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Changeset 11:a712b378e090 (2015-02-21)

Previous changeset 10:3378d12591ea (2015-02-21) Next changeset 12:0773b11fb822 (2015-02-21)

Commit message:
cutadapt added

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/cutadapt.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/cutadapt.xml Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,481 @@\n+<tool id="cutadapt" name="Cutadapt" version="1.6">\n+ <description>Remove adapter sequences from Fastq/Fasta</description>\n+ <requirements>\n+ <requirement type="package" version="1.6">cutadapt</requirement>\n+ </requirements>\n+ <version_command>cutadapt --version</version_command>\n+ \n+ <command>cutadapt\n+ #if $input.extension.startswith( "fastq"):\n+ --format=fastq\n+ #if $input.extension == "fastqillumina":\n+ --quality-base=64\n+ #end if\n+ #if $input.extension == "fastqsolexa":\n+ --quality-base=64\n+ #end if\n+ #else\n+ --format=$input.extension\n+ #end if\n+ #for $a in $adapters\n+ #if $a.adapter_source.adapter_source_list == \'prebuilt\':\n+ --adapter="${a.adapter_source.adapter.fields.name}"=\'${a.adapter_source.adapter}\'\n+ #else if str($a.adapter_source.adapter_name) != "":\n+ --adapter=\'${a.adapter_source.adapter_name}\'=\'${a.adapter_source.adapter}\'\n+ #else\n+ --adapter=\'${a.adapter_source.adapter}\'\n+ #end if\n+ #end for\n+ \n+ $anywhere_adapters_textbox\n+ \n+ #for $aa in $anywhere_adapters\n+ #if $aa.anywhere_adapter_source.anywhere_adapter_source_list == \'prebuilt\':\n+ --anywhere="${aa.anywhere_adapter_source.anywhere_adapter.fields.name}"=\'${aa.anywhere_adapter_source.anywhere_adapter}\'\n+ #else if str($aa.anywhere_adapter_source.anywhere_adapter_name) != "":\n+ --anywhere=\'${aa.anywhere_adapter_source.anywhere_adapter_name}\'=\'${aa.anywhere_adapter_source.anywhere_adapter}\'\n+ #else\n+ --anywhere=\'${aa.anywhere_adapter_source.anywhere_adapter}\'\n+ #end if\n+ #end for\n+ #for $fa in $front_adapters\n+ #if $fa.front_adapter_source.front_adapter_source_list == \'prebuilt\':\n+ --front="${fa.front_adapter_source.front_adapter.fields.name}"=\'${fa.front_adapter_source.front_adapter}\'\n+ #else if str($fa.front_adapter_source.front_adapter_name) != "":\n+ --front=\'${fa.front_adapter_source.front_adapter_name}\'=\'${fa.front_adapter_source.front_adapter}\'\n+ #else\n+ --front=\'${fa.front_adapter_source.front_adapter}\'\n+ #end if\n+ #end for\n+ --error-rate=$error_rate\n+ --times=$count\n+ --overlap=$overlap\n+ $no_indels\n+ $match_read_wildcards\n+ \n+ #if str( $output_filtering_options.output_filtering) == "filter":\n+ $output_filtering_options.discard\n+ $output_filtering_options.discard_untrimmed\n+ $output_filtering_options.no_trim\n+ $output_filtering_options.mask_adapter\n+ #if str($output_filtering_options.min) != \'0\':\n+ --minimum-length=$output_filtering_options.min\n+ #end if\n+ #if str($output_filtering_options.max) != \'0\':\n+ --maximum-length=$output_filtering_options.max\n+ #end if\n+ #end if\n+ \n+ --output=\'$output\'\n+ \n+ #if $paired_end.paired_end_boolean:\n+ --paired-output=\'$paired_output\'\n+ #end if\n+ \n+ #if str( $output_params.output_type ) == "additional":\n+ #if $output_params.rest_file:\n+ --rest-file=$rest_output\n+ #end if\n+ #if $output_params.wildcard_file:\n+ --wildcard-file=$wild_output\n+ #end if\n+ #if $output_params.too_short_file:\n+ --too-short-output=$too_short_output\n+ #end if\n+ #if $output_params.too_long_file:\n+ --too-long-output=$too_long_output\n+ #end if\n+ #if $output_params.untrimmed_file:\n+ --untrimmed-output=$untrimmed_output\n+ #if $paired_end.paired_end_boolean:\n+ --untrimmed-paired-output=$untrimmed_paired_output\n+ #end if\n+ #end if\n+ #if $output_params.info_file:\n+ --info-file=$info_file\n+ #end if\n+ \n+ #end if\n+ \n+ #if str( $read_modification_params.read_modification) == "modify'..b"adapter. For example when the adapter sequence is\n+ ``ADAPTER``::\n+ \n+ HELLOADAPTERTHERE\n+ APTERTHERE\n+ \n+ will both be trimmed to ``THERE``. To avoid this, you can prefix the adapter with the character\n+ ``^``. This will restrict the search, forcing the adapter to be a prefix of the read. With\n+ the adapter sequence set to ``^ADAPTER``, only reads like this will be trimmed::\n+ \n+ ADAPTERHELLO\n+ \n+ \n+ Allowing adapters anywhere\n+ --------------------------\n+ \n+ Cutadapt assumes that any adapter specified via the 3' Adapter parameter\n+ was ligated to the 3\\' end of the sequence. This is the correct assumption for\n+ at least the SOLiD and Illumina small RNA protocols and probably others.\n+ The assumption is enforced by the alignment algorithm, which only finds the adapter\n+ when its starting position is within the read. In other words, the 5' base of\n+ the adapter must appear within the read. The adapter and all bases following\n+ it are removed.\n+ \n+ If, on the other hand, your adapter can also be ligated to the 5' end (on\n+ purpose or by accident), you should tell cutadapt so by using the Anywhere Adapter\n+ parameter. It will then use a slightly different alignment algorithm\n+ (so-called semiglobal alignment), which allows any type of overlap between the\n+ adapter and the sequence. In particular, the adapter may appear only partially\n+ in the beginning of the read, like this::\n+ \n+ PTERMYSEQUENCE\n+ \n+ The decision which part of the read to remove is made as follows: If there is at\n+ least one base before the found adapter, then the adapter is considered to be\n+ a 3' adapter and the adapter itself and everything following it is removed.\n+ Otherwise, the adapter is considered to be a 5' adapter and it is removed from\n+ the read.\n+ \n+ Here are some examples, which may make this clearer (left: read, right: trimmed\n+ read)::\n+ \n+ MYSEQUENCEADAPTER -> MYSEQUENCE (3' adapter)\n+ MADAPTER -> M (3' adapter)\n+ ADAPTERMYSEQUENCE -> MYSEQUENCE (5' adapter)\n+ PTERMYSEQUENCE -> MYSEQUENCE (5' adapter)\n+ \n+ The regular algorithm (3' Adapter) would trim the first two examples in the same way,\n+ but trim the third to an empty sequence and trim the fourth not at all.\n+ \n+ \n+ Format of the info file\n+ -----------------------\n+ The info file contains information about the found adapters. The output is a tab-separated text file. Each line corresponds to one read of the input file. The fields are:\n+ \n+ 1. Read name\n+ 2. Number of errors\n+ 3. 0-based start coordinate of the adapter match\n+ 4. 0-based end coordinate of the adapter match\n+ 5. Sequence of the read to the left of the adapter match (can be empty)\n+ 6. Sequence of the read that was matched to the adapter\n+ 7. Sequence of the read to the right of the adapter match (can be empty)\n+ 8. Name of the found adapter.\n+ \n+ The concatenation of the fields 5-7 yields the full read sequence. In column 8, adapters without a name are numbered starting from 1.\n+ \n+ If no adapter was found, the format is as follows:\n+ \n+ 1. Read name\n+ 2. The value -1\n+ 3. The read sequence\n+ \n+ When parsing that file, be aware that additional columns may be added in the future. Note also that some fields can be empty, resulting in consecutive tabs within a line. Also, in the current version, when the *Match times* option is set to a value other than 1 (the default value), multiple lines are written to the info file for each read.\n+ \n+ .. _cutadapt: http://code.google.com/p/cutadapt/\n+ </help>\n+ \n+</tool>\n+\n"

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/1.axt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/1.axt Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,85 @@\n+##matrix=axtChain 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91\n+##matrix=axtChain 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91\n+0 chrX 3022176 3023241 chrX 132722808 132723933 - 67671\n+tcttcatgtgacttgcttgtgccttttaggacctgctcaagcctgatcacatatgtacaacttccagttgataatggattgttgctgtgcacaagctactttttagcttcattggttagataatactcagctcatgagatgcaggtcagattacatggcaatttggtagctcattgtcaaatgtttagtttctactgagacctaatatcaggccaagaactgtcactcaaatagagaatcgctatctgcaaaaatcatttgtccaaagtacctagggtttc----atctgtaatacatgtgtaggggcctgctaaatgctccaagcagcatccccatctgccactgtcacctc---atgtgcc--------------------------tagtcatagaaaaacatgcacagcagcctggacctgttaaagaaacttctcctatttctgtacccacacaaagctagcttctcttcaagtcacttggtatatggTATGCTTACCTTAATCTGTTGTGTGAGCCATTTATTAttattttcccattttctgactgtataatttggatattatacttataagttggcagaTATATG---------CATCAGAACATGGAATATGTTGGAAGAATCAAAAGGAGAGTTAGAAGGGGGCAATAGGAAGATGAACATAAACAGGGTACGTACAGA---------------AAATTTTTCAAAGAATAAATAAAACCATTAAAAAAACAAACAAATATACAATGACCATAAAATATTGCTATACTAAATTATAAAA------CAGAAATATTTATATGTACAAAGAAACAAATTCCAAGCCAGAAATTCAACAGGGAATATACAGCATAATAAGATATATATCAATTAGAAAAA-TATCAAATTAAAATTATAAGCTAGAAAGTATTAAAGGGAAAAAATGGATGAATTTAATAGCTTA-------TGCTTAAGAATAATTGGCAAATCAGAAGCCTTGTAAGAAACAATAGAAATAAAGTTT-AAGAGGAATAGAAGAGAAAAATAATAATGCTGAAGGCAGAGGTCAGCATAACAGGAGTGTGAATTGGAATCTCAGACTCACAGGGAAGGTAGAAAGAAGCAGAAGATATTTAAACAAataaa\n+tcttcatgtgacttgcttgtgccttttaggacctgctcaggcctgatgacacacatataacttccagttgataatgcattactgctgtgcacaagctatcttttggcttcattggctagataatactcagctcattaggtgcagttcagatcacatggtaatttggtggctaattgtcaaatgtttattttctactgagccccaatatcagtccaagaactgtcactcaaatagaggattgttgtctgcaaaa-tcatttgtccaaagtccttcgtgtttctttcctctgtaatttatacataggggccttctaaatgctc-aagcagcatccctatctgccactgtcaccaccacaagtgccctccagtctgctggatcataaaatcctagtcatagaacaacatgcacagcagcctggacctgttgaagaactttctccaattcctgtactcacacgaagctagccactccctaagtcacttggtatatgCTATGCATATCTTAATCTGTGGTGTGAACTACCTATTATT----TCCCCGTTTCAGACTGTATAATTGTGATAATATATTTAGAAGTTAGtatatatataatatatatatatCAGAATATGGGATATGCTGAAAGAATCACAAGGAGAGTTAGAAGGAGGCAATAGGAAGATGAACATAAACAGtatatatatatatatacatgtatatataATTTTTTCAAAGAATAAATAAAAATATTGTAAAAG-AAACAAACACACAATG-TCATAAAATATTGCTCTACTATATTATGAAATAGCAACAGCAATATTTGTATGTACAAAGAAATAAATTCCAAGCCAGAAACTCAGCAGAGAATTTACAACATAA---GGCATTTATCAATTGGAAAAAATACTAAATTAAAATTATAAGATAGGAAGTATTCAAAAGAAGCA-TGGATAAATTTAATAGCTCACTAAGAATGCTTAAGAATAATTGGCAAATAAGAGGACCTGCAAGAAATAATAGAAATAAAGTTTTAAGAGGAATAGAAGATAAAAATAAAAATGCCTTAGGCAGAGGTTAGCATAACATGAGTGTGAATTGGAATCTCAGAGTCACAGGAAAAGTAGAAAGAAGCAGAAGATATTTAAAGGAATGAA\n+\n+1 chrX 3025132 3025662 chrX 132731310 132731841 - 23012\n+ggagaaagggaatgggggatga-gagtgggactgggaggagaggagggaggagaggctgtaatcaggatgtaaagtgaataagcaaataaGTTAAGGAAAACAACAACAAAAAGAAACTGGATTAATTTCAATTTATTCAAGAACATTGGTTATTTCCATTAAGTACTGTAGTATTATGTATATGAATATAAAAATCCTTTCATCAAAGCAAGGAAGAGAGCACAAAGCTGCCCTTAAGTCATTGAAGACCTGGAGCACCTATGGGCCTCCCAAGAGGTTCTCACAAAACCTACAACCTCCATCCCAAGAGCCTGTGTCTGACAGAGCTGGTATGAGAAAAGGAGACAATTCTTCCC-----CAGG------------TTTTAGCCAGACTTTGAGTACACAATGGGATAGTGAGGAGCC----------------------CAGTGAAAGCAA------------TTAGTGATTTGGCCTGTGACCCTCTAGCACAATGTTTTGCAGGTCCAGTTGGACATGACATGTTTTCATTGGAAAGGCACATTTATAGTACCTAATGACAGCCCATGTCAA-GTGGCA\n+ggaggaggaggaggaggaataacaagaagaagaagaagaagaagaagaagaagaag--------aagaagaagaagaagaagaagaagaag--aagaagaagaagaagaagaagaaACAGGATTGATTCAAATTTATTCAGGAATACTAGTTATTTCGAATAAGCCCTATAGAATTATGTACATGAATCAAAAAATCCTTTCATCAAAGCTAGAAAGAGAGCACAAAACTGACCATAAGTCATTGAATACCTGGAG-----------------------------------------CTCCATCCCAAGAGCCTATGTCTGGCAGAGCTGGTGTGAGAAAAAGAGGCAATCCTTCCCTGCTGCAGGAATAATCAAGCATGTTGGCTGGACCTTGAGTACACATCAGGATAGTGAGGGGCCTGGCAAAAAGCACAGACTATGGCACTGAAAGAAATTAATAAGGGACTTAGTGATTTGGCTTATGACCCTCCAGCACAATGTTTTGCAGGTCCAGTTGGAGATGACATG-TTTCATTGGCAAGCCACGATTATGGGACTTAATGACAGCCCCTGTCAAGGTGGTG\n+\n+2 chrX 3030008 3030565 chrX 132731842 132732393 - 30932\n+CATTGTTTTTGACAAATCAGTTTCCTTTAGACTACACCTTCAAGCCACTTAAGGTTGCATTTACAACAAAAATTTATAATCTAAATATCAACAGTAATGGCAATATTTATCTTGATAATCTCAGATCACAGTGTCTCCTGCTTTAACTA-TTTCTAATGTTCATTTATCC'..b'-------ATTTCTGCATTGCCTTGCCTGCTGACAAAGGGAC\n+\n+18 chrX 3049058 3049300 chrX 132770073 132770321 - 14281\n+ctcctgtaccatgcctgcctggatgctgccatgctcctgcctagatgatagtagactgaacttctgaacctctaagccagcccaaattaaatgttgtccttataaaagatgccttggtcatagtgt----tctcatcagtaaaaccctaa----GACAGAAGTTGGTACCAGATACGGGGGTTATTTGTTTCTTGAGGAATCATGAACTCTGAATACTGTG--------CCCAGGGGCATTCTGAAGATCTCATTAGAA\n+ctcctgcaccatgcctgcctggatactcccatactcccaacttgatgataatggactgaacctttgaacctgtaagccagccccaattaaatgttgtccttataagagttgccttggtcatggtgtctgttcacagcagtaaaatcctaactaagacaGGAC----------ATATGGGTTTTATCTGCTTCTTGGGGAATCATGAACTCTGAACATTGTGCTAATATACCTAGGGCCAttctgaagatcatattagaa\n+\n+19 chrX 3049301 3049850 chr15 879492 880081 - 31160\n+GGTTTTGTTAGATATTCTTTCAGATTAAAACATTCCATCCTAGAAGGAGGAAGAGGGTTTATAAAACTCAAGGACTATCACAATTTAA--GACTAATGAAACTCTGGGAA-TTCACAAAAGTCACATGGCCATCCCCAATGTTCTACAAGTAGTGAACAATTGCAGGCAGGAGTG-AGGGGTTTCCTTCAGTGGGGATTCCTGAAAGTTGGTCAGAGAGCTCTAGGGACGTAGTTTTCATTAATCATTATCAACACTGAGTAAGGCTTTCTGGTAATGGAGCTGACATTGAAtcatctgtgttcctttcagtgacctcaataaactcattggttcactaagctaaaatcaggtgCAATGATGTTGGCTTTGTTTCACTC--------------------------------------------AACGTCCTACTTGGAGTAAACATATACTTGTTCATATATTTTCAGGAAAATTTACACAACAGAAGGTAGAAACTTCTAAACAAAAGAATATTTCTCTTTGTTAGTTTAGTCTACTCACTCTATATGGAAAATAAGGATGGAAAAGAACACCACCACCCCCTACAttaatttgggc\n+GTTTTTCTTAGGTGTTCCTTCAGATTAAAATATTCCATG-TGGAAGGAGGAAAAAGGTTTATAAATCTCAAGGACTATCTCAATTTAAAAGACTCATGAAACTCTGAAAACTTAACAAAAATCACATAGCCTCCCCCAATATTACATAAGTAGTGAACAATTGTGGGCAGGAGTGAAGGGGTTTCCTTCAGTGTGGGTTTTtgcaagttgggcagagagttctagggaatcaattttcataaatcagcatcagcattggggcaagctttctgttaatggagctgatg-tgagtcatccgtgttcctttcaatgacctcaacaaactcattggttctccaagctaaaatcaggtgctatggtgtagtctttgtttcactctgattaattaattaattaattaattaattaatcaagtaattgttaatgtcctacttg--gtaaacatacgtttatctaactattttcaggaaaattcacacaacaGAAGGTCGAAACTTCTAAACAAAAGAGTATTTCTCTTTGTTAGTTGAGTCTA--CACTCGATAGGGAAA--AATGAAGGAAAAGAAATCCCCCATTAAGTAAACTCACTTAGAC\n+\n+20 chrX 3055000 3055956 chrX 27929767 27930764 + 46154\n+CATCTGTCTAAGATGt---aattatatattttattaataa---ttatattaGCCTAGTTGTTAAACAAG----TTAAGTGTTTCTAATgtgatcctatttaaatataataag-------------cttaactgcataaatgccaaaaatatctccttctctcactcaaggtaaaggcaaaattcacctgtagagtttgtaacctgcagagctttgagctttctgactccactatgacttctagaaaatcacct--cacagttctctgcctccctccatcagttccagccatgcctctatcccagctgcttctcctcatgcatgcaaggtcttctctgacaactgagcctcagcaactgtcatcactttagctggaatgcatatttctcTTGACTGCTGCTGGAGGCCACAGTCTACCTGCATGT-----------------------------------------TTTCATTCCACACCCAAAGGTTCCTTGATAACTTTCCTGGCTATTCTGACTCTCTGAAAAGAATGCTCACCCTGGAATTTCATTTCCTTGAAGCTAGGCCTTGTCATGCTCCCTCTTATCACTTACCAATATGAAAATATTTCATACTGACTTAATAGCTACATGGCTATATGGCTCAtttcccagactaggatgagaactccatgaggataagatctgttcatttgctgcctctggtccttgcagtgtccaaaacactgcactgCAGAGACCACTCACAGTGTTTATGGGACATAGGTAAAACAAATGAACTGAGTGATAATCCATGGGATTGAGCATGTAAAATTACACAGGCATGCCTGGGTCTAGCCATATAGCTACCTACTAATGCACTTCCCACCAGGATCTAGGCTTGCAGGGCACGGTGAAATAGGGCAACTGGAGGCATGGCCAAGAGAAATCTTTCCAAGGTTGAAAT------GACTTTTCCATATACCAGGGTGATTTTATCCTTTTTTTAGAATGTGAGGCCTATTCCAAAGCCATTACATGATATGAACt\n+CACCTACTTACAATGTGGAATTTATATATTTGATTTTCATGCTCCAAATT--CCAAGATTTTTGAGAAGATTTTCAGGAGTTGCTGcagtgtgcctgttaaaatatgacaaaaactatgagatgcttcaactttaaaagcactaa---catgtccccctctcactcaaggtaaaagcaaaattcctctgtagaagttttaacctgcagggctttgggctctctgacacccctgtgacttctgagaaatcacttttcacaattttctaccacccttcatcatatccagccatgccttcatcccagctgcttctcctcatgcatgccaggtcttctctggc---------ccagcaattgtcatcacataagctggaatgcacattccccTTGACTGCTGTTGGAtctctctctctctctctctctctctctctctctctctctctctctctctctctctctcCTTGTTCCATTCTAAACCTAGAGCTTCCTTGATACCTTTCCTGACCATTGTAACTCTCTGAAAAGAATGCTGGCCCTGAAATTTCATTTTCTTGAACCTAGACTTGGT-GTGTCCCCTCTTATCACTTACCAATATGAAAATGCTTCAGATAGGCTTATTAGCTACAGGAATATATTGCTCATTTCCCACACTAGGAGGAGAACTCCAAAGGGATACGATCTGTCCATTTGCTGCCTCTGCTGACTGCAGTATATAGAACACTGCATGGC----------CAGAGTGTTTATGTGACAAAGGTAAAACAAATCAATTGGGTGAGAATCTGTGGAATCAAGCATGTAAAGTGAGACAAGTATCCCTGGGTCTAGCCATAATGCTATA----AATGCACTTCCTAACAGGGTATGAGCTTGAAGGGCAGGGTAAAGCAGGGCAACTGGAGGCATGCTCAACAGAAACCTTTCCAAGGTTGAAATGTGATGGCCTCTTCCTTACACCATGGTGCTTGTATCC--TTGTTGGAATGTGGGTCCTGTTCAAATGCCTTTACATGATATGAACT\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/1.bam

Binary file rnaseq/cutadapt/test-data/1.bam has changed

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/1.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/1.bed Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,65 @@
+chr1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 -
+chr1 147984545 147984630 CCDS990.1_cds_0_0_chr1_147984546_f 0 +
+chr1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 -
+chr1 148185136 148185276 CCDS996.1_cds_0_0_chr1_148185137_f 0 +
+chr10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 -
+chr11 116124407 116124501 CCDS8374.1_cds_0_0_chr11_116124408_r 0 -
+chr11 116206508 116206563 CCDS8377.1_cds_0_0_chr11_116206509_f 0 +
+chr11 116211733 116212337 CCDS8378.1_cds_0_0_chr11_116211734_r 0 -
+chr11 1812377 1812407 CCDS7726.1_cds_0_0_chr11_1812378_f 0 +
+chr12 38440094 38440321 CCDS8736.1_cds_0_0_chr12_38440095_r 0 -
+chr13 112381694 112381953 CCDS9526.1_cds_0_0_chr13_112381695_f 0 +
+chr14 98710240 98712285 CCDS9949.1_cds_0_0_chr14_98710241_r 0 -
+chr15 41486872 41487060 CCDS10096.1_cds_0_0_chr15_41486873_r 0 -
+chr15 41673708 41673857 CCDS10097.1_cds_0_0_chr15_41673709_f 0 +
+chr15 41679161 41679250 CCDS10098.1_cds_0_0_chr15_41679162_r 0 -
+chr15 41826029 41826196 CCDS10101.1_cds_0_0_chr15_41826030_f 0 +
+chr16 142908 143003 CCDS10397.1_cds_0_0_chr16_142909_f 0 +
+chr16 179963 180135 CCDS10401.1_cds_0_0_chr16_179964_r 0 -
+chr16 244413 244681 CCDS10402.1_cds_0_0_chr16_244414_f 0 +
+chr16 259268 259383 CCDS10403.1_cds_0_0_chr16_259269_r 0 -
+chr18 23786114 23786321 CCDS11891.1_cds_0_0_chr18_23786115_r 0 -
+chr18 59406881 59407046 CCDS11985.1_cds_0_0_chr18_59406882_f 0 +
+chr18 59455932 59456337 CCDS11986.1_cds_0_0_chr18_59455933_r 0 -
+chr18 59600586 59600754 CCDS11988.1_cds_0_0_chr18_59600587_f 0 +
+chr19 59068595 59069564 CCDS12866.1_cds_0_0_chr19_59068596_f 0 +
+chr19 59236026 59236146 CCDS12872.1_cds_0_0_chr19_59236027_r 0 -
+chr19 59297998 59298008 CCDS12877.1_cds_0_0_chr19_59297999_f 0 +
+chr19 59302168 59302288 CCDS12878.1_cds_0_0_chr19_59302169_r 0 -
+chr2 118288583 118288668 CCDS2120.1_cds_0_0_chr2_118288584_f 0 +
+chr2 118394148 118394202 CCDS2121.1_cds_0_0_chr2_118394149_r 0 -
+chr2 220190202 220190242 CCDS2441.1_cds_0_0_chr2_220190203_f 0 +
+chr2 220229609 220230869 CCDS2443.1_cds_0_0_chr2_220229610_r 0 -
+chr20 33330413 33330423 CCDS13249.1_cds_0_0_chr20_33330414_r 0 -
+chr20 33513606 33513792 CCDS13255.1_cds_0_0_chr20_33513607_f 0 +
+chr20 33579500 33579527 CCDS13256.1_cds_0_0_chr20_33579501_r 0 -
+chr20 33593260 33593348 CCDS13257.1_cds_0_0_chr20_33593261_f 0 +
+chr21 32707032 32707192 CCDS13614.1_cds_0_0_chr21_32707033_f 0 +
+chr21 32869641 32870022 CCDS13615.1_cds_0_0_chr21_32869642_r 0 -
+chr21 33321040 33322012 CCDS13620.1_cds_0_0_chr21_33321041_f 0 +
+chr21 33744994 33745040 CCDS13625.1_cds_0_0_chr21_33744995_r 0 -
+chr22 30120223 30120265 CCDS13897.1_cds_0_0_chr22_30120224_f 0 +
+chr22 30160419 30160661 CCDS13898.1_cds_0_0_chr22_30160420_r 0 -
+chr22 30665273 30665360 CCDS13901.1_cds_0_0_chr22_30665274_f 0 +
+chr22 30939054 30939266 CCDS13903.1_cds_0_0_chr22_30939055_r 0 -
+chr5 131424298 131424460 CCDS4149.1_cds_0_0_chr5_131424299_f 0 +
+chr5 131556601 131556672 CCDS4151.1_cds_0_0_chr5_131556602_r 0 -
+chr5 131621326 131621419 CCDS4152.1_cds_0_0_chr5_131621327_f 0 +
+chr5 131847541 131847666 CCDS4155.1_cds_0_0_chr5_131847542_r 0 -
+chr6 108299600 108299744 CCDS5061.1_cds_0_0_chr6_108299601_r 0 -
+chr6 108594662 108594687 CCDS5063.1_cds_0_0_chr6_108594663_f 0 +
+chr6 108640045 108640151 CCDS5064.1_cds_0_0_chr6_108640046_r 0 -
+chr6 108722976 108723115 CCDS5067.1_cds_0_0_chr6_108722977_f 0 +
+chr7 113660517 113660685 CCDS5760.1_cds_0_0_chr7_113660518_f 0 +
+chr7 116512159 116512389 CCDS5771.1_cds_0_0_chr7_116512160_r 0 -
+chr7 116714099 116714152 CCDS5773.1_cds_0_0_chr7_116714100_f 0 +
+chr7 116945541 116945787 CCDS5774.1_cds_0_0_chr7_116945542_r 0 -
+chr8 118881131 118881317 CCDS6324.1_cds_0_0_chr8_118881132_r 0 -
+chr9 128764156 128764189 CCDS6914.1_cds_0_0_chr9_128764157_f 0 +
+chr9 128787519 128789136 CCDS6915.1_cds_0_0_chr9_128787520_r 0 -
+chr9 128882427 128882523 CCDS6917.1_cds_0_0_chr9_128882428_f 0 +
+chr9 128937229 128937445 CCDS6919.1_cds_0_0_chr9_128937230_r 0 -
+chrX 122745047 122745924 CCDS14606.1_cds_0_0_chrX_122745048_f 0 +
+chrX 152648964 152649196 CCDS14733.1_cds_0_0_chrX_152648965_r 0 -
+chrX 152691446 152691471 CCDS14735.1_cds_0_0_chrX_152691447_f 0 +
+chrX 152694029 152694263 CCDS14736.1_cds_0_0_chrX_152694030_r 0 -

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/1.bed.spaces
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/1.bed.spaces Sat Feb 21 16:33:42 2015 +0100

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/1.bedgraph
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/1.bedgraph Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,30 @@
+chr1 0 14361 0
+chr1 14361 14829 1
+chr1 14829 14969 0
+chr1 14969 15038 1
+chr1 15038 15795 0
+chr1 15795 15947 1
+chr1 15947 16606 0
+chr1 16606 16765 1
+chr1 16765 16857 0
+chr1 16857 17055 1
+chr1 17055 17232 0
+chr1 17232 17368 1
+chr1 17368 17605 0
+chr1 17605 17742 1
+chr1 17742 17914 0
+chr1 17914 18061 1
+chr1 18061 18267 0
+chr1 18267 18366 1
+chr1 18366 24737 0
+chr1 24737 24891 1
+chr1 24891 29320 0
+chr1 29320 29370 1
+chr1 29370 34610 0
+chr1 34610 35174 2
+chr1 35174 35276 0
+chr1 35276 35481 2
+chr1 35481 35720 0
+chr1 35720 36081 2
+chr1 36081 69090 0
+chr1 69090 69093 3

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/1.bigbed

Binary file rnaseq/cutadapt/test-data/1.bigbed has changed

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/1.bigwig

Binary file rnaseq/cutadapt/test-data/1.bigwig has changed

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/1.customtrack
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/1.customtrack Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,3 @@
+track name="User Track" description="User Supplied Track (from Galaxy)" color=0,0,0 visibility=1
+chr7 127475281 127491632 NM_000230 0 + 127486022 127488767 0 3 29,172,3225, 0,10713,13126,
+chr7 127486011 127488900 D49487 0 + 127486022 127488767 0 2 155,490, 0,2399,

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/1.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/1.fasta Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,2 @@\n+>hg17\n+gtttgccatcttttgctgctctagggaatccagcagctgtcaccatgtaaacaagcccaggctagaccaGTTACCCTCATCATCTTAGCTGATAGCCAGCCAGCCACCACAGGCAtgagtcaggccatattgctggacccacagaattatgagctaaataaatagtcttgggttaagccactaagttttaggcatagtgtgttatgtaTCTCACAAACATATAAGACTGTGTGTTTGTTGACTGGAGGAAGAGATGCTATAAAGACCACCTTTTAAAACTTCCC-------------------------------AAATACT-GCCACTGATGTCCTG-----ATGGAGGTA-------TGAA-------------------AACATCCACTAAAATTTGTGGTTTATTCATTTTTCATTATTTTGTTTAAGGAGGTCTATAGTGGAAGAGGGAGATATTTGGggaaatt---ttgtatagactagctttcacgatgttagggaattattattgtgtgataatggtcttgcagttaca-cagaaattcttccttattttttgggaa---gcaccaaag----tagggat---aaaatgtcatgatgtgtgcaatacactttaaaatgtttttg-----ccaaaataatt----------------aatgaagc--aaatatggaaa-ataataattattaaatctaggtgatgggtatattgtagttcactatagtattgcacacttttctgtatgtttaaatttttcatttaaaaaaaaactttgagc-----tagacaccaggctatgagctaggagcatagcaatgaccaa----------------------------------------------------------------------------------------------atagactcctaccaa--------------------------------------------------ctc-aaagaatgcacattctCTGGGAAACATGTTTCCATTAGGAAGCCTCGAATGCAATGTGACTGTGGTCTCCAGGACCTG-TGTGATCCTGGCTTTTCCTGTTCCCTCCG---CATCATCACTGCAGGTGTGTTTTCCCAAGTTTTAAACATTTA------CCTTCCCAGTGGCCTTGCGTCTAGAGGAATCCCTGTATAGTGGT-ACATGAATATAACACATAACAAA-AATCATCTCTATGGTGTGTGTTGTTCCTGGGGTTCAattcagcaaattttccctg-ggcacccatgtgttcttggcactggaaaagtaccgggactgaaacagttgatggccca-atccctgtcctct---taaaacctaagggaggagaTGGAAAGGGG-CACCCAACCCAGACTGAGAGACAGGAATTAGCTGCAAGGGGAACTAGGAAAAGCTTCTTTA---AGGATGGAGAGGCCCTAGTGGAAT-GGGGAGATTCTTCCGGGAGAAGCGATGGATGCACAGTTGGGCATCCCCACAGACGGACTGGAAAGAAAAAAGGCCTGGAGGAATCAATGTG-------CAATGTATGTGTGTTCCCTGGTTcaagggctgg-gaactttctcta-aagggccaggtagaaaacattttaggctttctaagccaag--gcaaaat-tgaggatattacatgggtacttatacaacaagaataaacaatt---tacacaattttttgttgacagaattcaaaactttat----agacacagaaatgcaaatttcctgtaattttcccat-gagaactattcttct--tttgttttgttttgcgacAGGGTTGCGCtgatcctcccgcctcagtctccctaagtgctgagatgttgcaggaagtcagggaccccgaacagagagatcggctggagccgtggcagaggaacataaattttgaagatttcattttaatatggacacttatcagttcccaaataatacttttataattttttatgcctgtctttgctttaatctcttaatcctgttatcttcataagctaaggatgtacgtcacctcaggaccactgtgataattgtgttaactgtacagattgattgcaaaacatgtgtgtttgaacaatatgaaatcagtgcaccttgaaaaagagcagaataacagcaatttttagggaacaagggaagacaactataaggtctgactgcctgcggggtcgggcaaagggagccatatttttcttcttgcagagagcctataaatagacctgcaagtaggagagatattgctaatttcttttgctagcatggaatattaatattaacaccctgggaaaggaatgcattcctggggggaggtctataaatggccgctctgggaatgtctatcctacgcaatggagataaggactgagatacgccctggtctcctgcagtaccctcaggcttactagggtggtgaaaaactccgccctggtaaatttgtggtcagaccagttttctgctctcgaacactgttttctgttgtttaagatgtttatcaagacaatacgtgcaccgctgaacacagacccttatcagtagttctcctttttgccctttgaagcatgtgatctactccctgttttacaccccctcaccttttgaaacccttaataaaaaacttgctggttt-gaggctcaggtgggcatcacagtactaccgatatgtgatgtcacccccggcggcccagctgtaaaattcctctctttgtactctctctctttatttctcagccagctgacacttatggaaaatagaaagaacctacgttgaaatattgggggcaggttcccccaataTCTGGTGCCCAACGTGGGAtactgagattacaagcatgagccactgcatctggcctcttcttttgatttttttttttcaaacttttacaaatgtagaaaccattcttagcttttgggcattaccaaacccggcagtgg-caggctcggttcaccaacgtcatttgcagttccccgCTTTATGTTATGGgttttgttttgttttgtttttttt-attgagacagagtttcactcttgttgcccaggctgtagtgcaatggtctgatcttggctcactgcaacctccacttcccaggttcaagccattctcctgcctcagcctctcaagtagctgggattacagacactcaccaccacacctggctaattttgtatttttagtagagatgaggtttcaccatgttggccaggctggtctcgaaatcctgacctcaggtgatccacccaccttggcctcccaaagtgctgggattacaggcttgagctaccacgcctggctGGGTTGGTTCTCAATGGAGTGGTTTGTTTTTGGAGCTGCTCT-GCGCAGtggggaccagaataggcctg-------------------ggttcctagcccattgctattcctt----accagctgtggattctaaggaaagtcatttaacctcgctggaccttag-attcctcatccctgaaGCCCAAGGGTaaaacaaaacaaaacaaaacaaaacaaaccaaCCCATCATGTAAAGCGGGGAACTACAAACGATACAGGTGAAACATGCCTACCACACCACTCACAGGCT--ATGATGACAAAAACGTGGCTACATCTGGGACCACCCCCCAACCCCCACTTTGTACGTAGGAAATACGGAGTTGAGGATGGAGACCCACAGTATGTCCAGAGTGTCCCCAAAGGCCACAGTGCCCGCCTGGAGCCCTCCAGAGAGCGTGCACTCCCTGGGGTGCCAGCCAGAGACAACTTGCCCTGAGGCTTGGAACTCGATTCTCCGCGTGCCAGAGAAGGGGTGGGACTTCAGAACCCCCAACCCCGCAATCTGGGTCGGGGAGCCTGGCGCACTGCGGGCCGCTCCCTCTAACCCTGGGCTTCCCTG------GCGTCCAGGGCCGTCGG------'..b'gataatggggatatcacacacta-ttcacaaggttgttatgaggcctaaattagctaaagcaATTGAATCCTCCTTACCCCCTGCATGGAGCTCTCTGGAGACTTCCACGTCTCCTGGTCATTGTGGGTGTCTTATGGTA-GTCTTGGGCAGTTAGGGAGAAGTTAGGTGTCTGGAAGCAAAGATGGCTCAGAACTAGATAGAGTC-TTGGGCATTTTATA-GATAAAAACTCTT--GTCTCCtttaaaaataataaaaaaaaattaGCTGGGCATATTAGCCACTCAGCAAGACTGCACGTGATAGATCCCGAGTGCCCCACCTTGGGTGGTGTAATACACAATATCACGGGAGCCCCGGGTAGTAACCACGGAGGTGTCAGCCTCAGTGCTGTGGGCAGATG-GATGGGGAGAGCC--TCCCGG-AACTGGAGTCACTGGAGCA----------------------------GGGTTGGGGGGCCTCACTGAGGGTACGGCCTTGATCTCTAAGGAGGAGGGACTGCCTGGAAAAGC-TGACTGGGAGGGAGGACTCGGCTGGGGGTAGAAGGGA----------CTAGGGAAGGCTGGGGGTGGGGGTGCTTATGGAGGACCTCAGATGCCTGGGGAACAGACTCCACTAAATAAAACATATGAAACCATGGCTGGTTCTTCAGCAGAGGCCATGTAGAGAAAGGAATGACCTAGGAAAGTTGGCCTGGAAGTGGAGGGAAGGATGGTGTGGGAAAAGCAGGAA--------TCTCGGAGACCAGCTTAGAGGCTTGGCAGTCACCTGGGTGCAGG-ATACAAGGGCCTGAGCCAAAGTGGTGAGGGAGGGTGGAAGGAGGCAGCCCAGAGAATGACCCTCCATGCCCACGGGGAAGGCAGAGGGCTCT-GAGAGCGA--TTCCTCCCACATG-CT-GAGCACTTGTTCTCCCTCTTCCTCCTGCATAGCAGTCAGTCTCCTCCAAACAGAAAGTCACCGGTTTGGACTTCATTCCTGGGCTCCACCCCATCCTGACCTTATCCAAGATGGACCAGACACTGGCAGTCTACCAACAGATCCTCACCAGTATGCCTTCCAGAAACGTGATCCAAATATCCAACGACCTGGAGAACCTCCGGGATCTTCTTCACGTGCTGGCCTTCTCTAAGAGCTGCCACTTGCCCTGGGCCAGTGGCCTGGAGACCTTGGACAGCCTGGGGGGTGTCCTGGAAGCTTCAGGCTACTCCACAGAGGTGGTGGCCCTGAGCAGGCTGCAGGGGTCTCTGCAGGACATGCTGTGGCAGCTGGACCTCAGCCCTGGGTGCTGAGGCCTTGAAGGTCACTCTTCCTGCAAGGACTACGTTAAGGGAAGGAACTCTGGCTTCCAGGTATCTCCAGGATTGAAGAGCATTGCATGGACACCCCTTATCCAGGACTCTGTCAATT--TCCCTGACTCCTCTAAGCCACTCTTCCAAAGGCATAAGACCCTAAGCCTCCTTTTGCTTGAAACCAAAGATATATACACAGGATCCTATTCTCACCAGGAAGGGGG-TCCACCC-AGCAAAGAGTGGGCTGCATCTGGGATTCCCACCAAGGTCTTCAGCCATCA---ACAAGAGTTGTCTTGTCCCCTCT-TGACCCATCT-----------------CCCCCTCACTGAATGCCTCAATGTGACCAGGGGTGATTTCAGAGAGGGCAGAGGGGTAGGCAGAGCCTTTGGATGACCA--GAACAAGGTTCCCTCTGAGAATTCCAAGGAGTTCCATGAAGACCACATCCACACACG--CAGGAACTCCC--AGCAACACAAGCTGGAA---GCACATGTTTATTTATTCTGCATTTTATTCTGGATGGATTTGAAGCAAAGCACCAGCTTCTCCAGGCTCTTTGGGGTCAGCCAGGGCCAGGGGTCTCCCTGGAGTGCAGTTTCCAATCCCATAGATGGGTC-TGGCTGAGCTGAACCCA---TTTTGAGTGACT----CGAGGGTTGGG-TTCATCTGAGCAAGAGCTGGCAAAGGTGGCTCTCCAGTTAGTTCTCTCGTAACTGGTTTCATTTCTACTGTGACTGATGTTACATCACAGTGTTTGCAATGGTGTTGCCCTGAGTGGATCTCCAAGGACCAGGTTATTTTAAAA---AGATTTGTTTTGTCAAGTGTCATATGTAGGTGTCTGCACCCAGGGGTGGG-GAATGTTTGGGCAGAAGGGAGAAGGATCTAGAATGTGTTTTCTGAATAACATTTGTGTGGTGGGTTCTTTGGAAGGAGTGAGA-TCATTTTCTTATCTTCTGCAATTGCTTAGGATGTTTTTCATGAAAA------------TAGCTCTTTCAG-GGGGGTTGTGAGGCCTGGCCAGGCACCCCCTGGAGAGAAGTTTCTGGCCCTGGCTGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAAAGGGCTGAAAGCCATTTGTTGGGGCAGTGGTAAGCTCTGGCTTTCTCCGACTGCTAGGGAGTGGTCTTTCCTATCATGGAGTGACGGTCCCACACTGGTGACTGCGATCTTCAGAGCAGGGGTCCTTGGTGT-GACCCTCTGAATGGTCCAGGGTTGATCACACTCTGGGTTTATTACATGGCAG-----TGTTCCTATTTGGGGCTTGCATGCCAAATTGTAGTTCTTGTCTGATTGGCTCACCC-AAGCAAGGCCAAAATTACCAAAAATCTTGGGGGG--TTTTTACTC-CAGTGGTGAAGAAAACTCCTTTAGCAGG-TGGTCCTGAGACCT-GACAAGCACTGCTAGGCGAGTGCCAGGACTCCCCAGGCCAGGCCACCAGGATGGCCCTTCCCACTGGAGGTCACATTCAGGAAGATGAAAGAGGAGGTTTGGGGTCTGCCACCATCCTGCTGCTGTGTTTTTGCTATCACACAGTGGGTGGTGGATCTGTCCAAGGAAACTTGAATCAAAGCAGTTAAC-TTTAAGactgagcacctgcttcatgctcagccctgactggtgctataggctggagaagctcacccaataaacattaagatt-gaggcctgccctcagggatcttgcattcccagtggTCAAACC-GCACTCACCCATGTGCCAAGGTGGGGTA-TTTACCACAGCAG--CTGAACAGCCAAATGCATGGTGCAGTTGACAGCAGGTGGGAAATGGTATGAGCTGAGGGGGGCCGTGCCCAGGGGCCCACAGG-GAACCCTGCTTGCACTTTGTAACATGTTTA-----CTTTTCagggcatcttagctt---ctatta-----tagccacatccctttga---aacaagataactgagaatttaaaaataagaa-----aata--TGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAAATGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCATGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCA\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/1.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/1.fastq Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,8 @@
+@HANNIBAL_1_FC302VTAAXX:2:1:228:167
+GAATTGATCAGGACATAGGACAACTGTAGGCACCAT
++HANNIBAL_1_FC302VTAAXX:2:1:228:167
+40 40 40 40 35 40 40 40 25 40 40 26 40 9 33 11 40 35 17 40 40 33 40 7 9 15 3 22 15 30 11 17 9 4 9 4
+@HANNIBAL_1_FC302VTAAXX:2:1:156:340
+GAGTTCTCGTCGCCTGTAGGCACCATCAATCGTATG
++HANNIBAL_1_FC302VTAAXX:2:1:156:340
+40 15 40 17 6 36 40 40 40 25 40 9 35 33 40 14 14 18 15 17 19 28 31 4 24 18 27 14 15 18 2 8 12 8 11 9
\ No newline at end of file

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/1.fastqsanger
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/1.fastqsanger Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,8 @@
+@1831_573_1004/1
+AATACTTTCGGCGCCCTAAACCAGCTCACTGGGG
++
+><C&&9952+C>5<.?<79,=42<292:<(9/-7
+@1831_573_1050/1
+TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT
++
+;@@17?@=>7??@A8?==@4A?A4)&+.'&+'1,
\ No newline at end of file

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/1.fastqsolexa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/1.fastqsolexa Sat Feb 21 16:33:42 2015 +0100

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/1.interval
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/1.interval Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,5 @@
+chr1 4348187 4348589 3.70 4.90 2.55 0.24 0.46
+chr1 4488177 4488442 4.03 5.77 1.92 -0.67 0.81
+chr1 4774091 4774440 8.07 8.33 7.82 0.85 -0.40
+chr1 4800122 4800409 6.40 7.35 5.44 1.19 -0.42
+chr1 4878925 4879277 2.18 0.28 4.93 -0.96 1.24

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/1.lav
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/1.lav Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,178 @@
+#:lav
+d {
+  "blastz out.seq1m seq2data Y=3400 H=0 W=8 B=2 K=3000 C=0 m=83886080 P=0
+     A    C    G    T
+    91 -114  -31 -123
+  -114  100 -125  -31
+   -31 -125  100 -114
+  -123  -31 -114   91
+  O = 400, E = 30, K = 3000, L = 3000, M = 50"
+}
+#:lav
+s {
+  "out.seq1m" 1 1680 0 1
+  "seq2data" 1 1680 0 1
+}
+h {
+   ">seqmask seq1data out.repeats"
+   ">seq2"
+}
+a {
+  s 161304
+  b 1 1
+  e 1680 1680
+  l 1 1 1680 1680 100
+}
+a {
+  s 15173
+  b 186 251
+  e 450 505
+  l 186 251 244 309 92
+  l 256 310 280 334 84
+  l 281 336 307 362 78
+  l 308 374 329 395 91
+  l 341 396 367 422 81
+  l 369 423 419 473 94
+  l 422 474 425 477 75
+  l 426 481 450 505 96
+}
+a {
+  s 12134
+  b 191 343
+  e 361 503
+  l 191 343 215 367 80
+  l 216 369 244 397 86
+  l 256 398 361 503 95
+}
+a {
+  s 4422
+  b 192 431
+  e 276 505
+  l 192 431 212 451 100
+  l 223 452 244 473 95
+  l 247 474 254 481 63
+  l 255 484 276 505 91
+}
+a {
+  s 6872
+  b 192 311
+  e 330 450
+  l 192 311 215 334 83
+  l 216 336 275 395 73
+  l 286 396 307 417 91
+  l 308 428 330 450 96
+}
+a {
+  s 14437
+  b 192 224
+  e 472 505
+  l 192 224 223 255 84
+  l 224 257 255 288 84
+  l 257 289 277 309 90
+  l 288 310 308 330 90
+  l 309 342 362 395 85
+  l 374 396 395 417 91
+  l 396 428 417 449 95
+  l 428 450 449 471 95
+  l 450 483 472 505 91
+}
+a {
+  s 7306
+  b 192 399
+  e 308 505
+  l 192 399 244 451 94
+  l 256 452 277 473 91
+  l 280 474 283 477 100
+  l 284 481 308 505 92
+}
+a {
+  s 11180
+  b 193 290
+  e 396 505
+  l 193 290 212 309 100
+  l 223 310 280 367 76
+  l 281 369 332 420 88
+  l 333 422 335 424 100
+  l 336 429 341 434 83
+  l 342 451 396 505 87
+}
+a {
+  s 14437
+  b 224 192
+  e 505 472
+  l 224 192 255 223 84
+  l 257 224 288 255 84
+  l 289 257 309 277 90
+  l 310 288 330 308 90
+  l 342 309 395 362 85
+  l 396 374 417 395 91
+  l 428 396 449 417 95
+  l 450 428 471 449 95
+  l 483 450 505 472 91
+}
+a {
+  s 15173
+  b 251 186
+  e 505 450
+  l 251 186 309 244 92
+  l 310 256 334 280 84
+  l 336 281 362 307 78
+  l 374 308 395 329 91
+  l 396 341 422 367 81
+  l 423 369 473 419 94
+  l 474 422 477 425 75
+  l 481 426 505 450 96
+}
+a {
+  s 11180
+  b 290 193
+  e 505 396
+  l 290 193 309 212 100
+  l 310 223 367 280 76
+  l 369 281 420 332 88
+  l 422 333 424 335 100
+  l 429 336 434 341 83
+  l 451 342 505 396 87
+}
+a {
+  s 6872
+  b 311 192
+  e 450 330
+  l 311 192 334 215 83
+  l 336 216 395 275 73
+  l 396 286 417 307 91
+  l 428 308 450 330 96
+}
+a {
+  s 12134
+  b 343 191
+  e 503 361
+  l 343 191 367 215 80
+  l 369 216 397 244 86
+  l 398 256 503 361 95
+}
+a {
+  s 7306
+  b 399 192
+  e 505 308
+  l 399 192 451 244 94
+  l 452 256 473 277 91
+  l 474 280 477 283 100
+  l 481 284 505 308 92
+}
+a {
+  s 4422
+  b 431 192
+  e 505 276
+  l 431 192 451 212 100
+  l 452 223 473 244 95
+  l 474 247 481 254 63
+  l 484 255 505 276 91
+}
+x {
+  n 0
+}
+m {
+  n 0
+}
+#:eof

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/1.pileup
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/1.pileup Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,1000 @@\n+chrM\t42\tC\t1\t^:.\tI\n+chrM\t43\tC\t2\t.^:.\tII\n+chrM\t44\tT\t2\t..\tII\n+chrM\t45\tA\t3\t..^:.\tIII\n+chrM\t46\tG\t4\t...^:.\tIIII\n+chrM\t47\tA\t5\t....^:,\tIIIII\n+chrM\t48\tT\t5\t....,\tIIIII\n+chrM\t49\tG\t5\t....,\tIIIII\n+chrM\t50\tA\t5\t....,\tIIIII\n+chrM\t51\tG\t5\t....,\tIIIII\n+chrM\t52\tT\t5\t....,\tIIIII\n+chrM\t53\tA\t5\t....,\tIIIII\n+chrM\t54\tT\t5\t....,\tIIIII\n+chrM\t55\tT\t5\t....,\tIIIII\n+chrM\t56\tC\t5\t....,\tIIIII\n+chrM\t57\tT\t5\t....,\tIIIII\n+chrM\t58\tT\t5\t....,\tIIIII\n+chrM\t59\tA\t5\t....,\tIIIII\n+chrM\t60\tC\t5\t....,\tIIIII\n+chrM\t61\tT\t5\t....,\tIIIII\n+chrM\t62\tC\t5\t....,\tIIIII\n+chrM\t63\tC\t5\t....,\tIIIII\n+chrM\t64\tA\t5\t....,\tIIIII\n+chrM\t65\tT\t5\t....,\tIIIII\n+chrM\t66\tA\t5\t....,\tIIIII\n+chrM\t67\tA\t5\t....,\tIIIII\n+chrM\t68\tA\t5\t....,\tIIICI\n+chrM\t69\tC\t5\t....,\tIIIII\n+chrM\t70\tA\t5\t....,\tIIIII\n+chrM\t71\tC\t5\t....,\tIIIII\n+chrM\t72\tA\t5\t....,\tIAIII\n+chrM\t73\tT\t5\t....,\tIIIII\n+chrM\t74\tA\t5\t....,\tIIIII\n+chrM\t75\tG\t5\t....,\t%IIII\n+chrM\t76\tG\t5\tT...,\t*IIII\n+chrM\t77\tC\t5\t.$...,\tGIIII\n+chrM\t78\tT\t4\t.$..,\tIIII\n+chrM\t79\tT\t3\t..,\tIII\n+chrM\t80\tG\t3\t.$.,\tI1I\n+chrM\t81\tG\t2\t.$,\tII\n+chrM\t82\tT\t1\t,$\tI\n+chrM\t83\tC\t2\t^:.^:.\tII\n+chrM\t84\tC\t2\t..\tII\n+chrM\t85\tT\t2\t..\tII\n+chrM\t86\tA\t2\t..\tII\n+chrM\t87\tG\t2\t..\tII\n+chrM\t88\tC\t2\t..\tII\n+chrM\t89\tC\t2\t..\tII\n+chrM\t90\tT\t2\t..\tII\n+chrM\t91\tT\t2\t..\tII\n+chrM\t92\tT\t2\t..\tII\n+chrM\t93\tT\t2\t..\tII\n+chrM\t94\tT\t2\t..\tII\n+chrM\t95\tA\t2\t..\tII\n+chrM\t96\tT\t2\t..\tII\n+chrM\t97\tT\t2\t..\tII\n+chrM\t98\tA\t2\t..\tII\n+chrM\t99\tG\t2\t..\tII\n+chrM\t100\tT\t2\t..\tII\n+chrM\t101\tT\t2\t..\tII\n+chrM\t102\tA\t2\t..\tII\n+chrM\t103\tT\t2\t..\tII\n+chrM\t104\tT\t2\t..\tII\n+chrM\t105\tA\t2\t..\tIE\n+chrM\t106\tA\t2\t..\tII\n+chrM\t107\tT\t2\t..\tII\n+chrM\t108\tA\t2\t..\tII\n+chrM\t109\tG\t2\t..\tII\n+chrM\t110\tA\t2\t..\tII\n+chrM\t111\tA\t2\t..\tI2\n+chrM\t112\tT\t2\t..\tII\n+chrM\t113\tT\t2\t..\tII\n+chrM\t114\tA\t2\t..\tH7\n+chrM\t115\tC\t2\t..\tII\n+chrM\t116\tA\t2\t..\tII\n+chrM\t117\tC\t2\t..\tII\n+chrM\t118\tA\t2\t.$.$\tF8\n+chrM\t156\tT\t1\t^:,\t&\n+chrM\t157\tC\t1\t,\tI\n+chrM\t158\tA\t2\tg^:g\tI>\n+chrM\t159\tC\t2\t,,\t/F\n+chrM\t160\tG\t2\t,,\tII\n+chrM\t161\tT\t2\t,,\tI>\n+chrM\t162\tC\t2\t,,\t.-\n+chrM\t163\tT\t2\t,,\tI8\n+chrM\t164\tC\t2\t,,\t4F\n+chrM\t165\tT\t2\t,,\tII\n+chrM\t166\tA\t2\t,,\tII\n+chrM\t167\tC\t2\t,,\t;6\n+chrM\t168\tG\t2\t,,\tII\n+chrM\t169\tA\t2\t,,\tII\n+chrM\t170\tT\t2\t,,\tII\n+chrM\t171\tT\t2\t,,\tIB\n+chrM\t172\tA\t2\t,,\tII\n+chrM\t173\tA\t2\t,,\tII\n+chrM\t174\tA\t2\t,,\tII\n+chrM\t175\tA\t2\t,,\tII\n+chrM\t176\tG\t2\t,,\tII\n+chrM\t177\tG\t2\t,,\tII\n+chrM\t178\tA\t2\t,,\tII\n+chrM\t179\tG\t2\t,,\tII\n+chrM\t180\tC\t2\t,,\tII\n+chrM\t181\tA\t3\t,,^:,\tIII\n+chrM\t182\tG\t3\t,,,\tIII\n+chrM\t183\tG\t3\t,,,\tIII\n+chrM\t184\tT\t3\t,,,\tIII\n+chrM\t185\tA\t3\t,,,\tIII\n+chrM\t186\tT\t3\t,,,\tIII\n+chrM\t187\tC\t3\t,,,\tIII\n+chrM\t188\tA\t3\t,,,\tIII\n+chrM\t189\tA\t3\t,,,\tIII\n+chrM\t190\tG\t3\t,,,\tIII\n+chrM\t191\tC\t3\t,$,,\tIII\n+chrM\t192\tA\t2\t,,\tII\n+chrM\t193\tC\t2\t,$,\tII\n+chrM\t194\tA\t1\t,\tI\n+chrM\t195\tC\t1\t,\tI\n+chrM\t196\tT\t1\t,\tF\n+chrM\t197\tA\t1\t,\tI\n+chrM\t198\tG\t1\t,\tI\n+chrM\t199\tA\t1\t,\tI\n+chrM\t200\tA\t1\t,\tI\n+chrM\t201\tA\t2\t,^:.\tI-\n+chrM\t202\tG\t2\t,.\tII\n+chrM\t203\tT\t2\t,.\tII\n+chrM\t204\tA\t2\t,.\tII\n+chrM\t205\tG\t2\t,.\tI6\n+chrM\t206\tC\t2\t,.\tII\n+chrM\t207\tT\t2\t,.\tI,\n+chrM\t208\tC\t2\t,.\tII\n+chrM\t209\tA\t2\t,.\tII\n+chrM\t210\tT\t2\t,.\tII\n+chrM\t211\tA\t2\t,.\tII\n+chrM\t212\tA\t2\t,.\tIE\n+chrM\t213\tC\t2\t,.\tIC\n+chrM\t214\tA\t2\t,.\tI;\n+chrM\t215\tC\t2\t,.\tII\n+chrM\t216\tC\t2\t,$.\tII\n+chrM\t217\tT\t1\t.\tI\n+chrM\t218\tT\t1\t.\tI\n+chrM\t219\tG\t1\tT\tI\n+chrM\t220\tC\t1\t.\tI\n+chrM\t221\tT\t1\t.\tI\n+chrM\t222\tC\t1\t.\tE\n+chrM\t223\tA\t1\t.\t4\n+chrM\t224\tG\t1\tT\t9\n+chrM\t225\tC\t1\t.\t:\n+chrM\t226\tC\t1\t.\t?\n+chrM\t227\tA\t1\t.\t.\n+chrM\t228\tC\t1\t.\tC\n+chrM\t229\tA\t3\t.^:,^:,\t%II\n+chrM\t230\tC\t3\t.,,\t8II\n+chrM\t231\tC\t3\t.,,\t9II\n+chrM\t232\tC\t3\t.,,\tIII\n+chrM\t233\tC\t3\t.,,\tAI\'\n+chrM\t234\tC\t3\t.,,\tDI+\n+chrM\t235\tA\t3\t.,,\t&I@\n+chrM\t236\tC\t3\t.$,a\t+I$\n+chrM\t237\tG\t2\t,,\tII\n+chrM\t238\tG\t2\t,,\tII\n+chrM\t239\tG\t2\t,,\tII\n+chrM\t240\tA\t2\t,,\tII\n+chrM\t241\tC\t2\t,,\tI+\n+chrM\t242\tA\t2\t,,\tII\n+chrM\t243\tC\t2\t,,\tII\n+chrM\t244\tA\t3\t,,^:,\tII;\n+chrM\t245\tG\t3\t,,,\tII*\n+chrM\t246\tC\t3\t,,n\tII"\n+chrM\t247\tA\t3\t,,,\tIII\n+chrM\t248\tG\t4\t,,,^:.\tIIII\n+chrM\t249\tT\t4\t,,,.\tII)I\n+chrM\t250\tG\t4\t,,,.\tII2I\n+chrM\t251\tA\t4\t,,,.\tII(I\n+chrM\t252\tT\t4\t,,,.\tII*I\n+chrM\t253\tA\t4\t,,,.\tII7I\n+chrM\t254\tA\t4\t,,,.\tII1I\n+chrM\t255\tA\t4\t,,,.\tII?I\n+chrM\t256\tA\t4\t,,,.\tII9I\n+chrM\t257\tA\t4\t,,,.\tII?I\n+chrM\t258\tT\t4\t,,,.\tII$I\n+chrM\t259\tT\t5\t,,,.^:.\tII&II\n+chrM\t260\tA\t5\t,,,..\tII,II\n+chrM\t261\tA\t5\t,,,..\tII/II\n+chrM\t262\tG\t5\t,,,..\tII5II\n+chrM\t263\tC\t5\t,,a..\tII%II\n+chrM\t264\tT\t5\t,$,$,..'..b'\t,.,,\tIIII\n+chrM\t915\tA\t4\t,.,,\tIIII\n+chrM\t916\tG\t4\t,.,,\tIII5\n+chrM\t917\tC\t4\t,.,,\tIII5\n+chrM\t918\tG\t4\t,.,,\tIIII\n+chrM\t919\tC\t4\t,.,,\tIII<\n+chrM\t920\tG\t4\t,.,,\tIIII\n+chrM\t921\tC\t4\t,.,,\tIIII\n+chrM\t922\tA\t4\t,.,,\tIIII\n+chrM\t923\tC\t4\t,.,,\tIII8\n+chrM\t924\tA\t4\t,.,,\tIFII\n+chrM\t925\tC\t4\t,.,,\tIIII\n+chrM\t926\tA\t4\t,.,,\tIIII\n+chrM\t927\tC\t4\t,.,,\tIIII\n+chrM\t928\tC\t5\t,.,,^:,\tIIII:\n+chrM\t929\tG\t5\t,.,,,\tIIIE:\n+chrM\t930\tC\t5\t,.,,,\tIIIII\n+chrM\t931\tC\t5\t,.,,,\tIIIIF\n+chrM\t932\tC\t5\t,.,,,\tIIIIC\n+chrM\t933\tG\t5\t,$.,,,\tI?II:\n+chrM\t934\tT\t4\t.$,,,\t4II>\n+chrM\t935\tC\t3\t,,,\tIII\n+chrM\t936\tA\t3\t,,,\tIII\n+chrM\t937\tC\t3\t,,,\tII1\n+chrM\t938\tC\t3\t,,,\tIII\n+chrM\t939\tC\t3\t,,,\tIII\n+chrM\t940\tT\t3\t,$,,\tIII\n+chrM\t941\tC\t2\t,,\tII\n+chrM\t942\tC\t2\t,,\tI\'\n+chrM\t943\tT\t2\t,,\tII\n+chrM\t944\tT\t2\t,,\tII\n+chrM\t945\tA\t2\t,,\tII\n+chrM\t946\tA\t2\t,$,\tII\n+chrM\t947\tA\t1\t,\tI\n+chrM\t948\tT\t1\t,\tI\n+chrM\t949\tA\t1\t,\tI\n+chrM\t950\tT\t1\t,\tI\n+chrM\t951\tC\t1\t,\tI\n+chrM\t952\tA\t1\t,\tI\n+chrM\t953\tC\t1\t,\tI\n+chrM\t954\tA\t1\t,\tI\n+chrM\t955\tA\t2\t,^:.\tII\n+chrM\t956\tA\t2\t,.\tII\n+chrM\t957\tT\t2\t,.\tII\n+chrM\t958\tC\t3\t,.^:.\tIII\n+chrM\t959\tA\t3\t,..\tIII\n+chrM\t960\tT\t3\t,..\tIII\n+chrM\t961\tA\t3\t,..\tIII\n+chrM\t962\tA\t3\t,..\tIII\n+chrM\t963\tC\t4\t,$..^:.\tIIII\n+chrM\t964\tA\t3\t...\tI(;\n+chrM\t965\tT\t3\t...\tIII\n+chrM\t966\tA\t4\t...^:.\tIIII\n+chrM\t967\tA\t4\t....\tIIII\n+chrM\t968\tC\t4\t....\tIEII\n+chrM\t969\tA\t4\t....\tIIII\n+chrM\t970\tT\t4\t....\tIIII\n+chrM\t971\tA\t4\t....\tIIII\n+chrM\t972\tA\t4\t....\tIIII\n+chrM\t973\tA\t4\t....\tII0I\n+chrM\t974\tA\t5\t....^:.\tIIIII\n+chrM\t975\tC\t5\t.....\tIIIII\n+chrM\t976\tC\t5\t.....\tIIIII\n+chrM\t977\tG\t5\t.....\tIIIII\n+chrM\t978\tT\t5\t.....\tIIIII\n+chrM\t979\tG\t5\t.....\tI0III\n+chrM\t980\tA\t5\t.....\tIIII4\n+chrM\t981\tC\t5\t.....\tIIIII\n+chrM\t982\tC\t5\t.....\tIIIII\n+chrM\t983\tC\t5\t.....\tIIIII\n+chrM\t984\tA\t5\t.....\t-IGII\n+chrM\t985\tA\t5\t.....\t4GIII\n+chrM\t986\tA\t5\t.....\tBDGII\n+chrM\t987\tC\t5\t.....\tIDIII\n+chrM\t988\tA\t5\t.....\t@<III\n+chrM\t989\tT\t5\t.....\tIIIII\n+chrM\t990\tA\t5\t.$....\tI@III\n+chrM\t991\tT\t4\t....\tIICI\n+chrM\t992\tG\t4\tT...\t)III\n+chrM\t993\tA\t4\t.$...\t?ICI\n+chrM\t994\tA\t3\t...\tIII\n+chrM\t995\tA\t3\t...\tIII\n+chrM\t996\tG\t3\t...\tIII\n+chrM\t997\tG\t3\t...\tIII\n+chrM\t998\tA\t3\t.$..\t4II\n+chrM\t999\tG\t3\t..^:.\tIII\n+chrM\t1000\tA\t3\t...\tIII\n+chrM\t1001\tC\t3\t.$..\tIII\n+chrM\t1002\tA\t2\t..\tII\n+chrM\t1003\tA\t2\t..\tII\n+chrM\t1004\tG\t2\t..\tII\n+chrM\t1005\tT\t2\t..\tII\n+chrM\t1006\tC\t2\t..\tII\n+chrM\t1007\tG\t2\t..\tCI\n+chrM\t1008\tT\t2\t..\tII\n+chrM\t1009\tA\t2\t.$.\tII\n+chrM\t1010\tA\t1\t.\tI\n+chrM\t1011\tC\t1\t.\tI\n+chrM\t1012\tA\t1\t.\tI\n+chrM\t1013\tA\t1\t.\tI\n+chrM\t1014\tG\t1\t.\tI\n+chrM\t1015\tG\t1\t.\tI\n+chrM\t1016\tT\t1\t.\tI\n+chrM\t1017\tA\t1\t.\tI\n+chrM\t1018\tA\t1\t.\tI\n+chrM\t1019\tG\t1\t.\tI\n+chrM\t1020\tT\t1\t.\tI\n+chrM\t1021\tA\t1\t.\tI\n+chrM\t1022\tT\t1\t.\tI\n+chrM\t1023\tA\t1\t.\tI\n+chrM\t1024\tC\t1\t.\tI\n+chrM\t1025\tC\t1\t.\tI\n+chrM\t1026\tG\t1\t.\tI\n+chrM\t1027\tG\t1\t.\tI\n+chrM\t1028\tA\t1\t.\tI\n+chrM\t1029\tA\t1\t.\tI\n+chrM\t1030\tG\t1\t.\tI\n+chrM\t1031\tG\t2\t.^:.\tII\n+chrM\t1032\tT\t2\t..\tEI\n+chrM\t1033\tG\t2\t..\tII\n+chrM\t1034\tT\t2\t.$.\tII\n+chrM\t1035\tA\t2\t.^:.\tII\n+chrM\t1036\tC\t2\t..\tII\n+chrM\t1037\tT\t2\t..\tII\n+chrM\t1038\tT\t2\t..\tII\n+chrM\t1039\tG\t2\t..\tII\n+chrM\t1040\tG\t2\t..\tII\n+chrM\t1041\tA\t2\t..\tII\n+chrM\t1042\tT\t2\t..\tII\n+chrM\t1043\tA\t3\t..^:,\tIII\n+chrM\t1044\tA\t3\t..,\tIII\n+chrM\t1045\tC\t3\t..,\tII7\n+chrM\t1046\tC\t3\t..,\tII-\n+chrM\t1047\tA\t3\t..,\tIII\n+chrM\t1048\tA\t3\t..,\tIII\n+chrM\t1049\tA\t3\t..,\tIII\n+chrM\t1050\tG\t3\t..,\tIII\n+chrM\t1051\tT\t3\t..,\tIII\n+chrM\t1052\tG\t3\t..,\tIII\n+chrM\t1053\tT\t3\t..,\tGII\n+chrM\t1054\tA\t3\t..,\tIII\n+chrM\t1055\tG\t3\t..,\t:II\n+chrM\t1056\tC\t3\t..a\tHI%\n+chrM\t1057\tT\t3\t..,\tIII\n+chrM\t1058\tT\t3\t..,\tIII\n+chrM\t1059\tA\t3\t..,\tBII\n+chrM\t1060\tA\t3\t..,\tGII\n+chrM\t1061\tA\t3\t..,\tHII\n+chrM\t1062\tC\t3\t..,\tIII\n+chrM\t1063\tA\t3\t..,\tDII\n+chrM\t1064\tA\t3\t..,\tBII\n+chrM\t1065\tA\t3\t..,\t1II\n+chrM\t1066\tG\t3\t.$.,\t&II\n+chrM\t1067\tC\t2\t.,\tII\n+chrM\t1068\tA\t2\t.,\tII\n+chrM\t1069\tT\t2\t.,\tII\n+chrM\t1070\tC\t2\t.$,\tII\n+chrM\t1071\tC\t1\t,\tI\n+chrM\t1072\tA\t1\t,\tI\n+chrM\t1073\tG\t1\t,\tI\n+chrM\t1074\tC\t1\t,\tI\n+chrM\t1075\tT\t1\t,\tI\n+chrM\t1076\tT\t1\t,\tI\n+chrM\t1077\tA\t1\t,\tI\n+chrM\t1078\tC\t1\t,$\tI\n+chrM\t1090\tT\t1\t^:,\tI\n+chrM\t1091\tT\t1\t,\tI\n+chrM\t1092\tC\t1\tn\t"\n+chrM\t1093\tA\t1\t,\tI\n+chrM\t1094\tC\t1\t,\tI\n+chrM\t1095\tT\t1\t,\t7\n+chrM\t1096\tC\t1\ta\tB\n+chrM\t1097\tA\t1\t,\tI\n+chrM\t1098\tA\t1\t,\tI\n+chrM\t1099\tA\t1\t,\tI\n+chrM\t1100\tA\t1\t,\tI\n+chrM\t1101\tT\t1\t,\tI\n+chrM\t1102\tG\t2\t,^:,\t(I\n+chrM\t1103\tA\t2\t,,\tII\n+chrM\t1104\tA\t2\t,,\tI+\n+chrM\t1105\tC\t2\t,,\t.I\n+chrM\t1106\tA\t2\t,,\t8I\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/1.sam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/1.sam Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,29 @@
+@QNAME FLAG RNAME POS MAPQ CIGAR MRNM MPOS ISIZE SEQ QUAL OPT
+1378_11_329 69 * 0 0 * * 0 0 AGACCGGGCGGGGTGGCGTTCGGT %##+'#######%###$#$##$(#
+1378_11_329 133 * 0 0 * * 0 0 GTTCGTGGCCGGTGGGTGTTTGGG ###$$#$#$&#####$'$#$###$
+1378_17_1788 69 * 0 0 * * 0 0 TGCCGTGTCTTGCTAACGCCGATT #'#$$#$###%%##$$$$######
+1378_17_1788 133 * 0 0 * * 0 0 TGGGTGGATGTGTTGTCGTTCATG #$#$###$#$#######$#$####
+1378_25_2035 69 * 0 0 * * 0 0 CTGCGTGTTGGTGTCTACTGGGGT #%#'##$#$##&%#%$$$%#%#'#
+1378_25_2035 133 * 0 0 * * 0 0 GTGCGTCGGGGAGGGTGCTGTCGG ######%#$%#$$###($###&&%
+1378_28_770 89 chr11.nib:1-134452384 72131356 37 17M1I5M = 72131356 0 CACACTGTGACAGACAGCGCAGC 00/02!!0//1200210!!44/1 XT:A:U CM:i:2 SM:i:37 AM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:22
+1378_28_770 181 chr11.nib:1-134452384 72131356 0 24M = 72131356 0 TTGGTGCGCGCGGTTGAGGGTTGG $$(#%%#$%#%####$%%##$###
+1378_33_1945 113 chr2.nib:1-242951149 181247988 0 23M chr12.nib:1-132349534 41710908 0 GAGAGAGAGAGAGAGAGAGAGAG PQRVUMNXYRPUXYXWXSOSZ]M XT:A:R CM:i:0 SM:i:0 AM:i:0 X0:i:163148 XM:i:0 XO:i:0 XG:i:0 MD:Z:23
+1378_33_1945 177 chr12.nib:1-132349534 41710908 0 23M chr2.nib:1-242951149 181247988 0 AGAGAGAGAGAGAGAGAGAGAGA SQQWZYURVYWX]]YXTSY]]ZM XT:A:R CM:i:0 SM:i:0 AM:i:0 X0:i:163148 XM:i:0 XO:i:0 XG:i:0 MD:Z:23
+1378_34_789 69 * 0 0 * * 0 0 ATGGTGGCTGACGCGTTTGACTGT #$##%#$##$&$#%##$##$###$
+1378_34_789 133 * 0 0 * * 0 0 GGGCTTGCGTTAGTGAGAGGTTGT ###%$%$%%###$####$###$#&
+1378_35_263 115 chr16.nib:1-88827254 19671878 0 23M = 19671877 -1 AGAGAGAGAGAGAGAGAGAGTCT 77543:<55#"4!&=964518A> XT:A:R CM:i:2 SM:i:0 AM:i:0 X0:i:4 X1:i:137 XM:i:2 XO:i:0 XG:i:0 MD:Z:23
+1378_35_263 179 chr16.nib:1-88827254 19671877 0 23M = 19671878 1 GAGAGAGAGAGAGAGAGAGAGTC LE7402DD34FL:27AKE>;432 XT:A:R CM:i:0 SM:i:0 AM:i:0 X0:i:265 XM:i:0 XO:i:0 XG:i:0 MD:Z:23
+1378_43_186 69 * 0 0 * * 0 0 ATACTAGTTGGGACGCGTTGTGCT #$(4%$########$#$###$$$#
+1378_43_186 133 * 0 0 * * 0 0 GCTAGGGTTTGGGTTTGCGGTGGG $%#$########%##%#$###'#'
+1378_51_1671 117 chr2.nib:1-242951149 190342418 0 24M = 190342418 0 CTGGCGTTCTCGGCGTGGATGGGT #####$$##$#%#%%###%$#$##
+1378_51_1671 153 chr2.nib:1-242951149 190342418 37 16M1I6M = 190342418 0 TCTAACTTAGCCTCATAATAGCT /<<!"0///////00/!!0121/ XT:A:U CM:i:2 SM:i:37 AM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:22
+1378_56_324 117 chr2.nib:1-242951149 80324999 0 24M = 80324999 0 TCCAGTCGCGTTGTTAGGTTCGGA #$#$$$#####%##%%###**#+/
+1378_56_324 153 chr2.nib:1-242951149 80324999 37 8M1I14M = 80324999 0 TTTAGCCCGAAATGCCTAGAGCA 4;6//11!"11100110////00 XT:A:U CM:i:2 SM:i:37 AM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:22
+1378_56_773 69 * 0 0 * * 0 0 TGTCGTGAGGTCACTTATCCCCAT &%#%##%%#####&#$%##$%##$
+1378_56_773 133 * 0 0 * * 0 0 TCTGGTCGGTTTCGGGGAGTGGAA ##%%#&$###$#$##%$####%%$
+1378_62_2027 69 * 0 0 * * 0 0 CTTCCACGATCTGCTCGCTGTGGT (#&&$##$$#$%#%$$$#$###'#
+1378_62_2027 133 * 0 0 * * 0 0 GTTGGCCTGGCCTGCCGTGCTGCG *##),/%##$)#%##1$#'%.#&#
+1378_62_2029 69 * 0 0 * * 0 0 TCTGGGCTGTCTTCGGGTCGGTGT $%$$####$##$$#)##%%#$###
+1378_62_2029 133 * 0 0 * * 0 0 GGCGGTGTGTGGTGCGGCTGTGCG /$$$=(####%####)$$%$-&%#
+1378_67_1795 81 chr16.nib:1-88827254 26739130 0 23M chrY.nib:1-57772954 57401793 0 TGGCATTCCTGTAGGCAGAGAGG AZWWZS]!"QNXZ]VQ]]]/2]] XT:A:R CM:i:2 SM:i:0 AM:i:0 X0:i:3 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:23
+1378_67_1795 161 chrY.nib:1-57772954 57401793 37 23M chr16.nib:1-88827254 26739130 0 GATCACCCAGGTGATGTAACTCC ]WV]]]]WW]]]]]]]]]]PU]] XT:A:U CM:i:0 SM:i:37 AM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:23
\ No newline at end of file

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/1.scf

Binary file rnaseq/cutadapt/test-data/1.scf has changed

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/1.sff

Binary file rnaseq/cutadapt/test-data/1.sff has changed

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/1.tabular Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,6 @@
+chr22 1000 NM_17
+chr22 2000 NM_18
+chr10 2200 NM_10
+chr10 hap test
+chr10 1200 NM_11
+chr22 1600 NM_19
\ No newline at end of file

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/1.txt Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,10 @@
+chr1    4225    19670
+chr10   6       8
+chr1    24417   24420
+chr6_hla_hap2   0       150
+chr2    1       5
+chr10   2       10
+chr1    30      55
+chrY    1       20
+chr1    1225979 42287290
+chr10   7       8

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/1.wig
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/1.wig Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,3 @@
+track type=wiggle_0 name="tb_knownGene" description="table browser query on knownGene" visibility=3 url=
+chr7 127475281 127491632 NM_000230 0 + 127486022 127488767 0 3 29,172,3225, 0,10713,13126,
+chr7 127486011 127488900 D49487 0 + 127486022 127488767 0 2 155,490, 0,2399,

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/13.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/13.bed Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,96 @@
+chr16 20682314 20682813 ENSG00000005187
+chrX 123339504 123340003 ENSG00000009694
+chr3 52503897 52504396 ENSG00000010327
+chr6 112089190 112089689 ENSG00000010810
+chr6 112089249 112089748 ENSG00000010810
+chr6 112089261 112089760 ENSG00000010810
+chr2 31310208 31310707 ENSG00000013016
+chr22 16598265 16598764 ENSG00000015475
+chr22 16598139 16598638 ENSG00000015475
+chr22 16596941 16597440 ENSG00000015475
+chr22 16596908 16597407 ENSG00000015475
+chr12 101335726 101336225 ENSG00000017427
+chr12 101320236 101320735 ENSG00000017427
+chr12 101320163 101320662 ENSG00000017427
+chr12 101313809 101314308 ENSG00000017427
+chr7 99282701 99283200 ENSG00000021461
+chr7 99263073 99263572 ENSG00000021461
+chr19 38013262 38013761 ENSG00000021488
+chr3 52206685 52207184 ENSG00000023330
+chr3 52206657 52207156 ENSG00000023330
+chr10 101532011 101532510 ENSG00000023839
+chr10 101531994 101532493 ENSG00000023839
+chr5 71651457 71651956 ENSG00000049883
+chr3 52796382 52796881 ENSG00000055957
+chr3 52786149 52786648 ENSG00000055957
+chr6 166698400 166698899 ENSG00000060762
+chr6 166698708 166699207 ENSG00000060762
+chr16 2029817 2030316 ENSG00000065057
+chr10 126075862 126076361 ENSG00000065154
+chr10 126075869 126076368 ENSG00000065154
+chr10 123223889 123224388 ENSG00000066468
+chr10 123227846 123228345 ENSG00000066468
+chr10 123229123 123229622 ENSG00000066468
+chr10 123229361 123229860 ENSG00000066468
+chr10 123229555 123230054 ENSG00000066468
+chr10 123231339 123231838 ENSG00000066468
+chr10 123231360 123231859 ENSG00000066468
+chr10 123287470 123287969 ENSG00000066468
+chr1 92746841 92747340 ENSG00000067208
+chr1 92860438 92860937 ENSG00000067208
+chr3 151165384 151165883 ENSG00000070087
+chr16 56546748 56547247 ENSG00000070729
+chr16 56475004 56475503 ENSG00000070729
+chr8 145589254 145589753 ENSG00000071894
+chr1 159899157 159899656 ENSG00000072694
+chr1 159899076 159899575 ENSG00000072694
+chr4 5763326 5763825 ENSG00000072840
+chr2 70753968 70754467 ENSG00000075340
+chr2 70744123 70744622 ENSG00000075340
+chr2 70744138 70744637 ENSG00000075340
+chr2 70742773 70743272 ENSG00000075340
+chr2 70744065 70744564 ENSG00000075340
+chr3 172801314 172801813 ENSG00000075651
+chr3 172812085 172812584 ENSG00000075651
+chr4 74565827 74566326 ENSG00000079557
+chr19 10684644 10685143 ENSG00000079805
+chr19 10689340 10689839 ENSG00000079805
+chr19 10689256 10689755 ENSG00000079805
+chr13 93889844 93890343 ENSG00000080166
+chr2 151974175 151974674 ENSG00000080345
+chr2 151974202 151974701 ENSG00000080345
+chr5 113796627 113797126 ENSG00000080709
+chr5 113725416 113725915 ENSG00000080709
+chr5 113725066 113725565 ENSG00000080709
+chr2 165249579 165250078 ENSG00000082438
+chr2 165249502 165250001 ENSG00000082438
+chr4 187745932 187746431 ENSG00000083857
+chr2 27572711 27573210 ENSG00000084734
+chr1 111758461 111758960 ENSG00000085465
+chr11 49124766 49125265 ENSG00000086205
+chr11 49124879 49125378 ENSG00000086205
+chr7 26298700 26299199 ENSG00000086300
+chr7 26297541 26298040 ENSG00000086300
+chr16 80625865 80626364 ENSG00000086696
+chr19 54159879 54160378 ENSG00000087086
+chr16 55552764 55553263 ENSG00000087237
+chr3 187840344 187840843 ENSG00000090512
+chr3 187840445 187840944 ENSG00000090512
+chr4 25358148 25358647 ENSG00000091490
+chr3 113535219 113535718 ENSG00000091972
+chr3 113534107 113534606 ENSG00000091972
+chr15 40483770 40484269 ENSG00000092529
+chr15 40427094 40427593 ENSG00000092529
+chr15 40481381 40481880 ENSG00000092529
+chr15 40457707 40458206 ENSG00000092529
+chr15 40438491 40438990 ENSG00000092529
+chr1 120055534 120056033 ENSG00000092621
+chr1 120063274 120063773 ENSG00000092621
+chr6 159106769 159107268 ENSG00000092820
+chr6 159106768 159107267 ENSG00000092820
+chr6 159106766 159107265 ENSG00000092820
+chr9 111041832 111042331 ENSG00000095203
+chr9 110974075 110974574 ENSG00000095203
+chr10 94822723 94823222 ENSG00000095596
+chr10 94823138 94823637 ENSG00000095596
+chr10 29005931 29006430 ENSG00000095739

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/1_bed_random_lines_1_seed_asdf_out.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/1_bed_random_lines_1_seed_asdf_out.bed Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,1 @@
+chr5 131424298 131424460 CCDS4149.1_cds_0_0_chr5_131424299_f 0 +

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/2.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/2.bed Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,68 @@
+chr1 147962192 147962580 NM_005997_cds_0_0_chr1_147962193_r 0 -
+chr1 147984545 147984630 BC007833_cds_0_0_chr1_147984546_f 0 +
+chr1 148078400 148078582 AJ011123_cds_0_0_chr1_148078401_r 0 -
+chr1 148185136 148185276 NM_002796_cds_0_0_chr1_148185137_f 0 +
+chr10 55251623 55253124 AY029205_cds_0_0_chr10_55251624_r 0 -
+chr11 116124407 116124501 AK057832_cds_0_0_chr11_116124408_r 0 -
+chr11 116206508 116206563 NM_000040_cds_1_0_chr11_116206509_f 0 +
+chr11 116211733 116212337 BC005380_cds_0_0_chr11_116211734_r 0 -
+chr11 130745911 130745993 AY358331_cds_0_0_chr11_130745912_f 0 +
+chr12 38440094 38440321 NM_052885_cds_0_0_chr12_38440095_r 0 -
+chr12 38905200 38905351 AY792511_cds_0_0_chr12_38905201_f 0 +
+chr13 112381694 112381953 NM_207440_cds_1_0_chr13_112381695_f 0 +
+chr13 29680676 29680875 NM_032116_cds_0_0_chr13_29680677_r 0 -
+chr14 98521864 98521922 U88895_cds_0_0_chr14_98521865_f 0 +
+chr14 98710240 98712285 NM_022898_cds_0_0_chr14_98710241_r 0 -
+chr15 41486872 41487060 BX537418_cds_0_0_chr15_41486873_r 0 -
+chr15 41673708 41673857 AK223365_cds_0_0_chr15_41673709_f 0 +
+chr15 41679161 41679250 NM_153700_cds_0_0_chr15_41679162_r 0 -
+chr15 41773540 41773689 AK223365_cds_0_0_chr15_41773541_f 0 +
+chr16 142908 143003 NM_005332_cds_0_0_chr16_142909_f 0 +
+chr16 179197 179339 BC065198_cds_0_0_chr16_179198_r 0 -
+chr16 244413 244681 AK057165_cds_2_0_chr16_244414_f 0 +
+chr16 259268 259383 AB016929_cds_0_0_chr16_259269_r 0 -
+chr18 23786114 23786321 NM_001792_cds_0_0_chr18_23786115_r 0 -
+chr18 59406881 59407046 NM_012397_cds_1_0_chr18_59406882_f 0 +
+chr18 59455932 59456337 AB046400_cds_0_0_chr18_59455933_r 0 -
+chr18 59528407 59528575 AY792326_cds_0_0_chr18_59528408_f 0 +
+chr19 59068595 59069564 BC013995_cds_1_0_chr19_59068596_f 0 +
+chr19 59236026 59236146 NM_198481_cds_0_0_chr19_59236027_r 0 -
+chr19 59297998 59298008 NM_004542_cds_0_0_chr19_59297999_f 0 +
+chr19 59318205 59318718 AK128544_cds_3_0_chr19_59318206_r 0 -
+chr2 118288583 118288668 NM_006773_cds_0_0_chr2_118288584_f 0 +
+chr2 118390395 118390500 BC005078_cds_0_0_chr2_118390396_r 0 -
+chr2 220108689 220109267 AY125465_cds_0_0_chr2_220108690_f 0 +
+chr2 220229609 220230869 NM_024536_cds_0_0_chr2_220229610_r 0 -
+chr20 33330413 33330423 NM_181466_cds_0_0_chr20_33330414_r 0 -
+chr20 33485370 33486123 BC085019_cds_1_0_chr20_33485371_f 0 +
+chr20 33488491 33489122 NM_000557_cds_1_0_chr20_33488492_r 0 -
+chr20 33513606 33513792 AF022655_cds_1_0_chr20_33513607_f 0 +
+chr21 32687402 32687588 NM_032910_cds_0_0_chr21_32687403_f 0 +
+chr21 32869641 32870022 NM_018277_cds_3_0_chr21_32869642_r 0 -
+chr21 33321040 33322012 NM_005806_cds_1_0_chr21_33321041_f 0 +
+chr21 33728358 33728724 AK129657_cds_0_0_chr21_33728359_r 0 -
+chr22 30120223 30120265 NM_004147_cds_0_0_chr22_30120224_f 0 +
+chr22 30160419 30160661 BC032941_cds_0_0_chr22_30160420_r 0 -
+chr22 30228824 30228916 NM_001007467_cds_1_0_chr22_30228825_f 0 +
+chr22 30340151 30340376 CR456540_cds_0_0_chr22_30340152_r 0 -
+chr5 131311206 131311254 AF099740_cds_11_0_chr5_131311207_r 0 -
+chr5 131424298 131424460 NM_000588_cds_0_0_chr5_131424299_f 0 +
+chr5 131556601 131556672 BC035813_cds_0_0_chr5_131556602_r 0 -
+chr5 131621326 131621419 BC003096_cds_0_0_chr5_131621327_f 0 +
+chr6 108299600 108299744 NM_007214_cds_0_0_chr6_108299601_r 0 -
+chr6 108594662 108594687 NM_003269_cds_0_0_chr6_108594663_f 0 +
+chr6 108640045 108640151 NM_003795_cds_0_0_chr6_108640046_r 0 -
+chr6 108722976 108723115 NM_145315_cds_0_0_chr6_108722977_f 0 +
+chr7 113660517 113660685 AF467257_cds_1_0_chr7_113660518_f 0 +
+chr7 116512159 116512389 NM_003391_cds_0_0_chr7_116512160_r 0 -
+chr7 116714099 116714152 NM_000492_cds_0_0_chr7_116714100_f 0 +
+chr7 116945541 116945787 AF377960_cds_0_0_chr7_116945542_r 0 -
+chr8 118881131 118881317 NM_000127_cds_0_0_chr8_118881132_r 0 -
+chr9 128764156 128764189 BC051300_cds_0_0_chr9_128764157_f 0 +
+chr9 128787519 128789136 NM_014908_cds_0_0_chr9_128787520_r 0 -
+chr9 128789552 128789584 NM_015354_cds_0_0_chr9_128789553_f 0 +
+chr9 128850516 128850624 AB058751_cds_0_0_chr9_128850517_r 0 -
+chrX 122745047 122745924 NM_001167_cds_1_0_chrX_122745048_f 0 +
+chrX 152648964 152649196 NM_000425_cds_0_0_chrX_152648965_r 0 -
+chrX 152691446 152691471 AF101728_cds_0_0_chrX_152691447_f 0 +
+chrX 152694029 152694263 BC052303_cds_0_0_chrX_152694030_r 0 -

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/2.bigwig

Binary file rnaseq/cutadapt/test-data/2.bigwig has changed

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/2.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/2.fasta Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,11 @@
+>Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+gttcgatgcc taaaatacct tcttttgtcc ctacacagac cacagttttc ctaatggctt
+tacaccgact agaaattctt gtgcaagcac taattgaaag cggttggcct agagtgttac
+cggtttgtat agctgagcgc gtctcttgcc ctgatcaaag gttcattttc tctactttgg
+aagacgttgt ggaagaatac aacaagtacg agtctctccc ccctggtttg ctgattactg
+gatacagttg taataccctt cgcaacaccg cgtaactatc tatatgaatt attttccctt
+tattatatgt agtaggttcg tctttaatct tcctttagca agtcttttac tgttttcgac
+ctcaatgttc atgttcttag gttgttttgg ataatatgcg gtcagtttaa tcttcgttgt
+ttcttcttaa aatatttatt catggtttaa tttttggttt gtacttgttc aggggccagt
+tcattattta ctctgtttgt atacagcagt tcttttattt ttagtatgat tttaatttaa
+aacaattcta atggtcaaaa a
\ No newline at end of file

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/2.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/2.fastq Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,12 @@
+@EAS54_6_R1_2_1_413_324
+CCCTTCTTGTCTTCAGCGTTTCTCC
++
+;;3;;;;;;;;;;;;7;;;;;;;88
+@EAS54_6_R1_2_1_540_792
+TTGGCAGGCCAAGGCCGATGGATCA
++
+;;;;;;;;;;;7;;;;;-;;;3;83
+@EAS54_6_R1_2_1_443_348
+GTTGCTTCTGGCGTGGGTGGGGGGG
++EAS54_6_R1_2_1_443_348
+;;;;;;;;;;;9;7;;.7;393333
\ No newline at end of file

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/2.fastqsanger
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/2.fastqsanger Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,8 @@
+@1831_573_1004/1
+AATACTTTCGGCGCCCTAAACCAGCTCACTGGGG
++
+29 27 34 5 5 24 24 20 17 10 34 29 20 27 13 30 27 22 24 11 28 19 17 27 17 24 17 25 27 7 24 14 12 22
+@1831_573_1050/1
+TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT
++
+26 31 31 16 22 30 31 28 29 22 30 30 31 32 23 30 28 28 31 19 32 30 32 19 8 5 10 13 6 5 10 6 16 11
\ No newline at end of file

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/2.fastqsolexa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/2.fastqsolexa Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,8 @@
+@seq1
+GACAGCTTGGTTTTTAGTGAGTTGTTCCTTTCTTT
++seq1
+hhhhhhhhhhhhhhhhhhhhhhhhhhPW@hhhhhh
+@seq2
+GCAATGACGGCAGCAATAAACTCAACAGGTGCTGG
++seq2
+hhhhhhhhhhhhhhYhhahhhhWhAhFhSIJGChO
\ No newline at end of file

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/2.interval
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/2.interval Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,14 @@
+chrX 151117436 151117437 + 0.14351
+chrX 151117437 151117438 + 0.139843
+chrX 151117438 151117439 + 0.132509
+chrX 151117439 151117440 + 0.139843
+chrX 151117440 151117441 + 0.169179
+chrX 151117441 151117442 + 0.257185
+chrX 151117442 151117443 + 0.319523
+chrX 151117443 151117444 + 0.367193
+chrX 151117444 151117445 + 0.400195
+chrX 151117445 151117446 + 0.425864
+chrX 151117446 151117447 + 0.444198
+chrX 151117447 151117448 + 0.455199
+chrX 151117448 151117449 + 0.462533
+chrX 151117449 151117450 + 0.4662

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/2.lav
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/2.lav Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,22 @@
+#:lav
+s {
+  "/galaxy/data/hg16/seq/chr19.nib" 1 63811651 0 1
+  "/galaxy/data/mm5/seq/chr11.nib" 1 121648857 0 1
+}
+h {
+  "> hg16.chr19"
+  "> mm5.chr11 (reverse complement)"
+}
+a {
+  s 3500
+  b 3001012 70568380
+  e 3001075 70568443
+  l 3001012 70568380 3001075 70568443 81
+}
+a {
+  s 3900
+  b 3008279 70573976
+  e 3008357 70574054
+  l 3008279 70573976 3008357 70574054 78
+}
+#:eof

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/2.sam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/2.sam Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,10 @@
+HWI-EAS91_1_30788AAXX:1:1:1095:605 0 chrM 23 25 36M * 0 0 AAGCAAGNNACTGAAAATGCCTAGATGAGTATTCTT IIIIIII""IIIIIIIIIIIIIIIEIIIIIIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27
+HWI-EAS91_1_30788AAXX:1:1:1650:1185 0 chrM 14956 25 36M * 0 0 ACCCCAGNNAACCCTCTCAGCACTCCCCCTCATATT IIIIIII""IIIIIIIIIIII6IIIIIIIII5I-II NM:i:1 X1:i:1 MD:Z:7N0N27
+HWI-EAS91_1_30788AAXX:1:1:799:192 16 chrM 8421 25 36M * 0 0 CCTGTAGCCCTAGCCGTGCGGCTAACCNNTAACATT II%::I<IIIIIEIII8IIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27
+HWI-EAS91_1_30788AAXX:1:1:1082:719 16 chrM 7191 25 36M * 0 0 TAAATTAACCCATACCAGCACCATAGANNCTCAAGA <III0EII3+3I29I>III8AIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27
+HWI-EAS91_1_30788AAXX:1:1:1746:1180 16 chrM 12013 25 36M * 0 0 CCTAAGCTTCAAACTAGATTACTTCTCNNTAATTTT IIIIIIIIFIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27
+HWI-EAS91_1_30788AAXX:1:1:606:460 0 chrM 4552 25 36M * 0 0 TTAATTTNNATTATAATAACACTCACAATATTCATA IIIIIII""IIIIIIIIIIIIIIIIII?I6IIIII6 NM:i:1 X1:i:1 MD:Z:7N0N27
+HWI-EAS91_1_30788AAXX:1:1:1059:362 16 chrM 7348 25 36M * 0 0 GGCCACCAATGATACTGAAGCTACGAGNNTACCGAT II/<)2IIIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27
+HWI-EAS91_1_30788AAXX:1:1:1483:1161 16 chrM 15080 25 36M * 0 0 TCCTGATCCTAGCACTCATCCCCACCCNNCACATAT HIIIIIFIIAIHIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27
+HWI-EAS91_1_30788AAXX:1:1:1273:600 16 chrM 13855 25 36M * 0 0 GTATTAGACACCCATACCTCAGGATACNNCTCAGTA IIIIIIIIIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27
+HWI-EAS91_1_30788AAXX:1:1:1190:1283 16 chrM 15338 25 36M * 0 0 TATATCGCACATTACCCTGGTCTTGTANNCCAGAAA EIII?-IIIIIAIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/2.sff

Binary file rnaseq/cutadapt/test-data/2.sff has changed

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/2.tabular Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,10 @@
+1 68 4.1
+2 71 4.6
+3 62 3.8
+4 75 4.4
+5 58 3.2
+6 60 3.1
+7 67 3.8
+8 68 4.1
+9 71 4.3
+10 69 3.7

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/2.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/2.txt Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,8 @@
+chr1    4225    19670
+chr10   6       8
+chr1    24417   24420
+chr6_hla_hap2   0       150
+chr2    1       5
+chr1    30      55
+chrY    1       20
+chr1    1225979 42287290

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/2.wig
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/2.wig Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,23 @@
+track type=wiggle_0 name="Conservation" description="Human/Chimp/Mouse/Rat/Chicken Multiz Alignments & PhyloHMM Cons"
+# output date: 2007-10-23 14:29:10 UTC
+# chrom specified: chrX
+# position specified: 151073054-151383976
+# This data has been compressed with a minor loss in resolution.
+# (Worst case: 0.00747734) The original source data
+# (before querying and compression) is available at
+# http://hgdownload.cse.ucsc.edu/downloads.html
+variableStep chrom=chrX span=1
+151117437 0.14351
+151117438 0.139843
+151117439 0.132509
+151117440 0.139843
+151117441 0.169179
+151117442 0.257185
+151117443 0.319523
+151117444 0.367193
+151117445 0.400195
+151117446 0.425864
+151117447 0.444198
+151117448 0.455199
+151117449 0.462533
+151117450 0.4662

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/2gen.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/2gen.fastq Sat Feb 21 16:33:42 2015 +0100

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/3.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/3.bed Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,25 @@
+chr1 147962006 147975713 NM_005997 0 - 147962192 147975670 0 6 574,145,177,115,153,160, 0,1543,7859,9048,9340,13547,
+chr1 147984101 148035079 BC007833 0 + 147984545 148033414 0 14 529,32,81,131,118,153,300,206,84,49,85,130,46,1668, 0,25695,28767,33118,33695,33998,35644,38005,39629,40577,41402,43885,48367,49310,
+chr1 148077485 148111797 NM_002651 0 - 148078400 148111728 0 12 1097,121,133,266,124,105,110,228,228,45,937,77, 0,2081,2472,6871,9907,10257,11604,14199,15637,18274,23636,34235,
+chr1 148185113 148187485 NM_002796 0 + 148185136 148187378 0 7 163,207,147,82,117,89,120, 0,416,877,1199,1674,1977,2252,
+chr2 118288484 118306183 NM_006773 0 + 118288583 118304530 0 14 184,285,144,136,101,200,115,140,162,153,114,57,178,1796, 0,2765,4970,6482,6971,7183,7468,9890,10261,10768,11590,14270,14610,15903,
+chr2 118389378 118390700 BC005078 0 - 118390395 118390500 0 1 1322, 0,
+chr2 220108603 220116964 NM_001927 0 + 220108689 220116217 0 9 664,61,96,162,126,221,44,83,789, 0,1718,1874,2118,2451,2963,5400,7286,7572,
+chr2 220229182 220233943 NM_024536 0 - 220229609 220233765 0 4 1687,180,574,492, 0,1990,2660,4269,
+chr5 131170738 131357870 AF099740 0 - 131311206 131357817 0 31 112,124,120,81,65,40,120,129,61,88,94,79,72,102,144,117,89,73,96,135,135,78,74,52,33,179,100,102,65,115,248, 0,11593,44117,47607,104668,109739,114675,126366,135488,137518,138009,140437,152389,153373,155388,159269,160793,162981,164403,165577,166119,167611,169501,178260,179675,180901,181658,182260,182953,183706,186884,
+chr5 131424245 131426795 NM_000588 0 + 131424298 131426383 0 5 215,42,90,42,535, 0,313,1658,1872,2015,
+chr5 131556201 131590458 NM_004199 0 - 131556601 131582218 0 15 471,97,69,66,54,100,71,177,194,240,138,152,97,100,170, 0,2316,2802,5596,6269,11138,11472,15098,16528,17674,21306,24587,25142,25935,34087,
+chr5 131621285 131637046 NM_003687 0 + 131621326 131635821 0 7 134,152,82,179,164,118,1430, 0,4915,8770,13221,13609,14097,14331,
+chr6 108298214 108386086 NM_007214 0 - 108299600 108385906 0 21 1530,105,99,102,159,174,60,83,148,155,93,133,95,109,51,59,62,113,115,100,304, 0,2490,6246,10831,12670,23164,23520,27331,31052,32526,34311,36130,36365,38609,41028,42398,43048,51479,54500,59097,87568,
+chr6 108593954 108616704 NM_003269 0 + 108594662 108615360 0 9 733,146,88,236,147,97,150,106,1507, 0,5400,8778,10445,12037,14265,14749,15488,21243,
+chr6 108639410 108689143 NM_152827 0 - 108640045 108688818 0 3 741,125,487, 0,2984,49246,
+chr6 108722790 108950942 NM_145315 0 + 108722976 108950321 0 13 325,224,52,102,131,100,59,83,71,101,141,114,750, 0,28931,52094,60760,61796,71339,107102,152319,181970,182297,215317,224802,227402,
+chr7 113320332 113924911 AK131266 0 + 113862563 113893433 0 20 285,91,178,90,58,75,138,51,201,178,214,105,88,84,77,102,122,70,164,1124, 0,201692,340175,448290,451999,484480,542213,543265,543478,545201,556083,558358,565876,567599,573029,573245,575738,577123,577946,603455,
+chr7 116511232 116557294 NM_003391 0 - 116512159 116556994 0 5 1157,265,278,227,383, 0,20384,37843,43339,45679,
+chr7 116713967 116902666 NM_000492 0 + 116714099 116901113 0 27 185,111,109,216,90,164,126,247,93,183,192,95,87,724,129,38,251,80,151,228,101,249,156,90,173,106,1754, 0,24290,29071,50936,54313,55285,56585,60137,62053,68678,79501,107776,110390,111971,114967,122863,123569,126711,130556,131618,134650,147559,162475,172879,184725,185496,186945,
+chr7 116944658 117107512 AF377960 0 - 116945541 116979926 0 23 1129,102,133,64,186,206,179,188,153,100,87,80,96,276,118,255,151,100,204,1654,225,108,173, 0,7364,8850,10413,13893,14398,17435,24259,24615,35177,35359,45901,47221,49781,56405,66857,69787,72208,73597,80474,100111,150555,162681,
+chr8 118880786 119193239 NM_000127 0 - 118881131 119192466 0 11 531,172,161,90,96,119,133,120,108,94,1735, 0,5355,7850,13505,19068,20309,23098,30863,36077,37741,310718,
+chr9 128763240 128783870 NM_174933 0 + 128764156 128783586 0 12 261,118,74,159,76,48,56,63,129,117,127,370, 0,522,875,5630,12374,12603,15040,15175,18961,19191,20037,20260,
+chr9 128787362 128789566 NM_014908 0 - 128787519 128789136 0 1 2204, 0,
+chr9 128789530 128848928 NM_015354 0 + 128789552 128848511 0 44 54,55,74,85,81,45,93,120,212,115,201,90,66,120,127,153,127,88,77,115,121,67,129,140,107,207,170,70,68,196,78,86,146,182,201,93,159,138,75,228,132,74,130,594, 0,1491,5075,8652,9254,10312,11104,11317,20808,21702,23060,25462,31564,32908,33566,34851,35204,35595,35776,37202,38860,39111,39891,40349,42422,45499,45827,46675,47158,47621,50453,50840,51474,51926,53831,54186,55119,55619,57449,57605,57947,58352,58541,58804,
+chr9 128849867 128870133 NM_020145 0 - 128850516 128869987 0 11 757,241,101,90,24,63,93,134,129,142,209, 0,1071,1736,2085,2635,4201,6376,6736,13056,14247,20057,

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/3.bigwig

Binary file rnaseq/cutadapt/test-data/3.bigwig has changed

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/3.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/3.fasta Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,50 @@
+>HSFAU1
+ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgc
+agctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcg
+cccagatcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgc
+tcctggcaggccccctggaggatgaggccactctgggccagtgcggggtggaggccc
+tgactaccctggaagtagcaggccgcatgcttggaggtaaagttcatggttccctggccc
+gtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaagaaga
+agacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgccca
+cctttggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttc
+tctaataaaaaagccacttagttcagtcaaaaaaaaaa
+>HSFAU2
+ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgc
+agctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcg
+cccagatcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgc
+tcctggcaggcgcgcccctggaggatgcactctgggccagtgcggggtggaggccc
+tgactaccctggaagtagcaggccgcatgcttggaggtaaagttcatggttccctggccc
+gtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaagaaga
+agacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgccca
+cctttggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttc
+tctaataaaaaagccacttagttcagtcaaaaaaaaaa
+>HSFAU3
+ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgc
+agctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcg
+cccagatcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgc
+tcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggccc
+tgactaccctggaagtagcaggccgcatgcttggaggtaaagttcatggttccctggccc
+gtgctggaaaagtgagaggtcagactcctaagggggccaaacaggagaagaagaagaaga
+agacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgccca
+cctttggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttc
+tctaataaaaaagccacttagttcagtcaaaaaaaaaa
+>HSFAU4
+ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgc
+agctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcg
+cccagatcaaggctcatgaaatagcctcactggagggcattgccccggaagatcaagtcgtgc
+tcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggccc
+tgactaccctggaagtagcaggccgcatgcttgcccgaggtaaagttcatggttccctggccc
+gtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaagaaga
+agacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgccca
+cctttggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttc
+tctaataaaaaagccacttagttcagtcaaaaaaaaaa
+>HSFAU5
+ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgc
+agctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcg
+cccagatcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgc
+tcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggccc
+tgactaccctggaagtaggccgcatgctttttggaggtaaagttcatggttccctggccc
+gtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaagaaga
+agacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgccca
+cctttggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttc
+tctaataaaaaagccacttagttcagtcaaaaaaaaaa
\ No newline at end of file

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/3.fastqsanger
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/3.fastqsanger Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,20 @@
+@HWI-EAS91_1_30788AAXX:7:21:1542:1758
+GTCAATTGTACTGGTCAATACTAAAAGAATAGGATCGCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA
++HWI-EAS91_1_30788AAXX:7:21:1542:1758
+hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR
+@HWI-EAS91_1_30788AAXX:7:22:1621:462
+ATAATGGCTATTATTGTGGGGGGGATGATGCTGGAAACTAGCCCCAATATCAATCCTATATCAAATCTCACC
++HWI-EAS91_1_30788AAXX:7:22:1621:462
+hhhhhhhhhhhhQAhh@hhhhNhhhfhMbCIScC?hhJhhhhChhhJhhhRhhKhePhc\KhhV\KhXhJhh
+@HWI-EAS91_1_30788AAXX:7:45:408:807
+TACCCGATTTTTTGCTTTCCACTTTATCCTACCCTTATGAGTGCTAGGATCAGGATGGAGAGGATTAGGGCT
++HWI-EAS91_1_30788AAXX:7:45:408:807
+hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh`hhhZh`hhhhhRXhhYh
+@HWI-EAS91_1_30788AAXX:7:49:654:1439
+CTAACTCTATTTATTGTATTTCAACTAAAAATCTCATAGGTTTATTGATAGTTGTGTTGTTGGTGTAAATGG
++HWI-EAS91_1_30788AAXX:7:49:654:1439
+hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhdhh_hG\XhU@
+@HWI-EAS91_1_30788AAXX:7:64:947:234
+TATCAAAAAAGAATATAATCTGAATCAACACTACAACCTATTAGTGTGTAGAATAGGAAGTAGAGGCCTGCG
++HWI-EAS91_1_30788AAXX:7:64:947:234
+hhhhhhhhhhhhhhhhhhhhhhhRhhehhahhhhhJhhhhhhhh^hPhWfhhhhThWUhhfhh_hhNIVPUd

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/3.maf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/3.maf Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,55 @@\n+##maf version=1\n+a score=60426.0\n+s hg17.chr7 127471195 331 + 158628139 gtttgccatcttttgctgctctagggaatccagcagctgtcaccatgtaaacaagcccaggctagaccaGTTACCCTCATCATCTTAGCTGATAGCCAGCCAGCCACCACAGGCAtgagtcaggccatattgctggacccacagaattatgagctaaataaatagtcttgggttaagccactaagttttaggcatagtgtgttatgtaTCTCACAAACATATAAGACTGTGTGTTTGTTGACTGGAGGAAGAGATGCTATAAAGACCACCTTTTAAAACTTCCC-------------------------------AAATACT-GCCACTGATGTCCTG-----ATGGAGGTA-------TGAA-------------------AACATCCACTAA\n+s panTro1.chr6 129885076 331 + 161576975 gtttgccatcttttgctgctcttgggaatccagcagctgtcaccatgtaaacaagcccaggctagaccaGTTACCCTCATCATCTTAGCTGATAGCCAGCCAGCCACCACAGGCAtgagtcaggccatattgctggacccacagaattatgagctaaataaatagtcttgggttaagccactaagttttaggcatagtgtgttatgtaTCTCACAAACATATAAGACTGTGTGTTTGTTGACTGGAGGAAGAGATGCTATAAAGACCACCTTTTGAAACTTCCC-------------------------------AAATACT-GCCACTGATGTCCTG-----ATGGAGGTA-------TGAA-------------------AACATCCACTAA\n+s mm5.chr6 28904571 357 + 149721531 CTCCACTCTCGTTTGCTGTT----------------CTGTCACCATGGAAACAAA-CGAGGGTGGTCCAGTTACTATCTTGACTGCAGCTGGCAGTCAGTT-GCCACT-----CAGGAATAAGGCTATGCCATT-GATCCACTGAACCGTGATCTGGAAACCTGGCTGTTGTTT-------CAAGCCTTGGGGCCAGTTTGCGGTGTTACTCATGA--CTCTAAGATCGTGTGCTTG----CTGCAGGAAGAGACAGCAAGGGGGTTACATTTAAAAAGCCCCCAGTTTAGCTATAGGCAGGCCAACAGGTGTAAAAATACTCACTAGTAATGGGCTGAACTCATGGAGGTAGCATTAGTGAGACACTGTAACTGTTTTTTTAAAAATCACTAA\n+s rn3.chr4 56178191 282 + 187371129 CTTCACTCTCATTTGCTGTT----------------CTGTCACTATGGAGACAAACACAGGCTAGCCCAGTTACTATCTTGATCACAGCAGCT-GTCAGCTAGCTGCCACTCACAGGAATAAGGCCATACCATT-GATCCACTGAACCTTGATCTAGGAATTTGGC----------------------TGGGGCCAGTTTGCGGTGTCACTCATGA--CTCTAAGATTGTGTGTTTG----CTCCAGGAAGAGACGGCAAGAGGATTACCTTTAAAAGGTTC---------------------------------GGAGTCTAGCTGTAGACAGCCCA-----ATG--GGTA-------TAAC-------------------AATACTCACTAA\n+\n+a score=8157.0\n+s hg17.chr7 127471526 58 + 158628139 AATTTGTGGTTTATTCATTTTTCATTATTTTGTTTAAGGAGGTCTATAGTGGAAGAGG\n+s panTro1.chr6 129885407 58 + 161576975 AATTTGTGGTTTATTCGTTTTTCATTATTTTGTTTAAGGAGGTCTATAGTGGAAGAGG\n+s mm5.chr6 28904928 54 + 149721531 AA----CGTTTCATTGATTGCTCATCATTTAAAAAAAGAAATTCCTCAGTGGAAGAGG\n+\n+a score=43613.0\n+s hg17.chr7 127471584 104 + 158628139 GAGATATTTGGggaaatt---ttgtatagactagctttcacgatgttagggaattattattgtgtgataatggtcttgcagttaca-cagaaattcttccttattttt\n+s panTro1.chr6 129885465 104 + 161576975 GAGACATTTGGggaaatt---ttgtatagactagctttcacgatgttagggagttattattgtgtgataatggtcttgcagttaca-cagaaattcttccttattttt\n+s mm5.chr6 28909125 102 + 149721531 GAGACATTTGGGGGAAATACGATGTATA------CTTTCATGATCTTAAAGAATTGCTATTGTTTGATAGTGATATTATGGTTAAATTAAAAAAAAACCCTTACTTTT\n+s rn3.chr4 56182196 99 + 187371129 GAGATATTTGGGGGAAATATGATGTGCA------CTTCCATGATCTTAAAGAATTGCTACTGTTTGATAGTGATCTTATGGTTAAA-TAAAAAAAAT--CTTAGTTGT\n+s canFam1.chr14 52864846 108 - 63549963 GAGATATTTGGGGGAATTTGAATGTAGTGTTGCTCTTTTGTGATGCTAAGAAATTATAATTGTCTGATGATAGTCTCGTGGTTATGGGGGAAATGCTTCCTTATTTTT\n+\n+a score=63217.0\n+s hg17.chr7 127471688 183 + 158628139 tgggaa---gcaccaaag----tagggat---aaaatgtcatgatgtgtgcaatacactttaaaatgtttttg-----ccaaaataatt----------------aatgaagc--aaatatggaaa-ataataattattaaatctaggtgatgggtatattgtagttcactatagtattgcacacttttctgtatgtttaaatttttcatttaaaaa\n+s panTro1.chr6 129885569 183 + 161576975 tgggaa---acaccaaag----tagggat---aaaatgtcatgatgtgtgcaatacgctttaaaatatttttg-----ccaaaataatt----------------aatgaagc--aaatatggaaa-ataataattattaaatctaggtgatgggtatattgtagttcactatagtattgcacacttttctgtatgtttaaaattttcatttaaaaa\n+s mm5.chr6 28909227 176 + 149721531 CATAAA---ATACTCAAATATTTAGGGGTATGACAATGTCATAGTGTCTGCAATTTGCTTTAAAATAATTTTG-------AAAAC---------------------CTGAGGCTAAACTATGGGAA-ATAGCAATTATTACATATGGGTAATAAGTA-----TAACTCACTATATTATTTTTCACTAT----TGTGTTTGAAATTTTCATTTTAAAA\n+s rn3.chr4 56182295 194 + 187371129 TAGAAA---ATACTCAAATATTTAGGGGCGTGACAATGTCACAGTGTCTGCAATTTGCTTTAAAG-ATTTTTAAATATTTAAAAAAGTTTTAATAATTTTGAAAAACTGAAGCTACACTATGGGAA-GTGGTAATTGTTACATATGGGTAATAAGTA-----TAATTCGTTATATTATT-------------TTTCTTAGAATTTTTCATTTGAAAA\n+s canFam1.chr14 52865149 163 - 635499'..b'CCATAAGAAAGTCTCCAATGTGATCTGATGGT-GCCGCCAGGACCTA-TGTCAGCCTACCGTTCCATGTCCCCTCCACACCATCATCACTGCAGGTGTGTTTTCCCACATTTTAAATATCTG-------CTTCCCGGTGGCCTTGAGTCTAGAGGAGTCCCCCCACTATGGTGGCACTAATACTGAAGGTCAGAAATAATCAGTTCTGTGGTGCATGTTGCCCCTGAGGTTCTGTTCGGGAAACTTCTTCTG-AGCAC----ATGCACCTGGCACTGCAAACGTACCAGGA\n+\n+a score=82819.0\n+s hg17.chr7 127472258 423 + 158628139 gatggccca-atccctgtcctct---taaaacctaagggaggagaTGGAAAGGGG-CACCCAACCCAGACTGAGAGACAGGAATTAGCTGCAAGGGGAACTAGGAAAAGCTTCTTTA---AGGATGGAGAGGCCCTAGTGGAAT-GGGGAGATTCTTCCGGGAGAAGCGATGGATGCACAGTTGGGCATCCCCACAGACGGACTGGAAAGAAAAAAGGCCTGGAGGAATCAATGTG-------CAATGTATGTGTGTTCCCTGGTTcaagggctgg-gaactttctcta-aagggccaggtagaaaacattttaggctttctaagccaag--gcaaaat-tgaggatattacatgggtacttatacaacaagaataaacaatt---tacacaattttttgttgacagaattcaaaactttat----agacacagaaatgcaaatttcctgt\n+s panTro1.chr6 129886139 423 + 161576975 gatggccca-atccctgtcctct---taaaacctaagggaggagaTGGAAAGGGG-CACCCAACCCAGACTGAGAGACAGGAATTAGCTGCAAGGGGAACTAGGAAAAGCTTCTTTA---AGGATGGAGAGACCCTAGTGGAAT-GGGGAGATTCTTCCGGGAGAAGCGATGGATGCGCAGTTGGGCATCCCCACAGACGGACTGGAAAGAAAAAAGGCCTGGAGGAATCAATGTG-------CAATGTATGTGTGTTCCCTGGTTcaagggctgg-gaactttctcta-aagggccaggtagaaaacattttaggctttctaagccaag--gcaaaat-tgaggatattacatgggtacttatacaacaagaataaacaatt---tacacaattttttgttgacagaattcaaaactttat----agacacagaaatgtaaatttcctgt\n+s mm5.chr6 28911067 334 + 149721531 AATGGCAGAGGGCTCTGTTCTCT----------------------------------GTCCA---TAGACAAGGAAGC---------CTGCCAGTGG-----------------------TGGAGAGCAGGGCCTATGCAAAACAGGGGGGGTTCTGTGGGCAGAAGGGATGGACCTGACTCCAGGAACGCCCATA-AGAGACGGGCAGGACTGGGAGCCAGGAGCAGCCAGCGCA--------GGTGTGTGTAGGTTTCATAGTTT---------------------------GCAGGTTAGCAAACAATTCTCGCTTGGCAGGCCAAGA-GGGAAAT-AAAGGTTACCCCGTGGGTACTTAT---ACAAGAGAAAACAAG-------ACAATTTTTGGTTGACCAAATTCAGAACTTTATTTGAGGATGCTAAAGTTTTAATTTCTTAA\n+s rn3.chr4 56183879 340 + 187371129 AATGGCAGAGGCCCCTGTTCTCT----------------------------------GTCCA---TAGTCAAAGAAGC---------CTCTCAG----------------------A---TGGAGAGCAGGGCCTATGCAAAAG-AGGGGGCTTCTGTAGGCAGAAGGGATGGACTAGCCTCCGGACATAGCCATAGAGAGGCTGGCAGGACTGAGACCCAGGAGAAGCCAGCGCAGGTGTGCGGGCGTGTGTATATTTCATAGTTT---------------------------GCAGGTTGGCAAACAATTCCTGCTTTGCAGGCCAAGA-GGAAACT-GAAGGTGACCCCGTGAGTGCTTAC---ACAAGAGAAAACAAG-------ACAATTTTTGGTTGACCAAATTCAGAACTTTATTTGAGGATGCTAAAGTTTAAATTTCTTTT\n+s canFam1.chr14 52866108 405 - 63549963 GGAGACTTG-ATGCCTGCCTTCCACTTACAGCCTGTGGGCAGAGGTGGGAAGAGGTCACGCAAGCCAGTTGGAATGAGGGGAGTTGGCTGGAAAGGTGACCAGGACAAGCTACTTCAACCAGGAAGAAGAGACCCC---------GG--------TGCTTGGAGAAGGCCTGATTGAGCAGTCCTGCATGCCCGCCCAC-GACTGGCAGGAATAAAGACCCAGAAGAGCTAACGTG-------CAATGTA------TTTTCTAGTTCCAgggttggcaaactttctctctaagggtgggatgataaacattttaggcttttcagaccaagaggcgacatcagagggtat---gtaggt---------acaagagggaaaagttgcccccggaattttttg--gataaaattcaaaactttacttagggatgccaaaatgtaaacttcatat\n+\n+a score=15522.0\n+s hg17.chr7 127473809 97 + 158628139 tttttttttcaaacttttacaaatgtagaaaccattcttagcttttgggcattaccaaacccggcagtgg-caggctcggttcaccaacgtcatttgc\n+s panTro1.chr6 129887686 97 + 161576975 tttttttttcaaacttttacaaatgtagaaaccattcttagcttttgggcattaccaaacccggcagtgg-AAGGCTCGGTTCACCAACATCATTTGC\n+s canFam1.chr14 52866548 97 - 63549963 tatatttttcaactctttaaaaatgcaaaaaccattcctagc-tcggggccatggtggtcctggtggtggtcggatttggctcacccacataacttgc\n+\n+a score=28088.0\n+s hg17.chr7 127473906 331 + 158628139 agttccccgCTTTATGTTATGGgttttgttttgttttgtttttttt-attgagacagagtttcactcttgttgcccaggctgtagtgcaatggtctgatcttggctcactgcaacctccacttcccaggttcaagccattctcctgcctcagcctctcaagtagctgggattacagacactcaccaccacacctggctaattttgtatttttagtagagatgaggtttcaccatgttggccaggctggtctcgaaatcctgacctcaggtgatccacccaccttggcctcccaaagtgctgggattacaggcttgagctaccacgcctggct\n+s panTro1.chr6 129887783 318 + 161576975 AGTTCCCCGCTTTATATTATGGGttttttttttttttttttttttttattgagacagagtttcactcttgttgcccaggctgtagtg--------------tggctcactgcaacctccacttcccaggttcaagccattctcctgcctcagcctctcaagtagctgggattacagacactcaccaccacacctggctaattttgtatttttagtagagatgaggtttcatcatgttggccaggctggtctcgaaatcctgacctcaggtgatccacccaccttggcctcccaaagtgctgggattacaggcttgagctaccacgcctggct\n+\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/3.sam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/3.sam Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,10 @@
+HWI-EAS91_1_30788AAXX:1:1:1513:715 16 chrM 9563 25 36M * 0 0 CTGACTACCACAACTAAACATCTATGCNNAAAAAAC I+-II?IDIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27
+HWI-EAS91_1_30788AAXX:1:1:1698:516 16 chrM 2735 25 36M * 0 0 TTTACACTCAGAGGTTCAACTCCTCTCNNTAACAAC I9IIIII5IIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27
+HWI-EAS91_1_30788AAXX:1:1:1491:637 16 chrM 10864 25 36M * 0 0 TGTAGAAGCCCCAATTGCCGGATCCATNNTGCTAGC DBAIIIIIIIIIIIFIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27
+HWI-EAS91_1_30788AAXX:1:1:1711:249 16 chrM 10617 25 36M * 0 0 ACCAAACAGAACGCCTGAACGCAGGCCNNTACTTCC IIIIIIIIIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27
+HWI-EAS91_1_30788AAXX:1:1:1634:211 0 chrM 9350 25 36M * 0 0 GAAGCAGNNGCTTGATACTGACACTTCGTCGACGTA IIIIIII""IIIIIIIIIIIIIIIIIIIIII9IIDF NM:i:1 X1:i:1 MD:Z:7N0N27
+HWI-EAS91_1_30788AAXX:1:1:1218:141 16 chrM 14062 25 36M * 0 0 ACAAAACTAACAACAAAAATAACACTCNNAATAAAC I+IIII1IIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27
+HWI-EAS91_1_30788AAXX:1:1:1398:854 16 chrM 3921 25 36M * 0 0 CACCCTTCCCGTACTAATAAATCCCCTNNTCTTCAC IIIII=AIIIIIIIIIIIIIIBIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27
+HWI-EAS91_1_30788AAXX:1:1:1310:991 16 chrM 10002 25 36M * 0 0 CTCCTATGCCTAGAAGGAATAATACTANNACTATTC I:2IEI:IIDIIIIII4IIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27
+HWI-EAS91_1_30788AAXX:1:1:1716:413 0 chrM 6040 25 36M * 0 0 GATCCAANNCTTTATCAACACCTATTCTGATTCTTC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27
+HWI-EAS91_1_30788AAXX:1:1:1630:59 16 chrM 12387 25 36M * 0 0 TCATACTCGACCCCAACCTTACCAACCNNCCGCTCC FIIHII;IIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/3.wig
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/3.wig Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,37 @@
+track type=wiggle_0 name="LaminB1 (Tig3)" description="NKI LaminB1 DamID Map (log2-ratio scores, Tig3 cells)"
+# output date: 2009-07-22 15:55:44 UTC
+# chrom specified: chr20
+# position specified: 1-62435964
+# data values >= 4
+# This data has been compressed with a minor loss in resolution.
+# (Worst case: 0.0448672) The original source data
+# (before querying and compression) is available at
+# http://hgdownload.cse.ucsc.edu/downloads.html
+variableStep chrom=chr20 span=60
+1953668 4.029
+9749454 4.033
+12219969 4.053
+12571904 4.548
+12663417 4.207
+15198014 4.041
+16613945 4.526
+16994767 4.08
+19456653 4.014
+37706076 4.293
+38010695 4.14
+38418792 4.133
+38595669 4.032
+40038834 4.144
+50693133 4.206
+51294426 4
+52890600 4.12
+57414708 4.026
+57623989 4.031
+58977191 5.678
+59059925 4.325
+variableStep chrom=chr12 span=60
+1953668 -4.029
+9749454 -4.033
+12219969 -4.053
+12571904 -4.548
+12663417 -4.207

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/3_wig.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/3_wig.bed Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,26 @@
+chr20 1953667 1953727 + 4.029
+chr20 9749453 9749513 + 4.033
+chr20 12219968 12220028 + 4.053
+chr20 12571903 12571963 + 4.548
+chr20 12663416 12663476 + 4.207
+chr20 15198013 15198073 + 4.041
+chr20 16613944 16614004 + 4.526
+chr20 16994766 16994826 + 4.08
+chr20 19456652 19456712 + 4.014
+chr20 37706075 37706135 + 4.293
+chr20 38010694 38010754 + 4.14
+chr20 38418791 38418851 + 4.133
+chr20 38595668 38595728 + 4.032
+chr20 40038833 40038893 + 4.144
+chr20 50693132 50693192 + 4.206
+chr20 51294425 51294485 + 4.0
+chr20 52890599 52890659 + 4.12
+chr20 57414707 57414767 + 4.026
+chr20 57623988 57624048 + 4.031
+chr20 58977190 58977250 + 5.678
+chr20 59059924 59059984 + 4.325
+chr12 1953667 1953727 + -4.029
+chr12 9749453 9749513 + -4.033
+chr12 12219968 12220028 + -4.053
+chr12 12571903 12571963 + -4.548
+chr12 12663416 12663476 + -4.207

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/3unsorted.bam

Binary file rnaseq/cutadapt/test-data/3unsorted.bam has changed

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/4.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/4.bed Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,1 @@
+chr22 30128507 31828507 uc003bnx.1_cds_2_0_chr22_29227_f 0 +

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/4.bed.bz2

Binary file rnaseq/cutadapt/test-data/4.bed.bz2 has changed

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/4.bed.gz

Binary file rnaseq/cutadapt/test-data/4.bed.gz has changed

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/4.bed.zip

Binary file rnaseq/cutadapt/test-data/4.bed.zip has changed

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/4.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/4.fasta Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,7 @@
+>EYKX4VC01B65GS length=54 xy=0784_1754 region=1 run=R_2007_11_07_16_15_57_
+CCGGTATCCGGGTGCCGTGATGAGCGCCACCGGAACGAATTCGACTATGCCGAA
+>EYKX4VC01BNCSP length=187 xy=0558_3831 region=1 run=R_2007_11_07_16_15_57_
+CTTACCGGTCACCACCGTGCCTTCAGGATTGATCGCCAGATCGGTCGGTGCGTCAGGCGG
+GGTGACATCGCCCACCACGGTACTCACTGGCTGGCTCTGGTTCCCGGCGGCATCGGAGGC
+CACCACGTTGAGGGTATTCCCCTCGGTTTGTGGCTCGGTGAGAACCACGTTGTAGTCGCC
+ATTGGTC

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/4.maf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/4.maf Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,193 @@\n+##maf version=1\n+a score=121487.000000\n+s hg17.chr7 127471195 331 + 158628139 gtttgccatcttttgctgctctagggaatccagcagctgtcaccatgtaaacaagcccaggctagaccaGTTACCCTCATC---ATCTTAGCTGATAGCCAGCCAGCCACCACAGGCAtgagtcaggccatattgctggacccacagaattatgagctaaataaatagtcttgggttaagccactaagttttaggcatagtgtgttatgtaTCTCACAAACATATAAGACTGTGTGTTTGTTGACTGGAGGAAGAGATGCTATAAAGACCACCTTTTAAAACTTCCCAAATACTGCCACTGATGTCCTGATGGAGG-------------------------------------------------------TATGAA---------AACATCCACTAA\n+s panTro1.chr6 129885076 331 + 161576975 gtttgccatcttttgctgctcttgggaatccagcagctgtcaccatgtaaacaagcccaggctagaccaGTTACCCTCATC---ATCTTAGCTGATAGCCAGCCAGCCACCACAGGCAtgagtcaggccatattgctggacccacagaattatgagctaaataaatagtcttgggttaagccactaagttttaggcatagtgtgttatgtaTCTCACAAACATATAAGACTGTGTGTTTGTTGACTGGAGGAAGAGATGCTATAAAGACCACCTTTTGAAACTTCCCAAATACTGCCACTGATGTCCTGATGGAGG-------------------------------------------------------TATGAA---------AACATCCACTAA\n+i panTro1.chr6 C 0 C 0\n+s rheMac2.chr3 165787989 330 + 196418989 gcttgccatcttttgatgctcttgggaatccagcagctgtcaccat-taaacaagcccaggctagaccaGTTACCCTCATC---ATCTTAGCTGATAGCCAGCCAGCCACCATAGGCAtgagtcaggccatagtgctggacccacagaattatgagctaaataagtagtgttgggttaagtcactaagttttaggcatagtgtgttatgtagcTCACAAACATATAAGACTGTGTGTTTTTTGACTGGAGGAAGAGATGCCATAAAGACCACCTTTTGAAACTTCTCAAATACTGCCATTGATGTGCTGATGGAGG-------------------------------------------------------TATGAA---------AACATCCACTAA\n+i rheMac2.chr3 C 0 C 0\n+s rn3.chr4 56178191 282 + 187371129 CTTCACTCTCATTTGCTGTT----------------CTGTCACTATGGAGACAAACACAGGCTAGCCCAGTTACTATCTTGATCACAGCAGCTGT----CAGCTAGCTGCCACTCACAGGAATAAGGCCATACCATT-GATCCACTGAACCTTGATCTAGGAATTTGGC----------------------TGGGGCCAGTTTGCGGTGTCACTCATGA--CTCTAAGATTGTGTGTTTG----CTCCAGGAAGAGACGGCAAGAGGATTACCTTTAAAAGGTTCGG-AGTCTAGCTGTAGACAGCCCAATGGG---------------------------------------------------------TATAAC---------AATACTCACTAA\n+i rn3.chr4 C 0 I 3727\n+s mm7.chr6 28984529 357 + 149646834 CTCCACTCTCGTTTGCTGTT----------------CTGTCACCATGGAAACAAACG-AGGGTGGTCCAGTTACTATCTTG---ACTGCAGCTGG----CAGTCAGTTGCCACT--CAGGAATAAGGCTATGCCATT-GATCCACTGAACCGTGATCTGGAAACCTGGCTGTTGTTT-------CAAGCCTTGGGGCCAGTTTGCGGTGTTACTCATGA--CTCTAAGATCGTGTGCTTG----CTGCAGGAAGAGACAGCAAGGGGGTTACATTTAAAAAGCCCCC-AGTTTAGCTATAGGCAGGCCAACAGGTGTAAAAATACTCACTAGTAATGGGCTGAACTCATGGAGGTAGCATTAGTGAGACACTGTAACTGTTTTTTTAAAAATCACTAA\n+i mm7.chr6 C 0 C 0\n+e monDom2.scaffold_22 30245538 51850 - 46578359 I\n+e echTel1.scaffold_309554 3896 34801 + 42008 I\n+e dasNov1.scaffold_60130 12867 0 - 12883 I\n+e loxAfr1.scaffold_2979 11430 3597 - 113413 I\n+e canFam2.chr14 52842678 4750 - 63938239 I\n+e bosTau2.scaffold741 358386 0 + 359342 I\n+e oryCun1.scaffold_213837 7852 41067 + 53501 I\n+\n+a score=20323.000000\n+s hg17.chr7 127471526 58 + 158628139 AATTTGTGGTTTATTCATTTTTCATTATTTTGTTTAAGGAGGTCTATAGTGGAAGAGG\n+s mm7.chr6 28984886 54 + 149646834 ----AACGTTTCATTGATTGCTCATCATTTAAAAAAAGAAATTCCTCAGTGGAAGAGG\n+i mm7.chr6 C 0 I 5774\n+s rheMac2.chr3 165788319 58 + 196418989 AATTTGTGGTTTATTTATTTTTCATTATTTTGTTTAAGGAGGTCTATAGTGGAAGAGG\n+i rheMac2.chr3 C 0 C 0\n+s panTro1.chr6 129885407 58 + 161576975 AATTTGTGGTTTATTCGTTTTTCATTATTTTGTTTAAGGAGGTCTATAGTGGAAGAGG\n+i panTro1.chr6 C 0 C 0\n+e monDom2.scaffold_22 30245538 51850 - 46578359 I\n+e echTel1.scaffold_309554 3896 34801 + 42008 I\n+e dasNov1.scaffold_60130 12867 0 - 12883 I\n+e loxAfr1.scaffold_2979 11430 3597 - 113413 I\n+e canFam2.chr14 52842678 4750 - 63938239 I\n+e rn3.chr4 56178473 3727 + 187371129 I\n+e bosTau2.scaffold741 358386 0 + 359342 I\n+e oryCun1.scaffold_213837 7852 41067 + 53501 I\n+\n+a score=85620.000000\n+s hg17.chr7 127471584 104 + 158628139 GAGATATTT-GGggaaatttt-gtatagactagctt--tcacgat'..b'gacac---agaaatgcaaatttcctgt\n+s panTro1.chr6 129886161 401 + 161576975 taaaacctaagggaggagaTGGAAAG-GGGCACCCAACCCAGACTGAGAGACAGGAATTAGCTGCAAGGGGAACTAGGAAAAGCTTCTTTA---AGGATG--GAGAGACCCTA-GTGGAATGGGGAGATTCTTCCGGGAGAAGCGATGGATGCGCAGTTGGGCATCCCCACAGACGGACTGGAAAGAAAAAAGGCCTGGAGGAATCA------ATGTGC-AATGTATGTGTGTTCCCTGGTTcaagggctgg-gaactttctcta--aagggccaggtagaaaacattttaggctttctaagccaagg---caaaattgaggat-attacatgggtacttatacaacaagaataaacaatt---tacacaa-ttttttgttgacagaattcaaaa---ctttat----agacac---agaaatgtaaatttcctgt\n+i panTro1.chr6 C 0 C 0\n+s rheMac2.chr3 165789091 401 + 196418989 taaaacctaatggaggagatggaATG-GGTCACCCAACCCGGACTGAGAGACAGGAATTAGCTGCAAGGGTAACCAGGACAAGCTTCTCTA---ATGATG--GAGAGACCCTA-GTGGAATGGGGAGATTCTTCTGGGAGAAGCGATGGATTCGTAGTTGGGCATCCCCACAGAGGGACTGGAAAGAAAAAAGACCTGGAGGAACCA------ATGTGC-AATGTATGTGTGTTTCCTGGTTcaagggctggcaaactttctcta--aagggccagatagaaaacattttaggctttgtaagccaagg---caaaatcgaggag-attacatgggtacttatacaacaagaataaacaatt---tccacaa--tttttattcacagaattcaaaa---ctttat----agacac---agaaatgtaaatttcctgt\n+i rheMac2.chr3 C 0 C 0\n+s rn3.chr4 56183902 317 + 187371129 ------------------------------------GTCCATAGTCAAAG------------------------------AAGCCTCTCAG---ATGGAG--AGCAGGGCCTATGCAAAAGAGGGGGCTTCTGTAGGCAGAAGGGATGGACTAGCCTCCGGACATAGCCATAGAGAGGCTGGCAGGACTGAGACCCAGGAGAAGCCAGCGCAGGTGTGCGGGCGTGTGTATATTTCATAGTTTGCAGGTTGG----------------------------CAAACAATTCCTGCTTTGCAGGCCAAGA---GGAAACTGAAGGTGACCCCGTGAGTGCTTAC---ACAAGAGAAAACAAG-------ACAA-TTTTTGGTTGACCAAATTCAGAA---CTTTATTTGAGGATGC---TAAAGTTTAAATTTCTTTT\n+i rn3.chr4 C 0 I 329\n+s canFam2.chr14 52848716 380 - 63938239 TACAGCCTGTGGGCAGAGGTGGGAAGAGGTCACGCAAGCCAGTTGGAATGAGGGGAGTTGGCTGGAAAGGTGACCAGGACAAGCTACTTCAACCAGGAAG--AAGAGACCCCG-GTG----------------CTTGGAGAAGGCCTGATTGAGCAGTCCTGCATGCCCGCCCAC-GACTGGCAGGAATAAAGACCCAGAAGAGCTA------ACGTGC-AATGTA------TTTTCTAGTTCCAgggttggcaaactttctctct-aagggtgggatgataaacattttaggcttttcagaccaaga---ggcgacatcagag-ggtatgtaggt---------acaagagggaaaagttgcccccggaa-ttttttg--gataaaattcaaaa---ctttacttagggatgc---caaaatgtaaacttcatat\n+i canFam2.chr14 I 3 C 0\n+s dasNov1.scaffold_256527 987 414 + 1837 CTAAATCTCGCGGAGAAGGTGGAACA-GGTTACCCAAACCCGACCGAG-GAGGCGAGTTG---GAAACGGCGACTGGGACAAGCTCCCTCA---GAGACGGAGAGAGACCCCA-GTGGAAGGGGGGAGAGGCTCTTAGGGAAACGATGGGGGGACCCGCCCGCACCCGCACAGAGGCGCTGGCAGGCACAGCGGCCCCGAGGAGCCC------AGGAGC-AGGGC-TGTGT-TCCCCTGCATcaggggttggcaaactttttctgcaaagggccagatagtaaatattttaggctttgcaaaccaagaagtagaaagggaggcc-attatgtacgtatttatatagcaagagagaacattt---cccacaatttttttattgacagaatttaaaacttctttattgatgaacaccaaagaaacttgaatttcatat\n+i dasNov1.scaffold_256527 C 0 C 0\n+e monDom2.scaffold_22 30245538 51850 - 46578359 I\n+e echTel1.scaffold_309554 3896 34801 + 42008 I\n+e loxAfr1.scaffold_2979 11430 3597 - 113413 I\n+e mm7.chr6 28991048 471 + 149646834 I\n+e bosTau2.chr4 19312883 12 - 69556449 I\n+e oryCun1.scaffold_213837 7852 41067 + 53501 I\n+\n+a score=14948.000000\n+s hg17.chr7 127472681 34 + 158628139 aattttcccat---gagaactattcttcttttgtttt\n+s rheMac2.chr3 165789492 34 + 196418989 aattttcacat---aagaactattcttcttttgtttt\n+i rheMac2.chr3 C 0 C 0\n+s panTro1.chr6 129886562 34 + 161576975 aattttcccgt---gagaactattcttcttttgtttt\n+i panTro1.chr6 C 0 C 0\n+s canFam2.chr14 52849096 35 - 63938239 aatggtcatgt--ccataactattcttcttttatttt\n+i canFam2.chr14 C 0 C 0\n+s dasNov1.scaffold_256527 1401 32 + 1837 aattttcacatatcacgaagtatttttttttt-----\n+i dasNov1.scaffold_256527 C 0 n 0\n+e monDom2.scaffold_22 30245538 51850 - 46578359 I\n+e echTel1.scaffold_309554 3896 34801 + 42008 I\n+e loxAfr1.scaffold_2979 11430 3597 - 113413 I\n+e rn3.chr4 56184219 329 + 187371129 I\n+e mm7.chr6 28991048 471 + 149646834 I\n+e bosTau2.chr4 19312883 12 - 69556449 I\n+e oryCun1.scaffold_213837 7852 41067 + 53501 I\n+\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/454.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/454.fasta Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,52 @@
+>EYKX4VC01B65GS length=54 xy=0784_1754 region=1 run=R_2007_11_07_16_15_57_
+CCGGTATCCGGGTGCCGTGATGAGCGCCACCGGAACGAATTCGACTATGCCGAA
+>EYKX4VC01BNCSP length=187 xy=0558_3831 region=1 run=R_2007_11_07_16_15_57_
+CTTACCGGTCACCACCGTGCCTTCAGGATTGATCGCCAGATCGGTCGGTGCGTCAGGCGG
+GGTGACATCGCCCACCACGGTACTCACTGGCTGGCTCTGGTTCCCGGCGGCATCGGAGGC
+CACCACGTTGAGGGTATTCCCCTCGGTTTGTGGCTCGGTGAGAACCACGTTGTAGTCGCC
+ATTGGTC
+>EYKX4VC01CD9FT length=115 xy=0865_1719 region=1 run=R_2007_11_07_16_15_57_
+GGGGGCTTTGGCCTGTCGTCCGGCACCTCGCAAGAGCTACAGCAGGCGCGGCTGGCGATC
+ATCGGCGGCACGCCGGCCTATATGTCGCCGGAACACACCACCCGCACCCAACGCG
+>EYKX4VC01B8FW0 length=95 xy=0799_0514 region=1 run=R_2007_11_07_16_15_57_
+TAAATTTCAAGGAATGCAAATCAGGGTCGTGTGTTTAGACTTCGGCTTTAGAGACCTGAA
+TACGTCAAAAACATAACTTCATGATATCTTGCAGT
+>EYKX4VC01BCGYW length=115 xy=0434_3926 region=1 run=R_2007_11_07_16_15_57_
+GGCCAGCCGGGACAGCGTTGTTGGGCTGCATGGCGACGAGCTAAAAGTCGCCATCACCGC
+CCCGCCGGTTGATGGGCAGGCTAATGCCCATCTGGTAAAAACTTTCTCGCCAAAC
+>EYKX4VC01AZXC6 length=116 xy=0292_0280 region=1 run=R_2007_11_07_16_15_57_
+GGGGGCGTTTGGCCTGTCGTCCGGCACCTCGCAAGAGCTACAGCAGGCGCGGCTGGCGAT
+CATCGGCGGCACGCCGGCCTATATGTCGCCGGAACACACCACCCGCACCCAACGCG
+>EYKX4VC01CATH5 length=82 xy=0826_0843 region=1 run=R_2007_11_07_16_15_57_
+CGAAATTGCACATTCTCGGCCATATCTCTGGACCTACATGACCGATTTGATCATCTTCGA
+ACTTAGCCTTCCTTTNTTAACG
+>EYKX4VC01BCEIV length=47 xy=0434_0757 region=1 run=R_2007_11_07_16_15_57_
+TGACGTCGTGCCGAGCTACGACAATGCCGACATGGTGATCGTTAACA
+>EYKX4VC01BWERM length=83 xy=0662_0304 region=1 run=R_2007_11_07_16_15_57_
+CGGTCGGCCTCACCATGGAGAAGATCCCGCCCCGGCCGAGGTCATGGTGGATCTCGGCCA
+GGGCGTGCTGATGAAGTTCAAAT
+>EYKX4VC01BT2O7 length=69 xy=0635_1945 region=1 run=R_2007_11_07_16_15_57_
+AGCGTTTCTCCAGCCGGTCGGCTACGCCGTTTGCCCCTGAAAGACGCTGTTCAGACCGAA
+CGCGGTAAA
+>EYKX4VC01BO0UO length=222 xy=0577_3838 region=1 run=R_2007_11_07_16_15_57_
+AGACCTGGGACAGCGGCGGGCTGCTGAAGCCGCAGGCGATAGAGGACAAACTGCAGTACC
+GCTTCTGGCTGCACTATGCCGAAGGCTCGCTGATGCCGCTGCTGTTAATGAAGCTGGTGT
+TCGCCAGCCTGGGTAAACCCCCTGTGCCCTTTGGCGTCCGCTCGCTGGGCGCCCTGCTGG
+GCAAGGGCATTCAGAAAGCGTGGCTGGATCCCCAGCTGGCCA
+>EYKX4VC01CBCPK length=83 xy=0832_1158 region=1 run=R_2007_11_07_16_15_57_
+CGGTCGGCCTCACCATGGAGAAGATCCCGCCCCGGCCGAGGTCATGGTGGATCTCGGCCA
+GGGCGTGCTGATGAAGTTCAAAT
+>EYKX4VC01B474S length=54 xy=0762_2010 region=1 run=R_2007_11_07_16_15_57_
+AGCAGTTTTCCAGCGCTTTCGAAGAGCGCTGGCGCGCGCGGGCTTCCAGCATAT
+>EYKX4VC01BB4QL length=57 xy=0431_0363 region=1 run=R_2007_11_07_16_15_57_
+GGGGAGGAGCTAATAATATGCTCTTGGGGAGGAGCTAATTATATGCTCTTGGGGAGG
+>EYKX4VC01BJ37M length=64 xy=0522_0192 region=1 run=R_2007_11_07_16_15_57_
+TCGAGTATGTATCAAGGACTACATACAAATTTGCCAAAAGAGATTATGCACTATCCCGAC
+TTCC
+>EYKX4VC01BV9R8 length=54 xy=0660_2038 region=1 run=R_2007_11_07_16_15_57_
+AAAACTCGGAGAAACTATTCAGCAGCACTGCGTTTCGCTGAATTTTAGACCGTT
+>EYKX4VC01CEPP8 length=60 xy=0870_2350 region=1 run=R_2007_11_07_16_15_57_
+CTGGGTGGGTGCACTACAGGAACGTCATTTGTTCAATCCTCACGTTGTTGTTAGTGTCAG
+>EYKX4VC01BTLME length=78 xy=0630_0292 region=1 run=R_2007_11_07_16_15_57_
+TTATCCACACGCTGTCCGGATCCAGCGCCAGGCGCCGACGCTGGACTTCCGCCGCCTGCG
+CCCAGTTGCCCTGACTTC

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/454.qual
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/454.qual Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,52 @@
+>EYKX4VC01B65GS length=54 xy=0784_1754 region=1 run=R_2007_11_07_16_15_57_
+33 23 34 25 28 28 28 32 23 34 27 4 28 28 31 21 28 27 27 28 28 28 28 28 28 28 33 23 28 33 24 36 27 31 21 28 28 33 26 33 24 27 28 28 28 28 28 28 28 32 23 28 34 25
+>EYKX4VC01BNCSP length=187 xy=0558_3831 region=1 run=R_2007_11_07_16_15_57_
+27 35 26 25 37 28 37 28 25 28 27 36 27 28 36 27 28 28 27 36 27 30 19 27 28 36 28 23 36 27 27 28 27 27 28 37 29 27 26 27 24 24 36 27 26 28 36 28 24 25 21 28 24 28 26 34 25 26 43 36
+22 9 23 19 28 28 28 28 26 28 39 32 12 27 36 28 28 26 37 28 28 26 28 28 28 27 28 26 36 27 27 27 36 28 27 27 28 28 36 27 36 28 39 32 12 35 28 26 37 29 28 28 28 28 37 29 28 36 28 35
+26 27 37 29 28 26 28 36 28 26 24 38 32 11 28 26 32 24 36 32 18 2 27 25 33 26 32 28 6 18 22 26 17 15 14 28 20 8 22 21 14 22 26 16 26 16 28 20 22 27 18 27 18 27 28 27 20 25 34 27
+27 33 25 34 28 8 26
+>EYKX4VC01CD9FT length=115 xy=0865_1719 region=1 run=R_2007_11_07_16_15_57_
+35 24 16 9 2 27 39 33 13 36 27 36 27 28 28 28 27 28 28 33 23 37 28 28 28 36 27 28 28 28 28 36 27 28 28 28 27 28 28 28 28 28 28 28 37 28 28 28 28 37 28 26 28 36 27 28 28 28 28 28
+28 28 28 37 28 28 35 26 27 28 28 27 36 27 35 25 32 22 28 28 28 28 28 28 28 28 28 34 25 36 27 34 25 28 27 28 28 36 27 28 35 29 6 28 28 28 37 30 8 33 24 28 27 27 27
+>EYKX4VC01B8FW0 length=95 xy=0799_0514 region=1 run=R_2007_11_07_16_15_57_
+28 40 34 15 35 28 6 27 33 23 34 24 32 22 28 28 28 41 34 17 28 28 28 37 30 9 28 28 28 28 28 27 28 37 30 8 28 28 27 28 35 26 27 35 26 28 37 30 9 28 27 28 28 28 34 25 28 28 32 22
+26 28 28 28 28 27 43 36 23 12 1 28 21 28 27 16 28 32 23 27 28 27 28 28 27 28 28 28 32 22 28 26 26 27 28
+>EYKX4VC01BCGYW length=115 xy=0434_3926 region=1 run=R_2007_11_07_16_15_57_
+28 6 26 15 27 28 37 28 41 35 17 28 21 28 23 21 27 36 27 24 36 28 40 34 14 22 25 28 24 27 28 37 28 26 28 27 27 28 28 28 28 27 43 36 22 8 28 26 28 27 26 14 28 25 20 28 34 24 25 40
+33 18 1 19 27 16 36 28 36 28 21 27 25 41 34 16 22 28 37 29 26 26 35 27 28 26 41 34 16 28 28 27 28 37 29 25 43 36 23 12 1 11 39 32 12 28 17 20 28 28 17 36 29 7 24
+>EYKX4VC01AZXC6 length=116 xy=0292_0280 region=1 run=R_2007_11_07_16_15_57_
+35 24 17 11 5 26 24 40 33 14 34 25 33 24 28 27 27 26 28 28 33 24 36 27 28 27 36 27 27 28 27 28 35 26 27 27 28 27 28 28 28 28 28 27 28 36 27 28 28 28 37 28 27 26 35 26 27 28 28 28
+27 28 28 28 37 29 28 35 26 28 27 28 28 35 26 35 26 31 21 28 28 28 28 28 28 28 28 28 34 25 35 26 35 26 28 28 28 28 37 28 27 37 30 9 28 28 28 37 30 9 33 23 28 28 28 27
+>EYKX4VC01CATH5 length=82 xy=0826_0843 region=1 run=R_2007_11_07_16_15_57_
+28 28 41 35 17 33 24 28 27 28 28 28 36 27 28 28 28 36 27 34 25 27 28 28 28 28 28 28 28 37 28 27 35 25 28 26 28 27 28 28 24 36 27 26 26 37 30 9 28 28 28 28 28 25 25 35 26 26 27 35
+25 28 36 28 28 28 31 21 25 13 32 22 41 34 17 0 22 10 32 23 24 28
+>EYKX4VC01BCEIV length=47 xy=0434_0757 region=1 run=R_2007_11_07_16_15_57_
+28 28 26 26 28 26 28 27 28 25 32 22 27 26 25 27 28 28 27 26 27 28 32 23 28 28 34 25 27 22 26 26 27 28 17 28 28 28 28 28 28 34 24 35 25 28 28
+>EYKX4VC01BWERM length=83 xy=0662_0304 region=1 run=R_2007_11_07_16_15_57_
+28 36 27 28 28 35 26 34 24 28 28 28 32 22 28 28 32 23 28 28 32 23 27 28 27 34 27 3 27 43 36 22 9 35 26 37 29 26 27 32 23 28 28 27 28 36 27 28 36 27 28 28 28 28 28 35 26 34 25 28
+36 30 8 28 28 28 28 27 27 28 28 28 28 37 28 28 36 27 28 39 33 13 27
+>EYKX4VC01BT2O7 length=69 xy=0635_1945 region=1 run=R_2007_11_07_16_15_57_
+28 28 28 28 41 34 17 27 28 31 21 28 27 32 23 36 27 28 28 33 24 28 27 28 28 27 32 22 28 34 27 3 27 43 36 22 8 27 28 34 27 3 28 28 28 28 28 28 28 33 23 28 28 28 28 34 24 28 34 24
+28 28 27 36 27 28 37 30 9
+>EYKX4VC01BO0UO length=222 xy=0577_3838 region=1 run=R_2007_11_07_16_15_57_
+27 27 28 36 27 28 39 33 13 28 28 28 27 28 37 28 28 41 35 17 28 28 28 27 28 26 36 27 28 36 27 27 28 27 35 26 27 26 28 28 28 28 28 36 27 28 28 38 31 10 24 27 27 27 27 27 28 28 37 28
+27 28 35 26 28 28 36 27 28 28 27 28 28 28 28 28 28 27 36 28 27 36 27 37 28 27 28 27 28 28 28 27 28 28 27 36 27 26 27 28 28 28 28 28 37 28 37 29 25 28 36 27 28 27 28 34 27 26 24 34
+28 28 28 31 23 27 28 34 27 28 37 33 14 23 37 33 15 38 34 23 13 2 26 24 28 26 35 31 12 36 32 14 31 22 24 28 27 33 26 26 27 27 27 27 28 27 35 30 11 26 27 35 31 12 28 27 26 27 36 32
+14 27 34 27 37 33 15 27 27 34 28 27 23 27 35 31 11 27 28 28 26 34 26 27 28 34 28 28 28 39 35 22 9 27 27 23 27 35 28 34 27 27
+>EYKX4VC01CBCPK length=83 xy=0832_1158 region=1 run=R_2007_11_07_16_15_57_
+28 35 26 28 28 35 26 35 26 28 28 28 34 24 28 28 35 25 28 28 34 25 28 28 27 35 28 5 28 43 36 22 9 35 26 37 28 28 27 32 23 27 28 28 28 36 27 28 36 27 28 28 28 28 28 36 27 35 25 28
+37 30 9 28 28 28 28 28 28 28 28 28 28 36 27 28 35 26 28 38 31 10 28
+>EYKX4VC01B474S length=54 xy=0762_2010 region=1 run=R_2007_11_07_16_15_57_
+28 28 28 28 27 43 36 23 11 33 23 27 25 26 28 28 39 33 13 28 27 29 18 28 26 27 26 28 27 28 36 27 26 28 28 28 28 25 28 41 34 17 24 36 28 37 28 28 26 28 17 27 28 26
+>EYKX4VC01BB4QL length=57 xy=0431_0363 region=1 run=R_2007_11_07_16_15_57_
+36 24 15 7 28 33 26 28 27 27 26 29 18 28 35 26 28 26 28 25 27 27 28 36 27 41 34 20 5 27 36 28 28 28 27 28 32 22 34 25 28 28 28 28 26 28 27 28 36 27 40 34 18 3 28 37 28
+>EYKX4VC01BJ37M length=64 xy=0522_0192 region=1 run=R_2007_11_07_16_15_57_
+28 26 28 28 28 28 28 28 27 28 28 27 27 36 27 37 28 28 28 28 28 28 28 28 28 27 36 29 8 39 33 13 28 36 27 41 34 20 5 28 28 28 27 36 28 28 28 28 27 28 28 28 28 27 37 30 8 27 28 26
+33 26 35 26
+>EYKX4VC01BV9R8 length=54 xy=0660_2038 region=1 run=R_2007_11_07_16_15_57_
+41 34 19 4 27 28 28 30 20 28 28 34 27 4 28 28 27 34 25 27 28 28 28 28 28 28 28 28 28 28 28 28 38 31 11 27 28 28 28 28 37 28 40 33 18 2 24 15 25 24 12 26 34 27
+>EYKX4VC01CEPP8 length=60 xy=0870_2350 region=1 run=R_2007_11_07_16_15_57_
+26 21 40 34 17 26 36 29 8 26 28 22 26 28 28 20 24 28 34 26 23 11 28 28 26 27 26 40 33 14 27 35 26 26 23 10 28 31 21 28 23 27 23 28 36 27 26 36 28 27 36 28 28 27 25 27 27 27 26 28
+>EYKX4VC01BTLME length=78 xy=0630_0292 region=1 run=R_2007_11_07_16_15_57_
+36 27 25 24 33 23 28 26 28 28 28 28 27 27 26 36 27 36 28 28 28 36 27 28 28 27 27 36 28 28 37 29 28 26 36 27 27 28 27 27 28 27 36 28 28 28 36 27 36 27 28 36 28 25 36 28 28 28 27 28
+39 33 13 28 28 37 28 28 41 34 16 28 28 28 26 36 28 24

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/454Score.pdf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/454Score.pdf Sat Feb 21 16:33:42 2015 +0100

[

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diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/5.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/5.bed Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,134 @@\n+chr7\t115444712\t115444739\tCCDS5763.1_cds_0_0_chr7_115444713_f\t0\t+\n+chr7\t115468538\t115468624\tCCDS5763.1_cds_1_0_chr7_115468539_f\t0\t+\n+chr7\t115483024\t115483277\tCCDS5763.1_cds_2_0_chr7_115483025_f\t0\t+\n+chr7\t115484165\t115484501\tCCDS5763.1_cds_3_0_chr7_115484166_f\t0\t+\n+chr7\t115485764\t115485980\tCCDS5763.1_cds_4_0_chr7_115485765_f\t0\t+\n+chr7\t115486322\t115486481\tCCDS5763.1_cds_5_0_chr7_115486323_f\t0\t+\n+chr7\t115491298\t115491487\tCCDS5763.1_cds_6_0_chr7_115491299_f\t0\t+\n+chr7\t115468538\t115468624\tCCDS5764.1_cds_0_0_chr7_115468539_f\t0\t+\n+chr7\t115483024\t115483277\tCCDS5764.1_cds_1_0_chr7_115483025_f\t0\t+\n+chr7\t115484165\t115484501\tCCDS5764.1_cds_2_0_chr7_115484166_f\t0\t+\n+chr7\t115485764\t115485980\tCCDS5764.1_cds_3_0_chr7_115485765_f\t0\t+\n+chr7\t115486322\t115486481\tCCDS5764.1_cds_4_0_chr7_115486323_f\t0\t+\n+chr7\t115491298\t115491487\tCCDS5764.1_cds_5_0_chr7_115491299_f\t0\t+\n+chr7\t115733786\t115733936\tCCDS5766.1_cds_0_0_chr7_115733787_f\t0\t+\n+chr7\t115734264\t115734452\tCCDS5766.1_cds_1_0_chr7_115734265_f\t0\t+\n+chr7\t115739975\t115740126\tCCDS5766.1_cds_2_0_chr7_115739976_f\t0\t+\n+chr7\t115733786\t115733936\tCCDS5765.1_cds_0_0_chr7_115733787_f\t0\t+\n+chr7\t115739975\t115740164\tCCDS5765.1_cds_1_0_chr7_115739976_f\t0\t+\n+chr7\t115759067\t115759097\tCCDS5767.1_cds_0_0_chr7_115759068_f\t0\t+\n+chr7\t115760529\t115760694\tCCDS5767.1_cds_1_0_chr7_115760530_f\t0\t+\n+chr7\t115792950\t115793292\tCCDS5767.1_cds_2_0_chr7_115792951_f\t0\t+\n+chr7\t116096616\t116096655\tCCDS5768.1_cds_0_0_chr7_116096617_f\t0\t+\n+chr7\t116122131\t116122195\tCCDS5768.1_cds_1_0_chr7_116122132_f\t0\t+\n+chr7\t116126998\t116127050\tCCDS5768.1_cds_2_0_chr7_116126999_f\t0\t+\n+chr7\t116132776\t116132840\tCCDS5768.1_cds_3_0_chr7_116132777_f\t0\t+\n+chr7\t116138181\t116138388\tCCDS5768.1_cds_4_0_chr7_116138182_f\t0\t+\n+chr7\t116140267\t116140347\tCCDS5768.1_cds_5_0_chr7_116140268_f\t0\t+\n+chr7\t116144237\t116144316\tCCDS5768.1_cds_6_0_chr7_116144238_f\t0\t+\n+chr7\t116146073\t116146145\tCCDS5768.1_cds_7_0_chr7_116146074_f\t0\t+\n+chr7\t116150064\t116150127\tCCDS5768.1_cds_8_0_chr7_116150065_f\t0\t+\n+chr7\t116151731\t116151872\tCCDS5768.1_cds_9_0_chr7_116151732_f\t0\t+\n+chr7\t116187545\t116187696\tCCDS5770.1_cds_0_0_chr7_116187546_f\t0\t+\n+chr7\t116333766\t116333849\tCCDS5770.1_cds_1_0_chr7_116333767_f\t0\t+\n+chr7\t116353565\t116353725\tCCDS5770.1_cds_2_0_chr7_116353566_f\t0\t+\n+chr7\t116363797\t116363852\tCCDS5770.1_cds_3_0_chr7_116363798_f\t0\t+\n+chr7\t116364495\t116364611\tCCDS5770.1_cds_4_0_chr7_116364496_f\t0\t+\n+chr7\t116365889\t116365965\tCCDS5770.1_cds_5_0_chr7_116365890_f\t0\t+\n+chr7\t116368128\t116368197\tCCDS5770.1_cds_6_0_chr7_116368129_f\t0\t+\n+chr7\t116370085\t116370240\tCCDS5770.1_cds_7_0_chr7_116370086_f\t0\t+\n+chr7\t116372439\t116372537\tCCDS5770.1_cds_8_0_chr7_116372440_f\t0\t+\n+chr7\t116404866\t116404981\tCCDS5770.1_cds_9_0_chr7_116404867_f\t0\t+\n+chr7\t116423325\t116423398\tCCDS5770.1_cds_10_0_chr7_116423326_f\t0\t+\n+chr7\t116424838\t116424941\tCCDS5770.1_cds_11_0_chr7_116424839_f\t0\t+\n+chr7\t116443791\t116443942\tCCDS5770.1_cds_12_0_chr7_116443792_f\t0\t+\n+chr7\t116453088\t116453181\tCCDS5770.1_cds_13_0_chr7_116453089_f\t0\t+\n+chr7\t116455927\t116456067\tCCDS5770.1_cds_14_0_chr7_116455928_f\t0\t+\n+chr7\t116456865\t116456985\tCCDS5770.1_cds_15_0_chr7_116456866_f\t0\t+\n+chr7\t116187545\t116187696\tCCDS5769.1_cds_0_0_chr7_116187546_f\t0\t+\n+chr7\t116333766\t116333849\tCCDS5769.1_cds_1_0_chr7_116333767_f\t0\t+\n+chr7\t116353565\t116353725\tCCDS5769.1_cds_2_0_chr7_116353566_f\t0\t+\n+chr7\t116363797\t116363852\tCCDS5769.1_cds_3_0_chr7_116363798_f\t0\t+\n+chr7\t116364495\t116364611\tCCDS5769.1_cds_4_0_chr7_116364496_f\t0\t+\n+chr7\t116365889\t116365965\tCCDS5769.1_cds_5_0_chr7_116365890_f\t0\t+\n+chr7\t116370085\t116370240\tCCDS5769.1_cds_6_0_chr7_116370086_f\t0\t+\n+chr7\t116372439\t116372537\tCCDS5769.1_cds_7_0_chr7_116372440_f\t0\t+\n+chr7\t116404866\t116404981\tCCDS5769.1_cds_8_0_chr7_116404867_f\t0\t+\n+chr7\t116423325\t116423398\tCCDS5769.1_cds_9_0_chr7_116423326_f\t0\t+\n+chr7\t116424838\t116424941\tCCDS5769.1_cds_10_0_chr7_116424839_f\t0\t+\n+chr7\t116443791\t116443942\tCCDS5769.1_cds_11_0_chr7_116443792_f\t0\t+\n+chr7\t116453088\t116453181\tCCDS5769.1_cds_12_0_chr7_116453089_f\t0\t+\n+chr7\t116455'..b'r\t0\t-\n+chr7\t116618730\t116618865\tCCDS5772.1_cds_7_0_chr7_116618731_r\t0\t-\n+chr7\t116619702\t116619814\tCCDS5772.1_cds_8_0_chr7_116619703_r\t0\t-\n+chr7\t116654167\t116654279\tCCDS5772.1_cds_9_0_chr7_116654168_r\t0\t-\n+chr7\t116656241\t116656364\tCCDS5772.1_cds_10_0_chr7_116656242_r\t0\t-\n+chr7\t116660840\t116660940\tCCDS5772.1_cds_11_0_chr7_116660841_r\t0\t-\n+chr7\t116661360\t116661465\tCCDS5772.1_cds_12_0_chr7_116661361_r\t0\t-\n+chr7\t116714099\t116714152\tCCDS5773.1_cds_0_0_chr7_116714100_f\t0\t+\n+chr7\t116738257\t116738368\tCCDS5773.1_cds_1_0_chr7_116738258_f\t0\t+\n+chr7\t116743038\t116743147\tCCDS5773.1_cds_2_0_chr7_116743039_f\t0\t+\n+chr7\t116764903\t116765119\tCCDS5773.1_cds_3_0_chr7_116764904_f\t0\t+\n+chr7\t116768280\t116768370\tCCDS5773.1_cds_4_0_chr7_116768281_f\t0\t+\n+chr7\t116769252\t116769416\tCCDS5773.1_cds_5_0_chr7_116769253_f\t0\t+\n+chr7\t116770552\t116770678\tCCDS5773.1_cds_6_0_chr7_116770553_f\t0\t+\n+chr7\t116774104\t116774351\tCCDS5773.1_cds_7_0_chr7_116774105_f\t0\t+\n+chr7\t116776020\t116776113\tCCDS5773.1_cds_8_0_chr7_116776021_f\t0\t+\n+chr7\t116782645\t116782828\tCCDS5773.1_cds_9_0_chr7_116782646_f\t0\t+\n+chr7\t116793468\t116793660\tCCDS5773.1_cds_10_0_chr7_116793469_f\t0\t+\n+chr7\t116821743\t116821838\tCCDS5773.1_cds_11_0_chr7_116821744_f\t0\t+\n+chr7\t116824357\t116824444\tCCDS5773.1_cds_12_0_chr7_116824358_f\t0\t+\n+chr7\t116825938\t116826662\tCCDS5773.1_cds_13_0_chr7_116825939_f\t0\t+\n+chr7\t116828934\t116829063\tCCDS5773.1_cds_14_0_chr7_116828935_f\t0\t+\n+chr7\t116836830\t116836868\tCCDS5773.1_cds_15_0_chr7_116836831_f\t0\t+\n+chr7\t116837536\t116837787\tCCDS5773.1_cds_16_0_chr7_116837537_f\t0\t+\n+chr7\t116840678\t116840758\tCCDS5773.1_cds_17_0_chr7_116840679_f\t0\t+\n+chr7\t116844523\t116844674\tCCDS5773.1_cds_18_0_chr7_116844524_f\t0\t+\n+chr7\t116845585\t116845813\tCCDS5773.1_cds_19_0_chr7_116845586_f\t0\t+\n+chr7\t116848617\t116848718\tCCDS5773.1_cds_20_0_chr7_116848618_f\t0\t+\n+chr7\t116861526\t116861775\tCCDS5773.1_cds_21_0_chr7_116861527_f\t0\t+\n+chr7\t116876442\t116876598\tCCDS5773.1_cds_22_0_chr7_116876443_f\t0\t+\n+chr7\t116886846\t116886936\tCCDS5773.1_cds_23_0_chr7_116886847_f\t0\t+\n+chr7\t116898692\t116898865\tCCDS5773.1_cds_24_0_chr7_116898693_f\t0\t+\n+chr7\t116899463\t116899569\tCCDS5773.1_cds_25_0_chr7_116899464_f\t0\t+\n+chr7\t116900912\t116901113\tCCDS5773.1_cds_26_0_chr7_116900913_f\t0\t+\n+chr7\t116945541\t116945787\tCCDS5774.1_cds_0_0_chr7_116945542_r\t0\t-\n+chr7\t116952022\t116952124\tCCDS5774.1_cds_1_0_chr7_116952023_r\t0\t-\n+chr7\t116953508\t116953641\tCCDS5774.1_cds_2_0_chr7_116953509_r\t0\t-\n+chr7\t116955071\t116955135\tCCDS5774.1_cds_3_0_chr7_116955072_r\t0\t-\n+chr7\t116958551\t116958737\tCCDS5774.1_cds_4_0_chr7_116958552_r\t0\t-\n+chr7\t116959056\t116959262\tCCDS5774.1_cds_5_0_chr7_116959057_r\t0\t-\n+chr7\t116962093\t116962272\tCCDS5774.1_cds_6_0_chr7_116962094_r\t0\t-\n+chr7\t116968917\t116969105\tCCDS5774.1_cds_7_0_chr7_116968918_r\t0\t-\n+chr7\t116969273\t116969426\tCCDS5774.1_cds_8_0_chr7_116969274_r\t0\t-\n+chr7\t116979835\t116979935\tCCDS5774.1_cds_9_0_chr7_116979836_r\t0\t-\n+chr7\t116980017\t116980104\tCCDS5774.1_cds_10_0_chr7_116980018_r\t0\t-\n+chr7\t116990559\t116990639\tCCDS5774.1_cds_11_0_chr7_116990560_r\t0\t-\n+chr7\t116991879\t116991975\tCCDS5774.1_cds_12_0_chr7_116991880_r\t0\t-\n+chr7\t116994439\t116994715\tCCDS5774.1_cds_13_0_chr7_116994440_r\t0\t-\n+chr7\t117001063\t117001181\tCCDS5774.1_cds_14_0_chr7_117001064_r\t0\t-\n+chr7\t117011515\t117011770\tCCDS5774.1_cds_15_0_chr7_117011516_r\t0\t-\n+chr7\t117014445\t117014596\tCCDS5774.1_cds_16_0_chr7_117014446_r\t0\t-\n+chr7\t117016866\t117016966\tCCDS5774.1_cds_17_0_chr7_117016867_r\t0\t-\n+chr7\t117018255\t117018459\tCCDS5774.1_cds_18_0_chr7_117018256_r\t0\t-\n+chr7\t117025132\t117026786\tCCDS5774.1_cds_19_0_chr7_117025133_r\t0\t-\n+chr7\t117044769\t117044994\tCCDS5774.1_cds_20_0_chr7_117044770_r\t0\t-\n+chr7\t117095213\t117095321\tCCDS5774.1_cds_21_0_chr7_117095214_r\t0\t-\n+chr7\t117107339\t117107420\tCCDS5774.1_cds_22_0_chr7_117107340_r\t0\t-\n+chr5\t131424298\t131424460\tCCDS4149.1_cds_0_0_chr5_131424299_f\t0\t+\n+chr5\t131424558\t131424600\tCCDS4149.1_cds_1_0_chr5_131424559_f\t0\t+\n+chr5\t131425903\t131425993\tCCDS4149.1_cds_2_0_chr5_131425904_f\t0\t+\n+chr5\t131426117\t131426159\tCCDS4149.1_cds_3_0_chr5_131426118_f\t0\t+\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/5.gff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/5.gff Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,25 @@
+##gff-version 2
+##Date: Thu Mar 23 11:21:17 2006
+##bed2gff.pl $Rev: 601 $
+##Input file: ./database/files/61c6c604e0ef50b280e2fd9f1aa7da61.dat
+
+chr1 bed2gff CCDS1000.1_cds_0_0_chr1_148325916_f 148325916 148325975 . + . score "0";
+chr2 bed2gff CCDS2120.1_cds_0_0_chr2_118288584_f 118288584 118288668 . + . score "0";
+chr5 bed2gff CCDS3972.1_cds_0_0_chr5_56241230_f 56241230 56241327 . + . score "0";
+chr6 bed2gff CCDS4855.1_cds_0_0_chr6_41411593_f 41411593 41411644 . + . score "0";
+chr7 bed2gff CCDS5401.1_cds_0_0_chr7_26907299_r 26907299 26907654 . + . score "0";
+chr8 bed2gff CCDS6324.1_cds_0_0_chr8_118881132_r 118881132 118881317 . + . score "0";
+chr9 bed2gff CCDS6914.1_cds_0_0_chr9_128764157_f 128764157 128764189 . + . score "0";
+chr10 bed2gff CCDS7248.1_cds_0_0_chr10_55251624_r 55251624 55253124 . + . score "0";
+chr11 bed2gff CCDS7725.1_cds_0_0_chr11_1731309_r 1731309 1731476 . + . score "0";
+chr12 bed2gff CCDS8736.1_cds_0_0_chr12_38440095_r 38440095 38440321 . + . score "0";
+chr13 bed2gff CCDS9526.1_cds_0_0_chr13_112381695_f 112381695 112381953 . + . score "0";
+chr14 bed2gff CCDS9949.1_cds_0_0_chr14_98710241_r 98710241 98712285 . + . score "0";
+chr15 bed2gff CCDS10096.1_cds_0_0_chr15_41486873_r 41486873 41487060 . + . score "0";
+chr16 bed2gff CCDS10395.1_cds_0_0_chr16_37430_r 37430 37557 . + . score "0";
+chr18 bed2gff CCDS11891.1_cds_0_0_chr18_23786115_r 23786115 23786321 . + . score "0";
+chr19 bed2gff CCDS12866.1_cds_0_0_chr19_59068596_f 59068596 59069564 . + . score "0";
+chr20 bed2gff CCDS13249.1_cds_0_0_chr20_33330414_r 33330414 33330423 . + . score "0";
+chr21 bed2gff CCDS13614.1_cds_0_0_chr21_32707033_f 32707033 32707192 . + . score "0";
+chr22 bed2gff CCDS13897.1_cds_0_0_chr22_30120224_f 30120224 30120265 . + . score "0";
+chrX bed2gff CCDS14606.1_cds_0_0_chrX_122745048_f 122745048 122745924 . + . score "0";

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/5.gff3
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/5.gff3 Sat Feb 21 16:33:42 2015 +0100

b"@@ -0,0 +1,150 @@\n+##gff-version 3\n+##date Tue Jun 26 10:48:17 2007\n+##sequence-region ctgA 1 50000\n+##source gbrowse GFFToGalaxyDumper plugin\n+##NOTE: All features dumped.\n+ctgA\texample\tmy_feature\t22132\t24633\t.\t+\t.\tID=My_feature:f15\n+ctgA\texample\tmy_feature\t46990\t48410\t.\t-\t.\tID=My_feature:f11\n+ctgA\texample\tmy_feature\t44705\t47713\t.\t-\t.\tID=My_feature:f01\n+ctgA\texample\tmy_feature\t36649\t40440\t.\t-\t.\tID=My_feature:f03\n+ctgA\texample\tmy_feature\t23072\t23185\t.\t+\t.\tID=My_feature:f14\n+ctgA\texample\tmy_feature\t37242\t38653\t.\t+\t.\tID=My_feature:f04\n+ctgA\texample\tmotif\t37497\t40559\t.\t-\t.\tID=Motif:m15;Note=7-transmembrane\n+ctgA\texample\tmy_feature\t36034\t38167\t.\t+\t.\tID=My_feature:f09\n+ctgA\texample\tmotif\t28332\t30033\t.\t-\t.\tID=Motif:m02;Note=HOX\n+ctgA\texample\tmy_feature\t4715\t5968\t.\t-\t.\tID=My_feature:f05\n+ctgA\texample\tmotif\t48253\t48366\t.\t+\t.\tID=Motif:m01;Note=WD40\n+ctgA\texample\tBAC\t1000\t20000\t.\t.\t.\tID=BAC:b101.2;Note=Fingerprinted+BAC+with+end+reads\n+ctgA\texample\tright_end_read\t19500\t20000\t.\t-\t.\tParent=BAC:b101.2\n+ctgA\texample\tleft_end_read\t1000\t1500\t.\t+\t.\tParent=BAC:b101.2\n+ctgA\texample\tmotif\t13801\t14007\t.\t-\t.\tID=Motif:m05;Note=helix+loop+helix\n+ctgA\texample\tcoding\t1050\t9000\t.\t+\t.\tID=mRNA:EDEN.1;Gene=EDEN\n+ctgA\texample\tCDS\t1201\t1500\t.\t+\t0\tParent=mRNA:EDEN.1\n+ctgA\texample\tCDS\t3000\t3902\t.\t+\t0\tParent=mRNA:EDEN.1\n+ctgA\texample\tCDS\t5000\t5500\t.\t+\t0\tParent=mRNA:EDEN.1\n+ctgA\texample\tCDS\t7000\t7608\t.\t+\t0\tParent=mRNA:EDEN.1\n+ctgA\texample\tprocessed_transcript\t1050\t9000\t.\t+\t.\tID=mRNA:EDEN.1\n+ctgA\texample\t5'-UTR\t1050\t1200\t.\t+\t.\tParent=mRNA:EDEN.1\n+ctgA\texample\t3'-UTR\t7609\t9000\t.\t+\t.\tParent=mRNA:EDEN.1\n+ctgA\test\tmatch\t5410\t7503\t.\t-\t.\tID=EST:agt830.3;Target=agt830.3+1+595\n+ctgA\test\tHSP\t7000\t7503\t.\t-\t.\tParent=EST:agt830.3;Target=agt830.3+1+504\n+ctgA\test\tHSP\t5410\t5500\t.\t-\t.\tParent=EST:agt830.3;Target=agt830.3+505+595\n+ctgA\texample\tmotif\t46012\t48851\t.\t+\t.\tID=Motif:m09;Note=kinase\n+ctgA\texample\tmatch\t6885\t8999\t.\t-\t.\tID=Match:seg03\n+ctgA\texample\tHSP\t8306\t8999\t.\t-\t.\tParent=Match:seg03\n+ctgA\texample\tHSP\t8055\t8080\t.\t-\t.\tParent=Match:seg03\n+ctgA\texample\tHSP\t7410\t7737\t.\t-\t.\tParent=Match:seg03\n+ctgA\texample\tHSP\t6885\t7241\t.\t-\t.\tParent=Match:seg03\n+ctgA\texample\tmy_feature\t13280\t16394\t.\t+\t.\tID=My_feature:f08\n+ctgA\texample\tmatch\t29771\t32937\t.\t+\t.\tID=Match:seg10\n+ctgA\texample\tHSP\t29771\t29942\t.\t+\t.\tParent=Match:seg10\n+ctgA\texample\tHSP\t30042\t30340\t.\t+\t.\tParent=Match:seg10\n+ctgA\texample\tHSP\t30810\t31307\t.\t+\t.\tParent=Match:seg10\n+ctgA\texample\tHSP\t31761\t31984\t.\t+\t.\tParent=Match:seg10\n+ctgA\texample\tHSP\t32374\t32937\t.\t+\t.\tParent=Match:seg10\n+ctgA\texample\tmatch\t36616\t37227\t.\t-\t.\tID=Match:seg09\n+ctgA\texample\tHSP\t37208\t37227\t.\t-\t.\tParent=Match:seg09\n+ctgA\texample\tHSP\t36616\t37057\t.\t-\t.\tParent=Match:seg09\n+ctgA\texample\tmotif\t11911\t15561\t.\t+\t.\tID=Motif:m11;Note=kinase\n+ctgA\test\tmatch\t1050\t3202\t.\t+\t.\tID=EST:agt830.5;Target=agt830.5+1+654\n+ctgA\test\tHSP\t1050\t1500\t.\t+\t.\tParent=EST:agt830.5;Target=agt830.5+1+451\n+ctgA\test\tHSP\t3000\t3202\t.\t+\t.\tParent=EST:agt830.5;Target=agt830.5+452+654\n+ctgA\texample\tmotif\t15396\t16159\t.\t+\t.\tID=Motif:m03;Note=zinc+finger\n+ctgA\test\tmatch\t1150\t7200\t.\t+\t.\tID=EST:agt767.5;Target=agt767.5+1+1153\n+ctgA\test\tHSP\t1150\t1500\t.\t+\t.\tParent=EST:agt767.5;Target=agt767.5+1+351\n+ctgA\test\tHSP\t5000\t5500\t.\t+\t.\tParent=EST:agt767.5;Target=agt767.5+352+852\n+ctgA\test\tHSP\t7000\t7200\t.\t+\t.\tParent=EST:agt767.5;Target=agt767.5+853+1153\n+ctgA\test\tmatch\t1050\t7300\t.\t+\t.\tID=EST:agt221.5;Target=agt221.5+1+1253\n+ctgA\test\tHSP\t1050\t1500\t.\t+\t.\tParent=EST:agt221.5;Target=agt221.5+1+451\n+ctgA\test\tHSP\t5000\t5500\t.\t+\t.\tParent=EST:agt221.5;Target=agt221.5+452+952\n+ctgA\test\tHSP\t7000\t7300\t.\t+\t.\tParent=EST:agt221.5;Target=agt221.5+953+1253\n+ctgA\texample\tmy_feature\t19157\t22915\t.\t-\t.\tID=My_feature:f13\n+ctgA\test\tmatch\t8000\t9000\t.\t-\t.\tID=EST:agt767.3;Target=agt767.3+1+1001\n+ctgA\test\tHSP\t8000\t9000\t.\t-\t.\tParent=EST:agt767.3;Target=agt767.3+1+1001\n+ctgA\texample\tmotif\t28342\t28447\t.\t-\t.\tID=Motif:m10;Note=DEAD+box\n+ctgA\texample\tmotif\t17667\t17690\t.\t+\t.\tID=Motif:m13;Note=DEAD+box\n+ctgA\texample\ttrace\t44401\t45925\t.\t+\t.\tID=name:tr"..b"SP\t30329\t30774\t.\t+\t.\tParent=Match:seg02\n+ctgA\texample\tHSP\t30808\t31306\t.\t+\t.\tParent=Match:seg02\n+ctgA\texample\tHSP\t31516\t31729\t.\t+\t.\tParent=Match:seg02\n+ctgA\texample\tHSP\t31753\t32154\t.\t+\t.\tParent=Match:seg02\n+ctgA\texample\tHSP\t32595\t32696\t.\t+\t.\tParent=Match:seg02\n+ctgA\texample\tHSP\t32892\t32901\t.\t+\t.\tParent=Match:seg02\n+ctgA\texample\tHSP\t33127\t33388\t.\t+\t.\tParent=Match:seg02\n+ctgA\texample\tHSP\t33439\t33443\t.\t+\t.\tParent=Match:seg02\n+ctgA\texample\tHSP\t33759\t34209\t.\t+\t.\tParent=Match:seg02\n+ctgA\texample\tHSP\t34401\t34466\t.\t+\t.\tParent=Match:seg02\n+ctgA\texample\tcontig\t1\t50000\t.\t.\t.\tID=Contig:ctgA\n+ctgA\texample\tmatch\t41137\t47829\t.\t-\t.\tID=Match:seg14\n+ctgA\texample\tHSP\t47449\t47829\t.\t-\t.\tParent=Match:seg14\n+ctgA\texample\tHSP\t46816\t46992\t.\t-\t.\tParent=Match:seg14\n+ctgA\texample\tHSP\t46092\t46318\t.\t-\t.\tParent=Match:seg14\n+ctgA\texample\tHSP\t45790\t46022\t.\t-\t.\tParent=Match:seg14\n+ctgA\texample\tHSP\t45231\t45488\t.\t-\t.\tParent=Match:seg14\n+ctgA\texample\tHSP\t44763\t45030\t.\t-\t.\tParent=Match:seg14\n+ctgA\texample\tHSP\t44065\t44556\t.\t-\t.\tParent=Match:seg14\n+ctgA\texample\tHSP\t43395\t43811\t.\t-\t.\tParent=Match:seg14\n+ctgA\texample\tHSP\t42890\t43270\t.\t-\t.\tParent=Match:seg14\n+ctgA\texample\tHSP\t42057\t42474\t.\t-\t.\tParent=Match:seg14\n+ctgA\texample\tHSP\t41754\t41948\t.\t-\t.\tParent=Match:seg14\n+ctgA\texample\tHSP\t41137\t41318\t.\t-\t.\tParent=Match:seg14\n+ctgA\texample\tmatch\t12531\t15870\t.\t+\t.\tID=Match:seg12\n+ctgA\texample\tHSP\t12531\t12895\t.\t+\t.\tParent=Match:seg12\n+ctgA\texample\tHSP\t13122\t13449\t.\t+\t.\tParent=Match:seg12\n+ctgA\texample\tHSP\t13452\t13745\t.\t+\t.\tParent=Match:seg12\n+ctgA\texample\tHSP\t13908\t13965\t.\t+\t.\tParent=Match:seg12\n+ctgA\texample\tHSP\t13998\t14488\t.\t+\t.\tParent=Match:seg12\n+ctgA\texample\tHSP\t14564\t14899\t.\t+\t.\tParent=Match:seg12\n+ctgA\texample\tHSP\t15185\t15276\t.\t+\t.\tParent=Match:seg12\n+ctgA\texample\tHSP\t15639\t15736\t.\t+\t.\tParent=Match:seg12\n+ctgA\texample\tHSP\t15745\t15870\t.\t+\t.\tParent=Match:seg12\n+ctgA\test\tmatch\t7500\t8000\t.\t-\t.\tID=EST:agt221.3;Target=agt221.3+1+501\n+ctgA\test\tHSP\t7500\t8000\t.\t-\t.\tParent=EST:agt221.3;Target=agt221.3+1+501\n+ctgA\texample\tcoding\t1300\t9000\t.\t+\t.\tID=mRNA:EDEN.3;Gene=EDEN\n+ctgA\texample\tCDS\t3301\t3902\t.\t+\t0\tParent=mRNA:EDEN.3\n+ctgA\texample\tCDS\t5000\t5500\t.\t+\t1\tParent=mRNA:EDEN.3\n+ctgA\texample\tCDS\t7000\t7600\t.\t+\t1\tParent=mRNA:EDEN.3\n+ctgA\texample\tprocessed_transcript\t1300\t9000\t.\t+\t.\tID=mRNA:EDEN.3\n+ctgA\texample\t5'-UTR\t1300\t1500\t.\t+\t.\tParent=mRNA:EDEN.3\n+ctgA\texample\t5'-UTR\t3000\t3300\t.\t+\t.\tParent=mRNA:EDEN.3\n+ctgA\texample\t3'-UTR\t7601\t9000\t.\t+\t.\tParent=mRNA:EDEN.3\n+ctgA\texample\tmatch\t26503\t35904\t.\t-\t.\tID=Match:seg05\n+ctgA\texample\tHSP\t35642\t35904\t.\t-\t.\tParent=Match:seg05\n+ctgA\texample\tHSP\t35333\t35507\t.\t-\t.\tParent=Match:seg05\n+ctgA\texample\tHSP\t34605\t34983\t.\t-\t.\tParent=Match:seg05\n+ctgA\texample\tHSP\t34244\t34313\t.\t-\t.\tParent=Match:seg05\n+ctgA\texample\tHSP\t33438\t33868\t.\t-\t.\tParent=Match:seg05\n+ctgA\texample\tHSP\t33053\t33325\t.\t-\t.\tParent=Match:seg05\n+ctgA\texample\tHSP\t32208\t32680\t.\t-\t.\tParent=Match:seg05\n+ctgA\texample\tHSP\t32010\t32057\t.\t-\t.\tParent=Match:seg05\n+ctgA\texample\tHSP\t31421\t31817\t.\t-\t.\tParent=Match:seg05\n+ctgA\texample\tHSP\t31232\t31236\t.\t-\t.\tParent=Match:seg05\n+ctgA\texample\tHSP\t30465\t30798\t.\t-\t.\tParent=Match:seg05\n+ctgA\texample\tHSP\t30108\t30216\t.\t-\t.\tParent=Match:seg05\n+ctgA\texample\tHSP\t29513\t29647\t.\t-\t.\tParent=Match:seg05\n+ctgA\texample\tHSP\t28777\t29058\t.\t-\t.\tParent=Match:seg05\n+ctgA\texample\tHSP\t28225\t28316\t.\t-\t.\tParent=Match:seg05\n+ctgA\texample\tHSP\t27887\t28076\t.\t-\t.\tParent=Match:seg05\n+ctgA\texample\tHSP\t27448\t27860\t.\t-\t.\tParent=Match:seg05\n+ctgA\texample\tHSP\t27172\t27185\t.\t-\t.\tParent=Match:seg05\n+ctgA\texample\tHSP\t26503\t26799\t.\t-\t.\tParent=Match:seg05\n+ctgA\texample\tmatch\t49406\t50000\t.\t+\t.\tID=Match:seg13\n+ctgA\texample\tHSP\t49406\t49476\t.\t+\t.\tParent=Match:seg13\n+ctgA\texample\tHSP\t49762\t50000\t.\t+\t.\tParent=Match:seg13\n+ctgA\texample\tgene\t1050\t9000\t.\t+\t.\tID=Gene:EDEN;Note=protein+kinase\n+ctgA\texample\tmotif\t33325\t35791\t.\t+\t.\tID=Motif:m04;Note=Ig-like\n+ctgA\texample\tmatch\t31785\t32359\t.\t+\t.\tID=Match:seg01\n+ctgA\texample\tHSP\t31785\t31939\t.\t+\t.\tParent=Match:seg01\n+ctgA\texample\tHSP\t32329\t32359\t.\t+\t.\tParent=Match:seg01\n"

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/5.maf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/5.maf Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,1513 @@\n+##maf version=1\n+a score=64549.0\n+s hg17.chr1 147962192 9 + 245522847 TCATTTAAT \n+s panTro1.chr1 129698808 9 + 229575298 TCATTTAAT \n+s mm5.chr3 65458475 7 - 160575607 --ATTTGAT \n+s rn3.chr2 68236843 7 - 258222147 --ATTTGAT \n+s canFam1.chr17 62929731 9 + 66886099 TTATTTGAT \n+\n+a score=37247.0\n+s hg17.chr1 147962201 43 + 245522847 GACAATTTTCTGGCGCAAGGCTCGGGGCCCAGAGCCAGGGAGG \n+s panTro1.chr1 129698817 43 + 229575298 GACAATTTTCTGGCGCAAGGCTCGGGGCCCAGAGCCAGGGAGG \n+s mm5.chr3 65458482 43 - 160575607 GACAATCTTCTGACGCAAGGCTCGAGGCCCAGAGCCAGGTAGT \n+s rn3.chr2 68236850 43 - 258222147 GACAATCTTCTGACGCAAGGCTCGGGGCCCAGCGCCAGGGAGT \n+s canFam1.chr17 62929740 43 + 66886099 GACAATTTTCTGGCGCAAGGCTCGGGGCCCAGAACCAGGGAGG \n+s danRer1.chr10 19400803 43 + 25436222 GGCGCTCTGCTTGAGCACAGCTTTGGGTCGTGCGCTCTTCAAA \n+\n+a score=1000.0\n+s hg17.chr1 147962244 1 + 245522847 G \n+s panTro1.chr1 129698860 1 + 229575298 G \n+s mm5.chr3 65458525 1 - 160575607 G \n+s rn3.chr2 68236893 1 - 258222147 G \n+s canFam1.chr17 62929783 1 + 66886099 G \n+\n+a score=0.0\n+s hg17.chr1 147962244 3 + 245522847 GGC \n+\n+a score=3000.0\n+s hg17.chr1 147962245 2 + 245522847 GC \n+s panTro1.chr1 129698861 2 + 229575298 GC \n+s mm5.chr3 65458526 2 - 160575607 GC \n+s rn3.chr2 68236894 2 - 258222147 GC \n+s canFam1.chr17 62929784 2 + 66886099 GC \n+s fr1.chrUn 290886762 2 + 349519338 GC \n+\n+a score=18092.0\n+s hg17.chr1 147962247 26 + 245522847 TCAGGAGGTGGCGGGCCGGGGCC-----CAG \n+s panTro1.chr1 129698863 26 + 229575298 TCAGGAGGTGGCGGGCCAGGGCC-----CAG \n+s mm5.chr3 65458528 26 - 160575607 TCGGGGGGTGGGGGCCCGGGGCC-----CAG \n+s rn3.chr2 68236896 26 - 258222147 TCGGGGGGTGGGGGCCCGGGGCC-----CAG \n+s canFam1.chr17 62929786 26 + 66886099 TCGGGAGGTGGTGGGCCAGGGCC-----CAG \n+s fr1.chrUn 290886764 26 + 349519338 TGATGAGGAATCGAGTCCTGTGG-----CAG \n+s danRer1.chr10 19400846 31 + 25436222 TTAGCAGGTGAATCGCTAGCGTCGGTGTTAG \n+\n+a score=219213.0\n+s hg17.chr1 147962273 178 + 245522847 GGCTGAGGCAGTGGGCGGCAGTCCATGGGCAGTAATGTACTTCTTGTAAGCCTCACGAATGATCTTGAAGGCTCGAGCAGTGGCATAGGGTATGTCTGTAACAGGGTCCCGGTATAGGGCTGGACGATGGGTCACTGGACAGACCTCACGAACAGGGACTTTTGGG---GGCCGCCCTTGG \n+s panTro1.chr1 129698889 178 + 229575298 GGCTGAGGCAGTGGGCGGCAGTCCATGGGCAGTAATGTACTTCTTGTAAGCCTCACGAATGATCTTGAAGGCTCGAGCAGTGGCATAGGGTATGTCTGTAACAGGGTCCCGGTATAGGGCTGGACGATGGGTCACTGGACAAACCTCACGAACAGGGACTTTTGGG---GGCCGCCCTTGG \n+s mm5.chr3 65458554 178 - 160575607 CGCCGAGGCGGTGGGTGGAAGTCCGTGGGCAGTGATGTACTTCTTGTACGCCTCACGGATGATCTTGAAGGCTCTAGCAGTGGCATAGGGTATGTCTGTAACAGGGTCCCGGTACAAAGCTGGACGGTGGGTCACTGGGCAGACCTCCCGCACCGGGACCTTCGGG---GGTCGCCCCTGG \n+s rn3.chr2 68236922 178 - 258222147 CGCTGAGGCAGTGGGTGGTAGTCCGTGGGCAGTGATGTACTTCTTGTACGCCTCACGGATGATCTTGAAGGCTCTAGCAGTGGCATAGGGTATGTCTGTAACAGGGTCCCGGTACAAAGCTGGACGGTGGGTCACTGGGCAGACCTCCCGAACAGGGACCTTTGGT---GGTCGCCCTTGG \n+s canFam1.chr17 62929812 178 + 66886099 GGCTGAGGCAGTGGGCGGCAGTCCGTGGGCAGTGATGTACTTCTTGTAGGCCTCACGGATGATCTTGAAGGCTCGAGCAGTGGCGTAGGGGATGTCTGTGACAGGGTCCCGGTACAGGGCTGGGCGATGGGTCACGGGGCAGACCTCCCGAACAGGGACCTTTGGG---GGCCGGCCTTGG \n+s fr1.chrUn 290886790 179 + 349519338 CTCCAGG--AGTGTTTGGGAAGCCGTGTGCAGCCACGTATTTACGGTAAGCTTCTCGGATGATGCGGAAGGCTCGTGCGTTAGCATAAGGTATGTCTGTGACCGGATCTCTGTACAGTGCGATCTTATGCGTGACGGGACAAATCTCCTGGACGGGCAGCTGAGGGCTCGGCTGCCCCTTG \n+s danRer1.chrUn 128306408 178 - 367113659 GGATGGGCCAGTGCAGGGCAGGCCATGAGCAGCCACATACTTCTTATAGGCCTCCCGAATTATCCTGAAGGCCTGTACATTAGCGTAAGGAATGTCAGTGATGGGGTCCCGGTAGAGCGCAGGCTTATGGGTAACAGGACAGACCTCCTGGACAGGTACTCGAGGA---GCAGGCGACTGG \n+\n+a score=84843.0\n+s hg17.chr1 147962451 56 + 245522847 GGGAACCATTCCTCGAAAGTTGCATCATCACTAAAAGTGATGAAGGTACGTGAGCA \n+s panTro1.chr1 129699067 56 + 229575298 GGGAACCATTCCTCGAAAGTTGCATCATCACTAAAAGTGATGAAGGTACGTGAGCA \n+s mm5.chr3 65458732 56 - 160575607 GGGAACCACTCTTCAAACGTTGCATCATCACTGAACGTGATGAAGGTGCGAGAGCA \n+s rn3.chr2 68237100 56 - 258222147 GGGAACCATTCTTCAAACGTGGCATCATCACTGAATGTGATGAAGGTACGTGAGC'..b'GCTCCGGCC-------CCTCGCTGTGGCGGCTGAACTGGCTGGCCAGGGACTCGTCCATGTTGAGCTCCGTGGTTACGGCGCTGCTGCCGTTGAAGTCCAGGTTGTCCTCGCTGCACA---GCTTGCTGTCCTCGCCCAGCGAAGGCTGGCTGGCTGT----GCGCTTCTCTTCGAGGTCA \n+s danRer1.chr10 12185578 200 + 25436222 TGTTGGGGTTGACCGGCGACACGGCGCCAGAGCTGT-CGTGCCCGCGTG---------GATCCCTTCGACCGCTGTACTGCCCGATGAAGGAGCCGTCCTCATTGAACTGGATGTCCA---CGCTGTCCCCGTAATCCGCCAGACTGTCGTTGCTGCT---GCGCTTGCTCTCGCACCC---CGACGGCTGGCT-GATGG---AGCACTTCTCCATATCACTG \n+\n+a score=102002.0\n+s hg17.chrX 152691446 25 + 154824264 ATGCTCATGGCGTCCACCACTTCCG \n+s mm5.chrX 65450627 25 + 160634946 ATGATCCTGGTGTCTACCACGTCTG \n+s rn3.chrX 159897295 25 + 160775580 ATGCTCCTGGTGTCTACCGTGTCCG \n+s canFam1.chrX 124808548 25 + 126913094 ATGCTCCTGGCATCCACCACCTCGG \n+\n+a score=45779.0\n+s hg17.chrX 152694029 80 + 154824264 TCAGTGTG---GCTTGGGGGTCGTGTCTAGGCCCTGGGGGTGGGAAGCTGAGGGTGAGGCTGGGGCCCCAGGGCCCCGGGAGA \n+s panTro1.chrX 158011192 80 + 160174553 TCAGTGTG---GCTTGGGGGTCGTGTCTAGGCCCTGGGGGTGGGAAGCTGAGGGTGAGGCTGGGGCCCCAGGGCCCCGGGAGA \n+s mm5.chrX 65453119 80 + 160634946 TCAGACTG---GCTTGCGAGTTGAATCTGGACCCTGGGGATGGGAGGTTGAGGGGGAAATTGGAGCCCCAGGTCCCCGGGAGA \n+s rn3.chrX 159899770 80 + 160775580 TCAGACTG---GCTTGCGAGTTGAATCTGGACCCTGGGGATGGGAAACTGAGGGGGAAACTGGAGCCCCAGGTCCCCGGGAGA \n+s canFam1.chrX 124811065 77 + 126913094 TCAGT------GCTTAAGTGGAGAGTCCAGGCCCTGGGGATGGGACGCCGAGGGGGACGCCGGGGCCCCGGAGCCGCGGGAGA \n+s galGal2.chr26 3294210 66 - 4255270 TCAGGGCG---GCT--------------GCGCCATGGAACTGAAATGCACACCGTGCCCTGGCACCCCCATCACCCCTGGGGA \n+s danRer1.chrNA 128898465 70 + 390413307 CCAGACTGCAAGCACAGGGAGAGTGTCTGGCCCCCAGGGC-----AGCT--------CGCTGGGGCCAGAGAGCCTCTGGTGA \n+\n+a score=18883.0\n+s hg17.chrX 152694109 35 + 154824264 AGCCTTTGTTCCTGCCCAGGCGGCTGCTGGGCGGG \n+s panTro1.chrX 158011272 35 + 160174553 AGCCTTTGTTCCTGCCCAGGCGGCTGCTGGGCGGG \n+s mm5.chrX 65453199 35 + 160634946 AGACTTTGTTTTTGCTGATGCTGCTGCAGGCCAGG \n+s rn3.chrX 159899850 35 + 160775580 AGACTTTGTTTTTGCTGAAGCTGCTGCAGGCCAGG \n+s canFam1.chrX 124811142 35 + 126913094 AGCCTTTGCTCCTACCCAGGCGGCCGGAGGCCGGA \n+s galGal2.chr26 3294276 30 - 4255270 CATC----CCCCTGTCAGCACTGCT-CGGGGCGGG \n+\n+a score=7409.0\n+s hg17.chrX 152694144 26 + 154824264 GCCTTTGGGCTTCGGGGCCCAGGACT \n+s panTro1.chrX 158011307 26 + 160174553 GCCTTTGGGCTTCGGGGCCCAGGACT \n+s mm5.chrX 65453234 20 + 160634946 GGCGTCAGAGTT------CCTAGACT \n+s rn3.chrX 159899885 26 + 160775580 GGCTTCAGGTTTCGAGTTCCTAGACT \n+s canFam1.chrX 124811177 26 + 126913094 GGCTTCAGGCTGCAgggcccggggcc \n+s galGal2.chrUn 50576950 22 + 165033910 -GTTCTGAG---CGAGGAACAGCACC \n+\n+a score=24632.0\n+s hg17.chrX 152694170 31 + 154824264 GGGAGAGGTGGTAGATGCTGGCCCAAGGCCC \n+s panTro1.chrX 158011333 31 + 160174553 GGGAGAGGTGGTAGATGCTGGCCCAAGGCCC \n+s mm5.chrX 65453254 31 + 160634946 CGGGGAGGCTGTAGATGCTAACCCATGGCCC \n+s rn3.chrX 159899911 31 + 160775580 GGGGGAGGCTGTAGATGCTAGCCCATGGCCC \n+s canFam1.chrX 124811203 31 + 126913094 gggggagccggtggacgcgggccccgcgccc \n+s galGal2.chrUn 50576972 31 + 165033910 GGGAGAGGCGGCAGCGGCTGCCCCCGAGCTC \n+s fr1.chrUn 329777075 24 - 349519338 GGACGAGGAGGTGGAGGAAGGATC------- \n+\n+a score=47489.0\n+s hg17.chrX 152694201 49 + 154824264 TGGCGGACAGAGGTCTTTCCCAAGAGCTCCTTAAACACAGAGTCCATGT \n+s panTro1.chrX 158011364 49 + 160174553 TGGCGGACAGAGGTCTTTCCCAAGAGCTCCTTAAACACAGAGTCCATGT \n+s mm5.chrX 65453285 49 + 160634946 TGGCGGACAGCAGTCTTTCCCAAGAGCTCCTTAAACACAGAATTCATGT \n+s rn3.chrX 159899942 49 + 160775580 TGGCGGACAGCAGCCTTTCCCAAGAGCTCCTTAAACACAGAATCCATGT \n+s canFam1.chrX 124811234 49 + 126913094 tggcgggcggAGGTCTTTCCCAGGAGCTCCTTAAACACGGAATCCATGG \n+s fr1.chrUn 329777109 37 - 349519338 TGGCGTGTG------------AGGAGCTCCTTAAAAACAGAGTCCATGT \n+\n+a score=175616.0\n+s hg17.chrX 152694250 13 + 154824264 TCTGTGCCACAGC \n+s panTro1.chrX 158011413 13 + 160174553 TCTGTGCCACAGC \n+s mm5.chrX 65453334 13 + 160634946 TCTGTGCCACAGC \n+s rn3.chrX 159899991 13 + 160775580 TCTGCGCCACAGC \n+s canFam1.chrX 124811283 13 + 126913094 TCTGTGCCACAGC \n+\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/5_liftover_mapped.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/5_liftover_mapped.bed Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,131 @@\n+chr7\t116197893\t116197920\tCCDS5763.1_cds_0_0_chr7_115444713_f\t0\t+\n+chr7\t116222929\t116223015\tCCDS5763.1_cds_1_0_chr7_115468539_f\t0\t+\n+chr7\t116237938\t116238188\tCCDS5763.1_cds_2_0_chr7_115483025_f\t0\t+\n+chr7\t116239076\t116239412\tCCDS5763.1_cds_3_0_chr7_115484166_f\t0\t+\n+chr7\t116240675\t116240891\tCCDS5763.1_cds_4_0_chr7_115485765_f\t0\t+\n+chr7\t116241233\t116241396\tCCDS5763.1_cds_5_0_chr7_115486323_f\t0\t+\n+chr7\t116246193\t116246382\tCCDS5763.1_cds_6_0_chr7_115491299_f\t0\t+\n+chr7\t116222929\t116223015\tCCDS5764.1_cds_0_0_chr7_115468539_f\t0\t+\n+chr7\t116237938\t116238188\tCCDS5764.1_cds_1_0_chr7_115483025_f\t0\t+\n+chr7\t116239076\t116239412\tCCDS5764.1_cds_2_0_chr7_115484166_f\t0\t+\n+chr7\t116240675\t116240891\tCCDS5764.1_cds_3_0_chr7_115485765_f\t0\t+\n+chr7\t116241233\t116241396\tCCDS5764.1_cds_4_0_chr7_115486323_f\t0\t+\n+chr7\t116246193\t116246382\tCCDS5764.1_cds_5_0_chr7_115491299_f\t0\t+\n+chr7\t116495075\t116495225\tCCDS5766.1_cds_0_0_chr7_115733787_f\t0\t+\n+chr7\t116495546\t116495734\tCCDS5766.1_cds_1_0_chr7_115734265_f\t0\t+\n+chr7\t116501260\t116501411\tCCDS5766.1_cds_2_0_chr7_115739976_f\t0\t+\n+chr7\t116495075\t116495225\tCCDS5765.1_cds_0_0_chr7_115733787_f\t0\t+\n+chr7\t116501260\t116501449\tCCDS5765.1_cds_1_0_chr7_115739976_f\t0\t+\n+chr7\t116522088\t116522118\tCCDS5767.1_cds_0_0_chr7_115759068_f\t0\t+\n+chr7\t116523550\t116523715\tCCDS5767.1_cds_1_0_chr7_115760530_f\t0\t+\n+chr7\t116562770\t116563112\tCCDS5767.1_cds_2_0_chr7_115792951_f\t0\t+\n+chr7\t116872904\t116872943\tCCDS5768.1_cds_0_0_chr7_116096617_f\t0\t+\n+chr7\t116899050\t116899114\tCCDS5768.1_cds_1_0_chr7_116122132_f\t0\t+\n+chr7\t116903933\t116903985\tCCDS5768.1_cds_2_0_chr7_116126999_f\t0\t+\n+chr7\t116909709\t116909773\tCCDS5768.1_cds_3_0_chr7_116132777_f\t0\t+\n+chr7\t116915110\t116915317\tCCDS5768.1_cds_4_0_chr7_116138182_f\t0\t+\n+chr7\t116917198\t116917278\tCCDS5768.1_cds_5_0_chr7_116140268_f\t0\t+\n+chr7\t116921242\t116921321\tCCDS5768.1_cds_6_0_chr7_116144238_f\t0\t+\n+chr7\t116923078\t116923150\tCCDS5768.1_cds_7_0_chr7_116146074_f\t0\t+\n+chr7\t116927214\t116927277\tCCDS5768.1_cds_8_0_chr7_116150065_f\t0\t+\n+chr7\t116928880\t116929021\tCCDS5768.1_cds_9_0_chr7_116151732_f\t0\t+\n+chr7\t116964784\t116964932\tCCDS5770.1_cds_0_0_chr7_116187546_f\t0\t+\n+chr7\t117108894\t117108977\tCCDS5770.1_cds_1_0_chr7_116333767_f\t0\t+\n+chr7\t117128694\t117128854\tCCDS5770.1_cds_2_0_chr7_116353566_f\t0\t+\n+chr7\t117138899\t117138954\tCCDS5770.1_cds_3_0_chr7_116363798_f\t0\t+\n+chr7\t117139597\t117139713\tCCDS5770.1_cds_4_0_chr7_116364496_f\t0\t+\n+chr7\t117140988\t117141064\tCCDS5770.1_cds_5_0_chr7_116365890_f\t0\t+\n+chr7\t117143259\t117143328\tCCDS5770.1_cds_6_0_chr7_116368129_f\t0\t+\n+chr7\t117145226\t117145381\tCCDS5770.1_cds_7_0_chr7_116370086_f\t0\t+\n+chr7\t117147574\t117147672\tCCDS5770.1_cds_8_0_chr7_116372440_f\t0\t+\n+chr7_random\t2679423\t2679538\tCCDS5770.1_cds_9_0_chr7_116404867_f\t0\t+\n+chr7\t117201671\t117201751\tCCDS5770.1_cds_10_0_chr7_116423326_f\t0\t+\n+chr7\t117203227\t117203330\tCCDS5770.1_cds_11_0_chr7_116424839_f\t0\t+\n+chr7\t117222109\t117222260\tCCDS5770.1_cds_12_0_chr7_116443792_f\t0\t+\n+chr7\t117231432\t117231525\tCCDS5770.1_cds_13_0_chr7_116453089_f\t0\t+\n+chr7\t117234203\t117234343\tCCDS5770.1_cds_14_0_chr7_116455928_f\t0\t+\n+chr7\t117235141\t117235261\tCCDS5770.1_cds_15_0_chr7_116456866_f\t0\t+\n+chr7\t116964784\t116964932\tCCDS5769.1_cds_0_0_chr7_116187546_f\t0\t+\n+chr7\t117108894\t117108977\tCCDS5769.1_cds_1_0_chr7_116333767_f\t0\t+\n+chr7\t117128694\t117128854\tCCDS5769.1_cds_2_0_chr7_116353566_f\t0\t+\n+chr7\t117138899\t117138954\tCCDS5769.1_cds_3_0_chr7_116363798_f\t0\t+\n+chr7\t117139597\t117139713\tCCDS5769.1_cds_4_0_chr7_116364496_f\t0\t+\n+chr7\t117140988\t117141064\tCCDS5769.1_cds_5_0_chr7_116365890_f\t0\t+\n+chr7\t117145226\t117145381\tCCDS5769.1_cds_6_0_chr7_116370086_f\t0\t+\n+chr7\t117147574\t117147672\tCCDS5769.1_cds_7_0_chr7_116372440_f\t0\t+\n+chr7_random\t2679423\t2679538\tCCDS5769.1_cds_8_0_chr7_116404867_f\t0\t+\n+chr7\t117201671\t117201751\tCCDS5769.1_cds_9_0_chr7_116423326_f\t0\t+\n+chr7\t117203227\t117203330\tCCDS5769.1_cds_10_0_chr7_116424839_f\t0\t+\n+chr7\t117222109\t117222260\tCCDS5769.1_cds_11_0_chr7_116443792_f\t0\t+\n+chr7\t117231432\t117231525\tCCDS5769.1_cds_12_0_chr7_116453089_f\t0\t+\n+chr7\t'..b'r\t0\t-\n+chr7\t117399808\t117399884\tCCDS5772.1_cds_5_0_chr7_116616074_r\t0\t-\n+chr7\t117400724\t117400849\tCCDS5772.1_cds_6_0_chr7_116616991_r\t0\t-\n+chr7\t117402466\t117402602\tCCDS5772.1_cds_7_0_chr7_116618731_r\t0\t-\n+chr7\t117403442\t117403554\tCCDS5772.1_cds_8_0_chr7_116619703_r\t0\t-\n+chr7\t117438281\t117438393\tCCDS5772.1_cds_9_0_chr7_116654168_r\t0\t-\n+chr7\t117440357\t117440480\tCCDS5772.1_cds_10_0_chr7_116656242_r\t0\t-\n+chr7\t117444948\t117445048\tCCDS5772.1_cds_11_0_chr7_116660841_r\t0\t-\n+chr7\t117445468\t117445573\tCCDS5772.1_cds_12_0_chr7_116661361_r\t0\t-\n+chr7\t117499706\t117499759\tCCDS5773.1_cds_0_0_chr7_116714100_f\t0\t+\n+chr7\t117523820\t117523931\tCCDS5773.1_cds_1_0_chr7_116738258_f\t0\t+\n+chr7\t117528597\t117528706\tCCDS5773.1_cds_2_0_chr7_116743039_f\t0\t+\n+chr7\t117550464\t117550680\tCCDS5773.1_cds_3_0_chr7_116764904_f\t0\t+\n+chr7\t117553829\t117553919\tCCDS5773.1_cds_4_0_chr7_116768281_f\t0\t+\n+chr7\t117554806\t117554970\tCCDS5773.1_cds_5_0_chr7_116769253_f\t0\t+\n+chr7\t117556111\t117556237\tCCDS5773.1_cds_6_0_chr7_116770553_f\t0\t+\n+chr7\t117559659\t117559905\tCCDS5773.1_cds_7_0_chr7_116774105_f\t0\t+\n+chr7\t117561568\t117561660\tCCDS5773.1_cds_8_0_chr7_116776021_f\t0\t+\n+chr7\t117568199\t117568382\tCCDS5773.1_cds_9_0_chr7_116782646_f\t0\t+\n+chr7\t117579005\t117579197\tCCDS5773.1_cds_10_0_chr7_116793469_f\t0\t+\n+chr7\t117609945\t117610041\tCCDS5773.1_cds_11_0_chr7_116821744_f\t0\t+\n+chr7\t117612558\t117612645\tCCDS5773.1_cds_12_0_chr7_116824358_f\t0\t+\n+chr7\t117614292\t117615016\tCCDS5773.1_cds_13_0_chr7_116825939_f\t0\t+\n+chr7\t117617279\t117617408\tCCDS5773.1_cds_14_0_chr7_116828935_f\t0\t+\n+chr7\t117625173\t117625211\tCCDS5773.1_cds_15_0_chr7_116836831_f\t0\t+\n+chr7\t117625879\t117626130\tCCDS5773.1_cds_16_0_chr7_116837537_f\t0\t+\n+chr7\t117628986\t117629066\tCCDS5773.1_cds_17_0_chr7_116840679_f\t0\t+\n+chr7\t117632825\t117632976\tCCDS5773.1_cds_18_0_chr7_116844524_f\t0\t+\n+chr7\t117633887\t117634115\tCCDS5773.1_cds_19_0_chr7_116845586_f\t0\t+\n+chr7\t117636923\t117637024\tCCDS5773.1_cds_20_0_chr7_116848618_f\t0\t+\n+chr7\t117649505\t117649753\tCCDS5773.1_cds_21_0_chr7_116861527_f\t0\t+\n+chr7\t117664146\t117664302\tCCDS5773.1_cds_22_0_chr7_116876443_f\t0\t+\n+chr7\t117674548\t117674638\tCCDS5773.1_cds_23_0_chr7_116886847_f\t0\t+\n+chr7\t117686685\t117686858\tCCDS5773.1_cds_24_0_chr7_116898693_f\t0\t+\n+chr7\t117687456\t117687562\tCCDS5773.1_cds_25_0_chr7_116899464_f\t0\t+\n+chr7\t117688902\t117689103\tCCDS5773.1_cds_26_0_chr7_116900913_f\t0\t+\n+chr7\t117734744\t117734996\tCCDS5774.1_cds_0_0_chr7_116945542_r\t0\t-\n+chr7\t117741224\t117741326\tCCDS5774.1_cds_1_0_chr7_116952023_r\t0\t-\n+chr7\t117743450\t117743638\tCCDS5774.1_cds_4_0_chr7_116958552_r\t0\t-\n+chr7\t117743957\t117744164\tCCDS5774.1_cds_5_0_chr7_116959057_r\t0\t-\n+chr7\t117746996\t117747175\tCCDS5774.1_cds_6_0_chr7_116962094_r\t0\t-\n+chr7\t117753794\t117753981\tCCDS5774.1_cds_7_0_chr7_116968918_r\t0\t-\n+chr7\t117754149\t117754302\tCCDS5774.1_cds_8_0_chr7_116969274_r\t0\t-\n+chr7\t117764699\t117764799\tCCDS5774.1_cds_9_0_chr7_116979836_r\t0\t-\n+chr7\t117764881\t117764968\tCCDS5774.1_cds_10_0_chr7_116980018_r\t0\t-\n+chr7\t117775103\t117775183\tCCDS5774.1_cds_11_0_chr7_116990560_r\t0\t-\n+chr7\t117776423\t117776519\tCCDS5774.1_cds_12_0_chr7_116991880_r\t0\t-\n+chr7\t117779436\t117779712\tCCDS5774.1_cds_13_0_chr7_116994440_r\t0\t-\n+chr7\t117786062\t117786180\tCCDS5774.1_cds_14_0_chr7_117001064_r\t0\t-\n+chr7\t117796458\t117796713\tCCDS5774.1_cds_15_0_chr7_117011516_r\t0\t-\n+chr7\t117799369\t117799520\tCCDS5774.1_cds_16_0_chr7_117014446_r\t0\t-\n+chr7\t117801790\t117801890\tCCDS5774.1_cds_17_0_chr7_117016867_r\t0\t-\n+chr7\t117803186\t117803390\tCCDS5774.1_cds_18_0_chr7_117018256_r\t0\t-\n+chr7\t117810065\t117811719\tCCDS5774.1_cds_19_0_chr7_117025133_r\t0\t-\n+chr7\t117829639\t117829865\tCCDS5774.1_cds_20_0_chr7_117044770_r\t0\t-\n+chr7\t117880732\t117880840\tCCDS5774.1_cds_21_0_chr7_117095214_r\t0\t-\n+chr7\t117893163\t117893244\tCCDS5774.1_cds_22_0_chr7_117107340_r\t0\t-\n+chr5\t133682646\t133682808\tCCDS4149.1_cds_0_0_chr5_131424299_f\t0\t+\n+chr5\t133682906\t133682948\tCCDS4149.1_cds_1_0_chr5_131424559_f\t0\t+\n+chr5\t133684249\t133684339\tCCDS4149.1_cds_2_0_chr5_131425904_f\t0\t+\n+chr5\t133684463\t133684505\tCCDS4149.1_cds_3_0_chr5_131426118_f\t0\t+\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/5_liftover_unmapped.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/5_liftover_unmapped.bed Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,6 @@
+#Partially deleted in new
+chr7 116549075 116549353 CCDS5771.1_cds_2_0_chr7_116549076_r 0 -
+#Deleted in new
+chr7 116953508 116953641 CCDS5774.1_cds_2_0_chr7_116953509_r 0 -
+#Deleted in new
+chr7 116955071 116955135 CCDS5774.1_cds_3_0_chr7_116955072_r 0 -

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/5_mult_liftover_mapped.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/5_mult_liftover_mapped.bed Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,132 @@\n+chr7\t116197893\t116197920\tCCDS5763.1_cds_0_0_chr7_115444713_f\t1\t+\n+chr7\t116222929\t116223015\tCCDS5763.1_cds_1_0_chr7_115468539_f\t1\t+\n+chr7\t116237938\t116238188\tCCDS5763.1_cds_2_0_chr7_115483025_f\t1\t+\n+chr7\t116239076\t116239412\tCCDS5763.1_cds_3_0_chr7_115484166_f\t1\t+\n+chr7\t116240675\t116240891\tCCDS5763.1_cds_4_0_chr7_115485765_f\t1\t+\n+chr7\t116241233\t116241396\tCCDS5763.1_cds_5_0_chr7_115486323_f\t1\t+\n+chr7\t116246193\t116246382\tCCDS5763.1_cds_6_0_chr7_115491299_f\t1\t+\n+chr7\t116222929\t116223015\tCCDS5764.1_cds_0_0_chr7_115468539_f\t1\t+\n+chr7\t116237938\t116238188\tCCDS5764.1_cds_1_0_chr7_115483025_f\t1\t+\n+chr7\t116239076\t116239412\tCCDS5764.1_cds_2_0_chr7_115484166_f\t1\t+\n+chr7\t116240675\t116240891\tCCDS5764.1_cds_3_0_chr7_115485765_f\t1\t+\n+chr7\t116241233\t116241396\tCCDS5764.1_cds_4_0_chr7_115486323_f\t1\t+\n+chr7\t116246193\t116246382\tCCDS5764.1_cds_5_0_chr7_115491299_f\t1\t+\n+chr7\t116495075\t116495225\tCCDS5766.1_cds_0_0_chr7_115733787_f\t1\t+\n+chr7\t116495546\t116495734\tCCDS5766.1_cds_1_0_chr7_115734265_f\t1\t+\n+chr7\t116501260\t116501411\tCCDS5766.1_cds_2_0_chr7_115739976_f\t1\t+\n+chr7\t116495075\t116495225\tCCDS5765.1_cds_0_0_chr7_115733787_f\t1\t+\n+chr7\t116501260\t116501449\tCCDS5765.1_cds_1_0_chr7_115739976_f\t1\t+\n+chr7\t116522088\t116522118\tCCDS5767.1_cds_0_0_chr7_115759068_f\t1\t+\n+chr7\t116523550\t116523715\tCCDS5767.1_cds_1_0_chr7_115760530_f\t1\t+\n+chr7\t116562770\t116563112\tCCDS5767.1_cds_2_0_chr7_115792951_f\t1\t+\n+chr7\t116872904\t116872943\tCCDS5768.1_cds_0_0_chr7_116096617_f\t1\t+\n+chr7\t116899050\t116899114\tCCDS5768.1_cds_1_0_chr7_116122132_f\t1\t+\n+chr7\t116903933\t116903985\tCCDS5768.1_cds_2_0_chr7_116126999_f\t1\t+\n+chr7\t116909709\t116909773\tCCDS5768.1_cds_3_0_chr7_116132777_f\t1\t+\n+chr7\t116915110\t116915317\tCCDS5768.1_cds_4_0_chr7_116138182_f\t1\t+\n+chr7\t116917198\t116917278\tCCDS5768.1_cds_5_0_chr7_116140268_f\t1\t+\n+chr7\t116921242\t116921321\tCCDS5768.1_cds_6_0_chr7_116144238_f\t1\t+\n+chr7\t116923078\t116923150\tCCDS5768.1_cds_7_0_chr7_116146074_f\t1\t+\n+chr7\t116927214\t116927277\tCCDS5768.1_cds_8_0_chr7_116150065_f\t1\t+\n+chr7\t116928880\t116929021\tCCDS5768.1_cds_9_0_chr7_116151732_f\t1\t+\n+chr7\t116964784\t116964932\tCCDS5770.1_cds_0_0_chr7_116187546_f\t1\t+\n+chr7\t117108894\t117108977\tCCDS5770.1_cds_1_0_chr7_116333767_f\t1\t+\n+chr7\t117128694\t117128854\tCCDS5770.1_cds_2_0_chr7_116353566_f\t1\t+\n+chr7\t117138899\t117138954\tCCDS5770.1_cds_3_0_chr7_116363798_f\t1\t+\n+chr7\t117139597\t117139713\tCCDS5770.1_cds_4_0_chr7_116364496_f\t1\t+\n+chr7\t117140988\t117141064\tCCDS5770.1_cds_5_0_chr7_116365890_f\t1\t+\n+chr7\t117143259\t117143328\tCCDS5770.1_cds_6_0_chr7_116368129_f\t1\t+\n+chr7\t117145226\t117145381\tCCDS5770.1_cds_7_0_chr7_116370086_f\t1\t+\n+chr7\t117147574\t117147672\tCCDS5770.1_cds_8_0_chr7_116372440_f\t1\t+\n+chr7_random\t2679423\t2679538\tCCDS5770.1_cds_9_0_chr7_116404867_f\t1\t+\n+chr7\t117201671\t117201751\tCCDS5770.1_cds_10_0_chr7_116423326_f\t1\t+\n+chr7\t117203227\t117203330\tCCDS5770.1_cds_11_0_chr7_116424839_f\t1\t+\n+chr7\t117222109\t117222260\tCCDS5770.1_cds_12_0_chr7_116443792_f\t1\t+\n+chr7\t117231432\t117231525\tCCDS5770.1_cds_13_0_chr7_116453089_f\t1\t+\n+chr7\t117234203\t117234343\tCCDS5770.1_cds_14_0_chr7_116455928_f\t1\t+\n+chr7\t117235141\t117235261\tCCDS5770.1_cds_15_0_chr7_116456866_f\t1\t+\n+chr7\t116964784\t116964932\tCCDS5769.1_cds_0_0_chr7_116187546_f\t1\t+\n+chr7\t117108894\t117108977\tCCDS5769.1_cds_1_0_chr7_116333767_f\t1\t+\n+chr7\t117128694\t117128854\tCCDS5769.1_cds_2_0_chr7_116353566_f\t1\t+\n+chr7\t117138899\t117138954\tCCDS5769.1_cds_3_0_chr7_116363798_f\t1\t+\n+chr7\t117139597\t117139713\tCCDS5769.1_cds_4_0_chr7_116364496_f\t1\t+\n+chr7\t117140988\t117141064\tCCDS5769.1_cds_5_0_chr7_116365890_f\t1\t+\n+chr7\t117145226\t117145381\tCCDS5769.1_cds_6_0_chr7_116370086_f\t1\t+\n+chr7\t117147574\t117147672\tCCDS5769.1_cds_7_0_chr7_116372440_f\t1\t+\n+chr7_random\t2679423\t2679538\tCCDS5769.1_cds_8_0_chr7_116404867_f\t1\t+\n+chr7\t117201671\t117201751\tCCDS5769.1_cds_9_0_chr7_116423326_f\t1\t+\n+chr7\t117203227\t117203330\tCCDS5769.1_cds_10_0_chr7_116424839_f\t1\t+\n+chr7\t117222109\t117222260\tCCDS5769.1_cds_11_0_chr7_116443792_f\t1\t+\n+chr7\t117231432\t117231525\tCCDS5769.1_cds_12_0_chr7_116453089_f\t1\t+\n+chr7\t'..b'r\t1\t-\n+chr7\t117399808\t117399884\tCCDS5772.1_cds_5_0_chr7_116616074_r\t1\t-\n+chr7\t117400724\t117400849\tCCDS5772.1_cds_6_0_chr7_116616991_r\t1\t-\n+chr7\t117402466\t117402602\tCCDS5772.1_cds_7_0_chr7_116618731_r\t1\t-\n+chr7\t117403442\t117403554\tCCDS5772.1_cds_8_0_chr7_116619703_r\t1\t-\n+chr7\t117438281\t117438393\tCCDS5772.1_cds_9_0_chr7_116654168_r\t1\t-\n+chr7\t117440357\t117440480\tCCDS5772.1_cds_10_0_chr7_116656242_r\t1\t-\n+chr7\t117444948\t117445048\tCCDS5772.1_cds_11_0_chr7_116660841_r\t1\t-\n+chr7\t117445468\t117445573\tCCDS5772.1_cds_12_0_chr7_116661361_r\t1\t-\n+chr7\t117499706\t117499759\tCCDS5773.1_cds_0_0_chr7_116714100_f\t1\t+\n+chr7\t117523820\t117523931\tCCDS5773.1_cds_1_0_chr7_116738258_f\t1\t+\n+chr7\t117528597\t117528706\tCCDS5773.1_cds_2_0_chr7_116743039_f\t1\t+\n+chr7\t117550464\t117550680\tCCDS5773.1_cds_3_0_chr7_116764904_f\t1\t+\n+chr7\t117553829\t117553919\tCCDS5773.1_cds_4_0_chr7_116768281_f\t1\t+\n+chr7\t117554806\t117554970\tCCDS5773.1_cds_5_0_chr7_116769253_f\t1\t+\n+chr7\t117556111\t117556237\tCCDS5773.1_cds_6_0_chr7_116770553_f\t1\t+\n+chr7\t117559659\t117559905\tCCDS5773.1_cds_7_0_chr7_116774105_f\t1\t+\n+chr7\t117561568\t117561660\tCCDS5773.1_cds_8_0_chr7_116776021_f\t1\t+\n+chr7\t117568199\t117568382\tCCDS5773.1_cds_9_0_chr7_116782646_f\t1\t+\n+chr7\t117579005\t117579197\tCCDS5773.1_cds_10_0_chr7_116793469_f\t1\t+\n+chr7\t117609945\t117610041\tCCDS5773.1_cds_11_0_chr7_116821744_f\t1\t+\n+chr7\t117612558\t117612645\tCCDS5773.1_cds_12_0_chr7_116824358_f\t1\t+\n+chr7\t117614292\t117615016\tCCDS5773.1_cds_13_0_chr7_116825939_f\t1\t+\n+chr7\t117617279\t117617408\tCCDS5773.1_cds_14_0_chr7_116828935_f\t1\t+\n+chr7\t117625173\t117625211\tCCDS5773.1_cds_15_0_chr7_116836831_f\t1\t+\n+chr7\t117625879\t117626130\tCCDS5773.1_cds_16_0_chr7_116837537_f\t1\t+\n+chr7\t117628986\t117629066\tCCDS5773.1_cds_17_0_chr7_116840679_f\t1\t+\n+chr7\t117632825\t117632976\tCCDS5773.1_cds_18_0_chr7_116844524_f\t1\t+\n+chr7\t117633887\t117634115\tCCDS5773.1_cds_19_0_chr7_116845586_f\t1\t+\n+chr7\t117636923\t117637024\tCCDS5773.1_cds_20_0_chr7_116848618_f\t1\t+\n+chr7\t117649505\t117649753\tCCDS5773.1_cds_21_0_chr7_116861527_f\t1\t+\n+chr7\t117664146\t117664302\tCCDS5773.1_cds_22_0_chr7_116876443_f\t1\t+\n+chr7\t117674548\t117674638\tCCDS5773.1_cds_23_0_chr7_116886847_f\t1\t+\n+chr7\t117686685\t117686858\tCCDS5773.1_cds_24_0_chr7_116898693_f\t1\t+\n+chr7\t117687456\t117687562\tCCDS5773.1_cds_25_0_chr7_116899464_f\t1\t+\n+chr7\t117688902\t117689103\tCCDS5773.1_cds_26_0_chr7_116900913_f\t1\t+\n+chr7\t117734744\t117734996\tCCDS5774.1_cds_0_0_chr7_116945542_r\t1\t-\n+chr7\t117741224\t117741326\tCCDS5774.1_cds_1_0_chr7_116952023_r\t1\t-\n+chr7\t117743450\t117743638\tCCDS5774.1_cds_4_0_chr7_116958552_r\t1\t-\n+chr7\t117743957\t117744164\tCCDS5774.1_cds_5_0_chr7_116959057_r\t1\t-\n+chr7\t117746996\t117747175\tCCDS5774.1_cds_6_0_chr7_116962094_r\t1\t-\n+chr7\t117753794\t117753981\tCCDS5774.1_cds_7_0_chr7_116968918_r\t1\t-\n+chr7\t117754149\t117754302\tCCDS5774.1_cds_8_0_chr7_116969274_r\t1\t-\n+chr7\t117764699\t117764799\tCCDS5774.1_cds_9_0_chr7_116979836_r\t1\t-\n+chr7\t117764881\t117764968\tCCDS5774.1_cds_10_0_chr7_116980018_r\t1\t-\n+chr7\t117775103\t117775183\tCCDS5774.1_cds_11_0_chr7_116990560_r\t1\t-\n+chr7\t117776423\t117776519\tCCDS5774.1_cds_12_0_chr7_116991880_r\t1\t-\n+chr7\t117779436\t117779712\tCCDS5774.1_cds_13_0_chr7_116994440_r\t1\t-\n+chr7\t117786062\t117786180\tCCDS5774.1_cds_14_0_chr7_117001064_r\t1\t-\n+chr7\t117796458\t117796713\tCCDS5774.1_cds_15_0_chr7_117011516_r\t1\t-\n+chr7\t117799369\t117799520\tCCDS5774.1_cds_16_0_chr7_117014446_r\t1\t-\n+chr7\t117801790\t117801890\tCCDS5774.1_cds_17_0_chr7_117016867_r\t1\t-\n+chr7\t117803186\t117803390\tCCDS5774.1_cds_18_0_chr7_117018256_r\t1\t-\n+chr7\t117810065\t117811719\tCCDS5774.1_cds_19_0_chr7_117025133_r\t1\t-\n+chr7\t117829639\t117829865\tCCDS5774.1_cds_20_0_chr7_117044770_r\t1\t-\n+chr7\t117880732\t117880840\tCCDS5774.1_cds_21_0_chr7_117095214_r\t1\t-\n+chr7\t117893163\t117893244\tCCDS5774.1_cds_22_0_chr7_117107340_r\t1\t-\n+chr5\t133682646\t133682808\tCCDS4149.1_cds_0_0_chr5_131424299_f\t1\t+\n+chr5\t133682906\t133682948\tCCDS4149.1_cds_1_0_chr5_131424559_f\t1\t+\n+chr5\t133684249\t133684339\tCCDS4149.1_cds_2_0_chr5_131425904_f\t1\t+\n+chr5\t133684463\t133684505\tCCDS4149.1_cds_3_0_chr5_131426118_f\t1\t+\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/5_mult_liftover_unmapped.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/5_mult_liftover_unmapped.bed Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,4 @@
+#Deleted in new
+chr7 116953508 116953641 CCDS5774.1_cds_2_0_chr7_116953509_r 0 -
+#Deleted in new
+chr7 116955071 116955135 CCDS5774.1_cds_3_0_chr7_116955072_r 0 -

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/6.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/6.bed Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,10 @@
+chr7 115444712 115444739 CCDS5763.1_cds_0_0_chr7_115444713_f 0 +
+chr7 115468538 115468624 CCDS5763.1_cds_1_0_chr7_115468539_f 0 +
+chr7 115483024 115483277 CCDS5763.1_cds_2_0_chr7_115483025_f 0 +
+chr7 115484165 115484501 CCDS5763.1_cds_3_0_chr7_115484166_f 0 +
+chr7 115485764 115485980 CCDS5763.1_cds_4_0_chr7_115485765_f 0 +
+chr7 115486322 115486481 CCDS5763.1_cds_5_0_chr7_115486323_f 0 +
+chr7 115491298 115491487 CCDS5763.1_cds_6_0_chr7_115491299_f 0 +
+chr7 115468538 115468624 CCDS5764.1_cds_0_0_chr7_115468539_f 0 +
+chr7 115483024 115483277 CCDS5764.1_cds_1_0_chr7_115483025_f 0 +
+chr7 115484165 115484501 CCDS5764.1_cds_2_0_chr7_115484166_f 0 +

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/7.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/7.bed Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,29 @@
+chr1 147962006 147975713 NM_005997 0 - 147962192 147975670 0 6 574,145,177,115,153,160, 0,1543,7859,9048,9340,13547,
+chr1 147984101 148035079 BC007833 0 + 147984545 148033414 0 14 529,32,81,131,118,153,300,206,84,49,85,130,46,1668, 0,25695,28767,33118,33695,33998,35644,38005,39629,40577,41402,43885,48367,49310,
+chr1 148077485 148111797 NM_002651 0 - 148078400 148111728 0 12 1097,121,133,266,124,105,110,228,228,45,937,77, 0,2081,2472,6871,9907,10257,11604,14199,15637,18274,23636,34235,
+chr1 148185113 148187485 NM_002796 0 + 148185136 148187378 0 7 163,207,147,82,117,89,120, 0,416,877,1199,1674,1977,2252,
+chr2 118288484 118306183 NM_006773 0 + 118288583 118304530 0 14 184,285,144,136,101,200,115,140,162,153,114,57,178,1796, 0,2765,4970,6482,6971,7183,7468,9890,10261,10768,11590,14270,14610,15903,
+chr2 118389378 118390700 BC005078 0 - 118390395 118390500 0 1 1322, 0,
+chr2 220108603 220116964 NM_001927 0 + 220108689 220116217 0 9 664,61,96,162,126,221,44,83,789, 0,1718,1874,2118,2451,2963,5400,7286,7572,
+chr2 220229182 220233943 NM_024536 0 - 220229609 220233765 0 4 1687,180,574,492, 0,1990,2660,4269,
+chr5 131170738 131357870 AF099740 0 - 131311206 131357817 0 31 112,124,120,81,65,40,120,129,61,88,94,79,72,102,144,117,89,73,96,135,135,78,74,52,33,179,100,102,65,115,248, 0,11593,44117,47607,104668,109739,114675,126366,135488,137518,138009,140437,152389,153373,155388,159269,160793,162981,164403,165577,166119,167611,169501,178260,179675,180901,181658,182260,182953,183706,186884,
+chr5 131424245 131426795 NM_000588 0 + 131424298 131426383 0 5 215,42,90,42,535, 0,313,1658,1872,2015,
+chr5 131556201 131590458 NM_004199 0 - 131556601 131582218 0 15 471,97,69,66,54,100,71,177,194,240,138,152,97,100,170, 0,2316,2802,5596,6269,11138,11472,15098,16528,17674,21306,24587,25142,25935,34087,
+chr5 131621285 131637046 NM_003687 0 + 131621326 131635821 0 7 134,152,82,179,164,118,1430, 0,4915,8770,13221,13609,14097,14331,
+chr6 108298214 108386086 NM_007214 0 - 108299600 108385906 0 21 1530,105,99,102,159,174,60,83,148,155,93,133,95,109,51,59,62,113,115,100,304, 0,2490,6246,10831,12670,23164,23520,27331,31052,32526,34311,36130,36365,38609,41028,42398,43048,51479,54500,59097,87568,
+chr6 108593954 108616704 NM_003269 0 + 108594662 108615360 0 9 733,146,88,236,147,97,150,106,1507, 0,5400,8778,10445,12037,14265,14749,15488,21243,
+chr6 108639410 108689143 NM_152827 0 - 108640045 108688818 0 3 741,125,487, 0,2984,49246,
+chr6 108722790 108950942 NM_145315 0 + 108722976 108950321 0 13 325,224,52,102,131,100,59,83,71,101,141,114,750, 0,28931,52094,60760,61796,71339,107102,152319,181970,182297,215317,224802,227402,
+chr7 113320332 113924911 AK131266 0 + 113862563 113893433 0 20 285,91,178,90,58,75,138,51,201,178,214,105,88,84,77,102,122,70,164,1124, 0,201692,340175,448290,451999,484480,542213,543265,543478,545201,556083,558358,565876,567599,573029,573245,575738,577123,577946,603455,
+chr7 116511232 116557294 NM_003391 0 - 116512159 116556994 0 5 1157,265,278,227,383, 0,20384,37843,43339,45679,
+chr7 116713967 116902666 NM_000492 0 + 116714099 116901113 0 27 185,111,109,216,90,164,126,247,93,183,192,95,87,724,129,38,251,80,151,228,101,249,156,90,173,106,1754, 0,24290,29071,50936,54313,55285,56585,60137,62053,68678,79501,107776,110390,111971,114967,122863,123569,126711,130556,131618,134650,147559,162475,172879,184725,185496,186945,
+chr7 116944658 117107512 AF377960 0 - 116945541 116979926 0 23 1129,102,133,64,186,206,179,188,153,100,87,80,96,276,118,255,151,100,204,1654,225,108,173, 0,7364,8850,10413,13893,14398,17435,24259,24615,35177,35359,45901,47221,49781,56405,66857,69787,72208,73597,80474,100111,150555,162681,
+chr8 118880786 119193239 NM_000127 0 - 118881131 119192466 0 11 531,172,161,90,96,119,133,120,108,94,1735, 0,5355,7850,13505,19068,20309,23098,30863,36077,37741,310718,
+chr9 128763240 128783870 NM_174933 0 + 128764156 128783586 0 12 261,118,74,159,76,48,56,63,129,117,127,370, 0,522,875,5630,12374,12603,15040,15175,18961,19191,20037,20260,
+chr9 128787362 128789566 NM_014908 0 - 128787519 128789136 0 1 2204, 0,
+chr9 128789530 128848928 NM_015354 0 + 128789552 128848511 0 44 54,55,74,85,81,45,93,120,212,115,201,90,66,120,127,153,127,88,77,115,121,67,129,140,107,207,170,70,68,196,78,86,146,182,201,93,159,138,75,228,132,74,130,594, 0,1491,5075,8652,9254,10312,11104,11317,20808,21702,23060,25462,31564,32908,33566,34851,35204,35595,35776,37202,38860,39111,39891,40349,42422,45499,45827,46675,47158,47621,50453,50840,51474,51926,53831,54186,55119,55619,57449,57605,57947,58352,58541,58804,
+chr9 128849867 128870133 NM_020145 0 - 128850516 128869987 0 11 757,241,101,90,24,63,93,134,129,142,209, 0,1071,1736,2085,2635,4201,6376,6736,13056,14247,20057,
+chrX 122719582 122773357 NM_001167 0 + 122745047 122766566 0 7 96,909,100,79,43,201,6985, 0,25433,28421,31040,32533,40295,46790,
+chrX 152648233 152662158 NM_000425 0 - 152648964 152662138 0 28 963,12,73,135,156,120,174,123,202,116,223,71,198,111,125,157,167,112,144,132,185,112,171,123,203,106,11,100, 0,1436,1545,1951,2390,2653,2889,3156,3367,3772,4717,5122,5424,5868,6066,6370,6629,6909,7588,7871,8124,8456,8858,9125,10220,10660,11296,13825,
+chrX 152691216 152693487 NM_000054 0 + 152691446 152693029 0 3 255,885,664, 0,616,1607,
+chrX 152693677 152712545 NM_001666 0 - 152694029 152712503 0 22 586,100,93,184,74,234,106,135,78,61,103,28,85,192,102,222,129,183,63,163,205,109, 0,1693,2066,2364,2635,2794,3129,3323,3545,3752,5323,5647,5841,6032,6401,11455,11778,13249,13719,13987,14227,18759,

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/7.bigbed

Binary file rnaseq/cutadapt/test-data/7.bigbed has changed

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/8.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/8.bed Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,1 @@
+chrX 151007096 151290393 BC028629 0 - 151007267 151203610 0 10 507,212,153,144,83,221,68,122,166,208, 0,21673,29576,39944,56706,87721,116611,177524,196374,283089,
\ No newline at end of file

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/9.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/9.bed Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,1 @@
+chr28 346187 388197 BC114771 0 + 346187 388197 0 9 144,81,115,63,155,96,134,105,112, 0,24095,26190,31006,32131,33534,36994,41793,41898,
\ No newline at end of file

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/9_hg18.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/9_hg18.bed Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,2 @@
+chr22 1000 5000 cloneA 960 + 1000 5000 0 2 567,488, 0,3512
+chr22 2000 6000 cloneB 900 - 2000 6000 0 2 433,399, 0,3601

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/DNAseHSS.dat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/DNAseHSS.dat Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,1927 @@\n+chr22\t15456460\t15456683\tchr22.1\t362\n+chr22\t15458364\t15459404\tchr22.2\t504\n+chr22\t15815475\t15815875\tchr22.3\t400\n+chr22\t15825100\t15825400\tchr22.4\t392\n+chr22\t15842616\t15842716\tchr22.5\t324\n+chr22\t15842942\t15843082\tchr22.6\t391\n+chr22\t15930393\t15930681\tchr22.7\t461\n+chr22\t15939982\t15943768\tchr22.8\t733\n+chr22\t15953744\t15954492\tchr22.9\t491\n+chr22\t15962252\t15962574\tchr22.10\t374\n+chr22\t15973029\t15973901\tchr22.11\t423\n+chr22\t15975816\t15976065\tchr22.12\t422\n+chr22\t15976121\t15976201\tchr22.13\t452\n+chr22\t15976381\t15976394\tchr22.14\t444\n+chr22\t16013705\t16013885\tchr22.15\t450\n+chr22\t16013915\t16015621\tchr22.16\t738\n+chr22\t16026660\t16027656\tchr22.17\t634\n+chr22\t16072331\t16072502\tchr22.18\t450\n+chr22\t16072634\t16072981\tchr22.19\t480\n+chr22\t16074512\t16075141\tchr22.20\t564\n+chr22\t16076677\t16076793\tchr22.21\t400\n+chr22\t16092232\t16093072\tchr22.22\t535\n+chr22\t16112922\t16114222\tchr22.23\t623\n+chr22\t16123515\t16123655\tchr22.24\t353\n+chr22\t16123982\t16124182\tchr22.25\t374\n+chr22\t16135896\t16135934\tchr22.26\t356\n+chr22\t16135938\t16136134\tchr22.27\t365\n+chr22\t16137004\t16137183\tchr22.28\t419\n+chr22\t16159027\t16159069\tchr22.29\t303\n+chr22\t16159320\t16159852\tchr22.30\t516\n+chr22\t16160037\t16160317\tchr22.31\t421\n+chr22\t16160505\t16161102\tchr22.32\t427\n+chr22\t16224127\t16224777\tchr22.33\t428\n+chr22\t16331688\t16331928\tchr22.34\t359\n+chr22\t16355092\t16355756\tchr22.35\t519\n+chr22\t16427660\t16427974\tchr22.36\t393\n+chr22\t16428100\t16428200\tchr22.37\t391\n+chr22\t16485520\t16486465\tchr22.38\t737\n+chr22\t16486657\t16486695\tchr22.39\t336\n+chr22\t16495212\t16497144\tchr22.40\t725\n+chr22\t16535713\t16535723\tchr22.41\t316\n+chr22\t16546333\t16546873\tchr22.42\t458\n+chr22\t16549059\t16549226\tchr22.43\t333\n+chr22\t16563774\t16564614\tchr22.44\t485\n+chr22\t16591507\t16591854\tchr22.45\t370\n+chr22\t16600035\t16600064\tchr22.46\t459\n+chr22\t16624508\t16625289\tchr22.47\t589\n+chr22\t16625347\t16625979\tchr22.48\t450\n+chr22\t16630672\t16632992\tchr22.49\t543\n+chr22\t16633415\t16633795\tchr22.50\t507\n+chr22\t16634342\t16635155\tchr22.51\t626\n+chr22\t16637813\t16637855\tchr22.52\t453\n+chr22\t16638763\t16639001\tchr22.53\t438\n+chr22\t16639509\t16639672\tchr22.54\t336\n+chr22\t16642705\t16642835\tchr22.55\t359\n+chr22\t16678480\t16678580\tchr22.56\t359\n+chr22\t16687063\t16688043\tchr22.57\t646\n+chr22\t16699615\t16700067\tchr22.58\t527\n+chr22\t16700125\t16700139\tchr22.59\t368\n+chr22\t16777477\t16777677\tchr22.60\t389\n+chr22\t16837383\t16838363\tchr22.61\t565\n+chr22\t16853715\t16854395\tchr22.62\t505\n+chr22\t16858180\t16859332\tchr22.63\t616\n+chr22\t16878282\t16878622\tchr22.64\t400\n+chr22\t16878638\t16878722\tchr22.65\t355\n+chr22\t16880955\t16882198\tchr22.67\t606\n+chr22\t16884476\t16884876\tchr22.68\t438\n+chr22\t16929730\t16929970\tchr22.69\t392\n+chr22\t16933036\t16933676\tchr22.70\t495\n+chr22\t16933818\t16934179\tchr22.71\t473\n+chr22\t16934258\t16934398\tchr22.72\t378\n+chr22\t16934572\t16935974\tchr22.73\t846\n+chr22\t16937089\t16937189\tchr22.74\t374\n+chr22\t16937289\t16937297\tchr22.75\t304\n+chr22\t16949257\t16949557\tchr22.76\t407\n+chr22\t16968242\t16968371\tchr22.77\t329\n+chr22\t17006709\t17007978\tchr22.78\t674\n+chr22\t17009339\t17010349\tchr22.79\t556\n+chr22\t17010382\t17010419\tchr22.80\t336\n+chr22\t17050992\t17051532\tchr22.81\t455\n+chr22\t17103519\t17104159\tchr22.82\t486\n+chr22\t17216177\t17216977\tchr22.83\t526\n+chr22\t17216988\t17217077\tchr22.84\t312\n+chr22\t17242993\t17243556\tchr22.85\t501\n+chr22\t17267712\t17269152\tchr22.86\t888\n+chr22\t17270546\t17270694\tchr22.87\t373\n+chr22\t17316592\t17316705\tchr22.88\t364\n+chr22\t17332026\t17332280\tchr22.89\t401\n+chr22\t17332348\t17332838\tchr22.90\t456\n+chr22\t17430173\t17430273\tchr22.91\t386\n+chr22\t17471428\t17472268\tchr22.92\t579\n+chr22\t17480580\t17480594\tchr22.93\t366\n+chr22\t17481759\t17482262\tchr22.94\t427\n+chr22\t17483372\t17485317\tchr22.95\t919\n+chr22\t17506030\t17507178\tchr22.96\t776\n+chr22\t17511616\t17511950\tchr22.97\t465\n+chr22\t17533019\t17533068\tchr22.98\t453\n+chr22\t17533079\t17534240\tchr22.99\t688\n+chr22\t17539938\t17541938\tchr22.100\t646\n+chr22\t17621742\t17621961\tchr22.101\t418\n+chr22\t17634964\t17635544\tchr22.102\t392\n+chr22\t17652823\t17654497\tchr22.103\t781\n+chr22\t17654513\t17655354\tchr22.104\t486\n+chr22\t17781893\t17782125\tchr22.105\t412\n+chr22\t17792116\t17792866\tchr22.'..b'chr22\t48639740\t48640643\tchr22.1874\t603\n+chr22\t48643992\t48644020\tchr22.1875\t455\n+chr22\t48644024\t48644538\tchr22.1876\t582\n+chr22\t48645391\t48645781\tchr22.1877\t520\n+chr22\t48649413\t48651524\tchr22.1878\t657\n+chr22\t48659231\t48660371\tchr22.1879\t587\n+chr22\t48660404\t48660690\tchr22.1880\t446\n+chr22\t48663512\t48664112\tchr22.1881\t445\n+chr22\t48674179\t48675681\tchr22.1882\t809\n+chr22\t48675921\t48676099\tchr22.1883\t392\n+chr22\t48676199\t48677453\tchr22.1884\t596\n+chr22\t48734115\t48734651\tchr22.1885\t519\n+chr22\t48749768\t48749777\tchr22.1886\t325\n+chr22\t48750381\t48750521\tchr22.1887\t386\n+chr22\t48751551\t48752137\tchr22.1888\t451\n+chr22\t48755315\t48756619\tchr22.1889\t516\n+chr22\t48759370\t48759755\tchr22.1890\t416\n+chr22\t48759818\t48760403\tchr22.1891\t484\n+chr22\t48768575\t48769075\tchr22.1892\t465\n+chr22\t48770712\t48771712\tchr22.1893\t748\n+chr22\t48785745\t48786645\tchr22.1894\t501\n+chr22\t48798627\t48798677\tchr22.1895\t339\n+chr22\t48798883\t48798907\tchr22.1896\t319\n+chr22\t48799087\t48799534\tchr22.1897\t420\n+chr22\t48817391\t48817931\tchr22.1898\t467\n+chr22\t48826025\t48826657\tchr22.1899\t532\n+chr22\t48846735\t48846853\tchr22.1900\t355\n+chr22\t48871222\t48871702\tchr22.1901\t429\n+chr22\t48890006\t48890524\tchr22.1902\t588\n+chr22\t48908749\t48910049\tchr22.1903\t563\n+chr22\t48911005\t48912081\tchr22.1905\t507\n+chr22\t48918985\t48919731\tchr22.1906\t433\n+chr22\t48925325\t48925965\tchr22.1907\t443\n+chr22\t48926072\t48927031\tchr22.1908\t742\n+chr22\t48927533\t48928160\tchr22.1909\t456\n+chr22\t48929552\t48930092\tchr22.1910\t435\n+chr22\t48930809\t48932759\tchr22.1911\t707\n+chr22\t48933523\t48934523\tchr22.1912\t593\n+chr22\t48941058\t48942875\tchr22.1913\t751\n+chr22\t48942904\t48943044\tchr22.1914\t394\n+chr22\t48944348\t48944444\tchr22.1915\t342\n+chr22\t48950468\t48951062\tchr22.1916\t469\n+chr22\t48960702\t48960802\tchr22.1917\t370\n+chr22\t48970246\t48970646\tchr22.1918\t434\n+chr22\t48970818\t48970846\tchr22.1919\t330\n+chr22\t48982080\t48982292\tchr22.1920\t424\n+chr22\t48984707\t48986622\tchr22.1921\t711\n+chr22\t48988793\t48989293\tchr22.1922\t436\n+chr22\t48991385\t48993432\tchr22.1923\t625\n+chr22\t49002024\t49002114\tchr22.1924\t362\n+chr22\t49002124\t49002437\tchr22.1925\t399\n+chr22\t49002479\t49002601\tchr22.1926\t367\n+chr22\t49008521\t49008892\tchr22.1927\t543\n+chr22\t49010762\t49012305\tchr22.1928\t664\n+chr22\t49012445\t49012545\tchr22.1929\t370\n+chr22\t49012570\t49012892\tchr22.1930\t462\n+chr22\t49015865\t49016378\tchr22.1931\t447\n+chr22\t49070624\t49075418\tchr22.1932\t679\n+chr22\t49111690\t49112267\tchr22.1933\t466\n+chr22\t49148760\t49149100\tchr22.1934\t338\n+chr22\t49153627\t49153639\tchr22.1935\t302\n+chr22\t49159697\t49159797\tchr22.1936\t380\n+chr22\t49173809\t49173916\tchr22.1937\t362\n+chr22\t49197906\t49199406\tchr22.1938\t838\n+chr22\t49201713\t49202421\tchr22.1939\t524\n+chr22\t49202440\t49202498\tchr22.1940\t364\n+chr22\t49203051\t49204433\tchr22.1941\t676\n+chr22\t49209854\t49210782\tchr22.1942\t654\n+chr22\t49219181\t49219736\tchr22.1943\t458\n+chr22\t49226956\t49227163\tchr22.1944\t412\n+chr22\t49232935\t49233051\tchr22.1945\t359\n+chr22\t49235484\t49235647\tchr22.1946\t351\n+chr22\t49235684\t49237583\tchr22.1947\t821\n+chr22\t49253478\t49256010\tchr22.1948\t806\n+chr22\t49258252\t49260636\tchr22.1949\t646\n+chr22\t49267773\t49268606\tchr22.1950\t627\n+chr22\t49272646\t49274495\tchr22.1951\t644\n+chr22\t49275790\t49275818\tchr22.1952\t327\n+chr22\t49276675\t49277826\tchr22.1953\t745\n+chr22\t49289917\t49290017\tchr22.1954\t385\n+chr22\t49291185\t49292251\tchr22.1955\t687\n+chr22\t49292350\t49292490\tchr22.1956\t394\n+chr22\t49302144\t49302344\tchr22.1957\t361\n+chr22\t49310578\t49312317\tchr22.1958\t845\n+chr22\t49328526\t49329577\tchr22.1959\t611\n+chr22\t49339237\t49339737\tchr22.1960\t443\n+chr22\t49348359\t49348839\tchr22.1961\t499\n+chr22\t49349012\t49350493\tchr22.1962\t594\n+chr22\t49350929\t49350946\tchr22.1963\t344\n+chr22\t49356120\t49357265\tchr22.1964\t702\n+chr22\t49399918\t49400118\tchr22.1965\t419\n+chr22\t49401218\t49403850\tchr22.1966\t576\n+chr22\t49406600\t49406830\tchr22.1967\t354\n+chr22\t49430891\t49431185\tchr22.1968\t432\n+chr22\t49450962\t49451762\tchr22.1969\t484\n+chr22\t49456871\t49456955\tchr22.1970\t337\n+chr22\t49460431\t49461357\tchr22.1971\t599\n+chr22\t49485746\t49485837\tchr22.1972\t346\n+chr22\t49506364\t49506904\tchr22.1973\t382\n+chr22\t49511756\t49512736\tchr22.1974\t606\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/Extract_features1_out.gff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/Extract_features1_out.gff Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,8 @@
+##gff-version 2
+##Date: Thu Mar 23 11:21:17 2006
+##bed2gff.pl $Rev: 601 $
+##Input file: ./database/files/61c6c604e0ef50b280e2fd9f1aa7da61.dat
+chr5 bed2gff CCDS3972.1_cds_0_0_chr5_56241230_f 56241230 56241327 . + . score "0";
+chr6 bed2gff CCDS4855.1_cds_0_0_chr6_41411593_f 41411593 41411644 . + . score "0";
+chr7 bed2gff CCDS5401.1_cds_0_0_chr7_26907299_r 26907299 26907654 . + . score "0";
+chr8 bed2gff CCDS6324.1_cds_0_0_chr8_118881132_r 118881132 118881317 . + . score "0";

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/GRCm38mm10_chr5_34761740-34912521.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/GRCm38mm10_chr5_34761740-34912521.fa Sat Feb 21 16:33:42 2015 +0100

b"@@ -0,0 +1,5421 @@\n+>mm10_knownGene_uc008xda.1 range=chr5:34761740-34814709 5'pad=0 3'pad=0 strand=+ repeatMasking=none\n+GCACTCGCCGCGAGGGTTGCCGGGACGGGCCCAAGATGGCTGAGCGCCTT\n+GGTTCCGCTTCTGCCTGCCGCGCAGAGCCCCATTCATTGCCTTGCTGCTA\n+AGTGGCGCCGCGTAGTGCCAGTAGGCTCCAAGTCTTCAGGGTCTGTCCCA\n+TCGGGCAGGAAGCCGTCATGGCAACCCTGGAAAAGCTGATGAAGGCTTTC\n+GAGTCGCTCAAGTCGTTTCAGCAGCAACAGCAGCAGCAGCCACCGCCGCA\n+GGCGCCGCCGCCACCGCCGCCGCCGCCTCCGCCTCAACCCCCTCAGCCGC\n+CGCCTCAGGGGCAGCCGCCGCCGCCACCACCGCCGCTGCCAGGTCCGGCA\n+GAGGAACCGCTGCACCGACCGTGAGTCCGGGCGCCGCAGCTCCCGCCCGG\n+GCCCCGCGCCCCTGGCCTGCGTGCTGGGCATGGCCAACACTGTTCCCTGT\n+CCAGAGGGTCGCGGTACCTCCCTGAGGCCAGGCTTTCCCGGCCCGGGCCC\n+TCGTCTTGCGGGGTCTCTGGCCTCCCTCAGAGGAGACAGAGCCGGGTCAG\n+GCCAGCCAGGGACTCGCTGAGGGGCGTCACGACTCCAGTGCCTTCGCCGT\n+TCCCAGTTTGCGAAGTTAGGGAACGAACTTGTTTCTCTCTTCTGGAGAAA\n+CTGGGGCGGTGGCGCACATGACTGTTGTGAAGAGAACTTGGAGAGGCAGA\n+GATCTCTAGGGTTACCTCCTCATCAGGCCTAAGAGCTGGGAGTGCAGGAC\n+AGCGTGAGAGATGTGCGGGTAGTGGATGACATAATGCTTTTAGGAGGTCT\n+CGGCGGGAGTGCTGAGGGCGGGGGAGTGTGAACGCATCCAATGGGATATT\n+CTTTTTCCAAGTGACACTTGAAGCAGCCTGTGACTCGAGGCACTTCGTAC\n+TCTCCTGGCGTTTCATTTAGTTTGTGGTGTAGTGTAGTTAAACCAGGTTT\n+TAAGCATAGCCAGAGAGGTGTGCTTCTGTGTGTCTGCAGGCAGTTGGATG\n+AGTTGTATTTGTCAAGTACATGGTGAGTTACTTAGGTGTGATTATTAATA\n+AAAAACTATATGTGTGCATATATATGAAAGAGTCGACTTATACTTAACTG\n+CCTATCGATTTTTTGTTCTATATAAAACGGATACATTGGTGGTGCTCAGT\n+TTTCACCGGGGAATGAATTTTACTAGTGTTGCAGACAGGCTTGTTTTAGA\n+ACATAGGCCACTCTGACTCTGACTTTGTGCCAGTAAAAGTTCCTGTTTAG\n+TTCTTTGCTGACATCTTATAGATCTTTGGAAGCTAGCTGCTTGTGACTGG\n+AGAGAATATTGAAACAGAAGAGAGACCATGAGTCACAGTGCTCTAAGAGA\n+AAAGAGACGCTCAAAACATTTCCTGGAAATCCATGCTGAGTGTTGAGCCC\n+TGTGCTCTCTTGCAGCTCAGTCCTTTCTCTCAACTCTGGGCATTTTATTT\n+CTAATCTGGATTTGTATAATTAATAAGGAGAACTTTTGGGAACAACCTAC\n+TAAAGAATGTCATCATTAAAACTCACTTAGAAAATAAGTGTTCTGGTGAT\n+ATCATTGAGCTATGTTCCCAGTCCTGAGAGTTTGTTTTTTTTTTTTTTTT\n+TAAATAAAGATTTGGGGAGAAAAGGTGGCTTACTTGATAGAACAAAATAT\n+AGGAATAAAATTTCCTTCTATAAGGTGAAAAGTGTGAATAGAAAACTTCT\n+TATCCTCTAGATAAGTAGTTTCTTTTTGCTTTTGAGAGTCTCACTATGTA\n+ACTCTTGACCTGAACTCAGAGAGATCCATCCTCCTGCCTCTGCCTCCTCT\n+CTCTGGGATTAAAGGCATGTGGCACCATGCTGGGCTGTCCAAGTATGCCA\n+CAGACCCTCTAGGTCCCTGGTCTTCGAGGAACGGGATTTCTTAGGCAGAT\n+GGGTAAGGAGTCGGATGAAAATGACAATCAGCCACACACAAGAGAGGTGT\n+TGAATCTGAATGTAATGTTCTGGTTGAGCTTCAGACTTATATAACAACGA\n+ATTATCAGAGGATACAAATCACAAAAAGACAAGATACACTGAAATTCACC\n+AGTTACAGCAGAAAGGAATTTGCAGGGACTAATTAAATGTTTACATTAGG\n+GATAACAAGCCCTGCCTAGGATCAGCCTAATGCCAGGCAAGAATTTCACA\n+CTTTAAGGTTAAAAGCATCAGGGGGTTGTTAACTCTTGACAGGCCTTAAG\n+AGTAATGTGCTATCACTGAGCTCTAAATTCTTAGGTCTAGTAAAACTTAT\n+CCTGTCTGGAGAGTTCCCCCTTATCAGGGTAGTATATCAACTTATACTTG\n+ACATGGAATGAAGCCTGTAGTAAAACATTTCTATCTCAGTGAGACTTTTA\n+GTCTCTATCTGTAAACAGCTGAGTAAAATGGCAAGTGCTTAATTGTTTAC\n+TGAATGGGTTAAGCTCCTTGCTGCTATCTGGAATCTAAGAACACTGGGGA\n+AAGGCTTTAGCTATGTTAGAATACAATATTAAAAGGCATTTACTATAAGG\n+TGATGCTTAATAGAGTGCACGTGAATCTATACACTAGATTAATGTGGTGG\n+AAATTTGAATATAATGGGTTAGGGAAAGAGATGCCATAACTCTGGGAGGA\n+AAATTTCCCTGGACTCTTATCCTCGTGAAACAGCTTCCAGGCTTTTCGCC\n+TGACAAACCGATCCAAACTGGAGAGTTGGCTTTCGCCAGAATATCCAGGA\n+GGAGAGTCCTAGAAATTCATTTCTCATGAGCAGCTTTTTGGCATTTTTGC\n+CTCACAAGCTGACTCCACCAGAGTACCCTGACACAAGTATTGTCTAGTTA\n+TTTTGATTATTACCATGACTCTGCCTCTGGGTGAGAGGAATTGTGGAAGT\n+TTACATATTCCCCATATCTTCTATAAACCTCTGTGTGTGTGTGTGTGTGT\n+GTGTGTGTGTGTGTGTGTGTGTGTATGAGGGAGAGAGAGGGAGAGAGAGA\n+GAGGGAGGGAGGAAGAGAGAGAGAGAGATTGTTCTGTGCCTGCTTCGAAC\n+ACAAATTAGTTTGCAAAAGTAATTCATTAACATGATACAGTCCCAAAGAT\n+AAAAATGGTTAAATAATGAAAACATCTCCCTCCCCATTTTCCTAACTTTG\n+TACCCAGGAGCAAGCTCTGTTACACTTCATTTGTCCTTCCAGATAAAATT\n+TGGGCATATGTTAGGACAGAATTTTAAATTATTTACAAACAAAAGTATTT\n+TGGAACAAAAGCTTTTAAAAGCTTTTATTTTAATAAAATAACTTGTTACT\n+ACACTGTATATAACTAACTAACATTTTCCAAAATTAGCTCCATTAGCATC\n+TATCTCATATTTCTATGTACTTTGCTGTTGAAAAACCAAGTGTTCATTAA\n+TAATAAGTAACAAACTCACTGCTTGGAAGCTTTGATTTTTGGCATTTTGT\n+CCACTTGACTCAGTTAAAAGTCCTTTTTTTCGAAATGAGAACAGCCAAAA\n+CAGTTTTAGAATGAGTCTGTTCTGCTTTTGTGACTCTCATTGTGTTCTGT\n+AGAACCAGTGTCACAGCCATATGTGGGCCTCTGTTGAAGTAGCTGAGAAC\n+TTGTTCTCTGCTCTGCTAGCTGCTGTCGATCTGATAGGCCTTGAACAGTT\n+GACATTCACCCTTAATAGTCCTCATTAGTCTTCCTGAGCATAGTCATTCA\n+TTTATCAATATTTGCTGATCATCTCCTATGTGCCTAGCATTGTTCTAGTT\n+GCAGGTTTTAGCAGGGAACAAAGTCATGTC"..b'ACACCAAGAGGTTATTATCTCCTCAGCAGTTGTAGAACTG\n+CTACGCTGACATCAGTATTAACCATTACACCCATCATGTAGTGAGGCACC\n+TTGTCCCTGTAGATAAAGAGGCATTCTGTCATGTAGTGAGGTACCCCGTC\n+CTCTCTAGATATAGAGGAATTACCTCATGTAGTCAGATGCCCTGTACTGT\n+CTAGATACAGAGCAATTCTCCTCCACTTACCCCTCGAATACCAGAAAGCA\n+TACTGAGAGCTGGTGCAGGCCTTGAAAGCATTCAATTCCCTTCCTTGTCT\n+TCTTTGCCAAGCACTCTTAGGCCACTACCTTAGTGGGGTTCTTTGTTGCC\n+CAGTGAAGACAAGGACCTCATTGCCCCTTGATACATGCCAAATGGTTATG\n+GGGAAGCAGGAACTGAGCAGGTTAATAGAAGGTGTGTGTGTTGTGGAGAG\n+AGAGGGTTCTCACATAGGAAGATATCTAAAGCACAGGACCCAGTTTGTTA\n+TATTTTCCAAGTCGTTAGGTGGACTATTAGCAGCTTGCAAGTTCCATCCA\n+TGACCATAGAAATGTTTGATTTGGGGGAACTAATGATGAAATACAGTGTT\n+TAATATTAAAGCTTATGTTCTACTTGAAAAAATTGTGACTCTCTCTAAAT\n+CCTTAAATGGCTTAAAATAAGTTTTTGACAAAACATAATAAAAACTGTCA\n+TATGAGGCCAGACATGGTAGTGCATATCTTTAATTCCAATACTTGGGAGT\n+CAGACACTTGAGGATCTCTGTTTGTGACATGTCTGGTTGACTTAAGTTCC\n+AGGCCAGCCAGGGCTACATAGTAAGACTATCTCCAAATCAAAAAAAAAAA\n+AAGAAAATTAAAAGTTTTTGGCATGTGAAATGTTGTGTGTGTGTTTTTTT\n+AAGCAGATTTTTGTCTAATATAAGATGCTCTGTGTGCCTTCTCAGGCTGC\n+AGCATTGCTTGGCATCCCACTGGATTCTTAGATGGCATATTAAACTTGGT\n+GCGCTGTCTACATCAATTAAGATTTGTCATCCTAGAATTATTTCAATGAA\n+ATATAAGATCATAAAAATTAAAAATATTGCTCTTTCTCTCTTTCCCTCCC\n+CCCTCTCTCCACGTGGCCATGGCCAGTCTCTCTCTCTTTCTACCTTCTCT\n+CCTTTCTCCCTGACTTTCTACAATAAAGCTCTAAAACCATTTTAAAAAAT\n+TAAAAATATTACTTTAAAATTCAAATATGACAGTGACCAGAAATATTTAT\n+TAAGCATGTTAAGTGGAGTTGTTGATATATTTATTAATATATATAACATA\n+GGATATACTTTTTAAAATAGAGAATTCAACTTAGTTTTATCTGTCTTTTA\n+ACTTTATTTGTAGTCTAAGATCTTTTCTAGAGAGTATTTCCCACTTTTAT\n+TATTATAAGTTACTTGAGACAAGCTACATCATAAGAGAAAAAGATTTATT\n+TTGACTGATAGTTCTGCACATACAACATCCAAGGGCTCATCTGGTGATGA\n+CTTTACTGTCAGAGTCCCAGTGTGGTGCAGAAAACCTCCCATGGCAAACA\n+ATAAGGAGCTTGAGTGTCTCTGTTTCTAGAATATTCTCAGAAGCATTCCT\n+TACAGTTCTTTGGTCTGGATTATCTCAGAAACAAATGCTTATTGCATTAA\n+CTGTGTGTGTTCCAGCCTGAAGGAAAGCTTACTGTCTTTGCTGTTGTTTG\n+TCTTGCATGTAAACTTCTGACCCAGGAGTTCAACCTAAGCCTTTTGGCTC\n+CCTGTTTAAGCCTTGGCATGAGCGAGATTGCTAATGGCCAAAAGAGTCCC\n+CTCTTTGAAGCAGCCCGTGGGGTGATTCTGAACCGGGTGACCAGTGTTGT\n+TCAGCAGCTTCCTGCTGTCCATCAAGTCTTCCAGCCCTTCCTGCCTATAG\n+AGCCCACGGCCTACTGGAACAAGTTGAATGATCTGCTTGGTAATTAAATA\n+CAGTTCCCTTGGATGCTTGTCTGTCTATCTTCTCTGTCACTCTGTCTCTC\n+TTTATGGGTGATAGGAATGGCAGTAGCAGAATGGACAAGCCAGAGGGACA\n+CTGAGTCACACATTGAACCTAGAGCTGCCAACTCTGGTAGATCAGCTGAC\n+CAAGCCTCTAGGACCCTCCTGTCTCAGCCCTAAGTGCTGAGGTTACAGGT\n+GTACACCCACAGCCAGGTTTTACATAAGATCTTAAATTCCAAACTCAAGT\n+CCTCATGCTTGCACAGGAAGCACTTATCCACCGACTCATCCTCTCAGCTC\n+AAGTTATCTTAGTGTTTTAGTTATTTTATATTATGTTATAGTTGTCTGCA\n+TGTATGTCTTCACCAGATGCATACAGTGCCCATGGAGACAGAAGATGGCA\n+TCAAATCCCATGGGACTGGAATTACAGGTGGCTGTGAACACACTATGTGG\n+CAGCTAGAGATTTAACTTAGGTCCTCTGGAAGTGCAGCTCATGCTCTCAG\n+CTCCCGAGCTGTCTATCTAGCTACAAGTTGTCACCGTTTTTAAAAGTATT\n+ACAGATTCAGCACCGTGCTTTTCCTCAAGCACGCATATAGTCAGGACTGT\n+TGATCTAAAAGGCTGACAAAAATAGCTGAGAAACTGCACCAAATCCTTAG\n+CTCTAAACTTCTTTCTTTGTTGCTTGACCTGGACATAGAAAGTCAGGTTC\n+TAAGCCCTTCAGGATCAGTGGGTTAGACTCAGGGCAAACCATGTCCTGAC\n+TTTATGTAGCACGTATGAGTGAGCATGTACAGATGTGCTTGCTCTCTTGG\n+TCTTGGCAACCTCAAATTCACATAGTTGTGTGAAGGCTTCTGAAGGGGCG\n+GGCCTGTGCTCACAGTCAAAGTCACTCATGTCAGTCTCATGTTTCAGGTG\n+ATACCACATCATACCAGTCTCTGACCATACTTGCCCGTGCCCTGGCACAG\n+TACCTGGTGGTGCTCTCCAAAGTGCCTGCTCATTTGCACCTTCCTCCTGA\n+GAAGGAGGGGGACACGGTGAAGTTTGTGGTAATGACAGTTGAGGTAAGAG\n+CAGCTCTGAAATTATGTGTCCCTGTGAGGACAGGATATGTGAGTAGCACT\n+AAGATGAAAGTCCTTGAAAACCGACAGTGTGGAGTACAATAGTGCACACA\n+TTAGCCCAGCTGCCTTGGAGGCAGAGGCAGAATTGTGGGTTCCTGGTCTG\n+TAAGGATGTGCCTGAGTATACAGCTAGACCCTATTTGAATAAACAGGAAG\n+GCAGGGAATACCTATTGGCAAAGTCTGATTCACCTGATGGTACAGAGTGC\n+CTTTCACCCTCACCACTGGGAAGCAAGGAGGTCTGTAAGACATCCTGTTA\n+TCCCTACACTATAAACCTAATGTGGGTCCTAAATAAAATCTAGACAGTGT\n+TACATTTTAAATTGGGCAGTGAAGCTGGACATTTCACCCAGAAACACTTG\n+GCCCCTCAAAATGTATCTATACGTGCACTATAGTTTTATTACCTTGCCAT\n+GGGCATGCTGGGAAAGAGCCTCACTGTGCCAGAGCTGTGCTGCCAATCCT\n+GAACAAGGGTTGACACCTTACCCTAAGAGAAGAAAGTCAGTATCCTGAGG\n+GTGTATGGTACAAAGGCACCAGGTGAACCAGGCTAAGTTAGGTGGTCTTT\n+GAGCTTGTCTTAGCCCAGTGAAGACAGGAAAGCAAATGTGTGTGTAAAGT\n+ATTGGGTGGCAGCTCCTAGTCATACTCTGCGCTGCACAGGCCATGCCATG\n+ACACTTGTTTCCTATAAAAACTCTGTCCCCATTTCACACATGGGGAAAGA\n+AGCTCAGAGAGGTTCGGGGACTTGCTAGAAGTCACTAGTCATAAATCATA\n+CTCCAAAACTCAGTGTTGTGACTGAGATACAAAACAAAACACATTCTGTT\n+TCTT\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/Interval2Maf_pairwise_out.maf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/Interval2Maf_pairwise_out.maf Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,49 @@\n+##maf version=1\n+a score=10458\n+s hg17.chrX 3816458 525 - 154824264 tGATGCACGTTTTCTCTTTTCATACTCATCTT--CAGTTATTCCTTGACACAAACCTGGTTA---CTAGTGCTATTGGCTACATGGCCCCTGTGCCTTAACTTCCCTCATGGCTCCTCCTCCCTGCAGCCTCTGAAGGTTCTCTGTGTAATGAATT--AATTAGCTTTGCTTTTTTCTCCCTTTCCCCC-----CCTCTTTTTCCTGGCCTCT---------AGAAGAAAACACCAGCAGCCCCAGCAAAGAAAACCAGCACTACCTTCAACATCGTGGGGACCACCTATCCCATCAACCTGGCCAAGGACACTGAATTTTCCACCATCTCCAAGGGCGCTGCTCCCAGTGCCTCCTCAACCCCAACAATCATTGCTTCACCCAAGGCCACCTACGTGCAGGACAGCCCGACTGAGACCAAGA---CCTACAACAGTGTCAGCAAGGTTGACAAAATTTCCCGCATCATCTTTCCTGTGCTCTTTGCCATATTCAATCTGGTCTATTGGGCCACATATGTCAACCGGGAGTCAGCTATCAAGGGCATGA \n+s fr1.chrUn 343715247 529 - 349519338 TGGTCAACATTTTTTTCTTTTCTACTTTTCTTTTCAGGAACCGTTTCAGGCTAACATGGCCAGGATTAAAGATAT-GGTTAGGCTTTTGTTTTGTTCTTGTGTGTGTCGTGTCTCGTGGT----GTTGCTTCTATTTCCTCTTCATGAGTTCAAATGGAAGTATTGTTAAGTTTGTTGCCCCCGACCCTAACGACCTCTGCTTTATGGCCTCTTCTCTTTTCAGAGGAGAGAATCTGAGAATCTGACCAAAAAGACGAACAACACCTTCAACATCGTCGGGACGACCTACGCCATCAACGTGGCGAAGGACCAGGGCTTAACCACCATCTCCAAAAGCGCCACCACCGGCGCGCC----GGCCAAACAGCACTACCTGCACAAAA-----------TGGACGACCCCTACACAGAGGCCAAGAAATCCTACAACCGAGTCAGCATAGTGGACAAAATATCACGCATCATTTTCCCAGTTCTGTTCTTCATCTTCAACTTGGGCTACTGGGCCACATATATCAACAGGAAGCCCATTATTATGAACGCGA \n+\n+a score=12779\n+s hg17.chrX 3795168 357 - 154824264 aGGGCCATTTTGAGTGGGGTAAAGCTTCTCCTTTCAAATAGGAAA----TTAGTGATTTCATCG--AATAAGC-------TCTCAATGTCTTCCAGTTGCAACTGGTTCTCATCTTTCCTCT----CCTCAGGTGTCACCACTGTGCTTACCATGACCACCTTGAGTATCAGTGCCAGAAATTCCTTACCTAAAGTGGCATATGCGACGGCCATGGACTGGTTCATAGCCGTCTGTTATGCCTTTGTATTTTCTGCACTGATTGAATTTGCCACTGTCAACTATTTCACCAAGCGGAGTTGGGCTTGGGAAGGCAAGAAGGTGCCAGAGGCCCTGGAGATGAAGGTGAGATA----TAGCAAAAGAGAAACTGAGAAG \n+s fr1.chrUn 343710815 364 - 349519338 TGAGCCAATTT--------TGAAGTGACAATTTTCAAATGTGCCACATTTTAGTAGCAGCAAAGTCAGAAAGCGACTTTTCCTCTACATCACTTCTCTGATCTGTGTTCTGATGTTTTCCTTTCATCCTCAGGGGTCACCACTGTGCTTACCATGACCACCCTGAGCATCAGTGCTAGAAACTCCCTCCCTAAGGTGGCCTACGCCACCGCCATGGACTGGTTCATGGCGGTGTGCTACGCCTTTGTCTTCTCTGCCTTGATTGAGTTTGCGACGGTCAACTACTTCACCAAACGCAGCTGGGCATGGGATGGGAAAAA------AGAGGGCATGGAAATAAGGGTGAGTGATTTTTAATCAAATATATACTGATACG \n+\n+a score=10363\n+s hg17.chrX 3787425 174 - 154824264 TACTCTCTCTTTAGGAGAATATGTCGTCATGACAACCCACTTCCATCTCAAGCGAAAAATTGGCTACTTTGTGATCCAGACCTACTTGCCATGTATCATGACTGTCATTCTGTCACAAGTGTCGTTCTGGCTCAACAGAGAGTCTGTTCCTGCCCGTACAGTCTTTGGTGAGTG \n+s fr1.chrUn 343708230 174 - 349519338 TCCTCCCGCTGCAGGCGAATATGTTGTGATGACAACATATTTCCATTTGAAAAGGAAAATTGGCTATTTCGTGATTCAAACCTACCTCCCGTGCATCATGACTGTCATTCTGTCTCAAGTCTCCTTCTGGCTGAACCGAGAATCGGTCCCTGCTCGCACCGTGTTCGGTGAGTG \n+\n+a score=31\n+s hg17.chrX 3787284 100 - 154824264 ATTTTGTGATTATTAAAGGGCTCTAGTTATATGAACTTGGGAGATGCTGGAATATTGAATATAAG----ATTAAAGAGCTTTGTGAAT--------TGAATT-----GGGGCCCAAC \n+s fr1.chrUn 62078707 109 - 349519338 AGTTTGTGAGGCCTAAATGCCAAAAGT-------ACTTGA-ACAGGCTTAAGAATGGATCATGAATTTTCTTAAATAAATCTGTTAATCCAGAAAGTAAACTCTGGGGGGGTCCAGA \n+\n+a score=4963\n+s hg17.chrX 3776942 285 - 154824264 aCTTCAGTTGAAGACAGACCACATACCCAGAACTCTTTGAAGATGGAAGTTTTATTTCGATCTCATTTGAGTTTAGTATCAAGGGTAATCATTCTCCATTTCCTTCAACTTCTCTTTATTGACCCTTCTCTGCC--TTAGATGCCTATACAACAGCTGAAGTGGTTTATTCTTGGACTCTCGGAAAGAACAAATCCGTGGAAGTGGCACAGGATGGTTCTCGCTTGAACCAGTATGACCTTTTGGGCCATGTTGTTGGGACAGAGATAATCCGGTCTAGTACAGGTA \n+s fr1.chrUn 343707053 283 - 349519338 AACTTAAATCAACACCAAGTAAAGGCAAAGAATCTTTTAAACTAAGAA----TCTATTAAACTAGATAAACTAAAGCATCGACACTGACGCGTTGATCTGTCATCCACGTTTCCCCTGTTTCCTTTCCTTCTCCATCTAGACGCTTACACCAACAATGAGGTGATTTACCTGTGGACTCAGGGGGACGAGAGGTCTGTGTCTGTCGCAGAGGACGGCTCCAGGCTGAACCAGTATGATTTACTGGGACACGTTATTGGCAAAGAAACCATCAGCTCCAGCACAGGTA \n+\n+a score=5912\n+s hg17.chrX 3760375 93 - 154824264 TTAGGTTAACAATTCATGCTGAGTGTCCCATGCATTTGGAAGATTTTCCCATGGATGTGCATGCCTGCCCACTGAAGTTTGGAAGCTGTATGT \n+s fr1.chrUn 343706399 93 - 349519338 TCAGGTTGACCATCCACGCTGAGTGCCCCATGCACCTGGAGGACTTCCCCATGGACTCGCACGCCTGTCCTCTCAAGTTTGGAAGTTGTAAGT \n+\n+a score=4332\n+s hg17.chrX 3733405 476 - 154824264 ATCAAGGAGAATTTGGGGAAACAGAGCATTAGGGAAGGAATAGATGGAAGAGAGGCATGCTTGTAATAAATTATAGGAAAGAGAAGAGTTTGAAAAAGAGATAAGAGTTCACACAATTGTGGAAAGAATGG'..b'-GTGGATGGGCAGAAGACAGTAAGCAAATGGAAGAGAAGCAAGA-----GGAAGGAGAGAGTAATGGGCAGGAAAGGATCTGAACCCAGTAGAGATTGCAAATAGTGAGGAGAAATAGAGAATGAATGAAAAGAACAGG--ATAGAGGAGAAACAACAATAAAAGGAATAAAGCATAGAGAATAGGTTTAAGTTTTGGAGGAGGGATAGAGAA-----GAGAGAAGAAAGGAGAGAGGATGGGAATATTGAAATACAAAAAAATAGAAGGTGCAGGTTGAGGA \n+s fr1.chrUn 303515824 444 + 349519338 AACACGGAATATGGAGGGAAAACGGGGAATATGGAGGGAACAG--GGAATATGG-------------------TGGGAACACAGAGGGAATATGGAGGGAACACGGG-------GAATATGGAGGGAA---AACGGGGAATATGGAGGGAACGGGGAATATGGAGGGAACGAGGAATATGGAGGGAACGGGGAATATGGAGGGAACACAGGGAATATGGAGGGAACACAGGGAATATGGAGGGAACACAGGGAATATGGAGGGAACGAGGAATATGGAGGGAACACAGGGAATATGGAGGGAACGAGGAATATGGAGGGAACACAGGGAAT--ATGGAGGGAACGGGGAATATGGAGGGAACACAGGGAATATGGAGGGAACACAGGGAATAT--------------GGAGGGAACGAGGAATATGGAGGGAACACAGGGAATATGGAGGGAACGAGGAATATGGAGGGAACACGGGGTACTCAGTGAGAA \n+\n+a score=719\n+s hg17.chrX 3731355 108 - 154824264 TATGTAAGTAGAATGCAGTCAAGAAACTTGTAGGTGGATAGGTAGAGGCAGAAGGAAGAGAGGAAGGACGTTCTAGACAGAGAAAACCAAGTGAGCAGTTGCAGGGAA \n+s fr1.chrUn 303515724 91 + 349519338 TATGGAGGGAACACG------GGGAATATGGAGG-GAATATAGAGGGGAGACGGGGAATATGGAGGGA------ACACGGGGAATATGGAGGGAACA----CAGGGAA \n+\n+a score=3647\n+s hg17.chrX 3730591 447 - 154824264 CAAGGAAAAAAGGATAATACTTCAGAGAGAAGTTGGATGAGAGATGGGAGGAA--AAATGAACATAGAGGAGAAATGAGCATAGAGTGGAGGATAAAATAATGAAGAAGGAAAGTGGATAGAAGTGGGAAGATGAGGGTCAAGAGGGGAGGAGAAGACTAATTACACAGAGTACATAGAGGCATGTATATTGGAGAAATGAGAATGGTGAAAAGAAAGAGAGTATGAGAAGAGAGGACAAAAAGAGTAGAGAAGTTGAGAAGACAAAGGATAAGATGGTGTAAAATAAAGAAGCTAGATTAGATATTAGGATATTCTAAAGAGATAGGCGAATATAATGAAGTGGATGTAGTAGATGGGAATAAAGAGGAAAAGACATAGAGAAGTAGGGGAAGGGACATGGGAGGAGATGAACAAGAGGGAGGGAAATTGTAGACGAAAGAAAGAGAA \n+s fr1.chrUn 303515378 346 + 349519338 CACGGGGAATATGGCGGGAACACAGAGGGAATATGGAGGGAACACGGGGAATATGGAGGGAATATAGAGGGGAGACGGG--GAATATGGAGGG-AACATGGGGAATATGGAGGGAATATAGA---GGGGAGACGGGGAATATGGAGGGA--------------ACACGGGGAATATGGAGG---GAACACAGG------GAATATGGCGGGAACACAGGGAATATG----GAGGGAACACGGGGAATATGGAGG----GAACACAGGGAATATGGAGG----AAATATAGAGGGAAAACGGGAAAT------------------------------ATGGAGGGAATATGGT----GGGAACACAGGGAATA----------------TGGAGGGAACACGGGG----------AATATGGAGGGAA--TATAGAGGGGAGACGGGGAA \n+\n+a score=13113\n+s hg17.chrX 3729219 238 - 154824264 CCCCTAGGAGTACACTATTGATGTATTTTTTCGGCAGACATGGCATGATGAAAGACTGAAATTTGATGGCCCCATGAAGATCCTTCCACTGAACAATCTCCTGGCTAGTAAGATCTGGACACCGGACACCTTCTTCCACAATGGCAAGAAATCAGTGGCTCATAACATGACCACGCCCAACAAGCTGCTCAGATTGGTGGACAACGGAACCCTCCTCTATACAATGAGGTCAGAGAGT \n+s fr1.chrUn 343703525 238 - 349519338 CCCTCAGGAGTACACCATCGACGTCTTCTTCCGTCAGAGTTGGAGAGACGAGAGGCTAAAGTTTGATGGACCTATGCAGGTTTTACCCCTGAACAACCTCCTGGCCAGTAAGATTTGGACTCCTGACACCTTTTTCCACAACGGAAAGAAGTCTGTTGCCCACAACATGACGACTCCGAACAAACTGCTGCGCCTGGTCGACAACGGCACGCTTCTATATACAATGAGGTGAGGCGGT \n+\n+a score=3528\n+s hg17.chrX 3700391 307 - 154824264 AGTAAGTTGGCTGTCATTCAGAGT-ACTGCACTG-GACTCT---CTCTGAGCTAAGACAAAAGCCTTTCCTGACATTCTGCTTTTCTACTTTCTTTCACGCAGATGCAGTGACTGAAGTGAAGACTGACATCTACGTGACCAGTTTTGGCCCTGTGTCAGACACTGACATGGTA---------AGTTCTTGCAAAGGTAAATGTA---AAAGAGGATGCACT----AGACCAAAGAAAATAAATTGGAGCTTTCCTAAGGC---AGGGCCTTGTAGCTATATTCTAAGGAGTGGTCTTTTCTCA--TATGAATTT--CCTACCCTCGCCACCCTA \n+s fr1.chrUn 241017738 330 - 349519338 ATTCATTTGTATGTCCTTTTGTGTTACTAAGCTGTGTCTCTAATTCCAGAGCGAAAACAAAACTCATTAGATTTGTGTCATTTGTTCATTTGCTC---CATAGGTCCTGTAACTGAGGTCAAGACAGATATTTATGTGACAAGTTTTGGGCCTGTGTCAGATGTTGAAATGGTACGTACACCGAGTGTTATTGATGCTAAATTTACCTCAGGAGGGGACACTTTTAATACCTTATAGAACATTATAGAGATTCTGGGACGTGCAAGGGCAGTGCAGGAAAGGCC--AGGTGGGGTCAGGTCTTAGTTATGAAGCGGACATACTGTCGCAGCCCTA \n+\n+a score=5471\n+s hg17.chrX 3639441 205 - 154824264 TCTTGAATTACGATATCTA-GTCATGT---ATTTTTTTTCCTATTAAGAACTATTATTTTTTTTCTTTTC---CTTGCATTGCCTCAGGCTGTCTC---CTAAGCATGCCCCAGATATTCCTGATGACAGCACTGACAACATCACTATCTTCACCAGAATCTTGGATCGTCTTCTGGACGGCTATGACAACCGGCTGCGACCTGGGCTTGGAGGT \n+s fr1.chrUn 333536350 213 + 349519338 TCATTAATCACAAAGACCACGTCATGTTTGACGTCTTGTGGTTTTAAGAAGCGCAAGCCTTGTTCTTTTCACTCTCCCCTTCCTCTCGTCTCTTCCAGGCTCTGCTTGTCCCAGTCTGAGCCGCCTAC--CAACGACAACAGCACAGTTTTCACCAGGATCCTGGATGGGCTCCTTGACGGTTACGACAACAGGCTGCGACCTGGGCTTGGGGGT \n+\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/Ssuis.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/Ssuis.fasta Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,33460 @@\n+>Streptococcus_suis\n+ATGAACCAAGAACAACTTTTTTGGCAACGATTTATTGAATTGGCAAAGGTAAATTTTAAG\n+CCATCTATTTATGATTTTTATGTCGCTGATGCAAAATTACTCGGAATCAACCAGCAAGTT\n+GCCAATATTTTCTTAAATCGTCCATTTAAAAAAGATTTCTGGGAAAAAAACTTCGAAGAG\n+TTAATGATTGCCGCTAGTTTTGAAAGCTACGGAGAGCCTCTTACCATCCAATATCAATTT\n+ACAGAGGATGAACAGGAGATTAGGAATACTACAAACACAAGAAGTTCAATAGTTCACCAG\n+GTACAGACACTTGAGCCGGCTACTCCTCAAGAAACTTTTAAACCGGTTCATTCTGATATA\n+AAATCCCAGTACACCTTTGCTAATTTTGTACAAGGAGACAATAATCACTGGGCAAAGGCT\n+GCAGCTTTAGCTGTATCTGATAACCTAGGTGAGCTCTACAATCCATTATTCATTTTTGGT\n+GGTCCTGGTCTTGGAAAAACTCATATTTTAAATGCGATTGGAAATAAGGTTCTAGCCGAT\n+AATCCCCAGGCAAGGATAAAATATGTCTCATCGGAAACATTCATCAATGAATTTTTAGAA\n+CACCTCCGTCTCAATGATATGGAAAGTTTCAAAAAAACCTATCGCAATCTGGACTTACTT\n+CTAATTGATGACATTCAGTCTCTCCGTAATAAAGCAACAACACAGGAAGAATTTTTCCAT\n+ACTTTTAATGCGCTTCATGAAAAAAATAAGCAGATTGTACTCACAAGCGACCGTAATCCC\n+GATCACTTAGACAATTTGGAAGAAAGACTAGTAACACGTTTCAAATGGGGGTTAACCAGT\n+GAAATCACTCCACCTGATTTTGAAACACGTATCGCAATTTTACGTAACAAGTGCGAGAAC\n+CTGCCTTACAACTTTACAAATGAGACGCTATCCTATCTAGCTGGGCAATTTGATTCGAAC\n+GTACGTGACCTTGAAGGTGCCTTAAAAGATATCCATTTGATAGCCACTATGCGTCAACTG\n+TCTGAGATAAGTGTCGAGGTTGCTGCTGAGGCTATTCGATCAAGAAAACAAACAAATCCA\n+CAAAACATGGTTATTCCTATTGAGAAAATCCAAACCGAAGTGGGAAATTTCTACGGTGTC\n+AGCTTGAAAGAATTAAAAGGTTCTAAGCGTGTTCAACATATCGTTCACGCGCGACAAGTT\n+GCTATGTTTTTAGCACGTGAAATGACAGACAATTCCCTTCCAAAAATTGGGAAAGAATTT\n+GGTAATCGAGACCATACAACCGTTATGCATGCATACAATAAAATAAAAACTCTCCTCTTG\n+GATGATGAGAATTTAGAAATAGAGATTACCAGTATAAAAAATAAACTTCGTTAACCTGTG\n+TATAACTTTTTTAAAAAACTCTGTTTTTTCCACAAGTTGTGAACAAGTTAATTTCCGCAG\n+TTTTATTGGTCTTTCATCACTTTTCCACAGAATACACAGAGACTACTATTACTATTAACC\n+TTATAGATAATAAATAAAGGAGAATCCATGATTCAATTTTCTATTAATAAAAATATATTT\n+CTACAAGCACTTAGTATTACTAAACGGGCAATCAGTACAAAAAATGCTATTCCAATTCTT\n+TCAACAGTAAAAATTACAGTAACTAGTGAAGGAATCACTTTAACTGGTTCAAATGGACAA\n+ATCTCGATAGAACATTTTATTTCTATTCAAGATGAAAATGCAGGGCTTTTGATCAGTTCT\n+CCAGGTTCCATTCTCTTAGAAGCTGGTTTCTTTATTAATGTCGTATCCAGTATGCCGGAT\n+TTGGTCCTTGACTTCAATGAAATTGAACAAAAGCAAATCGTTTTGACAAGTGGTAAGTCT\n+GAAATCACATTAAAGGGAAAAGAAGCAGAACAGTATCCTCGTTTACAGGAAGTTCCAACT\n+TCAAAACCATTGGTGTTAGAAACCAAAGTATTAAAACAAACAATTAATGAAACAGCATTT\n+GCAGCTTCTACACAAGAAAGTCGTCCTATTCTTACGGGTGTTCATTTTGTTTTAACAGAA\n+AATAAAAATCTAAAAACTGTTGCAACAGATTCACACCGTATGAGCCAACGGAAATTGGTC\n+CTTGATACCTCTGGTGATGATTTTAATGTTGTCATTCCAAGTCGTTCTCTCCGTGAATTT\n+ACTGCAGTTTTTACAGATGATATTGAAACAGTAGAAGTCTTCTTTTCAAATAATCAAATC\n+CTTTTTAGAAGCGAGCATATTAGCTTCTATACACGCTTATTAGAAGGTACCTACCCTGAT\n+ACCGACCGCTTAATTCCAACTGAGTTTAAAACAACTGCAATTTTTGATACTGCAAATCTT\n+CGTCACTCGATGGAGCGTGCTCGTCTTCTTTCAAATGCAACCCAAAATGGTACAGTAAAA\n+CTAGAAATTGCTAATAATGTTGTATCGGCTCATGTAAATTCTCCAGAAGTTGGACGTGTG\n+AATGAGGAATTAGATACTGTAGAAGTATCAGGTGAAGATTTAGTAATCAGCTTTAACCCA\n+ACTTACTTGATAGAAGCATTGAAAGCCACAACTAGTGAACAAGTGAAAATTAGCTTTATC\n+TCTTCTGTCCGTCCATTTACATTGATTCCAAATAATGAAGGGGAAGATTTTATTCAATTG\n+GTTACACCAGTTCGTACCAACTAAATAATATTAAGAACGGCTAAACTAGCCGTTTTTATG\n+TTATACTAAAAAATAGCACCTAGCTTATTTTTATATATTTAGTGATGGGGAATAAATGAC\n+GTTATATATATTAGCTAATCCTAATGCTGGTAGCCATACTGCTGAACATATCATATTCAA\n+AATAAAAGAAAGTTATCCACAGCTTGCAGTTAACATTTTTATGACAGTTGGTCCTGAGGA\n+TGAAAAAAGTCAAATAGAGGCTATTTTAAAGGAGTTTGTCAGTAGTGAAGATCAATTAAT\n+GATTTTAGGCGGAGACGGCACACTATCTAAAGCTTTGCGTTTTTGGCCAGCTAGTCTACC\n+GTTTGCTTATTATCCAACAGGATCTGGAAATGATTTTGCTAAGGCAATGAATATAACATC\n+GCTATATAGAAGTGTAGATGCCATTTTAGAGAGAAAAACAAGTCGGATATATGTTTTAAA\n+CAGTTCATACGGAACGGTTGTAAACAGTATGGATTTTGGCTTTGCAGCTCAAGTTATCAA\n+TGGTTCAACGAATTCAATTTTGAAAAAAATTCTGAACAAGGTAAAACTTGGGAAGTTAAC\n+TTATCTATTCTTTGGTATTAAAACATTATTTTCAAAACAAGCTATAAACTTAGAATTAAC\n+TCTTGATGAAAAATCTTATCAGTTAGATAATCTCTTTTTTATTTCTGTAGCAAATAGTCT\n+TTATTTTGGTGGAGGAATCATGATATGGCCAACAGCAAGTGCTAAAAAGAAGGAAGTAGA\n+TATTGTTTACTTCAAAAATGGAAATTTCTACCAACGTCTACAATCATTGTTAGCCTTATT\n+AACGAAGAGGCATGAATCTTCTCATACGATTCAGCATTTAACAGGGGTAGATGTAGTTTT\n+AAAATCAAAAGAAAAATTATTATTGCAAATAGATGGAGAGACATGCACTGCAAATGAGGT\n+AACGTTAACCTATCAGGAAAGAAGTATGTATCTTTAAGGAGGAAGTATGTACCAATTAGG\n+AACCTTTGTCGAAATGAAAAAGCCCCATGCCTGTGTCATCAAATCGACCGGAAAGAAGGC\n+TAATAAATGGGAGGTTATCCGTCTAGGAGCGGATATTAAAATCCGCTGTACCAACTGTGA\n+CCATGTCGTTATGATGAGCCGGCATGATTTTGAACGAAAAATGAAACAAGT'..b'CTCTACCAACTGAGCTA\n+TGGCGGAAGAAATAGTCCGTACGGGATTCGAACCCGTGTTACCGCCGTGAAAAGGCGGTG\n+TCTTAACCCCTTGACCAACGGACCATTTTTAGAACAATAACTAGTATAATACATGTGACT\n+TTGTTTGTCAATACATTTTTTGATTTTTTATTGTATTGACAGAGTGCTTTGTTTAATGTA\n+AAATAAAATGGTTAAGGTTCCATAGCTCAGCTGGATAGAGCATTCGCCTTCTAAGCGAAC\n+GGTCGCAGGTTCGAATCCTGCTGGAATCATTTAGACCTACCTCGAGTAGGTCTTTTTTCT\n+TGCCATAATTCATAATTAATATATAACACTGGCAAAATCAGACCAATAAGGGCATATTCT\n+TCAAATTGGAAGGATAGGTGAGTAGATATGATGACACCTAGCATAAACCCTATAATGGTC\n+AATAAGATGTTTCTACCTGTTTTTCTAAGTTCTGAATCTTTTTCAATAACTCCTTTAAAC\n+CAGAGATAAGCAGCATTTTTGACATTCCCTGTCATCATCACATTGGCATACGGAGCACCT\n+CGTAACCTTCTAAATGTTTCTACTTGAATAGAGGCTACGAAGGCTAGACTAGCAATTGTA\n+AAAGACGCAGGCATTATAGGTGAGAGAATGATAGTTAGTAAAATAAGAACTAACATCATT\n+ACACTACTACCAAAGTGCCAAGACCATGTTTGTTTTTCAAAATACCTTCTTGCTAAGTAG\n+GTAAAAAATTGTCCGAATACAAAAAATAAAATGGGAATGGAAAAATTAACTACCTGCGCA\n+AAATCACCTTTAGCTAAAAAATAAGCTAGGGAAATAACATTTCCAGATTGTACGCCAGCA\n+AAGCGACCACCCTGAGTCACAAAAGTAAAGGCATTTAAATAACCACTGATAAACGTTAAT\n+GAACAAGCAATTCTCAATCCCTCAAAAACACGATACTCTTTTTGATTCATTTTCACTCCT\n+TGTTTCACGTGAAACTACTTATGATATGGGCTTCCCTGCTGAATCATAAATGCACGATAA\n+ATCTGCTCGATGAGAACTAATTTCATTAGTTGATGGGGAAGTGTCAACTGTCCAAAACTC\n+ATCAACAAATTAGCTCTTTTTTTAATACAAGAATCGAGACCCAAACTACCACCGATGATA\n+AAAGTTATATCTGAATACCCATTTACTGCAATGTCAGATATCCTTTGACTAAATTCTTCC\n+GATGGAAATTGTTTCCCTTCTATCGCTAAGGCAATGACAAAATCTCGCTCTCCAATTTTA\n+GACATAATTCTATCGGCTTCTTTTTTTAATATTTGTTCATTCTCTGCCTGACTGGCTTTA\n+TCTGGTGTTTTTTCATCAGGAAGCTCAATCATATCCAACTTAGTAAATCGTCCCAATCGT\n+TTACTATATTCTGCAATACCTTCTTTGAGGTACTTTTCTTTCAATTTTCCAACGGTAATC\n+AATTTTATTTTCATAAAATAATTGTAACATATCCACAAGCATACGACAGAAAATATTTTT\n+AGAAAATCAGGATATGGCTACAGTTTTTCACATAATTCACAGAGTTATCCACAGGTTGTG\n+GATTGATTTTTGAAAACTTTAAGTTATAATTAAGAAAGAAATAGTACTCTTAAGGAAAAT\n+TAAAGAAATGGAAAGGATTCCTTATATGAAAAAATATTTGAAATTTGCGATTTTATTTGT\n+AATTGGATTTTTTGGGGGTCTTATCGGGGCCTTGTCAGCCTCTTTCTTCCAGCCACAGGT\n+GCAACAAGCAAATTCTGCTATCACTAGTGTCAGCAATGTTCAATATAATAATGAAACTTC\n+CACCACAAAAGCTGTAGAGAAAGTACAAAATGCTGTTGTGTCTGTTATTAATTACCAAAA\n+ATCAGCCAACAATAGTCTTGGTGTTATCTTTGGAAATATTGAATCATCTGACGAACTAGC\n+TGTTGCTGGAGAGGGGTCTGGGGTTATCTATAAAAAATATGGTCAATATGCCTATATTGT\n+GACAAATACGCATGTTATTAATAACGCAGAAAAGATTGATATCCTTTTAGCATCTGGAGA\n+AAAAATTAGCGGTGAACTTGTTGGTTCCGATACATATTCTGATATAGCTGTTATAAAAAT\n+ATCAGCAGATAAAGTCACTGCTGTTGCTGAATTTGCTGATTCCGATACAATTAAAGTTGG\n+AGAAACTGCTATCGCAATTGGTAGTCCTCTAGGTAGCGTCTACGCCAATACAGTTACCCA\n+GGGTATTATTTCTAGCTTAAGTCGGACAGTTACTTCACAATCAAAAGATGGACAAACAAT\n+CTCAACTAACGCTATTCAAACTGATACAGCTATCAACCCTGGAAACTCTGGCGGACCGTT\n+AATCAATACCCAAGGACAAGTGATAGGCATTACCTCTAGCAAAATTACCTCAAGTTCTGC\n+AAATAGCTCAGGCGTGGCTGTAGAAGGGTTGGGATTTGCTATTCCTGCAAATGATGCCGT\n+AGCTATTATCAATCAGCTTGAAAAAACTGGACAAGTTAGCCGACCTGCTCTTGGAGTTCA\n+TATGGTTAACTTGACGACCTTGTCAACTAGTCAATTAGAAAAAGCTGGATTATCAAATAC\n+GGAATTAACATCCGGTGTAGTAATTGTCTCTACACAAAGTGGGCTACCTGCAGATGGAAA\n+ATTAGAAACTTTTGATGTTATTACTGAGATTGACGGAGAAGCTATTCAAAATAAGAGTGA\n+CCTCCAGAGCGCTCTCTACAAACATCAAATTGGAGATACAATCACTGTAACTTATTACCG\n+CAATAATCAGAAACAAACTGTTGACATTAAGTTGACACATTCTACAGAAGAACTTAGCGA\n+ATAATTGACAAATGAGACTTTACACAATTGTAAAGTCTCATTTTTTTTGCTAGAATAAGG\n+ATATATGGAAGAATTACGTACACTAAATATTTCAGAAATCCATCCCAATCCCTATCAGCC\n+AAGAATTCATTTTGATGAAAAGGAGCTACTTGAGCTCGCTCAATCTATTAAGGAAAATGG\n+CTTAATTCAACCGATTATTGTAAGAAAATCTTCTATTATCGGATACGAATTATTAGCTGG\n+AGAAAGAAGGTTGCGAGCCAGTCAATTAGCTGGACTGACTACAATACCAGCAGTGGTAAA\n+AGAACTGACTGATGATGATTTACTCTATCAGGCTATCATAGAGAATCTGCAGCGTTCTAA\n+CTTAAATCCGATAGAAGAAGCAGCCTCTTATCAAAAATTGATTAGTAGAGGGTTAACACA\n+TGATGAAGTTGCTCAAATCATGGGAAAATCAAGACCATATATCAGTAATTTATTGCGCCT\n+ACTAAATCTATCATCTCAGACTAAACAAGCTGTAGAAGAAGGAAAAATTTCACAAGGGCA\n+CGCGCGACAATTGGTGTCATTTTCAGAAGAAAAGCAAGCCGAATGGGTTCAACTCATTTT\n+ATCAAAGGATTTAAGTGTGCGTACGCTTGAAAAATTAATAGCTGCAAATAAGAAAAAACA\n+CACTAAGCTTAAACAACGCGACCAATTTTTAAAAGAACAGGAAGATTCACTCAGTAAAAC\n+TCTTGGAACAGCTACAAAAATTATCAAGAAGAAAAACGGGAGCGGAGAAATTCGGATTAG\n+CTTTAATGACCTCGATGAATTCGAAAGAATTATCAACAATTTTAAATAGACTTGTTTACA\n+ATTTATTTTTATAAACACTCTTTTCCACACTAAAATCATTACAAAAAGTCAGGACCAGCA\n+AGGGTTCTGACTTTTATTCACATCTTGTGGAAAACTTTTCTTAACAGTGTGGATTTTAAA\n+AATTATCTGTGGAAAACTTTTGTTTTTTATGGTACACTATTCTAACGAATATAATGTGAA\n+AGGGGGAAAAT\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/a.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/a.tab Sat Feb 21 16:33:42 2015 +0100

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/a.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/a.txt Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,15 @@
+ CHR        SNP         BP   A1       TEST    NMISS       BETA         STAT            P
+   1  rs1181876    3671541    T     DOMDEV      958     -1.415       -3.326    0.0009161
+   1 rs10492923    5092886    C        ADD     1007      5.105        4.368    1.382e-05
+   1 rs10492923    5092886    C     DOMDEV     1007     -5.612       -4.249     2.35e-05
+   1 rs10492923    5092886    C   GENO_2DF     1007         NA         19.9    4.775e-05
+   1  rs1801133   11778965    T        ADD     1022       1.23         3.97    7.682e-05
+   1  rs1801133   11778965    T   GENO_2DF     1022         NA        16.07    0.0003233
+   1  rs1361912   12663121    A        ADD     1021      12.69        4.093    4.596e-05
+   1  rs1361912   12663121    A     DOMDEV     1021     -12.37       -3.945    8.533e-05
+   1  rs1361912   12663121    A   GENO_2DF     1021         NA        17.05    0.0001982
+   1  rs1009806   19373138    G        ADD     1021     -1.334       -3.756    0.0001826
+   1  rs1009806   19373138    G   GENO_2DF     1021         NA        19.36    6.244e-05
+   1   rs873654   29550948    A     DOMDEV     1012      1.526          3.6    0.0003339
+   1 rs10489527   36800027    C        ADD     1016      12.67        4.114    4.211e-05
+   1 rs10489527   36800027    C     DOMDEV     1016     -13.05        -4.02    6.249e-05
\ No newline at end of file

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/add_scores_input1.interval
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/add_scores_input1.interval Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,20 @@
+chr20 74149 74150 G G
+chr22 14642921 14642922 C A
+chr20 74148 74149 T C
+chr22 15452519 15452520 C C
+chr22 15472687 15472688 C N
+chr22 15508088 15508089 G G
+chr22 15534573 15534574 C C
+chr20 24770 24771 C C
+chr20 24961 24962 T T
+chr22 15451993 15451994 C C
+chr22 14667850 14667851 G G
+chr22 15452482 15452483 A G
+chr20 71317 71318 T T
+chr20 74223 74224 A A
+chr22 15453065 15453066 A G
+chr20 74284 74285 T T
+chr20 74309 74310 A A
+chr22 15472610 15472611 G N
+chr20 86193 86194 C C
+chr20 87418 87419 C C

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/add_scores_input2.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/add_scores_input2.bed Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,25 @@
+chr1 90000 90001 A
+chr2 90000 90001 A
+chr3 90000 90001 A
+chr4 90000 90001 A
+chr5 90000 90001 A
+chr6 90000 90001 A
+chr7 90000 90001 A
+chr8 90000 90001 A
+chr9 90000 90001 A
+chr10 90000 90001 A
+chr11 90000 90001 A
+chr12 90000 90001 A
+chr13 90000 90001 A
+chr14 90000 90001 A
+chr15 90000 90001 A
+chr16 90000 90001 A
+chr17 90000 90001 A
+chr18 90000 90001 A
+chr19 90000 90001 A
+chr20 90000 90001 A
+chr21 90000 90001 A
+chr22 90000 90001 A
+chrX 90000 90001 A
+chrY 90000 90001 A
+chrM 9000 9001 A

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/add_scores_output1.interval
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/add_scores_output1.interval Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,20 @@
+chr20 74149 74150 G G 0.885
+chr22 14642921 14642922 C A -1.844
+chr20 74148 74149 T C -3.161
+chr22 15452519 15452520 C C -1.138
+chr22 15472687 15472688 C N NA
+chr22 15508088 15508089 G G -1.398
+chr22 15534573 15534574 C C 0.460
+chr20 24770 24771 C C -1.374
+chr20 24961 24962 T T -1.599
+chr22 15451993 15451994 C C 0.645
+chr22 14667850 14667851 G G 0.469
+chr22 15452482 15452483 A G -1.246
+chr20 71317 71318 T T -0.825
+chr20 74223 74224 A A -1.451
+chr22 15453065 15453066 A G -0.776
+chr20 74284 74285 T T -0.701
+chr20 74309 74310 A A -0.863
+chr22 15472610 15472611 G N NA
+chr20 86193 86194 C C 0.887
+chr20 87418 87419 C C -1.703

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/add_scores_output2.interval
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/add_scores_output2.interval Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,25 @@
+chr1 90000 90001 A 0.431
+chr2 90000 90001 A 0.514
+chr3 90000 90001 A 0.808
+chr4 90000 90001 A 0.456
+chr5 90000 90001 A 0.446
+chr6 90000 90001 A 0.397
+chr7 90000 90001 A 0.446
+chr8 90000 90001 A NA
+chr9 90000 90001 A 0.470
+chr10 90000 90001 A 0.463
+chr11 90000 90001 A 0.369
+chr12 90000 90001 A 0.557
+chr13 90000 90001 A NA
+chr14 90000 90001 A NA
+chr15 90000 90001 A NA
+chr16 90000 90001 A 0.819
+chr17 90000 90001 A -0.993
+chr18 90000 90001 A 0.657
+chr19 90000 90001 A 0.372
+chr20 90000 90001 A 0.360
+chr21 90000 90001 A NA
+chr22 90000 90001 A NA
+chrX 90000 90001 A 0.414
+chrY 90000 90001 A 0.414
+chrM 9000 9001 A -0.587

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/aggregate_binned_scores_3.wig
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/aggregate_binned_scores_3.wig Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,1000 @@\n+track type=wiggle_0 name="Conservation" description="Vertebrate Multiz Alignment & Conservation"\n+#\toutput date: 2008-02-18 20:43:07 UTC\n+#\tchrom specified: chr7\n+#\tposition specified: 115444712-115484501\n+#\tThis data has been compressed with a minor loss in resolution.\n+#\t(Worst case: 0.0078125) The original source data\n+#\t(before querying and compression) is available at \n+#\t\thttp://hgdownload.cse.ucsc.edu/downloads.html\n+variableStep chrom=chr7 span=1\n+115444712\t0.0472441\n+115444713\t0.84252\n+115444714\t0.952756\n+115444715\t0.968504\n+115444716\t0.976378\n+115444717\t0.976378\n+115444718\t0.976378\n+115444719\t0.976378\n+115444720\t0.976378\n+115444721\t0.968504\n+115444722\t0.96063\n+115444723\t0.905512\n+115444724\t0.566929\n+115444725\t0.559055\n+115444726\t0.598425\n+115444727\t0.76378\n+115444728\t0.818898\n+115444729\t0.858268\n+115444730\t0.889764\n+115444731\t0.905512\n+115444732\t0.984252\n+115444733\t0.992126\n+115444734\t1\n+115444735\t1\n+115444736\t1\n+115444737\t1\n+115444738\t1\n+115444739\t0.992126\n+115444740\t0.992126\n+115444741\t0.968504\n+115444742\t0.0472441\n+115444743\t0\n+115444744\t0\n+115444745\t0\n+115444746\t0\n+115444747\t0\n+115444748\t0\n+115444749\t0\n+115444750\t0\n+115444751\t0\n+115444752\t0\n+115444753\t0\n+115444754\t0\n+115444755\t0\n+115444756\t0\n+115444757\t0\n+115444758\t0\n+115444759\t0\n+115444760\t0\n+115444761\t0\n+115444762\t0\n+115444763\t0\n+115444764\t0\n+115444765\t0\n+115444766\t0\n+115444767\t0\n+115444768\t0\n+115444769\t0\n+115444770\t0\n+115444771\t0\n+115444772\t0\n+115444773\t0.015748\n+115444774\t0.0314961\n+115444775\t0.0314961\n+115444776\t0.0314961\n+115444777\t0.015748\n+115444778\t0.015748\n+115444779\t0\n+115444780\t0\n+115444781\t0\n+115444782\t0\n+115444783\t0\n+115444784\t0\n+115444785\t0\n+115444786\t0\n+115444787\t0\n+115444788\t0\n+115444789\t0\n+115444790\t0\n+115444791\t0\n+115444792\t0\n+115444793\t0\n+115444794\t0\n+115444795\t0\n+115444796\t0\n+115444797\t0\n+115444798\t0\n+115444799\t0\n+115444800\t0\n+115444801\t0\n+115444802\t0\n+115444803\t0\n+115444804\t0\n+115444805\t0\n+115444806\t0\n+115444807\t0\n+115444808\t0\n+115444809\t0\n+115444810\t0\n+115444811\t0\n+115444812\t0\n+115444813\t0\n+115444814\t0\n+115444815\t0\n+115444816\t0\n+115444817\t0\n+115444818\t0\n+115444819\t0\n+115444820\t0\n+115444821\t0\n+115444822\t0\n+115444823\t0\n+115444824\t0\n+115444825\t0\n+115444826\t0\n+115444827\t0\n+115444828\t0\n+115444829\t0\n+115444830\t0\n+115444831\t0\n+115444832\t0\n+115444833\t0\n+115444834\t0\n+115444835\t0\n+115444836\t0\n+115444837\t0\n+115444838\t0\n+115444839\t0\n+115444840\t0\n+115444841\t0\n+115444842\t0\n+115444843\t0\n+115444844\t0\n+115444845\t0\n+115444846\t0\n+115444847\t0\n+115444848\t0\n+115444849\t0\n+115444850\t0\n+115444851\t0\n+115444852\t0\n+115444853\t0\n+115444854\t0\n+115444855\t0\n+115444856\t0\n+115444857\t0\n+115444858\t0\n+115444859\t0\n+115444860\t0\n+115444861\t0\n+115444862\t0\n+115444863\t0\n+115444864\t0\n+115444865\t0\n+115444866\t0\n+115444867\t0\n+115444868\t0\n+115444869\t0\n+115444870\t0\n+115444871\t0\n+115444872\t0\n+115444873\t0\n+115444874\t0\n+115444875\t0\n+115444876\t0\n+115444877\t0\n+115444878\t0\n+115444879\t0\n+115444880\t0\n+115444881\t0\n+115444882\t0\n+115444883\t0\n+115444884\t0\n+115444885\t0\n+115444886\t0\n+115444887\t0\n+115444888\t0\n+115444889\t0\n+115444890\t0\n+115444891\t0\n+115444892\t0\n+115444893\t0\n+115444894\t0\n+115444895\t0\n+115444896\t0\n+115444897\t0\n+115444898\t0\n+115444899\t0\n+115444900\t0\n+115444901\t0\n+115444902\t0\n+115444903\t0\n+115444904\t0\n+115444905\t0\n+115444906\t0\n+115444907\t0\n+115444908\t0\n+115444909\t0\n+115444910\t0\n+115444911\t0\n+115444912\t0\n+115444913\t0\n+115444914\t0\n+115444915\t0\n+115444916\t0\n+115444917\t0\n+115444918\t0\n+115444919\t0\n+115444920\t0\n+115444921\t0\n+115444922\t0\n+115444923\t0\n+115444924\t0\n+115444925\t0\n+115444926\t0\n+115444927\t0\n+115444928\t0\n+115444929\t0\n+115444930\t0\n+115444931\t0\n+115444932\t0\n+115444933\t0\n+115444934\t0\n+115444935\t0\n+115444936\t0\n+115444937\t0\n+115444938\t0\n+115444939\t0\n+115444940\t0\n+115444941\t0\n+115444942\t0\n+115444943\t0\n+115444944\t0\n+115444945\t0\n+115444946\t0\n+115444947\t0\n+115444948\t0\n+115444949\t0\n+115444950\t0\n+115444951\t0\n+115444952\t0\n+115444953\t0\n+115444954\t0\n+115444955\t0\n+115444956\t0\n+115444957\t0\n+115444958\t0\n+115444959\t0\n+115444960\t0\n+115444961\t0\n+115444962\t0\n+115444963\t0\n+115444964\t0\n+115'..b'115445440\t0\n+115445441\t0\n+115445442\t0\n+115445443\t0\n+115445444\t0\n+115445445\t0\n+115445446\t0\n+115445447\t0\n+115445448\t0\n+115445449\t0\n+115445450\t0\n+115445451\t0\n+115445452\t0\n+115445453\t0\n+115445454\t0\n+115445455\t0\n+115445456\t0\n+115445457\t0\n+115445458\t0\n+115445459\t0\n+115445460\t0\n+115445461\t0\n+115445462\t0\n+115445463\t0\n+115445464\t0\n+115445465\t0\n+115445466\t0\n+115445467\t0\n+115445468\t0\n+115445469\t0\n+115445470\t0\n+115445471\t0\n+115445472\t0\n+115445473\t0\n+115445474\t0\n+115445475\t0\n+115445476\t0\n+115445477\t0\n+115445478\t0\n+115445479\t0\n+115445480\t0\n+115445481\t0\n+115445482\t0\n+115445483\t0\n+115445484\t0\n+115445485\t0\n+115445486\t0\n+115445487\t0\n+115445488\t0\n+115445489\t0\n+115445490\t0\n+115445491\t0\n+115445492\t0\n+115445493\t0\n+115445494\t0\n+115445495\t0\n+115445496\t0\n+115445497\t0\n+115445498\t0\n+115445499\t0\n+115445500\t0\n+115445501\t0\n+115445502\t0\n+115445503\t0\n+11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diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/aggregate_binned_scores_in_intervals.out
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/aggregate_binned_scores_in_intervals.out Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,10 @@
+chr7 115444712 115444739 CCDS5763.1_cds_0_0_chr7_115444713_f 0 + 0.842925922462 0.059 1.0
+chr7 115468538 115468624 CCDS5763.1_cds_1_0_chr7_115468539_f 0 + 0.999697674152 0.982 1.0
+chr7 115483024 115483277 CCDS5763.1_cds_2_0_chr7_115483025_f 0 + 0.99544268823 0.837 1.0
+chr7 115484165 115484501 CCDS5763.1_cds_3_0_chr7_115484166_f 0 + 0.750726190992 0.0 1.0
+chr7 115485764 115485980 CCDS5763.1_cds_4_0_chr7_115485765_f 0 + 0.984907407314 0.354 1.0
+chr7 115486322 115486481 CCDS5763.1_cds_5_0_chr7_115486323_f 0 + 0.994924527669 0.739 1.0
+chr7 115491298 115491487 CCDS5763.1_cds_6_0_chr7_115491299_f 0 + 0.946195768256 0.007 1.0
+chr7 115468538 115468624 CCDS5764.1_cds_0_0_chr7_115468539_f 0 + 0.999697674152 0.982 1.0
+chr7 115483024 115483277 CCDS5764.1_cds_1_0_chr7_115483025_f 0 + 0.99544268823 0.837 1.0
+chr7 115484165 115484501 CCDS5764.1_cds_2_0_chr7_115484166_f 0 + 0.750726190992 0.0 1.0

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/aggregate_binned_scores_in_intervals2.interval
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/aggregate_binned_scores_in_intervals2.interval Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,2 @@
+chr22 1000 5000 cloneA 960 + 1000 5000 0 2 567,488, 0,3512 nan nan nan
+chr22 2000 6000 cloneB 900 - 2000 6000 0 2 433,399, 0,3601 nan nan nan

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/aggregate_binned_scores_in_intervals3.out
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/aggregate_binned_scores_in_intervals3.out Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,10 @@
+chr7 115444712 115444739 CCDS5763.1_cds_0_0_chr7_115444713_f 0 + 0.904053741031 0.559055 1.0
+chr7 115468538 115468624 CCDS5763.1_cds_1_0_chr7_115468539_f 0 + nan nan nan
+chr7 115483024 115483277 CCDS5763.1_cds_2_0_chr7_115483025_f 0 + nan nan nan
+chr7 115484165 115484501 CCDS5763.1_cds_3_0_chr7_115484166_f 0 + nan nan nan
+chr7 115485764 115485980 CCDS5763.1_cds_4_0_chr7_115485765_f 0 + nan nan nan
+chr7 115486322 115486481 CCDS5763.1_cds_5_0_chr7_115486323_f 0 + nan nan nan
+chr7 115491298 115491487 CCDS5763.1_cds_6_0_chr7_115491299_f 0 + nan nan nan
+chr7 115468538 115468624 CCDS5764.1_cds_0_0_chr7_115468539_f 0 + nan nan nan
+chr7 115483024 115483277 CCDS5764.1_cds_1_0_chr7_115483025_f 0 + nan nan nan
+chr7 115484165 115484501 CCDS5764.1_cds_2_0_chr7_115484166_f 0 + nan nan nan

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/asian_chars_1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/asian_chars_1.txt Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,1 @@
+蛋白質核酸酵素:制癌性物質の化学修飾による効果の向上.
\ No newline at end of file

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/axt_to_concat_fasta.dat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/axt_to_concat_fasta.dat Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,4 @@\n+>hg17\n+tcttcatgtgacttgcttgtgccttttaggacctgctcaagcctgatcacatatgtacaacttccagttgataatggattgttgctgtgcacaagctactttttagcttcattggttagataatactcagctcatgagatgcaggtcagattacatggcaatttggtagctcattgtcaaatgtttagtttctactgagacctaatatcaggccaagaactgtcactcaaatagagaatcgctatctgcaaaaatcatttgtccaaagtacctagggtttc----atctgtaatacatgtgtaggggcctgctaaatgctccaagcagcatccccatctgccactgtcacctc---atgtgcc--------------------------tagtcatagaaaaacatgcacagcagcctggacctgttaaagaaacttctcctatttctgtacccacacaaagctagcttctcttcaagtcacttggtatatggTATGCTTACCTTAATCTGTTGTGTGAGCCATTTATTAttattttcccattttctgactgtataatttggatattatacttataagttggcagaTATATG---------CATCAGAACATGGAATATGTTGGAAGAATCAAAAGGAGAGTTAGAAGGGGGCAATAGGAAGATGAACATAAACAGGGTACGTACAGA---------------AAATTTTTCAAAGAATAAATAAAACCATTAAAAAAACAAACAAATATACAATGACCATAAAATATTGCTATACTAAATTATAAAA------CAGAAATATTTATATGTACAAAGAAACAAATTCCAAGCCAGAAATTCAACAGGGAATATACAGCATAATAAGATATATATCAATTAGAAAAA-TATCAAATTAAAATTATAAGCTAGAAAGTATTAAAGGGAAAAAATGGATGAATTTAATAGCTTA-------TGCTTAAGAATAATTGGCAAATCAGAAGCCTTGTAAGAAACAATAGAAATAAAGTTT-AAGAGGAATAGAAGAGAAAAATAATAATGCTGAAGGCAGAGGTCAGCATAACAGGAGTGTGAATTGGAATCTCAGACTCACAGGGAAGGTAGAAAGAAGCAGAAGATATTTAAACAAataaaggagaaagggaatgggggatga-gagtgggactgggaggagaggagggaggagaggctgtaatcaggatgtaaagtgaataagcaaataaGTTAAGGAAAACAACAACAAAAAGAAACTGGATTAATTTCAATTTATTCAAGAACATTGGTTATTTCCATTAAGTACTGTAGTATTATGTATATGAATATAAAAATCCTTTCATCAAAGCAAGGAAGAGAGCACAAAGCTGCCCTTAAGTCATTGAAGACCTGGAGCACCTATGGGCCTCCCAAGAGGTTCTCACAAAACCTACAACCTCCATCCCAAGAGCCTGTGTCTGACAGAGCTGGTATGAGAAAAGGAGACAATTCTTCCC-----CAGG------------TTTTAGCCAGACTTTGAGTACACAATGGGATAGTGAGGAGCC----------------------CAGTGAAAGCAA------------TTAGTGATTTGGCCTGTGACCCTCTAGCACAATGTTTTGCAGGTCCAGTTGGACATGACATGTTTTCATTGGAAAGGCACATTTATAGTACCTAATGACAGCCCATGTCAA-GTGGCACATTGTTTTTGACAAATCAGTTTCCTTTAGACTACACCTTCAAGCCACTTAAGGTTGCATTTACAACAAAAATTTATAATCTAAATATCAACAGTAATGGCAATATTTATCTTGATAATCTCAGATCACAGTGTCTCCTGCTTTAACTA-TTTCTAATGTTCATTTATCCATTTGTTCACTGCTATGTGATCCAAACCCTGATGATCTCCTAGTGCCAGAGACTGCACAGATCT--AAAACAGATAGTGATAAATACAACAGAATATCTTGGGAATGGACTCAGAAGTATGCCATGTGATGTTACCTTAAAGTCAGAATAACTTGCATTTTATAGCTGGAATAAACTTCAAATTCCTATTCCTTTTTTTGATCTCATGTTTTTCATTTT--TTTCTTTTTATTTCCCTCCTTTCATTCACATGTTTATCTAAG-AGACTTAAATTCTTTCAGCTTTAGACAATAACTACTTTTAGAATCTGCAAAGTAGTTACAAGAAAACAGTTGCCCAAGATTCAGAATCTTTTTAAAAAACTGGAGCTTGTCCAGATACA-TATGTAGCCAAttgtttgagacagtgtttctctgtgtagccacatctgttgtggaactcaatttgcaaatcaggctggcctcaaactcacagagatctacctgcctctgcctcttgagtgctagtattaaaggcatatgcaaccactgcctggctaaaataatatttttaaaataaCATGGTTACATGCCAAATTGACAAGGGGTGGATA------AGCCTATACtgatagataatttcacagaatctagaaacaccctggggaaaaatgtttgcacatgcctggg----gccagggagat--gttaatttctttggttatcgaaggagggagacctaatctaattgcctaa-tgaatgaaaagaagtaagtgaagtacctgagctcatctcctgttggttcctaaatgcaaaagcaatgagaccagctagcctcctgtttcttccatttctttcgccaatatcttctctgctatgatggattgtctttcttaaattgattgccaaaatcatctcttattttcttaaattgtttcttgttggttattttgacacatctatgagaaaaggaactaatataGAATGGACATGGTGGTGACTTGGAAAAGTTATGGAGTTACATATGA-TGACCGTGGTCTGACCAGGAAGAGACAGGGACAGATAGTCCAGGTGTCTAAGCACAAAAAAGTAAATAGATATGTCTCAGATAACTGAGAGCCCTATGTGGTTAACAAGCAATTGGGGCATACCAGGGCTTACAAATAAATGCTCTATATGATCCATGTTTCACCTTCTACTTTCCTTCATTGTTACATCCTACCCCATCACATAAAGAAAATATcacacacacacacacacacacatacacacagacagacagatagactgacacacacaaacacacacacacacacagagagagagagagagagagagagagagagagagagagagagagagagagagagTCAAACAGCATTTAATTCCTGTGTAGCAACAAGGACATCTTGCATGCAGTTCAGTCTGGTTAAGGAATGGGAGAAGCAAAATGAGGCTTTAGTCAATGATAGAGGAAGGAAGGGATTTAGATGGGTCTTGAGGCTTTGAAGATGAAGTATTAACCAGGTTGCTTGAAAGATCGCTGTGTCTTCCCTTTTGATGACCCCAAGCACAGAGTACATCACCGTTGTCTTCATATTCTTTTTCACTTTCTGAGGAGCTTTCACCAAAAGCACGTTGCTTTTCATAAACAAAACAACATTTGGATGAGCGACGGCCCAAGTGTTCATTGTCAATAGTGTCACTAGAACACCCAACCTTATTGCCTGACTTCCCCTTCTCTAACTTGTTGGACATATTGCTACTTTTTGGCTTATCACCCAGAACAACTGTGGGATCTGAGATGGATCTTCAGTCAGCTTAG------------------CAGAACTGGAAGCCTGGCAGAGGAGAGAAATCAATGTATCCAAAGAGTCTGAGGAAATAGGAATTTGAAATCAAGTCAGAGTCACAATTAAAATTTAATGTTGCAATTATTTTTATCTTAGAATTC----------GTACACAACTTACTCTTGTTTCTCAGTTGTTGTATGTTCAAATTCATATTTTGAGATCACAGAAAATAATTTGGTTATAAGGGAAATGGTAGAAAGAAAATTTGGGTCTGACTATTTCATTT'..b'ttgcgcttcctaggcaagcgctctaccactgagctaaatccccaacccctaaagcctatctttgagataagccaaggcaaaaactcaagTTATTCTTTTTGAAAATACAGTAATTTCACATCATCattcattgattcaacacatatttatggaatattggctatgATATAGATcagtggttcttaaccttcctaatgctacaaccctttatgctgtggtaaccacaaccataaaattacttttgtttctacttcataactgtaattttgttactgttatgaattataatataaatatgtgatatgcaggatatctgatgtatgacccctgaaagagttatgacccacaggttgagaaGTAGTGCTCTAGATCCTTTTCAAGAGACTAAGATGTAACTGAATGGGACACAGTGTTGT---ATTCAAGATGATAATTTTTTGGAGTAAAACTGAAAGTAATAAACTgg-actaaagagatagctcagacagtaaagtgcttgcag-------------------------tctccagcatccacagaaaagactgggcattgcaacttgcacctgtagtcacaggactggggatgtgaagacaggaggaccactggagtgtgctgagcaaattggtgagctctagattcattgagcgatcctatctcaaaactgaaggagacaccctaatgacttctggcctctacaaccatgcacttgtatacacaTGTGCTACACACATTTAAATtctctctctctctctctctctctctctctctctctctctctctctctctctctctctctctntAATAAAAA-AATTCA-ATAATATCCTACAGTAAAAAA-----AAACCCATTCATGGGTTTAAAAAATTTTGAACAAGTGATGTTTAATTCAAGACAGGAAAGACATCAACTTTGAAAAGTTATGAAAAGCTCT----GTAAGAAATAATTTTAGTGCAAAAGCTTTCAAACCCAAAACAAACTTGTTACCTTGAAGAATGCACAGAGACCATTAGTATGGCTGTCATACATACTCAAAAGAAAGAA--AATCTCCCAGAGCAGCACTTTACTACTTTTCATCATTGTGTTTTCCCGACTAAAAATACATTTTTTAAACTGGCATAGTGGTACACAATTGAAATCCTAGCTCCTGAGACTCTAGGGCAGGAGGGTCATGGCTACATAATGGTACACTCTCAAAAAGAAAGAA---AACTCTTAAAGTAAGAAGCTTCTAAAATATGTTTTCCAATTGTTTCTTCACGAAAATTTAATATCA-----GTGTTCTGTATCTTTTTAATACA-TGTATCTGCATATGTGTTTATAGTTAATTTATAAAATAGTAAACTTTATCTAGAACTAAGAATGAGTAAAATTTGTAAGTTAAAAATCAAAAAGTTGTTATCTAACAAGTACACTTGACATATGGTATTACTGAAAATTATT----TATGTACATTATAAC--AAAATTATATGTACAAATTATCAATTTATAAAATTATACAATAGAAA----------------------------------------TTTTGGTAACTTCATACATAAACGAAATGTACATAGGGAGACAATTAACTTCCTAGATA----TTTAGTAAATATAACATCTGAATTTTGCTTAATGTAAGAAAATACATTTctagatacacatataatatcaatatatt-----ttcatcacttataaacagtgacaagttataaagctacttaataagatgtaaactacatctaattttaaaaagcataagacacaaggatactaaagataatacatgagacgaggtgagggcagccagtagacatacacgggctacttGTTAATGAATGAATTCATGAATGATCTCTGAATTGTAAATTCTTCTGAtggtatggggagctcatcagagatgagcactcagacacagtgtatagccaataaaaagtctttattctagcCTGGAAGGAACTACACCCAAGTACAGCCTTGAGTGTCCAGAACATAGGATTAGTTTAACCTGCAGTGGCCTCAGCAAGAATACAAGATGGAGGA-------ATTTCTGCATTGCCTTGCCTGCTGACAAAGGGACctcctgcaccatgcctgcctggatactcccatactcccaacttgatgataatggactgaacctttgaacctgtaagccagccccaattaaatgttgtccttataagagttgccttggtcatggtgtctgttcacagcagtaaaatcctaactaagacaGGAC----------ATATGGGTTTTATCTGCTTCTTGGGGAATCATGAACTCTGAACATTGTGCTAATATACCTAGGGCCAttctgaagatcatattagaaGTTTTTCTTAGGTGTTCCTTCAGATTAAAATATTCCATG-TGGAAGGAGGAAAAAGGTTTATAAATCTCAAGGACTATCTCAATTTAAAAGACTCATGAAACTCTGAAAACTTAACAAAAATCACATAGCCTCCCCCAATATTACATAAGTAGTGAACAATTGTGGGCAGGAGTGAAGGGGTTTCCTTCAGTGTGGGTTTTtgcaagttgggcagagagttctagggaatcaattttcataaatcagcatcagcattggggcaagctttctgttaatggagctgatg-tgagtcatccgtgttcctttcaatgacctcaacaaactcattggttctccaagctaaaatcaggtgctatggtgtagtctttgtttcactctgattaattaattaattaattaattaattaatcaagtaattgttaatgtcctacttg--gtaaacatacgtttatctaactattttcaggaaaattcacacaacaGAAGGTCGAAACTTCTAAACAAAAGAGTATTTCTCTTTGTTAGTTGAGTCTA--CACTCGATAGGGAAA--AATGAAGGAAAAGAAATCCCCCATTAAGTAAACTCACTTAGACCACCTACTTACAATGTGGAATTTATATATTTGATTTTCATGCTCCAAATT--CCAAGATTTTTGAGAAGATTTTCAGGAGTTGCTGcagtgtgcctgttaaaatatgacaaaaactatgagatgcttcaactttaaaagcactaa---catgtccccctctcactcaaggtaaaagcaaaattcctctgtagaagttttaacctgcagggctttgggctctctgacacccctgtgacttctgagaaatcacttttcacaattttctaccacccttcatcatatccagccatgccttcatcccagctgcttctcctcatgcatgccaggtcttctctggc---------ccagcaattgtcatcacataagctggaatgcacattccccTTGACTGCTGTTGGAtctctctctctctctctctctctctctctctctctctctctctctctctctctctctcCTTGTTCCATTCTAAACCTAGAGCTTCCTTGATACCTTTCCTGACCATTGTAACTCTCTGAAAAGAATGCTGGCCCTGAAATTTCATTTTCTTGAACCTAGACTTGGT-GTGTCCCCTCTTATCACTTACCAATATGAAAATGCTTCAGATAGGCTTATTAGCTACAGGAATATATTGCTCATTTCCCACACTAGGAGGAGAACTCCAAAGGGATACGATCTGTCCATTTGCTGCCTCTGCTGACTGCAGTATATAGAACACTGCATGGC----------CAGAGTGTTTATGTGACAAAGGTAAAACAAATCAATTGGGTGAGAATCTGTGGAATCAAGCATGTAAAGTGAGACAAGTATCCCTGGGTCTAGCCATAATGCTATA----AATGCACTTCCTAACAGGGTATGAGCTTGAAGGGCAGGGTAAAGCAGGGCAACTGGAGGCATGCTCAACAGAAACCTTTCCAAGGTTGAAATGTGATGGCCTCTTCCTTACACCATGGTGCTTGTATCC--TTGTTGGAATGTGGGTCCTGTTCAAATGCCTTTACATGATATGAACT\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/axt_to_fasta.dat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/axt_to_fasta.dat Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,105 @@\n+>hg17.chrX_3022175_3023241\n+tcttcatgtgacttgcttgtgccttttaggacctgctcaagcctgatcacatatgtacaacttccagttgataatggattgttgctgtgcacaagctactttttagcttcattggttagataatactcagctcatgagatgcaggtcagattacatggcaatttggtagctcattgtcaaatgtttagtttctactgagacctaatatcaggccaagaactgtcactcaaatagagaatcgctatctgcaaaaatcatttgtccaaagtacctagggtttc----atctgtaatacatgtgtaggggcctgctaaatgctccaagcagcatccccatctgccactgtcacctc---atgtgcc--------------------------tagtcatagaaaaacatgcacagcagcctggacctgttaaagaaacttctcctatttctgtacccacacaaagctagcttctcttcaagtcacttggtatatggTATGCTTACCTTAATCTGTTGTGTGAGCCATTTATTAttattttcccattttctgactgtataatttggatattatacttataagttggcagaTATATG---------CATCAGAACATGGAATATGTTGGAAGAATCAAAAGGAGAGTTAGAAGGGGGCAATAGGAAGATGAACATAAACAGGGTACGTACAGA---------------AAATTTTTCAAAGAATAAATAAAACCATTAAAAAAACAAACAAATATACAATGACCATAAAATATTGCTATACTAAATTATAAAA------CAGAAATATTTATATGTACAAAGAAACAAATTCCAAGCCAGAAATTCAACAGGGAATATACAGCATAATAAGATATATATCAATTAGAAAAA-TATCAAATTAAAATTATAAGCTAGAAAGTATTAAAGGGAAAAAATGGATGAATTTAATAGCTTA-------TGCTTAAGAATAATTGGCAAATCAGAAGCCTTGTAAGAAACAATAGAAATAAAGTTT-AAGAGGAATAGAAGAGAAAAATAATAATGCTGAAGGCAGAGGTCAGCATAACAGGAGTGTGAATTGGAATCTCAGACTCACAGGGAAGGTAGAAAGAAGCAGAAGATATTTAAACAAataaa\n+>panTro1.chrX_132722807_132723933\n+tcttcatgtgacttgcttgtgccttttaggacctgctcaggcctgatgacacacatataacttccagttgataatgcattactgctgtgcacaagctatcttttggcttcattggctagataatactcagctcattaggtgcagttcagatcacatggtaatttggtggctaattgtcaaatgtttattttctactgagccccaatatcagtccaagaactgtcactcaaatagaggattgttgtctgcaaaa-tcatttgtccaaagtccttcgtgtttctttcctctgtaatttatacataggggccttctaaatgctc-aagcagcatccctatctgccactgtcaccaccacaagtgccctccagtctgctggatcataaaatcctagtcatagaacaacatgcacagcagcctggacctgttgaagaactttctccaattcctgtactcacacgaagctagccactccctaagtcacttggtatatgCTATGCATATCTTAATCTGTGGTGTGAACTACCTATTATT----TCCCCGTTTCAGACTGTATAATTGTGATAATATATTTAGAAGTTAGtatatatataatatatatatatCAGAATATGGGATATGCTGAAAGAATCACAAGGAGAGTTAGAAGGAGGCAATAGGAAGATGAACATAAACAGtatatatatatatatacatgtatatataATTTTTTCAAAGAATAAATAAAAATATTGTAAAAG-AAACAAACACACAATG-TCATAAAATATTGCTCTACTATATTATGAAATAGCAACAGCAATATTTGTATGTACAAAGAAATAAATTCCAAGCCAGAAACTCAGCAGAGAATTTACAACATAA---GGCATTTATCAATTGGAAAAAATACTAAATTAAAATTATAAGATAGGAAGTATTCAAAAGAAGCA-TGGATAAATTTAATAGCTCACTAAGAATGCTTAAGAATAATTGGCAAATAAGAGGACCTGCAAGAAATAATAGAAATAAAGTTTTAAGAGGAATAGAAGATAAAAATAAAAATGCCTTAGGCAGAGGTTAGCATAACATGAGTGTGAATTGGAATCTCAGAGTCACAGGAAAAGTAGAAAGAAGCAGAAGATATTTAAAGGAATGAA\n+\n+>hg17.chrX_3025131_3025662\n+ggagaaagggaatgggggatga-gagtgggactgggaggagaggagggaggagaggctgtaatcaggatgtaaagtgaataagcaaataaGTTAAGGAAAACAACAACAAAAAGAAACTGGATTAATTTCAATTTATTCAAGAACATTGGTTATTTCCATTAAGTACTGTAGTATTATGTATATGAATATAAAAATCCTTTCATCAAAGCAAGGAAGAGAGCACAAAGCTGCCCTTAAGTCATTGAAGACCTGGAGCACCTATGGGCCTCCCAAGAGGTTCTCACAAAACCTACAACCTCCATCCCAAGAGCCTGTGTCTGACAGAGCTGGTATGAGAAAAGGAGACAATTCTTCCC-----CAGG------------TTTTAGCCAGACTTTGAGTACACAATGGGATAGTGAGGAGCC----------------------CAGTGAAAGCAA------------TTAGTGATTTGGCCTGTGACCCTCTAGCACAATGTTTTGCAGGTCCAGTTGGACATGACATGTTTTCATTGGAAAGGCACATTTATAGTACCTAATGACAGCCCATGTCAA-GTGGCA\n+>panTro1.chrX_132731309_132731841\n+ggaggaggaggaggaggaataacaagaagaagaagaagaagaagaagaagaagaag--------aagaagaagaagaagaagaagaagaag--aagaagaagaagaagaagaagaaACAGGATTGATTCAAATTTATTCAGGAATACTAGTTATTTCGAATAAGCCCTATAGAATTATGTACATGAATCAAAAAATCCTTTCATCAAAGCTAGAAAGAGAGCACAAAACTGACCATAAGTCATTGAATACCTGGAG-----------------------------------------CTCCATCCCAAGAGCCTATGTCTGGCAGAGCTGGTGTGAGAAAAAGAGGCAATCCTTCCCTGCTGCAGGAATAATCAAGCATGTTGGCTGGACCTTGAGTACACATCAGGATAGTGAGGGGCCTGGCAAAAAGCACAGACTATGGCACTGAAAGAAATTAATAAGGGACTTAGTGATTTGGCTTATGACCCTCCAGCACAATGTTTTGCAGGTCCAGTTGGAGATGACATG-TTTCATTGGCAAGCCACGATTATGGGACTTAATGACAGCCCCTGTCAAGGTGGTG\n+\n+>hg17.chrX_3030007_3030565\n+CATTGTTTTTGACAAATCAGTTTCCTTTAGACTACACCTTCAAGCCACTTAAGGTTGCATTTACAACAAAAATTTATAATCTAAATATCAACAGTAATGGCAATATTTATCTTGATAATCTCAGATCACAGTGTCTCCTGCTTTAACTA-TTTCTAATGTTCATTTATCCATTTGTTCACTGCTATGTGATCCAAACCCTGATGATCTCCTAGTGCCAGAGACTGCACAGATCT--AAAACAGATAGTGATAAATACAACAGAATATCTTGGGAATGGACTCAGAAGTATGCCATGTGATGTTACCTTAAAGTCAGAATAACTTGCATTTTATAGCTGGAATAAACTTCAAATTCCTATTCCTTTTTTTG'..b'TGCCTTGCCTGCTGACAAAGGGAC\n+\n+>hg17.chrX_3049057_3049300\n+ctcctgtaccatgcctgcctggatgctgccatgctcctgcctagatgatagtagactgaacttctgaacctctaagccagcccaaattaaatgttgtccttataaaagatgccttggtcatagtgt----tctcatcagtaaaaccctaa----GACAGAAGTTGGTACCAGATACGGGGGTTATTTGTTTCTTGAGGAATCATGAACTCTGAATACTGTG--------CCCAGGGGCATTCTGAAGATCTCATTAGAA\n+>panTro1.chrX_132770072_132770321\n+ctcctgcaccatgcctgcctggatactcccatactcccaacttgatgataatggactgaacctttgaacctgtaagccagccccaattaaatgttgtccttataagagttgccttggtcatggtgtctgttcacagcagtaaaatcctaactaagacaGGAC----------ATATGGGTTTTATCTGCTTCTTGGGGAATCATGAACTCTGAACATTGTGCTAATATACCTAGGGCCAttctgaagatcatattagaa\n+\n+>hg17.chrX_3049300_3049850\n+GGTTTTGTTAGATATTCTTTCAGATTAAAACATTCCATCCTAGAAGGAGGAAGAGGGTTTATAAAACTCAAGGACTATCACAATTTAA--GACTAATGAAACTCTGGGAA-TTCACAAAAGTCACATGGCCATCCCCAATGTTCTACAAGTAGTGAACAATTGCAGGCAGGAGTG-AGGGGTTTCCTTCAGTGGGGATTCCTGAAAGTTGGTCAGAGAGCTCTAGGGACGTAGTTTTCATTAATCATTATCAACACTGAGTAAGGCTTTCTGGTAATGGAGCTGACATTGAAtcatctgtgttcctttcagtgacctcaataaactcattggttcactaagctaaaatcaggtgCAATGATGTTGGCTTTGTTTCACTC--------------------------------------------AACGTCCTACTTGGAGTAAACATATACTTGTTCATATATTTTCAGGAAAATTTACACAACAGAAGGTAGAAACTTCTAAACAAAAGAATATTTCTCTTTGTTAGTTTAGTCTACTCACTCTATATGGAAAATAAGGATGGAAAAGAACACCACCACCCCCTACAttaatttgggc\n+>panTro1.chr15_879491_880081\n+GTTTTTCTTAGGTGTTCCTTCAGATTAAAATATTCCATG-TGGAAGGAGGAAAAAGGTTTATAAATCTCAAGGACTATCTCAATTTAAAAGACTCATGAAACTCTGAAAACTTAACAAAAATCACATAGCCTCCCCCAATATTACATAAGTAGTGAACAATTGTGGGCAGGAGTGAAGGGGTTTCCTTCAGTGTGGGTTTTtgcaagttgggcagagagttctagggaatcaattttcataaatcagcatcagcattggggcaagctttctgttaatggagctgatg-tgagtcatccgtgttcctttcaatgacctcaacaaactcattggttctccaagctaaaatcaggtgctatggtgtagtctttgtttcactctgattaattaattaattaattaattaattaatcaagtaattgttaatgtcctacttg--gtaaacatacgtttatctaactattttcaggaaaattcacacaacaGAAGGTCGAAACTTCTAAACAAAAGAGTATTTCTCTTTGTTAGTTGAGTCTA--CACTCGATAGGGAAA--AATGAAGGAAAAGAAATCCCCCATTAAGTAAACTCACTTAGAC\n+\n+>hg17.chrX_3054999_3055956\n+CATCTGTCTAAGATGt---aattatatattttattaataa---ttatattaGCCTAGTTGTTAAACAAG----TTAAGTGTTTCTAATgtgatcctatttaaatataataag-------------cttaactgcataaatgccaaaaatatctccttctctcactcaaggtaaaggcaaaattcacctgtagagtttgtaacctgcagagctttgagctttctgactccactatgacttctagaaaatcacct--cacagttctctgcctccctccatcagttccagccatgcctctatcccagctgcttctcctcatgcatgcaaggtcttctctgacaactgagcctcagcaactgtcatcactttagctggaatgcatatttctcTTGACTGCTGCTGGAGGCCACAGTCTACCTGCATGT-----------------------------------------TTTCATTCCACACCCAAAGGTTCCTTGATAACTTTCCTGGCTATTCTGACTCTCTGAAAAGAATGCTCACCCTGGAATTTCATTTCCTTGAAGCTAGGCCTTGTCATGCTCCCTCTTATCACTTACCAATATGAAAATATTTCATACTGACTTAATAGCTACATGGCTATATGGCTCAtttcccagactaggatgagaactccatgaggataagatctgttcatttgctgcctctggtccttgcagtgtccaaaacactgcactgCAGAGACCACTCACAGTGTTTATGGGACATAGGTAAAACAAATGAACTGAGTGATAATCCATGGGATTGAGCATGTAAAATTACACAGGCATGCCTGGGTCTAGCCATATAGCTACCTACTAATGCACTTCCCACCAGGATCTAGGCTTGCAGGGCACGGTGAAATAGGGCAACTGGAGGCATGGCCAAGAGAAATCTTTCCAAGGTTGAAAT------GACTTTTCCATATACCAGGGTGATTTTATCCTTTTTTTAGAATGTGAGGCCTATTCCAAAGCCATTACATGATATGAACt\n+>panTro1.chrX_27929766_27930764\n+CACCTACTTACAATGTGGAATTTATATATTTGATTTTCATGCTCCAAATT--CCAAGATTTTTGAGAAGATTTTCAGGAGTTGCTGcagtgtgcctgttaaaatatgacaaaaactatgagatgcttcaactttaaaagcactaa---catgtccccctctcactcaaggtaaaagcaaaattcctctgtagaagttttaacctgcagggctttgggctctctgacacccctgtgacttctgagaaatcacttttcacaattttctaccacccttcatcatatccagccatgccttcatcccagctgcttctcctcatgcatgccaggtcttctctggc---------ccagcaattgtcatcacataagctggaatgcacattccccTTGACTGCTGTTGGAtctctctctctctctctctctctctctctctctctctctctctctctctctctctctcCTTGTTCCATTCTAAACCTAGAGCTTCCTTGATACCTTTCCTGACCATTGTAACTCTCTGAAAAGAATGCTGGCCCTGAAATTTCATTTTCTTGAACCTAGACTTGGT-GTGTCCCCTCTTATCACTTACCAATATGAAAATGCTTCAGATAGGCTTATTAGCTACAGGAATATATTGCTCATTTCCCACACTAGGAGGAGAACTCCAAAGGGATACGATCTGTCCATTTGCTGCCTCTGCTGACTGCAGTATATAGAACACTGCATGGC----------CAGAGTGTTTATGTGACAAAGGTAAAACAAATCAATTGGGTGAGAATCTGTGGAATCAAGCATGTAAAGTGAGACAAGTATCCCTGGGTCTAGCCATAATGCTATA----AATGCACTTCCTAACAGGGTATGAGCTTGAAGGGCAGGGTAAAGCAGGGCAACTGGAGGCATGCTCAACAGAAACCTTTCCAAGGTTGAAATGTGATGGCCTCTTCCTTACACCATGGTGCTTGTATCC--TTGTTGGAATGTGGGTCCTGTTCAAATGCCTTTACATGATATGAACT\n+\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/beam_output1.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/beam_output1.tab Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,2 @@
+ID chr position results
+rs0 chr1 738547 10 20 score= 45.101397 , df= 8 , p= 0.000431 , N=1225

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/beam_output2.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/beam_output2.tab Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,103 @@
+id: chr position marginal + interaction = total posterior
+0: 1 738547 0.0000 + 0.0000 = 0.0000
+1: 1 5597094 0.0000 + 0.0000 = 0.0000
+2: 1 9424115 0.0000 + 0.0000 = 0.0000
+3: 1 13879818 0.0000 + 0.0000 = 0.0000
+4: 1 13934751 0.0000 + 0.0000 = 0.0000
+5: 1 16803491 0.0000 + 0.0000 = 0.0000
+6: 1 17236854 0.0000 + 0.0000 = 0.0000
+7: 1 18445387 0.0000 + 0.0000 = 0.0000
+8: 1 21222571 0.0000 + 0.0000 = 0.0000
+9: 1 24988555 0.0000 + 0.0000 = 0.0000
+10: 1 29047517 0.1200 + 0.0000 = 0.1200
+11: 1 39100314 0.0000 + 0.0000 = 0.0000
+12: 1 43177587 0.0000 + 0.0000 = 0.0000
+13: 1 48982207 0.0200 + 0.0000 = 0.0200
+14: 1 54316843 0.0000 + 0.0000 = 0.0000
+15: 1 62764366 0.0000 + 0.0000 = 0.0000
+16: 1 68056276 0.0000 + 0.0000 = 0.0000
+17: 1 71657460 0.0000 + 0.0000 = 0.0000
+18: 1 83962523 0.0000 + 0.0000 = 0.0000
+19: 1 84078493 0.0000 + 0.0000 = 0.0000
+20: 1 85518967 0.0550 + 0.0000 = 0.0550
+21: 1 89040803 0.0000 + 0.0000 = 0.0000
+22: 1 90237128 0.0000 + 0.0000 = 0.0000
+23: 1 94936979 0.0000 + 0.0000 = 0.0000
+24: 1 97915585 0.0450 + 0.0000 = 0.0450
+25: 1 104312265 0.0000 + 0.0000 = 0.0000
+26: 1 108987701 0.0000 + 0.0000 = 0.0000
+27: 1 112558366 0.0000 + 0.0000 = 0.0000
+28: 1 116025269 0.0000 + 0.0000 = 0.0000
+29: 1 120010986 0.0000 + 0.0000 = 0.0000
+30: 1 121353801 0.0000 + 0.0000 = 0.0000
+31: 1 125064851 0.0000 + 0.0000 = 0.0000
+32: 1 125803399 0.0000 + 0.0000 = 0.0000
+33: 1 125998718 0.0000 + 0.0000 = 0.0000
+34: 1 133890804 0.0000 + 0.0000 = 0.0000
+35: 1 136606952 0.0000 + 0.0000 = 0.0000
+36: 1 137748344 0.0100 + 0.0000 = 0.0100
+37: 1 173015533 0.0000 + 0.0000 = 0.0000
+38: 1 174492629 0.0000 + 0.0000 = 0.0000
+39: 1 181023590 0.0050 + 0.0000 = 0.0050
+40: 1 183428449 0.0000 + 0.0000 = 0.0000
+41: 1 186040833 0.0000 + 0.0000 = 0.0000
+42: 2 1861629 0.0000 + 0.0000 = 0.0000
+43: 2 7306131 0.0000 + 0.0000 = 0.0000
+44: 2 14423047 0.0000 + 0.0000 = 0.0000
+45: 2 19837031 0.0250 + 0.0000 = 0.0250
+46: 2 22309030 0.0000 + 0.0000 = 0.0000
+47: 2 34730063 0.0000 + 0.0000 = 0.0000
+48: 2 42219306 0.0100 + 0.0000 = 0.0100
+49: 2 46150090 0.0000 + 0.0000 = 0.0000
+
+id: chr position block_boundary | allele counts in cases and controls
+0: 1 738547 1.000 | 157 93 250 | 167 83 250
+1: 1 5597094 1.000 | 157 18 325 | 157 17 326
+2: 1 9424115 1.000 | 127 6 367 | 121 11 368
+3: 1 13879818 1.000 | 217 31 252 | 190 32 278
+4: 1 13934751 1.000 | 190 65 245 | 218 57 225
+5: 1 16803491 1.000 | 247 161 92 | 237 174 89
+6: 1 17236854 1.000 | 204 42 254 | 208 45 247
+7: 1 18445387 1.000 | 204 67 229 | 217 55 228
+8: 1 21222571 1.000 | 356 9 135 | 348 8 144
+9: 1 24988555 1.000 | 79 2 419 | 77 4 419
+10: 1 29047517 1.000 | 365 15 120 | 409 9 82
+11: 1 39100314 1.000 | 243 50 207 | 225 48 227
+12: 1 43177587 1.000 | 28 283 189 | 41 276 183
+13: 1 48982207 1.000 | 243 83 174 | 231 58 211
+14: 1 54316843 1.000 | 158 17 325 | 151 25 324
+15: 1 62764366 1.000 | 115 377 8 | 99 392 9
+16: 1 68056276 1.000 | 245 84 171 | 249 84 167
+17: 1 71657460 1.000 | 243 49 208 | 228 57 215
+18: 1 83962523 1.000 | 101 392 7 | 104 386 10
+19: 1 84078493 1.000 | 239 180 81 | 240 177 83
+20: 1 85518967 1.000 | 142 7 351 | 99 12 389
+21: 1 89040803 1.000 | 79 176 245 | 76 172 252
+22: 1 90237128 1.000 | 255 167 78 | 231 186 83
+23: 1 94936979 1.000 | 279 33 188 | 272 40 188
+24: 1 97915585 1.000 | 62 7 431 | 86 1 413
+25: 1 104312265 1.000 | 308 22 170 | 293 28 179
+26: 1 108987701 1.000 | 137 351 12 | 135 352 13
+27: 1 112558366 1.000 | 261 173 66 | 241 193 66
+28: 1 116025269 1.000 | 68 201 231 | 79 185 236
+29: 1 120010986 1.000 | 242 138 120 | 271 122 107
+30: 1 121353801 1.000 | 373 12 115 | 390 9 101
+31: 1 125064851 1.000 | 128 14 358 | 128 8 364
+32: 1 125803399 1.000 | 165 310 25 | 165 320 15
+33: 1 125998718 1.000 | 206 247 47 | 226 225 49
+34: 1 133890804 1.000 | 150 96 254 | 168 98 234
+35: 1 136606952 1.000 | 125 369 6 | 139 353 8
+36: 1 137748344 1.000 | 154 86 260 | 163 110 227
+37: 1 173015533 1.000 | 67 186 247 | 93 181 226
+38: 1 174492629 1.000 | 125 7 368 | 121 9 370
+39: 1 181023590 1.000 | 258 119 123 | 236 118 146
+40: 1 183428449 1.000 | 229 63 208 | 247 64 189
+41: 1 186040833 1.000 | 95 154 251 | 97 139 264
+42: 2 1861629 1.000 | 135 109 256 | 129 119 252
+43: 2 7306131 1.000 | 67 195 238 | 66 206 228
+44: 2 14423047 1.000 | 58 235 207 | 62 250 188
+45: 2 19837031 1.000 | 214 263 23 | 201 254 45
+46: 2 22309030 1.000 | 125 17 358 | 144 9 347
+47: 2 34730063 1.000 | 238 125 137 | 229 116 155
+48: 2 42219306 1.000 | 211 41 248 | 200 59 241
+49: 2 46150090 1.000 | 182 286 32 | 173 299 28

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/bed2gff_out.gff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/bed2gff_out.gff Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,13 @@
+##gff-version 2
+##bed_to_gff_converter.py
+
+chr28 bed2gff mRNA 346188 388197 0 + . mRNA BC114771;
+chr28 bed2gff exon 346188 346331 0 + . exon BC114771;
+chr28 bed2gff exon 370283 370363 0 + . exon BC114771;
+chr28 bed2gff exon 372378 372492 0 + . exon BC114771;
+chr28 bed2gff exon 377194 377256 0 + . exon BC114771;
+chr28 bed2gff exon 378319 378473 0 + . exon BC114771;
+chr28 bed2gff exon 379722 379817 0 + . exon BC114771;
+chr28 bed2gff exon 383182 383315 0 + . exon BC114771;
+chr28 bed2gff exon 387981 388085 0 + . exon BC114771;
+chr28 bed2gff exon 388086 388197 0 + . exon BC114771;

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/bfast_out1.sam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/bfast_out1.sam Sat Feb 21 16:33:42 2015 +0100

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/bfast_out2.sam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/bfast_out2.sam Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,23 @@
+@HD VN:0.1.2 SO:unsorted GO:none
+@SQ SN:phiX174 LN:5386
+@PG ID:bfast VN:0.6.4d
+random_phiX_region_0 0 phiX174 553 255 50M * 0 0 TTGAGGCTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTT """""""""""""""""""""""""""""""""""""""""""""""""` PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 CS:Z:G10122032013310033101313321021200111002331002233200 CQ:Z:~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CM:i:0 XA:i:0 XE:Z:--------------------------------------------------
+random_phiX_region_1 0 phiX174 3693 255 50M * 0 0 GTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTA """""""""""""""""""""""""""""""""""""""""""""""""` PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 CS:Z:G01032113212201012120321021321231001331220321233013 CQ:Z:~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CM:i:0 XA:i:0 XE:Z:--------------------------------------------------
+random_phiX_region_2 0 phiX174 375 255 50M * 0 0 AATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTTTCCA """""""""""""""""""""""""""""""""""""""""""""""""` PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 CS:Z:G20332013022003213122121021031212011032031313100201 CQ:Z:~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CM:i:0 XA:i:0 XE:Z:--------------------------------------------------
+random_phiX_region_3 0 phiX174 3168 255 50M * 0 0 GGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTC """""""""""""""""""""""""""""""""""""""""""""""""` PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 CS:Z:G00130020212022012020131310131203210311202213031002 CQ:Z:~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CM:i:0 XA:i:0 XE:Z:--------------------------------------------------
+random_phiX_region_4 0 phiX174 5254 255 50M * 0 0 ACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGAC """""""""""""""""""""""""""""""""""""""""""""""""` PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 CS:Z:G21331000022222231222301220321002000210312113230321 CQ:Z:~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CM:i:0 XA:i:0 XE:Z:--------------------------------------------------
+random_phiX_region_5 0 phiX174 5066 255 50M * 0 0 AGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACTTCCCA """""""""""""""""""""""""""""""""""""""""""""""""` PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 CS:Z:G22323002203102011012211230000101023211233231202001 CQ:Z:~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CM:i:0 XA:i:0 XE:Z:--------------------------------------------------
+random_phiX_region_6 0 phiX174 1226 255 50M * 0 0 CACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGTGTTAATGC """""""""""""""""""""""""""""""""""""""""""""""""` PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 CS:Z:G31131003310112011211023030210213120202310111030313 CQ:Z:~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CM:i:0 XA:i:0 XE:Z:--------------------------------------------------
+random_phiX_region_7 0 phiX174 1096 255 50M * 0 0 AACTACTCCGGTTATCGCTGGCGACTCCTTCGAGATGGACGCCGTTGGCG """""""""""""""""""""""""""""""""""""""""""""""""` PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 CS:Z:G20123122030103323321033212202023222310213303101033 CQ:Z:~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CM:i:0 XA:i:0 XE:Z:--------------------------------------------------
+random_phiX_region_8 0 phiX174 535 255 50M * 0 0 CTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTATGGTACGCTGGACTTT """""""""""""""""""""""""""""""""""""""""""""""""` PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 CS:Z:G32231132231233213310122032013310033101313321021200 CQ:Z:~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CM:i:0 XA:i:0 XE:Z:--------------------------------------------------
+random_phiX_region_9 0 phiX174 3669 255 50M * 0 0 CAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGACTTAGTTCA """""""""""""""""""""""""""""""""""""""""""""""""` PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 CS:Z:G31003210022003121223310201032113212201012120321021 CQ:Z:~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CM:i:0 XA:i:0 XE:Z:--------------------------------------------------
+random_phiX_region_10 0 phiX174 4887 255 50M * 0 0 TACAGTATGCCCATCGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTC """""""""""""""""""""""""""""""""""""""""""""""""` PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 CS:Z:G13112133130013233121023323111331202133200002113102 CQ:Z:~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CM:i:0 XA:i:0 XE:Z:--------------------------------------------------
+random_phiX_region_11 0 phiX174 1849 255 50M * 0 0 TATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGA """""""""""""""""""""""""""""""""""""""""""""""""` PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 CS:Z:G13311003122201333201102310002033023121332123002222 CQ:Z:~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CM:i:0 XA:i:0 XE:Z:--------------------------------------------------
+random_phiX_region_12 0 phiX174 4145 255 50M * 0 0 AGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATA """""""""""""""""""""""""""""""""""""""""""""""""` PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 CS:Z:G22222302211220002313313120033101221023233031011233 CQ:Z:~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CM:i:0 XA:i:0 XE:Z:--------------------------------------------------
+random_phiX_region_13 0 phiX174 1853 255 50M * 0 0 TTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCA """""""""""""""""""""""""""""""""""""""""""""""""` PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 CS:Z:G10031222013332011023100020330231213321230022223021 CQ:Z:~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CM:i:0 XA:i:0 XE:Z:--------------------------------------------------
+random_phiX_region_14 0 phiX174 2800 255 50M * 0 0 CCGGGCAATAACGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGC """""""""""""""""""""""""""""""""""""""""""""""""` PG:Z:bfast AS:i:2300 NM:i:1 NH:i:1 IH:i:1 HI:i:1 MD:Z:11T38 CS:Z:G30300310330131003311010100213101001012230120031033 CQ:Z:~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CM:i:0 XA:i:0 XE:Z:--------------------------------------------------
+random_phiX_region_15 0 phiX174 1910 255 50M * 0 0 AACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTT """""""""""""""""""""""""""""""""""""""""""""""""` PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 CS:Z:G20133230020113200121203331032333013210332100211000 CQ:Z:~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CM:i:0 XA:i:0 XE:Z:--------------------------------------------------
+random_phiX_region_16 0 phiX174 3366 255 50M * 0 0 GCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCA """""""""""""""""""""""""""""""""""""""""""""""""` PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 CS:Z:G03030230012220321000022232031230003131012102110321 CQ:Z:~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CM:i:0 XA:i:0 XE:Z:--------------------------------------------------
+random_phiX_region_17 0 phiX174 2165 255 50M * 0 0 CATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAG """""""""""""""""""""""""""""""""""""""""""""""""` PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 CS:Z:G31312303312101211100201212031021210110131211020332 CQ:Z:~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CM:i:0 XA:i:0 XE:Z:--------------------------------------------------
+random_phiX_region_18 0 phiX174 2051 255 50M * 0 0 TGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA """""""""""""""""""""""""""""""""""""""""""""""""` PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 CS:Z:G11013323103313330202313311002220213203321102022012 CQ:Z:~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CM:i:0 XA:i:0 XE:Z:--------------------------------------------------
+random_phiX_region_19 0 phiX174 5099 255 50M * 0 0 GCTGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACT """""""""""""""""""""""""""""""""""""""""""""""""` PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 CS:Z:G03211233231202001022023211021220321220312230331012 CQ:Z:~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CM:i:0 XA:i:0 XE:Z:--------------------------------------------------

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/bfast_out3.sam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/bfast_out3.sam Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,23 @@
+@HD VN:0.1.2 SO:unsorted GO:none
+@SQ SN:phiX LN:5386
+@PG ID:bfast VN:0.6.4d
+random_phiX_region_0 0 phiX 553 255 50M * 0 0 TTGAGGCTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTT ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0
+random_phiX_region_1 0 phiX 3693 255 50M * 0 0 GTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0
+random_phiX_region_2 0 phiX 375 255 50M * 0 0 AATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTTTCCA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0
+random_phiX_region_3 0 phiX 3168 255 50M * 0 0 GGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTC ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0
+random_phiX_region_4 0 phiX 5254 255 50M * 0 0 ACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGAC ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0
+random_phiX_region_5 0 phiX 5066 255 50M * 0 0 AGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACTTCCCA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0
+random_phiX_region_6 0 phiX 1226 255 50M * 0 0 CACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGTGTTAATGC ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0
+random_phiX_region_7 0 phiX 1096 255 50M * 0 0 AACTACTCCGGTTATCGCTGGCGACTCCTTCGAGATGGACGCCGTTGGCG ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0
+random_phiX_region_8 0 phiX 535 255 50M * 0 0 CTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTATGGTACGCTGGACTTT ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0
+random_phiX_region_9 0 phiX 3669 255 50M * 0 0 CAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGACTTAGTTCA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0
+random_phiX_region_10 0 phiX 4887 255 50M * 0 0 TACAGTATGCCCATCGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTC ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0
+random_phiX_region_11 0 phiX 1849 255 50M * 0 0 TATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0
+random_phiX_region_12 0 phiX 4145 255 50M * 0 0 AGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0
+random_phiX_region_13 0 phiX 1853 255 50M * 0 0 TTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0
+random_phiX_region_14 0 phiX 2800 255 50M * 0 0 CCGGGCAATAACGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGC ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2300 NM:i:1 NH:i:1 IH:i:1 HI:i:1 MD:Z:11T38 XA:i:0
+random_phiX_region_15 0 phiX 1910 255 50M * 0 0 AACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTT ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0
+random_phiX_region_16 0 phiX 3366 255 50M * 0 0 GCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0
+random_phiX_region_17 0 phiX 2165 255 50M * 0 0 CATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAG ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0
+random_phiX_region_18 0 phiX 2051 255 50M * 0 0 TGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0
+random_phiX_region_19 0 phiX 5099 255 50M * 0 0 GCTGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACT ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/blat_wrapper_test1.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/blat_wrapper_test1.fa Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,200 @@
+>0_0.666667
+CGGACAGCGCCGCCACCAACAAAGCCACCA
+>1_0.600000
+AAAACACCGGATGCTCCGGCGCTGGCAGAT
+>2_0.400000
+TTTGCTTTTAGTACACCGGATTCAGAACCA
+>3_0.566667
+CCGTCCCCATGAATACACCTTTCTGGACGG
+>4_0.766667
+CACGCTACGTGCGCCCCCGCCCAGAAGGCG
+>5_0.533333
+AAACAAAACCCGCCGAAGCGGGTTAAGTGC
+>6_0.533333
+TAAGCCGTTACTGGCAGCAAGTGCAGGCAA
+>7_0.400000
+TGAATTTACCGTTATCTATCTTGCCTGCCT
+>8_0.500000
+TTAGCGGGAATAAAACAGGCTGTCAGCCAG
+>9_0.400000
+GCGTTTTGCTAAACTTCTGCCGGAATATAA
+>10_0.500000
+AAAGAGGCGAGCAGAGTAAAACGCAGGCAA
+>11_0.533333
+CAAAAGCAGAGTCTGTTGACCCATACGCGC
+>12_0.700000
+GCGGACGATCTTCACGGTCGCCACGCGGAC
+>13_0.533333
+TTCTTGTTGGATGGCATACTCCGGCAGCCA
+>14_0.666667
+ACCCCGATATCGTCGCAGGCGTTGCCGCAC
+>15_0.666667
+GGCTGCTGTCTCCGCTGGAAGAGGCGCTTC
+>16_0.566667
+ATGTCCTGATCGAGCGGCGTTTTACCGACC
+>17_0.533333
+GGTGTTGAGTGTCCAGGTAATACGCTCTCG
+>18_0.566667
+GTGGTCTCAAGCCCAAAGGAAGAGTGAGGC
+>19_0.566667
+GTTGTAAGCGTCAGAACCGATGCGGTCGGT
+>20_0.566667
+CGACATCCTGTAGGCTGGCTTCAATGCGAC
+>21_0.733333
+GGGAAGGCTGACGGGCGTCCACACCACGGC
+>22_0.566667
+CGGTATTCCTCAGTTCTCGCTGCATGCCTG
+>23_0.600000
+TTGCCGTTACGCACCACGCCTTCAGTAGCG
+>24_0.733333
+CGCGGGCGCACCACGTCGCTGCTGCTGTTC
+>25_0.266667
+TTTTGGGAAAACTAAATACGCATCAAAAAT
+>26_0.566667
+CAACGAGGCGCTACCGAGTTGTTCAATGCG
+>27_0.600000
+TTACCGAGGCCAGAACCGATACCACGACCC
+>28_0.666667
+CGCTCAATCTGCTCGCGCCTGGCTGGCGTT
+>29_0.700000
+CTCGTCCGGCGGGCGGTTTTGCCGACAAGG
+>30_0.233333
+GGAAATTGTACAATAGAAAAATTACTGTAT
+>31_0.533333
+GTGCTGAACTGTTCCACGACCATGGAGATG
+>32_0.600000
+TGAGGATGGTCCTCTGACTCTGCAGGCGCA
+>33_0.300000
+TAGTAACCCTTTAATAAGATTGTCGATTAG
+>34_0.533333
+TGATGTTAAATGCATGGCACCTGCCGGTGC
+>35_0.466667
+ACTGCTTTGCCGAGATATTCGAGGTTAACC
+>36_0.433333
+TGTTGGCAACATGGCGAGCGTAATCAATTA
+>37_0.366667
+ACTTCGTCAGTAAGGATGAGATTAGCAAAT
+>38_0.533333
+GCAGCAGGATCGGATCGAACTCTGGTTTCT
+>39_0.400000
+TAATGCGGCATTCTCCTGATTTATTGTCAC
+>40_0.400000
+AGCGTAATGATAATCGCTATCACTGCGATT
+>41_0.566667
+AGCTGACGGTCAGCAGGGATACTTCCTGCA
+>42_0.566667
+GCAGTGACTACATCCGCGAGGTGAATGTGG
+>43_0.466667
+GCTTTTTCCAGCATCAACGCCACTGAACAA
+>44_0.433333
+AAAGTGGTAGATAACGTGGTGCAGACTATG
+>45_0.500000
+TTCCTGATACCGGATGACCTTATCGCGGAT
+>46_0.466667
+ACCTGTACCCCAGGACCATGGTACATTTAT
+>47_0.533333
+ACAATGCAACCAGACCAGCCCGGATCGATA
+>48_0.500000
+GGGTAACCAGCTGATGATGGCCATTAACCT
+>49_0.433333
+CGTTATACGGAACAACATTTAACTCCAGCG
+>50_0.466667
+TTGCTGTTGCCATCGCTTTTCAGGACATAC
+>51_0.533333
+CGACGGTATCGGTACGCAGATTGTGATGGA
+>52_0.366667
+ATGAGCATCAACATCGAAATCTCAAACCAA
+>53_0.533333
+CCAGGCACTCCGCCATATTTTTGCCATGAC
+>54_0.400000
+GTATTCTTCATTGATTTGTAAGCGGGTACC
+>55_0.466667
+AAGCGCTGTTCAACATAAATTGGCTGACGG
+>56_0.433333
+AACCGTCAGCTCTTTACGCAATATTTTGCC
+>57_0.566667
+CGCGAAATCCTCGACGTCCAGGCACGTATT
+>58_0.300000
+GTTATCCATTAAAATAGATCGGATCGATAT
+>59_0.300000
+AAAATCTGCATATCATGATAAGAGTGGTTA
+>60_0.533333
+AATCTGGCGAATGCTGATAGCGTGACCGGT
+>61_0.366667
+TCAGTTTGAAAGCTTTGTCAGCCGTTTTTT
+>62_0.366667
+AATCCTAAACCTAGGAATGCCAGAATATCT
+>63_0.566667
+TCACGCTCGCAGTCAAGCTGGCTTATGCCA
+>64_0.500000
+GAGATGACGGTTGCAGAGTCATGCGTTTGA
+>65_0.533333
+TCTGGATCACGCGCAAACACTGGCTATCGT
+>66_0.466667
+TCTGCTTTAGCAAACAGAGTGTGGTCACGA
+>67_0.400000
+GCCTTTTGTCTGATCATCCACAATAATGAC
+>68_0.566667
+GAAGGATAGTTGGTCAGCAACACCAGCGGC
+>69_0.733333
+GGCGCGCTGTCGGCCACGGCGAAATCGACC
+>70_0.466667
+TGGTGTTCAGCATCTCAACGGTAATTCGCT
+>71_0.533333
+CAGGATGCAAACTGCCGGGAGATCCAGTTA
+>72_0.533333
+AACTGGAAGGGCTTGGGATGACACAACAGC
+>73_0.500000
+TTTAAGCGCCAACCAGGCTTCTTTGGTTGC
+>74_0.433333
+ACCCTTCTTTCGCCATATCAAACTGATGTC
+>75_0.533333
+ATAACCCTCTGCAACCGCCGCTTCAGCAAA
+>76_0.600000
+TGAAGCCGTACAACGGGCGCTGGAATTCGC
+>77_0.700000
+GAGCTGCAACGCGGTCAGCCAGCTGGCGGT
+>78_0.566667
+CGGAGTATCCGTTCCCCAACGACAAGCATC
+>79_0.500000
+AATACCGGGAAGAGACAACGGGGTCTCTTT
+>80_0.500000
+TAATGACAGGGTTGCGAAGCCCTGATTCTC
+>81_0.433333
+ATTAATGTTGCCGGCACAACATAATAGGGC
+>82_0.500000
+ACTGGGTTGCTCTGAACAAGAAAGGCGCTA
+>83_0.533333
+CGCCAGGGACGTATCGCGTCGATATCTATT
+>84_0.533333
+TGCTCGTTCCCGTCGTGATGAAGCTCGAAA
+>85_0.500000
+AGGAAAGCAAACAACACGACCACCATCAGC
+>86_0.566667
+GGCAACGCAGGCGCATGATTCTGCTTGGAA
+>87_0.433333
+CGCTGGATGAAAANCGTGAATATCACACCA
+>88_0.533333
+CGTACCGGGCTGAAAGTAGAAGAGCGTTTC
+>89_0.466667
+ATTAAAAAACAGGCGGTGCGTTTTCCCTGG
+>90_0.466667
+ATCACCGTTTCGCTAACCGGTACGTTTAAC
+>91_0.566667
+TTCGCCCGGCAAGCTTACCCAACGCTTATC
+>92_0.533333
+TTTTCCCCGCCGTTAGTAGCGACTGCAGTT
+>93_0.400000
+TTATTTGCCCGATGAGTCAGTTTATTGCAG
+>94_0.466667
+CCACGGTGATATCTGGTGCCATACTGATAA
+>95_0.466667
+TCCCCCGTAAGGCCTTTCTTTTTCTTTCGT
+>96_0.533333
+TTGCCGGGAAGAGAGATATCAATGGCAGGC
+>97_0.566667
+TGCGCCGCCGGATTGTTGCTCAACATGCTT
+>98_0.366667
+AACGCGCTAACCGCCAATAATAACAAAATT
+>99_0.366667
+TAAGAGTTTATTCATGATGTCATCCTGCGA

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/blat_wrapper_test1.out
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/blat_wrapper_test1.out Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,64 @@\n+30\t0\t0\t0\t0\t0\t0\t0\t+\t0_0.666667\t30\t0\t30\tchr\t4639675\t4549207\t4549237\t1\t30,\t0,\t4549207,\tcggacagcgccgccaccaacaaagccacca,\tcggacagcgccgccaccaacaaagccacca,\n+30\t0\t0\t0\t0\t0\t0\t0\t+\t1_0.600000\t30\t0\t30\tchr\t4639675\t614777\t614807\t1\t30,\t0,\t614777,\taaaacaccggatgctccggcgctggcagat,\taaaacaccggatgctccggcgctggcagat,\n+28\t1\t0\t0\t0\t0\t0\t0\t+\t2_0.400000\t30\t0\t29\tchr\t4639675\t3289283\t3289312\t1\t29,\t0,\t3289283,\ttttgcttttagtacaccggattcagaacc,\ttttgctttcagtacaccggattcagaacc,\n+30\t0\t0\t0\t0\t0\t0\t0\t+\t4_0.766667\t30\t0\t30\tchr\t4639675\t2665584\t2665614\t1\t30,\t0,\t2665584,\tcacgctacgtgcgcccccgcccagaaggcg,\tcacgctacgtgcgcccccgcccagaaggcg,\n+20\t0\t0\t0\t0\t0\t0\t0\t+\t5_0.533333\t30\t4\t24\tchr\t4639675\t3375780\t3375800\t1\t20,\t4,\t3375780,\taaaacccgccgaagcgggtt,\taaaacccgccgaagcgggtt,\n+30\t0\t0\t0\t0\t0\t0\t0\t+\t6_0.533333\t30\t0\t30\tchr\t4639675\t965481\t965511\t1\t30,\t0,\t965481,\ttaagccgttactggcagcaagtgcaggcaa,\ttaagccgttactggcagcaagtgcaggcaa,\n+30\t0\t0\t0\t0\t0\t0\t0\t+\t7_0.400000\t30\t0\t30\tchr\t4639675\t1781311\t1781341\t1\t30,\t0,\t1781311,\ttgaatttaccgttatctatcttgcctgcct,\ttgaatttaccgttatctatcttgcctgcct,\n+29\t1\t0\t0\t0\t0\t0\t0\t+\t9_0.400000\t30\t0\t30\tchr\t4639675\t4400977\t4401007\t1\t30,\t0,\t4400977,\tgcgttttgctaaacttctgccggaatataa,\tgcgctttgctaaacttctgccggaatataa,\n+30\t0\t0\t0\t0\t0\t0\t0\t+\t11_0.533333\t30\t0\t30\tchr\t4639675\t3923551\t3923581\t1\t30,\t0,\t3923551,\tcaaaagcagagtctgttgacccatacgcgc,\tcaaaagcagagtctgttgacccatacgcgc,\n+28\t2\t0\t0\t0\t0\t0\t0\t+\t12_0.700000\t30\t0\t30\tchr\t4639675\t3304453\t3304483\t1\t30,\t0,\t3304453,\tgcggacgatcttcacggtcgccacgcggac,\tgcggacgatcttcacggtcaccacgcgggc,\n+29\t1\t0\t0\t0\t0\t0\t0\t+\t13_0.533333\t30\t0\t30\tchr\t4639675\t4555547\t4555577\t1\t30,\t0,\t4555547,\tttcttgttggatggcatactccggcagcca,\tttcttgttggatggcgtactccggcagcca,\n+30\t0\t0\t0\t0\t0\t0\t0\t+\t14_0.666667\t30\t0\t30\tchr\t4639675\t3811672\t3811702\t1\t30,\t0,\t3811672,\taccccgatatcgtcgcaggcgttgccgcac,\taccccgatatcgtcgcaggcgttgccgcac,\n+29\t1\t0\t0\t0\t0\t0\t0\t+\t16_0.566667\t30\t0\t30\tchr\t4639675\t1916143\t1916173\t1\t30,\t0,\t1916143,\tatgtcctgatcgagcggcgttttaccgacc,\tatgtcctgatcgagcggcgttttaccgatc,\n+30\t0\t0\t0\t0\t0\t0\t0\t+\t18_0.566667\t30\t0\t30\tchr\t4639675\t1860631\t1860661\t1\t30,\t0,\t1860631,\tgtggtctcaagcccaaaggaagagtgaggc,\tgtggtctcaagcccaaaggaagagtgaggc,\n+30\t0\t0\t0\t0\t0\t0\t0\t+\t19_0.566667\t30\t0\t30\tchr\t4639675\t1018466\t1018496\t1\t30,\t0,\t1018466,\tgttgtaagcgtcagaaccgatgcggtcggt,\tgttgtaagcgtcagaaccgatgcggtcggt,\n+30\t0\t0\t0\t0\t0\t0\t0\t+\t22_0.566667\t30\t0\t30\tchr\t4639675\t2006716\t2006746\t1\t30,\t0,\t2006716,\tcggtattcctcagttctcgctgcatgcctg,\tcggtattcctcagttctcgctgcatgcctg,\n+30\t0\t0\t0\t0\t0\t0\t0\t-\t23_0.600000\t30\t0\t30\tchr\t4639675\t4516584\t4516614\t1\t30,\t0,\t4516584,\tcgctactgaaggcgtggtgcgtaacggcaa,\tcgctactgaaggcgtggtgcgtaacggcaa,\n+30\t0\t0\t0\t0\t0\t0\t0\t-\t24_0.733333\t30\t0\t30\tchr\t4639675\t1535123\t1535153\t1\t30,\t0,\t1535123,\tgaacagcagcagcgacgtggtgcgcccgcg,\tgaacagcagcagcgacgtggtgcgcccgcg,\n+30\t0\t0\t0\t0\t0\t0\t0\t+\t27_0.600000\t30\t0\t30\tchr\t4639675\t3442475\t3442505\t1\t30,\t0,\t3442475,\tttaccgaggccagaaccgataccacgaccc,\tttaccgaggccagaaccgataccacgaccc,\n+29\t1\t0\t0\t0\t0\t0\t0\t+\t29_0.700000\t30\t0\t30\tchr\t4639675\t2807120\t2807150\t1\t30,\t0,\t2807120,\tctcgtccggcgggcggttttgccgacaagg,\tctcgtccggcgggcggttttgccgataagg,\n+30\t0\t0\t0\t0\t0\t0\t0\t+\t34_0.533333\t30\t0\t30\tchr\t4639675\t421739\t421769\t1\t30,\t0,\t421739,\ttgatgttaaatgcatggcacctgccggtgc,\ttgatgttaaatgcatggcacctgccggtgc,\n+30\t0\t0\t0\t0\t0\t0\t0\t-\t35_0.466667\t30\t0\t30\tchr\t4639675\t1334399\t1334429\t1\t30,\t0,\t1334399,\tggttaacctcgaatatctcggcaaagcagt,\tggttaacctcgaatatctcggcaaagcagt,\n+30\t0\t0\t0\t0\t0\t0\t0\t+\t36_0.433333\t30\t0\t30\tchr\t4639675\t2906502\t2906532\t1\t30,\t0,\t2906502,\ttgttggcaacatggcgagcgtaatcaatta,\ttgttggcaacatggcgagcgtaatcaatta,\n+30\t0\t0\t0\t0\t0\t0\t0\t+\t38_0.533333\t30\t0\t30\tchr\t4639675\t3438288\t3438318\t1\t30,\t0,\t3438288,\tgcagcaggatcggatcgaactctggtttct,\tgcagcaggatcggatcgaactctggtttct,\n+29\t1\t0\t0\t0\t0\t0\t0\t+\t39_0.400000\t30\t0\t30\tchr\t4639675\t2893756\t2893786\t1\t30,\t0,\t2893756,\ttaatgcggcattctcctgatttattgtcac,\ttattgcggcattctcctgatttattgtcac,\n+29\t0\t0\t0\t0\t0\t0\t0\t+\t41_0.566667\t30\t1\t30\tchr\t4639675\t708504\t708533\t1\t29,\t1,\t708504,\tgctgacggtcagcagggatacttcctgca,\tgctgacggtcagcagggatacttcctgca,\n+30\t0\t0\t0\t0\t0\t0\t0\t+\t43_0.466667\t30\t0\t30\tchr\t4639675\t3483475\t3483505\t1\t30,\t0,\t3483475,\tgctttttccagcatcaacgccactgaacaa,\tgctttttc'..b'\tchr\t4639675\t2724848\t2724878\t1\t30,\t0,\t2724848,\ttcacgctcgcagtcaagctggcttatgcca,\ttcacgctcgcagtcaagctggcttatgcca,\n+30\t0\t0\t0\t0\t0\t0\t0\t-\t63_0.566667\t30\t0\t30\tchr\t4639675\t4210393\t4210423\t1\t30,\t0,\t4210393,\ttggcataagccagcttgactgcgagcgtga,\ttggcataagccagcttgactgcgagcgtga,\n+30\t0\t0\t0\t0\t0\t0\t0\t-\t63_0.566667\t30\t0\t30\tchr\t4639675\t3944054\t3944084\t1\t30,\t0,\t3944054,\ttggcataagccagcttgactgcgagcgtga,\ttggcataagccagcttgactgcgagcgtga,\n+29\t1\t0\t0\t0\t0\t0\t0\t+\t64_0.500000\t30\t0\t30\tchr\t4639675\t4553565\t4553595\t1\t30,\t0,\t4553565,\tgagatgacggttgcagagtcatgcgtttga,\tgagatgacggttgcagagtcatacgtttga,\n+30\t0\t0\t0\t0\t0\t0\t0\t+\t65_0.533333\t30\t0\t30\tchr\t4639675\t3154209\t3154239\t1\t30,\t0,\t3154209,\ttctggatcacgcgcaaacactggctatcgt,\ttctggatcacgcgcaaacactggctatcgt,\n+30\t0\t0\t0\t0\t0\t0\t0\t+\t66_0.466667\t30\t0\t30\tchr\t4639675\t3330950\t3330980\t1\t30,\t0,\t3330950,\ttctgctttagcaaacagagtgtggtcacga,\ttctgctttagcaaacagagtgtggtcacga,\n+30\t0\t0\t0\t0\t0\t0\t0\t+\t68_0.566667\t30\t0\t30\tchr\t4639675\t699412\t699442\t1\t30,\t0,\t699412,\tgaaggatagttggtcagcaacaccagcggc,\tgaaggatagttggtcagcaacaccagcggc,\n+30\t0\t0\t0\t0\t0\t0\t0\t+\t69_0.733333\t30\t0\t30\tchr\t4639675\t3218070\t3218100\t1\t30,\t0,\t3218070,\tggcgcgctgtcggccacggcgaaatcgacc,\tggcgcgctgtcggccacggcgaaatcgacc,\n+29\t1\t0\t0\t0\t0\t0\t0\t+\t72_0.533333\t30\t0\t30\tchr\t4639675\t2811982\t2812012\t1\t30,\t0,\t2811982,\taactggaagggcttgggatgacacaacagc,\taactggaagggcttgggatgacgcaacagc,\n+29\t1\t0\t0\t0\t0\t0\t0\t+\t73_0.500000\t30\t0\t30\tchr\t4639675\t2480740\t2480770\t1\t30,\t0,\t2480740,\ttttaagcgccaaccaggcttctttggttgc,\ttttaagcgccaaccaggcttctttagttgc,\n+30\t0\t0\t0\t0\t0\t0\t0\t+\t74_0.433333\t30\t0\t30\tchr\t4639675\t1904984\t1905014\t1\t30,\t0,\t1904984,\tacccttctttcgccatatcaaactgatgtc,\tacccttctttcgccatatcaaactgatgtc,\n+30\t0\t0\t0\t0\t0\t0\t0\t+\t78_0.566667\t30\t0\t30\tchr\t4639675\t4535164\t4535194\t1\t30,\t0,\t4535164,\tcggagtatccgttccccaacgacaagcatc,\tcggagtatccgttccccaacgacaagcatc,\n+30\t0\t0\t0\t0\t0\t0\t0\t+\t79_0.500000\t30\t0\t30\tchr\t4639675\t3598974\t3599004\t1\t30,\t0,\t3598974,\taataccgggaagagacaacggggtctcttt,\taataccgggaagagacaacggggtctcttt,\n+30\t0\t0\t0\t0\t0\t0\t0\t-\t80_0.500000\t30\t0\t30\tchr\t4639675\t1333814\t1333844\t1\t30,\t0,\t1333814,\tgagaatcagggcttcgcaaccctgtcatta,\tgagaatcagggcttcgcaaccctgtcatta,\n+30\t0\t0\t0\t0\t0\t0\t0\t+\t82_0.500000\t30\t0\t30\tchr\t4639675\t962544\t962574\t1\t30,\t0,\t962544,\tactgggttgctctgaacaagaaaggcgcta,\tactgggttgctctgaacaagaaaggcgcta,\n+30\t0\t0\t0\t0\t0\t0\t0\t+\t83_0.533333\t30\t0\t30\tchr\t4639675\t4543338\t4543368\t1\t30,\t0,\t4543338,\tcgccagggacgtatcgcgtcgatatctatt,\tcgccagggacgtatcgcgtcgatatctatt,\n+30\t0\t0\t0\t0\t0\t0\t0\t+\t86_0.566667\t30\t0\t30\tchr\t4639675\t159366\t159396\t1\t30,\t0,\t159366,\tggcaacgcaggcgcatgattctgcttggaa,\tggcaacgcaggcgcatgattctgcttggaa,\n+29\t0\t0\t1\t0\t0\t0\t0\t+\t87_0.433333\t30\t0\t30\tchr\t4639675\t2137315\t2137345\t1\t30,\t0,\t2137315,\tcgctggatgaaaancgtgaatatcacacca,\tcgctggatgaaaaacgtgaatatcacacca,\n+30\t0\t0\t0\t0\t0\t0\t0\t+\t88_0.533333\t30\t0\t30\tchr\t4639675\t2263609\t2263639\t1\t30,\t0,\t2263609,\tcgtaccgggctgaaagtagaagagcgtttc,\tcgtaccgggctgaaagtagaagagcgtttc,\n+30\t0\t0\t0\t0\t0\t0\t0\t+\t90_0.466667\t30\t0\t30\tchr\t4639675\t609915\t609945\t1\t30,\t0,\t609915,\tatcaccgtttcgctaaccggtacgtttaac,\tatcaccgtttcgctaaccggtacgtttaac,\n+29\t1\t0\t0\t0\t0\t0\t0\t+\t91_0.566667\t30\t0\t30\tchr\t4639675\t2506977\t2507007\t1\t30,\t0,\t2506977,\tttcgcccggcaagcttacccaacgcttatc,\tttcgcctggcaagcttacccaacgcttatc,\n+30\t0\t0\t0\t0\t0\t0\t0\t+\t92_0.533333\t30\t0\t30\tchr\t4639675\t4109771\t4109801\t1\t30,\t0,\t4109771,\tttttccccgccgttagtagcgactgcagtt,\tttttccccgccgttagtagcgactgcagtt,\n+30\t0\t0\t0\t0\t0\t0\t0\t+\t93_0.400000\t30\t0\t30\tchr\t4639675\t2250545\t2250575\t1\t30,\t0,\t2250545,\tttatttgcccgatgagtcagtttattgcag,\tttatttgcccgatgagtcagtttattgcag,\n+30\t0\t0\t0\t0\t0\t0\t0\t+\t94_0.466667\t30\t0\t30\tchr\t4639675\t1274949\t1274979\t1\t30,\t0,\t1274949,\tccacggtgatatctggtgccatactgataa,\tccacggtgatatctggtgccatactgataa,\n+30\t0\t0\t0\t0\t0\t0\t0\t+\t95_0.466667\t30\t0\t30\tchr\t4639675\t3279675\t3279705\t1\t30,\t0,\t3279675,\ttcccccgtaaggcctttctttttctttcgt,\ttcccccgtaaggcctttctttttctttcgt,\n+30\t0\t0\t0\t0\t0\t0\t0\t+\t97_0.566667\t30\t0\t30\tchr\t4639675\t2779110\t2779140\t1\t30,\t0,\t2779110,\ttgcgccgccggattgttgctcaacatgctt,\ttgcgccgccggattgttgctcaacatgctt,\n+30\t0\t0\t0\t0\t0\t0\t0\t+\t98_0.366667\t30\t0\t30\tchr\t4639675\t3729759\t3729789\t1\t30,\t0,\t3729759,\taacgcgctaaccgccaataataacaaaatt,\taacgcgctaaccgccaataataacaaaatt,\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/boxplot_summary_statistics_out.png

Binary file rnaseq/cutadapt/test-data/boxplot_summary_statistics_out.png has changed

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/build_ucsc_custom_track_out1.customtrack
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/build_ucsc_custom_track_out1.customtrack Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,8 @@
+track name="User Track" description="User Supplied Track (from Galaxy)" color=0,0,0 visibility=1
+chr2 31608 36385 NM_001077710 0 - 31608 36385 0 2 19,946, 0,3831,
+chr2 208154 246341 NM_015677 0 - 208810 232800 0 12 847,57,79,169,129,113,74,60,65,114,111,135, 0,6709,11811,12868,14946,16005,24643,25348,29383,31576,34850,38052,
+chr2 254871 262481 NM_001040649 0 + 254964 262258 0 3 136,74,445, 0,6994,7165,
+chr2 254895 268280 NM_004300 0 + 254964 267304 0 6 112,74,114,62,106,1054, 0,6970,7141,10244,12084,12331,
+chr2 254895 268280 NM_007099 0 + 254964 267304 0 6 112,74,114,62,106,1054, 0,6970,7296,10244,12084,12331,
+chr2 269928 277837 NM_001002919 0 - 270146 277835 0 6 221,65,81,54,22,53, 0,3182,6194,6361,7654,7856,
+

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/cat_wrapper_out1.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/cat_wrapper_out1.bed Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,133 @@\n+chr1\t147962192\t147962580\tCCDS989.1_cds_0_0_chr1_147962193_r\t0\t-\n+chr1\t147984545\t147984630\tCCDS990.1_cds_0_0_chr1_147984546_f\t0\t+\n+chr1\t148078400\t148078582\tCCDS993.1_cds_0_0_chr1_148078401_r\t0\t-\n+chr1\t148185136\t148185276\tCCDS996.1_cds_0_0_chr1_148185137_f\t0\t+\n+chr10\t55251623\t55253124\tCCDS7248.1_cds_0_0_chr10_55251624_r\t0\t-\n+chr11\t116124407\t116124501\tCCDS8374.1_cds_0_0_chr11_116124408_r\t0\t-\n+chr11\t116206508\t116206563\tCCDS8377.1_cds_0_0_chr11_116206509_f\t0\t+\n+chr11\t116211733\t116212337\tCCDS8378.1_cds_0_0_chr11_116211734_r\t0\t-\n+chr11\t1812377\t1812407\tCCDS7726.1_cds_0_0_chr11_1812378_f\t0\t+\n+chr12\t38440094\t38440321\tCCDS8736.1_cds_0_0_chr12_38440095_r\t0\t-\n+chr13\t112381694\t112381953\tCCDS9526.1_cds_0_0_chr13_112381695_f\t0\t+\n+chr14\t98710240\t98712285\tCCDS9949.1_cds_0_0_chr14_98710241_r\t0\t-\n+chr15\t41486872\t41487060\tCCDS10096.1_cds_0_0_chr15_41486873_r\t0\t-\n+chr15\t41673708\t41673857\tCCDS10097.1_cds_0_0_chr15_41673709_f\t0\t+\n+chr15\t41679161\t41679250\tCCDS10098.1_cds_0_0_chr15_41679162_r\t0\t-\n+chr15\t41826029\t41826196\tCCDS10101.1_cds_0_0_chr15_41826030_f\t0\t+\n+chr16\t142908\t143003\tCCDS10397.1_cds_0_0_chr16_142909_f\t0\t+\n+chr16\t179963\t180135\tCCDS10401.1_cds_0_0_chr16_179964_r\t0\t-\n+chr16\t244413\t244681\tCCDS10402.1_cds_0_0_chr16_244414_f\t0\t+\n+chr16\t259268\t259383\tCCDS10403.1_cds_0_0_chr16_259269_r\t0\t-\n+chr18\t23786114\t23786321\tCCDS11891.1_cds_0_0_chr18_23786115_r\t0\t-\n+chr18\t59406881\t59407046\tCCDS11985.1_cds_0_0_chr18_59406882_f\t0\t+\n+chr18\t59455932\t59456337\tCCDS11986.1_cds_0_0_chr18_59455933_r\t0\t-\n+chr18\t59600586\t59600754\tCCDS11988.1_cds_0_0_chr18_59600587_f\t0\t+\n+chr19\t59068595\t59069564\tCCDS12866.1_cds_0_0_chr19_59068596_f\t0\t+\n+chr19\t59236026\t59236146\tCCDS12872.1_cds_0_0_chr19_59236027_r\t0\t-\n+chr19\t59297998\t59298008\tCCDS12877.1_cds_0_0_chr19_59297999_f\t0\t+\n+chr19\t59302168\t59302288\tCCDS12878.1_cds_0_0_chr19_59302169_r\t0\t-\n+chr2\t118288583\t118288668\tCCDS2120.1_cds_0_0_chr2_118288584_f\t0\t+\n+chr2\t118394148\t118394202\tCCDS2121.1_cds_0_0_chr2_118394149_r\t0\t-\n+chr2\t220190202\t220190242\tCCDS2441.1_cds_0_0_chr2_220190203_f\t0\t+\n+chr2\t220229609\t220230869\tCCDS2443.1_cds_0_0_chr2_220229610_r\t0\t-\n+chr20\t33330413\t33330423\tCCDS13249.1_cds_0_0_chr20_33330414_r\t0\t-\n+chr20\t33513606\t33513792\tCCDS13255.1_cds_0_0_chr20_33513607_f\t0\t+\n+chr20\t33579500\t33579527\tCCDS13256.1_cds_0_0_chr20_33579501_r\t0\t-\n+chr20\t33593260\t33593348\tCCDS13257.1_cds_0_0_chr20_33593261_f\t0\t+\n+chr21\t32707032\t32707192\tCCDS13614.1_cds_0_0_chr21_32707033_f\t0\t+\n+chr21\t32869641\t32870022\tCCDS13615.1_cds_0_0_chr21_32869642_r\t0\t-\n+chr21\t33321040\t33322012\tCCDS13620.1_cds_0_0_chr21_33321041_f\t0\t+\n+chr21\t33744994\t33745040\tCCDS13625.1_cds_0_0_chr21_33744995_r\t0\t-\n+chr22\t30120223\t30120265\tCCDS13897.1_cds_0_0_chr22_30120224_f\t0\t+\n+chr22\t30160419\t30160661\tCCDS13898.1_cds_0_0_chr22_30160420_r\t0\t-\n+chr22\t30665273\t30665360\tCCDS13901.1_cds_0_0_chr22_30665274_f\t0\t+\n+chr22\t30939054\t30939266\tCCDS13903.1_cds_0_0_chr22_30939055_r\t0\t-\n+chr5\t131424298\t131424460\tCCDS4149.1_cds_0_0_chr5_131424299_f\t0\t+\n+chr5\t131556601\t131556672\tCCDS4151.1_cds_0_0_chr5_131556602_r\t0\t-\n+chr5\t131621326\t131621419\tCCDS4152.1_cds_0_0_chr5_131621327_f\t0\t+\n+chr5\t131847541\t131847666\tCCDS4155.1_cds_0_0_chr5_131847542_r\t0\t-\n+chr6\t108299600\t108299744\tCCDS5061.1_cds_0_0_chr6_108299601_r\t0\t-\n+chr6\t108594662\t108594687\tCCDS5063.1_cds_0_0_chr6_108594663_f\t0\t+\n+chr6\t108640045\t108640151\tCCDS5064.1_cds_0_0_chr6_108640046_r\t0\t-\n+chr6\t108722976\t108723115\tCCDS5067.1_cds_0_0_chr6_108722977_f\t0\t+\n+chr7\t113660517\t113660685\tCCDS5760.1_cds_0_0_chr7_113660518_f\t0\t+\n+chr7\t116512159\t116512389\tCCDS5771.1_cds_0_0_chr7_116512160_r\t0\t-\n+chr7\t116714099\t116714152\tCCDS5773.1_cds_0_0_chr7_116714100_f\t0\t+\n+chr7\t116945541\t116945787\tCCDS5774.1_cds_0_0_chr7_116945542_r\t0\t-\n+chr8\t118881131\t118881317\tCCDS6324.1_cds_0_0_chr8_118881132_r\t0\t-\n+chr9\t128764156\t128764189\tCCDS6914.1_cds_0_0_chr9_128764157_f\t0\t+\n+chr9\t128787519\t128789136\tCCDS6915.1_cds_0_0_chr9_128787520_r\t0\t-\n+chr9\t128882427\t128882523\tCCDS6917.1_cds_0_0_chr9_128882428_f\t0\t+\n+chr9\t128937229\t128937445\tCCDS6919.1_cds_0_0_chr'..b'124501\tAK057832_cds_0_0_chr11_116124408_r\t0\t-\n+chr11\t116206508\t116206563\tNM_000040_cds_1_0_chr11_116206509_f\t0\t+\n+chr11\t116211733\t116212337\tBC005380_cds_0_0_chr11_116211734_r\t0\t-\n+chr11\t130745911\t130745993\tAY358331_cds_0_0_chr11_130745912_f\t0\t+\n+chr12\t38440094\t38440321\tNM_052885_cds_0_0_chr12_38440095_r\t0\t-\n+chr12\t38905200\t38905351\tAY792511_cds_0_0_chr12_38905201_f\t0\t+\n+chr13\t112381694\t112381953\tNM_207440_cds_1_0_chr13_112381695_f\t0\t+\n+chr13\t29680676\t29680875\tNM_032116_cds_0_0_chr13_29680677_r\t0\t-\n+chr14\t98521864\t98521922\tU88895_cds_0_0_chr14_98521865_f\t0\t+\n+chr14\t98710240\t98712285\tNM_022898_cds_0_0_chr14_98710241_r\t0\t-\n+chr15\t41486872\t41487060\tBX537418_cds_0_0_chr15_41486873_r\t0\t-\n+chr15\t41673708\t41673857\tAK223365_cds_0_0_chr15_41673709_f\t0\t+\n+chr15\t41679161\t41679250\tNM_153700_cds_0_0_chr15_41679162_r\t0\t-\n+chr15\t41773540\t41773689\tAK223365_cds_0_0_chr15_41773541_f\t0\t+\n+chr16\t142908\t143003\tNM_005332_cds_0_0_chr16_142909_f\t0\t+\n+chr16\t179197\t179339\tBC065198_cds_0_0_chr16_179198_r\t0\t-\n+chr16\t244413\t244681\tAK057165_cds_2_0_chr16_244414_f\t0\t+\n+chr16\t259268\t259383\tAB016929_cds_0_0_chr16_259269_r\t0\t-\n+chr18\t23786114\t23786321\tNM_001792_cds_0_0_chr18_23786115_r\t0\t-\n+chr18\t59406881\t59407046\tNM_012397_cds_1_0_chr18_59406882_f\t0\t+\n+chr18\t59455932\t59456337\tAB046400_cds_0_0_chr18_59455933_r\t0\t-\n+chr18\t59528407\t59528575\tAY792326_cds_0_0_chr18_59528408_f\t0\t+\n+chr19\t59068595\t59069564\tBC013995_cds_1_0_chr19_59068596_f\t0\t+\n+chr19\t59236026\t59236146\tNM_198481_cds_0_0_chr19_59236027_r\t0\t-\n+chr19\t59297998\t59298008\tNM_004542_cds_0_0_chr19_59297999_f\t0\t+\n+chr19\t59318205\t59318718\tAK128544_cds_3_0_chr19_59318206_r\t0\t-\n+chr2\t118288583\t118288668\tNM_006773_cds_0_0_chr2_118288584_f\t0\t+\n+chr2\t118390395\t118390500\tBC005078_cds_0_0_chr2_118390396_r\t0\t-\n+chr2\t220108689\t220109267\tAY125465_cds_0_0_chr2_220108690_f\t0\t+\n+chr2\t220229609\t220230869\tNM_024536_cds_0_0_chr2_220229610_r\t0\t-\n+chr20\t33330413\t33330423\tNM_181466_cds_0_0_chr20_33330414_r\t0\t-\n+chr20\t33485370\t33486123\tBC085019_cds_1_0_chr20_33485371_f\t0\t+\n+chr20\t33488491\t33489122\tNM_000557_cds_1_0_chr20_33488492_r\t0\t-\n+chr20\t33513606\t33513792\tAF022655_cds_1_0_chr20_33513607_f\t0\t+\n+chr21\t32687402\t32687588\tNM_032910_cds_0_0_chr21_32687403_f\t0\t+\n+chr21\t32869641\t32870022\tNM_018277_cds_3_0_chr21_32869642_r\t0\t-\n+chr21\t33321040\t33322012\tNM_005806_cds_1_0_chr21_33321041_f\t0\t+\n+chr21\t33728358\t33728724\tAK129657_cds_0_0_chr21_33728359_r\t0\t-\n+chr22\t30120223\t30120265\tNM_004147_cds_0_0_chr22_30120224_f\t0\t+\n+chr22\t30160419\t30160661\tBC032941_cds_0_0_chr22_30160420_r\t0\t-\n+chr22\t30228824\t30228916\tNM_001007467_cds_1_0_chr22_30228825_f\t0\t+\n+chr22\t30340151\t30340376\tCR456540_cds_0_0_chr22_30340152_r\t0\t-\n+chr5\t131311206\t131311254\tAF099740_cds_11_0_chr5_131311207_r\t0\t-\n+chr5\t131424298\t131424460\tNM_000588_cds_0_0_chr5_131424299_f\t0\t+\n+chr5\t131556601\t131556672\tBC035813_cds_0_0_chr5_131556602_r\t0\t-\n+chr5\t131621326\t131621419\tBC003096_cds_0_0_chr5_131621327_f\t0\t+\n+chr6\t108299600\t108299744\tNM_007214_cds_0_0_chr6_108299601_r\t0\t-\n+chr6\t108594662\t108594687\tNM_003269_cds_0_0_chr6_108594663_f\t0\t+\n+chr6\t108640045\t108640151\tNM_003795_cds_0_0_chr6_108640046_r\t0\t-\n+chr6\t108722976\t108723115\tNM_145315_cds_0_0_chr6_108722977_f\t0\t+\n+chr7\t113660517\t113660685\tAF467257_cds_1_0_chr7_113660518_f\t0\t+\n+chr7\t116512159\t116512389\tNM_003391_cds_0_0_chr7_116512160_r\t0\t-\n+chr7\t116714099\t116714152\tNM_000492_cds_0_0_chr7_116714100_f\t0\t+\n+chr7\t116945541\t116945787\tAF377960_cds_0_0_chr7_116945542_r\t0\t-\n+chr8\t118881131\t118881317\tNM_000127_cds_0_0_chr8_118881132_r\t0\t-\n+chr9\t128764156\t128764189\tBC051300_cds_0_0_chr9_128764157_f\t0\t+\n+chr9\t128787519\t128789136\tNM_014908_cds_0_0_chr9_128787520_r\t0\t-\n+chr9\t128789552\t128789584\tNM_015354_cds_0_0_chr9_128789553_f\t0\t+\n+chr9\t128850516\t128850624\tAB058751_cds_0_0_chr9_128850517_r\t0\t-\n+chrX\t122745047\t122745924\tNM_001167_cds_1_0_chrX_122745048_f\t0\t+\n+chrX\t152648964\t152649196\tNM_000425_cds_0_0_chrX_152648965_r\t0\t-\n+chrX\t152691446\t152691471\tAF101728_cds_0_0_chrX_152691447_f\t0\t+\n+chrX\t152694029\t152694263\tBC052303_cds_0_0_chrX_152694030_r\t0\t-\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/cca_out1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/cca_out1.tabular Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,22 @@
+#Component 1 2
+#Correlation 0.9409 0.1311
+#F-statistic 144.4 2.57
+#p-value 6.213e-68 0.1111
+#X-Coefficients 1 2
+c3 1.507 -3.378
+c4 -0.5372 3.659
+#Y-Coefficients 1 2
+c1 6.35 3.379
+c2 -2.66 6.67
+#X-Loadings 1 2
+c3 0.9894 0.1452
+c4 0.9133 0.4073
+#Y-Loadings 1 2
+c1 0.9289 0.3704
+c2 -0.4698 0.8828
+#X-CrossLoadings 1 2
+c3 0.9309 0.01904
+c4 0.8593 0.05339
+#Y-CrossLoadings 1 2
+c1 0.874 0.04855
+c2 -0.442 0.1157

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/cca_out2.pdf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/cca_out2.pdf Sat Feb 21 16:33:42 2015 +0100

[

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diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/cf-gene2exon.dat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/cf-gene2exon.dat Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,325 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diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/cf_maf2fasta_concat.dat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/cf_maf2fasta_concat.dat Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,2 @@
+>canFam1
+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAGATATTTGGGGGAATTTGAATGTAGTGTTGCTCTTTTGTGATGCTAAGAAATTATAATTGTCTGATGATAGTCTCGTGGTTATGGGGGAAATGCTTCCTTATTTTTtagagacacaaactgaagtatttaaggat---gaaatgtcatgatgtttgcaattggctttaaaatattttag-----ccaaaa-agta----------------aatgaagc--aaatatgggaagacaataatcattaaatctaggtgaTGCATA---------------------------CTTTTCCATATGTTTGAAATTTTCATTTAAAAACATCAtgc-----tagatcctggactatgagctgggtatatagcagtgaacaa---------------------------------------------------------------------------------------------aacagagccctgcagt--------------------------------------------------cttgatggagcacacaACCTTTGGGGAACATGTTTCCATAAGAAAGTCTCCAATGTGATCTGATGGT-GCCGCCAGGACCTA-TGTCAGCCTACCGTTCCATGTCCCCTCCACACCATCATCACTGCAGGTGTGTTTTCCCACATTTTAAATATCTG-------CTTCCCGGTGGCCTTGAGTCTAGAGGAGTCCCCCCACTATGGTGGCACTAATACTGAAGGTCAGAAATAATCAGTTCTGTGGTGCATGTTGCCCCTGAGGTTCTGTTCGGGAAACTTCTTCTG-AGCAC----ATGCACCTGGCACTGCAAACGTACCAGGAGGAGACTTG-ATGCCTGCCTTCCACTTACAGCCTGTGGGCAGAGGTGGGAAGAGGTCACGCAAGCCAGTTGGAATGAGGGGAGTTGGCTGGAAAGGTGACCAGGACAAGCTACTTCAACCAGGAAGAAGAGACCCC---------GG--------TGCTTGGAGAAGGCCTGATTGAGCAGTCCTGCATGCCCGCCCAC-GACTGGCAGGAATAAAGACCCAGAAGAGCTAACGTG-------CAATGTA------TTTTCTAGTTCCAgggttggcaaactttctctctaagggtgggatgataaacattttaggcttttcagaccaagaggcgacatcagagggtat---gtaggt---------acaagagggaaaagttgcccccggaattttttg--gataaaattcaaaactttacttagggatgccaaaatgtaaacttcatattatatttttcaactctttaaaaatgcaaaaaccattcctagc-tcggggccatggtggtcctggtggtggtcggatttggctcacccacataacttgc--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/cf_maf2fasta_new.dat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/cf_maf2fasta_new.dat Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,134 @@\n+>hg17.chr7(+):127471195-127471526|sequence_index=0|block_index=0|species=hg17|hg17_0_0\n+gtttgccatcttttgctgctctagggaatccagcagctgtcaccatgtaaacaagcccaggctagaccaGTTACCCTCATC---ATCTTAGCTGATAGCCAGCCAGCCACCACAGGCAtgagtcaggccatattgctggacccacagaattatgagctaaataaatagtcttgggttaagccactaagttttaggcatagtgtgttatgtaTCTCACAAACATATAAGACTGTGTGTTTGTTGACTGGAGGAAGAGATGCTATAAAGACCACCTTTTAAAACTTCCCAAATACTGCCACTGATGTCCTGATGGAGG-------------------------------------------------------TATGAA---------AACATCCACTAA\n+>panTro1.chr6(+):129885076-129885407|sequence_index=0|block_index=0|species=panTro1|panTro1_0_0\n+gtttgccatcttttgctgctcttgggaatccagcagctgtcaccatgtaaacaagcccaggctagaccaGTTACCCTCATC---ATCTTAGCTGATAGCCAGCCAGCCACCACAGGCAtgagtcaggccatattgctggacccacagaattatgagctaaataaatagtcttgggttaagccactaagttttaggcatagtgtgttatgtaTCTCACAAACATATAAGACTGTGTGTTTGTTGACTGGAGGAAGAGATGCTATAAAGACCACCTTTTGAAACTTCCCAAATACTGCCACTGATGTCCTGATGGAGG-------------------------------------------------------TATGAA---------AACATCCACTAA\n+>rheMac2.chr3(+):165787989-165788319|sequence_index=0|block_index=0|species=rheMac2|rheMac2_0_0\n+gcttgccatcttttgatgctcttgggaatccagcagctgtcaccat-taaacaagcccaggctagaccaGTTACCCTCATC---ATCTTAGCTGATAGCCAGCCAGCCACCATAGGCAtgagtcaggccatagtgctggacccacagaattatgagctaaataagtagtgttgggttaagtcactaagttttaggcatagtgtgttatgtagcTCACAAACATATAAGACTGTGTGTTTTTTGACTGGAGGAAGAGATGCCATAAAGACCACCTTTTGAAACTTCTCAAATACTGCCATTGATGTGCTGATGGAGG-------------------------------------------------------TATGAA---------AACATCCACTAA\n+>rn3.chr4(+):56178191-56178473|sequence_index=0|block_index=0|species=rn3|rn3_0_0\n+CTTCACTCTCATTTGCTGTT----------------CTGTCACTATGGAGACAAACACAGGCTAGCCCAGTTACTATCTTGATCACAGCAGCTGT----CAGCTAGCTGCCACTCACAGGAATAAGGCCATACCATT-GATCCACTGAACCTTGATCTAGGAATTTGGC----------------------TGGGGCCAGTTTGCGGTGTCACTCATGA--CTCTAAGATTGTGTGTTTG----CTCCAGGAAGAGACGGCAAGAGGATTACCTTTAAAAGGTTCGG-AGTCTAGCTGTAGACAGCCCAATGGG---------------------------------------------------------TATAAC---------AATACTCACTAA\n+>mm7.chr6(+):28984529-28984886|sequence_index=0|block_index=0|species=mm7|mm7_0_0\n+CTCCACTCTCGTTTGCTGTT----------------CTGTCACCATGGAAACAAACG-AGGGTGGTCCAGTTACTATCTTG---ACTGCAGCTGG----CAGTCAGTTGCCACT--CAGGAATAAGGCTATGCCATT-GATCCACTGAACCGTGATCTGGAAACCTGGCTGTTGTTT-------CAAGCCTTGGGGCCAGTTTGCGGTGTTACTCATGA--CTCTAAGATCGTGTGCTTG----CTGCAGGAAGAGACAGCAAGGGGGTTACATTTAAAAAGCCCCC-AGTTTAGCTATAGGCAGGCCAACAGGTGTAAAAATACTCACTAGTAATGGGCTGAACTCATGGAGGTAGCATTAGTGAGACACTGTAACTGTTTTTTTAAAAATCACTAA\n+\n+>hg17.chr7(+):127471526-127471584|sequence_index=0|block_index=1|species=hg17|hg17_1_0\n+AATTTGTGGTTTATTCATTTTTCATTATTTTGTTTAAGGAGGTCTATAGTGGAAGAGG\n+>mm7.chr6(+):28984886-28984940|sequence_index=0|block_index=1|species=mm7|mm7_1_0\n+----AACGTTTCATTGATTGCTCATCATTTAAAAAAAGAAATTCCTCAGTGGAAGAGG\n+>rheMac2.chr3(+):165788319-165788377|sequence_index=0|block_index=1|species=rheMac2|rheMac2_1_0\n+AATTTGTGGTTTATTTATTTTTCATTATTTTGTTTAAGGAGGTCTATAGTGGAAGAGG\n+>panTro1.chr6(+):129885407-129885465|sequence_index=0|block_index=1|species=panTro1|panTro1_1_0\n+AATTTGTGGTTTATTCGTTTTTCATTATTTTGTTTAAGGAGGTCTATAGTGGAAGAGG\n+\n+>hg17.chr7(+):127471584-127471688|sequence_index=0|block_index=2|species=hg17|hg17_2_0\n+GAGATATTT-GGggaaatttt-gtatagactagctt--tcacgatgttagggaattattattgtgtgataatggtcttgcagttac-acagaaattcttcctta-ttttt\n+>panTro1.chr6(+):129885465-129885569|sequence_index=0|block_index=2|species=panTro1|panTro1_2_0\n+GAGACATTT-GGggaaatttt-gtatagactagctt--tcacgatgttagggagttattattgtgtgataatggtcttgcagttac-acagaaattcttcctta-ttttt\n+>rheMac2.chr3(+):165788377-165788482|sequence_index=0|block_index=2|species=rheMac2|rheMac2_2_0\n+GAGATATTT-GGggaaatttg-gtatagactagctt--tcatgatgtaagggagttatttttgtgtgataatggccctacagttac-acagaaattcttccttatttttt\n+>canFam2.chr14(-):11090703-11090811|sequence_index=0|block_index=2|species=canFam2|canFam2_2_0\n+gagatattt-gggggaatttgaatgtagtgttgctcttttgtgatgctaagaaattataattgtctgatgatagtctcgtggttatgggggaaatgcttcctta-ttttt\n+>bosTau2.chr4(-):50243931-50244034|sequence_index=0|block_index=2|species=bosTau2|bosTau2_2_0\n+-a'..b'TGCCTGCCTTCC-\n+>dasNov1.scaffold_256527(+):964-987|sequence_index=0|block_index=7|species=dasNov1|dasNov1_7_0\n+GACGGCCAG-ACCTCTGCCCTCGG\n+\n+>hg17.chr7(+):127472280-127472681|sequence_index=0|block_index=8|species=hg17|hg17_8_0\n+taaaacctaagggaggagaTGGAAAG-GGGCACCCAACCCAGACTGAGAGACAGGAATTAGCTGCAAGGGGAACTAGGAAAAGCTTCTTTA---AGGATG--GAGAGGCCCTA-GTGGAATGGGGAGATTCTTCCGGGAGAAGCGATGGATGCACAGTTGGGCATCCCCACAGACGGACTGGAAAGAAAAAAGGCCTGGAGGAATCA------ATGTGC-AATGTATGTGTGTTCCCTGGTTcaagggctgg-gaactttctcta--aagggccaggtagaaaacattttaggctttctaagccaagg---caaaattgaggat-attacatgggtacttatacaacaagaataaacaatt---tacacaa-ttttttgttgacagaattcaaaa---ctttat----agacac---agaaatgcaaatttcctgt\n+>panTro1.chr6(+):129886161-129886562|sequence_index=0|block_index=8|species=panTro1|panTro1_8_0\n+taaaacctaagggaggagaTGGAAAG-GGGCACCCAACCCAGACTGAGAGACAGGAATTAGCTGCAAGGGGAACTAGGAAAAGCTTCTTTA---AGGATG--GAGAGACCCTA-GTGGAATGGGGAGATTCTTCCGGGAGAAGCGATGGATGCGCAGTTGGGCATCCCCACAGACGGACTGGAAAGAAAAAAGGCCTGGAGGAATCA------ATGTGC-AATGTATGTGTGTTCCCTGGTTcaagggctgg-gaactttctcta--aagggccaggtagaaaacattttaggctttctaagccaagg---caaaattgaggat-attacatgggtacttatacaacaagaataaacaatt---tacacaa-ttttttgttgacagaattcaaaa---ctttat----agacac---agaaatgtaaatttcctgt\n+>rheMac2.chr3(+):165789091-165789492|sequence_index=0|block_index=8|species=rheMac2|rheMac2_8_0\n+taaaacctaatggaggagatggaATG-GGTCACCCAACCCGGACTGAGAGACAGGAATTAGCTGCAAGGGTAACCAGGACAAGCTTCTCTA---ATGATG--GAGAGACCCTA-GTGGAATGGGGAGATTCTTCTGGGAGAAGCGATGGATTCGTAGTTGGGCATCCCCACAGAGGGACTGGAAAGAAAAAAGACCTGGAGGAACCA------ATGTGC-AATGTATGTGTGTTTCCTGGTTcaagggctggcaaactttctcta--aagggccagatagaaaacattttaggctttgtaagccaagg---caaaatcgaggag-attacatgggtacttatacaacaagaataaacaatt---tccacaa--tttttattcacagaattcaaaa---ctttat----agacac---agaaatgtaaatttcctgt\n+>rn3.chr4(+):56183902-56184219|sequence_index=0|block_index=8|species=rn3|rn3_8_0\n+------------------------------------GTCCATAGTCAAAG------------------------------AAGCCTCTCAG---ATGGAG--AGCAGGGCCTATGCAAAAGAGGGGGCTTCTGTAGGCAGAAGGGATGGACTAGCCTCCGGACATAGCCATAGAGAGGCTGGCAGGACTGAGACCCAGGAGAAGCCAGCGCAGGTGTGCGGGCGTGTGTATATTTCATAGTTTGCAGGTTGG----------------------------CAAACAATTCCTGCTTTGCAGGCCAAGA---GGAAACTGAAGGTGACCCCGTGAGTGCTTAC---ACAAGAGAAAACAAG-------ACAA-TTTTTGGTTGACCAAATTCAGAA---CTTTATTTGAGGATGC---TAAAGTTTAAATTTCTTTT\n+>canFam2.chr14(-):11089143-11089523|sequence_index=0|block_index=8|species=canFam2|canFam2_8_0\n+TACAGCCTGTGGGCAGAGGTGGGAAGAGGTCACGCAAGCCAGTTGGAATGAGGGGAGTTGGCTGGAAAGGTGACCAGGACAAGCTACTTCAACCAGGAAG--AAGAGACCCCG-GTG----------------CTTGGAGAAGGCCTGATTGAGCAGTCCTGCATGCCCGCCCAC-GACTGGCAGGAATAAAGACCCAGAAGAGCTA------ACGTGC-AATGTA------TTTTCTAGTTCCAgggttggcaaactttctctct-aagggtgggatgataaacattttaggcttttcagaccaaga---ggcgacatcagag-ggtatgtaggt---------acaagagggaaaagttgcccccggaa-ttttttg--gataaaattcaaaa---ctttacttagggatgc---caaaatgtaaacttcatat\n+>dasNov1.scaffold_256527(+):987-1401|sequence_index=0|block_index=8|species=dasNov1|dasNov1_8_0\n+CTAAATCTCGCGGAGAAGGTGGAACA-GGTTACCCAAACCCGACCGAG-GAGGCGAGTTG---GAAACGGCGACTGGGACAAGCTCCCTCA---GAGACGGAGAGAGACCCCA-GTGGAAGGGGGGAGAGGCTCTTAGGGAAACGATGGGGGGACCCGCCCGCACCCGCACAGAGGCGCTGGCAGGCACAGCGGCCCCGAGGAGCCC------AGGAGC-AGGGC-TGTGT-TCCCCTGCATcaggggttggcaaactttttctgcaaagggccagatagtaaatattttaggctttgcaaaccaagaagtagaaagggaggcc-attatgtacgtatttatatagcaagagagaacattt---cccacaatttttttattgacagaatttaaaacttctttattgatgaacaccaaagaaacttgaatttcatat\n+\n+>hg17.chr7(+):127472681-127472715|sequence_index=0|block_index=9|species=hg17|hg17_9_0\n+aattttcccat---gagaactattcttcttttgtttt\n+>rheMac2.chr3(+):165789492-165789526|sequence_index=0|block_index=9|species=rheMac2|rheMac2_9_0\n+aattttcacat---aagaactattcttcttttgtttt\n+>panTro1.chr6(+):129886562-129886596|sequence_index=0|block_index=9|species=panTro1|panTro1_9_0\n+aattttcccgt---gagaactattcttcttttgtttt\n+>canFam2.chr14(-):11089108-11089143|sequence_index=0|block_index=9|species=canFam2|canFam2_9_0\n+aatggtcatgt--ccataactattcttcttttatttt\n+>dasNov1.scaffold_256527(+):1401-1433|sequence_index=0|block_index=9|species=dasNov1|dasNov1_9_0\n+aattttcacatatcacgaagtatttttttttt-----\n+\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/cf_maf_limit_to_species.dat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/cf_maf_limit_to_species.dat Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,40 @@\n+##maf version=1\n+a score=85620.0\n+s hg17.chr7 127471584 104 + 158628139 GAGATATTT-GGggaaatttt-gtatagactagctt--tcacgatgttagggaattattattgtgtgataatggtcttgcagttac-acagaaattcttcctta-ttttt \n+s panTro1.chr6 129885465 104 + 161576975 GAGACATTT-GGggaaatttt-gtatagactagctt--tcacgatgttagggagttattattgtgtgataatggtcttgcagttac-acagaaattcttcctta-ttttt \n+i panTro1.chr6 C 0 C 0 \n+s rheMac2.chr3 165788377 105 + 196418989 GAGATATTT-GGggaaatttg-gtatagactagctt--tcatgatgtaagggagttatttttgtgtgataatggccctacagttac-acagaaattcttccttatttttt \n+i rheMac2.chr3 C 0 C 0 \n+s canFam2.chr14 52847428 108 - 63938239 gagatattt-gggggaatttgaatgtagtgttgctcttttgtgatgctaagaaattataattgtctgatgatagtctcgtggttatgggggaaatgcttcctta-ttttt \n+i canFam2.chr14 I 4750 I 198 \n+s bosTau2.chr4 19312415 103 - 69556449 -agacattg-ggtaaaattcaaatgcagactagctc----atgatgttaaagaattactcttgtgtggtaatggtcttgtgatagagatagaaatgcttcctta-ttttt \n+i bosTau2.chr4 M 120077 I 1 \n+s rn3.chr4 56182200 95 + 187371129 ----TATTTGGGGGAAATATG-ATGTGCA----CTT--CCATGATCTTAAAGAATTGCTACTGTTTGATAGTGATCTTATGGTTAA-ATAAAAAAAAT--CTTA-GTTGT \n+i rn3.chr4 I 3727 C 0 \n+\n+a score=113319.0\n+s hg17.chr7 127471688 183 + 158628139 tgggaagcaccaaagta-------gggataaaatgtcatgatgtgtgcaatacactttaaaatgtttttgccaaaataattaa-------------------------tgaagc--aaatatg-gaaaataataattattaaatctaggtgatgggtatattgtagttcactatagtattgcacacttttctgtatgtttaaatttttcattta-------------------aaaa \n+s panTro1.chr6 129885569 183 + 161576975 tgggaaacaccaaagta-------gggataaaatgtcatgatgtgtgcaatacgctttaaaatatttttgccaaaataattaa-------------------------tgaagc--aaatatg-gaaaataataattattaaatctaggtgatgggtatattgtagttcactatagtattgcacacttttctgtatgtttaaaattttcattta-------------------aaaa \n+i panTro1.chr6 C 0 C 0 \n+s rheMac2.chr3 165788482 202 + 196418989 tgggaagcacaaaagta-------gggataaaatgtcatgatgtgtacaatatgctttaaaatatttttgccaaaataattaa-------------------------tgaagc--aaatatg-gaaaataataactgttaaatctaggtgttgggtatattgcagttcattatgttattgcacacttttctgtgtgtttaaaattttcatttaaaaatatgttttaaaaatgaaaa \n+i rheMac2.chr3 C 0 C 0 \n+s rn3.chr4 56182295 194 + 187371129 TAGAAAATACTCAAATATTTAGGGGCGTGACAATGTCACAGTGTCTGCAATTTGCTTTAAAGATTTTT-----AAATATTTAAAAAAGTTTTAATAATTTTGAAAAACTGAAGCTACACTATG-GGAAGTGGTAATTGTTACATATGGGTAATAAGTAT-----AATTCGTTATATTAT-------TTTTC------TTAGAATTTTTCATTTG-------------------AAAA \n+i rn3.chr4 C 0 I 959 \n+s bosTau2.chr4 19312519 138 - 69556449 agataaacacttaagtattta---aggatgaaacgccctgatgtttgtaatttgctttagaatattttagccaaaagaattaa-------------------------tgatgc--aaatatgcaaaaagagta--cgttaaacctaa------------------------------------------------atttgCGATT'..b' \n+s canFam2.chr14 52847734 160 - 63938239 agacacaaactgaagtattta---aggatgaaatgtcatgatgtttgcaattggctttaaaatattttagccaaaa-agtaaa-------------------------tgaagc--AAATATGGGAAGACAATAATCATTAAATCTAGGTGATGCATAC---------------------------TTTTCCATATGTTTGAAATTTTCATTTA-------------------AAAA \n+i canFam2.chr14 I 198 I 225 \n+\n+a score=94204.0\n+s hg17.chr7 127471910 164 + 158628139 caatgaccaa----------------------------------------------------------------------------------------------atagactcctaccaa-ctc-aaagaatgcacattctCTG-GGAAACATGTTTCCATTAGGAAGCCTCGAATGCAATGTGACTGTGGTCTCCAGGACCTG-TGTGATCCTGGCTTTTCCTGTTCCCTCCG---CATCATCACTGCAGGTGTGTTTTCCCAAG \n+s panTro1.chr6 129885791 164 + 161576975 caatgaccaa----------------------------------------------------------------------------------------------atagactcctaccaa-ctc-aaagaatgcacattctCTG-GGAAACATGTTTCCATTAGGAAGCCTCGAATGCAATGTGACTGTGGTCTCCAGGACATG-TGTGATCCTGGCTTTTCCTGTTCCCTCTG---CATCATCACTGCAGGTGTATTTTCCCAAG \n+i panTro1.chr6 C 0 C 0 \n+s rheMac2.chr3 165788723 162 + 196418989 caatgaccaa----------------------------------------------------------------------------------------------atagacccctaccga-ctc-aaagaatgtacattctTTG-GGAAACATGTTTCCATCAGAAAATCTCAAATGCAATGTGACTGGGGTCTCCAGGACCTG-TGTGAGCCTGGCTTTTCCTGTTCCCTCCA---CATCATCACTGCAGGTGTATTTTCCC--G \n+i rheMac2.chr3 C 0 C 0 \n+s rn3.chr4 56183448 257 + 187371129 --ATGACCAATATACACTGTTTACATGTATAGCATTGTGAATGGAGACATAAAAAGATAATCTAGCTTTGTGCTAGGTAGGTGCTGAGCTCTTAACAGTGCTGGGCAGAAACCTATAAC-CTC-ACAGGGTGGGTTGTCTTTG-AGGAGCGTGCTAACCCTAGGAAGTCTCAAATACAATGTGATGGTTGCCCCCAGGCACCACCTTGAACCTGGTCTTCCTGGTTTCTTTCA---CACCATTACCACAAATACATTTTCTCAGG \n+i rn3.chr4 I 959 C 0 \n+s bosTau2.chr4 19312715 168 - 69556449 atgtgaacaa---------------------------------------------------------------------------------------------aacggacccgtgtgggactcggcggagcacacagattttgcgggagCACGTTCCCGTTAGGAAGTCTCTGATGCAATACGACCGGTGCCTTCAGGACCTG-TG--AGGCTGACTTTCCTTA-CCCCTCCACACCATCATCAAGGCAGGTGTGATTTTCCAGG \n+i bosTau2.chr4 C 0 I 12 \n+s canFam2.chr14 52848158 168 - 63938239 cagtgaacaa---------------------------------------------------------------------------------------------aacagagccctgcagt-cttgatggagcacacaacctttg-gggaaCATGTTTCCATAAGAAAGTCTCCAATGTGATCTGA-TGGTGCCGCCAGGACCTA-TGTCAGCCTACCGTTCCATGTCCCCTCCACACCATCATCACTGCAGGTGTGTTTTCCCACA \n+i canFam2.chr14 C 0 C 0 \n+\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/cf_maf_to_bed.dat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/cf_maf_to_bed.dat Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,10 @@
+chr7 127471195 127471526 hg17_0 0 +
+chr7 127471526 127471584 hg17_1 0 +
+chr7 127471584 127471688 hg17_2 0 +
+chr7 127471688 127471871 hg17_3 0 +
+chr7 127471871 127471910 hg17_4 0 +
+chr7 127471910 127472074 hg17_5 0 +
+chr7 127472074 127472258 hg17_6 0 +
+chr7 127472258 127472280 hg17_7 0 +
+chr7 127472280 127472681 hg17_8 0 +
+chr7 127472681 127472715 hg17_9 0 +

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/changeCase_out1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/changeCase_out1.tabular Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,10 @@
+CHR1 4225 19670
+CHR10 6 8
+CHR1 24417 24420
+CHR6_HLA_HAP2 0 150
+CHR2 1 5
+CHR10 2 10
+CHR1 30 55
+CHRY 1 20
+CHR1 1225979 42287290
+CHR10 7 8

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/changeCase_out2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/changeCase_out2.tabular Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,65 @@
+CHR1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 -
+CHR1 147984545 147984630 CCDS990.1_cds_0_0_chr1_147984546_f 0 +
+CHR1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 -
+CHR1 148185136 148185276 CCDS996.1_cds_0_0_chr1_148185137_f 0 +
+CHR10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 -
+CHR11 116124407 116124501 CCDS8374.1_cds_0_0_chr11_116124408_r 0 -
+CHR11 116206508 116206563 CCDS8377.1_cds_0_0_chr11_116206509_f 0 +
+CHR11 116211733 116212337 CCDS8378.1_cds_0_0_chr11_116211734_r 0 -
+CHR11 1812377 1812407 CCDS7726.1_cds_0_0_chr11_1812378_f 0 +
+CHR12 38440094 38440321 CCDS8736.1_cds_0_0_chr12_38440095_r 0 -
+CHR13 112381694 112381953 CCDS9526.1_cds_0_0_chr13_112381695_f 0 +
+CHR14 98710240 98712285 CCDS9949.1_cds_0_0_chr14_98710241_r 0 -
+CHR15 41486872 41487060 CCDS10096.1_cds_0_0_chr15_41486873_r 0 -
+CHR15 41673708 41673857 CCDS10097.1_cds_0_0_chr15_41673709_f 0 +
+CHR15 41679161 41679250 CCDS10098.1_cds_0_0_chr15_41679162_r 0 -
+CHR15 41826029 41826196 CCDS10101.1_cds_0_0_chr15_41826030_f 0 +
+CHR16 142908 143003 CCDS10397.1_cds_0_0_chr16_142909_f 0 +
+CHR16 179963 180135 CCDS10401.1_cds_0_0_chr16_179964_r 0 -
+CHR16 244413 244681 CCDS10402.1_cds_0_0_chr16_244414_f 0 +
+CHR16 259268 259383 CCDS10403.1_cds_0_0_chr16_259269_r 0 -
+CHR18 23786114 23786321 CCDS11891.1_cds_0_0_chr18_23786115_r 0 -
+CHR18 59406881 59407046 CCDS11985.1_cds_0_0_chr18_59406882_f 0 +
+CHR18 59455932 59456337 CCDS11986.1_cds_0_0_chr18_59455933_r 0 -
+CHR18 59600586 59600754 CCDS11988.1_cds_0_0_chr18_59600587_f 0 +
+CHR19 59068595 59069564 CCDS12866.1_cds_0_0_chr19_59068596_f 0 +
+CHR19 59236026 59236146 CCDS12872.1_cds_0_0_chr19_59236027_r 0 -
+CHR19 59297998 59298008 CCDS12877.1_cds_0_0_chr19_59297999_f 0 +
+CHR19 59302168 59302288 CCDS12878.1_cds_0_0_chr19_59302169_r 0 -
+CHR2 118288583 118288668 CCDS2120.1_cds_0_0_chr2_118288584_f 0 +
+CHR2 118394148 118394202 CCDS2121.1_cds_0_0_chr2_118394149_r 0 -
+CHR2 220190202 220190242 CCDS2441.1_cds_0_0_chr2_220190203_f 0 +
+CHR2 220229609 220230869 CCDS2443.1_cds_0_0_chr2_220229610_r 0 -
+CHR20 33330413 33330423 CCDS13249.1_cds_0_0_chr20_33330414_r 0 -
+CHR20 33513606 33513792 CCDS13255.1_cds_0_0_chr20_33513607_f 0 +
+CHR20 33579500 33579527 CCDS13256.1_cds_0_0_chr20_33579501_r 0 -
+CHR20 33593260 33593348 CCDS13257.1_cds_0_0_chr20_33593261_f 0 +
+CHR21 32707032 32707192 CCDS13614.1_cds_0_0_chr21_32707033_f 0 +
+CHR21 32869641 32870022 CCDS13615.1_cds_0_0_chr21_32869642_r 0 -
+CHR21 33321040 33322012 CCDS13620.1_cds_0_0_chr21_33321041_f 0 +
+CHR21 33744994 33745040 CCDS13625.1_cds_0_0_chr21_33744995_r 0 -
+CHR22 30120223 30120265 CCDS13897.1_cds_0_0_chr22_30120224_f 0 +
+CHR22 30160419 30160661 CCDS13898.1_cds_0_0_chr22_30160420_r 0 -
+CHR22 30665273 30665360 CCDS13901.1_cds_0_0_chr22_30665274_f 0 +
+CHR22 30939054 30939266 CCDS13903.1_cds_0_0_chr22_30939055_r 0 -
+CHR5 131424298 131424460 CCDS4149.1_cds_0_0_chr5_131424299_f 0 +
+CHR5 131556601 131556672 CCDS4151.1_cds_0_0_chr5_131556602_r 0 -
+CHR5 131621326 131621419 CCDS4152.1_cds_0_0_chr5_131621327_f 0 +
+CHR5 131847541 131847666 CCDS4155.1_cds_0_0_chr5_131847542_r 0 -
+CHR6 108299600 108299744 CCDS5061.1_cds_0_0_chr6_108299601_r 0 -
+CHR6 108594662 108594687 CCDS5063.1_cds_0_0_chr6_108594663_f 0 +
+CHR6 108640045 108640151 CCDS5064.1_cds_0_0_chr6_108640046_r 0 -
+CHR6 108722976 108723115 CCDS5067.1_cds_0_0_chr6_108722977_f 0 +
+CHR7 113660517 113660685 CCDS5760.1_cds_0_0_chr7_113660518_f 0 +
+CHR7 116512159 116512389 CCDS5771.1_cds_0_0_chr7_116512160_r 0 -
+CHR7 116714099 116714152 CCDS5773.1_cds_0_0_chr7_116714100_f 0 +
+CHR7 116945541 116945787 CCDS5774.1_cds_0_0_chr7_116945542_r 0 -
+CHR8 118881131 118881317 CCDS6324.1_cds_0_0_chr8_118881132_r 0 -
+CHR9 128764156 128764189 CCDS6914.1_cds_0_0_chr9_128764157_f 0 +
+CHR9 128787519 128789136 CCDS6915.1_cds_0_0_chr9_128787520_r 0 -
+CHR9 128882427 128882523 CCDS6917.1_cds_0_0_chr9_128882428_f 0 +
+CHR9 128937229 128937445 CCDS6919.1_cds_0_0_chr9_128937230_r 0 -
+CHRX 122745047 122745924 CCDS14606.1_cds_0_0_chrX_122745048_f 0 +
+CHRX 152648964 152649196 CCDS14733.1_cds_0_0_chrX_152648965_r 0 -
+CHRX 152691446 152691471 CCDS14735.1_cds_0_0_chrX_152691447_f 0 +
+CHRX 152694029 152694263 CCDS14736.1_cds_0_0_chrX_152694030_r 0 -

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/chr_m.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/chr_m.fasta Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,335 @@\n+>chrM\n+GTTAATGTAGCTTAATAATATAAAGCAAGGCACTGAAAATGCCTAGATGA\n+GTATTCTTACTCCATAAACACATAGGCTTGGTCCTAGCCTTTTTATTAGT\n+TATTAATAGAATTACACATGCAAGTATCCGCACCCCAGTGAGAATGCCCT\n+CTAAATCACGTCTCTACGATTAAAAGGAGCAGGTATCAAGCACACTAGAA\n+AGTAGCTCATAACACCTTGCTCAGCCACACCCCCACGGGACACAGCAGTG\n+ATAAAAATTAAGCTATGAACGAAAGTTCGACTAAGTCATATTAAATAAGG\n+GTTGGTAAATTTCGTGCCAGCCACCGCGGTCATACGATTAACCCAAATTA\n+ATAAATCTCCGGCGTAAAGCGTGTCAAAGACTAATACCAAAATAAAGTTA\n+AAACCCAGTTAAGCCGTAAAAAGCTACAACCAAAGTAAAATAGACTACGA\n+AAGTGACTTTAATACCTCTGACTACACGATAGCTAAGACCCAAACTGGGA\n+TTAGATACCCCACTATGCTTAGCCCTAAACTAAAATAGCTTACCACAACA\n+AAGCTATTCGCCAGAGTACTACTAGCAACAGCCTAAAACTCAAAGGACTT\n+GGCGGTGCTTTACATCCCTCTAGAGGAGCCTGTTCCATAATCGATAAACC\n+CCGATAAACCCCACCATCCCTTGCTAATTCAGCCTATATACCGCCATCTT\n+CAGCAAACCCTAAACAAGGTACCGAAGTAAGCACAAATATCCAACATAAA\n+AACGTTAGGTCAAGGTGTAGCCCATGGGATGGAGAGAAATGGGCTACATT\n+TTCTACCCTAAGAACAAGAACTTTAACCCGGACGAAAGTCTCCATGAAAC\n+TGGAGACTAAAGGAGGATTTAGCAGTAAATTAAGAATAGAGAGCTTAATT\n+GAATCAGGCCATGAAGCGCGCACACACCGCCCGTCACCCTCCTTAAATAT\n+CACAAATCATAACATAACATAAAACCGTGACCCAAACATATGAAAGGAGA\n+CAAGTCGTAACAAGGTAAGTATACCGGAAGGTGTACTTGGATAACCAAAG\n+TGTAGCTTAAACAAAGCATCCAGCTTACACCTAGAAGATTTCACTCAAAA\n+TGAACACTTTGAACTAAAGCTAGCCCAAACAATACCTAATTCAATTACCC\n+TTAGTCACTTAACTAAAACATTCACCAAACCATTAAAGTATAGGAGATAG\n+AAATTTTAACTTGGCGCTATAGAGAAAGTACCGTAAGGGAACGATGAAAG\n+ATGCATTAAAAGTACTAAACAGCAAAGCTTACCCCTTTTACCTTTTGCAT\n+AATGATTTAACTAGAATAAACTTAGCAAAGAGAACTTAAGCTAAGCACCC\n+CGAAACCAGACGAGCTACCTATGAACAGTTACAAATGAACCAACTCATCT\n+ATGTCGCAAAATAGTGAGAAGATTCGTAGGTAGAGGTGAAAAGCCCAACG\n+AGCCTGGTGATAGCTGGTTGTCCAGAAACAGAATTTCAGTTCAAATTTAA\n+ATTTACCTAAAAACTACTCAATTCTAATGTAAATTTAAATTATAGTCTAA\n+AAAGGTACAGCTTTTTAGATACAGGTTACAACCTTCATTAGAGAGTAAGA\n+ACAAGATAAACCCATAGTTGGCTTAAAAGCAGCCATCAATTAAGAAAGCG\n+TTCAAGCTCAACGACACATCTATCTTAATCCCAACAATCAACCCAAACTA\n+ACTCCTAATCTCATACTGGACTATTCTATCAACACATAGAAGCAATAATG\n+TTAATATGAGTAACAAGAATTATTTCTCCTTGCATAAGCTTATATCAGAA\n+CGAATACTCACTGATAGTTAACAACAAGATAGGGATAATCCAAAAACTAA\n+TCATCTATTTAAACCATTGTTAACCCAACACAGGCATGCATCTATAAGGA\n+AAGATTAAAAGAAGTAAAAGGAACTCGGCAAACACAAACCCCGCCTGTTT\n+ACCAAAAACATCACCTCTAGCATTTCCAGTATTAGAGGCACTGCCTGCCC\n+AGTGACATCTGTTtaaacggccgcggtatcctaaccgtgcaaaggtagca\n+taatcacttgttccctaaatagggacttgtatgaatggccacacgagggt\n+tttactgtctcttacttccaatcagtgaaattgaccttcccgtgaagagg\n+cgggaatgactaaataagacgagaagaccctatggagcttTAATTAACTG\n+ATTCACAAAAAACAACACACAAACCTTAACCTTCAGGGACAACAAAACTT\n+TTGATTGAATCAGCAATTTCGGTTGGGGTGACCTCGGAGAACAAAACAAC\n+CTCCGAGTGATTTAAATCCAGACTAACCAGTCAAAATATATAATCACTTA\n+TTGATCCAAACCATTGATCAACGGAACAAGTTACCCTAGGGATAACAGCG\n+CAATCCTATTCCAGAGTCCATATCGACAATTAGGGTTTACGACCTCGATG\n+TTGGATCAAGACATCCTAATGGTGCAACCGCTATTAAGGGTTCGTTTGTT\n+CAACGATTAAAGTCTTACGTGATCTGAGTTCAGACCGGAGTAATCCAGGT\n+CGGTTTCTATCTATTCTATACTTTTCCCAGTACGAAAGGACAAGAAAAGT\n+AGGGCCCACTTTACAAGAAGCGCCCTCAAACTAATAGATGACATAATCTA\n+AATCTAACTAATTTATAACTTCTACCGCCCTAGAACAGGGCTCgttaggg\n+tggcagagcccggaaattgcataaaacttaaacctttacactcagaggtt\n+caactcctctccctaacaacaTGTTCATAATTAACGTCCTCCTCCTAATT\n+GTCCCAATCTTGCTCGCCGTAGCATTCCTCACACTAGTTGAACGAAAAGT\n+CTTAGGCTATATGCAACTTCGCAAAGGACCCAACATCGTAGGCCCCTATG\n+GCCTACTACAACCTATTGCCGATGCCCTCAAACTATTTATCAAAGAGCCA\n+CTACAACCACTAACATCATCGACATCCATATTCATCATCGCACCAATCCT\n+AGCCCTAACCCTGGCCTTAACCATATGAATCCCTCTGCCCATACCATACC\n+CACTAATCAACATAAACCTAGGAATTCTATTCATACTAGCCATGTCCAGC\n+CTAGCTGTCTACTCAATCCTTTGATCAGGATGGGCCTCAAACTCAAAATA\n+CGCCCTAATTGGAGCTCTACGAGCAGTAGCACAAACCATCTCATACGAAG\n+TAACTCTAGCAATCATCCTACTCTCAGTCCTCCTAATAAGCGGATCATTC\n+ACATTATCAACACTTATTATTACCCAAGAATACCTCTGATTAATCTTCCC\n+ATCATGACCCTTAGCCATAATGTGATTCATCTCAACATTAGCCGAAACCA\n+ACCGAGCTCCATTTGACCTAACAGAAGGAGAATCAGAACTCGTCTCTGGA\n+TTCAACGTTGAATACGCAGCCGGCCCATTTGCTCTATTCTTCCTAGCAGA\n+ATACGCAAACATCATCATGATAAACATCTTCACAACAACCCTATTTCTAG\n+GAGCATTTCACAACCCCTACCTGCCAGAACTCTACTCAATTAATTTCACC\n+ATTAAAGCTCTCCTTCTAACATGTTCCTTCCTATGAATCCGAGCATCCTA\n+CCCACGATTCCGATATGACCAACTTATACACCTCCTATGAAAGAACTTCC\n+TACCACTCACACTAGCCCTCTGCATATGACACGTCTCACTTCCAATCATA\n+CTATCCAGCATCCCACCACAAACATAGGAAATATGTCTGACAAAAGAGTT\n+ACTTTGATAGAGTAAAACATAGAGGCTCAAACCCTCTTATTTctagaact\n+acaggaattgaacctgctcct'..b'CATTATCCACAGCCTAAATGACGAGCAAGATATC\n+CGAAAAATAGGCGGACTATTTAATGCAATACCCTTCACCACCACATCTCT\n+AATTATTGGCAGCCTTGCACTCACCGGAATTCCTTTCCTCACAGGCTTCT\n+ACTCCAAAGACCTCATCATCGAAACCGCCAACACATCGTACACCAACGCC\n+TGAGCCCTACTAATAACTCTCATTGCCACATCCCTCACAGCTGTCTACAG\n+TACCCGAATCATCTTCTTTGCACTCCTAGGGCAACCCCGCTTCCTCCCTC\n+TGACCTCAATCAACGAAAATAACCCCTTTCTAATTAACTCCATCAAACGC\n+CTCTTAATTGGCAGCATTTTTGCCGGATTCTTCATCTCCAACAATATCTA\n+CCCCACAACCGTCCCAGAAATAACCATACCTACTTACATAAAACTCACCG\n+CCCTCGCAGTAACCATCCTAGGATTTACACTAGCCCTAGAACTAAGCTTG\n+ATAACCCATAACTTAAAACTAGAACACTCCACCAACGTATTCAAATTCTC\n+CAACCTCCTAGGATACTACCCAACAATTATACACCGACTCCCACCGCTCG\n+CTAACCTATCAATAAGCCAAAAATCAGCATCACTTCTACTAGACTCAATC\n+TGACTAGAAAACATCCTGCCAAAATCTATCTCCCAGTTCCAAATAAAAAC\n+CTCGATCCTAATTTCCACCCAAAAAGGACAAATCAAATTATATTTCCTCT\n+CATTCCTCATCACCCTTACCCTAAGCATACTACTTTTTAATCTCCACGAG\n+TAACCTCTAAAATTACCAAGACCCCAACAAGCAACGATCAACCAGTCACA\n+ATCACAACCCAAGCCCCATAACTATACAATGCAGCAGCCCCTATAATTTC\n+CTCACTAAACGCCCCAGAATCTCCAGTATCATAAATAGCTCAAGCCCCCA\n+CACCACTAAACTTAAACACTACCCCCACTTCCTCACTCTTCAGAACATAT\n+AAAACCAACATAACCTCCATCAACAACCCTAAAAGAAATACCCCCATAAC\n+AGTCGTATTAGACACCCATACCTCAGGATACTGCTCAGTAGCCATAGCCG\n+TTGTATAACCAAAAACAACCAACATTCCTCCCAAATAAATCAAAAACACC\n+ATCAACCCCAAAAAGGACCCTCCAAAATTCATAATAATACCACAACCTAC\n+CCCTCCACTTACAATCAGCACTAAACCCCCATAAATAGGTGAAGGTTTTG\n+AAGAAAACCCCACAAAACTAACAACAAAAATAACACTCAAAATAAACACA\n+ATATATGTCATCATTATTCCCACGTGGAATCTAACCACGACCAATGACAT\n+GAAAAATCATCGTTGTATTTCAACTATAAGAACACCAATGACAAACATCC\n+GGAAATCTCACCCACTAATTAAAATCATCAATCACTCTTTTATTGACCTA\n+CCAGCCCCCTCAAACATTTCATCATGATGAAACTTCGGCTCCCTCCTAGG\n+AATCTGCCTAATCCTCCAAATCTTAACAGGCCTATTCCTAGCCATACACT\n+ACACATCAGACACGACAACTGCCTTCTCATCCGTCACTCACATCTGCCGA\n+GACGTTAACTACGGATGAATTATTCGCTACCTCCATGCCAACGGAGCATC\n+AATATTTTTTATCTGCCTCTTCATTCACGTAGGACGCGGCCTCTACTACG\n+GCTCTTACACATTCCTAGAGACATGAAACATTGGAATCATCCTACTTTTC\n+ACAGTTATAGCTACAGCATTCATGGGCTATGTCCTACCATGAGGCCAAAT\n+ATCCTTTTGAGGAGCAACAGTCATCACGAACCTCCTATCAGCAATTCCCT\n+ACATCGGTACTACCCTCGTCGAGTGAATCTGAGGTGGATTCTCAGTAGAC\n+AAAGCCACCCTTACCCGATTTTTTGCTTTCCACTTCATCCTACCCTTCAT\n+CATCACAGCCCTGGTAGTCGTACATTTACTATTTCTTCACGAAACAGGAT\n+CTAATAACCCCTCAGGAATCCCATCCGATATGGACAAAATCCCATTCCAC\n+CCATATTATACAATTAAAGACATCCTAGGACTCCTCCTCCTGATCTTGCT\n+CCTACTAACTCTAGTATTATTCTCCCCCGACCTCCTAGGAGACCCAGACA\n+ACTACACCCCAGCTAACCCTCTCAGCACTCCCCCTCATATTAAACCAGAA\n+TGGTACTTCCTGTTTGCCTACGCCATCCTACGCTCCATTCCCAACAAACT\n+AGGCGGCGTATTAGCCCTAATCCTCTCCATCCTGATCCTAGCACTCATCC\n+CCACCCTCCACATATCAAAACAACGAAGCATAATATTCCGGCCTCTCAGC\n+CAATGCGTATTCTGACTCTTAGTGGCAGACTTACTGACACTAACATGAAT\n+CGGCGGACAGCCAGTGGAACACCCATACGTAATTATCGGCCAACTGGCCT\n+CAATCCTCTACTTCTCCCTAATTCTCATTTTTATACCACTCGCAAGCACC\n+ATCGAAAACAATCTTCTAAAATGAAGAGTCCCTGTAGTATATCGCACATT\n+ACCCTGGTCTTGTAAACCAGAAAAGGGGGAAAACGTTTCCTCCCAAGGAC\n+TATCAAGGAAGAAGCTCTAGCTCCACCATCAACACCCAAAGCTGAAATTC\n+TACTTAAACTATTCCTTGATTTCTTCCCCTAAACGACAACAATTTACCCT\n+CATGTGCTATGTCAGTATCAGATTATACCCCCACATAACACCATACCCAC\n+CTGACATGCAATATCTTATGAATGGCCTATGTACGTCGTGCATTAAATTG\n+TCTGCCCCATGAATAATAAGCATGTACATAATATCATTTATCTTACATAA\n+GTACATTATATTATTGATCGTGCATACCCCATCCAAGTCAAATCATTTCC\n+AGTCAACACGCATATCACAGCCCATGTTCCACGAGCTTAATCACCAAGCC\n+GCGGGAAATCAGCAACCCTCCCAACTACGTGTCCCAATCCTCGCTCCGGG\n+CCCATCCAAACGTGGGGGTTTCTACAATGAAACTATACCTGGCATCTGGT\n+TCTTTCTTCAGGGCCATTCCCACCCAACCTCGCCCATTCTTTCCCCTTAA\n+ATAAGACATCTCGATGGACTAATGACTAATCAGCCCATGCTCACACATAA\n+CTGTGATTTCATGCATTTGGTATCTTTTTATATTTGGGGATGCTATGACT\n+CAGCTATGGCCGTCAAAGGCCTCGACGCAGTCAATTAAATTGAAGCTGGA\n+CTTAAATTGAACGTTATTCCTCCGCATCAGCAACCATAAGGTGTTATTCA\n+GTCCATGGTAGCGGGACATAGGAAACAAgtgcacctgtgcacctgtgcac\n+ctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacct\n+gtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgt\n+gcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgc\n+acctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcac\n+ctgtgcacctACCCGCGCAGTAAGCAAGTAATATAGCTTTCTTAATCAAA\n+CCCCCCCTACCCCCCATTAAACTCCACATATGTACATTCAACACAATCTT\n+GCCAAACCCCAAAAACAAGACTAAACAATGCACAATACTTCATGAAGCTT\n+AACCCTCGCATGCCAACCATAATAACTCAACACACCTAACAATCTTAACA\n+GAACTTTCCCCCCGCCATTAATACCAACATGCTACTTTAATCAATAAAAT\n+TTCCATAGACAGGCATCCCCCTAGATCTAATTTTCTAAATCTGTCAACCC\n+TTCTTCCCCC\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/codingSnps_input1.interval
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/codingSnps_input1.interval Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,21 @@
+chr1 1415785 1415786 C C S N C N C N C
+chr1 1420777 1420778 C C Y N C N C N C
+chr1 1469195 1469196 A G R R G G G G G
+chr1 1541789 1541790 T C Y Y N Y N T N
+chr1 1548654 1548655 T T C N C N N N N
+chr1 1549089 1549090 T C A A T A N A N
+chr1 1551984 1551985 C C Y N C N N N N
+chr1 1571349 1571350 G A R N N N N N N
+chr1 1571354 1571355 G G R N N N N N N
+chr1 1589750 1589751 A G G N G N G N G
+chr1 1675899 1675900 G A C C G C G C N
+chr1 1714578 1714579 G G R N A N G N G
+chr1 1837838 1837839 T C Y N T N T N C
+chr1 1839388 1839389 A A T T A T A T A
+chr1 1839389 1839390 T T Y N T N T N C
+chr1 1839603 1839604 G G R N G N G N R
+chr1 1843968 1843969 A G G G R R A A G
+chr1 1844405 1844406 C C Y Y C C N C Y
+chr1 1876878 1876879 A G G N N N N N N
+chr1 1886192 1886193 G N R N G N N N N
+chr1 1890091 1890092 T C Y Y C C N C N

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/codingSnps_input2.interval
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/codingSnps_input2.interval Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,20 @@
+chr22 15452410 15452411 G/T
+chr22 15452482 15452483 A/G
+chr22 15644564 15644565 G/T
+chr22 15645123 15645124 A/C
+chr22 15645193 15645194 A/G
+chr22 15660821 15660822 A/G
+chr22 29352809 29352810 A/C
+chr22 25899978 25899979 C/G
+chr22 44339876 44339877 C/T
+chr22 44339947 44339948 C/G
+chr22 15824618 15824619 C/T
+chr22 15824639 15824640 C/T
+chr22 15825725 15825726 G/T
+chr22 15827035 15827036 G
+chr22 15827135 15827136 C/G
+chr22 15830928 15830929 A/G
+chr22 15830951 15830952 G
+chr22 15830955 15830956 C/T
+chr22 15848885 15848886 C/T
+chr22 15849048 15849049 A/C

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/codingSnps_inputGenes1.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/codingSnps_inputGenes1.bed Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,20 @@
+chr1 67051161 67163158 ENST00000371026 0 - 67052400 67163102 0 17 1290,157,227,99,122,158,152,87,203,195,156,140,157,113,185,175,226, 0,9470,13929,14921,20694,21100,22735,24819,27578,34593,49256,58479,61890,78263,80338,92310,111771,
+chr1 67075869 67163055 ENST00000371023 0 - 67075923 67162979 0 10 198,203,195,156,140,157,113,185,175,123, 0,2870,9885,24548,33771,37182,53555,55630,67602,87063,
+chr1 1843259 1849228 ENST00000378596 0 - 1843585 1847183 0 10 428,135,161,133,155,130,156,120,56,1278, 0,628,1024,1406,1814,2430,3822,4267,4496,4691,
+chr1 1874611 1925136 ENST00000270720 0 - 1876876 1912255 0 18 2538,165,90,67,119,174,156,199,158,103,111,174,105,99,144,85,86,137, 0,3307,5807,6651,10436,11575,13058,15322,17346,18667,19624,20712,32073,33624,35199,35576,37577,50388,
+chr1 1838889 1840572 ENST00000310991 0 - 1839180 1840564 0 5 572,179,42,44,92, 0,662,1302,1454,1591,
+chr1 1838888 1840096 ENST00000378602 0 - 1839180 1839855 0 2 573,545, 0,663,
+chr1 1672537 1699769 ENST00000344463 0 - 1674202 1686705 0 14 1822,83,158,100,155,103,86,155,204,143,169,84,219,182, 0,2328,2812,3045,3305,4135,5019,5264,5868,7862,8495,10713,13989,27050,
+chr1 1836125 1838593 ENST00000307786 0 + 1836579 1838492 0 6 481,51,175,145,101,148, 0,858,1614,1925,2147,2320,
+chr1 1672530 1701368 ENST00000378625 0 - 1674202 1686705 0 14 1829,83,158,100,155,103,86,155,204,143,169,84,219,165, 0,2335,2819,3052,3312,4142,5026,5271,5875,7869,8502,10720,13996,28673,
+chr1 1672537 1699769 ENST00000341426 0 - 1674202 1686705 0 12 1822,83,158,100,155,103,86,106,130,84,219,182, 0,2328,2812,3045,3305,4135,5019,5264,5942,10713,13989,27050,
+chr1 1540746 1555847 ENST00000378710 0 + 1540873 1555773 0 19 130,107,311,172,107,195,143,105,163,134,149,157,161,127,234,179,182,66,313, 0,1004,7885,8270,9291,9487,9782,11146,11333,11570,11792,12169,12515,12769,12985,13629,13881,14135,14788,
+chr1 1672530 1700089 ENST00000341991 0 - 1674202 1686705 0 12 1829,83,158,100,155,103,86,106,130,84,219,45, 0,2335,2819,3052,3312,4142,5026,5271,5949,10720,13996,27514,
+chr1 1540746 1555847 ENST00000355826 0 + 1540873 1555773 0 20 130,107,311,172,107,195,143,108,105,163,134,149,157,161,127,234,179,182,66,313, 0,1004,7885,8270,9291,9487,9782,10042,11146,11333,11570,11792,12169,12515,12769,12985,13629,13881,14135,14788,
+chr1 1836125 1838593 ENST00000378604 0 + 1836579 1838492 0 5 481,175,145,101,148, 0,1614,1925,2147,2320,
+chr1 1540746 1555847 ENST00000357882 0 + 1540873 1555773 0 19 130,107,311,172,107,143,108,105,163,134,149,157,161,127,234,179,182,66,313, 0,1004,7885,8270,9291,9782,10042,11146,11333,11570,11792,12169,12515,12769,12985,13629,13881,14135,14788,
+chr1 1540746 1555847 ENST00000357882 0 + 1540873 1555773 0 19 130,107,311,172,107,143,108,105,163,134,149,157,161,127,234,179,182,66,313, 0,1004,7885,8270,9291,9782,10042,11146,11333,11570,11792,12169,12515,12769,12985,13629,13881,14135,14788,
+chr1 67075991 67163158 ENST00000395250 0 - 67075991 67113089 0 11 27,45,203,195,156,140,157,113,185,175,226, 0,31,2748,9763,24426,33649,37060,53433,55508,67480,86941,
+chr1 201326404 201403155 ENST00000309502 0 + 201364592 201401651 0 6 81,18,100,155,398,2144, 0,1039,37175,37624,38131,74607,
+chr1 8335052 8508585 ENST00000377464 0 - 8337733 8508430 0 17 2715,181,147,721,223,1379,114,162,200,93,163,81,99,100,125,49,181, 0,3013,3694,5790,7358,7706,9357,10277,11650,12340,13406,70321,113519,142657,144999,156220,173352,
+chr1 8335054 8800286 ENST00000400908 0 - 8337733 8638943 0 23 2713,181,147,721,223,1379,114,162,200,93,163,81,99,100,125,49,105,97,106,126,71,469,481, 0,3011,3692,5788,7356,7704,9355,10275,11648,12338,13404,70319,113517,142655,144997,156218,188805,204066,205009,262152,271901,303564,464751,

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/codingSnps_inputGenes2.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/codingSnps_inputGenes2.bed Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,1647 @@\n+chr22\t14504263\t14572999\tuc002zkr.2\t0\t-\t14504263\t14504263\t0\t5\t710,91,136,138,94,\t0,38133,62547,62901,68642,\n+chr22\t14527995\t14572999\tuc002zks.2\t0\t-\t14527995\t14527995\t0\t8\t3826,91,136,138,112,148,111,94,\t0,14401,38815,39169,41036,41268,42685,44910,\n+chr22\t14527995\t14572999\tuc010gqo.1\t0\t-\t14527995\t14527995\t0\t4\t3826,91,136,94,\t0,14401,38815,44910,\n+chr22\t14542065\t14552264\tuc002zkt.2\t0\t+\t14542065\t14542065\t0\t3\t323,88,313,\t0,2416,9886,\n+chr22\t14559619\t14561004\tuc002zku.2\t0\t-\t14559619\t14559619\t0\t1\t1385,\t0,\n+chr22\t14567164\t14572999\tuc002zkv.2\t0\t-\t14567164\t14567164\t0\t5\t138,112,115,111,94,\t0,1867,2099,3516,5741,\n+chr22\t14620243\t14620281\tuc002zkw.1\t0\t-\t14620243\t14620243\t0\t1\t38,\t0,\n+chr22\t14620300\t14620339\tuc002zkx.1\t0\t-\t14620300\t14620300\t0\t1\t39,\t0,\n+chr22\t14621086\t14621125\tuc002zky.1\t0\t+\t14621086\t14621086\t0\t1\t39,\t0,\n+chr22\t14622000\t14622030\tuc002zkz.1\t0\t-\t14622000\t14622000\t0\t1\t30,\t0,\n+chr22\t14623380\t14623414\tuc002zla.1\t0\t-\t14623380\t14623380\t0\t1\t34,\t0,\n+chr22\t14623907\t14623948\tuc002zlb.1\t0\t-\t14623907\t14623907\t0\t1\t41,\t0,\n+chr22\t14625151\t14625185\tuc002zlc.1\t0\t-\t14625151\t14625151\t0\t1\t34,\t0,\n+chr22\t14625678\t14625719\tuc002zld.1\t0\t-\t14625678\t14625678\t0\t1\t41,\t0,\n+chr22\t14628998\t14629023\tuc002zle.1\t0\t-\t14628998\t14628998\t0\t1\t25,\t0,\n+chr22\t14631234\t14634941\tuc002zlf.1\t0\t-\t14631234\t14631234\t0\t1\t3707,\t0,\n+chr22\t14636331\t14667425\tuc002zlg.1\t0\t-\t14636331\t14636331\t0\t12\t346,119,49,167,45,71,71,138,107,174,115,172,\t0,1853,6572,10597,11805,13541,18875,21416,22863,25813,26146,30922,\n+chr22\t14636331\t14667425\tuc002zlh.1\t0\t-\t14638185\t14660411\t0\t12\t346,119,167,45,71,71,138,107,256,174,115,172,\t0,1853,10597,11805,13541,18875,21416,22863,24002,25813,26146,30922,\n+chr22\t14636331\t14667425\tuc010gqp.1\t0\t-\t14638185\t14667390\t0\t11\t346,119,167,45,71,71,138,107,174,115,172,\t0,1853,10597,11805,13541,18875,21416,22863,25813,26146,30922,\n+chr22\t14636331\t14667937\tuc002zli.1\t0\t-\t14662201\t14667885\t0\t12\t346,119,167,45,71,71,138,107,258,174,115,684,\t0,1853,10597,11805,13541,18875,21416,22863,24000,25813,26146,30922,\n+chr22\t14646928\t14667937\tuc002zlj.1\t0\t-\t14646930\t14667390\t0\t10\t167,45,71,71,138,107,174,115,172,400,\t0,1208,2944,8278,10819,12266,15216,15549,20325,20609,\n+chr22\t14654557\t14658598\tuc002zlk.2\t0\t+\t14654557\t14654557\t0\t2\t446,2118,\t0,1923,\n+chr22\t14753080\t14757057\tuc002zll.1\t0\t+\t14753080\t14753080\t0\t3\t41,82,1609,\t0,749,2368,\n+chr22\t14828823\t14829804\tuc002zlm.1\t0\t-\t14828823\t14829804\t0\t1\t981,\t0,\n+chr22\t14872811\t14872932\tuc002zln.1\t0\t+\t14872811\t14872811\t0\t1\t121,\t0,\n+chr22\t15409615\t15409643\tuc002zlo.1\t0\t+\t15409615\t15409615\t0\t1\t28,\t0,\n+chr22\t15451647\t15453700\tuc002zlp.1\t0\t-\t15451766\t15453440\t0\t1\t2053,\t0,\n+chr22\t15462800\t15476000\tuc010gqq.1\t0\t+\t15462800\t15462800\t0\t4\t305,236,102,412,\t0,9747,12166,12788,\n+chr22\t15462800\t15476000\tuc002zlq.2\t0\t+\t15462800\t15462800\t0\t3\t305,236,1034,\t0,9747,12166,\n+chr22\t15462800\t15509720\tuc002zlr.1\t0\t+\t15462800\t15462800\t0\t9\t305,236,102,57,51,162,90,123,304,\t0,9747,12166,20930,35129,36668,45257,45752,46616,\n+chr22\t15462800\t15559521\tuc002zls.1\t0\t+\t15462800\t15462800\t0\t3\t305,162,1136,\t0,36668,95585,\n+chr22\t15480506\t15514580\tuc002zlt.2\t0\t+\t15480506\t15480506\t0\t8\t104,109,57,51,162,181,122,181,\t0,435,3224,17423,18962,27988,28910,33893,\n+chr22\t15607759\t15609328\tuc002zlu.2\t0\t-\t15607759\t15607759\t0\t2\t870,163,\t0,1406,\n+chr22\t15644305\t15682584\tuc002zlv.1\t0\t-\t15644508\t15668963\t0\t4\t994,254,345,88,\t0,16355,24323,38191,\n+chr22\t15688363\t15690225\tuc010gqr.1\t0\t+\t15688363\t15688363\t0\t2\t587,794,\t0,1068,\n+chr22\t15822826\t15869112\tuc002zlw.1\t0\t-\t15823622\t15869004\t0\t10\t940,105,97,91,265,86,251,208,304,282,\t0,1788,2829,3241,4163,6361,8006,26023,29936,46004,\n+chr22\t15826991\t15869112\tuc010gqs.1\t0\t-\t15829218\t15869004\t0\t5\t1380,86,157,304,282,\t0,2196,21858,25771,41839,\n+chr22\t15897459\t15919682\tuc002zlx.1\t0\t+\t15897459\t15897459\t0\t4\t775,128,103,1720,\t0,8303,10754,20503,\n+chr22\t15945848\t15971389\tuc002zly.1\t0\t+\t15945981\t15970710\t0\t13\t271,25,147,113,127,48,164,84,85,12,102,42,2193,\t0,12103,12838,13816,15396,17037,17180,18535,19767,20632,20894,22768,23348,\n+chr22\t15945848\t1'..b'9357748\tuc003bmr.1\t0\t+\t49356293\t49356293\t0\t1\t1455,\t0,\n+chr22\t49364243\t49368260\tuc003bms.1\t0\t-\t49364475\t49368076\t0\t11\t307,82,104,109,82,59,96,134,114,109,408,\t0,477,778,1025,1241,1409,1616,2471,2800,3300,3609,\n+chr22\t49364253\t49368119\tuc003bmt.1\t0\t-\t49364475\t49365909\t0\t8\t297,82,104,109,82,59,96,576,\t0,467,768,1015,1231,1399,1606,3290,\n+chr22\t49364253\t49368260\tuc003bmu.1\t0\t-\t49364475\t49367127\t0\t10\t297,82,104,109,82,59,96,134,609,408,\t0,467,768,1015,1231,1399,1606,2461,2790,3599,\n+chr22\t49364253\t49368260\tuc003bmv.1\t0\t-\t49364475\t49368076\t0\t11\t297,82,104,109,82,59,96,134,114,109,408,\t0,467,768,1015,1231,1399,1606,2461,2790,3290,3599,\n+chr22\t49368320\t49369221\tuc003bmw.2\t0\t+\t49368320\t49368320\t0\t2\t298,329,\t0,572,\n+chr22\t49385996\t49396845\tuc003bmx.1\t0\t+\t49386113\t49396073\t0\t13\t182,106,276,94,242,979,76,173,110,108,71,99,845,\t0,1087,2521,2924,3139,3383,4665,4859,5122,5955,6218,9509,10004,\n+chr22\t49388427\t49396845\tuc003bmy.1\t0\t+\t49388427\t49396073\t0\t11\t366,94,242,979,76,173,110,108,71,99,845,\t0,493,708,952,2234,2428,2691,3524,3787,7078,7573,\n+chr22\t49410314\t49413473\tuc003bna.2\t0\t-\t49410438\t49412666\t0\t8\t444,103,128,125,170,219,241,234,\t0,558,915,1133,1570,1813,2145,2925,\n+chr22\t49410314\t49413473\tuc003bnb.2\t0\t-\t49410438\t49413067\t0\t9\t444,103,128,125,170,219,241,237,234,\t0,558,915,1133,1570,1813,2145,2535,2925,\n+chr22\t49410314\t49413473\tuc003bnc.2\t0\t-\t49410438\t49413067\t0\t8\t444,103,128,125,170,219,241,624,\t0,558,915,1133,1570,1813,2145,2535,\n+chr22\t49410314\t49413473\tuc003bnd.2\t0\t-\t49410438\t49413067\t0\t9\t444,103,128,125,170,219,241,237,189,\t0,558,915,1133,1570,1813,2145,2535,2970,\n+chr22\t49410314\t49413473\tuc003bmz.2\t0\t-\t49410438\t49413067\t0\t9\t444,103,128,125,170,219,241,237,282,\t0,558,915,1133,1570,1813,2145,2535,2877,\n+chr22\t49411884\t49413086\tuc010hbf.1\t0\t-\t49412327\t49413067\t0\t2\t816,237,\t0,965,\n+chr22\t49459935\t49518507\tuc003bne.1\t0\t+\t49459935\t49516606\t0\t23\t63,204,72,109,152,168,117,78,67,274,49,193,114,76,83,125,133,81,24,131,85,2254,2493,\t0,406,1980,3943,4127,4377,4670,8698,9943,20133,22601,22881,24048,29218,29524,30096,30322,31430,36973,40275,41027,45542,56079,\n+chr22\t49482816\t49507731\tuc003bnf.1\t0\t+\t49484072\t49507729\t0\t10\t193,114,76,83,125,133,81,131,85,2254,\t0,1167,6337,6643,7215,7441,8549,17394,18146,22661,\n+chr22\t49505477\t49518504\tuc010hbg.1\t0\t+\t49505533\t49518487\t0\t2\t2254,183,\t0,12844,\n+chr22\t49521122\t49523433\tuc003bng.1\t0\t-\t49521122\t49521122\t0\t2\t1276,750,\t0,1561,\n+chr22\t49523517\t49525653\tuc010hbh.1\t0\t+\t49523529\t49525450\t0\t3\t89,204,666,\t0,1047,1470,\n+chr22\t49523517\t49530593\tuc003bnh.2\t0\t+\t49523529\t49530501\t0\t5\t89,204,284,146,647,\t0,1047,1470,5837,6429,\n+chr22\t49542379\t49584800\tuc003bni.1\t0\t+\t49584070\t49584436\t0\t4\t241,175,121,852,\t0,26034,28087,41569,\n+chr22\t49552785\t49568953\tuc003bnk.1\t0\t-\t49554069\t49567588\t0\t9\t1383,84,98,112,80,80,30,164,159,\t0,1549,1963,2413,8280,9178,10460,14696,16009,\n+chr22\t49552785\t49568953\tuc003bnl.1\t0\t-\t49554069\t49567588\t0\t9\t1383,84,95,112,80,80,30,160,159,\t0,1549,1963,2413,8280,9178,10460,14696,16009,\n+chr22\t49552785\t49568953\tuc003bnm.1\t0\t-\t49554069\t49567588\t0\t10\t1383,84,125,112,80,80,30,164,155,159,\t0,1549,1933,2413,8280,9178,10460,14696,15399,16009,\n+chr22\t49552785\t49568953\tuc003bnn.1\t0\t-\t49554069\t49567588\t0\t10\t1383,84,98,112,80,80,30,164,248,159,\t0,1549,1963,2413,8280,9178,10460,14696,15547,16009,\n+chr22\t49552785\t49568953\tuc003bno.1\t0\t-\t49554069\t49567588\t0\t9\t1383,84,95,112,80,80,30,164,159,\t0,1549,1963,2413,8280,9178,10460,14696,16009,\n+chr22\t49552960\t49568953\tuc010hbi.1\t0\t-\t49552996\t49567588\t0\t10\t42,78,84,98,112,80,80,30,160,159,\t0,1130,1374,1788,2238,8105,9003,10285,14521,15834,\n+chr22\t49569090\t49574466\tuc003bnq.1\t0\t+\t49569090\t49569090\t0\t4\t225,121,49,278,\t0,1376,4953,5098,\n+chr22\t49569090\t49574647\tuc003bnr.1\t0\t+\t49569090\t49569090\t0\t4\t225,121,49,462,\t0,1376,4953,5095,\n+chr22\t49569090\t49584800\tuc003bns.1\t0\t+\t49584070\t49584436\t0\t3\t276,121,852,\t0,1376,14858,\n+chr22\t49569090\t49584800\tuc010hbj.1\t0\t+\t49569090\t49569090\t0\t3\t68,121,852,\t0,1376,14858,\n+chr22\t49584070\t49584436\tuc010hbk.1\t0\t+\t49584070\t49584436\t0\t1\t366,\t0,\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/codingSnps_output1.interval
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/codingSnps_output1.interval Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,21 @@
+chr1 1541789 1541790 C/T ENST00000355826 Phe:Leu/Phe 15 T TTC:CTC/TTC
+chr1 1541789 1541790 C/T ENST00000357882 Phe:Leu/Phe 15 T TTC:CTC/TTC
+chr1 1541789 1541790 C/T ENST00000357882 Phe:Leu/Phe 15 T TTC:CTC/TTC
+chr1 1541789 1541790 C/T ENST00000378710 Phe:Leu/Phe 15 T TTC:CTC/TTC
+chr1 1548654 1548655 C ENST00000355826 Met:Thr 45 T ATG:ACG
+chr1 1548654 1548655 C ENST00000357882 Met:Thr 45 T ATG:ACG
+chr1 1548654 1548655 C ENST00000357882 Met:Thr 45 T ATG:ACG
+chr1 1548654 1548655 C ENST00000378710 Met:Thr 45 T ATG:ACG
+chr1 1675899 1675900 C ENST00000341991 Asn:Lys 262 C AAC:AAG
+chr1 1675899 1675900 C ENST00000378625 Asn:Lys 407 C AAC:AAG
+chr1 1675899 1675900 C ENST00000341426 Asn:Lys 262 C AAC:AAG
+chr1 1675899 1675900 C ENST00000344463 Asn:Lys 407 C AAC:AAG
+chr1 1837838 1837839 C/T ENST00000307786 Trp:Arg/Trp 60 T TGG:CGG/TGG
+chr1 1837838 1837839 C/T ENST00000378604 Trp:Arg/Trp 43 T TGG:CGG/TGG
+chr1 1839388 1839389 T ENST00000378602 Met:Lys 126 T ATG:AAG
+chr1 1839388 1839389 T ENST00000310991 Met:Lys 141 T ATG:AAG
+chr1 1839389 1839390 C/T ENST00000378602 Met:Val/Met 126 A ATG:GTG/ATG
+chr1 1839389 1839390 C/T ENST00000310991 Met:Val/Met 141 A ATG:GTG/ATG
+chr1 1844405 1844406 C/T ENST00000378596 Glu:Glu/Lys 187 G GAG:GAG/AAG
+chr1 1876878 1876879 G ENST00000270720 Stop:Gln 763 T TAG:CAG
+chr1 1890091 1890092 C/T ENST00000270720 Ile:Val/Ile 363 A ATC:GTC/ATC

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/codingSnps_output2.interval
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/codingSnps_output2.interval Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,17 @@
+chr22 15452410 15452411 G/T uc002zlp.1 Pro:Pro/Thr 344 C CCA:CCA/ACA
+chr22 15452482 15452483 A/G uc002zlp.1 Trp:Trp/Arg 320 T TGG:TGG/CGG
+chr22 15644564 15644565 G/T uc002zlv.1 His:His/Asn 442 C CAC:CAC/AAC
+chr22 15645123 15645124 A/C uc002zlv.1 Phe:Phe/Leu 255 T TTT:TTT/TTG
+chr22 15645193 15645194 A/G uc002zlv.1 Pro:Leu/Pro 232 C CCG:CTG/CCG
+chr22 15660821 15660822 A/G uc002zlv.1 Thr:Met/Thr 143 C ACG:ATG/ACG
+chr22 15824618 15824619 C/T uc002zlw.1 Ser:Ser/Asn 526 G AGC:AGC/AAC
+chr22 15824639 15824640 C/T uc002zlw.1 Ala:Gly/Glu 519 C GCG:GGG/GAG
+chr22 15825725 15825726 G/T uc002zlw.1 Gln:Pro/Gln 469 A CAA:CCA/CAA
+chr22 15827035 15827036 G uc002zlw.1 Glu:Asp 414 G GAG:GAC
+chr22 15827135 15827136 C/G uc002zlw.1 Gly:Gly/Ala 381 G GGT:GGT/GCT
+chr22 15830928 15830929 A/G uc002zlw.1 Ala:Ser/Pro 281 G GCA:TCA/CCA
+chr22 15830951 15830952 G uc002zlw.1 Leu:Pro 273 T CTT:CCT
+chr22 15830955 15830956 C/T uc002zlw.1 Ser:Gly/Ser 272 A AGC:GGC/AGC
+chr22 15848885 15848886 C/T uc002zlw.1 Ser:Trp/Stop 217 C TCG:TGG/TAG
+chr22 15848885 15848886 C/T uc010gqs.1 Ser:Trp/Stop 200 C TCG:TGG/TAG
+chr22 15849048 15849049 A/C uc002zlw.1 Gly:Stop/Gly 163 G GGA:TGA/GGA

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/codingSnps_output3.interval
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/codingSnps_output3.interval Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,16 @@
+chr22 15452410 15452411 G/T uc002zlp.1 Pro:Ala/Ser 344 C CCA:GCA/TCA
+chr22 15452482 15452483 A/G uc002zlp.1 Trp:Arg/Gly 320 T TGG:AGG/GGG
+chr22 15644564 15644565 G/T uc002zlv.1 His:Asp/Tyr 442 C CAC:GAC/TAC
+chr22 15645123 15645124 A/C uc002zlv.1 Phe:Leu/Phe 255 T TTT:TTA/TTC
+chr22 15645193 15645194 A/G uc002zlv.1 Pro:Gln/Arg 232 C CCG:CAG/CGG
+chr22 15660821 15660822 A/G uc002zlv.1 Thr:Lys/Arg 143 C ACG:AAG/AGG
+chr22 15824618 15824619 C/T uc002zlw.1 Ser:Thr/Ile 526 G AGC:ACC/ATC
+chr22 15824639 15824640 C/T uc002zlw.1 Ala:Ala/Val 519 C GCG:GCG/GTG
+chr22 15825725 15825726 G/T uc002zlw.1 Gln:Arg/Leu 469 A CAA:CGA/CTA
+chr22 15827135 15827136 C/G uc002zlw.1 Gly:Ala/Gly 381 G GGT:GCT/GGT
+chr22 15830928 15830929 A/G uc002zlw.1 Ala:Thr/Ala 281 G GCA:ACA/GCA
+chr22 15830951 15830952 G uc002zlw.1 Leu:Arg 273 T CTT:CGT
+chr22 15830955 15830956 C/T uc002zlw.1 Ser:Arg/Cys 272 A AGC:CGC/TGC
+chr22 15848885 15848886 C/T uc002zlw.1 Ser:Ser/Leu 217 C TCG:TCG/TTG
+chr22 15848885 15848886 C/T uc010gqs.1 Ser:Ser/Leu 200 C TCG:TCG/TTG
+chr22 15849048 15849049 A/C uc002zlw.1 Gly:Arg/Arg 163 G GGA:AGA/CGA

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/column_maker_out1.interval
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/column_maker_out1.interval Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,65 @@
+chr1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 - 388.0
+chr1 147984545 147984630 CCDS990.1_cds_0_0_chr1_147984546_f 0 + 85.0
+chr1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 - 182.0
+chr1 148185136 148185276 CCDS996.1_cds_0_0_chr1_148185137_f 0 + 140.0
+chr10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 - 1501.0
+chr11 116124407 116124501 CCDS8374.1_cds_0_0_chr11_116124408_r 0 - 94.0
+chr11 116206508 116206563 CCDS8377.1_cds_0_0_chr11_116206509_f 0 + 55.0
+chr11 116211733 116212337 CCDS8378.1_cds_0_0_chr11_116211734_r 0 - 604.0
+chr11 1812377 1812407 CCDS7726.1_cds_0_0_chr11_1812378_f 0 + 30.0
+chr12 38440094 38440321 CCDS8736.1_cds_0_0_chr12_38440095_r 0 - 227.0
+chr13 112381694 112381953 CCDS9526.1_cds_0_0_chr13_112381695_f 0 + 259.0
+chr14 98710240 98712285 CCDS9949.1_cds_0_0_chr14_98710241_r 0 - 2045.0
+chr15 41486872 41487060 CCDS10096.1_cds_0_0_chr15_41486873_r 0 - 188.0
+chr15 41673708 41673857 CCDS10097.1_cds_0_0_chr15_41673709_f 0 + 149.0
+chr15 41679161 41679250 CCDS10098.1_cds_0_0_chr15_41679162_r 0 - 89.0
+chr15 41826029 41826196 CCDS10101.1_cds_0_0_chr15_41826030_f 0 + 167.0
+chr16 142908 143003 CCDS10397.1_cds_0_0_chr16_142909_f 0 + 95.0
+chr16 179963 180135 CCDS10401.1_cds_0_0_chr16_179964_r 0 - 172.0
+chr16 244413 244681 CCDS10402.1_cds_0_0_chr16_244414_f 0 + 268.0
+chr16 259268 259383 CCDS10403.1_cds_0_0_chr16_259269_r 0 - 115.0
+chr18 23786114 23786321 CCDS11891.1_cds_0_0_chr18_23786115_r 0 - 207.0
+chr18 59406881 59407046 CCDS11985.1_cds_0_0_chr18_59406882_f 0 + 165.0
+chr18 59455932 59456337 CCDS11986.1_cds_0_0_chr18_59455933_r 0 - 405.0
+chr18 59600586 59600754 CCDS11988.1_cds_0_0_chr18_59600587_f 0 + 168.0
+chr19 59068595 59069564 CCDS12866.1_cds_0_0_chr19_59068596_f 0 + 969.0
+chr19 59236026 59236146 CCDS12872.1_cds_0_0_chr19_59236027_r 0 - 120.0
+chr19 59297998 59298008 CCDS12877.1_cds_0_0_chr19_59297999_f 0 + 10.0
+chr19 59302168 59302288 CCDS12878.1_cds_0_0_chr19_59302169_r 0 - 120.0
+chr2 118288583 118288668 CCDS2120.1_cds_0_0_chr2_118288584_f 0 + 85.0
+chr2 118394148 118394202 CCDS2121.1_cds_0_0_chr2_118394149_r 0 - 54.0
+chr2 220190202 220190242 CCDS2441.1_cds_0_0_chr2_220190203_f 0 + 40.0
+chr2 220229609 220230869 CCDS2443.1_cds_0_0_chr2_220229610_r 0 - 1260.0
+chr20 33330413 33330423 CCDS13249.1_cds_0_0_chr20_33330414_r 0 - 10.0
+chr20 33513606 33513792 CCDS13255.1_cds_0_0_chr20_33513607_f 0 + 186.0
+chr20 33579500 33579527 CCDS13256.1_cds_0_0_chr20_33579501_r 0 - 27.0
+chr20 33593260 33593348 CCDS13257.1_cds_0_0_chr20_33593261_f 0 + 88.0
+chr21 32707032 32707192 CCDS13614.1_cds_0_0_chr21_32707033_f 0 + 160.0
+chr21 32869641 32870022 CCDS13615.1_cds_0_0_chr21_32869642_r 0 - 381.0
+chr21 33321040 33322012 CCDS13620.1_cds_0_0_chr21_33321041_f 0 + 972.0
+chr21 33744994 33745040 CCDS13625.1_cds_0_0_chr21_33744995_r 0 - 46.0
+chr22 30120223 30120265 CCDS13897.1_cds_0_0_chr22_30120224_f 0 + 42.0
+chr22 30160419 30160661 CCDS13898.1_cds_0_0_chr22_30160420_r 0 - 242.0
+chr22 30665273 30665360 CCDS13901.1_cds_0_0_chr22_30665274_f 0 + 87.0
+chr22 30939054 30939266 CCDS13903.1_cds_0_0_chr22_30939055_r 0 - 212.0
+chr5 131424298 131424460 CCDS4149.1_cds_0_0_chr5_131424299_f 0 + 162.0
+chr5 131556601 131556672 CCDS4151.1_cds_0_0_chr5_131556602_r 0 - 71.0
+chr5 131621326 131621419 CCDS4152.1_cds_0_0_chr5_131621327_f 0 + 93.0
+chr5 131847541 131847666 CCDS4155.1_cds_0_0_chr5_131847542_r 0 - 125.0
+chr6 108299600 108299744 CCDS5061.1_cds_0_0_chr6_108299601_r 0 - 144.0
+chr6 108594662 108594687 CCDS5063.1_cds_0_0_chr6_108594663_f 0 + 25.0
+chr6 108640045 108640151 CCDS5064.1_cds_0_0_chr6_108640046_r 0 - 106.0
+chr6 108722976 108723115 CCDS5067.1_cds_0_0_chr6_108722977_f 0 + 139.0
+chr7 113660517 113660685 CCDS5760.1_cds_0_0_chr7_113660518_f 0 + 168.0
+chr7 116512159 116512389 CCDS5771.1_cds_0_0_chr7_116512160_r 0 - 230.0
+chr7 116714099 116714152 CCDS5773.1_cds_0_0_chr7_116714100_f 0 + 53.0
+chr7 116945541 116945787 CCDS5774.1_cds_0_0_chr7_116945542_r 0 - 246.0
+chr8 118881131 118881317 CCDS6324.1_cds_0_0_chr8_118881132_r 0 - 186.0
+chr9 128764156 128764189 CCDS6914.1_cds_0_0_chr9_128764157_f 0 + 33.0
+chr9 128787519 128789136 CCDS6915.1_cds_0_0_chr9_128787520_r 0 - 1617.0
+chr9 128882427 128882523 CCDS6917.1_cds_0_0_chr9_128882428_f 0 + 96.0
+chr9 128937229 128937445 CCDS6919.1_cds_0_0_chr9_128937230_r 0 - 216.0
+chrX 122745047 122745924 CCDS14606.1_cds_0_0_chrX_122745048_f 0 + 877.0
+chrX 152648964 152649196 CCDS14733.1_cds_0_0_chrX_152648965_r 0 - 232.0
+chrX 152691446 152691471 CCDS14735.1_cds_0_0_chrX_152691447_f 0 + 25.0
+chrX 152694029 152694263 CCDS14736.1_cds_0_0_chrX_152694030_r 0 - 234.0

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/column_maker_out2.interval
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/column_maker_out2.interval Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,5 @@
+chr1 4348187 4348589 3.70 4.90 2.55 0.24 0.46 3.7
+chr1 4488177 4488442 4.03 5.77 1.92 -0.67 0.81 4.03
+chr1 4774091 4774440 8.07 8.33 7.82 0.85 -0.40 8.07
+chr1 4800122 4800409 6.40 7.35 5.44 1.19 -0.42 6.4
+chr1 4878925 4879277 2.18 0.28 4.93 -0.96 1.24 2.18

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/column_maker_out3.interval
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/column_maker_out3.interval Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,5 @@
+chr1 4348187 4348589 3.70 4.90 2.55 0.24 0.46 4
+chr1 4488177 4488442 4.03 5.77 1.92 -0.67 0.81 4
+chr1 4774091 4774440 8.07 8.33 7.82 0.85 -0.40 8
+chr1 4800122 4800409 6.40 7.35 5.44 1.19 -0.42 6
+chr1 4878925 4879277 2.18 0.28 4.93 -0.96 1.24 2

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/convert_SOLiD_color2nuc_test1.out
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/convert_SOLiD_color2nuc_test1.out Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,22 @@
+>2_14_26_F3
+TGTCATGAGAAAGACAGCCGACACTCAAGTCAACGTATCTCTGGT
+>2_14_192_F3
+GTTTCAGACAAATGGGCCAGGGAGGCTCTCACATCAAGACAGAGC
+>2_14_233_F3
+TGTTTGCGATGTGACTGATGAAGATGGAATACTCCACGACACTCG
+>2_14_294_F3
+CATTGACGATTTTTTTCATCGACTCGACCGCCCCGCAAGCGGCGA
+>2_14_463_F3
+GCTTAGGCCTTTCCTCCTTTAGTGCCTCTCTTCTAAAGACAAGAG
+>2_14_578_F3
+GCAACGGCTACCAGGAGATCAGTGGTTGCCACCTCATGACAAGAG
+>2_14_956_F3
+CAAGTAATTTCTGAAATCCCAACTTCATCAGAAACAGCTCCAGCA
+>2_14_988_F3
+CTGAAGGCATGGGCACCTTATTTCGGATAATTGCCAACCCTACGC
+>2_14_1028_F3
+GTCTAATTGTTGTTGTCCTTGCGTGTGCCTGTTTACAAGTGTAGT
+>2_14_1035_F3
+TTAATACCGCCGATCACCTTGTTCAAAATCTTATTGGATGTTATC
+>2_14_1157_F3
+ATTAAGTTCCTAGTCGCTCCTAAAAGCCAAGTTTTGCGTTGTCTT

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/convert_SOLiD_color2nuc_test1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/convert_SOLiD_color2nuc_test1.txt Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,22 @@
+>2_14_26_F3
+T011213122200221123032111221021210131332222101
+>2_14_192_F3
+T110021221100310030120022032222111321022112223
+>2_14_233_F3
+T011001332311121212312022310203312201132111223
+>2_14_294_F3
+T213012132300000021323212232103300033102330332
+>2_14_463_F3
+T132032030200202202003211302222202230022110222
+>2_14_578_F3
+T131013032310120222321211010130110221312110222
+>2_14_956_F3
+T210213030022120032001012021321220011232201231
+>2_14_988_F3
+T221202031310031102033002302330301301010023133
+>2_14_1028_F3
+T112230301101101120201331111302110031102111321
+>2_14_1035_F3
+T003033103303232110201102100032203301023110332
+>2_14_1157_F3
+T330302102023212332202300023010210001331011220
\ No newline at end of file

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/cor.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/cor.tabular Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,21 @@
+Person Height Self Esteem
+1 68 4.1
+2 71 4.6
+3 62 3.8
+4 75 4.4
+5 58 3.2
+6 60 3.1
+7 67 3.8
+8 68 4.1
+9 71 4.3
+1 69 3.7
+1 68 3.5
+1 67 3.2
+1 63 3.7
+1 62 3.3
+1 60 3.4
+1 63 4.0
+1 65 4.1
+1 67 3.8
+1 63 3.4
+2 61 3.6
\ No newline at end of file

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/cor_out.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/cor_out.txt Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,2 @@
+1.0 0.730635686279
+0.730635686279 1.0

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/count_gff_features_out1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/count_gff_features_out1.txt Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,1 @@
+3

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/count_gff_features_out2.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/count_gff_features_out2.txt Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,1 @@
+14

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/cuffcompare_in1.gtf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/cuffcompare_in1.gtf Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,100 @@\n+chr1\tCufflinks\ttranscript\t3111450\t3111490\t1000\t.\t.\tgene_id "CUFF.1"; transcript_id "CUFF.1.1"; FPKM "20.6079364877"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.751960"; cov "1.317073";\n+chr1\tCufflinks\texon\t3111450\t3111490\t1000\t.\t.\tgene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "1"; FPKM "20.6079364877"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.751960"; cov "1.317073";\n+chr1\tCufflinks\ttranscript\t3111546\t3111576\t1000\t.\t.\tgene_id "CUFF.3"; transcript_id "CUFF.3.1"; FPKM "27.2556579354"; frac "1.000000"; conf_lo "0.000000"; conf_hi "65.800979"; cov "1.741935";\n+chr1\tCufflinks\texon\t3111546\t3111576\t1000\t.\t.\tgene_id "CUFF.3"; transcript_id "CUFF.3.1"; exon_number "1"; FPKM "27.2556579354"; frac "1.000000"; conf_lo "0.000000"; conf_hi "65.800979"; cov "1.741935";\n+chr1\tCufflinks\ttranscript\t3200326\t3200352\t1000\t.\t.\tgene_id "CUFF.5"; transcript_id "CUFF.5.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";\n+chr1\tCufflinks\texon\t3200326\t3200352\t1000\t.\t.\tgene_id "CUFF.5"; transcript_id "CUFF.5.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";\n+chr1\tCufflinks\ttranscript\t3200023\t3200191\t1000\t.\t.\tgene_id "CUFF.7"; transcript_id "CUFF.7.1"; FPKM "9.9991171124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "19.998234"; cov "0.639053";\n+chr1\tCufflinks\texon\t3200023\t3200191\t1000\t.\t.\tgene_id "CUFF.7"; transcript_id "CUFF.7.1"; exon_number "1"; FPKM "9.9991171124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "19.998234"; cov "0.639053";\n+chr1\tCufflinks\ttranscript\t3201078\t3201481\t1000\t.\t.\tgene_id "CUFF.9"; transcript_id "CUFF.9.1"; FPKM "17.7768957078"; frac "1.000000"; conf_lo "9.153835"; conf_hi "26.399957"; cov "1.136139";\n+chr1\tCufflinks\texon\t3201078\t3201481\t1000\t.\t.\tgene_id "CUFF.9"; transcript_id "CUFF.9.1"; exon_number "1"; FPKM "17.7768957078"; frac "1.000000"; conf_lo "9.153835"; conf_hi "26.399957"; cov "1.136139";\n+chr1\tCufflinks\ttranscript\t3201673\t3201699\t1000\t.\t.\tgene_id "CUFF.11"; transcript_id "CUFF.11.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";\n+chr1\tCufflinks\texon\t3201673\t3201699\t1000\t.\t.\tgene_id "CUFF.11"; transcript_id "CUFF.11.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";\n+chr1\tCufflinks\ttranscript\t3204755\t3204833\t1000\t.\t.\tgene_id "CUFF.13"; transcript_id "CUFF.13.1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";\n+chr1\tCufflinks\texon\t3204755\t3204833\t1000\t.\t.\tgene_id "CUFF.13"; transcript_id "CUFF.13.1"; exon_number "1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";\n+chr1\tCufflinks\ttranscript\t3212214\t3212292\t1000\t.\t.\tgene_id "CUFF.15"; transcript_id "CUFF.15.1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";\n+chr1\tCufflinks\texon\t3212214\t3212292\t1000\t.\t.\tgene_id "CUFF.15"; transcript_id "CUFF.15.1"; exon_number "1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";\n+chr1\tCufflinks\ttranscript\t3213096\t3213192\t1000\t.\t.\tgene_id "CUFF.17"; transcript_id "CUFF.17.1"; FPKM "8.7105710927"; frac "1.000000"; conf_lo "0.000000"; conf_hi "21.029179"; cov "0.556701";\n+chr1\tCufflinks\texon\t3213096\t3213192\t1000\t.\t.\tgene_id "CUFF.17"; transcript_id "CUFF.17.1"; exon_number "1"; FPKM "8.7105710927"; frac "1.000000"; conf_lo "0.000000"; conf_hi "21.029179"; cov "0.556701";\n+chr1\tCufflinks\ttranscript\t3212368\t3212439\t1000\t.\t.\tgene_id "CUFF.19"; transcript_id "CUFF.19.1"; FPKM "29.3376873610"; frac "1.000000"; conf_lo "3.097262"; conf_hi "55.578113"; cov "1.875000";\n+chr1\tCufflinks\texon\t3212368\t3212439\t1000\t.\t.\tgene_id "CUFF.19"; transcript_id "CUFF.19.1"; exon_number "1"; FPKM "29.3376873610"; frac "1.000000"; conf_lo "3.097262"; conf_hi "55.578113"; cov "1.875000";\n+chr1\tCufflinks'..b'0000";\n+chr1\tCufflinks\ttranscript\t3363215\t3363278\t1000\t.\t.\tgene_id "CUFF.81"; transcript_id "CUFF.81.1"; FPKM "13.2019593124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.872349"; cov "0.843750";\n+chr1\tCufflinks\texon\t3363215\t3363278\t1000\t.\t.\tgene_id "CUFF.81"; transcript_id "CUFF.81.1"; exon_number "1"; FPKM "13.2019593124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.872349"; cov "0.843750";\n+chr1\tCufflinks\ttranscript\t3363754\t3363849\t1000\t.\t.\tgene_id "CUFF.83"; transcript_id "CUFF.83.1"; FPKM "13.2019593124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "28.446269"; cov "0.843750";\n+chr1\tCufflinks\texon\t3363754\t3363849\t1000\t.\t.\tgene_id "CUFF.83"; transcript_id "CUFF.83.1"; exon_number "1"; FPKM "13.2019593124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "28.446269"; cov "0.843750";\n+chr1\tCufflinks\ttranscript\t3367136\t3367162\t1000\t.\t.\tgene_id "CUFF.85"; transcript_id "CUFF.85.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";\n+chr1\tCufflinks\texon\t3367136\t3367162\t1000\t.\t.\tgene_id "CUFF.85"; transcript_id "CUFF.85.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";\n+chr1\tCufflinks\ttranscript\t3367334\t3367382\t1000\t.\t.\tgene_id "CUFF.87"; transcript_id "CUFF.87.1"; FPKM "17.2433754285"; frac "1.000000"; conf_lo "0.000000"; conf_hi "41.629191"; cov "1.102041";\n+chr1\tCufflinks\texon\t3367334\t3367382\t1000\t.\t.\tgene_id "CUFF.87"; transcript_id "CUFF.87.1"; exon_number "1"; FPKM "17.2433754285"; frac "1.000000"; conf_lo "0.000000"; conf_hi "41.629191"; cov "1.102041";\n+chr1\tCufflinks\ttranscript\t3377212\t3377262\t1000\t.\t.\tgene_id "CUFF.89"; transcript_id "CUFF.89.1"; FPKM "16.5671646274"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.996674"; cov "1.058824";\n+chr1\tCufflinks\texon\t3377212\t3377262\t1000\t.\t.\tgene_id "CUFF.89"; transcript_id "CUFF.89.1"; exon_number "1"; FPKM "16.5671646274"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.996674"; cov "1.058824";\n+chr1\tCufflinks\ttranscript\t3391326\t3391352\t1000\t.\t.\tgene_id "CUFF.91"; transcript_id "CUFF.91.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";\n+chr1\tCufflinks\texon\t3391326\t3391352\t1000\t.\t.\tgene_id "CUFF.91"; transcript_id "CUFF.91.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";\n+chr1\tCufflinks\ttranscript\t3435842\t3435880\t1000\t.\t.\tgene_id "CUFF.93"; transcript_id "CUFF.93.1"; FPKM "21.6647537435"; frac "1.000000"; conf_lo "0.000000"; conf_hi "52.303342"; cov "1.384615";\n+chr1\tCufflinks\texon\t3435842\t3435880\t1000\t.\t.\tgene_id "CUFF.93"; transcript_id "CUFF.93.1"; exon_number "1"; FPKM "21.6647537435"; frac "1.000000"; conf_lo "0.000000"; conf_hi "52.303342"; cov "1.384615";\n+chr1\tCufflinks\ttranscript\t3447762\t3447788\t1000\t.\t.\tgene_id "CUFF.95"; transcript_id "CUFF.95.1"; FPKM "46.9402997776"; frac "1.000000"; conf_lo "0.000000"; conf_hi "101.142289"; cov "3.000000";\n+chr1\tCufflinks\texon\t3447762\t3447788\t1000\t.\t.\tgene_id "CUFF.95"; transcript_id "CUFF.95.1"; exon_number "1"; FPKM "46.9402997776"; frac "1.000000"; conf_lo "0.000000"; conf_hi "101.142289"; cov "3.000000";\n+chr1\tCufflinks\ttranscript\t3450907\t3450965\t1000\t.\t.\tgene_id "CUFF.97"; transcript_id "CUFF.97.1"; FPKM "21.4811541355"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.285454"; cov "1.372881";\n+chr1\tCufflinks\texon\t3450907\t3450965\t1000\t.\t.\tgene_id "CUFF.97"; transcript_id "CUFF.97.1"; exon_number "1"; FPKM "21.4811541355"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.285454"; cov "1.372881";\n+chr1\tCufflinks\ttranscript\t3451052\t3451109\t1000\t.\t.\tgene_id "CUFF.99"; transcript_id "CUFF.99.1"; FPKM "14.5676792413"; frac "1.000000"; conf_lo "0.000000"; conf_hi "35.169489"; cov "0.931034";\n+chr1\tCufflinks\texon\t3451052\t3451109\t1000\t.\t.\tgene_id "CUFF.99"; transcript_id "CUFF.99.1"; exon_number "1"; FPKM "14.5676792413"; frac "1.000000"; conf_lo "0.000000"; conf_hi "35.169489"; cov "0.931034";\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/cuffcompare_in1_liftover_mapped.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/cuffcompare_in1_liftover_mapped.bed Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,86 @@\n+chr1\tCufflinks\ttranscript\t3022555\t3022596\t1000\t.\t.\tgene_id "CUFF.1"; transcript_id "CUFF.1.1"; FPKM "20.6079364877"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.751960"; cov "1.317073";\n+chr1\tCufflinks\texon\t3022555\t3022596\t1000\t.\t.\tgene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "1"; FPKM "20.6079364877"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.751960"; cov "1.317073";\n+chr1\tCufflinks\ttranscript\t3117334\t3117360\t1000\t.\t.\tgene_id "CUFF.5"; transcript_id "CUFF.5.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";\n+chr1\tCufflinks\texon\t3117334\t3117360\t1000\t.\t.\tgene_id "CUFF.5"; transcript_id "CUFF.5.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";\n+chr1\tCufflinks\ttranscript\t3117031\t3117199\t1000\t.\t.\tgene_id "CUFF.7"; transcript_id "CUFF.7.1"; FPKM "9.9991171124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "19.998234"; cov "0.639053";\n+chr1\tCufflinks\texon\t3117031\t3117199\t1000\t.\t.\tgene_id "CUFF.7"; transcript_id "CUFF.7.1"; exon_number "1"; FPKM "9.9991171124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "19.998234"; cov "0.639053";\n+chr1\tCufflinks\ttranscript\t3118118\t3118521\t1000\t.\t.\tgene_id "CUFF.9"; transcript_id "CUFF.9.1"; FPKM "17.7768957078"; frac "1.000000"; conf_lo "9.153835"; conf_hi "26.399957"; cov "1.136139";\n+chr1\tCufflinks\texon\t3118118\t3118521\t1000\t.\t.\tgene_id "CUFF.9"; transcript_id "CUFF.9.1"; exon_number "1"; FPKM "17.7768957078"; frac "1.000000"; conf_lo "9.153835"; conf_hi "26.399957"; cov "1.136139";\n+chr1\tCufflinks\ttranscript\t3118713\t3118739\t1000\t.\t.\tgene_id "CUFF.11"; transcript_id "CUFF.11.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";\n+chr1\tCufflinks\texon\t3118713\t3118739\t1000\t.\t.\tgene_id "CUFF.11"; transcript_id "CUFF.11.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";\n+chr1\tCufflinks\ttranscript\t3121789\t3121867\t1000\t.\t.\tgene_id "CUFF.13"; transcript_id "CUFF.13.1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";\n+chr1\tCufflinks\texon\t3121789\t3121867\t1000\t.\t.\tgene_id "CUFF.13"; transcript_id "CUFF.13.1"; exon_number "1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";\n+chr1\tCufflinks\ttranscript\t3128503\t3128581\t1000\t.\t.\tgene_id "CUFF.15"; transcript_id "CUFF.15.1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";\n+chr1\tCufflinks\texon\t3128503\t3128581\t1000\t.\t.\tgene_id "CUFF.15"; transcript_id "CUFF.15.1"; exon_number "1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";\n+chr1\tCufflinks\ttranscript\t3129386\t3129482\t1000\t.\t.\tgene_id "CUFF.17"; transcript_id "CUFF.17.1"; FPKM "8.7105710927"; frac "1.000000"; conf_lo "0.000000"; conf_hi "21.029179"; cov "0.556701";\n+chr1\tCufflinks\texon\t3129386\t3129482\t1000\t.\t.\tgene_id "CUFF.17"; transcript_id "CUFF.17.1"; exon_number "1"; FPKM "8.7105710927"; frac "1.000000"; conf_lo "0.000000"; conf_hi "21.029179"; cov "0.556701";\n+chr1\tCufflinks\ttranscript\t3128657\t3128728\t1000\t.\t.\tgene_id "CUFF.19"; transcript_id "CUFF.19.1"; FPKM "29.3376873610"; frac "1.000000"; conf_lo "3.097262"; conf_hi "55.578113"; cov "1.875000";\n+chr1\tCufflinks\texon\t3128657\t3128728\t1000\t.\t.\tgene_id "CUFF.19"; transcript_id "CUFF.19.1"; exon_number "1"; FPKM "29.3376873610"; frac "1.000000"; conf_lo "3.097262"; conf_hi "55.578113"; cov "1.875000";\n+chr1\tCufflinks\ttranscript\t3162445\t3162500\t1000\t.\t.\tgene_id "CUFF.23"; transcript_id "CUFF.23.1"; FPKM "23.4701498888"; frac "1.000000"; conf_lo "0.000000"; conf_hi "50.571145"; cov "1.500000";\n+chr1\tCufflinks\texon\t3162445\t3162500\t1000\t.\t.\tgene_id "CUFF.23"; transcript_id "CUFF.23.1"; exon_number "1"; FPKM "23.4701498888"; frac "1.000000"; conf_lo "0.000000"; conf_hi "50.571145"; cov "1.500000";\n+chr1\tCuffli'..b'0000";\n+chr1\tCufflinks\ttranscript\t3285318\t3285381\t1000\t.\t.\tgene_id "CUFF.81"; transcript_id "CUFF.81.1"; FPKM "13.2019593124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.872349"; cov "0.843750";\n+chr1\tCufflinks\texon\t3285318\t3285381\t1000\t.\t.\tgene_id "CUFF.81"; transcript_id "CUFF.81.1"; exon_number "1"; FPKM "13.2019593124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.872349"; cov "0.843750";\n+chr1\tCufflinks\ttranscript\t3285858\t3285953\t1000\t.\t.\tgene_id "CUFF.83"; transcript_id "CUFF.83.1"; FPKM "13.2019593124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "28.446269"; cov "0.843750";\n+chr1\tCufflinks\texon\t3285858\t3285953\t1000\t.\t.\tgene_id "CUFF.83"; transcript_id "CUFF.83.1"; exon_number "1"; FPKM "13.2019593124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "28.446269"; cov "0.843750";\n+chr1\tCufflinks\ttranscript\t3289268\t3289294\t1000\t.\t.\tgene_id "CUFF.85"; transcript_id "CUFF.85.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";\n+chr1\tCufflinks\texon\t3289268\t3289294\t1000\t.\t.\tgene_id "CUFF.85"; transcript_id "CUFF.85.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";\n+chr1\tCufflinks\ttranscript\t3289466\t3289514\t1000\t.\t.\tgene_id "CUFF.87"; transcript_id "CUFF.87.1"; FPKM "17.2433754285"; frac "1.000000"; conf_lo "0.000000"; conf_hi "41.629191"; cov "1.102041";\n+chr1\tCufflinks\texon\t3289466\t3289514\t1000\t.\t.\tgene_id "CUFF.87"; transcript_id "CUFF.87.1"; exon_number "1"; FPKM "17.2433754285"; frac "1.000000"; conf_lo "0.000000"; conf_hi "41.629191"; cov "1.102041";\n+chr1\tCufflinks\ttranscript\t3300382\t3300432\t1000\t.\t.\tgene_id "CUFF.89"; transcript_id "CUFF.89.1"; FPKM "16.5671646274"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.996674"; cov "1.058824";\n+chr1\tCufflinks\texon\t3300382\t3300432\t1000\t.\t.\tgene_id "CUFF.89"; transcript_id "CUFF.89.1"; exon_number "1"; FPKM "16.5671646274"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.996674"; cov "1.058824";\n+chr1\tCufflinks\ttranscript\t3317446\t3317472\t1000\t.\t.\tgene_id "CUFF.91"; transcript_id "CUFF.91.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";\n+chr1\tCufflinks\texon\t3317446\t3317472\t1000\t.\t.\tgene_id "CUFF.91"; transcript_id "CUFF.91.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";\n+chr1\tCufflinks\ttranscript\t3365246\t3365284\t1000\t.\t.\tgene_id "CUFF.93"; transcript_id "CUFF.93.1"; FPKM "21.6647537435"; frac "1.000000"; conf_lo "0.000000"; conf_hi "52.303342"; cov "1.384615";\n+chr1\tCufflinks\texon\t3365246\t3365284\t1000\t.\t.\tgene_id "CUFF.93"; transcript_id "CUFF.93.1"; exon_number "1"; FPKM "21.6647537435"; frac "1.000000"; conf_lo "0.000000"; conf_hi "52.303342"; cov "1.384615";\n+chr1\tCufflinks\ttranscript\t3377607\t3377633\t1000\t.\t.\tgene_id "CUFF.95"; transcript_id "CUFF.95.1"; FPKM "46.9402997776"; frac "1.000000"; conf_lo "0.000000"; conf_hi "101.142289"; cov "3.000000";\n+chr1\tCufflinks\texon\t3377607\t3377633\t1000\t.\t.\tgene_id "CUFF.95"; transcript_id "CUFF.95.1"; exon_number "1"; FPKM "46.9402997776"; frac "1.000000"; conf_lo "0.000000"; conf_hi "101.142289"; cov "3.000000";\n+chr1\tCufflinks\ttranscript\t3381259\t3381317\t1000\t.\t.\tgene_id "CUFF.97"; transcript_id "CUFF.97.1"; FPKM "21.4811541355"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.285454"; cov "1.372881";\n+chr1\tCufflinks\texon\t3381259\t3381317\t1000\t.\t.\tgene_id "CUFF.97"; transcript_id "CUFF.97.1"; exon_number "1"; FPKM "21.4811541355"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.285454"; cov "1.372881";\n+chr1\tCufflinks\ttranscript\t3381404\t3381474\t1000\t.\t.\tgene_id "CUFF.99"; transcript_id "CUFF.99.1"; FPKM "14.5676792413"; frac "1.000000"; conf_lo "0.000000"; conf_hi "35.169489"; cov "0.931034";\n+chr1\tCufflinks\texon\t3381404\t3381474\t1000\t.\t.\tgene_id "CUFF.99"; transcript_id "CUFF.99.1"; exon_number "1"; FPKM "14.5676792413"; frac "1.000000"; conf_lo "0.000000"; conf_hi "35.169489"; cov "0.931034";\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/cuffcompare_in1_liftover_unmapped.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/cuffcompare_in1_liftover_unmapped.bed Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,28 @@
+# Deleted in new
+chr1 Cufflinks transcript 3111546 3111576 1000 . . gene_id "CUFF.3"; transcript_id "CUFF.3.1"; FPKM "27.2556579354"; frac "1.000000"; conf_lo "0.000000"; conf_hi "65.800979"; cov "1.741935";
+# Deleted in new
+chr1 Cufflinks exon 3111546 3111576 1000 . . gene_id "CUFF.3"; transcript_id "CUFF.3.1"; exon_number "1"; FPKM "27.2556579354"; frac "1.000000"; conf_lo "0.000000"; conf_hi "65.800979"; cov "1.741935";
+# Partially deleted in new
+chr1 Cufflinks transcript 3243019 3243079 1000 . . gene_id "CUFF.21"; transcript_id "CUFF.21.1"; FPKM "13.8512359999"; frac "1.000000"; conf_lo "0.000000"; conf_hi "33.439842"; cov "0.885246";
+# Partially deleted in new
+chr1 Cufflinks exon 3243019 3243079 1000 . . gene_id "CUFF.21"; transcript_id "CUFF.21.1"; exon_number "1"; FPKM "13.8512359999"; frac "1.000000"; conf_lo "0.000000"; conf_hi "33.439842"; cov "0.885246";
+# Partially deleted in new
+chr1 Cufflinks transcript 3242634 3242923 1000 . . gene_id "CUFF.25"; transcript_id "CUFF.25.1"; FPKM "14.5676792413"; frac "1.000000"; conf_lo "5.354270"; conf_hi "23.781089"; cov "0.931034";
+# Partially deleted in new
+chr1 Cufflinks exon 3242634 3242923 1000 . . gene_id "CUFF.25"; transcript_id "CUFF.25.1"; exon_number "1"; FPKM "14.5676792413"; frac "1.000000"; conf_lo "5.354270"; conf_hi "23.781089"; cov "0.931034";
+# Partially deleted in new
+chr1 Cufflinks transcript 3191877 3191945 1000 . . gene_id "CUFF.37"; transcript_id "CUFF.37.1"; FPKM "104.0850125502"; frac "1.000000"; conf_lo "53.596365"; conf_hi "154.573660"; cov "6.652174";
+# Partially deleted in new
+chr1 Cufflinks exon 3191877 3191945 1000 . . gene_id "CUFF.37"; transcript_id "CUFF.37.1"; exon_number "1"; FPKM "104.0850125502"; frac "1.000000"; conf_lo "53.596365"; conf_hi "154.573660"; cov "6.652174";
+# Partially deleted in new
+chr1 Cufflinks transcript 3194186 3194226 1000 . . gene_id "CUFF.47"; transcript_id "CUFF.47.1"; FPKM "20.6079364877"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.751960"; cov "1.317073";
+# Partially deleted in new
+chr1 Cufflinks exon 3194186 3194226 1000 . . gene_id "CUFF.47"; transcript_id "CUFF.47.1"; exon_number "1"; FPKM "20.6079364877"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.751960"; cov "1.317073";
+# Deleted in new
+chr1 Cufflinks transcript 3277191 3277218 1000 . . gene_id "CUFF.61"; transcript_id "CUFF.61.1"; FPKM "45.2638604998"; frac "1.000000"; conf_lo "0.000000"; conf_hi "97.530065"; cov "2.892857";
+# Deleted in new
+chr1 Cufflinks exon 3277191 3277218 1000 . . gene_id "CUFF.61"; transcript_id "CUFF.61.1"; exon_number "1"; FPKM "45.2638604998"; frac "1.000000"; conf_lo "0.000000"; conf_hi "97.530065"; cov "2.892857";
+# Deleted in new
+chr1 Cufflinks transcript 3278237 3278263 1000 . . gene_id "CUFF.63"; transcript_id "CUFF.63.1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";
+# Deleted in new
+chr1 Cufflinks exon 3278237 3278263 1000 . . gene_id "CUFF.63"; transcript_id "CUFF.63.1"; exon_number "1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/cuffcompare_in1_mult_liftover_mapped.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/cuffcompare_in1_mult_liftover_mapped.bed Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,92 @@\n+chr1\tCufflinks\ttranscript\t3022555\t3022596\t1000\t.\t.\tgene_id "CUFF.1"; transcript_id "CUFF.1.1"; FPKM "20.6079364877"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.751960"; cov "1.317073";\n+chr1\tCufflinks\texon\t3022555\t3022596\t1000\t.\t.\tgene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "1"; FPKM "20.6079364877"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.751960"; cov "1.317073";\n+chr1\tCufflinks\ttranscript\t3117334\t3117360\t1000\t.\t.\tgene_id "CUFF.5"; transcript_id "CUFF.5.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";\n+chr1\tCufflinks\texon\t3117334\t3117360\t1000\t.\t.\tgene_id "CUFF.5"; transcript_id "CUFF.5.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";\n+chr1\tCufflinks\ttranscript\t3117031\t3117199\t1000\t.\t.\tgene_id "CUFF.7"; transcript_id "CUFF.7.1"; FPKM "9.9991171124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "19.998234"; cov "0.639053";\n+chr1\tCufflinks\texon\t3117031\t3117199\t1000\t.\t.\tgene_id "CUFF.7"; transcript_id "CUFF.7.1"; exon_number "1"; FPKM "9.9991171124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "19.998234"; cov "0.639053";\n+chr1\tCufflinks\ttranscript\t3118118\t3118521\t1000\t.\t.\tgene_id "CUFF.9"; transcript_id "CUFF.9.1"; FPKM "17.7768957078"; frac "1.000000"; conf_lo "9.153835"; conf_hi "26.399957"; cov "1.136139";\n+chr1\tCufflinks\texon\t3118118\t3118521\t1000\t.\t.\tgene_id "CUFF.9"; transcript_id "CUFF.9.1"; exon_number "1"; FPKM "17.7768957078"; frac "1.000000"; conf_lo "9.153835"; conf_hi "26.399957"; cov "1.136139";\n+chr1\tCufflinks\ttranscript\t3118713\t3118739\t1000\t.\t.\tgene_id "CUFF.11"; transcript_id "CUFF.11.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";\n+chr1\tCufflinks\texon\t3118713\t3118739\t1000\t.\t.\tgene_id "CUFF.11"; transcript_id "CUFF.11.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";\n+chr1\tCufflinks\ttranscript\t3121789\t3121867\t1000\t.\t.\tgene_id "CUFF.13"; transcript_id "CUFF.13.1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";\n+chr1\tCufflinks\texon\t3121789\t3121867\t1000\t.\t.\tgene_id "CUFF.13"; transcript_id "CUFF.13.1"; exon_number "1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";\n+chr1\tCufflinks\ttranscript\t3128503\t3128581\t1000\t.\t.\tgene_id "CUFF.15"; transcript_id "CUFF.15.1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";\n+chr1\tCufflinks\texon\t3128503\t3128581\t1000\t.\t.\tgene_id "CUFF.15"; transcript_id "CUFF.15.1"; exon_number "1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";\n+chr1\tCufflinks\ttranscript\t3129386\t3129482\t1000\t.\t.\tgene_id "CUFF.17"; transcript_id "CUFF.17.1"; FPKM "8.7105710927"; frac "1.000000"; conf_lo "0.000000"; conf_hi "21.029179"; cov "0.556701";\n+chr1\tCufflinks\texon\t3129386\t3129482\t1000\t.\t.\tgene_id "CUFF.17"; transcript_id "CUFF.17.1"; exon_number "1"; FPKM "8.7105710927"; frac "1.000000"; conf_lo "0.000000"; conf_hi "21.029179"; cov "0.556701";\n+chr1\tCufflinks\ttranscript\t3128657\t3128728\t1000\t.\t.\tgene_id "CUFF.19"; transcript_id "CUFF.19.1"; FPKM "29.3376873610"; frac "1.000000"; conf_lo "3.097262"; conf_hi "55.578113"; cov "1.875000";\n+chr1\tCufflinks\texon\t3128657\t3128728\t1000\t.\t.\tgene_id "CUFF.19"; transcript_id "CUFF.19.1"; exon_number "1"; FPKM "29.3376873610"; frac "1.000000"; conf_lo "3.097262"; conf_hi "55.578113"; cov "1.875000";\n+chr1\tCufflinks\ttranscript\t3162123\t3162179\t1000\t.\t.\tgene_id "CUFF.21"; transcript_id "CUFF.21.1"; FPKM "13.8512359999"; frac "1.000000"; conf_lo "0.000000"; conf_hi "33.439842"; cov "0.885246";\n+chr1\tCufflinks\texon\t3162123\t3162179\t1000\t.\t.\tgene_id "CUFF.21"; transcript_id "CUFF.21.1"; exon_number "1"; FPKM "13.8512359999"; frac "1.000000"; conf_lo "0.000000"; conf_hi "33.439842"; cov "0.885246";\n+chr1\tCuffli'..b'0000";\n+chr1\tCufflinks\ttranscript\t3285318\t3285381\t1000\t.\t.\tgene_id "CUFF.81"; transcript_id "CUFF.81.1"; FPKM "13.2019593124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.872349"; cov "0.843750";\n+chr1\tCufflinks\texon\t3285318\t3285381\t1000\t.\t.\tgene_id "CUFF.81"; transcript_id "CUFF.81.1"; exon_number "1"; FPKM "13.2019593124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.872349"; cov "0.843750";\n+chr1\tCufflinks\ttranscript\t3285858\t3285953\t1000\t.\t.\tgene_id "CUFF.83"; transcript_id "CUFF.83.1"; FPKM "13.2019593124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "28.446269"; cov "0.843750";\n+chr1\tCufflinks\texon\t3285858\t3285953\t1000\t.\t.\tgene_id "CUFF.83"; transcript_id "CUFF.83.1"; exon_number "1"; FPKM "13.2019593124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "28.446269"; cov "0.843750";\n+chr1\tCufflinks\ttranscript\t3289268\t3289294\t1000\t.\t.\tgene_id "CUFF.85"; transcript_id "CUFF.85.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";\n+chr1\tCufflinks\texon\t3289268\t3289294\t1000\t.\t.\tgene_id "CUFF.85"; transcript_id "CUFF.85.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";\n+chr1\tCufflinks\ttranscript\t3289466\t3289514\t1000\t.\t.\tgene_id "CUFF.87"; transcript_id "CUFF.87.1"; FPKM "17.2433754285"; frac "1.000000"; conf_lo "0.000000"; conf_hi "41.629191"; cov "1.102041";\n+chr1\tCufflinks\texon\t3289466\t3289514\t1000\t.\t.\tgene_id "CUFF.87"; transcript_id "CUFF.87.1"; exon_number "1"; FPKM "17.2433754285"; frac "1.000000"; conf_lo "0.000000"; conf_hi "41.629191"; cov "1.102041";\n+chr1\tCufflinks\ttranscript\t3300382\t3300432\t1000\t.\t.\tgene_id "CUFF.89"; transcript_id "CUFF.89.1"; FPKM "16.5671646274"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.996674"; cov "1.058824";\n+chr1\tCufflinks\texon\t3300382\t3300432\t1000\t.\t.\tgene_id "CUFF.89"; transcript_id "CUFF.89.1"; exon_number "1"; FPKM "16.5671646274"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.996674"; cov "1.058824";\n+chr1\tCufflinks\ttranscript\t3317446\t3317472\t1000\t.\t.\tgene_id "CUFF.91"; transcript_id "CUFF.91.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";\n+chr1\tCufflinks\texon\t3317446\t3317472\t1000\t.\t.\tgene_id "CUFF.91"; transcript_id "CUFF.91.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";\n+chr1\tCufflinks\ttranscript\t3365246\t3365284\t1000\t.\t.\tgene_id "CUFF.93"; transcript_id "CUFF.93.1"; FPKM "21.6647537435"; frac "1.000000"; conf_lo "0.000000"; conf_hi "52.303342"; cov "1.384615";\n+chr1\tCufflinks\texon\t3365246\t3365284\t1000\t.\t.\tgene_id "CUFF.93"; transcript_id "CUFF.93.1"; exon_number "1"; FPKM "21.6647537435"; frac "1.000000"; conf_lo "0.000000"; conf_hi "52.303342"; cov "1.384615";\n+chr1\tCufflinks\ttranscript\t3377607\t3377633\t1000\t.\t.\tgene_id "CUFF.95"; transcript_id "CUFF.95.1"; FPKM "46.9402997776"; frac "1.000000"; conf_lo "0.000000"; conf_hi "101.142289"; cov "3.000000";\n+chr1\tCufflinks\texon\t3377607\t3377633\t1000\t.\t.\tgene_id "CUFF.95"; transcript_id "CUFF.95.1"; exon_number "1"; FPKM "46.9402997776"; frac "1.000000"; conf_lo "0.000000"; conf_hi "101.142289"; cov "3.000000";\n+chr1\tCufflinks\ttranscript\t3381259\t3381317\t1000\t.\t.\tgene_id "CUFF.97"; transcript_id "CUFF.97.1"; FPKM "21.4811541355"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.285454"; cov "1.372881";\n+chr1\tCufflinks\texon\t3381259\t3381317\t1000\t.\t.\tgene_id "CUFF.97"; transcript_id "CUFF.97.1"; exon_number "1"; FPKM "21.4811541355"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.285454"; cov "1.372881";\n+chr1\tCufflinks\ttranscript\t3381404\t3381474\t1000\t.\t.\tgene_id "CUFF.99"; transcript_id "CUFF.99.1"; FPKM "14.5676792413"; frac "1.000000"; conf_lo "0.000000"; conf_hi "35.169489"; cov "0.931034";\n+chr1\tCufflinks\texon\t3381404\t3381474\t1000\t.\t.\tgene_id "CUFF.99"; transcript_id "CUFF.99.1"; exon_number "1"; FPKM "14.5676792413"; frac "1.000000"; conf_lo "0.000000"; conf_hi "35.169489"; cov "0.931034";\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/cuffcompare_in1_mult_liftover_unmapped.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/cuffcompare_in1_mult_liftover_unmapped.bed Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,16 @@
+# Deleted in new
+chr1 Cufflinks transcript 3111546 3111576 1000 . . gene_id "CUFF.3"; transcript_id "CUFF.3.1"; FPKM "27.2556579354"; frac "1.000000"; conf_lo "0.000000"; conf_hi "65.800979"; cov "1.741935";
+# Deleted in new
+chr1 Cufflinks exon 3111546 3111576 1000 . . gene_id "CUFF.3"; transcript_id "CUFF.3.1"; exon_number "1"; FPKM "27.2556579354"; frac "1.000000"; conf_lo "0.000000"; conf_hi "65.800979"; cov "1.741935";
+# Partially deleted in new
+chr1 Cufflinks transcript 3194186 3194226 1000 . . gene_id "CUFF.47"; transcript_id "CUFF.47.1"; FPKM "20.6079364877"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.751960"; cov "1.317073";
+# Partially deleted in new
+chr1 Cufflinks exon 3194186 3194226 1000 . . gene_id "CUFF.47"; transcript_id "CUFF.47.1"; exon_number "1"; FPKM "20.6079364877"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.751960"; cov "1.317073";
+# Deleted in new
+chr1 Cufflinks transcript 3277191 3277218 1000 . . gene_id "CUFF.61"; transcript_id "CUFF.61.1"; FPKM "45.2638604998"; frac "1.000000"; conf_lo "0.000000"; conf_hi "97.530065"; cov "2.892857";
+# Deleted in new
+chr1 Cufflinks exon 3277191 3277218 1000 . . gene_id "CUFF.61"; transcript_id "CUFF.61.1"; exon_number "1"; FPKM "45.2638604998"; frac "1.000000"; conf_lo "0.000000"; conf_hi "97.530065"; cov "2.892857";
+# Deleted in new
+chr1 Cufflinks transcript 3278237 3278263 1000 . . gene_id "CUFF.63"; transcript_id "CUFF.63.1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";
+# Deleted in new
+chr1 Cufflinks exon 3278237 3278263 1000 . . gene_id "CUFF.63"; transcript_id "CUFF.63.1"; exon_number "1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/cufflinks_out1.gtf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/cufflinks_out1.gtf Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,4 @@
+test_chromosome Cufflinks transcript 53 550 1000 + . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; FPKM "10679134.4063403048"; frac "1.000000"; conf_lo "8543307.525072"; conf_hi "12814961.287608"; cov "145.770185";
+test_chromosome Cufflinks exon 53 250 1000 + . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "1"; FPKM "10679134.4063403048"; frac "1.000000"; conf_lo "8543307.525072"; conf_hi "12814961.287608"; cov "145.770185";
+test_chromosome Cufflinks exon 351 400 1000 + . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "2"; FPKM "10679134.4063403048"; frac "1.000000"; conf_lo "8543307.525072"; conf_hi "12814961.287608"; cov "145.770185";
+test_chromosome Cufflinks exon 501 550 1000 + . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "3"; FPKM "10679134.4063403048"; frac "1.000000"; conf_lo "8543307.525072"; conf_hi "12814961.287608"; cov "145.770185";

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/customTrack1.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/customTrack1.bed Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,6 @@
+chr2 31608 36385 NM_001077710 0 - 31608 36385 0 2 19,946, 0,3831,
+chr2 208154 246341 NM_015677 0 - 208810 232800 0 12 847,57,79,169,129,113,74,60,65,114,111,135, 0,6709,11811,12868,14946,16005,24643,25348,29383,31576,34850,38052,
+chr2 254871 262481 NM_001040649 0 + 254964 262258 0 3 136,74,445, 0,6994,7165,
+chr2 254895 268280 NM_004300 0 + 254964 267304 0 6 112,74,114,62,106,1054, 0,6970,7141,10244,12084,12331,
+chr2 254895 268280 NM_007099 0 + 254964 267304 0 6 112,74,114,62,106,1054, 0,6970,7296,10244,12084,12331,
+chr2 269928 277837 NM_001002919 0 - 270146 277835 0 6 221,65,81,54,22,53, 0,3182,6194,6361,7654,7856,

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/dna_filter_in1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/dna_filter_in1.tabular Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,49 @@
+chr1 256 257 A N M N - M N U N N A N D N G N N K N N N +
+chr1 468 469 C C C N M N N K . N C U N H N G N N M N S -
+chr1 582 583 G G G N G R N R N - N M N V K N N N G C R +
+chr1 602 603 G G G N G N Y N R G G N N U N T N A K N R +
+chr1 4792 4793 A A M K N W S S N N Y N N N N N M R N R N +
+chr1 6119 6120 G G M N S N N W B N S D N N H V N B W N N +
+chr1 6357 6358 G G N M K N G - N N G U N N N B N N K N S -
+chr1 6433 6434 G G N R N N C N N N . N N . N N N N N R N +
+chr1 39160 39161 T T T N N Y N - N N N N N N N V N N N N Y +
+chr1 41920 41921 G C G N M C G N A N G N K N W S N N N V N +
+chr1 42100 42101 T T T Y R W N N N V N M R N N G N M Y N K -
+chr1 45026 45027 C A C N N Y N S Y N N X N A D N N K N N A +
+chr1 45161 45162 C T C . N X H V N N C R N Y N N N N R N Y +
+chr2 45407 45408 C N C S B N N N N N C N Y N N T K G N C N +
+chr2 45788 45789 T T T N W S N Y N R Y N S N W M N C T N C -
+chr2 46243 46244 T T T N W N N B V N U N T N N Y C N U N N +
+chr2 47814 47815 A C A S N X D N N H W N G N Y C N N M R N +
+chr2 48073 48074 A G A Y W . N K N N N G N N N G N N N Y N +
+chr2 48633 48634 T T T N G N N N . N N N N S N Y N . N N N +
+chr2 51304 51305 A G N N C N W - N S Y N . N N G N N N W R +
+chr2 51324 51325 T T N R N N N N N - N U N W A N N N N N N -
+chr2 52065 52066 T C T N N N S N . N T N M N S W N T Y C N -
+chr2 53130 53131 T C T K R . N B N N T N N M N Y N N Y N N +
+chr2 53505 53506 A A A M N N Y N N N N - K N W N N N S N R +
+chr2 53559 53560 T T T N N V R V N N T N U N N B N M N V Y +
+chr2 55607 55608 A N A U S N N H R K N N N Y N N G N N N N +
+chr10 55659 55660 T N T C N K N N N U N S N N N V C R S N N +
+chr10 55734 55735 T N T G N C N M M G C N B N . N G N N N N +
+chr10 55870 55871 C G C N H G - N N N C N H K N M G N N N N +
+chr10 56024 56025 A T A N D U N Y B N N X N N Y N T N - N N +
+chr10 56100 56101 T T A W N N W N S N K M N R N R N R N G N +
+chr10 56120 56121 A - A N A N N Y N N N W V N N Y G N N W N -
+chr10 56137 56138 A A A N A Y H . Y N G N . D N N T N N N N +
+chr10 56174 56175 A T A Y A N N N N N N N N N . S T Y N B N +
+chr10 59373 59374 A G A N N N N N N T N S N N N G N N N V N +
+chr10 68912 68913 G T G R N B R N H N U W Y N N N N N N N T +
+chr10 72946 72947 T A N N N N N N B N N . B D W U N U N D A -
+chr10 77052 77053 G A R N G N N Y N N N N N N B R N W N N R +
+chr18 78200 78201 G G G N N H N N V N G N N N N A A N K X N +
+chr18 81076 81077 T A T B N N G N N X W N X N V N N D N N N +
+chr18 81198 81199 A T A N N N N - N N X N K T N M N K X N W +
+chr18 81216 81217 G A G Y N N D N X N N N N A N S N N N D N -
+chr18 81398 81399 G T G N - W N N M N G C N K N S N N N N K +
+chr18 91548 91549 A A A S N X H S R N A K N N N N U A R N N +
+chr18 93895 93896 T T T H N N V W Y N N N - N N N N N N Y N +
+chr18 98172 98173 T T T N . N N N S N T N Y N N Y X D V N Y +
+chr18 110904 110905 T - A A N A N A W A N N A X N W N N N N N +
+chr18 140324 140325 A A A N M N N Y N S N V N N X N C N N . M +
+chr18 160592 160593 C G G G N G N G N G N N G N N M T N Y N N -
\ No newline at end of file

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/dna_filter_out1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/dna_filter_out1.tabular Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,35 @@
+chr1 582 583 G G G N G R N R N - N M N V K N N N G C R +
+chr1 602 603 G G G N G N Y N R G G N N U N T N A K N R +
+chr1 4792 4793 A A M K N W S S N N Y N N N N N M R N R N +
+chr1 6119 6120 G G M N S N N W B N S D N N H V N B W N N +
+chr1 6357 6358 G G N M K N G - N N G U N N N B N N K N S -
+chr1 6433 6434 G G N R N N C N N N . N N . N N N N N R N +
+chr1 39160 39161 T T T N N Y N - N N N N N N N V N N N N Y +
+chr1 42100 42101 T T T Y R W N N N V N M R N N G N M Y N K -
+chr1 45026 45027 C A C N N Y N S Y N N X N A D N N K N N A +
+chr1 45161 45162 C T C . N X H V N N C R N Y N N N N R N Y +
+chr2 45407 45408 C N C S B N N N N N C N Y N N T K G N C N +
+chr2 47814 47815 A C A S N X D N N H W N G N Y C N N M R N +
+chr2 48633 48634 T T T N G N N N . N N N N S N Y N . N N N +
+chr2 51324 51325 T T N R N N N N N - N U N W A N N N N N N -
+chr2 52065 52066 T C T N N N S N . N T N M N S W N T Y C N -
+chr2 53130 53131 T C T K R . N B N N T N N M N Y N N Y N N +
+chr2 53505 53506 A A A M N N Y N N N N - K N W N N N S N R +
+chr2 53559 53560 T T T N N V R V N N T N U N N B N M N V Y +
+chr2 55607 55608 A N A U S N N H R K N N N Y N N G N N N N +
+chr10 55659 55660 T N T C N K N N N U N S N N N V C R S N N +
+chr10 55734 55735 T N T G N C N M M G C N B N . N G N N N N +
+chr10 56024 56025 A T A N D U N Y B N N X N N Y N T N - N N +
+chr10 56100 56101 T T A W N N W N S N K M N R N R N R N G N +
+chr10 59373 59374 A G A N N N N N N T N S N N N G N N N V N +
+chr10 68912 68913 G T G R N B R N H N U W Y N N N N N N N T +
+chr10 72946 72947 T A N N N N N N B N N . B D W U N U N D A -
+chr10 77052 77053 G A R N G N N Y N N N N N N B R N W N N R +
+chr18 78200 78201 G G G N N H N N V N G N N N N A A N K X N +
+chr18 81076 81077 T A T B N N G N N X W N X N V N N D N N N +
+chr18 81198 81199 A T A N N N N - N N X N K T N M N K X N W +
+chr18 81216 81217 G A G Y N N D N X N N N N A N S N N N D N -
+chr18 91548 91549 A A A S N X H S R N A K N N N N U A R N N +
+chr18 93895 93896 T T T H N N V W Y N N N - N N N N N N Y N +
+chr18 110904 110905 T - A A N A N A W A N N A X N W N N N N N +
+chr18 160592 160593 C G G G N G N G N G N N G N N M T N Y N N -
\ No newline at end of file

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/dna_filter_out2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/dna_filter_out2.tabular Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,31 @@
+chr1 602 603 G G G N G N Y N R G G N N U N T N A K N R +
+chr1 39160 39161 T T T N N Y N - N N N N N N N V N N N N Y +
+chr1 41920 41921 G C G N M C G N A N G N K N W S N N N V N +
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+chr2 46243 46244 T T T N W N N B V N U N T N N Y C N U N N +
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+chr18 81216 81217 G A G Y N N D N X N N N N A N S N N N D N -
+chr18 81398 81399 G T G N - W N N M N G C N K N S N N N N K +
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\ No newline at end of file

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/dna_filter_out3.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/dna_filter_out3.tabular Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,42 @@
+chr1 468 469 C C C N M N N K . N C U N H N G N N M N S -
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+chr2 53130 53131 T C T K R . N B N N T N N M N Y N N Y N N +
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\ No newline at end of file

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/dna_filter_out4.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/dna_filter_out4.tabular Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,6 @@
+chr2 45788 45789 T T T N W S N Y N R Y N S N W M N C T N C -
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\ No newline at end of file

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/droPer1.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/droPer1.bed Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,2 @@
+super_1 139823 139913 AK028861 0 - 139823 139913 0 1 90, 0,
+super_1 156750 156844 BC126698 0 - 156750 156844 0 1 94, 0,

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/eq-addvalue.dat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/eq-addvalue.dat Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,65 @@
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diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/eq-condense.dat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/eq-condense.dat Sat Feb 21 16:33:42 2015 +0100

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/eq-convert.dat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/eq-convert.dat Sat Feb 21 16:33:42 2015 +0100

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/eq-createinterval.dat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/eq-createinterval.dat Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,1 @@
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diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/eq-cut.dat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/eq-cut.dat Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,65 @@
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+chr7 CCDS5760.1_cds_0_0_chr7_113660518_f 113660517 113660685
+chr7 CCDS5771.1_cds_0_0_chr7_116512160_r 116512159 116512389
+chr7 CCDS5773.1_cds_0_0_chr7_116714100_f 116714099 116714152
+chr7 CCDS5774.1_cds_0_0_chr7_116945542_r 116945541 116945787
+chr8 CCDS6324.1_cds_0_0_chr8_118881132_r 118881131 118881317
+chr9 CCDS6914.1_cds_0_0_chr9_128764157_f 128764156 128764189
+chr9 CCDS6915.1_cds_0_0_chr9_128787520_r 128787519 128789136
+chr9 CCDS6917.1_cds_0_0_chr9_128882428_f 128882427 128882523
+chr9 CCDS6919.1_cds_0_0_chr9_128937230_r 128937229 128937445
+chrX CCDS14606.1_cds_0_0_chrX_122745048_f 122745047 122745924
+chrX CCDS14733.1_cds_0_0_chrX_152648965_r 152648964 152649196
+chrX CCDS14735.1_cds_0_0_chrX_152691447_f 152691446 152691471
+chrX CCDS14736.1_cds_0_0_chrX_152694030_r 152694029 152694263

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/eq-paste.dat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/eq-paste.dat Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,68 @@\n+chr1\t147962192\t147962580\tCCDS989.1_cds_0_0_chr1_147962193_r\t0\t-\tchr1\t147962192\t147962580\tNM_005997_cds_0_0_chr1_147962193_r\t0\t-\n+chr1\t147984545\t147984630\tCCDS990.1_cds_0_0_chr1_147984546_f\t0\t+\tchr1\t147984545\t147984630\tBC007833_cds_0_0_chr1_147984546_f\t0\t+\n+chr1\t148078400\t148078582\tCCDS993.1_cds_0_0_chr1_148078401_r\t0\t-\tchr1\t148078400\t148078582\tAJ011123_cds_0_0_chr1_148078401_r\t0\t-\n+chr1\t148185136\t148185276\tCCDS996.1_cds_0_0_chr1_148185137_f\t0\t+\tchr1\t148185136\t148185276\tNM_002796_cds_0_0_chr1_148185137_f\t0\t+\n+chr10\t55251623\t55253124\tCCDS7248.1_cds_0_0_chr10_55251624_r\t0\t-\tchr10\t55251623\t55253124\tAY029205_cds_0_0_chr10_55251624_r\t0\t-\n+chr11\t116124407\t116124501\tCCDS8374.1_cds_0_0_chr11_116124408_r\t0\t-\tchr11\t116124407\t116124501\tAK057832_cds_0_0_chr11_116124408_r\t0\t-\n+chr11\t116206508\t116206563\tCCDS8377.1_cds_0_0_chr11_116206509_f\t0\t+\tchr11\t116206508\t116206563\tNM_000040_cds_1_0_chr11_116206509_f\t0\t+\n+chr11\t116211733\t116212337\tCCDS8378.1_cds_0_0_chr11_116211734_r\t0\t-\tchr11\t116211733\t116212337\tBC005380_cds_0_0_chr11_116211734_r\t0\t-\n+chr11\t1812377\t1812407\tCCDS7726.1_cds_0_0_chr11_1812378_f\t0\t+\tchr11\t130745911\t130745993\tAY358331_cds_0_0_chr11_130745912_f\t0\t+\n+chr12\t38440094\t38440321\tCCDS8736.1_cds_0_0_chr12_38440095_r\t0\t-\tchr12\t38440094\t38440321\tNM_052885_cds_0_0_chr12_38440095_r\t0\t-\n+chr13\t112381694\t112381953\tCCDS9526.1_cds_0_0_chr13_112381695_f\t0\t+\tchr12\t38905200\t38905351\tAY792511_cds_0_0_chr12_38905201_f\t0\t+\n+chr14\t98710240\t98712285\tCCDS9949.1_cds_0_0_chr14_98710241_r\t0\t-\tchr13\t112381694\t112381953\tNM_207440_cds_1_0_chr13_112381695_f\t0\t+\n+chr15\t41486872\t41487060\tCCDS10096.1_cds_0_0_chr15_41486873_r\t0\t-\tchr13\t29680676\t29680875\tNM_032116_cds_0_0_chr13_29680677_r\t0\t-\n+chr15\t41673708\t41673857\tCCDS10097.1_cds_0_0_chr15_41673709_f\t0\t+\tchr14\t98521864\t98521922\tU88895_cds_0_0_chr14_98521865_f\t0\t+\n+chr15\t41679161\t41679250\tCCDS10098.1_cds_0_0_chr15_41679162_r\t0\t-\tchr14\t98710240\t98712285\tNM_022898_cds_0_0_chr14_98710241_r\t0\t-\n+chr15\t41826029\t41826196\tCCDS10101.1_cds_0_0_chr15_41826030_f\t0\t+\tchr15\t41486872\t41487060\tBX537418_cds_0_0_chr15_41486873_r\t0\t-\n+chr16\t142908\t143003\tCCDS10397.1_cds_0_0_chr16_142909_f\t0\t+\tchr15\t41673708\t41673857\tAK223365_cds_0_0_chr15_41673709_f\t0\t+\n+chr16\t179963\t180135\tCCDS10401.1_cds_0_0_chr16_179964_r\t0\t-\tchr15\t41679161\t41679250\tNM_153700_cds_0_0_chr15_41679162_r\t0\t-\n+chr16\t244413\t244681\tCCDS10402.1_cds_0_0_chr16_244414_f\t0\t+\tchr15\t41773540\t41773689\tAK223365_cds_0_0_chr15_41773541_f\t0\t+\n+chr16\t259268\t259383\tCCDS10403.1_cds_0_0_chr16_259269_r\t0\t-\tchr16\t142908\t143003\tNM_005332_cds_0_0_chr16_142909_f\t0\t+\n+chr18\t23786114\t23786321\tCCDS11891.1_cds_0_0_chr18_23786115_r\t0\t-\tchr16\t179197\t179339\tBC065198_cds_0_0_chr16_179198_r\t0\t-\n+chr18\t59406881\t59407046\tCCDS11985.1_cds_0_0_chr18_59406882_f\t0\t+\tchr16\t244413\t244681\tAK057165_cds_2_0_chr16_244414_f\t0\t+\n+chr18\t59455932\t59456337\tCCDS11986.1_cds_0_0_chr18_59455933_r\t0\t-\tchr16\t259268\t259383\tAB016929_cds_0_0_chr16_259269_r\t0\t-\n+chr18\t59600586\t59600754\tCCDS11988.1_cds_0_0_chr18_59600587_f\t0\t+\tchr18\t23786114\t23786321\tNM_001792_cds_0_0_chr18_23786115_r\t0\t-\n+chr19\t59068595\t59069564\tCCDS12866.1_cds_0_0_chr19_59068596_f\t0\t+\tchr18\t59406881\t59407046\tNM_012397_cds_1_0_chr18_59406882_f\t0\t+\n+chr19\t59236026\t59236146\tCCDS12872.1_cds_0_0_chr19_59236027_r\t0\t-\tchr18\t59455932\t59456337\tAB046400_cds_0_0_chr18_59455933_r\t0\t-\n+chr19\t59297998\t59298008\tCCDS12877.1_cds_0_0_chr19_59297999_f\t0\t+\tchr18\t59528407\t59528575\tAY792326_cds_0_0_chr18_59528408_f\t0\t+\n+chr19\t59302168\t59302288\tCCDS12878.1_cds_0_0_chr19_59302169_r\t0\t-\tchr19\t59068595\t59069564\tBC013995_cds_1_0_chr19_59068596_f\t0\t+\n+chr2\t118288583\t118288668\tCCDS2120.1_cds_0_0_chr2_118288584_f\t0\t+\tchr19\t59236026\t59236146\tNM_198481_cds_0_0_chr19_59236027_r\t0\t-\n+chr2\t118394148\t118394202\tCCDS2121.1_cds_0_0_chr2_118394149_r\t0\t-\tchr19\t59297998\t59298008\tNM_004542_cds_0_0_chr19_59297999_f\t0\t+\n+chr2\t220190202\t220190242\tCCDS2441.1_cds_0_0_chr2_220190203_f\t0\t+\tchr19\t59318205\t59318718\tAK128544_cds_3_0_chr19_59318206_r\t0\t-\n+chr2\t220229609\t220230869\tCCDS2443.'..b'33330423\tNM_181466_cds_0_0_chr20_33330414_r\t0\t-\n+chr21\t32707032\t32707192\tCCDS13614.1_cds_0_0_chr21_32707033_f\t0\t+\tchr20\t33485370\t33486123\tBC085019_cds_1_0_chr20_33485371_f\t0\t+\n+chr21\t32869641\t32870022\tCCDS13615.1_cds_0_0_chr21_32869642_r\t0\t-\tchr20\t33488491\t33489122\tNM_000557_cds_1_0_chr20_33488492_r\t0\t-\n+chr21\t33321040\t33322012\tCCDS13620.1_cds_0_0_chr21_33321041_f\t0\t+\tchr20\t33513606\t33513792\tAF022655_cds_1_0_chr20_33513607_f\t0\t+\n+chr21\t33744994\t33745040\tCCDS13625.1_cds_0_0_chr21_33744995_r\t0\t-\tchr21\t32687402\t32687588\tNM_032910_cds_0_0_chr21_32687403_f\t0\t+\n+chr22\t30120223\t30120265\tCCDS13897.1_cds_0_0_chr22_30120224_f\t0\t+\tchr21\t32869641\t32870022\tNM_018277_cds_3_0_chr21_32869642_r\t0\t-\n+chr22\t30160419\t30160661\tCCDS13898.1_cds_0_0_chr22_30160420_r\t0\t-\tchr21\t33321040\t33322012\tNM_005806_cds_1_0_chr21_33321041_f\t0\t+\n+chr22\t30665273\t30665360\tCCDS13901.1_cds_0_0_chr22_30665274_f\t0\t+\tchr21\t33728358\t33728724\tAK129657_cds_0_0_chr21_33728359_r\t0\t-\n+chr22\t30939054\t30939266\tCCDS13903.1_cds_0_0_chr22_30939055_r\t0\t-\tchr22\t30120223\t30120265\tNM_004147_cds_0_0_chr22_30120224_f\t0\t+\n+chr5\t131424298\t131424460\tCCDS4149.1_cds_0_0_chr5_131424299_f\t0\t+\tchr22\t30160419\t30160661\tBC032941_cds_0_0_chr22_30160420_r\t0\t-\n+chr5\t131556601\t131556672\tCCDS4151.1_cds_0_0_chr5_131556602_r\t0\t-\tchr22\t30228824\t30228916\tNM_001007467_cds_1_0_chr22_30228825_f\t0\t+\n+chr5\t131621326\t131621419\tCCDS4152.1_cds_0_0_chr5_131621327_f\t0\t+\tchr22\t30340151\t30340376\tCR456540_cds_0_0_chr22_30340152_r\t0\t-\n+chr5\t131847541\t131847666\tCCDS4155.1_cds_0_0_chr5_131847542_r\t0\t-\tchr5\t131311206\t131311254\tAF099740_cds_11_0_chr5_131311207_r\t0\t-\n+chr6\t108299600\t108299744\tCCDS5061.1_cds_0_0_chr6_108299601_r\t0\t-\tchr5\t131424298\t131424460\tNM_000588_cds_0_0_chr5_131424299_f\t0\t+\n+chr6\t108594662\t108594687\tCCDS5063.1_cds_0_0_chr6_108594663_f\t0\t+\tchr5\t131556601\t131556672\tBC035813_cds_0_0_chr5_131556602_r\t0\t-\n+chr6\t108640045\t108640151\tCCDS5064.1_cds_0_0_chr6_108640046_r\t0\t-\tchr5\t131621326\t131621419\tBC003096_cds_0_0_chr5_131621327_f\t0\t+\n+chr6\t108722976\t108723115\tCCDS5067.1_cds_0_0_chr6_108722977_f\t0\t+\tchr6\t108299600\t108299744\tNM_007214_cds_0_0_chr6_108299601_r\t0\t-\n+chr7\t113660517\t113660685\tCCDS5760.1_cds_0_0_chr7_113660518_f\t0\t+\tchr6\t108594662\t108594687\tNM_003269_cds_0_0_chr6_108594663_f\t0\t+\n+chr7\t116512159\t116512389\tCCDS5771.1_cds_0_0_chr7_116512160_r\t0\t-\tchr6\t108640045\t108640151\tNM_003795_cds_0_0_chr6_108640046_r\t0\t-\n+chr7\t116714099\t116714152\tCCDS5773.1_cds_0_0_chr7_116714100_f\t0\t+\tchr6\t108722976\t108723115\tNM_145315_cds_0_0_chr6_108722977_f\t0\t+\n+chr7\t116945541\t116945787\tCCDS5774.1_cds_0_0_chr7_116945542_r\t0\t-\tchr7\t113660517\t113660685\tAF467257_cds_1_0_chr7_113660518_f\t0\t+\n+chr8\t118881131\t118881317\tCCDS6324.1_cds_0_0_chr8_118881132_r\t0\t-\tchr7\t116512159\t116512389\tNM_003391_cds_0_0_chr7_116512160_r\t0\t-\n+chr9\t128764156\t128764189\tCCDS6914.1_cds_0_0_chr9_128764157_f\t0\t+\tchr7\t116714099\t116714152\tNM_000492_cds_0_0_chr7_116714100_f\t0\t+\n+chr9\t128787519\t128789136\tCCDS6915.1_cds_0_0_chr9_128787520_r\t0\t-\tchr7\t116945541\t116945787\tAF377960_cds_0_0_chr7_116945542_r\t0\t-\n+chr9\t128882427\t128882523\tCCDS6917.1_cds_0_0_chr9_128882428_f\t0\t+\tchr8\t118881131\t118881317\tNM_000127_cds_0_0_chr8_118881132_r\t0\t-\n+chr9\t128937229\t128937445\tCCDS6919.1_cds_0_0_chr9_128937230_r\t0\t-\tchr9\t128764156\t128764189\tBC051300_cds_0_0_chr9_128764157_f\t0\t+\n+chrX\t122745047\t122745924\tCCDS14606.1_cds_0_0_chrX_122745048_f\t0\t+\tchr9\t128787519\t128789136\tNM_014908_cds_0_0_chr9_128787520_r\t0\t-\n+chrX\t152648964\t152649196\tCCDS14733.1_cds_0_0_chrX_152648965_r\t0\t-\tchr9\t128789552\t128789584\tNM_015354_cds_0_0_chr9_128789553_f\t0\t+\n+chrX\t152691446\t152691471\tCCDS14735.1_cds_0_0_chrX_152691447_f\t0\t+\tchr9\t128850516\t128850624\tAB058751_cds_0_0_chr9_128850517_r\t0\t-\n+chrX\t152694029\t152694263\tCCDS14736.1_cds_0_0_chrX_152694030_r\t0\t-\tchrX\t122745047\t122745924\tNM_001167_cds_1_0_chrX_122745048_f\t0\t+\n+\tchrX\t152648964\t152649196\tNM_000425_cds_0_0_chrX_152648965_r\t0\t-\n+\tchrX\t152691446\t152691471\tAF101728_cds_0_0_chrX_152691447_f\t0\t+\n+\tchrX\t152694029\t152694263\tBC052303_cds_0_0_chrX_152694030_r\t0\t-\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/eq-removebeginning.dat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/eq-removebeginning.dat Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,60 @@
+chr11 116124407 116124501 CCDS8374.1_cds_0_0_chr11_116124408_r 0 -
+chr11 116206508 116206563 CCDS8377.1_cds_0_0_chr11_116206509_f 0 +
+chr11 116211733 116212337 CCDS8378.1_cds_0_0_chr11_116211734_r 0 -
+chr11 1812377 1812407 CCDS7726.1_cds_0_0_chr11_1812378_f 0 +
+chr12 38440094 38440321 CCDS8736.1_cds_0_0_chr12_38440095_r 0 -
+chr13 112381694 112381953 CCDS9526.1_cds_0_0_chr13_112381695_f 0 +
+chr14 98710240 98712285 CCDS9949.1_cds_0_0_chr14_98710241_r 0 -
+chr15 41486872 41487060 CCDS10096.1_cds_0_0_chr15_41486873_r 0 -
+chr15 41673708 41673857 CCDS10097.1_cds_0_0_chr15_41673709_f 0 +
+chr15 41679161 41679250 CCDS10098.1_cds_0_0_chr15_41679162_r 0 -
+chr15 41826029 41826196 CCDS10101.1_cds_0_0_chr15_41826030_f 0 +
+chr16 142908 143003 CCDS10397.1_cds_0_0_chr16_142909_f 0 +
+chr16 179963 180135 CCDS10401.1_cds_0_0_chr16_179964_r 0 -
+chr16 244413 244681 CCDS10402.1_cds_0_0_chr16_244414_f 0 +
+chr16 259268 259383 CCDS10403.1_cds_0_0_chr16_259269_r 0 -
+chr18 23786114 23786321 CCDS11891.1_cds_0_0_chr18_23786115_r 0 -
+chr18 59406881 59407046 CCDS11985.1_cds_0_0_chr18_59406882_f 0 +
+chr18 59455932 59456337 CCDS11986.1_cds_0_0_chr18_59455933_r 0 -
+chr18 59600586 59600754 CCDS11988.1_cds_0_0_chr18_59600587_f 0 +
+chr19 59068595 59069564 CCDS12866.1_cds_0_0_chr19_59068596_f 0 +
+chr19 59236026 59236146 CCDS12872.1_cds_0_0_chr19_59236027_r 0 -
+chr19 59297998 59298008 CCDS12877.1_cds_0_0_chr19_59297999_f 0 +
+chr19 59302168 59302288 CCDS12878.1_cds_0_0_chr19_59302169_r 0 -
+chr2 118288583 118288668 CCDS2120.1_cds_0_0_chr2_118288584_f 0 +
+chr2 118394148 118394202 CCDS2121.1_cds_0_0_chr2_118394149_r 0 -
+chr2 220190202 220190242 CCDS2441.1_cds_0_0_chr2_220190203_f 0 +
+chr2 220229609 220230869 CCDS2443.1_cds_0_0_chr2_220229610_r 0 -
+chr20 33330413 33330423 CCDS13249.1_cds_0_0_chr20_33330414_r 0 -
+chr20 33513606 33513792 CCDS13255.1_cds_0_0_chr20_33513607_f 0 +
+chr20 33579500 33579527 CCDS13256.1_cds_0_0_chr20_33579501_r 0 -
+chr20 33593260 33593348 CCDS13257.1_cds_0_0_chr20_33593261_f 0 +
+chr21 32707032 32707192 CCDS13614.1_cds_0_0_chr21_32707033_f 0 +
+chr21 32869641 32870022 CCDS13615.1_cds_0_0_chr21_32869642_r 0 -
+chr21 33321040 33322012 CCDS13620.1_cds_0_0_chr21_33321041_f 0 +
+chr21 33744994 33745040 CCDS13625.1_cds_0_0_chr21_33744995_r 0 -
+chr22 30120223 30120265 CCDS13897.1_cds_0_0_chr22_30120224_f 0 +
+chr22 30160419 30160661 CCDS13898.1_cds_0_0_chr22_30160420_r 0 -
+chr22 30665273 30665360 CCDS13901.1_cds_0_0_chr22_30665274_f 0 +
+chr22 30939054 30939266 CCDS13903.1_cds_0_0_chr22_30939055_r 0 -
+chr5 131424298 131424460 CCDS4149.1_cds_0_0_chr5_131424299_f 0 +
+chr5 131556601 131556672 CCDS4151.1_cds_0_0_chr5_131556602_r 0 -
+chr5 131621326 131621419 CCDS4152.1_cds_0_0_chr5_131621327_f 0 +
+chr5 131847541 131847666 CCDS4155.1_cds_0_0_chr5_131847542_r 0 -
+chr6 108299600 108299744 CCDS5061.1_cds_0_0_chr6_108299601_r 0 -
+chr6 108594662 108594687 CCDS5063.1_cds_0_0_chr6_108594663_f 0 +
+chr6 108640045 108640151 CCDS5064.1_cds_0_0_chr6_108640046_r 0 -
+chr6 108722976 108723115 CCDS5067.1_cds_0_0_chr6_108722977_f 0 +
+chr7 113660517 113660685 CCDS5760.1_cds_0_0_chr7_113660518_f 0 +
+chr7 116512159 116512389 CCDS5771.1_cds_0_0_chr7_116512160_r 0 -
+chr7 116714099 116714152 CCDS5773.1_cds_0_0_chr7_116714100_f 0 +
+chr7 116945541 116945787 CCDS5774.1_cds_0_0_chr7_116945542_r 0 -
+chr8 118881131 118881317 CCDS6324.1_cds_0_0_chr8_118881132_r 0 -
+chr9 128764156 128764189 CCDS6914.1_cds_0_0_chr9_128764157_f 0 +
+chr9 128787519 128789136 CCDS6915.1_cds_0_0_chr9_128787520_r 0 -
+chr9 128882427 128882523 CCDS6917.1_cds_0_0_chr9_128882428_f 0 +
+chr9 128937229 128937445 CCDS6919.1_cds_0_0_chr9_128937230_r 0 -
+chrX 122745047 122745924 CCDS14606.1_cds_0_0_chrX_122745048_f 0 +
+chrX 152648964 152649196 CCDS14733.1_cds_0_0_chrX_152648965_r 0 -
+chrX 152691446 152691471 CCDS14735.1_cds_0_0_chrX_152691447_f 0 +
+chrX 152694029 152694263 CCDS14736.1_cds_0_0_chrX_152694030_r 0 -

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/eq-showbeginning.dat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/eq-showbeginning.dat Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,10 @@
+chr1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 -
+chr1 147984545 147984630 CCDS990.1_cds_0_0_chr1_147984546_f 0 +
+chr1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 -
+chr1 148185136 148185276 CCDS996.1_cds_0_0_chr1_148185137_f 0 +
+chr10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 -
+chr11 116124407 116124501 CCDS8374.1_cds_0_0_chr11_116124408_r 0 -
+chr11 116206508 116206563 CCDS8377.1_cds_0_0_chr11_116206509_f 0 +
+chr11 116211733 116212337 CCDS8378.1_cds_0_0_chr11_116211734_r 0 -
+chr11 1812377 1812407 CCDS7726.1_cds_0_0_chr11_1812378_f 0 +
+chr12 38440094 38440321 CCDS8736.1_cds_0_0_chr12_38440095_r 0 -

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/eq-showtail.dat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/eq-showtail.dat Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,10 @@
+chr7 116945541 116945787 CCDS5774.1_cds_0_0_chr7_116945542_r 0 -
+chr8 118881131 118881317 CCDS6324.1_cds_0_0_chr8_118881132_r 0 -
+chr9 128764156 128764189 CCDS6914.1_cds_0_0_chr9_128764157_f 0 +
+chr9 128787519 128789136 CCDS6915.1_cds_0_0_chr9_128787520_r 0 -
+chr9 128882427 128882523 CCDS6917.1_cds_0_0_chr9_128882428_f 0 +
+chr9 128937229 128937445 CCDS6919.1_cds_0_0_chr9_128937230_r 0 -
+chrX 122745047 122745924 CCDS14606.1_cds_0_0_chrX_122745048_f 0 +
+chrX 152648964 152649196 CCDS14733.1_cds_0_0_chrX_152648965_r 0 -
+chrX 152691446 152691471 CCDS14735.1_cds_0_0_chrX_152691447_f 0 +
+chrX 152694029 152694263 CCDS14736.1_cds_0_0_chrX_152694030_r 0 -

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/extract_genomic_dna_out1.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/extract_genomic_dna_out1.fasta Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,456 @@\n+>hg17_chr1_147962192_147962580_-\n+ACTTGATCCTGCTCCCTCGGTGTCTGCATTGACTCCTCATGCTGGGACTG\n+GACCCGTCAACCCCCCTGCTCGCTGCTCACGTACCTTCATCACTTTTAGT\n+GATGATGCAACTTTCGAGGAATGGTTCCCCCAAGGGCGGCCCCCAAAAGT\n+CCCTGTTCGTGAGGTCTGTCCAGTGACCCATCGTCCAGCCCTATACCGGG\n+ACCCTGTTACAGACATACCCTATGCCACTGCTCGAGCCTTCAAGATCATT\n+CGTGAGGCTTACAAGAAGTACATTACTGCCCATGGACTGCCGCCCACTGC\n+CTCAGCCCTGGGCCCCGGCCCGCCACCTCCTGAGCCCCTCCCTGGCTCTG\n+GGCCCCGAGCCTTGCGCCAGAAAATTGTCATTAAATGA\n+>hg17_chr1_147984545_147984630_+\n+ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTT\n+TGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG\n+>hg17_chr1_148078400_148078582_-\n+GTTCTCAGCTTCCTTGCTTCCATGGCTCCAGCACCATTCGAAACCTCAAA\n+GAGAGGTTCCACATGAGCATGACTGAGGAGCAGCTGCAGCTGCTGGTGGA\n+GCAGATGGTGGATGGCAGTATGCGGTCTATCACCACCAAACTCTATGACG\n+GCTTCCAGTACCTCACCAACGGCATCATGTGA\n+>hg17_chr1_148185136_148185276_+\n+ATGGAAGCGTTTTTGGGGTCGCGGTCCGGACTTTGGGCGGGGGGTCCGGC\n+CCCAGGACAGTTTTACCGCATTCCGTCCACTCCCGATTCCTTCATGGATC\n+CGGCGTCTGCACTTTACAGAGGTCCAATCACGCGGACCCA\n+>hg17_chr10_55251623_55253124_-\n+TCTTTTCCTTCTCTACCATTTTCAACAAAGCAGGGGAAATAACTCAGTCT\n+CAGAAGACAGGAAACATCAACAAGTTGTGATGCCCTTTTCTTCCAATACT\n+ATTGAGGCTCACAAGTCAGCTCATGTAGACGGATCACTTAAGAGCAACAA\n+ACTGAAGTCTGCAAGAAAATTCACATTTCTATCTGATGAGGATGACTTAA\n+GTGCCCATAATCCCCTTTATAAGGAAAACATAAGTCAAGTATCAACAAAT\n+TCAGACATTTCACAGAGAACAGATTTTGTAGACCCATTTTCACCCAAAAT\n+ACAAGCCAAGAGTAAGTCTCTGAGGGGCCCAAGAGAAAAGATTCAGAGGC\n+TGTGGAGTCAGTCAGTCAGCTTACCCAGGAGGCTGATGAGGAAAGTTCCA\n+AATAGACCAGAGATCATAGATCTGCAGCAGTGGCAAGGCACCAGGCAGAA\n+AGCTGAAAATGAAAACACTGGAATCTGTACAAACAAAAGAGGTAGCAGCA\n+ATCCATTGCTTACAACTGAAGAGGCAAATTTGACAGAGAAAGAGGAAATA\n+AGGCAAGGTGAAACACTGATGATAGAAGGAACAGAACAGTTGAAATCTCT\n+CTCTTCAGACTCTTCATTTTGCTTTCCCAGGCCTCACTTCTCATTCTCCA\n+CTTTGCCAACTGTTTCAAGAACTGTGGAACTCAAATCAGAACCTAATGTC\n+ATCAGTTCTCCTGCTGAGTGTTCCTTGGAACTTTCTCCTTCAAGGCCTTG\n+TGTTTTACATTCTTCACTCTCTAGGAGAGAGACACCTATTTGTATGTTAC\n+CTATTGAAACCGAAAGAAATATTTTTGAAAATTTTGCCCATCCACCAAAC\n+ATCTCTCCTTCTGCCTGtccccttccccctcctcctcctatttctcctcc\n+ttctcctcctcctgctcctgctcctcttgctcctcctcctgacatttctc\n+ctttttctcttttttgtcctcctccctctcctccttctatccctcttcct\n+cttcctcctcctACATTTTTTCCACTTTCCGTTTCAACGTCTGGTCCCCC\n+AACAccacctcttctacctccatttccaactcctcttcctccaccacctc\n+cttctattccttgccctccacctccttcAGCTTCATTTCTGTCCACAGAG\n+TGTGTCTGTATAACAGGTGTTAAATGCACGACCAACTTGATGCCTGCCGA\n+GAAAATTAAGTCCTCTATGACACAGCTATCAACAACGACAGTGTGTAAAA\n+CAGACCCTCAGAGAGAACCAAAAGGCATCCTCAGACACGTTAAAAACTTA\n+GCAGAACTTGAAAAATCAGTAGCTAACATGTACAGTCAAATAGAAAAAAA\n+CTATCTACGCACAAATGTTTCAGAACTTCAAACTATGTGCCCTTCAGAAG\n+TAACAAATATGGAAATCACATCTGAACAAAACAAGGGGAGTTTGAACAAT\n+ATTGTCGAGGGAACTGAAAAACAATCTCACAGTCAATCTACTTCACTGTA\n+A\n+>hg17_chr11_116124407_116124501_-\n+ATCCAATGGATTTGAACAGAAGCGCTTTGCCAGGCTTGCCAGCAAGAAGG\n+CAGTGGAGGAACTTGCCTACAAATGGAGTGTTGAGGATATGTAA\n+>hg17_chr11_116206508_116206563_+\n+ATGCAGCCCCGGGTACTCCTTGTTGTTGCCCTCCTGGCGCTCCTGGCCTC\n+TGCCC\n+>hg17_chr11_116211733_116212337_-\n+CCTAAAGCTCCTTGACAACTGGGACAGCGTGACCTCCACCTTCAGCAAGC\n+TGCGCGAACAGCTCGGCCCTGTGACCCAGGAGTTCTGGGATAACCTGGAA\n+AAGGAGACAGAGGGCCTGAGGCAGGAGATGAGCAAGGATCTGGAGGAGGT\n+GAAGGCCAAGGTGCAGCCCTACCTGGACGACTTCCAGAAGAAGTGGCAGG\n+AGGAGATGGAGCTCTACCGCCAGAAGGTGGAGCCGCTGCGCGCAGAGCTC\n+CAAGAGGGCGCGCGCCAGAAGCTGCACGAGCTGCAAGAGAAGCTGAGCCC\n+ACTGGGCGAGGAGATGCGCGACCGCGCGCGCGCCCATGTGGACGCGCTGC\n+GCACGCATCTGGCCCCCTACAGCGACGAGCTGCGCCAGCGCTTGGCCGCG\n+CGCCTTGAGGCTCTCAAGGAGAACGGCGGCGCCAGACTGGCCGAGTACCA\n+CGCCAAGGCCACCGAGCATCTGAGCACGCTCAGCGAGAAGGCCAAGCCCG\n+CGCTCGAGGACCTCCGCCAAGGCCTGCTGCCCGTGCTGGAGAGCTTCAAG\n+GTCAGCTTCCTGAGCGCTCTCGAGGAGTACACTAAGAAGCTCAACACCCA\n+GTGA\n+>hg17_chr11_1812377_1812407_+\n+ATGCTCCACCTGCATGGCTGGCAAACCATG\n+>hg17_chr12_38440094_38440321_-\n+GAGCTTTCTTCCTCTATGCTGGATTTGCTGCTGTGGGACTCCTTTTCATC\n+TATGGCTGTCTTCCTGAGACCAAAGGCAAAAAATTAGAGGAAATTGAATC\n+ACTCTTTGACAACAGGCTATGTACATGTGGCACTTCAGATTCTGATGAAG\n+GGAGATATATTGAATATATTCGGGTAAAGGGAAGTAACTATCATCTTTCT\n+GACAATGATGCTTCTGATGTGGAATAA\n+>hg17_chr13_112381694_112381953_+\n+ATGAACTCACCAGAGGCGAGGCTCTGCGTTGCTCAATGCAGAGACTCTTA\n+CCCAGGGTGTCAGCCTCTGAAAGATACACGTGCCTGGGCCTCTTCCCTGA\n+AGATGGACCCGGCAGGTCTGGAGGGAGGCCCCCGTGATGAATCCCGTGAT\n+GAG'..b'TGAACACCTAGAAAAACCTAACAAATAG\n+>hg17_chr8_118881131_118881317_-\n+ACTTCTCGGGCTTCCCGTTGGGCTGACCCTGACCACTTTGCCCAGCGACA\n+GAGCTGCATGAATACGTTTGCCAGCTGGTTTGGCTACATGCCGCTGATCC\n+ACTCTCAGATGAGGCTCGACCCCGTCCTCTTTAAAGACCAGGTCTCTATT\n+TTGAGGAAGAAATACCGAGACATTGAGCGACTTTGA\n+>hg17_chr9_128764156_128764189_+\n+ATGGCCTGCCTGAGCCCCTCGCAGCTCCAGAAG\n+>hg17_chr9_128787519_128789136_-\n+ATGACCCGAGAGTGCCCATCTCCGGCCCCGGGGCCTGGGGCTCCGCTGAG\n+TGGATCGGTGCTGGCAGAGGCGGCAGTAGTGTTTGCAGTGGTGCTGAGCA\n+TCCACGCAACCGTATGGGACCGATACTCGTGGTGCGCCGTGGCCCTCGCA\n+GTGCAGGCCTTCTACGTCCAATACAAGTGGGACCGGCTGCTACAGCAGGG\n+AAGCGCCGTCTTCCAGTTCCGAATGTCCGCAAACAGTGGCCTATTGCCCG\n+CCTCCATGGTCATGCCTTTGCTTGGACTAGTCATGAAGGAGCGGTGCCAG\n+ACTGCTGGGAACCCGTTCTTTGAGCGTTTTGGCATTGTGGTGGCAGCCAC\n+TGGCATGGCAGTGGCCCTCTTCTCATCAGTGTTGGCGCTCGGCATCACTC\n+GCCCAGTGCCAACCAACACTTGTGTCATCTTGGGCTTGGCTGGAGGTGTT\n+ATCATTTATATCATGAAGCACTCGTTGAGCGTGGGGGAGGTGATCGAAGT\n+CCTGGAAGTCCTTCTGATCTTCGTTTATCTCAACATGATCCTGCTGTACC\n+TGCTGCCCCGCTGCTTCACCCCTGGTGAGGCACTGCTGGTATTGGGTGGC\n+ATTAGCTTTGTCCTCAACCAGCTCATCAAGCGCTCTCTGACACTGGTGGA\n+AAGTCAGGGGGACCCAGTGGACTTCTTCCTGCTGGTGGTGGTAGTAGGGA\n+TGGTACTCATGGGCATTTTCTTCAGCACTCTGTTTGTCTTCATGGACTCA\n+GGCACCTGGGCCTCCTCCATCTTCTTCCACCTCATGACCTGTGTGCTGAG\n+CCTTGGTGTGGTCCTACCCTGGCTGCACCGGCTCATCCGCAGGAATCCCC\n+TGCTCTGGCTTCTTCAGTTTCTCTTCCAGACAGACACCCGCATCTACCTC\n+CTAGCCTATTGGTCTCTGCTGGCCACCTTGGCCTGCCTGGTGGTGCTGTA\n+CCAGAATGCCAAGCGGTCATCTTCCGAGTCCAAGAAGCACCAGGCCCCCA\n+CCATCGCCCGAAAGTATTTCCACCTCATTGTGGTAGCCACCTACATCCCA\n+GGTATCATCTTTGACCGGCCACTGCTCTATGTAGCCGCCACTGTATGCCT\n+GGCGGTCTTCATCTTCCTGGAGTATGTGCGCTACTTCCGCATCAAGCCTT\n+TGGGTCACACTCTACGGAGCTTCCTGTCCCTTTTTCTGGATGAACGAGAC\n+AGTGGACCACTCATTCTGACACACATCTACCTGCTCCTGGGCATGTCTCT\n+TCCCATCTGGCTGATCCCCAGACCCTGCACACAGAAGGGTAGCCTGGGAG\n+GAGCCAGGGCCCTCGTCCCCTATGCCGGTGTCCTGGCTGTGGGTGTGGGT\n+GATACTGTGGCCTCCATCTTCGGTAGCACCATGGGGGAGATCCGCTGGCC\n+TGGAACCAAAAAGACTTTTGAGGGGACCATGACATCTATATTTGCGCAGA\n+TCATTTCTGTAGCTCTGATCTTAATCTTTGACAGTGGAGTGGACCTAAAC\n+TACAGTTATGCTTGGATTTTGGGGTCCATCAGCACTGTGTCCCTCCTGGA\n+AGCATACACTACACAGATAGACAATCTCCTTCTGCCTCTCTACCTCCTGA\n+TATTGCTGATGGCCTAG\n+>hg17_chr9_128882427_128882523_+\n+ATGGCGTTCCGGAGGGCCGAGGGCACGTCTATGATCCAGGCCCTGGCCAT\n+GACGGTGGCCGAGATCCCCGTGTTCCTGTACACGACGTTTGGGCAG\n+>hg17_chr9_128937229_128937445_-\n+GTCCCTGCCAAGACAGACTGTGTCATGTTCTTCGGGCCCGTGGTCCCCGA\n+CGGCTACGGTGTCTGCTATAACCCCATGGAGGCCCACATCAACTTCTCCC\n+TGTCGGCCTACAACAGCTGCGCGGAGACCAACGCCGCCCGCCTGGCGCAT\n+TACCTGGAGAAGGCGCTCCTGGACATGCGTGCCCTGCTGCAGAGCCACCC\n+CCGGGCCAAGCTCTGA\n+>hg17_chrX_122745047_122745924_+\n+ATGACTTTTAACAGTTTTGAAGGATCTAAAACTTGTGTACCTGCAGACAT\n+CAATAAGGAAGAAGAATTTGTAGAAGAGTTTAATAGATTAAAAACTTTTG\n+CTAATTTTCCAAGTGGTAGTCCTGTTTCAGCATCAACACTGGCACGAGCA\n+GGGTTTCTTTATACTGGTGAAGGAGATACCGTGCGGTGCTTTAGTTGTCA\n+TGCAGCTGTAGATAGATGGCAATATGGAGACTCAGCAGTTGGAAGACACA\n+GGAAAGTATCCCCAAATTGCAGATTTATCAACGGCTTTTATCTTGAAAAT\n+AGTGCCACGCAGTCTACAAATTCTGGTATCCAGAATGGTCAGTACAAAGT\n+TGAAAACTATCTGGGAAGCAGAGATCATTTTGCCTTAGACAGGCCATCTG\n+AGACACATGCAGACTATCTTTTGAGAACTGGGCAGGTTGTAGATATATCA\n+GACACCATATACCCGAGGAACCCTGCCATGTATAGTGAAGAAGCTAGATT\n+AAAGTCCTTTCAGAACTGGCCAGACTATGCTCACCTAACCCCAAGAGAGT\n+TAGCAAGTGCTGGACTCTACTACACAGGTATTGGTGACCAAGTGCAGTGC\n+TTTTGTTGTGGTGGAAAACTGAAAAATTGGGAACCTTGTGATCGTGCCTG\n+GTCAGAACACAGGCGACACTTTCCTAATTGCTTCTTTGTTTTGGGCCGGA\n+ATCTTAATATTCGAAGTGAATCTGATGCTGTGAGTTCTGATAGGAATTTC\n+CCAAATTCAACAAATCTTCCAAGAAATCCATCCATGGCAGATTATGAAGC\n+ACGGATCTTTACTTTTGGGACATGGATATACTCAGTTAACAAGGAGCAGC\n+TTGCAAGAGCTGGATTTTATGCTTTAG\n+>hg17_chrX_152648964_152649196_-\n+TGACAACGAGGAGAAGGCCTTTGGCAGCAGCCAGCCATCGCTCAACGGGG\n+ACATCAAGCCCCTGGGCAGTGACGACAGCCTGGCCGATTATGGGGGCAGC\n+GTGGATGTTCAGTTCAACGAGGATGGTTCGTTCATTGGCCAGTACAGTGG\n+CAAGAAGGAGAAGGAGGCGGCAGGGGGCAATGACAGCTCAGGGGCCACTT\n+CCCCCATCAACCCTGCCGTGGCCCTAGAATAG\n+>hg17_chrX_152691446_152691471_+\n+ATGCTCATGGCGTCCACCACTTCCG\n+>hg17_chrX_152694029_152694263_-\n+GCTGTGGCACAGAACATGGACTCTGTGTTTAAGGAGCTCTTGGGAAAGAC\n+CTCTGTCCGCCAGGGCCTTGGGCCAGCATCTACCACCTCTCCCAGTCCTG\n+GGCCCCGAAGCCCAAAGGCCCCGCCCAGCAGCCGCCTGGGCAGGAACAAA\n+GGCTTCTCCCGGGGCCCTGGGGCCCCAGCCTCACCCTCAGCTTCCCACCC\n+CCAGGGCCTAGACACGACCCCCAAGCCACACTGA\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/extract_genomic_dna_out2.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/extract_genomic_dna_out2.fasta Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,6 @@
+>droPer1_super_1_139823_139913_- AK028861
+CGTCGGCTTCTGCTTCTGCTGATGATGGTCGTTCTTCTTCCTTTACTTCT
+TCCTATTTTTCTTCCTTCCCTTACACTATATCTTCCTTTA
+>droPer1_super_1_156750_156844_- BC126698
+CCGGGCTGCGGCAAGGGATTCACCTGCTCCAAACAGCTCAAGGTGCACTC
+CCGCACGCACACGGGCGAGAAGCCCTATCACTGCGACATCTGCT

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/extract_genomic_dna_out3.interval
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/extract_genomic_dna_out3.interval Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,65 @@\n+chr1\t147962192\t147962580\tCCDS989.1_cds_0_0_chr1_147962193_r\t0\t-\tACTTGATCCTGCTCCCTCGGTGTCTGCATTGACTCCTCATGCTGGGACTGGACCCGTCAACCCCCCTGCTCGCTGCTCACGTACCTTCATCACTTTTAGTGATGATGCAACTTTCGAGGAATGGTTCCCCCAAGGGCGGCCCCCAAAAGTCCCTGTTCGTGAGGTCTGTCCAGTGACCCATCGTCCAGCCCTATACCGGGACCCTGTTACAGACATACCCTATGCCACTGCTCGAGCCTTCAAGATCATTCGTGAGGCTTACAAGAAGTACATTACTGCCCATGGACTGCCGCCCACTGCCTCAGCCCTGGGCCCCGGCCCGCCACCTCCTGAGCCCCTCCCTGGCTCTGGGCCCCGAGCCTTGCGCCAGAAAATTGTCATTAAATGA\n+chr1\t147984545\t147984630\tCCDS990.1_cds_0_0_chr1_147984546_f\t0\t+\tATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG\n+chr1\t148078400\t148078582\tCCDS993.1_cds_0_0_chr1_148078401_r\t0\t-\tGTTCTCAGCTTCCTTGCTTCCATGGCTCCAGCACCATTCGAAACCTCAAAGAGAGGTTCCACATGAGCATGACTGAGGAGCAGCTGCAGCTGCTGGTGGAGCAGATGGTGGATGGCAGTATGCGGTCTATCACCACCAAACTCTATGACGGCTTCCAGTACCTCACCAACGGCATCATGTGA\n+chr1\t148185136\t148185276\tCCDS996.1_cds_0_0_chr1_148185137_f\t0\t+\tATGGAAGCGTTTTTGGGGTCGCGGTCCGGACTTTGGGCGGGGGGTCCGGCCCCAGGACAGTTTTACCGCATTCCGTCCACTCCCGATTCCTTCATGGATCCGGCGTCTGCACTTTACAGAGGTCCAATCACGCGGACCCA\n+chr10\t55251623\t55253124\tCCDS7248.1_cds_0_0_chr10_55251624_r\t0\t-\tTCTTTTCCTTCTCTACCATTTTCAACAAAGCAGGGGAAATAACTCAGTCTCAGAAGACAGGAAACATCAACAAGTTGTGATGCCCTTTTCTTCCAATACTATTGAGGCTCACAAGTCAGCTCATGTAGACGGATCACTTAAGAGCAACAAACTGAAGTCTGCAAGAAAATTCACATTTCTATCTGATGAGGATGACTTAAGTGCCCATAATCCCCTTTATAAGGAAAACATAAGTCAAGTATCAACAAATTCAGACATTTCACAGAGAACAGATTTTGTAGACCCATTTTCACCCAAAATACAAGCCAAGAGTAAGTCTCTGAGGGGCCCAAGAGAAAAGATTCAGAGGCTGTGGAGTCAGTCAGTCAGCTTACCCAGGAGGCTGATGAGGAAAGTTCCAAATAGACCAGAGATCATAGATCTGCAGCAGTGGCAAGGCACCAGGCAGAAAGCTGAAAATGAAAACACTGGAATCTGTACAAACAAAAGAGGTAGCAGCAATCCATTGCTTACAACTGAAGAGGCAAATTTGACAGAGAAAGAGGAAATAAGGCAAGGTGAAACACTGATGATAGAAGGAACAGAACAGTTGAAATCTCTCTCTTCAGACTCTTCATTTTGCTTTCCCAGGCCTCACTTCTCATTCTCCACTTTGCCAACTGTTTCAAGAACTGTGGAACTCAAATCAGAACCTAATGTCATCAGTTCTCCTGCTGAGTGTTCCTTGGAACTTTCTCCTTCAAGGCCTTGTGTTTTACATTCTTCACTCTCTAGGAGAGAGACACCTATTTGTATGTTACCTATTGAAACCGAAAGAAATATTTTTGAAAATTTTGCCCATCCACCAAACATCTCTCCTTCTGCCTGtccccttccccctcctcctcctatttctcctccttctcctcctcctgctcctgctcctcttgctcctcctcctgacatttctcctttttctcttttttgtcctcctccctctcctccttctatccctcttcctcttcctcctcctACATTTTTTCCACTTTCCGTTTCAACGTCTGGTCCCCCAACAccacctcttctacctccatttccaactcctcttcctccaccacctccttctattccttgccctccacctccttcAGCTTCATTTCTGTCCACAGAGTGTGTCTGTATAACAGGTGTTAAATGCACGACCAACTTGATGCCTGCCGAGAAAATTAAGTCCTCTATGACACAGCTATCAACAACGACAGTGTGTAAAACAGACCCTCAGAGAGAACCAAAAGGCATCCTCAGACACGTTAAAAACTTAGCAGAACTTGAAAAATCAGTAGCTAACATGTACAGTCAAATAGAAAAAAACTATCTACGCACAAATGTTTCAGAACTTCAAACTATGTGCCCTTCAGAAGTAACAAATATGGAAATCACATCTGAACAAAACAAGGGGAGTTTGAACAATATTGTCGAGGGAACTGAAAAACAATCTCACAGTCAATCTACTTCACTGTAA\n+chr11\t116124407\t116124501\tCCDS8374.1_cds_0_0_chr11_116124408_r\t0\t-\tATCCAATGGATTTGAACAGAAGCGCTTTGCCAGGCTTGCCAGCAAGAAGGCAGTGGAGGAACTTGCCTACAAATGGAGTGTTGAGGATATGTAA\n+chr11\t116206508\t116206563\tCCDS8377.1_cds_0_0_chr11_116206509_f\t0\t+\tATGCAGCCCCGGGTACTCCTTGTTGTTGCCCTCCTGGCGCTCCTGGCCTCTGCCC\n+chr11\t116211733\t116212337\tCCDS8378.1_cds_0_0_chr11_116211734_r\t0\t-\tCCTAAAGCTCCTTGACAACTGGGACAGCGTGACCTCCACCTTCAGCAAGCTGCGCGAACAGCTCGGCCCTGTGACCCAGGAGTTCTGGGATAACCTGGAAAAGGAGACAGAGGGCCTGAGGCAGGAGATGAGCAAGGATCTGGAGGAGGTGAAGGCCAAGGTGCAGCCCTACCTGGACGACTTCCAGAAGAAGTGGCAGGAGGAGATGGAGCTCTACCGCCAGAAGGTGGAGCCGCTGCGCGCAGAGCTCCAAGAGGGCGCGCGCCAGAAGCTGCACGAGCTGCAAGAGAAGCTGAGCCCACTGGGCGAGGAGATGCGCGACCGCGCGCGCGCCCATGTGGACGCGCTGCGCACGCATCTGGCCCCCTACAGCGACGAGCTGCGCCAGCGCTTGGCCGCGCGCCTTGAGGCTCTCAAGGAGAACGGCGGCGCCAGACTGGCCGAGTACCACGCCAAGGCCACCGAGCATCTGAGCACGCTCAGCGAGAAGGCCAAGCCCGCGCTCGAGGACCTCCGCCAAGGCCTGCTGCCCGTGCTGGAGAGCTTCAAGGTCAGCTTCCTGAGCGCTCTCGAGGAGTACACTAAGAAGCTCAACACCCAGTGA\n+chr11\t1812377\t1812407\tCCDS7726.1_cds_0_0_chr11_1812378_f\t0\t+\tATGCTCCACCTGCATGGCTGGCAAACCATG\n+chr12\t38440094\t38440321\tCCDS8736.1_cds_0_0_chr12_38440095_r\t0\t-\tGAGCTTTCTTCCTCTATGCTGGATTTGCTGCTGTGGGACTCCTTTTCATCTATGGCTGTCTTCCTGAGACCAAAGGCAAAAAATTAGAGGAAATTGAATCACTCTTTGACAACAGGCTATGTACATGTGGCACTTCAGATTCTGATGAAGGGAGATATATTGAATATATTCGGGTAAAGGGAAGTAACTATCATCTTTCTGACAATGATGCTTCTGATGTGGAATAA\n+chr13\t112'..b'TGAATACGTTTGCCAGCTGGTTTGGCTACATGCCGCTGATCCACTCTCAGATGAGGCTCGACCCCGTCCTCTTTAAAGACCAGGTCTCTATTTTGAGGAAGAAATACCGAGACATTGAGCGACTTTGA\n+chr9\t128764156\t128764189\tCCDS6914.1_cds_0_0_chr9_128764157_f\t0\t+\tATGGCCTGCCTGAGCCCCTCGCAGCTCCAGAAG\n+chr9\t128787519\t128789136\tCCDS6915.1_cds_0_0_chr9_128787520_r\t0\t-\tATGACCCGAGAGTGCCCATCTCCGGCCCCGGGGCCTGGGGCTCCGCTGAGTGGATCGGTGCTGGCAGAGGCGGCAGTAGTGTTTGCAGTGGTGCTGAGCATCCACGCAACCGTATGGGACCGATACTCGTGGTGCGCCGTGGCCCTCGCAGTGCAGGCCTTCTACGTCCAATACAAGTGGGACCGGCTGCTACAGCAGGGAAGCGCCGTCTTCCAGTTCCGAATGTCCGCAAACAGTGGCCTATTGCCCGCCTCCATGGTCATGCCTTTGCTTGGACTAGTCATGAAGGAGCGGTGCCAGACTGCTGGGAACCCGTTCTTTGAGCGTTTTGGCATTGTGGTGGCAGCCACTGGCATGGCAGTGGCCCTCTTCTCATCAGTGTTGGCGCTCGGCATCACTCGCCCAGTGCCAACCAACACTTGTGTCATCTTGGGCTTGGCTGGAGGTGTTATCATTTATATCATGAAGCACTCGTTGAGCGTGGGGGAGGTGATCGAAGTCCTGGAAGTCCTTCTGATCTTCGTTTATCTCAACATGATCCTGCTGTACCTGCTGCCCCGCTGCTTCACCCCTGGTGAGGCACTGCTGGTATTGGGTGGCATTAGCTTTGTCCTCAACCAGCTCATCAAGCGCTCTCTGACACTGGTGGAAAGTCAGGGGGACCCAGTGGACTTCTTCCTGCTGGTGGTGGTAGTAGGGATGGTACTCATGGGCATTTTCTTCAGCACTCTGTTTGTCTTCATGGACTCAGGCACCTGGGCCTCCTCCATCTTCTTCCACCTCATGACCTGTGTGCTGAGCCTTGGTGTGGTCCTACCCTGGCTGCACCGGCTCATCCGCAGGAATCCCCTGCTCTGGCTTCTTCAGTTTCTCTTCCAGACAGACACCCGCATCTACCTCCTAGCCTATTGGTCTCTGCTGGCCACCTTGGCCTGCCTGGTGGTGCTGTACCAGAATGCCAAGCGGTCATCTTCCGAGTCCAAGAAGCACCAGGCCCCCACCATCGCCCGAAAGTATTTCCACCTCATTGTGGTAGCCACCTACATCCCAGGTATCATCTTTGACCGGCCACTGCTCTATGTAGCCGCCACTGTATGCCTGGCGGTCTTCATCTTCCTGGAGTATGTGCGCTACTTCCGCATCAAGCCTTTGGGTCACACTCTACGGAGCTTCCTGTCCCTTTTTCTGGATGAACGAGACAGTGGACCACTCATTCTGACACACATCTACCTGCTCCTGGGCATGTCTCTTCCCATCTGGCTGATCCCCAGACCCTGCACACAGAAGGGTAGCCTGGGAGGAGCCAGGGCCCTCGTCCCCTATGCCGGTGTCCTGGCTGTGGGTGTGGGTGATACTGTGGCCTCCATCTTCGGTAGCACCATGGGGGAGATCCGCTGGCCTGGAACCAAAAAGACTTTTGAGGGGACCATGACATCTATATTTGCGCAGATCATTTCTGTAGCTCTGATCTTAATCTTTGACAGTGGAGTGGACCTAAACTACAGTTATGCTTGGATTTTGGGGTCCATCAGCACTGTGTCCCTCCTGGAAGCATACACTACACAGATAGACAATCTCCTTCTGCCTCTCTACCTCCTGATATTGCTGATGGCCTAG\n+chr9\t128882427\t128882523\tCCDS6917.1_cds_0_0_chr9_128882428_f\t0\t+\tATGGCGTTCCGGAGGGCCGAGGGCACGTCTATGATCCAGGCCCTGGCCATGACGGTGGCCGAGATCCCCGTGTTCCTGTACACGACGTTTGGGCAG\n+chr9\t128937229\t128937445\tCCDS6919.1_cds_0_0_chr9_128937230_r\t0\t-\tGTCCCTGCCAAGACAGACTGTGTCATGTTCTTCGGGCCCGTGGTCCCCGACGGCTACGGTGTCTGCTATAACCCCATGGAGGCCCACATCAACTTCTCCCTGTCGGCCTACAACAGCTGCGCGGAGACCAACGCCGCCCGCCTGGCGCATTACCTGGAGAAGGCGCTCCTGGACATGCGTGCCCTGCTGCAGAGCCACCCCCGGGCCAAGCTCTGA\n+chrX\t122745047\t122745924\tCCDS14606.1_cds_0_0_chrX_122745048_f\t0\t+\tATGACTTTTAACAGTTTTGAAGGATCTAAAACTTGTGTACCTGCAGACATCAATAAGGAAGAAGAATTTGTAGAAGAGTTTAATAGATTAAAAACTTTTGCTAATTTTCCAAGTGGTAGTCCTGTTTCAGCATCAACACTGGCACGAGCAGGGTTTCTTTATACTGGTGAAGGAGATACCGTGCGGTGCTTTAGTTGTCATGCAGCTGTAGATAGATGGCAATATGGAGACTCAGCAGTTGGAAGACACAGGAAAGTATCCCCAAATTGCAGATTTATCAACGGCTTTTATCTTGAAAATAGTGCCACGCAGTCTACAAATTCTGGTATCCAGAATGGTCAGTACAAAGTTGAAAACTATCTGGGAAGCAGAGATCATTTTGCCTTAGACAGGCCATCTGAGACACATGCAGACTATCTTTTGAGAACTGGGCAGGTTGTAGATATATCAGACACCATATACCCGAGGAACCCTGCCATGTATAGTGAAGAAGCTAGATTAAAGTCCTTTCAGAACTGGCCAGACTATGCTCACCTAACCCCAAGAGAGTTAGCAAGTGCTGGACTCTACTACACAGGTATTGGTGACCAAGTGCAGTGCTTTTGTTGTGGTGGAAAACTGAAAAATTGGGAACCTTGTGATCGTGCCTGGTCAGAACACAGGCGACACTTTCCTAATTGCTTCTTTGTTTTGGGCCGGAATCTTAATATTCGAAGTGAATCTGATGCTGTGAGTTCTGATAGGAATTTCCCAAATTCAACAAATCTTCCAAGAAATCCATCCATGGCAGATTATGAAGCACGGATCTTTACTTTTGGGACATGGATATACTCAGTTAACAAGGAGCAGCTTGCAAGAGCTGGATTTTATGCTTTAG\n+chrX\t152648964\t152649196\tCCDS14733.1_cds_0_0_chrX_152648965_r\t0\t-\tTGACAACGAGGAGAAGGCCTTTGGCAGCAGCCAGCCATCGCTCAACGGGGACATCAAGCCCCTGGGCAGTGACGACAGCCTGGCCGATTATGGGGGCAGCGTGGATGTTCAGTTCAACGAGGATGGTTCGTTCATTGGCCAGTACAGTGGCAAGAAGGAGAAGGAGGCGGCAGGGGGCAATGACAGCTCAGGGGCCACTTCCCCCATCAACCCTGCCGTGGCCCTAGAATAG\n+chrX\t152691446\t152691471\tCCDS14735.1_cds_0_0_chrX_152691447_f\t0\t+\tATGCTCATGGCGTCCACCACTTCCG\n+chrX\t152694029\t152694263\tCCDS14736.1_cds_0_0_chrX_152694030_r\t0\t-\tGCTGTGGCACAGAACATGGACTCTGTGTTTAAGGAGCTCTTGGGAAAGACCTCTGTCCGCCAGGGCCTTGGGCCAGCATCTACCACCTCTCCCAGTCCTGGGCCCCGAAGCCCAAAGGCCCCGCCCAGCAGCCGCCTGGGCAGGAACAAAGGCTTCTCCCGGGGCCCTGGGGCCCCAGCCTCACCCTCAGCTTCCCACCCCCAGGGCCTAGACACGACCCCCAAGCCACACTGA\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/extract_genomic_dna_out4.gff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/extract_genomic_dna_out4.gff Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,46 @@\n+chr10\tCufflinks\ttranscript\t62044837\t62045189\t1000\t.\t.\tgene_id "CUFF.23531"; transcript_id "CUFF.23531.1"; FPKM "19.5178121606"; frac "1.000000"; conf_lo "9.264456"; conf_hi "29.771168"; cov "1.108611"; seq "AATTACAAGATCGACACACCAAGATAGGCAGATCCATGGTTGGTTTTACTTTGTAAATCTAAAAGTATGTTGGAAAACGATGCAATGAATTCTTATCCTTTTTCAAAATGAAGAATTTGTGATGGTTAGTGGACAGTTCAGAAGCCTCTCTGCAAGAAAGGGGGCGCTGAGAAGTGGTAAAAAAAGGAAGGAAGCACTCGGGCTTTGTCAGCAGGGTGGACCCTGGGGTCCACAGTGGGAACAGTCCCTTCTGGCCTCTACTCACTGACCAAACGCTTTACTAAAACTCCGCTTCTGGCCTCTGTTGCCACCTCCTGGTCGCTGTCCTCGGAAGTTTCTACTTCCTCCTCGCT";\n+chr10\tCufflinks\ttranscript\t75372919\t75373002\t1000\t.\t.\tgene_id "CUFF.24985"; transcript_id "CUFF.24985.1"; FPKM "124.4970510798"; frac "1.000000"; conf_lo "71.411330"; conf_hi "177.582772"; cov "7.071429"; seq "GCGTCTCGCAGCTTCTGCCCGTCGATCTCCATGTCGAGCCGGATGGGCACCAGCACCTCAGGCTGTGACGCATTCTCATGGATC";\n+chr10\tCufflinks\ttranscript\t80362428\t80363292\t1000\t-\t.\tgene_id "CUFF.26065"; transcript_id "CUFF.26065.1"; FPKM "43.6170921216"; frac "1.000000"; conf_lo "32.260169"; conf_hi "54.974016"; cov "2.477449"; seq "ATGACGGACAAGTGTTTCCGGAAGTGCATCGGGAAGCCCGGGGGCTCCTTGGATAACTCGGAGCAGGTGAGACATCTCGGGAACCCGGGGTGGTGAGGGGCGCGGGGTCAGGAGCGTCTAGGAGGTTGAGAGATGTGCGCGTGCGCGGCCTCTAGCCTTAGCTACTGAGGAAGTTGTGCGCGTGCGCGGGGTGAGGACCCGGCTTCTGTGCCTAGATCGGTGCAGCCTTCATGGGTGATCCTCGGGTCGTGTGACCGTCAGTCAGGGATCCCCCTCCACGCTTTGCAGAAATGCATCGCCATGTGCATGGACCGCTACATGGACGCCTGGAATACCGTGTCCCGCGCCTACAACTCTCGACTGCAGCGGGAACGAGCCAACATGTGACCGGGACCTGTGCCTCGGGACACCGTGCTTATGGTCTGAACTGTTTTCCCTGCCAGTTAGGGTGTCTCCTCCTAGCCGCCCTGAAGTCTGGCAGCATGGAGGGCTTGGGGATCGAGGCCTCTCCCCTGGGTTGCTGCGTCCAGCTCAATCTCAGAAGAGAGTGAGGACCCGACAGAGCACAGGGATCTGGCTGGCCCCACTGACCTGTGACCTCAGGAGAGCAGGCCAATAAATCGCTGCTGGGGCAGTAAAGCAGGCGTGTCACCTCACTGCTTCAGGTCCCTTCCCCTGAGTAGGCCCAGACCTCCCAGGGTATCTTTCCCCTTGGGGTCAGTGGGCTGCTGGCTCTCAGGGAATTCGGAGCATGATCTCAGGTGTTTGGTCATCCCGGGGAGACCAGCCGAGGTTAAGAAGCAAGGCTTCATGTagccttcacctatcatgcatgaggcccagggtgctgaccttaactctgaat";\n+chr11\tCufflinks\ttranscript\t7904565\t7904642\t1000\t.\t.\tgene_id "CUFF.33508"; transcript_id "CUFF.33508.1"; FPKM "61.6484988869"; frac "1.000000"; conf_lo "22.882428"; conf_hi "100.414569"; cov "3.501633"; seq "CATCTTCTATTTGAGCCTCCATCCAGGCACCTCTGAAACAAAGGTGCACTCACTGCATGTCCACTTGTCACAGGAGCC";\n+chr11\tCufflinks\texon\t78140156\t78140259\t1000\t.\t.\tgene_id "CUFF.43148"; transcript_id "CUFF.43148.1"; exon_number "1"; FPKM "54.8483511750"; frac "1.000000"; conf_lo "23.181641"; conf_hi "86.515061"; cov "3.115385"; seq "CTGCTTGCTAATTTTCTCTCTTGGGATCAGGGGGACGTGAACTCCAGCCCTGACTCGTGCTCCTTATGCTCTGAGTACATAGCAAATAAATGAGAGCAAAACAC";\n+chr11\tCufflinks\texon\t105616462\t105616737\t1000\t.\t.\tgene_id "CUFF.48385"; transcript_id "CUFF.48385.1"; exon_number "1"; FPKM "18.9452034252"; frac "1.000000"; conf_lo "7.520816"; conf_hi "30.369591"; cov "1.076087"; seq "TAGGTGTAATAGTGGAAAACAATAGTTTTTAAACTTCAGAGTCCAGGGCTGTAACTCAGTAGTAACAGTGTTCTCTAAGTATGTTATTCTTCCTCTACATGCTGAAATTTTTCATATTTGGAGCATTCACTGTTCCATGTATCAGTAAATTATATTGTGAGCTGTCATCATATCTAAGCACCATATTGAATATTTTTCATGATTAAAATTTGTTGAAACAACAATTCTATGACCGAAAAAAGCAAGGCTTTGTAAATAACATGTTTGTTACTAGTA";\n+chr12\tCufflinks\texon\t30701762\t30702509\t1000\t.\t.\tgene_id "CUFF.53897"; transcript_id "CUFF.53897.1"; exon_number "1"; FPKM "48.9333329111"; frac "1.000000"; conf_lo "37.780391"; conf_hi "60.086275"; cov "2.779412"; seq "TGTGGAGTGTACTTATATGATCCCTATGCTGATAGGATTACCTTCCTAGACATAGCTAGACGCAAAGCCACATGTGTAAGGCTGCTGAGCAAAGACAGCATCCCAGCATGGGTGTGTTCACGGTGGATTCACCACGTTGCATATGTAAAGTGGTCCCCTTGGCTTACCCTTCACTTTGCTCATGAGATTCAGAAGCTGGTGGTCCAGCAGGGGTGAGCATTTGTGAAATAGTAAGCTGAACTTAGTGGTGAGATTTCAGAACAGACTTCTGTGAAGTAAGAGATGTAACCATGCATCTAAAATCAGATGGCCGTGTAACTGCTCGGGCATAGAAATGGTGGGAGAACCTGTCCTGGGTACCTGGCATTTCACATGAGCCCAGGGATATGTCTTGTGCCAAGGCACACAAGTGTCCATGGACTTGGACAGGTGCCAAGGGTTTTTGTCTCTGTTCCTATGTGGGAGGCTGGCTGTGATTTACATTAATTTCTGTATTTCAAACGAAGATGTCTGCAGATCTCCATTTTGATGTTACAGCCTCATTGCCCAGGCAGTGGGCAGTGCCCAGACACCCTTTCTGACTAGCCACTGCATTGGGCTTCTGTGATTCAAAGTAGTGTATATATTTATTTACTTCTCTGACTGTGGCCAACAGCCAAATGCCATTTTATGTTCCTTGTATTCAGTCCATTACCAAAGAGGTGTTT'..b'7.7370289869"; frac "1.000000"; conf_lo "1.872548"; conf_hi "33.601510"; cov "1.007463"; seq "GTGAAACATCATGCTTCTGCATCAAGTTATTAGTGGGAAACCTGTAAAAGTTGACATTGAATGCTGATAACAAATTACTTTCATCCTGTCTCATAATGAATCCTACATCAAGACAAGGCAAGTGAGAAAGAGGG";\n+chr7\tCufflinks\texon\t104055491\t104055589\t1000\t.\t.\tgene_id "CUFF.238474"; transcript_id "CUFF.238474.1"; exon_number "1"; FPKM "28.8092349606"; frac "1.000000"; conf_lo "5.286593"; conf_hi "52.331877"; cov "1.636364"; seq "ACATTTCTCCTCTCTTGGGGGAGCGCATCTCCTTGGGTGTGTCCACATCCGCCCCTAGGTACCCAGTGTGATGTGAGACACGAGTGTCTGTGCTAACTT";\n+chr8\tCufflinks\texon\t9970398\t9970545\t1000\t.\t.\tgene_id "CUFF.245320"; transcript_id "CUFF.245320.1"; exon_number "1"; FPKM "22.4828826889"; frac "1.000000"; conf_lo "5.487421"; conf_hi "39.478345"; cov "1.277027"; seq "AGTCTTCACCAAAATTAAGTCTCAGCTAACTTAAAAGTTGCAAGGATTTTTTTCAATAAAATTAATATCTTAAGTGTTTGGTGTTTAGATGATTCTCTCTCAACTTCCCCCACATTATCAAAAAACATTTGATGAACCTTAAAAACTC";\n+chr9\tCufflinks\ttranscript\t20449846\t20449932\t1000\t.\t.\tgene_id "CUFF.260747"; transcript_id "CUFF.260747.1"; FPKM "234.9313045507"; frac "1.000000"; conf_lo "163.275950"; conf_hi "306.586659"; cov "13.344091"; seq "CCAGCACCGATGACACCATCGGCGACTTGAAGAAACTGATAGCTGCTCAAACTGGCACCCGCTGGAACAAGATCGTTCTTAAAAAGT";\n+chr9\tCufflinks\texon\t107445870\t107445930\t1000\t.\t.\tgene_id "CUFF.272761"; transcript_id "CUFF.272761.1"; exon_number "1"; FPKM "38.9633095779"; frac "1.000000"; conf_lo "4.113466"; conf_hi "73.813153"; cov "2.213115"; seq "CAAGCAGAAGCTGGTGCCCATCATGACCATCCTGCTGGAAGAGCTGAATGCCTCCGGCCGC";\n+chr9\tCufflinks\ttranscript\t120860476\t120860606\t1000\t.\t.\tgene_id "CUFF.275115"; transcript_id "CUFF.275115.1"; FPKM "25.4005086867"; frac "1.000000"; conf_lo "6.199529"; conf_hi "44.601488"; cov "1.442748"; seq "CTGCCATTGTACGCACCATGCAGAATACAAATGATGTAGAGACAGCTCGTTGTACTGCTGGGACTCTGCACAACCTTTCTCACCACCGCGAGGGCTTGCTGGCCATCTTTAAGTCTGGTGGCATCCCAGCG";\n+chrX\tCufflinks\texon\t10274057\t10274087\t1000\t.\t.\tgene_id "CUFF.276147"; transcript_id "CUFF.276147.1"; exon_number "1"; FPKM "99.5432248142"; frac "1.000000"; conf_lo "21.405127"; conf_hi "177.681323"; cov "5.654052"; seq "ACTTCGCTGTCATCATTTGTACAAACTCTTT";\n+chrX\tCufflinks\ttranscript\t39881431\t39881678\t1000\t.\t.\tgene_id "CUFF.277419"; transcript_id "CUFF.277419.1"; FPKM "42.1683560109"; frac "1.000000"; conf_lo "24.187709"; conf_hi "60.149003"; cov "2.395161"; seq "AGCTAAAAAGAGTCCTTTTCTGACAGAAAGGCTGGACTTCTCCTTTTCACCGTTTCTCTTACTGATGCTTTTGCCAGAAGAACAGTAAAGATTTAGACACTGTCATGATTCATACACGTAAAATATTTTTCAAGGACACAATCTGATATACTAACATTTATTTAAGAGGTTAAAGTCCACCACTAAATCTAAGGAAAGATTTTTAACTGCCAAACACATTTCCTTTGACAAATAATGTAAGATGACAA";\n+chrX\tCufflinks\ttranscript\t148249672\t148249713\t1000\t.\t.\tgene_id "CUFF.282847"; transcript_id "CUFF.282847.1"; FPKM "56.5895686726"; frac "1.000000"; conf_lo "5.974320"; conf_hi "107.204818"; cov "3.214286"; seq "AATGCTAGTATGAACAGTGGGAGGAATGAGCAAAATGTTACA";\n+chrX\tCufflinks\ttranscript\t148481505\t148482455\t1000\t+\t.\tgene_id "CUFF.282965"; transcript_id "CUFF.282965.1"; FPKM "40.1706233958"; frac "1.000000"; conf_lo "16.978103"; conf_hi "63.363144"; cov "2.281690"; seq "CGCCACAACCTGCTACAGGCCTGTAAGATGCAGGACATCAAACTGCCACTGTCAAAGGGCACCATGGATGATATTAGTCAGGAAGAAGTGAGTATTATGGTGGGTGGTAGGAGTCATCTATGAATATTTAACCAGTAATGGGAGATTACAGATGGCCAGGAAGGGCAGGCAACAGATAGGACCACATAGAGTTGTGAGGGGCATAAAGATGGATGCAGAAGAAATGTGGCAAGGTGGAAGTAGTGAAGTCAGGCTTTGGTATGAGAGAGACATTGATTTGAGAGGAGAGCTGCAAGCCAGTGAGTACTCAGAAAGACCAAGAATGGGTCATTAATCTTAAGGATTTGAGCTCTTAGCTGCAGCAGATACTGGGCATGGGTAGGAGTGAGAATTGAGGAGCAGAGGAAGATGGGAAACTGGAGAACCTAAGGAGACTGATAGCTTAGCTGCAGTAAGGGAGGTTGGCCAGAAGAGGGTTGGGTAGGGGACTCAGCAAGGCAGAACTAAGGAAGCTTAGGTGGAGGGGAAGGAACAACATCTGAGCAACTAAAGCACTCTATCAACTGGAAGTGCAAGATGGTAGTGAGGGGTGGACAGGTGTAACTGAGTAACTCTTTGTAGGTAGCCTTTCAGTTTAATTCAGTAAAATATTTTGAACACTAGTATTCCAGATACTGGTAGGCCATGACTTAACCATTCCTAATGTTAATCTCAGCTGTGCTAGCTGAGCTTGTGTTCACATTAGACATGAAGAAACTTAGTAAAAGGTAGAGCCCAGTTTTCGGTTTGGACCTTCCTGTTGGCCTCTGCTTCCGTGCCATCTAGCAAAGGAGTTCCTAATCTCTAGAGGGATACAAATGACTAGTCTGCTCCATCTGCCTCTTCCAACATTGCAGGGTAGCTCCCAGGGAGAAGAGTCAGTGAGTGGTTCCCAGAGAACATCCAGTATCT";\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/extract_genomic_dna_out5.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/extract_genomic_dna_out5.fasta Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,258 @@\n+>mm9_chr10_62044837_62045189_+\n+AATTACAAGATCGACACACCAAGATAGGCAGATCCATGGTTGGTTTTACT\n+TTGTAAATCTAAAAGTATGTTGGAAAACGATGCAATGAATTCTTATCCTT\n+TTTCAAAATGAAGAATTTGTGATGGTTAGTGGACAGTTCAGAAGCCTCTC\n+TGCAAGAAAGGGGGCGCTGAGAAGTGGTAAAAAAAGGAAGGAAGCACTCG\n+GGCTTTGTCAGCAGGGTGGACCCTGGGGTCCACAGTGGGAACAGTCCCTT\n+CTGGCCTCTACTCACTGACCAAACGCTTTACTAAAACTCCGCTTCTGGCC\n+TCTGTTGCCACCTCCTGGTCGCTGTCCTCGGAAGTTTCTACTTCCTCCTC\n+GCT\n+>mm9_chr10_75372919_75373002_+\n+GCGTCTCGCAGCTTCTGCCCGTCGATCTCCATGTCGAGCCGGATGGGCAC\n+CAGCACCTCAGGCTGTGACGCATTCTCATGGATC\n+>mm9_chr10_80362428_80363292_-\n+ATGACGGACAAGTGTTTCCGGAAGTGCATCGGGAAGCCCGGGGGCTCCTT\n+GGATAACTCGGAGCAGGTGAGACATCTCGGGAACCCGGGGTGGTGAGGGG\n+CGCGGGGTCAGGAGCGTCTAGGAGGTTGAGAGATGTGCGCGTGCGCGGCC\n+TCTAGCCTTAGCTACTGAGGAAGTTGTGCGCGTGCGCGGGGTGAGGACCC\n+GGCTTCTGTGCCTAGATCGGTGCAGCCTTCATGGGTGATCCTCGGGTCGT\n+GTGACCGTCAGTCAGGGATCCCCCTCCACGCTTTGCAGAAATGCATCGCC\n+ATGTGCATGGACCGCTACATGGACGCCTGGAATACCGTGTCCCGCGCCTA\n+CAACTCTCGACTGCAGCGGGAACGAGCCAACATGTGACCGGGACCTGTGC\n+CTCGGGACACCGTGCTTATGGTCTGAACTGTTTTCCCTGCCAGTTAGGGT\n+GTCTCCTCCTAGCCGCCCTGAAGTCTGGCAGCATGGAGGGCTTGGGGATC\n+GAGGCCTCTCCCCTGGGTTGCTGCGTCCAGCTCAATCTCAGAAGAGAGTG\n+AGGACCCGACAGAGCACAGGGATCTGGCTGGCCCCACTGACCTGTGACCT\n+CAGGAGAGCAGGCCAATAAATCGCTGCTGGGGCAGTAAAGCAGGCGTGTC\n+ACCTCACTGCTTCAGGTCCCTTCCCCTGAGTAGGCCCAGACCTCCCAGGG\n+TATCTTTCCCCTTGGGGTCAGTGGGCTGCTGGCTCTCAGGGAATTCGGAG\n+CATGATCTCAGGTGTTTGGTCATCCCGGGGAGACCAGCCGAGGTTAAGAA\n+GCAAGGCTTCATGTagccttcacctatcatgcatgaggcccagggtgctg\n+accttaactctgaat\n+>mm9_chr11_7904565_7904642_+\n+CATCTTCTATTTGAGCCTCCATCCAGGCACCTCTGAAACAAAGGTGCACT\n+CACTGCATGTCCACTTGTCACAGGAGCC\n+>mm9_chr11_78140156_78140259_+\n+CTGCTTGCTAATTTTCTCTCTTGGGATCAGGGGGACGTGAACTCCAGCCC\n+TGACTCGTGCTCCTTATGCTCTGAGTACATAGCAAATAAATGAGAGCAAA\n+ACAC\n+>mm9_chr11_105616462_105616737_+\n+TAGGTGTAATAGTGGAAAACAATAGTTTTTAAACTTCAGAGTCCAGGGCT\n+GTAACTCAGTAGTAACAGTGTTCTCTAAGTATGTTATTCTTCCTCTACAT\n+GCTGAAATTTTTCATATTTGGAGCATTCACTGTTCCATGTATCAGTAAAT\n+TATATTGTGAGCTGTCATCATATCTAAGCACCATATTGAATATTTTTCAT\n+GATTAAAATTTGTTGAAACAACAATTCTATGACCGAAAAAAGCAAGGCTT\n+TGTAAATAACATGTTTGTTACTAGTA\n+>mm9_chr12_30701762_30702509_+\n+TGTGGAGTGTACTTATATGATCCCTATGCTGATAGGATTACCTTCCTAGA\n+CATAGCTAGACGCAAAGCCACATGTGTAAGGCTGCTGAGCAAAGACAGCA\n+TCCCAGCATGGGTGTGTTCACGGTGGATTCACCACGTTGCATATGTAAAG\n+TGGTCCCCTTGGCTTACCCTTCACTTTGCTCATGAGATTCAGAAGCTGGT\n+GGTCCAGCAGGGGTGAGCATTTGTGAAATAGTAAGCTGAACTTAGTGGTG\n+AGATTTCAGAACAGACTTCTGTGAAGTAAGAGATGTAACCATGCATCTAA\n+AATCAGATGGCCGTGTAACTGCTCGGGCATAGAAATGGTGGGAGAACCTG\n+TCCTGGGTACCTGGCATTTCACATGAGCCCAGGGATATGTCTTGTGCCAA\n+GGCACACAAGTGTCCATGGACTTGGACAGGTGCCAAGGGTTTTTGTCTCT\n+GTTCCTATGTGGGAGGCTGGCTGTGATTTACATTAATTTCTGTATTTCAA\n+ACGAAGATGTCTGCAGATCTCCATTTTGATGTTACAGCCTCATTGCCCAG\n+GCAGTGGGCAGTGCCCAGACACCCTTTCTGACTAGCCACTGCATTGGGCT\n+TCTGTGATTCAAAGTAGTGTATATATTTATTTACTTCTCTGACTGTGGCC\n+AACAGCCAAATGCCATTTTATGTTCCTTGTATTCAGTCCATTACCAAAGA\n+GGTGTTTGCACTTTGTAATGATACCTTTCAGTTCAAATAAAAGGACCA\n+>mm9_chr13_49159496_49159569_+\n+ttttcttttggattacttgatttttttttatttgatcttatttatgatga\n+ttttgagtacatttttgaacagtt\n+>mm9_chr13_100200304_100200330_+\n+TCTCATATGAATAGCCACCCTCTTCTG\n+>mm9_chr14_31949103_31949152_+\n+GGATGCTATCCGCGATGTGCATGTAAAGGGCCTCATGTACCAGTGGATCG\n+>mm9_chr14_67604227_67604668_+\n+TTCACCGTGAGAGTTTTCTCCATTTCACTCTTCACTGTGCTGTTCTCTGT\n+GCCGCTTTCCTCTTGACTTATAAACATCTGAGCCAGTTTTCAATAAACTT\n+AAAACGAAGCCTGCTTCTCATCCCAAATTGTAAACAGGAATAAAGCTTTT\n+TAAACCTTATCTTAAATTTTAACTTTGTTGAATTCTGCTTTGTGATAGGA\n+CAATCTGTTTCACCCAACAAGAATCTGTGTAGGAGGATGAACATCCCGCA\n+TGTTGGAGCTGCAAATCAGCACTGTACAAGCTCACTGATGGACAGCTGTT\n+CTGTGATGTATTCCATGATTTTACTAATACTTTCAAAAATGGCAAAACTA\n+ACTTCAGTTTTAATGTTGAAAGAAAATCATAAATGTTCCCATAGTTCAAT\n+GGCACTGTCGATGAAACTGCTACTGAATTTAGAGAGAAAACG\n+>mm9_chr14_75165582_75165744_+\n+ggccctgggatgataTAACAGAAGAGTCTAAAGGAGGCTTCTGAGATGTG\n+CAGTAGGAAAGCCTGGCACATAATAGGTTATTATCTAAATCCCTTCACTA\n+CTCTTCAAAGACAGCAGGATGCCTCTGCTCCCATGTTTTATCTCTACTTA\n+TGTGGAATTTATG\n+>mm9_chr16_57154027_57154067_+\n+GTTGAGGTTTATTTAAGTAAAATGATTTTTTAAAAAAGCAA\n+>mm9_chr16_74862302_74862560_+\n+GCATTGGCAGCAGATATTGGTACCCAGTGGCACTGCAGAGTACTTACAAT\n+CAGGACTCGCTACTGTGCTTCATTCTGCT'..b'GTGACGTCTCTTGAACTGTTGGCACGCCTAAGTTATTTCAGCAT\n+TTCTTGCTCAGCAGTTGTTCTCTTGGCTTCCTCTG\n+>mm9_chr4_13715310_13715630_+\n+AACACATGGCCACATCATGTGATATTTTCAAAACACTTACACATAGCTTT\n+GAGAAGGTCCCTGCAGGAATGATCCATCCTCTCACAGTTGGCCCATTTTT\n+TAACAGCATATCTGCATTTTCCATTTAGGAGAGCTATATATTATTAGCTT\n+ACATTTTTGGGTAGTAAAACAGTGCATTGCTGATTGTAAAACATGGACTT\n+TATTATCTGCTGAAAATTGATTTGGCATTTATAGCCACTGTGTATTAGAC\n+TGTTTTTCTGTTTTTAACATCAATGCTTAAAAGCGATGATTTGTGTTTaa\n+aaaaattaaaaaaataaaata\n+>mm9_chr4_147515029_147515097_+\n+GCTGACGTGCTCTCCGAGTTCCTGGAGGTGGCCGTGCACCTGATTCTCTA\n+TGTGCGCGAGGTCTACCCG\n+>mm9_chr5_3949522_3949685_+\n+AGTCCCAACCACCCCCTTGTTTAATGTATAACTTTCTGAAATGGGAGCGT\n+TAGAATGGATTAAAATGGTTGGTAGGTGGTTGGATCACCAACCAAGACCA\n+GAAATAGAGGGGTAGGCTGCTCAGGAGAGTATTGGGAGGGTAGCTATTAT\n+TTGCATTTTGTGCT\n+>mm9_chr5_68089694_68089831_+\n+CAATGATAGAGAAGACTAAAATAAAAGCAGGCATGCTGGCACAAGCGACA\n+GAAGGAAAAAGCCTCACCCGGCCCTGTTTGAGGCCACTCCTGGTGGCTCC\n+TTTTCCAAGGACCATGCGGTCAAGCCTCTGAGTTGTTC\n+>mm9_chr5_122819526_122819619_+\n+CTTTAGAAAAGATGCATCTGTCATTGATTTAGGGATATGAATTGTTTGGA\n+TTTGAGTAGTTTTCCATAACTCCTGCAGTTTGGCAATGTGTGCG\n+>mm9_chr5_145619548_145619710_+\n+CGGCGTTCTGAAAACTGTGCTCCGGGATGAGATCATTGCTTGGCACAAAA\n+AGACACAGGAGGACACTTCCTCTCCACTGTCGGCCGCAGGGCAGCCTGAG\n+AACATGGACAGCCAGCAGCTGGTTTCCTTAGTTCAGAAAGCCGTCACTGC\n+CATCATGACCCGC\n+>mm9_chr6_83928984_83929105_+\n+ACAGGAACCATTATTTACATTTAATTTGGATGAATTTGTTACTGTGGATG\n+AAGTCATAGAAGAAGTAAATCCTTCTCAAGCCAAGCAGAATCCATTAAAA\n+GGAAAAAGAAAGGAAGCCCTCA\n+>mm9_chr6_118857949_118858148_+\n+CCAGGCTTGCTAGTTGGTGCAGTTAGCTACATCTCAGGACAGAGACAAGG\n+TACTCTGAGCTCCCCTTGAACTGCCACACAAGCTGTCTCCTGGATGCCAA\n+GCAGAGAAACCTGGAGACAACAATCATCATACTCAAAACCAGGATCTCTT\n+TCTTAAGACTTTTGTATTTTGTCCCAGCCCTAACCCTGAGTTCTGCTGAA\n+>mm9_chr7_85554210_85554343_+\n+GTGAAACATCATGCTTCTGCATCAAGTTATTAGTGGGAAACCTGTAAAAG\n+TTGACATTGAATGCTGATAACAAATTACTTTCATCCTGTCTCATAATGAA\n+TCCTACATCAAGACAAGGCAAGTGAGAAAGAGGG\n+>mm9_chr7_104055491_104055589_+\n+ACATTTCTCCTCTCTTGGGGGAGCGCATCTCCTTGGGTGTGTCCACATCC\n+GCCCCTAGGTACCCAGTGTGATGTGAGACACGAGTGTCTGTGCTAACTT\n+>mm9_chr8_9970398_9970545_+\n+AGTCTTCACCAAAATTAAGTCTCAGCTAACTTAAAAGTTGCAAGGATTTT\n+TTTCAATAAAATTAATATCTTAAGTGTTTGGTGTTTAGATGATTCTCTCT\n+CAACTTCCCCCACATTATCAAAAAACATTTGATGAACCTTAAAAACTC\n+>mm9_chr9_20449846_20449932_+\n+CCAGCACCGATGACACCATCGGCGACTTGAAGAAACTGATAGCTGCTCAA\n+ACTGGCACCCGCTGGAACAAGATCGTTCTTAAAAAGT\n+>mm9_chr9_107445870_107445930_+\n+CAAGCAGAAGCTGGTGCCCATCATGACCATCCTGCTGGAAGAGCTGAATG\n+CCTCCGGCCGC\n+>mm9_chr9_120860476_120860606_+\n+CTGCCATTGTACGCACCATGCAGAATACAAATGATGTAGAGACAGCTCGT\n+TGTACTGCTGGGACTCTGCACAACCTTTCTCACCACCGCGAGGGCTTGCT\n+GGCCATCTTTAAGTCTGGTGGCATCCCAGCG\n+>mm9_chrX_10274057_10274087_+\n+ACTTCGCTGTCATCATTTGTACAAACTCTTT\n+>mm9_chrX_39881431_39881678_+\n+AGCTAAAAAGAGTCCTTTTCTGACAGAAAGGCTGGACTTCTCCTTTTCAC\n+CGTTTCTCTTACTGATGCTTTTGCCAGAAGAACAGTAAAGATTTAGACAC\n+TGTCATGATTCATACACGTAAAATATTTTTCAAGGACACAATCTGATATA\n+CTAACATTTATTTAAGAGGTTAAAGTCCACCACTAAATCTAAGGAAAGAT\n+TTTTAACTGCCAAACACATTTCCTTTGACAAATAATGTAAGATGACAA\n+>mm9_chrX_148249672_148249713_+\n+AATGCTAGTATGAACAGTGGGAGGAATGAGCAAAATGTTACA\n+>mm9_chrX_148481505_148482455_+\n+CGCCACAACCTGCTACAGGCCTGTAAGATGCAGGACATCAAACTGCCACT\n+GTCAAAGGGCACCATGGATGATATTAGTCAGGAAGAAGTGAGTATTATGG\n+TGGGTGGTAGGAGTCATCTATGAATATTTAACCAGTAATGGGAGATTACA\n+GATGGCCAGGAAGGGCAGGCAACAGATAGGACCACATAGAGTTGTGAGGG\n+GCATAAAGATGGATGCAGAAGAAATGTGGCAAGGTGGAAGTAGTGAAGTC\n+AGGCTTTGGTATGAGAGAGACATTGATTTGAGAGGAGAGCTGCAAGCCAG\n+TGAGTACTCAGAAAGACCAAGAATGGGTCATTAATCTTAAGGATTTGAGC\n+TCTTAGCTGCAGCAGATACTGGGCATGGGTAGGAGTGAGAATTGAGGAGC\n+AGAGGAAGATGGGAAACTGGAGAACCTAAGGAGACTGATAGCTTAGCTGC\n+AGTAAGGGAGGTTGGCCAGAAGAGGGTTGGGTAGGGGACTCAGCAAGGCA\n+GAACTAAGGAAGCTTAGGTGGAGGGGAAGGAACAACATCTGAGCAACTAA\n+AGCACTCTATCAACTGGAAGTGCAAGATGGTAGTGAGGGGTGGACAGGTG\n+TAACTGAGTAACTCTTTGTAGGTAGCCTTTCAGTTTAATTCAGTAAAATA\n+TTTTGAACACTAGTATTCCAGATACTGGTAGGCCATGACTTAACCATTCC\n+TAATGTTAATCTCAGCTGTGCTAGCTGAGCTTGTGTTCACATTAGACATG\n+AAGAAACTTAGTAAAAGGTAGAGCCCAGTTTTCGGTTTGGACCTTCCTGT\n+TGGCCTCTGCTTCCGTGCCATCTAGCAAAGGAGTTCCTAATCTCTAGAGG\n+GATACAAATGACTAGTCTGCTCCATCTGCCTCTTCCAACATTGCAGGGTA\n+GCTCCCAGGGAGAAGAGTCAGTGAGTGGTTCCCAGAGAACATCCAGTATC\n+T\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/extract_genomic_dna_out6.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/extract_genomic_dna_out6.fasta Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,20 @@
+>mm9_test_chromosome_53_550_+
+TACTATCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCAC
+TACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAG
+CGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTAC
+GTATTTGGCGCGCGGCGCTACGGCTGAGCGTCGAGCTTGCGATACGCCGT
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAC
+TATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTGT
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGTT
+TTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACTTGC
+>mm9_test_chromosome_53_250_+
+TACTATCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCAC
+TACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAG
+CGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTAC
+GTATTTGGCGCGCGGCGCTACGGCTGAGCGTCGAGCTTGCGATACGCC
+>mm9_test_chromosome_351_400_+
+ACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACT
+>mm9_test_chromosome_501_550_+
+TTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACTTGC

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/extract_genomic_dna_out7.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/extract_genomic_dna_out7.fasta Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,17 @@
+>mm9_test_chromosome_53_550_+
+TACTATCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCAC
+TACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAG
+CGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTAC
+GTATTTGGCGCGCGGCGCTACGGCTGAGCGTCGAGCTTGCGATACGCCGT
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAC
+TATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTGT
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGTT
+TTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACTTGCTA
+CTATCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCACTA
+CGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCG
+ACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGT
+ATTTGGCGCGCGGCGCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTA
+TTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTT
+CTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACTTGC

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/fasta_to_tabular_out1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/fasta_to_tabular_out1.tabular Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,18 @@
+EYKX4VC01B65GS length=54 xy=0784_1754 region=1 run=R_2007_11_07_16_15_57_ CCGGTATCCGGGTGCCGTGATGAGCGCCACCGGAACGAATTCGACTATGCCGAA
+EYKX4VC01BNCSP length=187 xy=0558_3831 region=1 run=R_2007_11_07_16_15_57_ CTTACCGGTCACCACCGTGCCTTCAGGATTGATCGCCAGATCGGTCGGTGCGTCAGGCGGGGTGACATCGCCCACCACGGTACTCACTGGCTGGCTCTGGTTCCCGGCGGCATCGGAGGCCACCACGTTGAGGGTATTCCCCTCGGTTTGTGGCTCGGTGAGAACCACGTTGTAGTCGCCATTGGTC
+EYKX4VC01CD9FT length=115 xy=0865_1719 region=1 run=R_2007_11_07_16_15_57_ GGGGGCTTTGGCCTGTCGTCCGGCACCTCGCAAGAGCTACAGCAGGCGCGGCTGGCGATCATCGGCGGCACGCCGGCCTATATGTCGCCGGAACACACCACCCGCACCCAACGCG
+EYKX4VC01B8FW0 length=95 xy=0799_0514 region=1 run=R_2007_11_07_16_15_57_ TAAATTTCAAGGAATGCAAATCAGGGTCGTGTGTTTAGACTTCGGCTTTAGAGACCTGAATACGTCAAAAACATAACTTCATGATATCTTGCAGT
+EYKX4VC01BCGYW length=115 xy=0434_3926 region=1 run=R_2007_11_07_16_15_57_ GGCCAGCCGGGACAGCGTTGTTGGGCTGCATGGCGACGAGCTAAAAGTCGCCATCACCGCCCCGCCGGTTGATGGGCAGGCTAATGCCCATCTGGTAAAAACTTTCTCGCCAAAC
+EYKX4VC01AZXC6 length=116 xy=0292_0280 region=1 run=R_2007_11_07_16_15_57_ GGGGGCGTTTGGCCTGTCGTCCGGCACCTCGCAAGAGCTACAGCAGGCGCGGCTGGCGATCATCGGCGGCACGCCGGCCTATATGTCGCCGGAACACACCACCCGCACCCAACGCG
+EYKX4VC01CATH5 length=82 xy=0826_0843 region=1 run=R_2007_11_07_16_15_57_ CGAAATTGCACATTCTCGGCCATATCTCTGGACCTACATGACCGATTTGATCATCTTCGAACTTAGCCTTCCTTTNTTAACG
+EYKX4VC01BCEIV length=47 xy=0434_0757 region=1 run=R_2007_11_07_16_15_57_ TGACGTCGTGCCGAGCTACGACAATGCCGACATGGTGATCGTTAACA
+EYKX4VC01BWERM length=83 xy=0662_0304 region=1 run=R_2007_11_07_16_15_57_ CGGTCGGCCTCACCATGGAGAAGATCCCGCCCCGGCCGAGGTCATGGTGGATCTCGGCCAGGGCGTGCTGATGAAGTTCAAAT
+EYKX4VC01BT2O7 length=69 xy=0635_1945 region=1 run=R_2007_11_07_16_15_57_ AGCGTTTCTCCAGCCGGTCGGCTACGCCGTTTGCCCCTGAAAGACGCTGTTCAGACCGAACGCGGTAAA
+EYKX4VC01BO0UO length=222 xy=0577_3838 region=1 run=R_2007_11_07_16_15_57_ AGACCTGGGACAGCGGCGGGCTGCTGAAGCCGCAGGCGATAGAGGACAAACTGCAGTACCGCTTCTGGCTGCACTATGCCGAAGGCTCGCTGATGCCGCTGCTGTTAATGAAGCTGGTGTTCGCCAGCCTGGGTAAACCCCCTGTGCCCTTTGGCGTCCGCTCGCTGGGCGCCCTGCTGGGCAAGGGCATTCAGAAAGCGTGGCTGGATCCCCAGCTGGCCA
+EYKX4VC01CBCPK length=83 xy=0832_1158 region=1 run=R_2007_11_07_16_15_57_ CGGTCGGCCTCACCATGGAGAAGATCCCGCCCCGGCCGAGGTCATGGTGGATCTCGGCCAGGGCGTGCTGATGAAGTTCAAAT
+EYKX4VC01B474S length=54 xy=0762_2010 region=1 run=R_2007_11_07_16_15_57_ AGCAGTTTTCCAGCGCTTTCGAAGAGCGCTGGCGCGCGCGGGCTTCCAGCATAT
+EYKX4VC01BB4QL length=57 xy=0431_0363 region=1 run=R_2007_11_07_16_15_57_ GGGGAGGAGCTAATAATATGCTCTTGGGGAGGAGCTAATTATATGCTCTTGGGGAGG
+EYKX4VC01BJ37M length=64 xy=0522_0192 region=1 run=R_2007_11_07_16_15_57_ TCGAGTATGTATCAAGGACTACATACAAATTTGCCAAAAGAGATTATGCACTATCCCGACTTCC
+EYKX4VC01BV9R8 length=54 xy=0660_2038 region=1 run=R_2007_11_07_16_15_57_ AAAACTCGGAGAAACTATTCAGCAGCACTGCGTTTCGCTGAATTTTAGACCGTT
+EYKX4VC01CEPP8 length=60 xy=0870_2350 region=1 run=R_2007_11_07_16_15_57_ CTGGGTGGGTGCACTACAGGAACGTCATTTGTTCAATCCTCACGTTGTTGTTAGTGTCAG
+EYKX4VC01BTLME length=78 xy=0630_0292 region=1 run=R_2007_11_07_16_15_57_ TTATCCACACGCTGTCCGGATCCAGCGCCAGGCGCCGACGCTGGACTTCCGCCGCCTGCGCCCAGTTGCCCTGACTTC

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/fasta_to_tabular_out2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/fasta_to_tabular_out2.tabular Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,2 @@
+EYKX4VC01B65GS length=54 xy=0784_1754 region=1 run=R_2007_11_07_16_15_57_ CCGGTATCCGGGTGCCGTGATGAGCGCCACCGGAACGAATTCGACTATGCCGAA
+EYKX4VC01BNCSP length=187 xy=0558_3831 region=1 run=R_2007_11_07_16_15_57_ CTTACCGGTCACCACCGTGCCTTCAGGATTGATCGCCAGATCGGTCGGTGCGTCAGGCGGGGTGACATCGCCCACCACGGTACTCACTGGCTGGCTCTGGTTCCCGGCGGCATCGGAGGCCACCACGTTGAGGGTATTCCCCTCGGTTTGTGGCTCGGTGAGAACCACGTTGTAGTCGCCATTGGTC

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/fasta_to_tabular_out3.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/fasta_to_tabular_out3.tabular Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,18 @@
+EYKX4VC01B65GS CCGGTATCCGGGTGCCGTGATGAGCGCCACCGGAACGAATTCGACTATGCCGAA
+EYKX4VC01BNCSP CTTACCGGTCACCACCGTGCCTTCAGGATTGATCGCCAGATCGGTCGGTGCGTCAGGCGGGGTGACATCGCCCACCACGGTACTCACTGGCTGGCTCTGGTTCCCGGCGGCATCGGAGGCCACCACGTTGAGGGTATTCCCCTCGGTTTGTGGCTCGGTGAGAACCACGTTGTAGTCGCCATTGGTC
+EYKX4VC01CD9FT GGGGGCTTTGGCCTGTCGTCCGGCACCTCGCAAGAGCTACAGCAGGCGCGGCTGGCGATCATCGGCGGCACGCCGGCCTATATGTCGCCGGAACACACCACCCGCACCCAACGCG
+EYKX4VC01B8FW0 TAAATTTCAAGGAATGCAAATCAGGGTCGTGTGTTTAGACTTCGGCTTTAGAGACCTGAATACGTCAAAAACATAACTTCATGATATCTTGCAGT
+EYKX4VC01BCGYW GGCCAGCCGGGACAGCGTTGTTGGGCTGCATGGCGACGAGCTAAAAGTCGCCATCACCGCCCCGCCGGTTGATGGGCAGGCTAATGCCCATCTGGTAAAAACTTTCTCGCCAAAC
+EYKX4VC01AZXC6 GGGGGCGTTTGGCCTGTCGTCCGGCACCTCGCAAGAGCTACAGCAGGCGCGGCTGGCGATCATCGGCGGCACGCCGGCCTATATGTCGCCGGAACACACCACCCGCACCCAACGCG
+EYKX4VC01CATH5 CGAAATTGCACATTCTCGGCCATATCTCTGGACCTACATGACCGATTTGATCATCTTCGAACTTAGCCTTCCTTTNTTAACG
+EYKX4VC01BCEIV TGACGTCGTGCCGAGCTACGACAATGCCGACATGGTGATCGTTAACA
+EYKX4VC01BWERM CGGTCGGCCTCACCATGGAGAAGATCCCGCCCCGGCCGAGGTCATGGTGGATCTCGGCCAGGGCGTGCTGATGAAGTTCAAAT
+EYKX4VC01BT2O7 AGCGTTTCTCCAGCCGGTCGGCTACGCCGTTTGCCCCTGAAAGACGCTGTTCAGACCGAACGCGGTAAA
+EYKX4VC01BO0UO AGACCTGGGACAGCGGCGGGCTGCTGAAGCCGCAGGCGATAGAGGACAAACTGCAGTACCGCTTCTGGCTGCACTATGCCGAAGGCTCGCTGATGCCGCTGCTGTTAATGAAGCTGGTGTTCGCCAGCCTGGGTAAACCCCCTGTGCCCTTTGGCGTCCGCTCGCTGGGCGCCCTGCTGGGCAAGGGCATTCAGAAAGCGTGGCTGGATCCCCAGCTGGCCA
+EYKX4VC01CBCPK CGGTCGGCCTCACCATGGAGAAGATCCCGCCCCGGCCGAGGTCATGGTGGATCTCGGCCAGGGCGTGCTGATGAAGTTCAAAT
+EYKX4VC01B474S AGCAGTTTTCCAGCGCTTTCGAAGAGCGCTGGCGCGCGCGGGCTTCCAGCATAT
+EYKX4VC01BB4QL GGGGAGGAGCTAATAATATGCTCTTGGGGAGGAGCTAATTATATGCTCTTGGGGAGG
+EYKX4VC01BJ37M TCGAGTATGTATCAAGGACTACATACAAATTTGCCAAAAGAGATTATGCACTATCCCGACTTCC
+EYKX4VC01BV9R8 AAAACTCGGAGAAACTATTCAGCAGCACTGCGTTTCGCTGAATTTTAGACCGTT
+EYKX4VC01CEPP8 CTGGGTGGGTGCACTACAGGAACGTCATTTGTTCAATCCTCACGTTGTTGTTAGTGTCAG
+EYKX4VC01BTLME TTATCCACACGCTGTCCGGATCCAGCGCCAGGCGCCGACGCTGGACTTCCGCCGCCTGCGCCCAGTTGCCCTGACTTC

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/fasta_to_tabular_out4.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/fasta_to_tabular_out4.tabular Sat Feb 21 16:33:42 2015 +0100

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/fasta_to_tabular_out5.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/fasta_to_tabular_out5.tabular Sat Feb 21 16:33:42 2015 +0100

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/fasta_to_tabular_out6.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/fasta_to_tabular_out6.tabular Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,18 @@
+EYKX4VC01B length=54 xy=0784_1754 region=1 run=R_2007_11_07_16_15_57_ CCGGTATCCGGGTGCCGTGATGAGCGCCACCGGAACGAATTCGACTATGCCGAA
+EYKX4VC01B length=187 xy=0558_3831 region=1 run=R_2007_11_07_16_15_57_ CTTACCGGTCACCACCGTGCCTTCAGGATTGATCGCCAGATCGGTCGGTGCGTCAGGCGGGGTGACATCGCCCACCACGGTACTCACTGGCTGGCTCTGGTTCCCGGCGGCATCGGAGGCCACCACGTTGAGGGTATTCCCCTCGGTTTGTGGCTCGGTGAGAACCACGTTGTAGTCGCCATTGGTC
+EYKX4VC01C length=115 xy=0865_1719 region=1 run=R_2007_11_07_16_15_57_ GGGGGCTTTGGCCTGTCGTCCGGCACCTCGCAAGAGCTACAGCAGGCGCGGCTGGCGATCATCGGCGGCACGCCGGCCTATATGTCGCCGGAACACACCACCCGCACCCAACGCG
+EYKX4VC01B length=95 xy=0799_0514 region=1 run=R_2007_11_07_16_15_57_ TAAATTTCAAGGAATGCAAATCAGGGTCGTGTGTTTAGACTTCGGCTTTAGAGACCTGAATACGTCAAAAACATAACTTCATGATATCTTGCAGT
+EYKX4VC01B length=115 xy=0434_3926 region=1 run=R_2007_11_07_16_15_57_ GGCCAGCCGGGACAGCGTTGTTGGGCTGCATGGCGACGAGCTAAAAGTCGCCATCACCGCCCCGCCGGTTGATGGGCAGGCTAATGCCCATCTGGTAAAAACTTTCTCGCCAAAC
+EYKX4VC01A length=116 xy=0292_0280 region=1 run=R_2007_11_07_16_15_57_ GGGGGCGTTTGGCCTGTCGTCCGGCACCTCGCAAGAGCTACAGCAGGCGCGGCTGGCGATCATCGGCGGCACGCCGGCCTATATGTCGCCGGAACACACCACCCGCACCCAACGCG
+EYKX4VC01C length=82 xy=0826_0843 region=1 run=R_2007_11_07_16_15_57_ CGAAATTGCACATTCTCGGCCATATCTCTGGACCTACATGACCGATTTGATCATCTTCGAACTTAGCCTTCCTTTNTTAACG
+EYKX4VC01B length=47 xy=0434_0757 region=1 run=R_2007_11_07_16_15_57_ TGACGTCGTGCCGAGCTACGACAATGCCGACATGGTGATCGTTAACA
+EYKX4VC01B length=83 xy=0662_0304 region=1 run=R_2007_11_07_16_15_57_ CGGTCGGCCTCACCATGGAGAAGATCCCGCCCCGGCCGAGGTCATGGTGGATCTCGGCCAGGGCGTGCTGATGAAGTTCAAAT
+EYKX4VC01B length=69 xy=0635_1945 region=1 run=R_2007_11_07_16_15_57_ AGCGTTTCTCCAGCCGGTCGGCTACGCCGTTTGCCCCTGAAAGACGCTGTTCAGACCGAACGCGGTAAA
+EYKX4VC01B length=222 xy=0577_3838 region=1 run=R_2007_11_07_16_15_57_ AGACCTGGGACAGCGGCGGGCTGCTGAAGCCGCAGGCGATAGAGGACAAACTGCAGTACCGCTTCTGGCTGCACTATGCCGAAGGCTCGCTGATGCCGCTGCTGTTAATGAAGCTGGTGTTCGCCAGCCTGGGTAAACCCCCTGTGCCCTTTGGCGTCCGCTCGCTGGGCGCCCTGCTGGGCAAGGGCATTCAGAAAGCGTGGCTGGATCCCCAGCTGGCCA
+EYKX4VC01C length=83 xy=0832_1158 region=1 run=R_2007_11_07_16_15_57_ CGGTCGGCCTCACCATGGAGAAGATCCCGCCCCGGCCGAGGTCATGGTGGATCTCGGCCAGGGCGTGCTGATGAAGTTCAAAT
+EYKX4VC01B length=54 xy=0762_2010 region=1 run=R_2007_11_07_16_15_57_ AGCAGTTTTCCAGCGCTTTCGAAGAGCGCTGGCGCGCGCGGGCTTCCAGCATAT
+EYKX4VC01B length=57 xy=0431_0363 region=1 run=R_2007_11_07_16_15_57_ GGGGAGGAGCTAATAATATGCTCTTGGGGAGGAGCTAATTATATGCTCTTGGGGAGG
+EYKX4VC01B length=64 xy=0522_0192 region=1 run=R_2007_11_07_16_15_57_ TCGAGTATGTATCAAGGACTACATACAAATTTGCCAAAAGAGATTATGCACTATCCCGACTTCC
+EYKX4VC01B length=54 xy=0660_2038 region=1 run=R_2007_11_07_16_15_57_ AAAACTCGGAGAAACTATTCAGCAGCACTGCGTTTCGCTGAATTTTAGACCGTT
+EYKX4VC01C length=60 xy=0870_2350 region=1 run=R_2007_11_07_16_15_57_ CTGGGTGGGTGCACTACAGGAACGTCATTTGTTCAATCCTCACGTTGTTGTTAGTGTCAG
+EYKX4VC01B length=78 xy=0630_0292 region=1 run=R_2007_11_07_16_15_57_ TTATCCACACGCTGTCCGGATCCAGCGCCAGGCGCCGACGCTGGACTTCCGCCGCCTGCGCCCAGTTGCCCTGACTTC

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/fasta_tool_compute_length_1.out
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/fasta_tool_compute_length_1.out Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,18 @@
+EYKX4VC01B65GS length=54 xy=0784_1754 region=1 run=R_2007_11_07_16_15_57_ 54
+EYKX4VC01BNCSP length=187 xy=0558_3831 region=1 run=R_2007_11_07_16_15_57_ 187
+EYKX4VC01CD9FT length=115 xy=0865_1719 region=1 run=R_2007_11_07_16_15_57_ 115
+EYKX4VC01B8FW0 length=95 xy=0799_0514 region=1 run=R_2007_11_07_16_15_57_ 95
+EYKX4VC01BCGYW length=115 xy=0434_3926 region=1 run=R_2007_11_07_16_15_57_ 115
+EYKX4VC01AZXC6 length=116 xy=0292_0280 region=1 run=R_2007_11_07_16_15_57_ 116
+EYKX4VC01CATH5 length=82 xy=0826_0843 region=1 run=R_2007_11_07_16_15_57_ 82
+EYKX4VC01BCEIV length=47 xy=0434_0757 region=1 run=R_2007_11_07_16_15_57_ 47
+EYKX4VC01BWERM length=83 xy=0662_0304 region=1 run=R_2007_11_07_16_15_57_ 83
+EYKX4VC01BT2O7 length=69 xy=0635_1945 region=1 run=R_2007_11_07_16_15_57_ 69
+EYKX4VC01BO0UO length=222 xy=0577_3838 region=1 run=R_2007_11_07_16_15_57_ 222
+EYKX4VC01CBCPK length=83 xy=0832_1158 region=1 run=R_2007_11_07_16_15_57_ 83
+EYKX4VC01B474S length=54 xy=0762_2010 region=1 run=R_2007_11_07_16_15_57_ 54
+EYKX4VC01BB4QL length=57 xy=0431_0363 region=1 run=R_2007_11_07_16_15_57_ 57
+EYKX4VC01BJ37M length=64 xy=0522_0192 region=1 run=R_2007_11_07_16_15_57_ 64
+EYKX4VC01BV9R8 length=54 xy=0660_2038 region=1 run=R_2007_11_07_16_15_57_ 54
+EYKX4VC01CEPP8 length=60 xy=0870_2350 region=1 run=R_2007_11_07_16_15_57_ 60
+EYKX4VC01BTLME length=78 xy=0630_0292 region=1 run=R_2007_11_07_16_15_57_ 78

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/fasta_tool_compute_length_2.out
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/fasta_tool_compute_length_2.out Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,65 @@
+hg17_chr1_147962192_147962580_- 388
+hg17_chr1_147984545_147984630_+ 85
+hg17_chr1_148078400_148078582_- 182
+hg17_chr1_148185136_148185276_+ 140
+hg17_chr10_55251623_55253124_- 1501
+hg17_chr11_116124407_116124501_- 94
+hg17_chr11_116206508_116206563_+ 55
+hg17_chr11_116211733_116212337_- 604
+hg17_chr11_1812377_1812407_+ 30
+hg17_chr12_38440094_38440321_- 227
+hg17_chr13_112381694_112381953_+ 259
+hg17_chr14_98710240_98712285_- 2045
+hg17_chr15_41486872_41487060_- 188
+hg17_chr15_41673708_41673857_+ 149
+hg17_chr15_41679161_41679250_- 89
+hg17_chr15_41826029_41826196_+ 167
+hg17_chr16_142908_143003_+ 95
+hg17_chr16_179963_180135_- 172
+hg17_chr16_244413_244681_+ 268
+hg17_chr16_259268_259383_- 115
+hg17_chr18_23786114_23786321_- 207
+hg17_chr18_59406881_59407046_+ 165
+hg17_chr18_59455932_59456337_- 405
+hg17_chr18_59600586_59600754_+ 168
+hg17_chr19_59068595_59069564_+ 969
+hg17_chr19_59236026_59236146_- 120
+hg17_chr19_59297998_59298008_+ 10
+hg17_chr19_59302168_59302288_- 120
+hg17_chr2_118288583_118288668_+ 85
+hg17_chr2_118394148_118394202_- 54
+hg17_chr2_220190202_220190242_+ 40
+hg17_chr2_220229609_220230869_- 1260
+hg17_chr20_33330413_33330423_- 10
+hg17_chr20_33513606_33513792_+ 186
+hg17_chr20_33579500_33579527_- 27
+hg17_chr20_33593260_33593348_+ 88
+hg17_chr21_32707032_32707192_+ 160
+hg17_chr21_32869641_32870022_- 381
+hg17_chr21_33321040_33322012_+ 972
+hg17_chr21_33744994_33745040_- 46
+hg17_chr22_30120223_30120265_+ 42
+hg17_chr22_30160419_30160661_- 242
+hg17_chr22_30665273_30665360_+ 87
+hg17_chr22_30939054_30939266_- 212
+hg17_chr5_131424298_131424460_+ 162
+hg17_chr5_131556601_131556672_- 71
+hg17_chr5_131621326_131621419_+ 93
+hg17_chr5_131847541_131847666_- 125
+hg17_chr6_108299600_108299744_- 144
+hg17_chr6_108594662_108594687_+ 25
+hg17_chr6_108640045_108640151_- 106
+hg17_chr6_108722976_108723115_+ 139
+hg17_chr7_113660517_113660685_+ 168
+hg17_chr7_116512159_116512389_- 230
+hg17_chr7_116714099_116714152_+ 53
+hg17_chr7_116945541_116945787_- 246
+hg17_chr8_118881131_118881317_- 186
+hg17_chr9_128764156_128764189_+ 33
+hg17_chr9_128787519_128789136_- 1617
+hg17_chr9_128882427_128882523_+ 96
+hg17_chr9_128937229_128937445_- 216
+hg17_chrX_122745047_122745924_+ 877
+hg17_chrX_152648964_152649196_- 232
+hg17_chrX_152691446_152691471_+ 25
+hg17_chrX_152694029_152694263_- 234

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/fasta_tool_compute_length_3.out
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/fasta_tool_compute_length_3.out Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,18 @@
+EYKX4VC01B65GS 54
+EYKX4VC01BNCSP 187
+EYKX4VC01CD9FT 115
+EYKX4VC01B8FW0 95
+EYKX4VC01BCGYW 115
+EYKX4VC01AZXC6 116
+EYKX4VC01CATH5 82
+EYKX4VC01BCEIV 47
+EYKX4VC01BWERM 83
+EYKX4VC01BT2O7 69
+EYKX4VC01BO0UO 222
+EYKX4VC01CBCPK 83
+EYKX4VC01B474S 54
+EYKX4VC01BB4QL 57
+EYKX4VC01BJ37M 64
+EYKX4VC01BV9R8 54
+EYKX4VC01CEPP8 60
+EYKX4VC01BTLME 78

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/fastq_conv_in1.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/fastq_conv_in1.fastq Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,4 @@
+@081017-and-081020:1:1:1715:1759
+GGACTCAGATAGTAATCCACGCTCCTTTAAAATATC
++
+II#IIIIIII$5+.(9IIIIIII$%*$G$A31I&&B

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/fastq_conv_out1.fastqsanger
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/fastq_conv_out1.fastqsanger Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,4 @@
+@081017-and-081020:1:1:1715:1759
+GGACTCAGATAGTAATCCACGCTCCTTTAAAATATC
++
+++!+++++++!!!!!"+++++++!!!!)!%!!+!!%!

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/fastq_conv_out2.fastqsolexa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/fastq_conv_out2.fastqsolexa Sat Feb 21 16:33:42 2015 +0100

[

@@ -0,0 +1,8 @@
+@1831_573_1004/1
+AATACTTTCGGCGCCCTAAACCAGCTCACTGGGG
++
+][bEEXXTQJb]T[M^[VXK\SQ[QXQY[GXNLV
+@1831_573_1050/1
+TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT
++
+Z__PV^_\]V^^_`W^\\_S`^`SHEJMFEJFPK

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/fastq_conv_out4.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/fastq_conv_out4.fasta Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,4 @@
+>1831_573_1004/1
+AATACTTTCGGCGCCCTAAACCAGCTCACTGGGG
+>1831_573_1050/1
+TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/fastq_gen_conv_in1.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/fastq_gen_conv_in1.fastq Sat Feb 21 16:33:42 2015 +0100

[

@@ -0,0 +1,16 @@
+@seq1
+AGTCGTGGTCATCGTGACTAGTCGATCTAGCTAGCTCTCTAGAGTGT
++
+;>@BCEFGHJKLMNOPQRSTUVWXYZ[\]^_?abcdefghijklmno
+@seq2
+AGTCGTTGTCATCGTGACTAGTCGATCTAGCTAGCTCTCTAGAGTGT
++
+;>@BCElcH@KLMNOPQ>STZVWbYu[\]^_?a=;d?fghijklmno
+@seq3
+AGTCGTCGTCATCGTGACTAGTCGATCTAGCTAGCTCTCTAGAGTGT
++
+7>@BCEFGHJKLMNOPQRSTUVWXYZ[\]^_?abcdefghijklmno
+@seq4
+AGTCGTAGTCATCGTGACTAGTCGATCTAGCTAGCTCTCTAGAGTGT
++
+;>@BCEFGHJKLMNOPQRSTUVWXYZ[\]^_?abcdefghijklmno

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/fastq_gen_conv_in2.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/fastq_gen_conv_in2.fastq Sat Feb 21 16:33:42 2015 +0100

[

@@ -0,0 +1,24 @@
+@seq1
+AAAGGTTTCTCTTTTGGAAATATCTAAATCCC
++
+!"#$%&\'()*+,-./0123456789:;<=>.
+@seq2
+GGGTCTCCCAGAATGATTAGAGCCGTATAGGA
++
+?@ABCDEFGHIJK MNOPQRSTUVWXYZ[\\]
+@seq3
+GCGGTTCAATACGATTACCACCATGATAAATA
++
+?Aa.1ghB2K!#lk(02GY[[II])Kwl+,5M
+@seq4
+AGTCTTTTCCTCTAAAATAACATAGGATACTA
++
+ghY)N375Nh.,Ol>==/<:2#i&d%#KdNII
+@seq5
+GAGGACTCATGGTAGGTATTTTACATGACATT
++
+IIgy%hf6#394bd&hNMWL$OPB63II*,+-
+@seq6
+GGCCTACATTCATTTACGAGACTAATTAGGGA
++
+IIIIIgd6#5%jKO&.,D+s3aW=cdGB#a1$
\ No newline at end of file

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/fastq_gen_conv_out1.fastqsanger
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/fastq_gen_conv_out1.fastqsanger Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,12 @@
+@seq1
+AGTCGTGGTCATCGTGACTAGTCGATCTAGCTAGCTCTCTAGAGTGT
++
+"#$%%''()+,-./0123456789:;<=>?@#BCDEFGHIJKLMNOP
+@seq2
+AGTCGTTGTCATCGTGACTAGTCGATCTAGCTAGCTCTCTAGAGTGT
++
+"#$%%'MD)$,-./012#45;78C:V<=>?@#B""E#GHIJKLMNOP
+@seq4
+AGTCGTAGTCATCGTGACTAGTCGATCTAGCTAGCTCTCTAGAGTGT
++
+"#$%%''()+,-./0123456789:;<=>?@#BCDEFGHIJKLMNOP

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/fastq_gen_conv_out2.fastqsanger
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/fastq_gen_conv_out2.fastqsanger Sat Feb 21 16:33:42 2015 +0100

[

@@ -0,0 +1,20 @@
+@seq1
+AAAGGTTTCTCTTTTGGAAATATCTAAATCCC
++
+!"#$%&\'()*+,-./0123456789:;<=>.
+@seq3
+GCGGTTCAATACGATTACCACCATGATAAATA
++
+?Aa.1ghB2K!#lk(02GY[[II])Kwl+,5M
+@seq4
+AGTCTTTTCCTCTAAAATAACATAGGATACTA
++
+ghY)N375Nh.,Ol>==/<:2#i&d%#KdNII
+@seq5
+GAGGACTCATGGTAGGTATTTTACATGACATT
++
+IIgy%hf6#394bd&hNMWL$OPB63II*,+-
+@seq6
+GGCCTACATTCATTTACGAGACTAATTAGGGA
++
+IIIIIgd6#5%jKO&.,D+s3aW=cdGB#a1$
\ No newline at end of file

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/fastq_stats_1_out.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/fastq_stats_1_out.tabular Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,37 @@
+#column count min max sum mean Q1 med Q3 IQR lW rW outliers A_Count C_Count G_Count T_Count N_Count other_bases other_base_count
+1 9 23 34 288 32.0 33.0 33.0 33.0 0.0 33 33 23,34 3 1 4 1 0
+2 9 28 33 287 31.8888888889 30.5 33.0 33.0 2.5 28 33 3 3 2 1 0
+3 9 13 34 268 29.7777777778 27.5 33.0 33.5 6.0 27 34 13 5 1 0 3 0
+4 9 17 33 261 29.0 24.5 33.0 33.0 8.5 17 33 1 2 3 3 0
+5 9 22 33 269 29.8888888889 26.0 33.0 33.0 7.0 22 33 3 3 3 0 0
+6 9 22 33 277 30.7777777778 29.0 33.0 33.0 4.0 28 33 22 5 3 0 1 0
+7 9 21 33 258 28.6666666667 23.0 33.0 33.0 10.0 21 33 4 1 3 1 0
+8 9 12 33 263 29.2222222222 26.5 33.0 33.0 6.5 21 33 12 2 1 1 5 0
+9 9 29 33 290 32.2222222222 31.5 33.0 33.0 1.5 30 33 29 3 3 2 1 0
+10 9 23 33 277 30.7777777778 28.0 33.0 33.0 5.0 23 33 1 4 2 2 0
+11 9 12 33 245 27.2222222222 21.0 31.0 33.0 12.0 12 33 5 2 1 1 0
+12 9 13 33 214 23.7777777778 14.0 24.0 33.0 19.0 13 33 2 4 2 1 0
+13 9 5 33 249 27.6666666667 26.5 31.0 33.0 6.5 24 33 5 2 1 1 5 0
+14 9 5 33 233 25.8888888889 19.5 33.0 33.0 13.5 5 33 3 3 2 1 0
+15 9 15 33 251 27.8888888889 22.5 33.0 33.0 10.5 15 33 5 1 1 2 0
+16 9 23 34 269 29.8888888889 23.5 33.0 33.0 9.5 23 34 3 1 2 3 0
+17 9 13 34 266 29.5555555556 27.0 33.0 33.0 6.0 21 34 13 2 3 1 3 0
+18 9 21 34 272 30.2222222222 26.0 33.0 33.0 7.0 21 34 0 5 1 3 0
+19 9 5 34 244 27.1111111111 24.0 30.0 33.0 9.0 21 34 5 4 4 1 0 0
+20 9 11 34 241 26.7777777778 17.0 32.0 33.0 16.0 11 34 3 4 2 0 0
+21 9 13 33 240 26.6666666667 22.5 27.0 33.0 10.5 13 33 1 4 0 4 0
+22 9 5 33 190 21.1111111111 9.0 21.0 33.0 24.0 5 33 1 4 0 3 1
+23 9 5 33 205 22.7777777778 14.0 26.0 33.0 19.0 5 33 4 4 1 0 0
+24 9 5 33 247 27.4444444444 24.5 31.0 33.0 8.5 21 33 5 1 5 1 2 0
+25 9 11 34 241 26.7777777778 18.5 33.0 33.0 14.5 11 34 3 4 0 2 0
+26 9 5 33 212 23.5555555556 11.5 31.0 33.0 21.5 5 33 0 6 0 3 0
+27 9 5 33 227 25.2222222222 20.0 26.0 33.0 13.0 5 33 3 4 1 1 0
+28 9 21 33 255 28.3333333333 22.5 31.0 33.0 10.5 21 33 2 4 3 0 0
+29 9 5 33 228 25.3333333333 19.5 30.0 33.0 13.5 5 33 2 4 1 2 0
+30 9 10 33 213 23.6666666667 13.5 28.0 33.0 19.5 10 33 3 4 2 0 0
+31 9 5 33 236 26.2222222222 21.0 31.0 33.0 12.0 5 33 1 4 1 3 0
+32 9 5 33 210 23.3333333333 11.5 29.0 33.0 21.5 5 33 3 3 0 3 0
+33 9 5 33 183 20.3333333333 8.0 21.0 33.0 25.0 5 33 1 4 2 2 0
+34 9 5 33 150 16.6666666667 6.0 17.0 25.5 19.5 5 33 3 4 1 1 0
+35 9 13 33 217 24.1111111111 19.5 24.0 31.0 11.5 13 33 1 4 1 3 0
+36 9 5 33 195 21.6666666667 11.5 21.0 32.5 21.0 5 33 3 2 1 3 0

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/fastqsolexa_to_fasta_qual_out2.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/fastqsolexa_to_fasta_qual_out2.fasta Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,4 @@
+>seq1
+GACAGCTTGGTTTTTAGTGAGTTGTTCCTTTCTTT
+>seq2
+GCAATGACGGCAGCAATAAACTCAACAGGTGCTGG

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/fastqsolexa_to_fasta_qual_out4.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/fastqsolexa_to_fasta_qual_out4.fasta Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,4 @@
+>HANNIBAL_1_FC302VTAAXX:2:1:228:167
+GAATTGATCAGGACATAGGACAACTGTAGGCACCAT
+>HANNIBAL_1_FC302VTAAXX:2:1:156:340
+GAGTTCTCGTCGCCTGTAGGCACCATCAATCGTATG

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/filter1_in3.sam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/filter1_in3.sam Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,100 @@\n+HWI-EAS269B:8:34:797:623\t145\tchr1\t16632182\t255\t27M\t=\t16631977\t0\tCCATTTCCTGTATGCTGTAAAGTACAA\tIIIIIIIIIIIIIIIIIIIIIIIIIII\tNM:i:0\tNH:i:1\n+HWI-EAS269B:8:40:39:1184\t145\tchr1\t24620331\t3\t27M\t=\t24620115\t0\tATTTATGTGGTTTCGTTTACCTTCTAT\tIIIIIIIIIIIIIIIIIIIIIIIIIII\tNM:i:0\tNH:i:2\tCC:Z:chrM\tCP:i:9060\n+HWI-EAS269B:8:58:533:1198\t81\tchr1\t88426079\t255\t27M\t=\t88423429\t0\tGAAGAGGAAGAAGGTGGGGAGGAAGAG\tIIIG?IIIIIIIIIIIIIIIIIIIIII\tNM:i:0\tNH:i:1\n+HWI-EAS269:3:89:1776:1815\t97\tchr1\t134085638\t255\t27M\t=\t134085824\t0\tGAATGATTCTCTGGGTGTTACTTTGCA\tIIIIIIIIIIIIIIIDIII:IIII>F5\tNM:i:0\tNH:i:1\n+HWI-EAS269B:8:74:1134:1670\t161\tchr1\t138166886\t255\t27M\t=\t138167084\t0\tTTACTAGTGTCTCTCTTACCATCATAT\t.IIIIIIIIIIIIIIIIIIIIIIIIII\tNM:i:1\tNH:i:1\n+HWI-EAS269:3:59:1321:1427\t147\tchr1\t173149715\t255\t27M\t=\t173149555\t0\tAAGGGCTAGGGTGACAGGCAGGGGACG\t-C<CID?IIIIIIIDIIIIIIIIIIII\tNM:i:0\tNH:i:1\n+HWI-EAS269B:8:8:164:1678\t145\tchr1\t178660716\t255\t27M\t=\t178660493\t0\tCAATTGGTGTTTTTCTTAAGAGACTCA\tIIIIIIIIIIIIIIIIIIIIIIIIIII\tNM:i:0\tNH:i:1\n+HWI-EAS269:3:1:1048:638\t137\tchr10\t12456478\t1\t27M\t*\t0\t0\tTAAAANAAATAAAACAAAACAATAAAA\t$\'&(+")\'%$(&*&#&$$#%%$$%%$$\tNM:i:2\tNH:i:4\tCC:Z:chr16\tCP:i:21639623\n+HWI-EAS269:3:62:1211:798\t147\tchr10\t28135294\t255\t27M\t=\t28135117\t0\tACATGGTGTGGGGACAGAGATGTGAAG\tI;IIIIIIAIIIIIIIIIIIIIIIIII\tNM:i:1\tNH:i:1\n+HWI-EAS269:3:27:410:424\t145\tchr10\t76950070\t255\t27M\t=\t76949871\t0\tGAGTCTGTGTCCAGGCCAATTCACTAT\t25-8I+.6B.IIIIIIIIIIIIIIIII\tNM:i:0\tNH:i:1\n+HWI-EAS269:3:48:1180:1122\t73\tchr10\t83772157\t0\t27M\t*\t0\t0\tGATCATCTTTTCTAAAACAATAAAGAC\t/IIIIIIIIIIIIIIIIIIIIIIIIII\tNM:i:0\tNH:i:6\tCC:Z:chr11\tCP:i:93811140\n+HWI-EAS269:3:77:654:131\t99\tchr10\t93419810\t255\t27M\t=\t93419993\t0\tTTGCATCCCTAGGAACTGGAGTTATAG\tIIIIIIGIHIIIED@CIIH5I3D9G6:\tNM:i:0\tNH:i:1\n+HWI-EAS269B:8:98:895:1810\t177\tchr11\t3371472\t255\t27M\t=\t37952212\t0\tCTACATAGTGGGAACCGGCGACCGCTG\tIIIIIIIIIIIIIIIIIIIIIIIIIII\tNM:i:2\tNH:i:1\n+HWI-EAS269B:8:58:1126:883\t97\tchr11\t30080486\t255\t27M\t=\t30080702\t0\tTACTTCCACCAGGCTCCAGTTTTGTGA\tIIIIIIIIIIIIIIIIIIIIIIIIII5\tNM:i:0\tNH:i:1\n+HWI-EAS269B:8:89:1763:1446\t81\tchr11\t59589605\t255\t27M\t=\t59589400\t0\tGTACCTGGCCACTGATGCAGCTTAGAA\tII<IIIIIIIIIIIIIIIIIIIIIIII\tNM:i:0\tNH:i:1\n+HWI-EAS269B:8:6:739:1329\t161\tchr11\t68629628\t3\t27M\t=\t68629835\t0\tGTTTTTGGTTGATAGTTGAGCAAACTG\tIIIIIIIIIIIIIIIIIIIIIIIIIII\tNM:i:0\tNH:i:2\tCC:Z:chr4\tCP:i:126661877\n+HWI-EAS269:3:19:1683:1350\t81\tchr11\t70846915\t255\t27M\t=\t70846725\t0\tCACGGGCAGATAAGCTGCTGAGACTAA\tH50BB:IF=IIGIIIIIIIIIIIIIII\tNM:i:0\tNH:i:1\n+HWI-EAS269B:8:9:1691:1087\t97\tchr11\t84640783\t255\t27M\t=\t84641010\t0\tACATTATCCATCTCTCTGTCATTGTCC\tIIIIIIIIIIIIIIIIIIIIIIIIIII\tNM:i:0\tNH:i:1\n+HWI-EAS269B:8:48:1350:424\t81\tchr11\t94150331\t255\t27M\t=\t94150113\t0\tTTGCAAGCCAACCCTGAGTGAAGTGTC\tIIDHIIIIIIIIIIIIIIIIIIIIIII\tNM:i:0\tNH:i:1\n+HWI-EAS269:3:22:1176:1405\t97\tchr11\t98629843\t255\t27M\t=\t98630030\t0\tCCCTCGGAGGGCAACGGGAAAGGAGAA\tIIIIIIIIIIIDIIIII?III/79E14\tNM:i:0\tNH:i:1\n+HWI-EAS269:3:67:1311:1512\t97\tchr11\t100488190\t255\t27M\t=\t100488374\t0\tCATGCCCTGAGACTTAGCAAGACTCTT\tIIIIIIIIIIIIIIIEIA3,I57GBI@\tNM:i:0\tNH:i:1\n+HWI-EAS269B:8:41:1142:1307\t161\tchr11\t101320424\t255\t27M\t=\t101320625\t0\tGCCTCCCTACATAGCAAAGGAAAGAAA\tIIIIIIIIIIIIIIIIIIIIIIIIIII\tNM:i:0\tNH:i:1\n+HWI-EAS269B:8:31:1101:21\t97\tchr11\t116711287\t255\t27M\t=\t116711485\t0\tCATAAGCAAAAGATACACCATGTTTTA\tIIIIIIIIIIIIIIIIIIIIIIIIIII\tNM:i:0\tNH:i:1\n+HWI-EAS269:3:84:637:1203\t145\tchr12\t35829424\t255\t27M\t=\t35829229\t0\tCTCCCTCAAGGATCTTGTGGGGCATCA\t</\'>I,I5B26$II;EB=%IIII1III\tNM:i:0\tNH:i:1\n+HWI-EAS269:3:65:1158:1081\t163\tchr12\t52234332\t255\t27M\t=\t52234505\t0\tTTTTTTTTTTAAGACAGGGAGTTTTTT\tIIIIIIIIIIIC4,,*>II%-,%III>\tNM:i:1\tNH:i:1\n+HWI-EAS269B:8:65:1325:1287\t137\tchr12\t52234513\t3\t27M\t*\t0\t0\tGCAGCACCTTGTGACATTTAATTTAGT\tIIIII+IIIIIIIIIIIIIIIIIIIII\tNM:i:0\tNH:i:2\tCC:Z:chr15\tCP:i:98780443\n+HWI-EAS269:3:38:488:1093\t97\tchr12\t80471642\t255\t27M\t=\t80471839\t0\tTGGAGAGATGACTCCTTGTTTGAGACA\tIIIIIIIIIIIIIIIIIIIBAE0B<7D\tNM:i:0\tNH:i:1\n+HWI-EAS269:3:76:290:1451\t99\tchr12\t117745566\t0\t27M\t=\t117745739\t0\tCAATCTGAAGATCCACAATCTTTTATA\tIIIIIIIIIIIIIIFII5I9IIII+I7\tNM:i:0\tNH:i:5\tCC:Z:chr4\tCP:i:133520935\n+HWI-EAS269B:8:39:353:1526\t65\tchr13\t18122558\t255\t2'..b":1\n+HWI-EAS269B:8:13:280:189\t161\tchr7\t29184615\t255\t27M\t=\t29184814\t0\tCTTTTCCAACAGCGAGAAAAATGTACA\tIIIIIIIIIIIIIIIIIIIIIIIIDII\tNM:i:0\tNH:i:1\n+HWI-EAS269B:8:19:72:273\t137\tchr7\t52258521\t255\t27M\t*\t0\t0\tATCAGAGGCACAGGGACAGGGTAAGGA\t&&2IIIII;E(IIIIIIIIIIIIIIII\tNM:i:1\tNH:i:1\n+HWI-EAS269B:8:40:235:869\t161\tchr7\t52631974\t255\t27M\t=\t52632179\t0\tGGCGCTGACTCCATCAGATATCCATTC\tIIIIIII7IIIIIII6IIIIIIIBIII\tNM:i:1\tNH:i:1\n+HWI-EAS269B:8:18:304:346\t129\tchr7\t107789557\t255\t27M\t=\t33158390\t0\tCACGTACTGTCACCTTGTAACATTTGG\tIIIIIIIIIIIIIIIIIIIIIIIIIIF\tNM:i:0\tNH:i:1\n+HWI-EAS269B:8:3:698:297\t161\tchr7\t110976065\t255\t27M\t=\t110976385\t0\tGCAGTTATCACTTTCTTGCCATGGGCC\tIIIIIIIIIIIIIIIIIIIIIIIIIII\tNM:i:0\tNH:i:1\n+HWI-EAS269B:8:50:1269:965\t145\tchr7\t118217605\t255\t27M\t=\t118216239\t0\tACCTGTAGATCCACATGATCATGAAGA\tIIIIIIIIIIIIIIIIIIIIIIIIIII\tNM:i:0\tNH:i:1\n+HWI-EAS269:3:38:1381:1429\t83\tchr7\t136141344\t255\t27M\t=\t136141280\t0\tATCTGAAGTATCCCACATGTTGAGCTC\t<III@IIIIIIIII>IIIIIIIIIIII\tNM:i:1\tNH:i:1\n+HWI-EAS269:3:25:781:386\t83\tchr8\t29844005\t255\t27M\t=\t29843841\t0\tTAAGGGAGGAAAGTGTTTCAGAGTGTA\t;83<159<<III@IIIIIIIIIIIIII\tNM:i:0\tNH:i:1\n+HWI-EAS269:3:25:979:679\t163\tchr8\t72664237\t255\t27M\t=\t72664413\t0\tCTGATGGGAGCCCTGCGTGGTAAGAGG\tIIIIIIIIIII=III@I(II$27I>I4\tNM:i:0\tNH:i:1\n+HWI-EAS269B:8:23:1069:816\t145\tchr8\t74704433\t255\t27M\t=\t74704222\t0\tTGTTCTCAGTTGTGGACAAGTGACAGC\tI<GII@IIIIIIII;IIIIIIIIII0I\tNM:i:0\tNH:i:1\n+HWI-EAS269B:8:34:435:1679\t73\tchr8\t87366211\t3\t27M\t*\t0\t0\tAAGCCTAGGGCTTCTCCTCTACACCCC\tI556I;FCAIIIFI<IIIIIIIIIIII\tNM:i:0\tNH:i:2\n+HWI-EAS269B:8:32:1486:294\t97\tchr8\t124121215\t255\t27M\t=\t124121411\t0\tTGTTACCATACGCCCTTCTGCTGAGGC\tIIIIIIIIIIIIIIIIIIDIIIIGIII\tNM:i:0\tNH:i:1\n+HWI-EAS269B:8:32:142:1471\t81\tchr8\t124496752\t3\t27M\t=\t124496536\t0\tGGATCTGCTTCATGAGTTGCCACATTG\tIIIIIIIIIIIIIIIIIIIIIIIIIII\tNM:i:1\tNH:i:2\n+HWI-EAS269B:8:60:82:1806\t97\tchr8\t125945215\t255\t27M\t=\t125945423\t0\tAGATGCTGGCCATCCAGAGTAAGAACA\tIIIIIIIIIIIIIIIIIIIHIIIIIII\tNM:i:0\tNH:i:1\n+HWI-EAS269B:8:16:1162:495\t81\tchr8\t125945584\t255\t27M\t=\t125945381\t0\tGTTGCTCGCAGCTGGGGTGTGGGGCCA\t<CIIIIIIIIIIIIIIIIIIIIIIIII\tNM:i:0\tNH:i:1\n+HWI-EAS269B:8:1:165:1889\t81\tchr8\t126016885\t255\t27M\t=\t126016469\t0\tTGAGCAGGAAAACACTTTAAACCAGAT\tIIIIIIIIIIIIIIIIIIIIIIIIIII\tNM:i:0\tNH:i:1\n+HWI-EAS269B:8:66:939:1154\t145\tchr9\t17537149\t255\t27M\t=\t17536959\t0\tCTCCTTCAAGTACGCCTGGGTCTTAGA\tIDIIIIIIIIIIIIIIIIIIIIIIIII\tNM:i:0\tNH:i:1\n+HWI-EAS269:3:68:1189:285\t81\tchr9\t61249807\t255\t27M\t=\t61242460\t0\tAGTCAAGCTCACTTGGCGGTGAAGGAT\t@.0;;A,?-F5I;7IIIIGIIIIIIII\tNM:i:0\tNH:i:1\n+HWI-EAS269:3:15:784:1754\t163\tchr9\t74846937\t255\t27M\t=\t74847108\t0\tGCACAGCACTGAGGAAAGGATCATCTC\tIIIIIIIIIIIIIIIIIIGII1CI7II\tNM:i:0\tNH:i:1\n+HWI-EAS269B:8:26:126:1382\t145\tchrM\t3413\t255\t27M\t=\t3190\t0\tGTTATTCTTTATAGCAGAGTACACTAA\tIIII8IB328I9IIIIIIIIIIIIIII\tNM:i:0\tNH:i:1\n+HWI-EAS269:3:90:320:1336\t73\tchrM\t6326\t255\t27M\t*\t0\t0\tATGATCTCCAGCTATCCTATGAGCCTT\tIIIIIIIIA.ICI.4'(=,C>7-*&@8\tNM:i:1\tNH:i:1\n+HWI-EAS269B:8:23:469:1215\t161\tchrM\t7472\t3\t27M\t=\t7676\t0\tATTTCATCTGAAGACGTCCTCCACTCA\tIIIIIIIIIIIIIIIIIIIIIIIIIII\tNM:i:0\tNH:i:2\n+HWI-EAS269:3:73:36:783\t161\tchrM\t7958\t3\t27M\t=\t8152\t0\tCCCCAACAATAATAGGATTCCCAATCG\tIIIIIIIIIIIIIIIIIIIII09I>>I\tNM:i:0\tNH:i:2\n+HWI-EAS269:3:33:1528:954\t99\tchrM\t8012\t3\t27M\t=\t8186\t0\tTCCTATTCCCATCCTCAAAACGCCTAA\tIIIIIIIIIIIIIIIIIIIIIIIDII:\tNM:i:0\tNH:i:2\n+HWI-EAS269:3:2:192:1456\t161\tchrM\t9071\t3\t27M\t=\t9255\t0\tACGAAACCACATAAATCAAGCCCTACT\tIII;IEIIDI7III+III*?I@CH+5I\tNM:i:0\tNH:i:2\n+HWI-EAS269:3:63:192:470\t97\tchrM\t14787\t255\t27M\t=\t14982\t0\tGCAGATAAAATTCCATTTCACCCCTAC\tIIIIIIIIIIIIIIFIII=B5042:4E\tNM:i:0\tNH:i:1\n+HWI-EAS269B:8:49:528:63\t83\tchrM\t14963\t255\t27M\t=\t14829\t0\tTTTCCTATTTGCATACGCCATTCTACG\tIIIIIIIIIIIIIIIIIIIIIIIIIII\tNM:i:0\tNH:i:1\n+HWI-EAS269B:8:98:856:1516\t145\tchrX\t20257960\t255\t27M\t=\t20256746\t0\tTACCCGGATTTAAGATGTACCCCATTG\tIIIIIIIIIIIIIIIIIIIIIIIIIII\tNM:i:0\tNH:i:1\n+HWI-EAS269B:8:28:1174:110\t145\tchrX\t53916348\t255\t27M\t=\t53916153\t0\tTGAATGTCAGCATCATTGACCCACAAA\tIIIIFIIIIIIIIIIIIIIIIIIIIII\tNM:i:0\tNH:i:1\n+HWI-EAS269B:8:58:663:410\t147\tchrX\t75006902\t255\t27M\t=\t75006834\t0\tTCAGGTGGTTTACAGTGTTCTGACAAA\tIIIIIIIIIIIIIIIIIIIIIIIIIII\tNM:i:0\tNH:i:1\n\\ No newline at end of file\n"

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/filter1_in5.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/filter1_in5.tab Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,5 @@
+tracking_id class_code nearest_ref_id gene_id gene_short_name tss_id locus length coverage replicate 1_FPKM replicate 1_conf_lo replicate 1_conf_hi replicate 1_status replicate 2_FPKM replicate 2_conf_lo replicate 2_conf_hi replicate 2_status
+CUFF.1.1 - - CUFF.1 - - chr19:305598-306225 627 - 0 0 0 OK 206.177 0 694.583 OK
+CUFF.10.1 - - CUFF.10 - - chr19:618402-618611 209 - 0 0 0 OK 767.201 0 2801.16 OK
+CUFF.100.1 - - CUFF.100 - - chr19:1625589-1652356 888 - 0 0 0 OK 172.566 0 2879.98 OK
+CUFF.100.2 - - CUFF.100 - - chr19:1625589-1652356 581 - 0 0 0 OK 1147.8 0 5922.31 OK

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/filter1_inbad.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/filter1_inbad.bed Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,6 @@
+# Should skip this line
+chr22 30120223 30120265 CCDS13897.1_cds_0_0_chr22_30120224_f 0 +
+chr22 foo foo foo foo foo
+chr22 30160419 30160661 CCDS13898.1_cds_0_0_chr22_30160420_r 0 -
+chr22 30665273 30665360 CCDS13901.1_cds_0_0_chr22_30665274_f 0 +
+chr22 30939054 30939266 CCDS13903.1_cds_0_0_chr22_30939055_r 0 -

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/filter1_test1.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/filter1_test1.bed Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,4 @@
+chr22 30120223 30120265 CCDS13897.1_cds_0_0_chr22_30120224_f 0 +
+chr22 30160419 30160661 CCDS13898.1_cds_0_0_chr22_30160420_r 0 -
+chr22 30665273 30665360 CCDS13901.1_cds_0_0_chr22_30665274_f 0 +
+chr22 30939054 30939266 CCDS13903.1_cds_0_0_chr22_30939055_r 0 -

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/filter1_test2.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/filter1_test2.bed Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,2 @@
+chr1 147984101 148035079 BC007833 0 + 147984545 148033414 0 14 529,32,81,131,118,153,300,206,84,49,85,130,46,1668, 0,25695,28767,33118,33695,33998,35644,38005,39629,40577,41402,43885,48367,49310,
+chr1 148185113 148187485 NM_002796 0 + 148185136 148187378 0 7 163,207,147,82,117,89,120, 0,416,877,1199,1674,1977,2252,

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/filter1_test3.sam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/filter1_test3.sam Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,6 @@
+HWI-EAS269B:8:34:797:623 145 chr1 16632182 255 27M = 16631977 0 CCATTTCCTGTATGCTGTAAAGTACAA IIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1
+HWI-EAS269B:8:58:533:1198 81 chr1 88426079 255 27M = 88423429 0 GAAGAGGAAGAAGGTGGGGAGGAAGAG IIIG?IIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1
+HWI-EAS269:3:89:1776:1815 97 chr1 134085638 255 27M = 134085824 0 GAATGATTCTCTGGGTGTTACTTTGCA IIIIIIIIIIIIIIIDIII:IIII>F5 NM:i:0 NH:i:1
+HWI-EAS269B:8:74:1134:1670 161 chr1 138166886 255 27M = 138167084 0 TTACTAGTGTCTCTCTTACCATCATAT .IIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1
+HWI-EAS269:3:59:1321:1427 147 chr1 173149715 255 27M = 173149555 0 AAGGGCTAGGGTGACAGGCAGGGGACG -C<CID?IIIIIIIDIIIIIIIIIIII NM:i:0 NH:i:1
+HWI-EAS269B:8:8:164:1678 145 chr1 178660716 255 27M = 178660493 0 CAATTGGTGTTTTTCTTAAGAGACTCA IIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/filter1_test4.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/filter1_test4.bed Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,5 @@
+chr22 30120223 30120265 CCDS13897.1_cds_0_0_chr22_30120224_f 0 +
+chr22 foo foo foo foo foo
+chr22 30160419 30160661 CCDS13898.1_cds_0_0_chr22_30160420_r 0 -
+chr22 30665273 30665360 CCDS13901.1_cds_0_0_chr22_30665274_f 0 +
+chr22 30939054 30939266 CCDS13903.1_cds_0_0_chr22_30939055_r 0 -

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/filter1_test5.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/filter1_test5.tab Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,4 @@
+tracking_id class_code nearest_ref_id gene_id gene_short_name tss_id locus length coverage replicate 1_FPKM replicate 1_conf_lo replicate 1_conf_hi replicate 1_status replicate 2_FPKM replicate 2_conf_lo replicate 2_conf_hi replicate 2_status
+CUFF.1.1 - - CUFF.1 - - chr19:305598-306225 627 - 0 0 0 OK 206.177 0 694.583 OK
+CUFF.100.1 - - CUFF.100 - - chr19:1625589-1652356 888 - 0 0 0 OK 172.566 0 2879.98 OK
+CUFF.100.2 - - CUFF.100 - - chr19:1625589-1652356 581 - 0 0 0 OK 1147.8 0 5922.31 OK

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/filteredJoinedFlanksDNAse.dat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/filteredJoinedFlanksDNAse.dat Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,1 @@
+chr22 20414625 20415125 NM_013313 0 - 20379971 20389587 0 5 3680,109,44,281,168, 0,5831,6300,13089,38076, chr22 20413245 20415213 chr22.303 1000

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/fr.csfasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/fr.csfasta Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,1001 @@\n+# Sun Oct 4 18:40:32 2009 /share/apps/corona/bin/filter_fasta.pl --output=/data/results/solid176/solid176_20090923/Somali_Wild_Ass_a/results.01/primary.20091004212559515 --name=solid176_20090923_Somali_Wild_Ass_a --tag=F3 --minlength=50 --mincalls=25 --prefix=T /data/results/solid176/solid176_20090923/Somali_Wild_Ass_a/jobs/postPrimerSetPrimary.1062/rawseq \n+# Cwd: /state/partition1/home/pipeline\n+# Title: solid176_20090923_Somali_Wild_Ass_a\n+>853_7_53_F3\n+T..02.1120..22.2..230.22.3..033212.1.1....2221...12\n+>853_7_78_F3\n+T..13.2222..22.2..222.22.2..222212.2.2....2222...22\n+>853_7_88_F3\n+T..23.2221..13.2..033.30.1..010220.1.2....2222...22\n+>853_7_132_F3\n+T..22.2032..32.2..222.22.2..222222.2.2....2222...22\n+>853_7_141_F3\n+T..22.2112..10.2..221.02.1..220112.0.2....0222...22\n+>853_7_146_F3\n+T..12.1011..21.2..213.22.2..222222.2.2....2222...22\n+>853_7_269_F3\n+T..12.2222..22.2..222.22.2..222222.2.2....2222...22\n+>853_7_321_F3\n+T..20.2322..21.3..222.12.1..120012.3.0....2000...22\n+>853_7_386_F3\n+T..12.2302..20.2..231.12.0..200232.3.2....0002...22\n+>853_7_405_F3\n+T..21.0221..31.2..000.23.2..020022.0.2....0313...12\n+>853_7_411_F3\n+T..10.2000..33.2..022.02.0..200222.2.0....0000...00\n+>853_7_445_F3\n+T..30.3210..01.1..120.11.3..301222.1.2....3222...22\n+>853_7_469_F3\n+T..22.0102..20.3..200.21.0..002202.2.2....0203...02\n+>853_7_474_F3\n+T..30.1122..22.3..111.21.3..222020.2.2....2203...23\n+>853_7_497_F3\n+T..10.0200..22.1..112.03.0..100121.2.2....3132...21\n+>853_7_587_F3\n+T..22.2022..01.2..323.23.0..323322.1.1....2212...20\n+>853_7_630_F3\n+T..13.0022..11.1..213.10.0..031113.3.3....1112...20\n+>853_7_655_F3\n+T..01.0023..02.2..301.32.3..232113.2.2....2222...22\n+>853_7_692_F3\n+T..00.0122..02.3..230.21.2..301213.2.1....1122...22\n+>853_7_715_F3\n+T..00.0213..21.3..131.12.0..202011.1.0....0221...22\n+>853_7_719_F3\n+T..00.2231..02.0..122.13.0..003022.0.1....1010...02\n+>853_7_743_F3\n+T..11.0201..00.1..303.01.1..021332.3.3....3223...23\n+>853_7_791_F3\n+T..20.3311..03.2..301.01.2..122002.2.1....3123...21\n+>853_7_801_F3\n+T..00.0323..21.1..112.23.3..132022.2.1....2122...22\n+>853_7_845_F3\n+T..01.3303..01.1..102.03.1..222102.0.0....0231...12\n+>853_7_868_F3\n+T..31.3103..12.1..211.32.2..223200.2.3....1031...21\n+>853_7_1026_F3\n+T..22.3032..03.3..110.32.3..212230.3.0....1111...13\n+>853_7_1057_F3\n+T..30.3112..22.2..132.21.0..332122.2.2....2220...32\n+>853_7_1066_F3\n+T..01.1122..00.0..131.32.0..230030.3.3....2000...30\n+>853_7_1107_F3\n+T..20.0301..13.2..003.10.0..300221.2.1....3300...32\n+>853_7_1179_F3\n+T..02.3301..32.0..310.03.3..312300.3.3....1320...03\n+>853_7_1198_F3\n+T..32.2203..31.2..111.13.1..312322.2.2....1103...22\n+>853_7_1261_F3\n+T..20.3233..32.2..223.22.3..232033.2.3....0322...23\n+>853_7_1321_F3\n+T..00.0321..22.2..100.11.1..120210.0.2....2211...02\n+>853_7_1406_F3\n+T..13.0310..13.2..031.32.0..002230.0.2....0231...11\n+>853_7_1431_F3\n+T..11.0032..21.1..310.00.0..321021.0.2....3030...02\n+>853_7_1439_F3\n+T..20.0132..13.1..212.32.2..222110.3.0....2132...22\n+>853_7_1524_F3\n+T..20.1110..13.3..201.33.3..320121.1.3....3321...20\n+>853_7_1537_F3\n+T..12.1030..02.0..011.30.1..111200.0.3....2033...11\n+>853_7_1592_F3\n+T..21.3233..02.1..000.22.0..121233.3.1....3223...22\n+>853_7_1597_F3\n+T..12.3100..33.0..312.02.1..000000.3.1....1100...00\n+>853_7_1650_F3\n+T..00.2212..12.1..203.13.3..102012.0.2....3333...30\n+>853_7_1790_F3\n+T..23.1021..32.0..130.13.0..012301.0.1....0001...10\n+>853_7_1795_F3\n+T..22.2123..01.0..222.31.3..233211.0.1....2312...03\n+>853_7_1807_F3\n+T..03.0310..02.3..121.20.1..333122.3.1....0302...12\n+>853_7_1872_F3\n+T..01.2331..12.2..200.02.3..302232.3.1....1203...23\n+>853_7_1885_F3\n+T..10.3010..11.2..331.21.2..230213.1.3....0132...32\n+>853_7_1910_F3\n+T..11.1002..20.1..000.20.1..111022.2.0....3311...23\n+>853_8_43_F3\n+T..32100023203.2..110.31.120321022.100.1.11202..211\n+>853_8_48_F3\n+T..21122022323.1..222.32.020211202.222.2.20222..222\n+>853_8_57_F3\n+T..23231203232.2..212.22.222222232.222.2.22222..222\n+>853_8_106_F3\n+T..23112221210.3..001.02.0322223'..b'.212123310.011310330302303122333.2233\n+>853_15_1794_F3\n+T2221231303022.022023010.221322032322120332311.3213\n+>853_15_1876_F3\n+T2221311021332.101230332.111000230102222310002.1031\n+>853_15_1915_F3\n+T1323002020313.110132112.012221202021132212100.0100\n+>853_15_1974_F3\n+T3200002312331.022233323.021320331222211031102.2110\n+>853_16_26_F3\n+T2200303003123.332202133.022202222221222222222.2222\n+>853_16_44_F3\n+T1010220033031.131100202.322222222222222222222.2222\n+>853_16_56_F3\n+T2222220320012.222222222.222222222222222222222.2222\n+>853_16_67_F3\n+T3020301230012.320302200.122222233212012222222.2222\n+>853_16_112_F3\n+T1200021122132.111211211.101321132100211222122.0222\n+>853_16_155_F3\n+T2211222000221.222212222.122222222222222222222.2222\n+>853_16_169_F3\n+T1200213123132.220001100.311323132102222222202.2212\n+>853_16_319_F3\n+T3212223211023.013011313.020220313111230111311.0111\n+>853_16_375_F3\n+T3332011121213.223022022.220021112220100221322.1222\n+>853_16_447_F3\n+T3302130221112.123102110.022103123222122220111.0203\n+>853_16_502_F3\n+T1023113011002.032210023.012230013110011223013.1000\n+>853_16_506_F3\n+T1022110220323.201110311.021300002020121031023.1000\n+>853_16_513_F3\n+T0332023210131.212020222.102202231311211133011.1122\n+>853_16_571_F3\n+T2010033331133.302200220.122102023123200012222.2222\n+>853_16_622_F3\n+T0013033001233.133330200.000000330003000000000.3000\n+>853_16_690_F3\n+T0021310130010.202032022.110223101101310102100.0112\n+>853_16_697_F3\n+T1231230012311.132303323.310130033010101111222.1310\n+>853_16_791_F3\n+T1110102111131.110203033.121212111131211113111.2111\n+>853_16_804_F3\n+T3133010300211.330333311.122313112302002200031.2333\n+>853_16_830_F3\n+T3230012031232.130212222.012232100113320211310.1221\n+>853_16_871_F3\n+T3201000013102.303333121.003330012300022302213.2223\n+>853_16_874_F3\n+T2301033231033.020002133.133030332300323313233.3133\n+>853_16_892_F3\n+T3321220311213.332101020.231311213111213212011.3011\n+>853_16_919_F3\n+T1220221133122.203221113.002222222222222213332.2212\n+>853_16_941_F3\n+T3310301301311.011321102.321223223120112231222.1222\n+>853_16_1040_F3\n+T3222002222223.332302032.322031103321223221212.3031\n+>853_16_1049_F3\n+T1100033003303.021320321.111301320233200033001.0000\n+>853_16_1063_F3\n+T1123202211000.302123303.122302023333231103220.1212\n+>853_16_1081_F3\n+T0012023221322.322222022.202022222222222222222.2222\n+>853_16_1142_F3\n+T2222003033021.112113112.023101132021212223001.1200\n+>853_16_1155_F3\n+T3211301033030.010023021.222211203303330033130.0203\n+>853_16_1188_F3\n+T3213220312022.213131000.032301320320100303322.3322\n+>853_16_1231_F3\n+T0032303211001.310313100.320000200213333000302.3232\n+>853_16_1285_F3\n+T1110130123031.110222221.003111112232000001113.1113\n+>853_16_1300_F3\n+T0011232200000.110012222.101002200130311033003.0300\n+>853_16_1391_F3\n+T3113212223000.101202111.201002121202012103121.1121\n+>853_16_1397_F3\n+T2120211222223.012212231.032321102311221213223.3133\n+>853_16_1528_F3\n+T1011223130211.130021111.233321321121322131121.1121\n+>853_16_1574_F3\n+T2103333220002.302023111.231021311232100032103.1212\n+>853_16_1593_F3\n+T1320102033202.110112100.103112112021110222002.2323\n+>853_16_1653_F3\n+T0300012120022.111332202.010231221033110201300.2102\n+>853_16_1698_F3\n+T3003323013003.033033222.211103000122022112121.1210\n+>853_16_1746_F3\n+T3003322312011.031233000.313001220020120330301.1330\n+>853_16_1806_F3\n+T3022322013100.301112103.001112221321112001312.2012\n+>853_16_1821_F3\n+T2133312220333.203003203.132322202222220113310.1220\n+>853_16_1842_F3\n+T2022031201310.230002012.310222131210221100011.0130\n+>853_16_1853_F3\n+T2332123123202.112200333.212101231122012220211.2203\n+>853_16_1871_F3\n+T1310331222123.031120212.231120302120122222221.2111\n+>853_16_1887_F3\n+T3332021100203.001331023.300022222012120111033.1003\n+>853_16_1919_F3\n+T3331012121211.303003033.131111320313213223300.0202\n+>853_16_1924_F3\n+T1201123330103.233221210.100211100211001133123.1002\n+>853_16_1982_F3\n+T0331130320230.220330112.210312121022203321222.2302\n+>853_16_2037_F3\n+T.13331.12..23.10..2..02.2323120.3.320..10.021.2..1\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/fr.qualsolid
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/fr.qualsolid Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,1001 @@\n+# Sun Oct 4 18:40:32 2009 /share/apps/corona/bin/filter_fasta.pl --output=/data/results/solid176/solid176_20090923/Somali_Wild_Ass_a/results.01/primary.20091004212559515 --name=solid176_20090923_Somali_Wild_Ass_a --tag=F3 --minlength=50 --mincalls=25 --prefix=T /data/results/solid176/solid176_20090923/Somali_Wild_Ass_a/jobs/postPrimerSetPrimary.1062/rawseq \n+# Cwd: /state/partition1/home/pipeline\n+# Title: solid176_20090923_Somali_Wild_Ass_a\n+>853_7_53_F3\n+-1 -1 16 19 -1 18 13 16 20 -1 -1 19 22 -1 19 -1 -1 23 10 16 -1 3 24 -1 7 -1 -1 11 13 13 16 8 5 -1 18 -1 7 -1 -1 -1 -1 16 14 24 5 -1 -1 -1 11 18 \n+>853_7_78_F3\n+-1 -1 2 2 -1 2 2 2 3 -1 -1 2 2 -1 5 -1 -1 2 3 5 -1 3 5 -1 5 -1 -1 4 5 8 6 2 6 -1 3 -1 2 -1 -1 -1 -1 5 8 9 7 -1 -1 -1 5 9 \n+>853_7_88_F3\n+-1 -1 21 16 -1 20 20 20 16 -1 -1 16 18 -1 19 -1 -1 13 11 8 -1 14 11 -1 18 -1 -1 13 8 14 16 22 10 -1 5 -1 20 -1 -1 -1 -1 12 6 15 13 -1 -1 -1 11 20 \n+>853_7_132_F3\n+-1 -1 3 7 -1 11 2 5 2 -1 -1 5 2 -1 2 -1 -1 2 7 3 -1 4 3 -1 2 -1 -1 2 5 4 2 3 7 -1 2 -1 2 -1 -1 -1 -1 8 7 9 10 -1 -1 -1 11 17 \n+>853_7_141_F3\n+-1 -1 20 19 -1 24 20 16 23 -1 -1 16 5 -1 20 -1 -1 14 18 16 -1 8 15 -1 21 -1 -1 8 20 18 18 14 25 -1 20 -1 21 -1 -1 -1 -1 8 14 27 25 -1 -1 -1 11 22 \n+>853_7_146_F3\n+-1 -1 16 15 -1 14 17 19 15 -1 -1 15 8 -1 17 -1 -1 2 5 6 -1 6 20 -1 7 -1 -1 7 13 12 9 3 18 -1 9 -1 19 -1 -1 -1 -1 10 2 7 13 -1 -1 -1 13 7 \n+>853_7_269_F3\n+-1 -1 4 5 -1 7 6 2 4 -1 -1 2 9 -1 2 -1 -1 14 2 2 -1 5 8 -1 3 -1 -1 6 3 6 11 4 11 -1 4 -1 17 -1 -1 -1 -1 18 11 11 9 -1 -1 -1 11 17 \n+>853_7_321_F3\n+-1 -1 10 3 -1 10 17 16 7 -1 -1 9 12 -1 13 -1 -1 8 2 16 -1 23 14 -1 24 -1 -1 21 11 18 10 4 21 -1 6 -1 11 -1 -1 -1 -1 17 5 21 11 -1 -1 -1 5 17 \n+>853_7_386_F3\n+-1 -1 18 16 -1 25 22 12 4 -1 -1 25 11 -1 12 -1 -1 17 16 11 -1 22 22 -1 8 -1 -1 17 17 22 25 24 25 -1 17 -1 26 -1 -1 -1 -1 8 6 11 4 -1 -1 -1 23 21 \n+>853_7_405_F3\n+-1 -1 27 23 -1 23 26 28 28 -1 -1 26 29 -1 25 -1 -1 22 25 22 -1 22 26 -1 23 -1 -1 22 25 29 19 23 28 -1 17 -1 28 -1 -1 -1 -1 20 18 21 9 -1 -1 -1 26 25 \n+>853_7_411_F3\n+-1 -1 11 14 -1 16 18 26 11 -1 -1 5 11 -1 10 -1 -1 17 14 4 -1 9 16 -1 3 -1 -1 4 9 8 10 2 11 -1 11 -1 5 -1 -1 -1 -1 6 12 6 5 -1 -1 -1 10 10 \n+>853_7_445_F3\n+-1 -1 5 6 -1 9 10 6 2 -1 -1 6 4 -1 5 -1 -1 11 4 2 -1 8 4 -1 7 -1 -1 6 2 2 3 5 6 -1 2 -1 3 -1 -1 -1 -1 3 3 2 11 -1 -1 -1 2 3 \n+>853_7_469_F3\n+-1 -1 2 2 -1 9 7 3 5 -1 -1 2 2 -1 2 -1 -1 4 8 8 -1 2 16 -1 4 -1 -1 7 11 2 2 3 13 -1 2 -1 7 -1 -1 -1 -1 2 2 6 2 -1 -1 -1 5 3 \n+>853_7_474_F3\n+-1 -1 20 19 -1 21 19 21 19 -1 -1 20 21 -1 25 -1 -1 24 22 25 -1 23 23 -1 23 -1 -1 22 14 20 8 19 14 -1 19 -1 23 -1 -1 -1 -1 19 2 19 20 -1 -1 -1 2 8 \n+>853_7_497_F3\n+-1 -1 24 25 -1 21 22 23 26 -1 -1 16 19 -1 24 -1 -1 25 27 25 -1 22 22 -1 26 -1 -1 13 22 21 13 7 27 -1 13 -1 14 -1 -1 -1 -1 17 8 7 24 -1 -1 -1 16 19 \n+>853_7_587_F3\n+-1 -1 17 11 -1 11 18 18 14 -1 -1 22 5 -1 22 -1 -1 24 16 21 -1 8 24 -1 27 -1 -1 26 11 27 21 11 16 -1 20 -1 14 -1 -1 -1 -1 11 18 16 26 -1 -1 -1 14 29 \n+>853_7_630_F3\n+-1 -1 11 23 -1 5 20 14 28 -1 -1 29 8 -1 8 -1 -1 26 8 13 -1 8 22 -1 21 -1 -1 14 17 29 11 7 6 -1 20 -1 17 -1 -1 -1 -1 8 28 11 5 -1 -1 -1 17 20 \n+>853_7_655_F3\n+-1 -1 2 2 -1 2 2 2 6 -1 -1 2 6 -1 2 -1 -1 11 2 2 -1 2 2 -1 3 -1 -1 4 3 2 2 2 7 -1 2 -1 2 -1 -1 -1 -1 2 6 2 2 -1 -1 -1 2 2 \n+>853_7_692_F3\n+-1 -1 15 19 -1 18 29 21 21 -1 -1 13 16 -1 22 -1 -1 20 29 20 -1 25 11 -1 11 -1 -1 16 25 5 26 20 24 -1 29 -1 11 -1 -1 -1 -1 20 13 5 13 -1 -1 -1 8 23 \n+>853_7_715_F3\n+-1 -1 5 15 -1 11 8 14 20 -1 -1 7 13 -1 16 -1 -1 8 6 11 -1 10 5 -1 20 -1 -1 5 23 14 17 21 18 -1 12 -1 2 -1 -1 -1 -1 5 21 5 5 -1 -1 -1 5 15 \n+>853_7_719_F3\n+-1 -1 21 9 -1 14 13 17 10 -1 -1 20 7 -1 2 -1 -1 3 13 3 -1 20 5 -1 11 -1 -1 16 11 5 17 9 13 -1 3 -1 2 -1 -1 -1 -1 2 10 5 2 -1 -1 -1 3 2 \n+>853_7_743_F3\n+-1 -1 23 18 -1 22 29 6 11 -1 -1 19 20 -1 24 -1 -1 21 7 23 -1 17 16 -1 27 -1 -1 13 5 28 11 22 13 -1 22 -1 19 -1 -1 -1 -1 13 24 21 18 -1 -1 -1 15 19 \n+>853_7_791_F3\n+-1 -1 15 26 -1 18 29 17 23 -1 -1 29 25 -1 19 -1 -1 20 19 5 -1 27 26 -1 6 -1 -1 24 11 5 6 23 23 -1 5 -1 1'..b'-1 22 9 5 5 21 29 10 8 8 -1 24 18 6 11 25 21 6 11 16 20 4 3 7 14 8 25 20 10 22 25 13 -1 22 23 14 14 \n+>853_16_1081_F3\n+2 2 2 2 2 2 2 2 2 2 2 2 2 -1 2 2 2 2 2 2 2 2 2 -1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 -1 2 2 2 2 \n+>853_16_1142_F3\n+11 11 12 8 12 15 14 4 12 18 20 8 9 -1 14 20 18 15 14 21 21 8 9 -1 15 15 14 22 20 20 15 17 4 22 18 4 2 3 2 12 2 5 2 5 15 -1 3 2 11 13 \n+>853_16_1155_F3\n+19 19 17 24 23 21 5 8 16 10 19 26 8 -1 5 25 19 16 10 26 5 15 12 -1 20 14 15 6 14 20 13 24 19 20 14 15 21 11 21 7 19 22 20 14 21 -1 18 6 18 14 \n+>853_16_1188_F3\n+6 5 12 13 12 19 19 2 2 2 11 2 7 -1 9 14 8 4 3 16 6 2 22 -1 2 2 2 3 18 2 9 4 4 3 11 13 2 11 4 4 2 2 2 3 7 -1 2 4 8 2 \n+>853_16_1231_F3\n+19 27 22 3 20 21 25 25 4 18 21 25 22 -1 26 11 25 23 17 25 11 22 19 -1 23 22 23 29 19 24 14 4 8 18 18 19 18 20 2 23 2 16 21 15 7 -1 16 8 5 13 \n+>853_16_1285_F3\n+14 9 10 2 2 2 2 3 2 2 2 2 4 -1 2 2 2 2 2 2 2 2 8 -1 2 7 2 5 2 2 2 2 3 2 2 2 2 2 2 2 2 2 2 2 2 -1 2 2 2 2 \n+>853_16_1300_F3\n+10 17 13 6 3 8 4 15 20 17 2 19 10 -1 19 15 14 5 7 3 2 12 5 -1 8 4 6 7 7 3 3 12 16 3 5 3 6 10 11 21 7 3 4 9 5 -1 6 2 8 22 \n+>853_16_1391_F3\n+29 32 32 27 32 32 32 32 30 28 29 29 28 -1 29 24 28 32 27 31 31 31 29 -1 31 23 29 27 27 32 26 20 29 32 23 27 18 30 31 31 22 22 25 30 26 -1 29 23 30 16 \n+>853_16_1397_F3\n+22 23 14 4 7 23 14 16 22 7 16 24 18 -1 21 28 7 25 22 16 25 14 16 -1 5 9 7 6 7 25 25 11 21 14 27 28 5 16 22 12 5 5 18 14 10 -1 28 11 20 28 \n+>853_16_1528_F3\n+29 24 29 32 29 30 28 31 27 28 31 30 32 -1 32 29 27 23 28 27 25 31 29 -1 27 27 26 29 32 25 29 27 29 20 21 23 25 5 5 21 18 8 15 14 5 -1 7 11 24 8 \n+>853_16_1574_F3\n+23 27 20 2 12 14 19 13 23 21 21 18 16 -1 2 14 21 18 6 2 11 24 4 -1 15 22 31 15 23 10 19 25 6 2 8 25 29 14 14 7 12 20 10 5 12 -1 23 11 5 21 \n+>853_16_1593_F3\n+6 5 3 18 6 5 4 6 6 11 5 11 6 -1 4 3 3 3 11 4 4 9 4 -1 3 8 11 3 19 12 9 14 6 5 10 5 11 3 3 6 18 18 7 13 11 -1 8 14 6 4 \n+>853_16_1653_F3\n+28 22 25 23 25 26 27 26 25 27 29 28 23 -1 28 27 25 27 26 26 28 27 27 -1 28 26 26 24 26 28 27 25 23 24 28 26 29 25 28 24 27 28 23 26 29 -1 24 20 25 20 \n+>853_16_1698_F3\n+24 21 27 23 24 26 26 29 27 23 23 27 26 -1 23 21 26 22 28 24 27 25 24 -1 22 24 27 22 17 22 21 26 25 22 12 24 16 23 26 10 23 21 23 24 11 -1 25 26 26 15 \n+>853_16_1746_F3\n+28 26 29 26 26 31 27 27 32 23 29 28 16 -1 26 25 28 23 25 26 28 23 24 -1 25 27 22 14 28 23 29 21 14 28 25 25 24 14 29 29 26 23 23 28 24 -1 28 21 24 11 \n+>853_16_1806_F3\n+23 32 26 23 21 21 29 28 27 22 31 30 30 -1 19 29 27 29 30 27 31 28 20 -1 32 29 28 26 27 25 25 19 27 5 17 14 15 2 3 15 2 14 3 15 3 -1 3 5 5 2 \n+>853_16_1821_F3\n+25 11 21 16 25 20 26 27 16 23 26 28 27 -1 25 11 28 7 17 24 19 11 21 -1 14 11 8 16 10 11 11 16 12 18 17 9 15 3 13 15 2 11 5 5 8 -1 7 11 25 8 \n+>853_16_1842_F3\n+21 29 26 23 32 27 25 27 29 23 25 22 30 -1 24 25 31 26 28 28 30 24 21 -1 23 28 23 24 27 29 28 18 28 24 27 28 26 26 24 28 28 29 24 22 28 -1 23 21 15 23 \n+>853_16_1853_F3\n+8 18 8 16 26 6 18 8 11 8 27 24 25 -1 16 27 8 21 6 22 8 22 28 -1 21 21 8 5 14 5 11 22 14 11 18 8 5 8 11 11 11 11 8 5 14 -1 8 25 11 19 \n+>853_16_1871_F3\n+25 13 7 21 6 16 14 8 7 13 26 11 6 -1 29 20 18 18 16 4 21 22 5 -1 11 17 10 21 6 7 8 6 5 19 12 8 18 13 23 13 5 7 5 8 11 -1 5 11 5 4 \n+>853_16_1887_F3\n+26 25 23 29 24 27 32 29 29 27 29 28 26 -1 28 28 27 25 25 22 29 25 24 -1 19 27 29 25 26 29 27 29 28 29 28 28 31 28 30 25 24 28 10 24 25 -1 28 21 25 20 \n+>853_16_1919_F3\n+17 11 9 25 26 28 24 25 24 25 22 23 20 -1 17 23 11 28 21 22 27 17 17 -1 26 23 23 27 27 24 20 16 26 17 24 17 22 17 19 17 24 16 11 26 27 -1 22 3 24 10 \n+>853_16_1924_F3\n+11 23 16 13 29 8 21 18 13 8 8 5 11 -1 14 19 3 14 6 5 11 14 14 -1 11 10 18 8 5 20 29 5 5 5 8 7 26 24 22 29 7 6 22 21 8 -1 21 25 8 12 \n+>853_16_1982_F3\n+27 23 23 27 26 24 27 21 27 28 23 26 27 -1 26 19 25 25 23 27 25 31 25 -1 29 25 26 26 25 28 21 25 21 24 28 28 28 24 22 26 24 25 24 29 28 -1 28 19 11 27 \n+>853_16_2037_F3\n+-1 24 22 24 24 28 -1 28 25 -1 -1 25 24 -1 28 28 -1 -1 23 -1 -1 29 25 -1 26 23 28 24 27 26 28 -1 24 -1 25 26 20 -1 -1 26 23 -1 21 22 24 -1 11 -1 -1 21 \n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/fs-compare-2.dat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/fs-compare-2.dat Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,40 @@
+chr10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 -
+chr11 116124407 116124501 CCDS8374.1_cds_0_0_chr11_116124408_r 0 -
+chr11 116206508 116206563 CCDS8377.1_cds_0_0_chr11_116206509_f 0 +
+chr11 116211733 116212337 CCDS8378.1_cds_0_0_chr11_116211734_r 0 -
+chr11 1812377 1812407 CCDS7726.1_cds_0_0_chr11_1812378_f 0 +
+chr12 38440094 38440321 CCDS8736.1_cds_0_0_chr12_38440095_r 0 -
+chr13 112381694 112381953 CCDS9526.1_cds_0_0_chr13_112381695_f 0 +
+chr14 98710240 98712285 CCDS9949.1_cds_0_0_chr14_98710241_r 0 -
+chr15 41486872 41487060 CCDS10096.1_cds_0_0_chr15_41486873_r 0 -
+chr15 41673708 41673857 CCDS10097.1_cds_0_0_chr15_41673709_f 0 +
+chr15 41679161 41679250 CCDS10098.1_cds_0_0_chr15_41679162_r 0 -
+chr15 41826029 41826196 CCDS10101.1_cds_0_0_chr15_41826030_f 0 +
+chr16 142908 143003 CCDS10397.1_cds_0_0_chr16_142909_f 0 +
+chr16 179963 180135 CCDS10401.1_cds_0_0_chr16_179964_r 0 -
+chr16 244413 244681 CCDS10402.1_cds_0_0_chr16_244414_f 0 +
+chr16 259268 259383 CCDS10403.1_cds_0_0_chr16_259269_r 0 -
+chr18 23786114 23786321 CCDS11891.1_cds_0_0_chr18_23786115_r 0 -
+chr18 59406881 59407046 CCDS11985.1_cds_0_0_chr18_59406882_f 0 +
+chr18 59455932 59456337 CCDS11986.1_cds_0_0_chr18_59455933_r 0 -
+chr18 59600586 59600754 CCDS11988.1_cds_0_0_chr18_59600587_f 0 +
+chr19 59068595 59069564 CCDS12866.1_cds_0_0_chr19_59068596_f 0 +
+chr19 59236026 59236146 CCDS12872.1_cds_0_0_chr19_59236027_r 0 -
+chr19 59297998 59298008 CCDS12877.1_cds_0_0_chr19_59297999_f 0 +
+chr19 59302168 59302288 CCDS12878.1_cds_0_0_chr19_59302169_r 0 -
+chr20 33330413 33330423 CCDS13249.1_cds_0_0_chr20_33330414_r 0 -
+chr20 33513606 33513792 CCDS13255.1_cds_0_0_chr20_33513607_f 0 +
+chr20 33579500 33579527 CCDS13256.1_cds_0_0_chr20_33579501_r 0 -
+chr20 33593260 33593348 CCDS13257.1_cds_0_0_chr20_33593261_f 0 +
+chr21 32707032 32707192 CCDS13614.1_cds_0_0_chr21_32707033_f 0 +
+chr21 32869641 32870022 CCDS13615.1_cds_0_0_chr21_32869642_r 0 -
+chr21 33321040 33322012 CCDS13620.1_cds_0_0_chr21_33321041_f 0 +
+chr21 33744994 33745040 CCDS13625.1_cds_0_0_chr21_33744995_r 0 -
+chr22 30120223 30120265 CCDS13897.1_cds_0_0_chr22_30120224_f 0 +
+chr22 30160419 30160661 CCDS13898.1_cds_0_0_chr22_30160420_r 0 -
+chr22 30665273 30665360 CCDS13901.1_cds_0_0_chr22_30665274_f 0 +
+chr22 30939054 30939266 CCDS13903.1_cds_0_0_chr22_30939055_r 0 -
+chrX 122745047 122745924 CCDS14606.1_cds_0_0_chrX_122745048_f 0 +
+chrX 152648964 152649196 CCDS14733.1_cds_0_0_chrX_152648965_r 0 -
+chrX 152691446 152691471 CCDS14735.1_cds_0_0_chrX_152691447_f 0 +
+chrX 152694029 152694263 CCDS14736.1_cds_0_0_chrX_152694030_r 0 -

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/fs-compare.dat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/fs-compare.dat Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,49 @@
+chr6 108299600 108299744 CCDS5061.1_cds_0_0_chr6_108299601_r 0 -
+chr6 108594662 108594687 CCDS5063.1_cds_0_0_chr6_108594663_f 0 +
+chr6 108640045 108640151 CCDS5064.1_cds_0_0_chr6_108640046_r 0 -
+chr6 108722976 108723115 CCDS5067.1_cds_0_0_chr6_108722977_f 0 +
+chr13 112381694 112381953 CCDS9526.1_cds_0_0_chr13_112381695_f 0 +
+chr7 113660517 113660685 CCDS5760.1_cds_0_0_chr7_113660518_f 0 +
+chr11 116124407 116124501 CCDS8374.1_cds_0_0_chr11_116124408_r 0 -
+chr11 116206508 116206563 CCDS8377.1_cds_0_0_chr11_116206509_f 0 +
+chr11 116211733 116212337 CCDS8378.1_cds_0_0_chr11_116211734_r 0 -
+chr7 116512159 116512389 CCDS5771.1_cds_0_0_chr7_116512160_r 0 -
+chr7 116714099 116714152 CCDS5773.1_cds_0_0_chr7_116714100_f 0 +
+chr7 116945541 116945787 CCDS5774.1_cds_0_0_chr7_116945542_r 0 -
+chr2 118288583 118288668 CCDS2120.1_cds_0_0_chr2_118288584_f 0 +
+chr8 118881131 118881317 CCDS6324.1_cds_0_0_chr8_118881132_r 0 -
+chrX 122745047 122745924 CCDS14606.1_cds_0_0_chrX_122745048_f 0 +
+chr9 128764156 128764189 CCDS6914.1_cds_0_0_chr9_128764157_f 0 +
+chr9 128787519 128789136 CCDS6915.1_cds_0_0_chr9_128787520_r 0 -
+chr5 131424298 131424460 CCDS4149.1_cds_0_0_chr5_131424299_f 0 +
+chr5 131556601 131556672 CCDS4151.1_cds_0_0_chr5_131556602_r 0 -
+chr5 131621326 131621419 CCDS4152.1_cds_0_0_chr5_131621327_f 0 +
+chr16 142908 143003 CCDS10397.1_cds_0_0_chr16_142909_f 0 +
+chr1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 -
+chr1 147984545 147984630 CCDS990.1_cds_0_0_chr1_147984546_f 0 +
+chr1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 -
+chr1 148185136 148185276 CCDS996.1_cds_0_0_chr1_148185137_f 0 +
+chrX 152648964 152649196 CCDS14733.1_cds_0_0_chrX_152648965_r 0 -
+chrX 152691446 152691471 CCDS14735.1_cds_0_0_chrX_152691447_f 0 +
+chrX 152694029 152694263 CCDS14736.1_cds_0_0_chrX_152694030_r 0 -
+chr2 220229609 220230869 CCDS2443.1_cds_0_0_chr2_220229610_r 0 -
+chr18 23786114 23786321 CCDS11891.1_cds_0_0_chr18_23786115_r 0 -
+chr16 244413 244681 CCDS10402.1_cds_0_0_chr16_244414_f 0 +
+chr16 259268 259383 CCDS10403.1_cds_0_0_chr16_259269_r 0 -
+chr22 30120223 30120265 CCDS13897.1_cds_0_0_chr22_30120224_f 0 +
+chr22 30160419 30160661 CCDS13898.1_cds_0_0_chr22_30160420_r 0 -
+chr21 32869641 32870022 CCDS13615.1_cds_0_0_chr21_32869642_r 0 -
+chr21 33321040 33322012 CCDS13620.1_cds_0_0_chr21_33321041_f 0 +
+chr20 33330413 33330423 CCDS13249.1_cds_0_0_chr20_33330414_r 0 -
+chr20 33513606 33513792 CCDS13255.1_cds_0_0_chr20_33513607_f 0 +
+chr12 38440094 38440321 CCDS8736.1_cds_0_0_chr12_38440095_r 0 -
+chr15 41486872 41487060 CCDS10096.1_cds_0_0_chr15_41486873_r 0 -
+chr15 41673708 41673857 CCDS10097.1_cds_0_0_chr15_41673709_f 0 +
+chr15 41679161 41679250 CCDS10098.1_cds_0_0_chr15_41679162_r 0 -
+chr10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 -
+chr19 59068595 59069564 CCDS12866.1_cds_0_0_chr19_59068596_f 0 +
+chr19 59236026 59236146 CCDS12872.1_cds_0_0_chr19_59236027_r 0 -
+chr19 59297998 59298008 CCDS12877.1_cds_0_0_chr19_59297999_f 0 +
+chr18 59406881 59407046 CCDS11985.1_cds_0_0_chr18_59406882_f 0 +
+chr18 59455932 59456337 CCDS11986.1_cds_0_0_chr18_59455933_r 0 -
+chr14 98710240 98712285 CCDS9949.1_cds_0_0_chr14_98710241_r 0 -

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/fs-grep.dat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/fs-grep.dat Sat Feb 21 16:33:42 2015 +0100

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/fsa_interval2maf.dat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/fsa_interval2maf.dat Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,2703 @@\n+##maf version=1\n+a score=2047408.0\n+s hg17.chr1 147984545 85 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG \n+s panTro1.chr1 129723125 85 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG \n+s baboon.ENr231_1 81874 85 + 657133 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG \n+s marmoset.ENr231_1 131543 85 + 772620 ATGGCGTCGGCCTCCTCCGGGATGTCGTCGGCGGTCGGTTTTTCATCCTTTGATCCCGGCGTCCCTTCCTGTACCTCGTCCTCAG \n+s galago.ENr231_1 75476 82 + 825110 ATGGCGTCGGCCTCCTCTGGGCCGCCGGCTCC---CGGATTTTCGTCCTGTGATCCCGGGGTCCCTCCCTGTGCCTCGACTTCAG \n+s rn3.chr2 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG \n+s mm6.chr3 64351392 76 - 158945675 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCCGGGTTTTCATCCCTTGATGCCGGGGCCCCTGCTGGTACCGC------AG \n+s rabbit.ENr231_1 70872 82 + 694075 ATGGCGTCGGCCTCTTCTGGGCCGTCGGC---GGTCGGGTGTTCAGCCTTGGATTCCGGGATCCCTTCCAGCACCTCGATCTCAG \n+s cow.ENr231_1 83601 82 + 1082283 ATGGCGTCTGCCTCCTCTGGGCCGTCGGC---GGTAGGGTTTTCATCCGCGGATTCCAGCGTCCCTCCCTGCACCTCGGCCTCAG \n+s canFam1.chr17 62947719 82 + 66886099 ATGGCGTCGGCCTCCTCTGGGCCGTCGGC---GGCTGGGGTTTCATCCTTTGATCCCGGGGTCCCTTCCTGTGCTTCGGCTTCAG \n+s rfbat.ENr231_1 76952 82 + 561098 ATGGCGTCGGTCTCCTCTGGGCCGTCGTC---GGGCGGGTTTTCGTCGGTGGATTCCGGGGTTCCTGGCTGCACCTCGTCCTCAG \n+s shrew.ENr231_8 4546 63 - 4749 ATGGCGTCGGCTCCGTTCGTAGTG----------------------CCTCCGATTCCGGGTCCTCCTCCTGCTCTATGATTATCT \n+s armadillo.ENr231_1 35525 82 + 758801 ATGGCGATGGCCTCCTCTGGACCGTCGAC---GACCGCGCTTTCATCCGTGGATACCGGAGTGCCTCCCTGCACCTTATCCTCAG \n+s tenrec.ENr231_3 2426 73 + 2724 ATGGCGACGGCCTCCTCTGGGCCGTCGAC---GACCGCGTATTCGCTCGCGGATTCCTG---------CAACACCTCGTCCGCAG \n+s monDom1.scaffold_18720 1604680 79 - 5714867 ATGGCGTCG---TCCTCCGGGTCGTCGTC---GGCCGGGAATACCTCCTTGGAGTTGGCGAGTAGCAGCGGCTCCTCCAGCTTCG \n+s tetNig1.chr21 1755128 81 + 5821691 CTAATGAAGAAATGCTCGGGGACGGCGCT---GGCCA-TCGCTCACAGCGTGGCCACACTCACCTTTCCCAGCCCTTCCCCCTGT \n+s fr1.chrUn 290894076 81 + 349519338 CTAATGAAGAAATGCTCGGGGACGGCGCT---GGCTA-TCGCTCACAGTGTGGCCACACTTAGCTTTCCCAGCCCTCCCCCCGCT \n+\n+a score=2837921.0\n+s hg17.chr1 97444265 182 - 245522847 GTTCTCAGCTT---------CCTTGCTTCCATGGCTCCAGCACCATTCGAAACCTCAAAGAGAGGTTCCACATGAGCA---------------------------------------------TGACTGAGGAGCAGCTGCAGCTGCTGGTGGAGCAGATGGTGGATGGCAGTATGCGGTCTATCACCACCAAACTCTATGACGGCTTCCAGTACCTCACCAACGGCATCATGTGA \n+s panTro1.chr1 99744907 182 - 229575298 GTTCTCAGCTT---------CCTTGCTTCCATGGCTCCAGCACCATTCGAAACCTCAAAGAGAGGTTCCACATGAGCA---------------------------------------------TGACTGAGGAGCAGCTGCAGCTGCTGGTGGAGCAGATGGTGGATGGCAGTATGCGGTCTATCACCACCAAACTCTATGACGGCTTCCAGTACCTCACCAACGGCATCATGTGA \n+s baboon.ENr231_1 479199 182 - 657133 GTTCTCAGCTT---------CCTTGCTTCCATGGCTCCAGCACCATTCGAAACCTCAAAGAGAGGTTCCACATGAGCA---------------------------------------------TGACTGAGGAGCAGCTGCAGCTGCTGGTGGAGCAGATGGTGGATGGCAGTATGCGGTCTATCACCACCAAACTCTATGACGGCTTCCAGTACCTCACCAACGGCATCATGTGA \n+s rheMac1.SCAFFOLD90935 33761 182 - 50918 GTTCTCAGCTT---------CCTTGCTTCCATGGCTCCAGCACCATTCGAAACCTCAAAGAGAGGTTCCACATGAGCA---------------------------------------------TGACTGAGGAGCAGCTGCAGCTGCTGGTGGAGCAGATGGTGGATGGCAGTATGCGGTCTATCACCACCAAACTCTATGACGGCTTCCAGTACCTCACCAACGGCATCATGTGA \n+s marmoset.ENr231_1 544638 182 - 772620 GTTCTCAGCTT---------CCTTGCTTCCATGGTTCCAGCACCATTCGAAACCTCAAAGAGAGGTTCCACATGAGCA---------------------------------------------TGACTGAGGAGCAGCTGCAGCTGCTGGTGGAGCAGATGGTGGATGGCAGTATGCGCTCTATCACCACCAAACTCTATGACGGCTTCCAGTACCTCACCAACGGCATCATGTGA \n+s galago.ENr231_1 619780 182 - 825110 GTTCTCAGCTT---------CCTTGCTTCCATGGCTCCAGCACCATTCGCAACCTCAAAGAGAGGTTCCACATGA'..b' 875680 17 - 160775580 TCGAAACCTGAA-----GCCCC \n+s mm6.chrX 95133465 11 - 163688980 TC------TGAC-----GCCCC \n+s rabbit.ENm006_53 67667 16 + 95848 -CGCAGCCAAAA-----GCAGA \n+s canFam1.chrX 2101902 17 - 126913094 cTGCAGCCTGAA-----GCCTC \n+s rfbat.ENm006_1 953313 17 - 1015308 CCGCAGCCCAAA-----GCCTC \n+s shrew.ENm006_28 13093 17 - 17919 CCGCAGCCCAAA-----GCTTC \n+s armadillo.ENm006_1 624067 17 - 637865 CCGCAGCCCACA-----GCCTC \n+s monDom1.scaffold_4966 7679 17 - 16700 CTGCCGCCCACA-----GCTGG \n+s platypus.ENm006_33 1989 17 + 24358 CCCAGGCAAAAA-----GGGTT \n+s xenTro1.scaffold_101 953965 22 + 2407444 CGGGAACTTAAACAAGTGACAC \n+\n+a score=49886.0\n+s hg17.chrX 2130082 23 - 154824264 ACCACCTCTCCCA--GTCCTGGGCC \n+s panTro1.chrX 2163208 23 - 160174553 ACCACCTCTCCCA--GTCCTGGGCC \n+s baboon.ENm006_1 737840 23 - 802484 GCCACCTCTCCCA--GCCCTGGGCC \n+s marmoset.ENm006_1 629796 23 - 677071 GTCACCTCTCCCA--GCCCTGGGTC \n+s galago.ENm006_1 899441 23 - 952237 GCCACCTCCCCCA--GCCCAGGGTC \n+s rn3.chrX 875657 23 - 160775580 ACAGCCTCCCCCA--GTCTAGGAAC \n+s mm6.chrX 95133442 23 - 163688980 ACAGCCTCCCCGA--GTCTAGGAAC \n+s rabbit.ENm006_53 67644 23 + 95848 GCCCCCCTTGTCG--GCCCTTGGGC \n+s canFam1.chrX 2101879 23 - 126913094 accggctcccccg--gccccgggcc \n+s rfbat.ENm006_1 953290 23 - 1015308 CCCGGCTCCCCCA--GCCCTGGGTC \n+s shrew.ENm006_28 13070 23 - 17919 AGCGATGCTCCTG--GCACCGGGCC \n+s armadillo.ENm006_1 624044 23 - 637865 CCCAGCTCCCCCA--GCCCCGGGCC \n+s monDom1.scaffold_4966 7656 23 - 16700 --GAGCTCCCCTGAGGCCTCCTGCT \n+s platypus.ENm006_33 1966 23 + 24358 CCAGAGTCACCCC--AACCTGGAGC \n+s xenTro1.scaffold_101 953938 23 + 2407444 GTGGACCCTGGTA--AAGCAGGAAA \n+\n+a score=406800.0\n+s hg17.chrX 2130001 81 - 154824264 GCTGTGGCACAGAACATGGACTCTGTGTTTAAGGAGCTCTTGGGAAAGACCTCTGTCCGCCA--------GGGCCTTGGGC-----------CAGCATCT \n+s panTro1.chrX 2163127 81 - 160174553 GCTGTGGCACAGAACATGGACTCTGTGTTTAAGGAGCTCTTGGGAAAGACCTCTGTCCGCCA--------GGGCCTTGGGC-----------CAGCATCT \n+s baboon.ENm006_1 737759 81 - 802484 GCCGTGGCACAGAACATGGACTCTGTGTTTAAGGAGCTCTTGGGAAAGACCTCTGTCCGCCA--------GGGCCTCGGGC-----------CAGCATCT \n+s marmoset.ENm006_1 629715 81 - 677071 GCTGTGGCGCAGAACATGGGCTCTGTGTTTAAGGAGCTCTTGGGAAAGGCCTCCGCCCGCCA--------GGGCCTTGGGC-----------CAGCACCT \n+s galago.ENm006_1 899360 81 - 952237 GCTGTGGCGCAGAACATGGACTCCGTGTTTCAGGAGCTCTTGGGAAAGACGGCTATTCGCCA--------GGGCCTCAGGC-----------CAGTGTCT \n+s rn3.chrX 875576 81 - 160775580 GCTGTGGCGCAGAACATGGATTCTGTGTTTAAGGAGCTCTTGGGAAAGGCTGCTGTCCGCCA--------GGGCCATGGGC-----------TAGCATCT \n+s mm6.chrX 95133361 81 - 163688980 GCTGTGGCACAGAACATGAATTCTGTGTTTAAGGAGCTCTTGGGAAAGACTGCTGTCCGCCA--------GGGCCATGGGT-----------TAGCATCT \n+s canFam1.chrX 2101798 81 - 126913094 GCTGTGGCACAGACCATGGATTCCGTGTTTAAGGAGCTCCTGGGAAAGACCTccgcccgcca--------gggcgcggggc-----------ccgcgtcc \n+s rfbat.ENm006_1 953209 81 - 1015308 GCTGTGGCACAGACTATGGATTCGGTCTTTAAGGAGCTCTTGGGAAAGACCGCTGTCCGCCA--------GGGCCTCGGGC-----------CAGCGTCC \n+s shrew.ENm006_28 12998 72 - 17919 GCCGTGGCCCAGACCATGGGCTCCGTGTTCAAGGAGCTCTTGGGGAAGACC---GCCCGCCA--------GGGTCTTGGGC-----------CC------ \n+s armadillo.ENm006_1 623963 81 - 637865 GCCGTGGCGCAGACCATGGACTCCGTGTTTAAGGAGCTCTTGGGGAAGACGGCTGGCCGCCA--------GGGCCTGGGGC-----------CAGCGTCC \n+s monDom1.scaffold_4966 7567 89 - 16700 AGCGTGGCCCAGAAGATGGAATCTGTCTTTAAGGAGCTCTTGGGGAAGGCCCATACCAGGCACCTGCCGAAGACCTCAGAG-----------ATACTTTT \n+s platypus.ENm006_33 1876 90 + 24358 GACATCACCAAGACCATGAACTACGTGTTTAAGGAGCTTATGGAGAAGACCA--GCCTGCGG--------CAAACTGGGGCGGATGATCCCCCGGCCTCT \n+s xenTro1.scaffold_101 953857 81 + 2407444 AATGTGACAAAGAACATGGACAGCGTGTTCAAAGAGCTGCTTGGAAAAACTGCTCTAAAGCA--------GGTGCATTTGG-----------AAGATCCT \n+\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/gene_bed_maf_to_fasta_out.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/gene_bed_maf_to_fasta_out.fasta Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,11 @@
+>hg17.BC028629
+ATGATAATCACACAAACAAGTCACTGTTACATGACCAGCCTTGGGATTCTTTTCCTGATTAATATTCTCCCTGGAACCACTGGTCAAGGGGAATCAAGACGACAAGAACCCGGGGACTTTGTGAAGCAGGACATTGGCGGGCTGTCTCCTAAGCATGCCCCAGATATTCCTGATGACAGCACTGACAACATCACTATCTTCACCAGAATCTTGGATCGTCTTCTGGACGGCTATGACAACCGGCTGCGACCTGGGCTTGGAGATGCAGTGACTGAAGTGAAGACTGACATCTACGTGACCAGTTTTGGCCCTGTGTCAGACACTGACATGGAGTACACTATTGATGTATTTTTTCGGCAGACATGGCATGATGAAAGACTGAAATTTGATGGCCCCATGAAGATCCTTCCACTGAACAATCTCCTGGCTAGTAAGATCTGGACACCGGACACCTTCTTCCACAATGGCAAGAAATCAGTGGCTCATAACATGACCACGCCCAACAAGCTGCTCAGATTGGTGGACAACGGAACCCTCCTCTATACAATGAGGTTAACAATTCATGCTGAGTGTCCCATGCATTTGGAAGATTTTCCCATGGATGTGCATGCCTGCCCACTGAAGTTTGGAAGCTATGCCTATACAACAGCTGAAGTGGTTTATTCTTGGACTCTCGGAAAGAACAAATCCGTGGAAGTGGCACAGGATGGTTCTCGCTTGAACCAGTATGACCTTTTGGGCCATGTTGTTGGGACAGAGATAATCCGGTCTAGTACAGGAGAATATGTCGTCATGACAACCCACTTCCATCTCAAGCGAAAAATTGGCTACTTTGTGATCCAGACCTACTTGCCATGTATCATGACTGTCATTCTGTCACAAGTGTCGTTCTGGCTCAACAGAGAGTCTGTTCCTGCCCGTACAGTCTTTGGTGTCACCACTGTGCTTACCATGACCACCTTGAGTATCAGTGCCAGAAATTCCTTACCTAAAGTGGCATATGCGACGGCCATGGACTGGTTCATAGCCGTCTGTTATGCCTTTGTATTTTCTGCACTGATTGAATTTGCCACTGTCAACTATTTCACCAAGCGGAGTTGGGCTTGGGAAGGCAAGAAGGTGCCAGAGGCCCTGGAGATGAAGAAGAAAACACCAGCAGCCCCAGCAAAGAAAACCAGCACTACCTTCAACATCGTGGGGACCACCTATCCCATCAACCTGGCCAAGGACACTGAATTTTCCACCATCTCCAAGGGCGCTGCTCCCAGTGCCTCCTCAACCCCAACAATCATTGCTTCACCCAAGGCCACCTACGTGCAGGACAGCCCGACTGAGACCAAGACCTACAACAGTGTCAGCAAGGTTGACAAAATTTCCCGCATCATCTTTCCTGTGCTCTTTGCCATATTCAATCTGGTCTATTGGGCCACATATGTCAACCGGGAGTCAGCTATCAAGGGCATGATCCGCAAACAGTAG
+>canFam1.BC028629
+ATGATAGTCACACAAATGAGTCACTTCTACACAATCATCCTTGGGCTTCTTTTCCTGATTAATATTTTTCCTGGAACAACTGGCCAAGGGGAATCAAGACGACAAGAACCTGGGGATTTTGTGAAGCAGGATATTGGCGGACTCTCTCCTAAGCATGCCCCAGATATTCCTGATGACAGCACTGACAACATCACTATATTCACCAGAATCTTAGATCGTCTTCTGGATGGCTATGACAACCGACTACGACCTGGGCTTGGAGATGCGGTGACTGAAGTGAAGACTGATATCTATGTGACCAGTTTTGGCCCCGTGTCAGACACTGACATGGAGTACACCATTGATGTATTTTTTCGACAGACATGGCATGATGAAAGACTAAAATTTGATGGACCCATGAAGATTCTTCCACTGAACAATCTCCTGGCTAGTAAGATCTGGACCCCTGACACCTTCTTTCATAATGGCAAGAAATCAGTAGCCCATAACATGACCACACCTAACAAGCTGCTCAGACTGGTGGACAATGGAACCCTCCTCTACACAATGAGGTTAACAATTCATGCTGAGTGCCCCATGCATTTGGAAGATTTTCCTATGGATGTACATGCCTGCCCACTGAAGTTTGGAAGCTATGCCTATACAACAGCTGAAGTGGTTTATTCCTGGACTCTTGGGAAGAACAAATCTGTGGAAGTAGCGCAGGACGGCTCCCGCCTGAATCAGTATGACCTGCTGGGCCATGTTGTTGGGACAGAGATAATCCGGTCTAGTACAGGAGAATATGTCGTCATGACAACCCACTTTCATCTCAAACGAAAAATTGGCTACTTTGTGATCCAGACTTACTTGCCATGTATCATGACTGTCATTCTGTCACAAGTGTCTTTCTGGCTCAACAGAGAATCTGTCCCTGCCCGCACGGTCTTTGGTGTCACCACTGTTCTCACCATGACCACTTTGAGTATCAGTGCCAGAAACTCCTTACCTAAAGTGGCATACGCGACGGCCATGGATTGGTTCATAGCCGTCTGTTATGCCTTTGTATTTTCTGCGCTGATTGAATTTGCCACTGTTAACTACTTCACCAAGCGGAGTTGGGCTTGGGAAGGCAAGAAGGTGCCGGAGGCCCTGGAGATGAAGAAGAAAACACCAGCAGCCCCAACAAAGAAAACCAGCACCACCTTCAACATCGTGGGAACCACCTATCCCATCAATCTGGCCAAGGACACTGAGTTCTCTACCATCTCCAAGGGCGCTGCTCCCAGTGCCTCCTCAACCCCAACAATTATTGCTTCACCCAAGACCACCTACGTGCAGGACATCCCGACTGAGACCAAGACCTACAACAGTGTCAGCAAGGTTGACAAAATTTCCCGCATCATCTTTCCTGTGCTTTTTGCCATTTTTAATCTGGTCTACTGGGCCACCTATGTCAACCGGGAGTCAGCTATCAAGGGCATGATCCGCAAACACTAG
+>mm5.BC028629
+ATGATAATCACACAAATGTGGCACTTTTATGTGACCAGAGTTGTACTTCTTCTCCTGATTAGTATTCTCCCTGGAACCACTAGCCAAGGGGAATCAAGACGACAAGAACCTGGGGACTTTGTGAAACAAGATATTGGAGGACTCTCTCCCAAGCATGCCCCAGATATTCCTGACGATAGTACAGATAATATCACTATCTTCACTAGAATCTTGGATCGGCTTTTGGATGGCTATGATAACCGGCTTCGACCTGGACTTGGAGATGCAGTGACTGAAGTGAAGACAGACATCTATGTGACCAGTTTTGGCCCTGTGTCAGACACTGATATGGAATATACTATTGATGTATTTTTTAGACAGACATGGCATGATGAAAGACTGAAATTTGATGGACCAATGAAGATCCTTCCACTGAACAATCTTCTGGCTAGTAAGATATGGACTCCTGATACCTTCTTCCACAATGGTAAAAAATCAGTGGCTCACAATATGACCACACCCAACAAGCTGCTCAGACTGGTAGATAATGGGACCCTCCTCTATACAATGAGGTTAACAATACACGCTGAATGCCCCATGCATTTGGAAGATTTCCCCATGGATGTGCATGCCTGCCCACTGAAGTTTGGAAGCTATGCCTATACCAAAGCTGAAGTAATTTATTCTTGGACTCTTGGGAAGAACAAATCTGTGGAAGTAGCACAGGATGGCTCACGCCTGAATCAGTATGACTTGCTTGGCCATGTTGTTGGGACAGAGATAATCCGGTCTAGTACAGGAGAATATGTCGTCATGACAACCCACTTTCATCTGAAGAGAAAAATTGGCTACTTTGTCATCCAGACCTACTTGCCATGTATCATGACTGTCATTCTGTCACAAGTGTCTTTCTGGCTTAATAGAGAATCTGTCCCTGCCCGCACAGTCTTTGGTGTCACCACTGTTCTCACCATGACCACCTTGAGTATCAGTGCCAGAAACTCTTTACCTAAAGTGGCATACGCGACGGCCATGGACTGGTTCATAGCCGTCTGTTATGCCTTTGTATTTTCTGCACTGATTGAATTTGCTACTGTCAACTACTTCACCAAGCGGAGTTGGGCTTGGGAAGGCAAGAAGGTACCAGAGGCCCTGGAGATGAAGAAGAAAACACCAGCAGCTCCAACAAAGAAAA---ACACCACCTTCAACATAGTGGGTACCACCTATCCTATCAATCTGGCCAAGGATACTGAGTTCTCCACCATCTCCAAGGCTGCTGCTCCCAGTGCTTCTTCAACTCCAACAGCGATTGCTTCACCCAAGGCTACTTATGTGCAAGACAGTCCTGCTGAGACCAAGACCTACAACAGTGTCAGCAAGGTTGACAAAATTTCCCGCATCATCTTCCCTGTGCTCTTTGCCATATTCAATCTTGTCTATTGGGCTACATATGTGAACCGGGAATCAGCTATCAAGGGCATGATCCGCAAACAGTAG
+>panTro1.BC028629
+ATGATAATCACACAAACGAGTCACTGTTACATGACCAGCCTTGGGATTCTTTTCCTGATTAATATTCTCCCTGGAACCACTGGTCAAGGGGAATCAAGACGACAAGAACCTGGGGACTTTGTGAAGCAGGACATTGGCGGGCTGTCTCCTAAGCATGCCCCAGATATTCCTGATGACAGCACTGACAACATCACTATCTTCACCAGAATCTTGGATCGTCTTCTGGACGGCTATGACAACCGGCTGCGACCTGGGCTTGGAG--------------------------------------------------------------------GAGTACACTATTGATGTATTTTTTCGGCAGACATGGCATGATGAAAGACTGAAATTTGATGGCCCCATGAAGATCCTTCCACTGAACAATCTCCTGGCTAGTAAGATCTGGACACCTGACACCTTCTTCCACAATGGCAAGAAATCGGTGGCTCATAACATGACCACGCCCAACAAGCTGCTCAGATTGGTGGACAACGGAACCCTCCTCTATACAATGAGGTTAACAATTCATGCTGAGTGTCCCATGCATTTGGAAGATTTTCCCATGGATGTGCATGCCTGCCCACTGAAGTTTGGAAGCTATGCCTATACAACAGCTGAAGTGGTTTATTCTTGGACTCTCGGAAAGAACAAATCCGTGGAAGTGGCACAGGATGGTTCTCGCTTGAACCAGTATGACCTTTTGGGCCATGTTGTTGGGACAGAGATAATCCGGTCTAGTACAGGAGAATATGTCGTCATGACAACCCACTTCCATCTCAAGCGAAAAATTGGCTACTTTGTGATCCAGACCTACTTGCCATGTATCATGACTGTCATTCTGTCACAAGTGTCGTTCTGGCTCAACAGAGAGTCTGTTCCTGCCCGTACAGTCTTTGGTGTCACCACTGTGCTTACCATGACCACCTTGAGTATCAGTGCCAGAAATTCCTTACCTAAAGTGGCATATGCGACGGCCATGGACTGGTTCATAGCCGTCTGTTATGCCTTTGTATTTTCTGCACTGATTGAATTTGCCACTGTCAACTATTTCACCAAGCGGAGTTGGGCTTGGGAAGGCAAGAAGGTGCCAGAGGCCCTGGAGATGAAG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>rn3.BC028629
+ATGATAACCACACAAATGTGGCACTTCTATGTGACCAGAGTTGGACTTCTTCTTCTGATTAGTATTCTACCTGGAACCACTGGCCAAGGGGAGTCAAGACGACAAGAACCTGGGGACTTTGTGAAGCAAGATATTGGAGGCCTCTCTCCCAAGCATGCCCCAGATATTCCTGACGATAGTACAGATAACATCACTATCTTCACTAGAATCTTGGATCGGCTTCTGGATGGCTATGACAACCGACTGCGACCTGGGCTTGGAGATGCAGTGACTGAAGTGAAGACAGATATCTATGTGACCAGTTTTGGCCCTGTGTCAGACACTGATATGGAATATACTATTGATGTGTTTTTTAGACAGACATGGCATGATGAAAGACTGAAATTTGATGGACCAATGAAGATCCTTCCACTGAATAATCTTCTGGCTAGTAAGATATGGACTCCAGATACCTTCTTCCACAACGGTAAAAAATCAGTGGCTCACAATATGACCACACCCAACAAGCTGCTCAGACTGGTAGACAATGGGACCCTCCTCTATACAATGAGGTTAACAATACATGCTGAATGCCCTATGCATTTAGAAGATTTCCCCATGGATGTGCATGCCTGTCCACTGAAGTTTGGAAGCTATGCCTATACCAAAGCTGAAGTAATTTATTCTTGGACTCTTGGGAAGAACAAATCTGTGGAAGTAGCTCAGGATGGCTCACGCCTGAATCAGTATGACTTGCTTGGTCATGTTGTTGGGACAGAGATAATCCGGTCTAGTACAGGAGAATATGTCGTCATGACAACCCACTTTCATCTGAAGAGAAAAATTGGCTACTTTGTCATCCAGACCTACTTGCCATGTATCATGACTGTCATTCTGTCACAAGTTTCTTTCTGGCTTAATAGAGAATCTGTCCCTGCTCGCACAGTCTTTGGTGTCACCACTGTTCTCACCATGACCACCTTGAGTATCAGTGCCAGAAACTCTTTACCTAAAGTGGCATACGCGACGGCCATGGACTGGTTCATAGCCGTCTGTTATGCCTTTGTATTTTCTGCACTGATTGAATTTGCTACTGTCAACTACTTCACCAAGCGAAGTTGGGCTTGGGAAGGCAAGAAGGTACCAGAGGCCCTGGAGATGAAG----------------------------------------------------------CCAACTACGCCCCGAATCTTTCCAAAGATCCTGTCCTCTCTACCATTTCCAAAAGTGCAACT---------------ACTCCAGAACCAA-------ACAAGAAGCCAG--------AGAACAAGCCAGCCGAAGCCAAGACTTTCAACAGTGTCAGCAAAATCGACAGAATGTCTAGAATAGTGTTCCCGGTTCTGTTTGGTACTTTTAATTTAGTTTACTGGGCTACGTATTTAAACCGGGAGCCTG-TATTAGGGG-------------------
+

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/gene_bed_maf_to_fasta_user_out.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/gene_bed_maf_to_fasta_user_out.fasta Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,5 @@
+>hg17.BC028629
+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>panTro1.BC028629
+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/gff2bed_in2.gff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/gff2bed_in2.gff Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,13 @@
+chr1 Cufflinks exon 3204563 3207049 1000 - . gene_id "Xkr4"; transcript_id "Xkr4"; exon_number "1"; FPKM "0.3924207844"; frac "1.000000"; conf_lo "0.000000"; conf_hi "0.845549"; cov "0.022289";
+chr1 Cufflinks exon 3411783 3411982 1000 - . gene_id "Xkr4"; transcript_id "Xkr4"; exon_number "2"; FPKM "0.3924207844"; frac "1.000000"; conf_lo "0.000000"; conf_hi "0.845549"; cov "0.022289";
+chr1 Cufflinks exon 3660633 3661579 1000 - . gene_id "Xkr4"; transcript_id "Xkr4"; exon_number "3"; FPKM "0.3924207844"; frac "1.000000"; conf_lo "0.000000"; conf_hi "0.845549"; cov "0.022289";
+chr1 Cufflinks exon 4481009 4482749 1000 - . gene_id "Sox17"; transcript_id "Sox17"; exon_number "1"; FPKM "1.5186976896"; frac "1.000000"; conf_lo "0.558189"; conf_hi "2.479206"; cov "0.086262";
+chr1 Cufflinks exon 4483181 4483547 1000 - . gene_id "Sox17"; transcript_id "Sox17"; exon_number "2"; FPKM "1.5186976896"; frac "1.000000"; conf_lo "0.558189"; conf_hi "2.479206"; cov "0.086262";
+chr1 Cufflinks exon 4483853 4483944 1000 - . gene_id "Sox17"; transcript_id "Sox17"; exon_number "3"; FPKM "1.5186976896"; frac "1.000000"; conf_lo "0.558189"; conf_hi "2.479206"; cov "0.086262";
+chr1 Cufflinks exon 4485217 4486023 1000 - . gene_id "Sox17"; transcript_id "Sox17"; exon_number "4"; FPKM "1.5186976896"; frac "1.000000"; conf_lo "0.558189"; conf_hi "2.479206"; cov "0.086262";
+chr1 Cufflinks exon 4486372 4486494 1000 - . gene_id "Sox17"; transcript_id "Sox17"; exon_number "5"; FPKM "1.5186976896"; frac "1.000000"; conf_lo "0.558189"; conf_hi "2.479206"; cov "0.086262";
+chr1 Cufflinks exon 4763279 4766882 1000 - . gene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "1"; FPKM "9.1596238357"; frac "1.000000"; conf_lo "7.124003"; conf_hi "11.195245"; cov "0.520266";
+chr1 Cufflinks exon 4767606 4767729 1000 - . gene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "2"; FPKM "9.1596238357"; frac "1.000000"; conf_lo "7.124003"; conf_hi "11.195245"; cov "0.520266";
+chr1 Cufflinks exon 4772649 4772814 1000 - . gene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "3"; FPKM "9.1596238357"; frac "1.000000"; conf_lo "7.124003"; conf_hi "11.195245"; cov "0.520266";
+chr1 Cufflinks exon 4774032 4774186 1000 - . gene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "4"; FPKM "9.1596238357"; frac "1.000000"; conf_lo "7.124003"; conf_hi "11.195245"; cov "0.520266";
+chr1 Cufflinks exon 4775654 4775807 1000 - . gene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "5"; FPKM "9.1596238357"; frac "1.000000"; conf_lo "7.124003"; conf_hi "11.195245"; cov "0.520266";

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/gff2bed_out.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/gff2bed_out.bed Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,20 @@
+chr1 148325915 148325975 CCDS1000.1_cds_0_0_chr1_148325916_f 0 +
+chr2 118288583 118288668 CCDS2120.1_cds_0_0_chr2_118288584_f 0 +
+chr5 56241229 56241327 CCDS3972.1_cds_0_0_chr5_56241230_f 0 +
+chr6 41411592 41411644 CCDS4855.1_cds_0_0_chr6_41411593_f 0 +
+chr7 26907298 26907654 CCDS5401.1_cds_0_0_chr7_26907299_r 0 +
+chr8 118881131 118881317 CCDS6324.1_cds_0_0_chr8_118881132_r 0 +
+chr9 128764156 128764189 CCDS6914.1_cds_0_0_chr9_128764157_f 0 +
+chr10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 +
+chr11 1731308 1731476 CCDS7725.1_cds_0_0_chr11_1731309_r 0 +
+chr12 38440094 38440321 CCDS8736.1_cds_0_0_chr12_38440095_r 0 +
+chr13 112381694 112381953 CCDS9526.1_cds_0_0_chr13_112381695_f 0 +
+chr14 98710240 98712285 CCDS9949.1_cds_0_0_chr14_98710241_r 0 +
+chr15 41486872 41487060 CCDS10096.1_cds_0_0_chr15_41486873_r 0 +
+chr16 37429 37557 CCDS10395.1_cds_0_0_chr16_37430_r 0 +
+chr18 23786114 23786321 CCDS11891.1_cds_0_0_chr18_23786115_r 0 +
+chr19 59068595 59069564 CCDS12866.1_cds_0_0_chr19_59068596_f 0 +
+chr20 33330413 33330423 CCDS13249.1_cds_0_0_chr20_33330414_r 0 +
+chr21 32707032 32707192 CCDS13614.1_cds_0_0_chr21_32707033_f 0 +
+chr22 30120223 30120265 CCDS13897.1_cds_0_0_chr22_30120224_f 0 +
+chrX 122745047 122745924 CCDS14606.1_cds_0_0_chrX_122745048_f 0 +

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/gff2bed_out2.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/gff2bed_out2.bed Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,3 @@
+chr1 3204562 3661579 Xkr4 0 - 3204562 3661579 0 3 2487,200,947 0,207220,456070
+chr1 4481008 4486494 Sox17 0 - 4481008 4486494 0 5 1741,367,92,807,123 0,2172,2844,4208,5363
+chr1 4763278 4775807 Mrpl15 0 - 4763278 4775807 0 5 3604,124,166,155,154 0,4327,9370,10753,12375

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/gff2bed_out3.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/gff2bed_out3.bed Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,145 @@
+ctgA 22131 24633 my_feature 0 +
+ctgA 46989 48410 my_feature 0 -
+ctgA 44704 47713 my_feature 0 -
+ctgA 36648 40440 my_feature 0 -
+ctgA 23071 23185 my_feature 0 +
+ctgA 37241 38653 my_feature 0 +
+ctgA 37496 40559 motif 0 -
+ctgA 36033 38167 my_feature 0 +
+ctgA 28331 30033 motif 0 -
+ctgA 4714 5968 my_feature 0 -
+ctgA 48252 48366 motif 0 +
+ctgA 999 20000 BAC 0 +
+ctgA 19499 20000 right_end_read 0 -
+ctgA 999 1500 left_end_read 0 +
+ctgA 13800 14007 motif 0 -
+ctgA 1049 9000 coding 0 +
+ctgA 1200 1500 CDS 0 +
+ctgA 2999 3902 CDS 0 +
+ctgA 4999 5500 CDS 0 +
+ctgA 6999 7608 CDS 0 +
+ctgA 1049 9000 processed_transcript 0 +
+ctgA 1049 1200 5'-UTR 0 +
+ctgA 7608 9000 3'-UTR 0 +
+ctgA 5409 7503 match 0 -
+ctgA 6999 7503 HSP 0 -
+ctgA 5409 5500 HSP 0 -
+ctgA 46011 48851 motif 0 +
+ctgA 6884 8999 match 0 -
+ctgA 8305 8999 HSP 0 -
+ctgA 8054 8080 HSP 0 -
+ctgA 7409 7737 HSP 0 -
+ctgA 6884 7241 HSP 0 -
+ctgA 13279 16394 my_feature 0 +
+ctgA 29770 32937 match 0 +
+ctgA 29770 29942 HSP 0 +
+ctgA 30041 30340 HSP 0 +
+ctgA 30809 31307 HSP 0 +
+ctgA 31760 31984 HSP 0 +
+ctgA 32373 32937 HSP 0 +
+ctgA 36615 37227 match 0 -
+ctgA 37207 37227 HSP 0 -
+ctgA 36615 37057 HSP 0 -
+ctgA 11910 15561 motif 0 +
+ctgA 1049 3202 match 0 +
+ctgA 1049 1500 HSP 0 +
+ctgA 2999 3202 HSP 0 +
+ctgA 15395 16159 motif 0 +
+ctgA 1149 7200 match 0 +
+ctgA 1149 1500 HSP 0 +
+ctgA 4999 5500 HSP 0 +
+ctgA 6999 7200 HSP 0 +
+ctgA 1049 7300 match 0 +
+ctgA 1049 1500 HSP 0 +
+ctgA 4999 5500 HSP 0 +
+ctgA 6999 7300 HSP 0 +
+ctgA 19156 22915 my_feature 0 -
+ctgA 7999 9000 match 0 -
+ctgA 7999 9000 HSP 0 -
+ctgA 28341 28447 motif 0 -
+ctgA 17666 17690 motif 0 +
+ctgA 44400 45925 trace 0 +
+ctgA 26121 34466 match 0 +
+ctgA 26121 26126 HSP 0 +
+ctgA 26496 26869 HSP 0 +
+ctgA 27200 27325 HSP 0 +
+ctgA 27371 27433 HSP 0 +
+ctgA 27564 27565 HSP 0 +
+ctgA 27812 28091 HSP 0 +
+ctgA 28092 28201 HSP 0 +
+ctgA 28328 28377 HSP 0 +
+ctgA 28828 29194 HSP 0 +
+ctgA 29516 29702 HSP 0 +
+ctgA 29712 30061 HSP 0 +
+ctgA 30328 30774 HSP 0 +
+ctgA 30807 31306 HSP 0 +
+ctgA 31515 31729 HSP 0 +
+ctgA 31752 32154 HSP 0 +
+ctgA 32594 32696 HSP 0 +
+ctgA 32891 32901 HSP 0 +
+ctgA 33126 33388 HSP 0 +
+ctgA 33438 33443 HSP 0 +
+ctgA 33758 34209 HSP 0 +
+ctgA 34400 34466 HSP 0 +
+ctgA 0 50000 contig 0 +
+ctgA 41136 47829 match 0 -
+ctgA 47448 47829 HSP 0 -
+ctgA 46815 46992 HSP 0 -
+ctgA 46091 46318 HSP 0 -
+ctgA 45789 46022 HSP 0 -
+ctgA 45230 45488 HSP 0 -
+ctgA 44762 45030 HSP 0 -
+ctgA 44064 44556 HSP 0 -
+ctgA 43394 43811 HSP 0 -
+ctgA 42889 43270 HSP 0 -
+ctgA 42056 42474 HSP 0 -
+ctgA 41753 41948 HSP 0 -
+ctgA 41136 41318 HSP 0 -
+ctgA 12530 15870 match 0 +
+ctgA 12530 12895 HSP 0 +
+ctgA 13121 13449 HSP 0 +
+ctgA 13451 13745 HSP 0 +
+ctgA 13907 13965 HSP 0 +
+ctgA 13997 14488 HSP 0 +
+ctgA 14563 14899 HSP 0 +
+ctgA 15184 15276 HSP 0 +
+ctgA 15638 15736 HSP 0 +
+ctgA 15744 15870 HSP 0 +
+ctgA 7499 8000 match 0 -
+ctgA 7499 8000 HSP 0 -
+ctgA 1299 9000 coding 0 +
+ctgA 3300 3902 CDS 0 +
+ctgA 4999 5500 CDS 0 +
+ctgA 6999 7600 CDS 0 +
+ctgA 1299 9000 processed_transcript 0 +
+ctgA 1299 1500 5'-UTR 0 +
+ctgA 2999 3300 5'-UTR 0 +
+ctgA 7600 9000 3'-UTR 0 +
+ctgA 26502 35904 match 0 -
+ctgA 35641 35904 HSP 0 -
+ctgA 35332 35507 HSP 0 -
+ctgA 34604 34983 HSP 0 -
+ctgA 34243 34313 HSP 0 -
+ctgA 33437 33868 HSP 0 -
+ctgA 33052 33325 HSP 0 -
+ctgA 32207 32680 HSP 0 -
+ctgA 32009 32057 HSP 0 -
+ctgA 31420 31817 HSP 0 -
+ctgA 31231 31236 HSP 0 -
+ctgA 30464 30798 HSP 0 -
+ctgA 30107 30216 HSP 0 -
+ctgA 29512 29647 HSP 0 -
+ctgA 28776 29058 HSP 0 -
+ctgA 28224 28316 HSP 0 -
+ctgA 27886 28076 HSP 0 -
+ctgA 27447 27860 HSP 0 -
+ctgA 27171 27185 HSP 0 -
+ctgA 26502 26799 HSP 0 -
+ctgA 49405 50000 match 0 +
+ctgA 49405 49476 HSP 0 +
+ctgA 49761 50000 HSP 0 +
+ctgA 1049 9000 gene 0 +
+ctgA 33324 35791 motif 0 +
+ctgA 31784 32359 match 0 +
+ctgA 31784 31939 HSP 0 +
+ctgA 32328 32359 HSP 0 +

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/gff_filter_attr_in1.gff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/gff_filter_attr_in1.gff Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,200 @@\n+chr1\tCufflinks\texon\t21199802\t21199861\t1000\t+\t.\tgene_id "CUFF.1383"; transcript_id "CUFF.1383.1"; exon_number "1"; FPKM "5.0037092300"; frac "1.000000"; conf_lo "0.000000"; conf_hi "15.011128"; cov "0.284211";\n+chr1\tCufflinks\ttranscript\t55716264\t55716295\t1000\t.\t.\tgene_id "CUFF.5021"; transcript_id "CUFF.5021.1"; FPKM "29.7095235531"; frac "1.000000"; conf_lo "0.000000"; conf_hi "71.725135"; cov "1.687500";\n+chr1\tCufflinks\ttranscript\t74904128\t74904154\t1000\t.\t.\tgene_id "CUFF.7563"; transcript_id "CUFF.7563.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";\n+chr1\tCufflinks\texon\t134487086\t134487123\t1000\t.\t.\tgene_id "CUFF.11837"; transcript_id "CUFF.11837.1"; exon_number "1"; FPKM "25.0185461500"; frac "1.000000"; conf_lo "0.000000"; conf_hi "60.400113"; cov "1.421053";\n+chr1\tCufflinks\texon\t136200923\t136200959\t1000\t.\t.\tgene_id "CUFF.12099"; transcript_id "CUFF.12099.1"; exon_number "1"; FPKM "38.5420846095"; frac "1.000000"; conf_lo "0.000000"; conf_hi "83.046650"; cov "2.189189";\n+chr1\tCufflinks\ttranscript\t138116837\t138116866\t1000\t.\t.\tgene_id "CUFF.12557"; transcript_id "CUFF.12557.1"; FPKM "31.6901584567"; frac "1.000000"; conf_lo "0.000000"; conf_hi "76.506810"; cov "1.800000";\n+chr1\tCufflinks\texon\t152240694\t152240779\t1000\t.\t.\tgene_id "CUFF.13107"; transcript_id "CUFF.13107.1"; exon_number "1"; FPKM "16.5820596576"; frac "1.000000"; conf_lo "0.000000"; conf_hi "35.729373"; cov "0.941860";\n+chr1\tCufflinks\texon\t157633998\t157634024\t1000\t.\t.\tgene_id "CUFF.13967"; transcript_id "CUFF.13967.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";\n+chr1\tCufflinks\texon\t167704819\t167704854\t1000\t.\t.\tgene_id "CUFF.15347"; transcript_id "CUFF.15347.1"; exon_number "1"; FPKM "26.4084653806"; frac "1.000000"; conf_lo "0.000000"; conf_hi "63.755675"; cov "1.500000";\n+chr1\tCufflinks\ttranscript\t184245403\t184245429\t1000\t.\t.\tgene_id "CUFF.17679"; transcript_id "CUFF.17679.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";\n+chr10\tCufflinks\texon\t12731734\t12731826\t1000\t.\t.\tgene_id "CUFF.19287"; transcript_id "CUFF.19287.1"; exon_number "1"; FPKM "10.2226317602"; frac "1.000000"; conf_lo "0.000000"; conf_hi "24.679616"; cov "0.580645";\n+chr10\tCufflinks\ttranscript\t42305464\t42305515\t1000\t.\t.\tgene_id "CUFF.21709"; transcript_id "CUFF.21709.1"; FPKM "18.2827837250"; frac "1.000000"; conf_lo "0.000000"; conf_hi "44.138544"; cov "1.038462";\n+chr10\tCufflinks\texon\t52431636\t52431662\t1000\t.\t.\tgene_id "CUFF.22495"; transcript_id "CUFF.22495.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";\n+chr10\tCufflinks\ttranscript\t62044837\t62045189\t1000\t.\t.\tgene_id "CUFF.23531"; transcript_id "CUFF.23531.1"; FPKM "19.5178121606"; frac "1.000000"; conf_lo "9.264456"; conf_hi "29.771168"; cov "1.108611";\n+chr10\tCufflinks\ttranscript\t75372919\t75373002\t1000\t.\t.\tgene_id "CUFF.24985"; transcript_id "CUFF.24985.1"; FPKM "124.4970510798"; frac "1.000000"; conf_lo "71.411330"; conf_hi "177.582772"; cov "7.071429";\n+chr10\tCufflinks\ttranscript\t80362428\t80363292\t1000\t-\t.\tgene_id "CUFF.26065"; transcript_id "CUFF.26065.1"; FPKM "43.6170921216"; frac "1.000000"; conf_lo "32.260169"; conf_hi "54.974016"; cov "2.477449";\n+chr10\tCufflinks\texon\t87908564\t87908597\t1000\t+\t.\tgene_id "CUFF.27209"; transcript_id "CUFF.27209.1"; exon_number "2"; FPKM "11.4913582411"; frac "1.000000"; conf_lo "0.000000"; conf_hi "30.264098"; cov "0.652709";\n+chr10\tCufflinks\texon\t89142681\t89142707\t1000\t.\t.\tgene_id "CUFF.27307"; transcript_id "CUFF.27307.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";\n+chr10\tCufflinks\texon\t93425781\t93425807\t1000\t.\t.\tgene_id "CUFF.28101"; transcript_id "CUFF.28101.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";\n+c'..b'r9\tCufflinks\texon\t25083606\t25083643\t1000\t.\t.\tgene_id "CUFF.261551"; transcript_id "CUFF.261551.1"; exon_number "1"; FPKM "25.0185461500"; frac "1.000000"; conf_lo "0.000000"; conf_hi "60.400113"; cov "1.421053";\n+chr9\tCufflinks\ttranscript\t27906894\t27906964\t1000\t.\t.\tgene_id "CUFF.261925"; transcript_id "CUFF.261925.1"; FPKM "26.7804155972"; frac "1.000000"; conf_lo "0.000000"; conf_hi "53.560831"; cov "1.521127";\n+chr9\tCufflinks\ttranscript\t34418034\t34418065\t1000\t.\t.\tgene_id "CUFF.262975"; transcript_id "CUFF.262975.1"; FPKM "29.7095235531"; frac "1.000000"; conf_lo "0.000000"; conf_hi "71.725135"; cov "1.687500";\n+chr9\tCufflinks\texon\t34710789\t34710815\t1000\t.\t.\tgene_id "CUFF.263065"; transcript_id "CUFF.263065.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";\n+chr9\tCufflinks\ttranscript\t40823051\t40823090\t1000\t.\t.\tgene_id "CUFF.263747"; transcript_id "CUFF.263747.1"; FPKM "23.7676188425"; frac "1.000000"; conf_lo "0.000000"; conf_hi "57.380108"; cov "1.350000";\n+chr9\tCufflinks\texon\t59236547\t59236671\t1000\t.\t.\tgene_id "CUFF.267045"; transcript_id "CUFF.267045.1"; exon_number "1"; FPKM "12.1905895442"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.808020"; cov "0.692425";\n+chr9\tCufflinks\ttranscript\t66418162\t66418188\t1000\t.\t.\tgene_id "CUFF.268423"; transcript_id "CUFF.268423.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";\n+chr9\tCufflinks\ttranscript\t95913236\t95913262\t1000\t.\t.\tgene_id "CUFF.270957"; transcript_id "CUFF.270957.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";\n+chr9\tCufflinks\texon\t103101949\t103102030\t1000\t.\t.\tgene_id "CUFF.271979"; transcript_id "CUFF.271979.1"; exon_number "1"; FPKM "11.5939604110"; frac "1.000000"; conf_lo "0.000000"; conf_hi "27.990296"; cov "0.658537";\n+chr9\tCufflinks\ttranscript\t105579135\t105579173\t1000\t.\t.\tgene_id "CUFF.272347"; transcript_id "CUFF.272347.1"; FPKM "24.3770449667"; frac "1.000000"; conf_lo "0.000000"; conf_hi "58.851393"; cov "1.384615";\n+chr9\tCufflinks\texon\t107445870\t107445930\t1000\t.\t.\tgene_id "CUFF.272761"; transcript_id "CUFF.272761.1"; exon_number "1"; FPKM "38.9633095779"; frac "1.000000"; conf_lo "4.113466"; conf_hi "73.813153"; cov "2.213115";\n+chr9\tCufflinks\texon\t113779194\t113779220\t1000\t.\t.\tgene_id "CUFF.274445"; transcript_id "CUFF.274445.1"; exon_number "1"; FPKM "52.8169307611"; frac "1.000000"; conf_lo "0.000000"; conf_hi "113.804669"; cov "3.000000";\n+chr9\tCufflinks\ttranscript\t120860476\t120860606\t1000\t.\t.\tgene_id "CUFF.275115"; transcript_id "CUFF.275115.1"; FPKM "25.4005086867"; frac "1.000000"; conf_lo "6.199529"; conf_hi "44.601488"; cov "1.442748";\n+chrX\tCufflinks\texon\t10274057\t10274087\t1000\t.\t.\tgene_id "CUFF.276147"; transcript_id "CUFF.276147.1"; exon_number "1"; FPKM "99.5432248142"; frac "1.000000"; conf_lo "21.405127"; conf_hi "177.681323"; cov "5.654052";\n+chrX\tCufflinks\ttranscript\t39881431\t39881678\t1000\t.\t.\tgene_id "CUFF.277419"; transcript_id "CUFF.277419.1"; FPKM "42.1683560109"; frac "1.000000"; conf_lo "24.187709"; conf_hi "60.149003"; cov "2.395161";\n+chrX\tCufflinks\ttranscript\t90114645\t90131913\t1000\t-\t.\tgene_id "CUFF.279771"; transcript_id "CUFF.279771.1"; FPKM "6.8891648819"; frac "1.000000"; conf_lo "0.000000"; conf_hi "20.667495"; cov "0.391304";\n+chrX\tCufflinks\ttranscript\t148249672\t148249713\t1000\t.\t.\tgene_id "CUFF.282847"; transcript_id "CUFF.282847.1"; FPKM "56.5895686726"; frac "1.000000"; conf_lo "5.974320"; conf_hi "107.204818"; cov "3.214286";\n+chrX\tCufflinks\ttranscript\t148481505\t148482455\t1000\t+\t.\tgene_id "CUFF.282965"; transcript_id "CUFF.282965.1"; FPKM "40.1706233958"; frac "1.000000"; conf_lo "16.978103"; conf_hi "63.363144"; cov "2.281690";\n+chrX\tCufflinks\ttranscript\t158986411\t158986471\t1000\t.\t.\tgene_id "CUFF.283831"; transcript_id "CUFF.283831.1"; FPKM "15.5853238312"; frac "1.000000"; conf_lo "0.000000"; conf_hi "37.626300"; cov "0.885246";\n\\ No newline at end of file\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/gff_filter_by_attribute_out1.gff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/gff_filter_by_attribute_out1.gff Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,46 @@\n+chr10\tCufflinks\ttranscript\t62044837\t62045189\t1000\t.\t.\tgene_id "CUFF.23531"; transcript_id "CUFF.23531.1"; FPKM "19.5178121606"; frac "1.000000"; conf_lo "9.264456"; conf_hi "29.771168"; cov "1.108611";\n+chr10\tCufflinks\ttranscript\t75372919\t75373002\t1000\t.\t.\tgene_id "CUFF.24985"; transcript_id "CUFF.24985.1"; FPKM "124.4970510798"; frac "1.000000"; conf_lo "71.411330"; conf_hi "177.582772"; cov "7.071429";\n+chr10\tCufflinks\ttranscript\t80362428\t80363292\t1000\t-\t.\tgene_id "CUFF.26065"; transcript_id "CUFF.26065.1"; FPKM "43.6170921216"; frac "1.000000"; conf_lo "32.260169"; conf_hi "54.974016"; cov "2.477449";\n+chr11\tCufflinks\ttranscript\t7904565\t7904642\t1000\t.\t.\tgene_id "CUFF.33508"; transcript_id "CUFF.33508.1"; FPKM "61.6484988869"; frac "1.000000"; conf_lo "22.882428"; conf_hi "100.414569"; cov "3.501633";\n+chr11\tCufflinks\texon\t78140156\t78140259\t1000\t.\t.\tgene_id "CUFF.43148"; transcript_id "CUFF.43148.1"; exon_number "1"; FPKM "54.8483511750"; frac "1.000000"; conf_lo "23.181641"; conf_hi "86.515061"; cov "3.115385";\n+chr11\tCufflinks\texon\t105616462\t105616737\t1000\t.\t.\tgene_id "CUFF.48385"; transcript_id "CUFF.48385.1"; exon_number "1"; FPKM "18.9452034252"; frac "1.000000"; conf_lo "7.520816"; conf_hi "30.369591"; cov "1.076087";\n+chr12\tCufflinks\texon\t30701762\t30702509\t1000\t.\t.\tgene_id "CUFF.53897"; transcript_id "CUFF.53897.1"; exon_number "1"; FPKM "48.9333329111"; frac "1.000000"; conf_lo "37.780391"; conf_hi "60.086275"; cov "2.779412";\n+chr13\tCufflinks\texon\t49159496\t49159569\t1000\t.\t.\tgene_id "CUFF.67788"; transcript_id "CUFF.67788.1"; exon_number "1"; FPKM "44.9657653777"; frac "1.000000"; conf_lo "10.974842"; conf_hi "78.956689"; cov "2.554054";\n+chr13\tCufflinks\ttranscript\t100200304\t100200330\t1000\t.\t.\tgene_id "CUFF.73108"; transcript_id "CUFF.73108.1"; FPKM "123.2395051093"; frac "1.000000"; conf_lo "30.079196"; conf_hi "216.399814"; cov "7.000000";\n+chr14\tCufflinks\ttranscript\t31949103\t31949152\t1000\t.\t.\tgene_id "CUFF.77316"; 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cov "1.080000";\n+chr7\tCufflinks\ttranscript\t85554210\t85554343\t1000\t.\t.\tgene_id "CUFF.235778"; transcript_id "CUFF.235778.1"; FPKM "17.7370289869"; frac "1.000000"; conf_lo "1.872548"; conf_hi "33.601510"; cov "1.007463";\n+chr7\tCufflinks\texon\t104055491\t104055589\t1000\t.\t.\tgene_id "CUFF.238474"; transcript_id "CUFF.238474.1"; exon_number "1"; FPKM "28.8092349606"; frac "1.000000"; conf_lo "5.286593"; conf_hi "52.331877"; cov "1.636364";\n+chr8\tCufflinks\texon\t9970398\t9970545\t1000\t.\t.\tgene_id "CUFF.245320"; transcript_id "CUFF.245320.1"; exon_number "1"; FPKM "22.4828826889"; frac "1.000000"; conf_lo "5.487421"; conf_hi "39.478345"; cov "1.277027";\n+chr9\tCufflinks\ttranscript\t20449846\t20449932\t1000\t.\t.\tgene_id "CUFF.260747"; transcript_id "CUFF.260747.1"; FPKM "234.9313045507"; frac "1.000000"; conf_lo "163.275950"; conf_hi "306.586659"; cov "13.344091";\n+chr9\tCufflinks\texon\t107445870\t107445930\t1000\t.\t.\tgene_id "CUFF.272761"; transcript_id "CUFF.272761.1"; exon_number "1"; FPKM "38.9633095779"; frac "1.000000"; conf_lo "4.113466"; conf_hi "73.813153"; cov "2.213115";\n+chr9\tCufflinks\ttranscript\t120860476\t120860606\t1000\t.\t.\tgene_id "CUFF.275115"; transcript_id "CUFF.275115.1"; FPKM "25.4005086867"; frac "1.000000"; conf_lo "6.199529"; conf_hi "44.601488"; cov "1.442748";\n+chrX\tCufflinks\texon\t10274057\t10274087\t1000\t.\t.\tgene_id "CUFF.276147"; transcript_id "CUFF.276147.1"; exon_number "1"; FPKM "99.5432248142"; frac "1.000000"; conf_lo "21.405127"; conf_hi "177.681323"; cov "5.654052";\n+chrX\tCufflinks\ttranscript\t39881431\t39881678\t1000\t.\t.\tgene_id "CUFF.277419"; transcript_id "CUFF.277419.1"; FPKM "42.1683560109"; frac "1.000000"; conf_lo "24.187709"; conf_hi "60.149003"; cov "2.395161";\n+chrX\tCufflinks\ttranscript\t148249672\t148249713\t1000\t.\t.\tgene_id "CUFF.282847"; transcript_id "CUFF.282847.1"; FPKM "56.5895686726"; frac "1.000000"; conf_lo "5.974320"; conf_hi "107.204818"; cov "3.214286";\n+chrX\tCufflinks\ttranscript\t148481505\t148482455\t1000\t+\t.\tgene_id "CUFF.282965"; transcript_id "CUFF.282965.1"; FPKM "40.1706233958"; frac "1.000000"; conf_lo "16.978103"; conf_hi "63.363144"; cov "2.281690";\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/gff_filter_by_attribute_out2.gff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/gff_filter_by_attribute_out2.gff Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,161 @@\n+chr1\tCufflinks\texon\t21199802\t21199861\t1000\t+\t.\tgene_id "CUFF.1383"; transcript_id "CUFF.1383.1"; exon_number "1"; FPKM "5.0037092300"; frac "1.000000"; conf_lo "0.000000"; conf_hi "15.011128"; cov "0.284211";\n+chr1\tCufflinks\ttranscript\t55716264\t55716295\t1000\t.\t.\tgene_id "CUFF.5021"; transcript_id "CUFF.5021.1"; FPKM "29.7095235531"; frac "1.000000"; conf_lo "0.000000"; conf_hi "71.725135"; cov "1.687500";\n+chr1\tCufflinks\ttranscript\t74904128\t74904154\t1000\t.\t.\tgene_id "CUFF.7563"; transcript_id "CUFF.7563.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";\n+chr1\tCufflinks\texon\t134487086\t134487123\t1000\t.\t.\tgene_id "CUFF.11837"; transcript_id "CUFF.11837.1"; exon_number "1"; FPKM "25.0185461500"; frac "1.000000"; conf_lo "0.000000"; conf_hi "60.400113"; cov "1.421053";\n+chr1\tCufflinks\texon\t136200923\t136200959\t1000\t.\t.\tgene_id "CUFF.12099"; transcript_id "CUFF.12099.1"; exon_number "1"; FPKM "38.5420846095"; frac "1.000000"; conf_lo "0.000000"; conf_hi "83.046650"; cov "2.189189";\n+chr1\tCufflinks\ttranscript\t138116837\t138116866\t1000\t.\t.\tgene_id "CUFF.12557"; transcript_id "CUFF.12557.1"; FPKM "31.6901584567"; frac "1.000000"; conf_lo "0.000000"; conf_hi "76.506810"; cov "1.800000";\n+chr1\tCufflinks\texon\t152240694\t152240779\t1000\t.\t.\tgene_id "CUFF.13107"; transcript_id "CUFF.13107.1"; exon_number "1"; FPKM "16.5820596576"; frac "1.000000"; conf_lo "0.000000"; conf_hi "35.729373"; cov "0.941860";\n+chr1\tCufflinks\texon\t157633998\t157634024\t1000\t.\t.\tgene_id "CUFF.13967"; transcript_id "CUFF.13967.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";\n+chr1\tCufflinks\texon\t167704819\t167704854\t1000\t.\t.\tgene_id "CUFF.15347"; transcript_id "CUFF.15347.1"; exon_number "1"; FPKM "26.4084653806"; frac "1.000000"; conf_lo "0.000000"; conf_hi "63.755675"; cov "1.500000";\n+chr1\tCufflinks\ttranscript\t184245403\t184245429\t1000\t.\t.\tgene_id "CUFF.17679"; 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transcript_id "CUFF.27209.1"; exon_number "2"; FPKM "11.4913582411"; frac "1.000000"; conf_lo "0.000000"; conf_hi "30.264098"; cov "0.652709";\n+chr10\tCufflinks\texon\t89142681\t89142707\t1000\t.\t.\tgene_id "CUFF.27307"; transcript_id "CUFF.27307.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";\n+chr10\tCufflinks\texon\t93425781\t93425807\t1000\t.\t.\tgene_id "CUFF.28101"; transcript_id "CUFF.28101.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";\n+chr10\tCufflinks\texon\t108207916\t108207986\t1000\t.\t.\tgene_id "CUFF.29319"; transcript_id "CUFF.29319.1"; exon_number "1"; FPKM "13.3902077986"; frac "1.000000"; conf_lo "0.000000"; conf_hi "32.326821"; cov "0.760563";\n+chr10\tCufflinks\ttranscript\t117583959\t117584039\t1000\t.\t.\tgene_id "CUFF.30522"; transcript_id "CUFF.30522.1"; FPKM "17.6056435870"; frac "1.000000"; conf_lo "0.000000"; conf_hi "37.934890"; cov '..b';\n+chr8\tCufflinks\ttranscript\t93627215\t93627241\t1000\t.\t.\tgene_id "CUFF.254225"; transcript_id "CUFF.254225.1"; FPKM "52.8169307611"; frac "1.000000"; conf_lo "0.000000"; conf_hi "113.804669"; cov "3.000000";\n+chr8\tCufflinks\texon\t108148187\t108148357\t1000\t.\t.\tgene_id "CUFF.255477"; transcript_id "CUFF.255477.1"; exon_number "1"; FPKM "11.1193538445"; frac "1.000000"; conf_lo "0.000000"; conf_hi "22.238708"; cov "0.631579";\n+chr8\tCufflinks\texon\t108190587\t108190664\t1000\t.\t.\tgene_id "CUFF.255507"; transcript_id "CUFF.255507.1"; exon_number "1"; FPKM "12.1885224833"; frac "1.000000"; conf_lo "0.000000"; conf_hi "29.425696"; cov "0.692308";\n+chr8\tCufflinks\texon\t120931685\t120931769\t1000\t.\t.\tgene_id "CUFF.257375"; transcript_id "CUFF.257375.1"; exon_number "1"; FPKM "16.7771427124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "36.149718"; cov "0.952941";\n+chr9\tCufflinks\ttranscript\t20449846\t20449932\t1000\t.\t.\tgene_id "CUFF.260747"; transcript_id "CUFF.260747.1"; 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transcript_id "CUFF.263747.1"; FPKM "23.7676188425"; frac "1.000000"; conf_lo "0.000000"; conf_hi "57.380108"; cov "1.350000";\n+chr9\tCufflinks\texon\t59236547\t59236671\t1000\t.\t.\tgene_id "CUFF.267045"; transcript_id "CUFF.267045.1"; exon_number "1"; FPKM "12.1905895442"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.808020"; cov "0.692425";\n+chr9\tCufflinks\ttranscript\t66418162\t66418188\t1000\t.\t.\tgene_id "CUFF.268423"; transcript_id "CUFF.268423.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";\n+chr9\tCufflinks\ttranscript\t95913236\t95913262\t1000\t.\t.\tgene_id "CUFF.270957"; transcript_id "CUFF.270957.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";\n+chr9\tCufflinks\texon\t103101949\t103102030\t1000\t.\t.\tgene_id "CUFF.271979"; transcript_id "CUFF.271979.1"; exon_number "1"; FPKM "11.5939604110"; frac "1.000000"; conf_lo "0.000000"; conf_hi "27.990296"; cov "0.658537";\n+chr9\tCufflinks\ttranscript\t105579135\t105579173\t1000\t.\t.\tgene_id "CUFF.272347"; transcript_id "CUFF.272347.1"; FPKM "24.3770449667"; frac "1.000000"; conf_lo "0.000000"; conf_hi "58.851393"; cov "1.384615";\n+chr9\tCufflinks\texon\t113779194\t113779220\t1000\t.\t.\tgene_id "CUFF.274445"; transcript_id "CUFF.274445.1"; exon_number "1"; FPKM "52.8169307611"; frac "1.000000"; conf_lo "0.000000"; conf_hi "113.804669"; cov "3.000000";\n+chrX\tCufflinks\texon\t10274057\t10274087\t1000\t.\t.\tgene_id "CUFF.276147"; transcript_id "CUFF.276147.1"; exon_number "1"; FPKM "99.5432248142"; frac "1.000000"; conf_lo "21.405127"; conf_hi "177.681323"; cov "5.654052";\n+chrX\tCufflinks\ttranscript\t90114645\t90131913\t1000\t-\t.\tgene_id "CUFF.279771"; transcript_id "CUFF.279771.1"; FPKM "6.8891648819"; frac "1.000000"; conf_lo "0.000000"; conf_hi "20.667495"; cov "0.391304";\n+chrX\tCufflinks\ttranscript\t158986411\t158986471\t1000\t.\t.\tgene_id "CUFF.283831"; transcript_id "CUFF.283831.1"; FPKM "15.5853238312"; frac "1.000000"; conf_lo "0.000000"; conf_hi "37.626300"; cov "0.885246";\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/gff_filter_by_feature_count_out1.gff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/gff_filter_by_feature_count_out1.gff Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,42 @@\n+chr13\tCufflinks\ttranscript\t3565855\t3566203\t1000\t-\t.\tgene_id "CUFF.50195"; transcript_id "CUFF.50195.1"; FPKM "29.8710998584"; frac "1.000000"; conf_lo "7.290671"; conf_hi "52.451529"; cov "1.909091";\n+chr13\tCufflinks\texon\t3565855\t3565913\t1000\t-\t.\tgene_id "CUFF.50195"; transcript_id "CUFF.50195.1"; exon_number "1"; FPKM "29.8710998584"; frac "1.000000"; conf_lo "7.290671"; conf_hi "52.451529"; cov "1.909091";\n+chr13\tCufflinks\texon\t3566164\t3566203\t1000\t-\t.\tgene_id "CUFF.50195"; transcript_id "CUFF.50195.1"; exon_number "2"; FPKM "29.8710998584"; frac "1.000000"; conf_lo "7.290671"; conf_hi "52.451529"; cov "1.909091";\n+chr13\tCufflinks\ttranscript\t3606116\t3613028\t1000\t-\t.\tgene_id "CUFF.50207"; transcript_id "CUFF.50207.1"; FPKM "19.6171377865"; frac "1.000000"; conf_lo "0.936995"; conf_hi "38.297281"; cov "1.253750";\n+chr13\tCufflinks\texon\t3606116\t3606146\t1000\t-\t.\tgene_id "CUFF.50207"; transcript_id "CUFF.50207.1"; exon_number "1"; FPKM "19.6171377865"; frac "1.000000"; conf_lo "0.936995"; conf_hi "38.297281"; cov "1.253750";\n+chr13\tCufflinks\texon\t3612965\t3613028\t1000\t-\t.\tgene_id "CUFF.50207"; transcript_id "CUFF.50207.1"; exon_number "2"; FPKM "19.6171377865"; frac "1.000000"; conf_lo "0.936995"; conf_hi "38.297281"; cov "1.253750";\n+chr13\tCufflinks\ttranscript\t4594319\t4594938\t1000\t-\t.\tgene_id "CUFF.50261"; transcript_id "CUFF.50261.1"; FPKM "29.3887094260"; frac "1.000000"; conf_lo "8.607754"; conf_hi "50.169665"; cov "1.878261";\n+chr13\tCufflinks\texon\t4594319\t4594400\t1000\t-\t.\tgene_id "CUFF.50261"; transcript_id "CUFF.50261.1"; exon_number "1"; FPKM "29.3887094260"; frac "1.000000"; conf_lo "8.607754"; conf_hi "50.169665"; cov "1.878261";\n+chr13\tCufflinks\texon\t4594906\t4594938\t1000\t-\t.\tgene_id "CUFF.50261"; transcript_id "CUFF.50261.1"; exon_number "2"; FPKM "29.3887094260"; frac "1.000000"; conf_lo "8.607754"; conf_hi "50.169665"; cov "1.878261";\n+chr13\tCufflinks\ttranscript\t4596799\t4598059\t1000\t-\t.\tgene_id "CUFF.50263"; transcript_id "CUFF.50263.1"; FPKM "22.8358215134"; frac "1.000000"; conf_lo "0.000000"; conf_hi "45.671643"; cov "1.459459";\n+chr13\tCufflinks\texon\t4596799\t4596828\t1000\t-\t.\tgene_id "CUFF.50263"; transcript_id "CUFF.50263.1"; exon_number "1"; FPKM "22.8358215134"; frac "1.000000"; conf_lo "0.000000"; conf_hi "45.671643"; cov "1.459459";\n+chr13\tCufflinks\texon\t4598016\t4598059\t1000\t-\t.\tgene_id "CUFF.50263"; transcript_id "CUFF.50263.1"; exon_number "2"; FPKM "22.8358215134"; frac "1.000000"; conf_lo "0.000000"; conf_hi "45.671643"; cov "1.459459";\n+chr13\tCufflinks\ttranscript\t5861035\t5872268\t1000\t-\t.\tgene_id "CUFF.50289"; transcript_id "CUFF.50289.1"; FPKM "7.5439767500"; frac "1.000000"; conf_lo "0.000000"; conf_hi "18.212771"; cov "0.482143";\n+chr13\tCufflinks\texon\t5861035\t5861117\t1000\t-\t.\tgene_id "CUFF.50289"; transcript_id "CUFF.50289.1"; exon_number "1"; FPKM "7.5439767500"; frac "1.000000"; conf_lo "0.000000"; conf_hi "18.212771"; cov "0.482143";\n+chr13\tCufflinks\texon\t5872240\t5872268\t1000\t-\t.\tgene_id "CUFF.50289"; transcript_id "CUFF.50289.1"; exon_number "2"; FPKM "7.5439767500"; frac "1.000000"; conf_lo "0.000000"; conf_hi "18.212771"; cov "0.482143";\n+chr13\tCufflinks\ttranscript\t5865442\t5866941\t1000\t+\t.\tgene_id "CUFF.50297"; transcript_id "CUFF.50297.1"; FPKM "13.2019593124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "28.446269"; cov "0.843750";\n+chr13\tCufflinks\texon\t5865442\t5865510\t1000\t+\t.\tgene_id "CUFF.50297"; transcript_id "CUFF.50297.1"; exon_number "1"; FPKM "13.2019593124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "28.446269"; cov "0.843750";\n+chr13\tCufflinks\texon\t5866915\t5866941\t1000\t+\t.\tgene_id "CUFF.50297"; transcript_id "CUFF.50297.1"; exon_number "2"; FPKM "13.2019593124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "28.446269"; cov "0.843750";\n+chr13\tCufflinks\ttranscript\t6583845\t6585843\t1000\t-\t.\tgene_id "CUFF.50339"; transcript_id "CUFF.50339.1"; FPKM "163.2242242265"; frac "1.000000"; conf_lo "127.815919"; conf_hi "198.632530"; cov "10.431818";\n+chr13\tCufflinks\texon\t6583845'..b'2"; cov "5.272727";\n+chr13\tCufflinks\texon\t6587735\t6587966\t1000\t-\t.\tgene_id "CUFF.50341"; transcript_id "CUFF.50341.1"; exon_number "2"; FPKM "82.5011329424"; frac "1.000000"; conf_lo "60.835274"; conf_hi "104.166992"; cov "5.272727";\n+chr13\tCufflinks\ttranscript\t6580385\t6581757\t1000\t-\t.\tgene_id "CUFF.50365"; transcript_id "CUFF.50365.1"; FPKM "324.9135847836"; frac "1.000000"; conf_lo "293.684884"; conf_hi "356.142286"; cov "20.765542";\n+chr13\tCufflinks\texon\t6580385\t6580838\t1000\t-\t.\tgene_id "CUFF.50365"; transcript_id "CUFF.50365.1"; exon_number "1"; FPKM "324.9135847836"; frac "1.000000"; conf_lo "293.684884"; conf_hi "356.142286"; cov "20.765542";\n+chr13\tCufflinks\texon\t6581649\t6581757\t1000\t-\t.\tgene_id "CUFF.50365"; transcript_id "CUFF.50365.1"; exon_number "2"; FPKM "324.9135847836"; frac "1.000000"; conf_lo "293.684884"; conf_hi "356.142286"; cov "20.765542";\n+chr13\tCufflinks\ttranscript\t8803760\t8819743\t1000\t+\t.\tgene_id "CUFF.50481"; transcript_id "CUFF.50481.1"; FPKM "15.1783005269"; frac "1.000000"; conf_lo "2.785270"; conf_hi "27.571331"; cov "0.970060";\n+chr13\tCufflinks\texon\t8803760\t8803879\t1000\t+\t.\tgene_id "CUFF.50481"; transcript_id "CUFF.50481.1"; exon_number "1"; FPKM "15.1783005269"; frac "1.000000"; conf_lo "2.785270"; conf_hi "27.571331"; cov "0.970060";\n+chr13\tCufflinks\texon\t8819697\t8819743\t1000\t+\t.\tgene_id "CUFF.50481"; transcript_id "CUFF.50481.1"; exon_number "2"; FPKM "15.1783005269"; frac "1.000000"; conf_lo "2.785270"; conf_hi "27.571331"; cov "0.970060";\n+chr13\tCufflinks\ttranscript\t8855128\t8864773\t1000\t-\t.\tgene_id "CUFF.50497"; transcript_id "CUFF.50497.1"; FPKM "6.4009499697"; frac "1.000000"; conf_lo "0.000000"; conf_hi "19.202850"; cov "0.409091";\n+chr13\tCufflinks\texon\t8855128\t8855158\t1000\t-\t.\tgene_id "CUFF.50497"; transcript_id "CUFF.50497.1"; exon_number "1"; FPKM "6.4009499697"; frac "1.000000"; conf_lo "0.000000"; conf_hi "19.202850"; cov "0.409091";\n+chr13\tCufflinks\texon\t8864739\t8864773\t1000\t-\t.\tgene_id "CUFF.50497"; transcript_id "CUFF.50497.1"; exon_number "2"; FPKM "6.4009499697"; frac "1.000000"; conf_lo "0.000000"; conf_hi "19.202850"; cov "0.409091";\n+chr13\tCufflinks\ttranscript\t9169898\t9172437\t1000\t+\t.\tgene_id "CUFF.50509"; transcript_id "CUFF.50509.1"; FPKM "41.4918721248"; frac "1.000000"; conf_lo "16.471332"; conf_hi "66.512412"; cov "2.651786";\n+chr13\tCufflinks\texon\t9169898\t9169928\t1000\t+\t.\tgene_id "CUFF.50509"; transcript_id "CUFF.50509.1"; exon_number "1"; FPKM "41.4918721248"; frac "1.000000"; conf_lo "16.471332"; conf_hi "66.512412"; cov "2.651786";\n+chr13\tCufflinks\texon\t9172357\t9172437\t1000\t+\t.\tgene_id "CUFF.50509"; transcript_id "CUFF.50509.1"; exon_number "2"; FPKM "41.4918721248"; frac "1.000000"; conf_lo "16.471332"; conf_hi "66.512412"; cov "2.651786";\n+chr13\tCufflinks\ttranscript\t9353602\t9373527\t1000\t-\t.\tgene_id "CUFF.50527"; transcript_id "CUFF.50527.1"; FPKM "16.2485653076"; frac "1.000000"; conf_lo "0.000000"; conf_hi "35.010792"; cov "1.038462";\n+chr13\tCufflinks\texon\t9353602\t9353648\t1000\t-\t.\tgene_id "CUFF.50527"; transcript_id "CUFF.50527.1"; exon_number "1"; FPKM "16.2485653076"; frac "1.000000"; conf_lo "0.000000"; conf_hi "35.010792"; cov "1.038462";\n+chr13\tCufflinks\texon\t9373497\t9373527\t1000\t-\t.\tgene_id "CUFF.50527"; transcript_id "CUFF.50527.1"; exon_number "2"; FPKM "16.2485653076"; frac "1.000000"; conf_lo "0.000000"; conf_hi "35.010792"; cov "1.038462";\n+chr13\tCufflinks\ttranscript\t9586173\t9593034\t1000\t-\t.\tgene_id "CUFF.50563"; transcript_id "CUFF.50563.1"; FPKM "10.3039682439"; frac "1.000000"; conf_lo "0.000000"; conf_hi "24.875980"; cov "0.658537";\n+chr13\tCufflinks\texon\t9586173\t9586218\t1000\t-\t.\tgene_id "CUFF.50563"; transcript_id "CUFF.50563.1"; exon_number "1"; FPKM "10.3039682439"; frac "1.000000"; conf_lo "0.000000"; conf_hi "24.875980"; cov "0.658537";\n+chr13\tCufflinks\texon\t9592999\t9593034\t1000\t-\t.\tgene_id "CUFF.50563"; transcript_id "CUFF.50563.1"; exon_number "2"; FPKM "10.3039682439"; frac "1.000000"; conf_lo "0.000000"; conf_hi "24.875980"; cov "0.658537";\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/gff_filter_by_feature_count_out2.gff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/gff_filter_by_feature_count_out2.gff Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,71 @@
+ctgA example match 29771 32937 . + . ID=Match:seg10
+ctgA example HSP 29771 29942 . + . Parent=Match:seg10
+ctgA example HSP 30042 30340 . + . Parent=Match:seg10
+ctgA example HSP 30810 31307 . + . Parent=Match:seg10
+ctgA example HSP 31761 31984 . + . Parent=Match:seg10
+ctgA example HSP 32374 32937 . + . Parent=Match:seg10
+ctgA example match 26122 34466 . + . ID=Match:seg02
+ctgA example HSP 26122 26126 . + . Parent=Match:seg02
+ctgA example HSP 26497 26869 . + . Parent=Match:seg02
+ctgA example HSP 27201 27325 . + . Parent=Match:seg02
+ctgA example HSP 27372 27433 . + . Parent=Match:seg02
+ctgA example HSP 27565 27565 . + . Parent=Match:seg02
+ctgA example HSP 27813 28091 . + . Parent=Match:seg02
+ctgA example HSP 28093 28201 . + . Parent=Match:seg02
+ctgA example HSP 28329 28377 . + . Parent=Match:seg02
+ctgA example HSP 28829 29194 . + . Parent=Match:seg02
+ctgA example HSP 29517 29702 . + . Parent=Match:seg02
+ctgA example HSP 29713 30061 . + . Parent=Match:seg02
+ctgA example HSP 30329 30774 . + . Parent=Match:seg02
+ctgA example HSP 30808 31306 . + . Parent=Match:seg02
+ctgA example HSP 31516 31729 . + . Parent=Match:seg02
+ctgA example HSP 31753 32154 . + . Parent=Match:seg02
+ctgA example HSP 32595 32696 . + . Parent=Match:seg02
+ctgA example HSP 32892 32901 . + . Parent=Match:seg02
+ctgA example HSP 33127 33388 . + . Parent=Match:seg02
+ctgA example HSP 33439 33443 . + . Parent=Match:seg02
+ctgA example HSP 33759 34209 . + . Parent=Match:seg02
+ctgA example HSP 34401 34466 . + . Parent=Match:seg02
+ctgA example match 41137 47829 . - . ID=Match:seg14
+ctgA example HSP 47449 47829 . - . Parent=Match:seg14
+ctgA example HSP 46816 46992 . - . Parent=Match:seg14
+ctgA example HSP 46092 46318 . - . Parent=Match:seg14
+ctgA example HSP 45790 46022 . - . Parent=Match:seg14
+ctgA example HSP 45231 45488 . - . Parent=Match:seg14
+ctgA example HSP 44763 45030 . - . Parent=Match:seg14
+ctgA example HSP 44065 44556 . - . Parent=Match:seg14
+ctgA example HSP 43395 43811 . - . Parent=Match:seg14
+ctgA example HSP 42890 43270 . - . Parent=Match:seg14
+ctgA example HSP 42057 42474 . - . Parent=Match:seg14
+ctgA example HSP 41754 41948 . - . Parent=Match:seg14
+ctgA example HSP 41137 41318 . - . Parent=Match:seg14
+ctgA example match 12531 15870 . + . ID=Match:seg12
+ctgA example HSP 12531 12895 . + . Parent=Match:seg12
+ctgA example HSP 13122 13449 . + . Parent=Match:seg12
+ctgA example HSP 13452 13745 . + . Parent=Match:seg12
+ctgA example HSP 13908 13965 . + . Parent=Match:seg12
+ctgA example HSP 13998 14488 . + . Parent=Match:seg12
+ctgA example HSP 14564 14899 . + . Parent=Match:seg12
+ctgA example HSP 15185 15276 . + . Parent=Match:seg12
+ctgA example HSP 15639 15736 . + . Parent=Match:seg12
+ctgA example HSP 15745 15870 . + . Parent=Match:seg12
+ctgA example match 26503 35904 . - . ID=Match:seg05
+ctgA example HSP 35642 35904 . - . Parent=Match:seg05
+ctgA example HSP 35333 35507 . - . Parent=Match:seg05
+ctgA example HSP 34605 34983 . - . Parent=Match:seg05
+ctgA example HSP 34244 34313 . - . Parent=Match:seg05
+ctgA example HSP 33438 33868 . - . Parent=Match:seg05
+ctgA example HSP 33053 33325 . - . Parent=Match:seg05
+ctgA example HSP 32208 32680 . - . Parent=Match:seg05
+ctgA example HSP 32010 32057 . - . Parent=Match:seg05
+ctgA example HSP 31421 31817 . - . Parent=Match:seg05
+ctgA example HSP 31232 31236 . - . Parent=Match:seg05
+ctgA example HSP 30465 30798 . - . Parent=Match:seg05
+ctgA example HSP 30108 30216 . - . Parent=Match:seg05
+ctgA example HSP 29513 29647 . - . Parent=Match:seg05
+ctgA example HSP 28777 29058 . - . Parent=Match:seg05
+ctgA example HSP 28225 28316 . - . Parent=Match:seg05
+ctgA example HSP 27887 28076 . - . Parent=Match:seg05
+ctgA example HSP 27448 27860 . - . Parent=Match:seg05
+ctgA example HSP 27172 27185 . - . Parent=Match:seg05
+ctgA example HSP 26503 26799 . - . Parent=Match:seg05

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/gops_subtract_in1.gff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/gops_subtract_in1.gff Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,500 @@\n+chr13\tCufflinks\ttranscript\t3405463\t3405542\t1000\t.\t.\tgene_id "CUFF.50189"; transcript_id "CUFF.50189.1"; FPKM "6.3668918357"; frac "1.000000"; conf_lo "0.000000"; conf_hi "17.963819"; cov "0.406914";\n+chr13\tCufflinks\texon\t3405463\t3405542\t1000\t.\t.\tgene_id "CUFF.50189"; transcript_id "CUFF.50189.1"; exon_number "1"; FPKM "6.3668918357"; frac "1.000000"; conf_lo "0.000000"; conf_hi "17.963819"; cov "0.406914";\n+chr13\tCufflinks\ttranscript\t3473337\t3473372\t1000\t.\t.\tgene_id "CUFF.50191"; transcript_id "CUFF.50191.1"; FPKM "11.7350749444"; frac "1.000000"; conf_lo "0.000000"; conf_hi "35.205225"; cov "0.750000";\n+chr13\tCufflinks\texon\t3473337\t3473372\t1000\t.\t.\tgene_id "CUFF.50191"; transcript_id "CUFF.50191.1"; exon_number "1"; FPKM "11.7350749444"; frac "1.000000"; conf_lo "0.000000"; conf_hi "35.205225"; cov "0.750000";\n+chr13\tCufflinks\ttranscript\t3490319\t3490350\t1000\t.\t.\tgene_id "CUFF.50193"; transcript_id "CUFF.50193.1"; FPKM "39.6058779373"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.338807"; cov "2.531250";\n+chr13\tCufflinks\texon\t3490319\t3490350\t1000\t.\t.\tgene_id "CUFF.50193"; transcript_id "CUFF.50193.1"; exon_number "1"; FPKM "39.6058779373"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.338807"; cov "2.531250";\n+chr13\tCufflinks\ttranscript\t3565855\t3566203\t1000\t-\t.\tgene_id "CUFF.50195"; transcript_id "CUFF.50195.1"; FPKM "29.8710998584"; frac "1.000000"; conf_lo "7.290671"; conf_hi "52.451529"; cov "1.909091";\n+chr13\tCufflinks\texon\t3565855\t3565913\t1000\t-\t.\tgene_id "CUFF.50195"; transcript_id "CUFF.50195.1"; exon_number "1"; FPKM "29.8710998584"; frac "1.000000"; conf_lo "7.290671"; conf_hi "52.451529"; cov "1.909091";\n+chr13\tCufflinks\texon\t3566164\t3566203\t1000\t-\t.\tgene_id "CUFF.50195"; transcript_id "CUFF.50195.1"; exon_number "2"; FPKM "29.8710998584"; frac "1.000000"; conf_lo "7.290671"; conf_hi "52.451529"; cov "1.909091";\n+chr13\tCufflinks\ttranscript\t3566475\t3566560\t1000\t.\t.\tgene_id "CUFF.50197"; transcript_id "CUFF.50197.1"; FPKM "14.7370708604"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.753975"; cov "0.941860";\n+chr13\tCufflinks\texon\t3566475\t3566560\t1000\t.\t.\tgene_id "CUFF.50197"; transcript_id "CUFF.50197.1"; exon_number "1"; FPKM "14.7370708604"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.753975"; cov "0.941860";\n+chr13\tCufflinks\ttranscript\t3566664\t3566942\t1000\t.\t.\tgene_id "CUFF.50199"; transcript_id "CUFF.50199.1"; FPKM "31.7874813134"; frac "1.000000"; conf_lo "17.911934"; conf_hi "45.663029"; cov "2.031569";\n+chr13\tCufflinks\texon\t3566664\t3566942\t1000\t.\t.\tgene_id "CUFF.50199"; transcript_id "CUFF.50199.1"; exon_number "1"; FPKM "31.7874813134"; frac "1.000000"; conf_lo "17.911934"; conf_hi "45.663029"; cov "2.031569";\n+chr13\tCufflinks\ttranscript\t3568042\t3568068\t1000\t.\t.\tgene_id "CUFF.50201"; transcript_id "CUFF.50201.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";\n+chr13\tCufflinks\texon\t3568042\t3568068\t1000\t.\t.\tgene_id "CUFF.50201"; transcript_id "CUFF.50201.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";\n+chr13\tCufflinks\ttranscript\t3569564\t3569626\t1000\t.\t.\tgene_id "CUFF.50203"; transcript_id "CUFF.50203.1"; FPKM "13.4115142222"; frac "1.000000"; conf_lo "0.000000"; conf_hi "32.378260"; cov "0.857143";\n+chr13\tCufflinks\texon\t3569564\t3569626\t1000\t.\t.\tgene_id "CUFF.50203"; transcript_id "CUFF.50203.1"; exon_number "1"; FPKM "13.4115142222"; frac "1.000000"; conf_lo "0.000000"; conf_hi "32.378260"; cov "0.857143";\n+chr13\tCufflinks\ttranscript\t3594171\t3594199\t1000\t.\t.\tgene_id "CUFF.50205"; transcript_id "CUFF.50205.1"; FPKM "29.1353584826"; frac "1.000000"; conf_lo "0.000000"; conf_hi "70.338978"; cov "1.862069";\n+chr13\tCufflinks\texon\t3594171\t3594199\t1000\t.\t.\tgene_id "CUFF.50205"; transcript_id "CUFF.50205.1"; exon_number "1"; FPKM "29.1353584826"; frac "1.000000"; conf_lo "0.000000"; conf_hi "70.338978"; cov "1.862069";\n+chr13\tCufflinks\ttranscript\t3606116\t3613028\t1000\t-\t.'..b' "44.344138"; cov "1.173913";\n+chr13\tCufflinks\texon\t10289392\t10289437\t1000\t.\t.\tgene_id "CUFF.50655"; transcript_id "CUFF.50655.1"; exon_number "1"; FPKM "18.3679433912"; frac "1.000000"; conf_lo "0.000000"; conf_hi "44.344138"; cov "1.173913";\n+chr13\tCufflinks\ttranscript\t10326745\t10326771\t1000\t.\t.\tgene_id "CUFF.50657"; transcript_id "CUFF.50657.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";\n+chr13\tCufflinks\texon\t10326745\t10326771\t1000\t.\t.\tgene_id "CUFF.50657"; transcript_id "CUFF.50657.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";\n+chr13\tCufflinks\ttranscript\t10346675\t10346701\t1000\t.\t.\tgene_id "CUFF.50659"; transcript_id "CUFF.50659.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";\n+chr13\tCufflinks\texon\t10346675\t10346701\t1000\t.\t.\tgene_id "CUFF.50659"; transcript_id "CUFF.50659.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";\n+chr13\tCufflinks\ttranscript\t10337071\t10337097\t1000\t.\t.\tgene_id "CUFF.50661"; transcript_id "CUFF.50661.1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";\n+chr13\tCufflinks\texon\t10337071\t10337097\t1000\t.\t.\tgene_id "CUFF.50661"; transcript_id "CUFF.50661.1"; exon_number "1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";\n+chr13\tCufflinks\ttranscript\t10337141\t10337167\t1000\t.\t.\tgene_id "CUFF.50663"; transcript_id "CUFF.50663.1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";\n+chr13\tCufflinks\texon\t10337141\t10337167\t1000\t.\t.\tgene_id "CUFF.50663"; transcript_id "CUFF.50663.1"; exon_number "1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";\n+chr13\tCufflinks\ttranscript\t10344376\t10344402\t1000\t.\t.\tgene_id "CUFF.50665"; transcript_id "CUFF.50665.1"; FPKM "46.9402997776"; frac "1.000000"; conf_lo "0.000000"; conf_hi "101.142289"; cov "3.000000";\n+chr13\tCufflinks\texon\t10344376\t10344402\t1000\t.\t.\tgene_id "CUFF.50665"; transcript_id "CUFF.50665.1"; exon_number "1"; FPKM "46.9402997776"; frac "1.000000"; conf_lo "0.000000"; conf_hi "101.142289"; cov "3.000000";\n+chr13\tCufflinks\ttranscript\t10344976\t10345002\t1000\t.\t.\tgene_id "CUFF.50667"; transcript_id "CUFF.50667.1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";\n+chr13\tCufflinks\texon\t10344976\t10345002\t1000\t.\t.\tgene_id "CUFF.50667"; transcript_id "CUFF.50667.1"; exon_number "1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";\n+chr13\tCufflinks\ttranscript\t10345008\t10345034\t1000\t.\t.\tgene_id "CUFF.50669"; transcript_id "CUFF.50669.1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";\n+chr13\tCufflinks\texon\t10345008\t10345034\t1000\t.\t.\tgene_id "CUFF.50669"; transcript_id "CUFF.50669.1"; exon_number "1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";\n+chr13\tCufflinks\ttranscript\t10345484\t10345510\t1000\t.\t.\tgene_id "CUFF.50671"; transcript_id "CUFF.50671.1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";\n+chr13\tCufflinks\texon\t10345484\t10345510\t1000\t.\t.\tgene_id "CUFF.50671"; transcript_id "CUFF.50671.1"; exon_number "1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";\n+chr13\tCufflinks\ttranscript\t10345538\t10345564\t1000\t.\t.\tgene_id "CUFF.50673"; transcript_id "CUFF.50673.1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";\n+chr13\tCufflinks\texon\t10345538\t10345564\t1000\t.\t.\tgene_id "CUFF.50673"; transcript_id "CUFF.50673.1"; exon_number "1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/gpass_and_beam_input.map
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/gpass_and_beam_input.map Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,50 @@
+1 rs0 0 738547
+1 rs1 0 5597094
+1 rs2 0 9424115
+1 rs3 0 13879818
+1 rs4 0 13934751
+1 rs5 0 16803491
+1 rs6 0 17236854
+1 rs7 0 18445387
+1 rs8 0 21222571
+1 rs9 0 24988555
+1 rs10 0 29047517
+1 rs11 0 39100314
+1 rs12 0 43177587
+1 rs13 0 48982207
+1 rs14 0 54316843
+1 rs15 0 62764366
+1 rs16 0 68056276
+1 rs17 0 71657460
+1 rs18 0 83962523
+1 rs19 0 84078493
+1 rs20 0 85518967
+1 rs21 0 89040803
+1 rs22 0 90237128
+1 rs23 0 94936979
+1 rs24 0 97915585
+1 rs25 0 104312265
+1 rs26 0 108987701
+1 rs27 0 112558366
+1 rs28 0 116025269
+1 rs29 0 120010986
+1 rs30 0 121353801
+1 rs31 0 125064851
+1 rs32 0 125803399
+1 rs33 0 125998718
+1 rs34 0 133890804
+1 rs35 0 136606952
+1 rs36 0 137748344
+1 rs37 0 173015533
+1 rs38 0 174492629
+1 rs39 0 181023590
+1 rs40 0 183428449
+1 rs41 0 186040833
+2 rs42 0 1861629
+2 rs43 0 7306131
+2 rs44 0 14423047
+2 rs45 0 19837031
+2 rs46 0 22309030
+2 rs47 0 34730063
+2 rs48 0 42219306
+2 rs49 0 46150090

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/gpass_and_beam_input.ped
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/gpass_and_beam_input.ped Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,1000 @@\n+1 1 0 0 1 1 G G A A A A A A A A A G A A G G G G A A G G G G G G A A A A A G A A G G A G A G A A G G A A G G A A G G A G A A G G A A G G A A A G A G G G A G G G G G A A A G A A G G G G G G G G A G A A A A A A A A\n+1 1 0 0 1 1 G G A G G G A A A A A G A A G G G G G G A A G G A G A G G G G G A G G G A G A A G G A G G G A A G G G G A G A G G G A G A A A A G G G G A G A G G G A G A A A A A G G G A G G G A G G G G G A A G G A G\n+1 1 0 0 1 1 A G A A G G A A A G A A G G A A G G A A G G A A A G A G A A A G A A A G A G G G G G A G A G G G G G G G A G G G A G A G G G G G A G G G G G G G A A A G G G G G A A A G G G A G G G A A G G G G A G G G\n+1 1 0 0 1 1 G G A A A A A A A A G G A G A A A A A A A A A A G G G G G G A G A A A A A G A G G G A G A G A A A A A A G G A G A G G G A A G G G G A G A A A G A A A A A A A G G G A G G G A G A G G G G G G G A A G G\n+1 1 0 0 1 1 A A G G A A A A A A A G A A A A A A A A A A G G A G A A A A A G G G A A A G A G G G G G A A G G A A A G A G A G G G G G G G A A A G A G A A A G A A G G G G G G A A G G A A A G G G G G A A G G G G A G\n+1 1 0 0 1 1 A A G G A A G G A G G G G G G G G G A A A G G G G G G G G G A G G G A A A A G G A A A G G G G G A A G G A A G G G G A G A A A A A G G G A A A G A A G G A A A G A A A A A G G G G G A G G G G G A A G G\n+1 1 0 0 1 1 A A A A A A G G G G A G G G A G G G A A A A G G A G A A A A A G G G A A A G A G A A A A A G A A G G A G G G A A A G G G A A A G G G A G G G A G A A A A G G G G A A G G G G G G G G A G A A G G A A G G\n+1 1 0 0 1 1 A A A A A A A A A A G G A A A A A A A A G G G G A G G G G G A G A G G G A G A G A A A G A G A A A A A A A G A G A G G G A A A A A G G G G G A G A A G G A A G G G G G G A A G G A A G G A A A G G G A G\n+1 1 0 0 1 1 G G A A A A A A G G G G G G A A G G A A A A G G A G G G A A A G G G G G A G G G G G A A A G A A G G A A A G G G A G A A G G A A A G A G G G G G G G A G G G G G A G A A G G G G G G G G A A G G A A G G\n+1 1 0 0 1 1 A A A A G G A A G G A G A A G G A A A A A A G G A G G G A A G G G G A A G G G G A A G G A G A A A A A A A G A G G G G G A A A A A G A G G G A G A A G G A A A G G G A G G G G G A G A G A A A A A A G G\n+1 1 0 0 1 2 A A A A G G G G A G G G A A G G A A G G A A G G A G G G G G G G A A G G A G A A A A G G A G G G A A G G A G A A G G G G G G A A A G A G G G A G G G G G A A A G G G G G G G G G G G A G A A A A G G A G\n+1 1 0 0 1 2 G G G G A A A A A A A G G G A G A A A A A A A A A A G G A A A G A G A G G G G G A A G G G G G G A A G G G G G G A G A A A A A A G G G G G G G G A A G G A A A G G G A G A G A G A G G G A A A A A A G G\n+1 1 0 0 1 2 G G A G A A G G A A G G G G A A A A G G A A A A A G G G A A A G A G G G A G G G A A A A A A A G A A G G A G G G A G A G A A A A A G G G G G A G G G A G A A A G A A G G G G A G G G G G A A G G A A A G\n+1 1 0 0 1 2 A A A A A A G G A A G G G G G G A A A A G G G G A G A A A A A G G G A A A G A G G G A A G G A A A A G G A G A G A G A G G G A A A G A G A A A G G G A G A A A A A A G G G G A G G G A G A A G G G G A G\n+1 1 0 0 1 2 G G A A A A A A A A A G G G G G G G A A A A A A G G A A A A A G G G A A A G A G G G G G A A A A A A A A A G A A G G A A A A A A A G G G A G A G G G A G G G A A G G G G G G A G A G A G A A A G G G A G\n+1 1 0 0 1 2 A A '..b'G G A G G G A G G G G G A A A G\n+1 1 0 0 1 1 A A A A A A A A A A A G A A G G A G A A G G A A A A A A G G A G A G A A A G A G A A A A G G A A A A A A A G A G G G G G A A A A A G A G G G G G G G G G A A A A G G A A A A G G G G A G G G A A G G A G\n+1 1 0 0 1 1 A A G G G G A A A A A G A A G G A A A A A A A A G G A A A A A G G G G G G G G G A A A G A A G G A A G G A G A G G G G G A A A A A G G G G G G G G G A G A A G G A G G G A G G G A G G G G G G G G G G G\n+1 1 0 0 1 1 A A G G A A G G A G A A G G A A A A A A A A A A G G A A A A A G G G A G A G A G G G G G G G A A G G G G G G G G A G G G A A G G A G A G G G A G A A G G A A G G G G G G G G G G A G G G G G A G G G A G\n+1 1 0 0 1 1 A A G G G G A A G G A G A A G G A A A A A A A A G G G G A A A G A A G G A G G G G G G G A A A A A A A A A G G G G G G G G G A A A G A G G G A G A A G G A A G G A G G G G G G G A G A G A A A G A G A G\n+1 1 0 0 1 1 A A A A A A A A G G G G A A G G G G G G A A A A G G G G A A A G A A A A A G G G G G G G G G A G A A G G G G G G G G G G A A A A G G G G G G G G A G A G A A A A A G A G A A G G A A A G A A G G G G A G\n+1 1 0 0 1 2 A A A A G G A A A A A G G G G G G G A A A A A A A G A A A A A G A A G G A G A G A A G G G G G G G G A A A G G G A A A G G G A A G G A G G G A G A A A G A A A A A A G G G G A A A G G G A A G G A A A G\n+1 1 0 0 1 2 A A A A A A G G G G A G A A A A A A A A A A G G A G A A A A A G A A G G A G A A G G A A G G A A A A A A A G A G A G G G A A A A G G A G G G A G G G A G A A G G A A G G A A G G A A G G A A A A A A G G\n+1 1 0 0 1 2 A A A A G G A A A G A A A A A G A A A A A A A A A G A A G G A G G G A A A G G G A A A G A A A A A A A A A G G G A G G G A A A G G G A G G G G G G G A A A A G G G G G G A G G G A G G G A A G G A A G G\n+1 1 0 0 1 2 A A A A A A A A A G G G G G G G A A A A A A A A G G G G G G A G A G A G A G G G G G A G A A A A A A A A A G A G A A A G A A G G G G A G G G A G A G G G G G A A G G A G G G G G A A A G A A G G A A A G\n+1 1 0 0 1 2 A A A G A A A A G G A G A A A A A A A A A A A A A G A A G G G G A A G G A G A G A A A G A A A G A A A A A G A G A G G G A A A A G G G G A A A G G G A G A A A A A A G G G G A G A G A G A A A A A A G G\n+1 1 0 0 1 2 G G A A A A A A A A A A A A A A G G A A A A A A G G A G A A G G G G G G G G G G G G A A A A A A A A A A G G G G G G G G A A A A A G A G A G G G G G G G A A A A G G G G A A G G G G A G A A G G A A A G\n+1 1 0 0 1 2 A A G G A A G G G G A A G G G G A A A A A A A G A G G G G G A G G G G G A G A G A A A A A G A A G G A A A G G G G G A A A A A A A G A G A A A G A G G G A A A G G G G G G G A G A G G G G G A A G G A G\n+1 1 0 0 1 2 G G A A A A A A A A G G A A G G A A A A A A A A A G A G A A A G G G A A A G G G G G G G G G G G A A A A A G G G A G G G G G A A A A G G A G G G G G G G A A A A G G G G G G A G A G G G A A A G A A G G\n+1 1 0 0 1 2 G G A A A A A A G G A G A A A A A A A A A A A A G G G G A A G G A G A A A G A G G G A G G G A A A A G G A G G G G G G G G G A A A G A G A G A G A A A G A A G G G G A G A G G G G G G G A A G G A A A G\n+1 1 0 0 1 2 A G A A A A A A A G A G A A A G A A A A G G A A A G A A A A A G A A G G A G G G A A A G G G G G A A A A A G A G G G A G A A G G G G A G G G A G A A A A G G G G A A A A G G G G G G G G A A G G A A A G\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/gpass_output.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/gpass_output.txt Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,8 @@
+#ID chr position Statistics adj-Pvalue FDR
+rs36 chr1 137748344 4.890849 0.991562 0.682138
+rs37 chr1 173015533 4.931934 0.991562 0.795827
+rs45 chr2 19837031 7.712832 0.665086 0.218776
+rs24 chr1 97915585 9.122863 0.407595 0.174521
+rs13 chr1 48982207 8.548830 0.514570 0.180680
+rs10 chr1 29047517 11.680067 0.134287 0.072101
+rs20 chr1 85518967 12.334287 0.099194 0.104465

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/groupby_out1.dat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/groupby_out1.dat Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,20 @@
+chr1 1.48053e+08
+chr10 5.52516e+07
+chr11 8.75888e+07
+chr12 3.84401e+07
+chr13 1.12382e+08
+chr14 9.87102e+07
+chr15 4.16664e+07
+chr16 206638
+chr18 5.05624e+07
+chr19 5.92262e+07
+chr2 1.69276e+08
+chr20 3.35042e+07
+chr21 3.31607e+07
+chr22 3.04712e+07
+chr5 1.31612e+08
+chr6 1.08564e+08
+chr7 1.15958e+08
+chr8 1.18881e+08
+chr9 1.28843e+08
+chrx 1.45195e+08

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/groupby_out2.dat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/groupby_out2.dat Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,2 @@
+chr10 1700
+chr22 1533.33
\ No newline at end of file

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/groupby_out3.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/groupby_out3.tabular Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,20 @@
+chr1 1.48053e+08 1.48031e+08 +,- 1.48185e+08 1.47962e+08 5.9221e+08 4 1 chr1,chr1,chr1,chr1 +,- 147962192 88085.9
+chr10 5.52516e+07 5.52516e+07 - 5.52516e+07 5.52516e+07 5.52516e+07 1 1 chr10 - 55251623 0
+chr11 8.75888e+07 1.16165e+08 +,- 1.16212e+08 1.81238e+06 3.50355e+08 4 1 chr11,chr11,chr11,chr11 +,- 116124407 4.9523e+07
+chr12 3.84401e+07 3.84401e+07 - 3.84401e+07 3.84401e+07 3.84401e+07 1 1 chr12 - 38440094 0
+chr13 1.12382e+08 1.12382e+08 + 1.12382e+08 1.12382e+08 1.12382e+08 1 1 chr13 + 112381694 0
+chr14 9.87102e+07 9.87102e+07 - 9.87102e+07 9.87102e+07 9.87102e+07 1 1 chr14 - 98710240 0
+chr15 4.16664e+07 4.16764e+07 +,- 4.1826e+07 4.14869e+07 1.66666e+08 4 1 chr15,chr15,chr15,chr15 +,- 41486872 120341
+chr16 206638 212188 +,- 259268 142908 826552 4 1 chr16,chr16,chr16,chr16 +,- 244413 47354.9
+chr18 5.05624e+07 5.94314e+07 +,- 5.96006e+07 2.37861e+07 2.0225e+08 4 1 chr18,chr18,chr18,chr18 +,- 59600586 1.54594e+07
+chr19 5.92262e+07 5.9267e+07 +,- 5.93022e+07 5.90686e+07 2.36905e+08 4 1 chr19,chr19,chr19,chr19 +,- 59297998 94686.3
+chr2 1.69276e+08 1.69292e+08 +,- 2.2023e+08 1.18289e+08 6.77103e+08 4 1 chr2,chr2,chr2,chr2 +,- 118394148 5.09343e+07
+chr20 3.35042e+07 3.35466e+07 +,- 3.35933e+07 3.33304e+07 1.34017e+08 4 1 chr20,chr20,chr20,chr20 +,- 33593260 104752
+chr21 3.31607e+07 3.30953e+07 +,- 3.3745e+07 3.2707e+07 1.32643e+08 4 1 chr21,chr21,chr21,chr21 +,- 32869641 405475
+chr22 3.04712e+07 3.04128e+07 +,- 3.09391e+07 3.01202e+07 1.21885e+08 4 1 chr22,chr22,chr22,chr22 +,- 30160419 345080
+chr5 1.31612e+08 1.31589e+08 +,- 1.31848e+08 1.31424e+08 5.2645e+08 4 1 chr5,chr5,chr5,chr5 +,- 131556601 153188
+chr6 1.08564e+08 1.08617e+08 +,- 1.08723e+08 1.083e+08 4.34257e+08 4 1 chr6,chr6,chr6,chr6 +,- 108640045 159611
+chr7 1.15958e+08 1.16613e+08 +,- 1.16946e+08 1.13661e+08 4.63832e+08 4 1 chr7,chr7,chr7,chr7 +,- 113660517 1.33533e+06
+chr8 1.18881e+08 1.18881e+08 - 1.18881e+08 1.18881e+08 1.18881e+08 1 1 chr8 - 118881131 0
+chr9 1.28843e+08 1.28835e+08 +,- 1.28937e+08 1.28764e+08 5.15371e+08 4 1 chr9,chr9,chr9,chr9 +,- 128764156 70228.2
+chrX 1.45195e+08 1.5267e+08 +,- 1.52694e+08 1.22745e+08 5.80779e+08 4 1 chrX,chrX,chrX,chrX +,- 122745047 1.29614e+07

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/gsummary_out1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/gsummary_out1.tabular Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,2 @@
+#sum mean stdev 0% 25% 50% 75% 100%
+5.55921e+09 8.55264e+07 5.37839e+07 142908 3.35933e+07 1.083e+08 1.28764e+08 2.2023e+08

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/gtf2bedgraph_in.gtf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/gtf2bedgraph_in.gtf Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,100 @@\n+chr1\tCufflinks\texon\t36425950\t36426026\t1000\t-\t.\tgene_id "uc007aqa.1"; transcript_id "uc007aqa.1"; exon_number "21"; FPKM "4.8386844109"; frac "0.515875"; conf_lo "0.000000"; conf_hi "9.779040"; cov "0.274837";\n+chr1\tCufflinks\texon\t46891972\t46892996\t1000\t-\t.\tgene_id "uc007axc.1"; transcript_id "uc007axc.1"; exon_number "9"; FPKM "8.4688567539"; frac "1.000000"; conf_lo "6.667227"; conf_hi "10.270487"; cov "0.481031";\n+chr1\tCufflinks\texon\t71654478\t71654594\t1000\t-\t.\tgene_id "uc007bkb.1"; transcript_id "uc007bkb.1"; exon_number "4"; FPKM "0.4686878995"; frac "0.186704"; conf_lo "0.300747"; conf_hi "0.636629"; cov "0.026621";\n+chr1\tCufflinks\ttranscript\t72629845\t72679706\t1000\t+\t.\tgene_id "uc007bks.1"; transcript_id "uc007bks.1"; FPKM "4.0695297327"; frac "1.000000"; conf_lo "2.473329"; conf_hi "5.665731"; cov "0.231149";\n+chr1\tCufflinks\texon\t75531753\t75532000\t1000\t+\t.\tgene_id "uc007bpt.1"; transcript_id "uc007bpt.1"; exon_number "24"; FPKM "3.6392661141"; frac "1.000000"; conf_lo "2.391008"; conf_hi "4.887524"; cov "0.206710";\n+chr1\tCufflinks\texon\t123389482\t123389564\t1000\t+\t.\tgene_id "uc007cju.1"; transcript_id "uc007cju.1"; exon_number "20"; FPKM "0.9948773061"; frac "1.000000"; conf_lo "0.105032"; conf_hi "1.884723"; cov "0.056509";\n+chr1\tCufflinks\texon\t129625990\t129626119\t1000\t+\t.\tgene_id "uc007ckv.1"; transcript_id "uc007ckv.1"; exon_number "1"; FPKM "0.0003267777"; frac "0.004692"; conf_lo "0.000000"; conf_hi "0.000915"; cov "0.000019";\n+chr1\tCufflinks\texon\t132059397\t132059512\t1000\t+\t.\tgene_id "uc007clw.1"; transcript_id "uc007clw.1"; exon_number "7"; FPKM "0.2051423010"; frac "0.886787"; conf_lo "0.000000"; conf_hi "0.509199"; cov "0.011652";\n+chr1\tCufflinks\texon\t175865141\t175865308\t1000\t-\t.\tgene_id "uc007dsf.1"; transcript_id "uc007dsf.1"; exon_number "5"; FPKM "0.6544444010"; frac "1.000000"; conf_lo "0.068952"; conf_hi "1.239936"; cov "0.037172";\n+chr10\tCufflinks\ttranscript\t7399380\t7400956\t1000\t-\t.\tgene_id "uc007eie.1"; transcript_id "uc007eie.1"; FPKM "2.1099978681"; frac "1.000000"; conf_lo "0.514989"; conf_hi "3.705006"; cov "0.119848";\n+chr10\tCufflinks\texon\t79784826\t79784954\t1000\t-\t.\tgene_id "uc007gcr.1"; transcript_id "uc007gcr.1"; exon_number "2"; FPKM "1.2054582676"; frac "1.000000"; conf_lo "0.000000"; conf_hi "2.597402"; cov "0.068470";\n+chr10\tCufflinks\texon\t79820729\t79820836\t1000\t+\t.\tgene_id "uc007gcy.1"; transcript_id "uc007gcy.1"; exon_number "2"; FPKM "1.8177911161"; frac "1.000000"; conf_lo "0.532419"; conf_hi "3.103164"; cov "0.103250";\n+chr10\tCufflinks\ttranscript\t105907395\t106369573\t1000\t+\t.\tgene_id "uc007gyr.1"; transcript_id "uc007gyr.1"; FPKM "4.2493607936"; frac "0.247216"; conf_lo "3.727223"; conf_hi "4.771499"; cov "0.241364";\n+chr10\tCufflinks\texon\t119487061\t119487172\t1000\t+\t.\tgene_id "uc007hep.1"; transcript_id "uc007hep.1"; exon_number "10"; FPKM "4.3105966126"; frac "0.341843"; conf_lo "3.127417"; conf_hi "5.493776"; cov "0.244842";\n+chr11\tCufflinks\texon\t29097093\t29097209\t1000\t+\t.\tgene_id "uc007igs.1"; transcript_id "uc007igs.1"; exon_number "7"; FPKM "4.2530782301"; frac "1.000000"; conf_lo "2.700074"; conf_hi "5.806083"; cov "0.241575";\n+chr11\tCufflinks\texon\t69404158\t69404264\t1000\t+\t.\tgene_id "uc007jqm.1"; transcript_id "uc007jqm.1"; exon_number "10"; FPKM "18.7450971965"; frac "0.685277"; conf_lo "11.773851"; conf_hi "25.716343"; cov "1.064721";\n+chr11\tCufflinks\ttranscript\t98249986\t98261804\t1000\t-\t.\tgene_id "uc007lgh.1"; transcript_id "uc007lgh.1"; FPKM "2.1571271227"; frac "1.000000"; conf_lo "0.856331"; conf_hi "3.457924"; cov "0.122525";\n+chr11\tCufflinks\texon\t102210141\t102211681\t1000\t-\t.\tgene_id "uc007lrp.1"; transcript_id "uc007lrp.1"; exon_number "1"; FPKM "0.8688186006"; frac "1.000000"; conf_lo "0.254471"; conf_hi "1.483166"; cov "0.049349";\n+chr11\tCufflinks\ttranscript\t105926400\t105927243\t1000\t-\t.\tgene_id "uc007lya.1"; transcript_id "uc007lya.1"; FPKM "3.6706747247"; frac "1.000000"; conf_lo "0.000000"; conf_hi "8.861793"; cov "0.208494";\n+chr11\tCufflinks\texon\t106633966\t'..b'chr6\tCufflinks\ttranscript\t17015149\t17055825\t1000\t+\t.\tgene_id "uc009azi.1"; transcript_id "uc009azi.1"; FPKM "12.3429992456"; frac "1.000000"; conf_lo "9.242902"; conf_hi "15.443097"; cov "0.701082";\n+chr6\tCufflinks\texon\t15361026\t15361102\t1000\t+\t.\tgene_id "uc009ayz.1"; transcript_id "uc009ayz.1"; exon_number "14"; FPKM "4.1692596952"; frac "0.281345"; conf_lo "2.894471"; conf_hi "5.444049"; cov "0.236814";\n+chr6\tCufflinks\texon\t115576309\t115576426\t1000\t-\t.\tgene_id "uc009dix.1"; transcript_id "uc009dix.1"; exon_number "8"; FPKM "34.7320589881"; frac "0.628311"; conf_lo "31.195284"; conf_hi "38.268834"; cov "1.972780";\n+chr6\tCufflinks\texon\t117820274\t117822784\t1000\t+\t.\tgene_id "uc009dld.1"; transcript_id "uc009dld.1"; exon_number "3"; FPKM "8.2141924772"; frac "1.000000"; conf_lo "5.778655"; conf_hi "10.649730"; cov "0.466566";\n+chr6\tCufflinks\texon\t121331667\t121331759\t1000\t-\t.\tgene_id "uc009don.1"; transcript_id "uc009don.1"; exon_number "4"; FPKM "0.9373248338"; frac "0.255959"; conf_lo "0.597786"; conf_hi "1.276864"; cov "0.053240";\n+chr6\tCufflinks\texon\t134837648\t134837803\t1000\t-\t.\tgene_id "uc009ekw.1"; transcript_id "uc009ekw.1"; exon_number "2"; FPKM "3.4342255434"; frac "0.337007"; conf_lo "2.099159"; conf_hi "4.769292"; cov "0.195064";\n+chr7\tCufflinks\texon\t19628774\t19628924\t1000\t+\t.\tgene_id "uc009fkg.1"; transcript_id "uc009fkg.1"; exon_number "14"; FPKM "3.4380795645"; frac "0.240903"; conf_lo "2.901335"; conf_hi "3.974824"; cov "0.195283";\n+chr7\tCufflinks\ttranscript\t51739887\t51740783\t1000\t+\t.\tgene_id "uc009gpo.1"; transcript_id "uc009gpo.1"; FPKM "3.5875651083"; frac "1.000000"; conf_lo "0.658330"; conf_hi "6.516800"; cov "0.203774";\n+chr7\tCufflinks\texon\t53085965\t53086159\t1000\t-\t.\tgene_id "uc009gxj.1"; transcript_id "uc009gxj.1"; exon_number "6"; FPKM "6.4200658663"; frac "0.543693"; conf_lo "4.666748"; conf_hi "8.173383"; cov "0.364660";\n+chr7\tCufflinks\texon\t77546982\t77547077\t1000\t+\t.\tgene_id "uc009hnk.1"; transcript_id "uc009hnk.1"; exon_number "7"; FPKM "0.4622078998"; frac "0.405823"; conf_lo "0.077413"; conf_hi "0.847003"; cov "0.026253";\n+chr7\tCufflinks\texon\t82788205\t82788350\t1000\t+\t.\tgene_id "uc009hwu.1"; transcript_id "uc009hwu.1"; exon_number "1"; FPKM "0.6859341657"; frac "0.576962"; conf_lo "0.055268"; conf_hi "1.316600"; cov "0.038961";\n+chr7\tCufflinks\texon\t85984891\t85985078\t1000\t-\t.\tgene_id "uc009hxo.1"; transcript_id "uc009hxo.1"; exon_number "3"; FPKM "3.0017741434"; frac "1.000000"; conf_lo "1.397258"; conf_hi "4.606290"; cov "0.170501";\n+chr7\tCufflinks\texon\t148509981\t148510078\t1000\t-\t.\tgene_id "uc009kkn.1"; transcript_id "uc009kkn.1"; exon_number "11"; FPKM "32.9197864125"; frac "1.000000"; conf_lo "27.375094"; conf_hi "38.464479"; cov "1.869843";\n+chr9\tCufflinks\texon\t15330072\t15330148\t1000\t+\t.\tgene_id "uc009ogc.1"; transcript_id "uc009ogc.1"; exon_number "2"; FPKM "1.0060367764"; frac "1.000000"; conf_lo "0.000000"; conf_hi "2.428788"; cov "0.057143";\n+chr9\tCufflinks\ttranscript\t21069743\t21078812\t1000\t+\t.\tgene_id "uc009okt.1"; transcript_id "uc009okt.1"; FPKM "7.9134805855"; frac "0.623402"; conf_lo "5.930640"; conf_hi "9.896321"; cov "0.449485";\n+chr9\tCufflinks\texon\t57867100\t57867303\t1000\t+\t.\tgene_id "uc009pwa.1"; transcript_id "uc009pwa.1"; exon_number "4"; FPKM "0.5359102332"; frac "1.000000"; conf_lo "0.000000"; conf_hi "1.293802"; cov "0.030440";\n+chr9\tCufflinks\texon\t49314958\t49315758\t1000\t-\t.\tgene_id "uc009pje.1"; transcript_id "uc009pje.1"; exon_number "2"; FPKM "156.0206032233"; frac "0.793945"; conf_lo "147.369898"; conf_hi "164.671308"; cov "8.861965";\n+chr9\tCufflinks\texon\t106815438\t106815604\t1000\t-\t.\tgene_id "uc009rkv.1"; transcript_id "uc009rkv.1"; exon_number "12"; FPKM "5.4023275754"; frac "1.000000"; conf_lo "4.337713"; conf_hi "6.466942"; cov "0.306852";\n+chr9\tCufflinks\texon\t119703054\t119703292\t1000\t-\t.\tgene_id "uc009sbk.1"; transcript_id "uc009sbk.1"; exon_number "15"; FPKM "0.0814657030"; frac "1.000000"; conf_lo "0.000000"; conf_hi "0.244397"; cov "0.004627";\n\\ No newline at end of file\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/gtf2bedgraph_out.bedgraph
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/gtf2bedgraph_out.bedgraph Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,101 @@
+track type=bedGraph
+chr1 36425949 36426026 4.8386844109
+chr1 46891971 46892996 8.4688567539
+chr1 71654477 71654594 0.4686878995
+chr1 72629844 72679706 4.0695297327
+chr1 75531752 75532000 3.6392661141
+chr1 123389481 123389564 0.9948773061
+chr1 129625989 129626119 0.0003267777
+chr1 132059396 132059512 0.2051423010
+chr1 175865140 175865308 0.6544444010
+chr10 7399379 7400956 2.1099978681
+chr10 79784825 79784954 1.2054582676
+chr10 79820728 79820836 1.8177911161
+chr10 105907394 106369573 4.2493607936
+chr10 119487060 119487172 4.3105966126
+chr11 29097092 29097209 4.2530782301
+chr11 69404157 69404264 18.7450971965
+chr11 98249985 98261804 2.1571271227
+chr11 102210140 102211681 0.8688186006
+chr11 105926399 105927243 3.6706747247
+chr11 106633965 106634066 2.4729108195
+chr11 120472426 120472492 10.2380258574
+chr12 100112716 100112852 1.8669402513
+chr13 8889563 8891614 9.4402522582
+chr13 13756206 13756380 0.0574771218
+chr13 93243917 93244083 6.9802111138
+chr14 13130095 13130170 4.0381928600
+chr14 32036105 32036250 0.1289615781
+chr14 56517079 56517223 15.7683764379
+chr14 62950941 62951013 10.1138803585
+chr14 66479006 66479052 14.3011267395
+chr14 70961618 70961783 2.0814553995
+chr14 96679221 96679434 1.7614342028
+chr14 99504387 99504488 3.1573312214
+chr15 12777807 12777962 12.7118803258
+chr15 28200048 28200282 0.0608801712
+chr15 34434713 34434889 2.1698982510
+chr15 51709055 51716160 5.0213279245
+chr15 54880181 54880296 9.7267082384
+chr15 59176892 59177072 4.5392702144
+chr15 76426649 76426779 3.5730073595
+chr15 76533503 76533613 3.3395072810
+chr15 88963182 88963261 1.5871531781
+chr15 102313590 102313719 37.5792165910
+chr15 102455469 102455519 0.2873090379
+chr16 3979122 3982204 4.1992546925
+chr16 4608597 4608818 5.7793602049
+chr16 20541819 20541939 68.0268643583
+chr17 24857053 24858867 22.0141466642
+chr17 25379603 25380686 1.7458387165
+chr17 27159195 27159462 1.7334774900
+chr18 34787706 34787836 5.0638001964
+chr18 61167369 61167501 2.4172869897
+chr18 61371051 61371250 0.1230526474
+chr18 86630591 86630719 2.2892787327
+chr19 5603633 5603715 2.1837193523
+chr2 28404474 28404676 10.9087431164
+chr2 29770253 29770439 7.2973656902
+chr2 30002171 30002382 12.8769808138
+chr2 32076599 32076704 43.8860660433
+chr2 32546709 32546774 8.1366623064
+chr2 35574279 35574458 2.0012109810
+chr2 117127696 117127757 1.6760710643
+chr2 122435404 122435623 10.5679023498
+chr2 130265171 130265261 3.6318426438
+chr2 152702302 152702428 2.5312142816
+chr2 158262738 158262887 5.0001206267
+chr2 178152210 178152296 1.6796903776
+chr3 97500912 97501137 4.1738869883
+chr3 101987873 101987902 0.6428024028
+chr3 127258213 127258303 0.4060755145
+chr3 144790794 144790854 1.1258808773
+chr4 17978868 17981846 0.6623587694
+chr4 21711839 21711940 0.9584930367
+chr4 108353506 108353731 2.6286767383
+chr4 131325667 131325803 4.0813960015
+chr4 153530640 153530927 21.2412511761
+chr5 3631588 3631765 4.6386616700
+chr5 3992045 3992138 23.3742995121
+chr5 34223635 34223836 4.1101744570
+chr5 115734399 115734621 15.3221708908
+chr5 137807768 137808016 0.7189248975
+chr6 15361025 15361102 4.1692596952
+chr6 17015148 17055825 12.3429992456
+chr6 115576308 115576426 34.7320589881
+chr6 117820273 117822784 8.2141924772
+chr6 121331666 121331759 0.9373248338
+chr6 134837647 134837803 3.4342255434
+chr7 19628773 19628924 3.4380795645
+chr7 51739886 51740783 3.5875651083
+chr7 53085964 53086159 6.4200658663
+chr7 77546981 77547077 0.4622078998
+chr7 82788204 82788350 0.6859341657
+chr7 85984890 85985078 3.0017741434
+chr7 148509980 148510078 32.9197864125
+chr9 15330071 15330148 1.0060367764
+chr9 21069742 21078812 7.9134805855
+chr9 49314957 49315758 156.0206032233
+chr9 57867099 57867303 0.5359102332
+chr9 106815437 106815604 5.4023275754
+chr9 119703053 119703292 0.0814657030

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/gtf_filter_by_attribute_values_list_in1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/gtf_filter_by_attribute_values_list_in1.txt Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,3 @@
+CUFF.50195
+CUFF.50341
+CUFF.50527

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/gtf_filter_by_attribute_values_list_in2.gtf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/gtf_filter_by_attribute_values_list_in2.gtf Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,100 @@\n+chr19\tCufflinks\texon\t22162\t22646\t.\t+\t.\tgene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "1"; oId "uc010drl.1"; class_code "."; tss_id "TSS1";\n+chr19\tCufflinks\texon\t23171\t23274\t.\t+\t.\tgene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "2"; oId "uc010drl.1"; class_code "."; tss_id "TSS1";\n+chr19\tCufflinks\texon\t23585\t23703\t.\t+\t.\tgene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "3"; oId "uc010drl.1"; class_code "."; tss_id "TSS1";\n+chr19\tCufflinks\texon\t58146\t58157\t.\t+\t.\tgene_id "XLOC_000002"; transcript_id "TCONS_00000002"; exon_number "1"; oId "uc002lob.1"; class_code "."; tss_id "TSS2";\n+chr19\tCufflinks\texon\t58473\t58555\t.\t+\t.\tgene_id "XLOC_000002"; transcript_id "TCONS_00000002"; exon_number "2"; oId "uc002lob.1"; class_code "."; tss_id "TSS2";\n+chr19\tCufflinks\texon\t61625\t62417\t.\t+\t.\tgene_id "XLOC_000002"; transcript_id "TCONS_00000002"; exon_number "3"; oId "uc002lob.1"; class_code "."; tss_id "TSS2";\n+chr19\tCufflinks\texon\t61679\t62596\t.\t+\t.\tgene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "1"; oId "uc002loc.1"; class_code ".";\n+chr19\tCufflinks\texon\t447490\t447551\t.\t+\t.\tgene_id "XLOC_000003"; transcript_id "TCONS_00000006"; exon_number "1"; oId "uc010drq.1"; class_code "."; tss_id "TSS3";\n+chr19\tCufflinks\texon\t449496\t449825\t.\t+\t.\tgene_id "XLOC_000003"; transcript_id "TCONS_00000006"; exon_number "2"; oId "uc010drq.1"; class_code "."; tss_id "TSS3";\n+chr19\tCufflinks\texon\t455745\t456343\t.\t+\t.\tgene_id "XLOC_000003"; transcript_id "TCONS_00000006"; exon_number "3"; oId "uc010drq.1"; class_code "."; tss_id "TSS3";\n+chr19\tCufflinks\texon\t447490\t447551\t.\t+\t.\tgene_id "XLOC_000003"; transcript_id "TCONS_00000005"; exon_number "1"; oId "uc002lot.1"; class_code "."; tss_id "TSS3";\n+chr19\tCufflinks\texon\t448833\t449117\t.\t+\t.\tgene_id "XLOC_000003"; transcript_id "TCONS_00000005"; exon_number "2"; oId "uc002lot.1"; class_code "."; tss_id "TSS3";\n+chr19\tCufflinks\texon\t449496\t449825\t.\t+\t.\tgene_id "XLOC_000003"; transcript_id "TCONS_00000005"; exon_number "3"; oId "uc002lot.1"; class_code "."; tss_id "TSS3";\n+chr19\tCufflinks\texon\t455745\t456343\t.\t+\t.\tgene_id "XLOC_000003"; transcript_id "TCONS_00000005"; exon_number "4"; oId "uc002lot.1"; class_code "."; tss_id "TSS3";\n+chr19\tCufflinks\texon\t447490\t447551\t.\t+\t.\tgene_id "XLOC_000003"; transcript_id "TCONS_00000004"; exon_number "1"; oId "uc002los.1"; class_code "."; tss_id "TSS3";\n+chr19\tCufflinks\texon\t448833\t449117\t.\t+\t.\tgene_id "XLOC_000003"; transcript_id "TCONS_00000004"; exon_number "2"; oId "uc002los.1"; class_code "."; tss_id "TSS3";\n+chr19\tCufflinks\texon\t449496\t449825\t.\t+\t.\tgene_id "XLOC_000003"; transcript_id "TCONS_00000004"; exon_number "3"; oId "uc002los.1"; class_code "."; tss_id "TSS3";\n+chr19\tCufflinks\texon\t452669\t452929\t.\t+\t.\tgene_id "XLOC_000003"; transcript_id "TCONS_00000004"; exon_number "4"; oId "uc002los.1"; class_code "."; tss_id "TSS3";\n+chr19\tCufflinks\texon\t455745\t456343\t.\t+\t.\tgene_id "XLOC_000003"; transcript_id "TCONS_00000004"; exon_number "5"; oId "uc002los.1"; class_code "."; tss_id "TSS3";\n+chr19\tCufflinks\texon\t458497\t458844\t.\t+\t.\tgene_id "XLOC_000004"; transcript_id "TCONS_00000007"; exon_number "1"; oId "uc002lou.1"; class_code "."; tss_id "TSS4";\n+chr19\tCufflinks\texon\t469889\t470654\t.\t+\t.\tgene_id "XLOC_000004"; transcript_id "TCONS_00000007"; exon_number "2"; oId "uc002lou.1"; class_code "."; tss_id "TSS4";\n+chr19\tCufflinks\texon\t482733\t483108\t.\t+\t.\tgene_id "XLOC_000005"; transcript_id "TCONS_00000008"; exon_number "1"; oId "uc002lov.1"; class_code "."; tss_id "TSS5";\n+chr19\tCufflinks\texon\t486837\t486923\t.\t+\t.\tgene_id "XLOC_000005"; transcript_id "TCONS_00000008"; exon_number "2"; oId "uc002lov.1"; class_code "."; tss_id "TSS5";\n+chr19\tCufflinks\texon\t487243\t487340\t.\t+\t.\tgene_id "XLOC_000005"; transcript_id "TCONS_00000008"; exon_number "3"; oId "uc002lov.1"; class_code "."; tss_id "TSS5";\n+chr19\tCufflinks\texon\t488013\t488147\t.\t+\t.\tgene_id "XLOC_000005"; transcript_id "TCONS_00000008"; e'..b'n_number "7"; oId "uc002lpc.1"; class_code "."; tss_id "TSS9";\n+chr19\tCufflinks\texon\t533496\t533582\t.\t+\t.\tgene_id "XLOC_000007"; transcript_id "TCONS_00000016"; exon_number "1"; oId "uc002lpd.1"; class_code "."; tss_id "TSS10";\n+chr19\tCufflinks\texon\t533750\t534493\t.\t+\t.\tgene_id "XLOC_000007"; transcript_id "TCONS_00000016"; exon_number "2"; oId "uc002lpd.1"; class_code "."; tss_id "TSS10";\n+chr19\tCufflinks\texon\t540893\t541577\t.\t+\t.\tgene_id "XLOC_000008"; transcript_id "TCONS_00000017"; exon_number "1"; oId "uc002lpe.1"; class_code "."; tss_id "TSS11";\n+chr19\tCufflinks\texon\t554544\t554967\t.\t+\t.\tgene_id "XLOC_000008"; transcript_id "TCONS_00000017"; exon_number "2"; oId "uc002lpe.1"; class_code "."; tss_id "TSS11";\n+chr19\tCufflinks\texon\t556061\t556222\t.\t+\t.\tgene_id "XLOC_000008"; transcript_id "TCONS_00000017"; exon_number "3"; oId "uc002lpe.1"; class_code "."; tss_id "TSS11";\n+chr19\tCufflinks\texon\t558964\t559182\t.\t+\t.\tgene_id "XLOC_000008"; transcript_id "TCONS_00000017"; exon_number "4"; oId "uc002lpe.1"; class_code "."; tss_id "TSS11";\n+chr19\tCufflinks\texon\t561259\t561405\t.\t+\t.\tgene_id "XLOC_000008"; transcript_id "TCONS_00000017"; exon_number "5"; oId "uc002lpe.1"; class_code "."; tss_id "TSS11";\n+chr19\tCufflinks\texon\t564248\t564488\t.\t+\t.\tgene_id "XLOC_000008"; transcript_id "TCONS_00000017"; exon_number "6"; oId "uc002lpe.1"; class_code "."; tss_id "TSS11";\n+chr19\tCufflinks\texon\t564852\t565016\t.\t+\t.\tgene_id "XLOC_000008"; transcript_id "TCONS_00000017"; exon_number "7"; oId "uc002lpe.1"; class_code "."; tss_id "TSS11";\n+chr19\tCufflinks\texon\t566795\t568159\t.\t+\t.\tgene_id "XLOC_000008"; transcript_id "TCONS_00000017"; exon_number "8"; oId "uc002lpe.1"; class_code "."; tss_id "TSS11";\n+chr19\tCufflinks\texon\t590926\t591139\t.\t+\t.\tgene_id "XLOC_000009"; transcript_id "TCONS_00000018"; exon_number "1"; oId "uc002lpg.1"; class_code "."; tss_id "TSS12";\n+chr19\tCufflinks\texon\t594235\t594338\t.\t+\t.\tgene_id "XLOC_000009"; transcript_id "TCONS_00000018"; exon_number "2"; oId "uc002lpg.1"; class_code "."; tss_id "TSS12";\n+chr19\tCufflinks\texon\t594410\t594604\t.\t+\t.\tgene_id "XLOC_000009"; transcript_id "TCONS_00000018"; exon_number "3"; oId "uc002lpg.1"; class_code "."; tss_id "TSS12";\n+chr19\tCufflinks\texon\t627389\t627526\t.\t+\t.\tgene_id "XLOC_000010"; transcript_id "TCONS_00000019"; exon_number "1"; oId "uc002lpk.1"; class_code "."; tss_id "TSS13";\n+chr19\tCufflinks\texon\t628792\t628977\t.\t+\t.\tgene_id "XLOC_000010"; transcript_id "TCONS_00000019"; exon_number "2"; oId "uc002lpk.1"; class_code "."; tss_id "TSS13";\n+chr19\tCufflinks\texon\t631274\t631489\t.\t+\t.\tgene_id "XLOC_000010"; transcript_id "TCONS_00000019"; exon_number "3"; oId "uc002lpk.1"; class_code "."; tss_id "TSS13";\n+chr19\tCufflinks\texon\t632333\t632560\t.\t+\t.\tgene_id "XLOC_000010"; transcript_id "TCONS_00000019"; exon_number "4"; oId "uc002lpk.1"; class_code "."; tss_id "TSS13";\n+chr19\tCufflinks\texon\t632650\t634392\t.\t+\t.\tgene_id "XLOC_000010"; transcript_id "TCONS_00000019"; exon_number "5"; oId "uc002lpk.1"; class_code "."; tss_id "TSS13";\n+chr19\tCufflinks\texon\t631715\t631879\t.\t+\t.\tgene_id "XLOC_000010"; transcript_id "TCONS_00000020"; exon_number "1"; oId "uc010drt.1"; class_code "."; tss_id "TSS14";\n+chr19\tCufflinks\texon\t632333\t632560\t.\t+\t.\tgene_id "XLOC_000010"; transcript_id "TCONS_00000020"; exon_number "2"; oId "uc010drt.1"; class_code "."; tss_id "TSS14";\n+chr19\tCufflinks\texon\t632650\t634392\t.\t+\t.\tgene_id "XLOC_000010"; transcript_id "TCONS_00000020"; exon_number "3"; oId "uc010drt.1"; class_code "."; tss_id "TSS14";\n+chr19\tCufflinks\texon\t659953\t660151\t.\t+\t.\tgene_id "XLOC_000011"; transcript_id "TCONS_00000022"; exon_number "1"; oId "uc002lpn.1"; class_code "."; tss_id "TSS15";\n+chr19\tCufflinks\texon\t677138\t677189\t.\t+\t.\tgene_id "XLOC_000011"; transcript_id "TCONS_00000022"; exon_number "2"; oId "uc002lpn.1"; class_code "."; tss_id "TSS15";\n+chr19\tCufflinks\texon\t678008\t678088\t.\t+\t.\tgene_id "XLOC_000011"; transcript_id "TCONS_00000022"; exon_number "3"; oId "uc002lpn.1"; class_code "."; tss_id "TSS15";\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/gtf_filter_by_attribute_values_list_in3.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/gtf_filter_by_attribute_values_list_in3.tabular Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,10 @@
+tracking_id class_code nearest_ref_id gene_short_name tss_id locus q1_FPKM q1_conf_lo q1_conf_hi q2_FPKM q2_conf_lo q2_conf_hi
+TCONS_00000003 - - - TSS1 chr14:64816731-64817486 5464.24 5316.39 5612.08 4938.79 4798.23 5079.34
+TCONS_00000006 - - - TSS2 chr19:486851-492890 1259.06 480.159 2037.96 1981.03 1161.83 2800.24
+TCONS_00000007 - - - TSS2 chr19:486851-492890 9975.16 9741.29 10209 2149.43 1991.62 2307.25
+TCONS_00000008 - - - TSS3 chr19:522317-532652 1260.19 918.688 1601.68 25755.1 24169.1 27341.1
+TCONS_00000009 - - - TSS4 chr19:522317-532652 66438.8 65553.7 67323.8 16095.5 15285.1 16905.9
+TCONS_00000010 - - - TSS4 chr19:522317-532652 12.8837 0 110.959 14580.2 11400.9 17759.4
+TCONS_00000011 - - - TSS5 chr19:533532-534490 21906.7 21610.7 22202.7 5488.26 5340.09 5636.42
+TCONS_00000012 - - - TSS6 chr19:748410-763253 7821.71 7147.91 8495.52 3711.15 3257.64 4164.67
+TCONS_00000013 - - - TSS6 chr19:748410-763253 15248.8 14297.2 16200.4 9310.77 8823.77 9797.77

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/gtf_filter_by_attribute_values_list_out1.gtf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/gtf_filter_by_attribute_values_list_out1.gtf Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,9 @@
+chr13 Cufflinks transcript 3565855 3566203 1000 - . gene_id "CUFF.50195"; transcript_id "CUFF.50195.1"; FPKM "29.8710998584"; frac "1.000000"; conf_lo "7.290671"; conf_hi "52.451529"; cov "1.909091";
+chr13 Cufflinks exon 3565855 3565913 1000 - . gene_id "CUFF.50195"; transcript_id "CUFF.50195.1"; exon_number "1"; FPKM "29.8710998584"; frac "1.000000"; conf_lo "7.290671"; conf_hi "52.451529"; cov "1.909091";
+chr13 Cufflinks exon 3566164 3566203 1000 - . gene_id "CUFF.50195"; transcript_id "CUFF.50195.1"; exon_number "2"; FPKM "29.8710998584"; frac "1.000000"; conf_lo "7.290671"; conf_hi "52.451529"; cov "1.909091";
+chr13 Cufflinks transcript 6586295 6587966 1000 - . gene_id "CUFF.50341"; transcript_id "CUFF.50341.1"; FPKM "82.5011329424"; frac "1.000000"; conf_lo "60.835274"; conf_hi "104.166992"; cov "5.272727";
+chr13 Cufflinks exon 6586295 6586359 1000 - . gene_id "CUFF.50341"; transcript_id "CUFF.50341.1"; exon_number "1"; FPKM "82.5011329424"; frac "1.000000"; conf_lo "60.835274"; conf_hi "104.166992"; cov "5.272727";
+chr13 Cufflinks exon 6587735 6587966 1000 - . gene_id "CUFF.50341"; transcript_id "CUFF.50341.1"; exon_number "2"; FPKM "82.5011329424"; frac "1.000000"; conf_lo "60.835274"; conf_hi "104.166992"; cov "5.272727";
+chr13 Cufflinks transcript 9353602 9373527 1000 - . gene_id "CUFF.50527"; transcript_id "CUFF.50527.1"; FPKM "16.2485653076"; frac "1.000000"; conf_lo "0.000000"; conf_hi "35.010792"; cov "1.038462";
+chr13 Cufflinks exon 9353602 9353648 1000 - . gene_id "CUFF.50527"; transcript_id "CUFF.50527.1"; exon_number "1"; FPKM "16.2485653076"; frac "1.000000"; conf_lo "0.000000"; conf_hi "35.010792"; cov "1.038462";
+chr13 Cufflinks exon 9373497 9373527 1000 - . gene_id "CUFF.50527"; transcript_id "CUFF.50527.1"; exon_number "2"; FPKM "16.2485653076"; frac "1.000000"; conf_lo "0.000000"; conf_hi "35.010792"; cov "1.038462";

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/gtf_filter_by_attribute_values_list_out2.gtf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/gtf_filter_by_attribute_values_list_out2.gtf Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,48 @@
+chr19 Cufflinks exon 61679 62596 . + . gene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "1"; oId "uc002loc.1"; class_code ".";
+chr19 Cufflinks exon 447490 447551 . + . gene_id "XLOC_000003"; transcript_id "TCONS_00000006"; exon_number "1"; oId "uc010drq.1"; class_code "."; tss_id "TSS3";
+chr19 Cufflinks exon 449496 449825 . + . gene_id "XLOC_000003"; transcript_id "TCONS_00000006"; exon_number "2"; oId "uc010drq.1"; class_code "."; tss_id "TSS3";
+chr19 Cufflinks exon 455745 456343 . + . gene_id "XLOC_000003"; transcript_id "TCONS_00000006"; exon_number "3"; oId "uc010drq.1"; class_code "."; tss_id "TSS3";
+chr19 Cufflinks exon 458497 458844 . + . gene_id "XLOC_000004"; transcript_id "TCONS_00000007"; exon_number "1"; oId "uc002lou.1"; class_code "."; tss_id "TSS4";
+chr19 Cufflinks exon 469889 470654 . + . gene_id "XLOC_000004"; transcript_id "TCONS_00000007"; exon_number "2"; oId "uc002lou.1"; class_code "."; tss_id "TSS4";
+chr19 Cufflinks exon 482733 483108 . + . gene_id "XLOC_000005"; transcript_id "TCONS_00000008"; exon_number "1"; oId "uc002lov.1"; class_code "."; tss_id "TSS5";
+chr19 Cufflinks exon 486837 486923 . + . gene_id "XLOC_000005"; transcript_id "TCONS_00000008"; exon_number "2"; oId "uc002lov.1"; class_code "."; tss_id "TSS5";
+chr19 Cufflinks exon 487243 487340 . + . gene_id "XLOC_000005"; transcript_id "TCONS_00000008"; exon_number "3"; oId "uc002lov.1"; class_code "."; tss_id "TSS5";
+chr19 Cufflinks exon 488013 488147 . + . gene_id "XLOC_000005"; transcript_id "TCONS_00000008"; exon_number "4"; oId "uc002lov.1"; class_code "."; tss_id "TSS5";
+chr19 Cufflinks exon 492339 493087 . + . gene_id "XLOC_000005"; transcript_id "TCONS_00000008"; exon_number "5"; oId "uc002lov.1"; class_code "."; tss_id "TSS5";
+chr19 Cufflinks exon 495027 495126 . + . gene_id "XLOC_000006"; transcript_id "TCONS_00000009"; exon_number "1"; oId "uc002low.1"; class_code "."; tss_id "TSS6";
+chr19 Cufflinks exon 498280 498436 . + . gene_id "XLOC_000006"; transcript_id "TCONS_00000009"; exon_number "2"; oId "uc002low.1"; class_code "."; tss_id "TSS6";
+chr19 Cufflinks exon 499542 499677 . + . gene_id "XLOC_000006"; transcript_id "TCONS_00000009"; exon_number "3"; oId "uc002low.1"; class_code "."; tss_id "TSS6";
+chr19 Cufflinks exon 499922 500185 . + . gene_id "XLOC_000006"; transcript_id "TCONS_00000009"; exon_number "4"; oId "uc002low.1"; class_code "."; tss_id "TSS6";
+chr19 Cufflinks exon 500630 500919 . + . gene_id "XLOC_000006"; transcript_id "TCONS_00000009"; exon_number "5"; oId "uc002low.1"; class_code "."; tss_id "TSS6";
+chr19 Cufflinks exon 522325 522579 . + . gene_id "XLOC_000007"; transcript_id "TCONS_00000010"; exon_number "1"; oId "uc002loy.1"; class_code "."; tss_id "TSS7";
+chr19 Cufflinks exon 531379 531461 . + . gene_id "XLOC_000007"; transcript_id "TCONS_00000010"; exon_number "2"; oId "uc002loy.1"; class_code "."; tss_id "TSS7";
+chr19 Cufflinks exon 531646 531782 . + . gene_id "XLOC_000007"; transcript_id "TCONS_00000010"; exon_number "3"; oId "uc002loy.1"; class_code "."; tss_id "TSS7";
+chr19 Cufflinks exon 532315 532591 . + . gene_id "XLOC_000007"; transcript_id "TCONS_00000010"; exon_number "4"; oId "uc002loy.1"; class_code "."; tss_id "TSS7";
+chr19 Cufflinks exon 533306 533330 . + . gene_id "XLOC_000007"; transcript_id "TCONS_00000010"; exon_number "5"; oId "uc002loy.1"; class_code "."; tss_id "TSS7";
+chr19 Cufflinks exon 533514 533582 . + . gene_id "XLOC_000007"; transcript_id "TCONS_00000010"; exon_number "6"; oId "uc002loy.1"; class_code "."; tss_id "TSS7";
+chr19 Cufflinks exon 533750 534493 . + . gene_id "XLOC_000007"; transcript_id "TCONS_00000010"; exon_number "7"; oId "uc002loy.1"; class_code "."; tss_id "TSS7";
+chr19 Cufflinks exon 523537 523701 . + . gene_id "XLOC_000007"; transcript_id "TCONS_00000013"; exon_number "1"; oId "uc002lpb.1"; class_code "."; tss_id "TSS8";
+chr19 Cufflinks exon 530500 530656 . + . gene_id "XLOC_000007"; transcript_id "TCONS_00000013"; exon_number "2"; oId "uc002lpb.1"; class_code "."; tss_id "TSS8";
+chr19 Cufflinks exon 531379 531461 . + . gene_id "XLOC_000007"; transcript_id "TCONS_00000013"; exon_number "3"; oId "uc002lpb.1"; class_code "."; tss_id "TSS8";
+chr19 Cufflinks exon 531646 531782 . + . gene_id "XLOC_000007"; transcript_id "TCONS_00000013"; exon_number "4"; oId "uc002lpb.1"; class_code "."; tss_id "TSS8";
+chr19 Cufflinks exon 532315 532581 . + . gene_id "XLOC_000007"; transcript_id "TCONS_00000013"; exon_number "5"; oId "uc002lpb.1"; class_code "."; tss_id "TSS8";
+chr19 Cufflinks exon 533306 533330 . + . gene_id "XLOC_000007"; transcript_id "TCONS_00000013"; exon_number "6"; oId "uc002lpb.1"; class_code "."; tss_id "TSS8";
+chr19 Cufflinks exon 533514 533582 . + . gene_id "XLOC_000007"; transcript_id "TCONS_00000013"; exon_number "7"; oId "uc002lpb.1"; class_code "."; tss_id "TSS8";
+chr19 Cufflinks exon 533750 534493 . + . gene_id "XLOC_000007"; transcript_id "TCONS_00000013"; exon_number "8"; oId "uc002lpb.1"; class_code "."; tss_id "TSS8";
+chr19 Cufflinks exon 523537 523701 . + . gene_id "XLOC_000007"; transcript_id "TCONS_00000012"; exon_number "1"; oId "uc002lpa.1"; class_code "."; tss_id "TSS8";
+chr19 Cufflinks exon 530500 530656 . + . gene_id "XLOC_000007"; transcript_id "TCONS_00000012"; exon_number "2"; oId "uc002lpa.1"; class_code "."; tss_id "TSS8";
+chr19 Cufflinks exon 531379 531461 . + . gene_id "XLOC_000007"; transcript_id "TCONS_00000012"; exon_number "3"; oId "uc002lpa.1"; class_code "."; tss_id "TSS8";
+chr19 Cufflinks exon 531646 531782 . + . gene_id "XLOC_000007"; transcript_id "TCONS_00000012"; exon_number "4"; oId "uc002lpa.1"; class_code "."; tss_id "TSS8";
+chr19 Cufflinks exon 532315 532591 . + . gene_id "XLOC_000007"; transcript_id "TCONS_00000012"; exon_number "5"; oId "uc002lpa.1"; class_code "."; tss_id "TSS8";
+chr19 Cufflinks exon 533306 533330 . + . gene_id "XLOC_000007"; transcript_id "TCONS_00000012"; exon_number "6"; oId "uc002lpa.1"; class_code "."; tss_id "TSS8";
+chr19 Cufflinks exon 533514 533582 . + . gene_id "XLOC_000007"; transcript_id "TCONS_00000012"; exon_number "7"; oId "uc002lpa.1"; class_code "."; tss_id "TSS8";
+chr19 Cufflinks exon 533750 534493 . + . gene_id "XLOC_000007"; transcript_id "TCONS_00000012"; exon_number "8"; oId "uc002lpa.1"; class_code "."; tss_id "TSS8";
+chr19 Cufflinks exon 523537 523701 . + . gene_id "XLOC_000007"; transcript_id "TCONS_00000011"; exon_number "1"; oId "uc002loz.1"; class_code "."; tss_id "TSS8";
+chr19 Cufflinks exon 528774 529121 . + . gene_id "XLOC_000007"; transcript_id "TCONS_00000011"; exon_number "2"; oId "uc002loz.1"; class_code "."; tss_id "TSS8";
+chr19 Cufflinks exon 530500 530656 . + . gene_id "XLOC_000007"; transcript_id "TCONS_00000011"; exon_number "3"; oId "uc002loz.1"; class_code "."; tss_id "TSS8";
+chr19 Cufflinks exon 531379 531461 . + . gene_id "XLOC_000007"; transcript_id "TCONS_00000011"; exon_number "4"; oId "uc002loz.1"; class_code "."; tss_id "TSS8";
+chr19 Cufflinks exon 531646 531782 . + . gene_id "XLOC_000007"; transcript_id "TCONS_00000011"; exon_number "5"; oId "uc002loz.1"; class_code "."; tss_id "TSS8";
+chr19 Cufflinks exon 532315 532591 . + . gene_id "XLOC_000007"; transcript_id "TCONS_00000011"; exon_number "6"; oId "uc002loz.1"; class_code "."; tss_id "TSS8";
+chr19 Cufflinks exon 533306 533330 . + . gene_id "XLOC_000007"; transcript_id "TCONS_00000011"; exon_number "7"; oId "uc002loz.1"; class_code "."; tss_id "TSS8";
+chr19 Cufflinks exon 533514 533582 . + . gene_id "XLOC_000007"; transcript_id "TCONS_00000011"; exon_number "8"; oId "uc002loz.1"; class_code "."; tss_id "TSS8";
+chr19 Cufflinks exon 533750 534493 . + . gene_id "XLOC_000007"; transcript_id "TCONS_00000011"; exon_number "9"; oId "uc002loz.1"; class_code "."; tss_id "TSS8";

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/hg17chr22KnownGenes.dat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/hg17chr22KnownGenes.dat Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,964 @@\n+chr22\t14535540\t14538299\tBC066547\t0\t-\t14537305\t14537938\t0\t1\t2759,\t0,\n+chr22\t14538790\t14572995\tBX248778\t0\t-\t14538811\t14539138\t0\t8\t599,91,136,114,112,148,111,90,\t0,3606,28020,28374,30241,30473,31890,34115,\n+chr22\t14823377\t14824358\tNM_001005239\t0\t-\t14823377\t14824358\t0\t1\t981,\t0,\n+chr22\t15342446\t15343766\tAY026350\t0\t+\t15342479\t15343061\t0\t1\t1320,\t0,\n+chr22\t15446203\t15448254\tNM_014406\t0\t-\t15446320\t15447994\t0\t1\t2051,\t0,\n+chr22\t15504251\t15506384\tAK095032\t0\t+\t15504572\t15504974\t0\t1\t2133,\t0,\n+chr22\t15638923\t15677136\tBC045548\t0\t-\t15639062\t15663517\t0\t4\t930,254,345,86,\t0,16291,24259,38127,\n+chr22\t15940411\t15965941\tNM_014339\t0\t+\t15940535\t15965264\t0\t13\t262,25,147,113,127,48,164,84,85,12,102,42,2191,\t0,12094,12829,13807,15387,17028,17171,18526,19758,20623,20885,22759,23339,\n+chr22\t15971743\t15976697\tNM_031890\t0\t-\t15974834\t15976571\t0\t1\t4954,\t0,\n+chr22\t15992964\t16014723\tNM_033070\t0\t-\t15993464\t16014695\t0\t8\t837,189,175,34,94,113,204,154,\t0,1029,3538,5577,7503,10927,12021,21605,\n+chr22\t15992964\t16020731\tNM_017829\t0\t-\t15993464\t16020688\t0\t8\t837,189,175,34,94,113,204,79,\t0,1029,3538,5577,7503,10927,12021,27688,\n+chr22\t16034745\t16055099\tNM_177405\t0\t-\t16036926\t16055022\t0\t7\t2275,203,158,109,91,128,107,\t0,2518,3302,9037,10640,12381,20247,\n+chr22\t16034747\t16065333\tNM_017424\t0\t-\t16036926\t16065121\t0\t9\t2273,203,158,109,91,128,211,220,534,\t0,2516,3300,9035,10638,12379,24259,27767,30052,\n+chr22\t16042774\t16053967\tAK130623\t0\t-\t16053157\t16053556\t0\t2\t33,1379,\t0,9814,\n+chr22\t16331181\t16407586\tAL832377\t0\t+\t16353079\t16407094\t0\t18\t97,184,140,105,50,170,84,154,130,38,92,127,389,129,847,1417,112,498,\t0,19807,21814,23035,25486,27251,34217,46516,60164,61581,61701,62054,63473,64900,65218,71210,75088,75907,\n+chr22\t16331181\t16408399\tAF336133\t0\t+\t16353079\t16407094\t0\t18\t97,184,140,105,50,170,84,210,134,38,92,127,389,129,847,1417,112,1311,\t0,19807,21814,23035,25486,27251,34217,46516,60160,61581,61701,62054,63473,64900,65218,71210,75088,75907,\n+chr22\t16403242\t16408387\tAK091754\t0\t+\t16403257\t16404572\t0\t4\t566,167,112,1299,\t0,1239,3027,3846,\n+chr22\t16417736\t16448201\tNM_031481\t0\t+\t16437264\t16447556\t0\t11\t231,63,220,123,56,91,119,166,155,76,787,\t0,6806,19328,20620,20941,22146,22999,26719,27508,29173,29678,\n+chr22\t16449478\t16486089\tNM_001696\t0\t-\t16449993\t16485955\t0\t9\t578,88,95,69,90,67,110,66,167,\t0,2370,6035,7868,8933,20653,21052,27302,36444,\n+chr22\t16496038\t16586541\tNM_015367\t0\t+\t16513031\t16584854\t0\t7\t168,171,108,157,70,144,2545,\t0,16943,44495,50267,57422,63524,87958,\n+chr22\t16496091\t16561053\tCR608603\t0\t+\t16513031\t16559712\t0\t6\t115,171,108,157,70,1491,\t0,16890,44442,50214,57369,63471,\n+chr22\t16496130\t16587937\tAL831982\t0\t+\t16513031\t16584126\t0\t5\t76,171,108,157,3941,\t0,16851,44403,50175,87866,\n+chr22\t16496144\t16586023\tBC007658\t0\t+\t16559592\t16584854\t0\t7\t62,171,108,157,70,144,2027,\t0,16837,44389,50161,57316,63418,87852,\n+chr22\t16513031\t16584854\tAF539453\t0\t+\t16513031\t16542014\t0\t5\t121,108,98,157,858,\t0,27502,28897,33274,70965,\n+chr22\t16546303\t16586541\tAF146568\t0\t+\t16546373\t16584854\t0\t4\t159,70,144,2545,\t0,7157,13259,37693,\n+chr22\t16591459\t16631812\tNM_001196\t0\t-\t16592899\t16607436\t0\t6\t1452,213,140,211,70,112,\t0,3877,5209,9663,15965,40241,\n+chr22\t16591459\t16631333\tNM_197966\t0\t-\t16592899\t16631009\t0\t6\t1452,213,140,211,70,404,\t0,3877,5209,9663,15965,39470,\n+chr22\t16592818\t16631732\tAY005151\t0\t-\t16596712\t16607436\t0\t7\t93,213,140,95,211,70,32,\t0,2518,3850,4583,8304,14606,38882,\n+chr22\t16634641\t16636801\tAK097861\t0\t+\t16634856\t16635369\t0\t1\t2160,\t0,\n+chr22\t16698994\t16764147\tCR456364\t0\t-\t16699095\t16764132\t0\t19\t343,88,89,187,174,63,113,197,148,97,127,116,258,101,156,102,117,208,279,\t0,23224,24249,30162,44203,45495,45648,47359,49810,52133,53609,54571,55049,57773,59167,60203,60956,62957,64874,\n+chr22\t16719761\t16721799\tAK124853\t0\t-\t16720930\t16721356\t0\t1\t2038,\t0,\n+chr22\t16816353\t16818604\tAK094477\t0\t-\t16817923\t16818349\t0\t1\t2251,\t0,\n+chr22\t16886704\t16895288\tAK123935\t0\t+\t16894400\t16894982\t0\t2\t170,2209,\t0,6375,\n+chr22\t16934505\t16936204\tAK000085\t0\t-\t16935437\t16936076\t0\t1\t1699,\t0,\n+chr22\t16935242\t1694879'..b'102,1491,2256,2444,2613,2748,2964,\n+chr22\t49231523\t49236257\tNM_033200\t0\t-\t49231963\t49235627\t0\t14\t749,97,112,169,183,97,106,135,142,179,218,29,339,103,\t0,857,1389,1608,1851,2106,2278,2452,2723,3084,3334,3687,3831,4631,\n+chr22\t49231527\t49236253\tBC002942\t0\t-\t49231963\t49236248\t0\t14\t745,97,112,169,183,97,106,135,142,179,218,29,254,99,\t0,853,1385,1604,1847,2102,2274,2448,2719,3080,3330,3683,3827,4627,\n+chr22\t49236815\t49248324\tNM_014551\t0\t+\t49245061\t49247932\t0\t9\t203,102,56,85,69,80,146,84,562,\t0,8204,9184,9334,9498,9730,9890,10406,10947,\n+chr22\t49236816\t49252044\tBC001298\t0\t+\t49245061\t49251832\t0\t19\t202,102,56,85,69,80,146,84,131,72,67,108,54,71,73,69,50,102,455,\t0,8203,9183,9333,9497,9729,9889,10405,10946,12721,13299,13497,13742,13937,14099,14257,14427,14577,14773,\n+chr22\t49236831\t49252044\tNM_152299\t0\t+\t49245061\t49251948\t0\t20\t187,102,56,85,69,80,146,84,131,72,67,108,54,71,73,69,50,102,150,237,\t0,8188,9168,9318,9482,9714,9874,10390,10931,12706,13284,13482,13727,13922,14084,14242,14412,14562,14758,14976,\n+chr22\t49236831\t49252044\tBC001937\t0\t+\t49236910\t49251948\t0\t20\t187,102,56,85,69,80,146,84,131,72,67,108,54,71,73,69,50,102,150,237,\t0,8188,9168,9318,9482,9714,9874,10390,10931,12706,13284,13482,13727,13922,14084,14242,14412,14562,14758,14976,\n+chr22\t49236832\t49252043\tBC009441\t0\t+\t49236910\t49251948\t0\t20\t186,102,56,85,69,80,146,84,131,72,67,108,54,71,73,72,50,102,150,236,\t0,8187,9167,9317,9481,9713,9873,10389,10930,12705,13283,13481,13726,13921,14083,14238,14411,14561,14757,14975,\n+chr22\t49236832\t49252043\tBC009441\t0\t+\t49245061\t49251948\t0\t20\t186,102,56,85,69,80,146,84,131,72,67,108,54,71,73,72,50,102,150,236,\t0,8187,9167,9317,9481,9713,9873,10389,10930,12705,13283,13481,13726,13921,14083,14238,14411,14561,14757,14975,\n+chr22\t49252142\t49254116\tNM_005138\t0\t-\t49252183\t49252984\t0\t2\t855,72,\t0,1902,\n+chr22\t49254324\t49258599\tNM_001953\t0\t-\t49254342\t49258282\t0\t10\t167,141,231,163,119,130,99,203,224,123,\t0,249,494,824,1413,1836,2760,3384,3744,4152,\n+chr22\t49258282\t49260395\tS72487\t0\t-\t49260065\t49260230\t0\t4\t851,117,122,632,\t0,1002,1227,1481,\n+chr22\t49276605\t49278685\tNM_138433\t0\t+\t49277036\t49278524\t0\t1\t2080,\t0,\n+chr22\t49297433\t49307022\tNM_004377\t0\t-\t49297910\t49306488\t0\t19\t561,93,114,153,135,165,117,106,186,196,85,108,78,138,102,178,140,160,64,\t0,715,1432,2030,2297,2514,3145,3342,4014,4659,5474,5632,7174,7337,7675,7996,8463,8914,9525,\n+chr22\t49307530\t49311538\tNM_005198\t0\t-\t49307753\t49311354\t0\t11\t298,82,104,109,82,59,96,134,114,109,408,\t0,468,769,1016,1232,1400,1607,2462,2791,3291,3600,\n+chr22\t49311598\t49312310\tCR456603\t0\t+\t49311602\t49311719\t0\t2\t298,140,\t0,572,\n+chr22\t49329274\t49340120\tNM_139124\t0\t+\t49329391\t49339351\t0\t11\t182,106,93,358,76,173,110,108,71,99,842,\t0,1087,2521,4004,4665,4859,5122,5955,6218,9509,10004,\n+chr22\t49353599\t49356720\tNM_000487\t0\t-\t49353716\t49356345\t0\t8\t437,103,128,125,170,219,241,593,\t0,551,908,1126,1563,1806,2138,2528,\n+chr22\t49353600\t49356715\tBC014210\t0\t-\t49353716\t49356351\t0\t8\t436,103,128,125,170,219,241,588,\t0,550,907,1125,1562,1805,2137,2527,\n+chr22\t49383785\t49386505\tAK127606\t0\t-\t49384128\t49384557\t0\t1\t2720,\t0,\n+chr22\t49466790\t49473870\tNM_001097\t0\t+\t49466807\t49473779\t0\t5\t94,204,284,146,646,\t0,1052,1475,5842,6434,\n+chr22\t49485657\t49528078\tNM_203477\t0\t+\t49527348\t49527714\t0\t4\t241,175,121,852,\t0,26034,28087,41569,\n+chr22\t49496063\t49512231\tNM_007081\t0\t-\t49497347\t49510866\t0\t9\t1383,84,95,112,80,80,30,160,159,\t0,1549,1963,2413,8280,9178,10460,14696,16009,\n+chr22\t49496063\t49512231\tNM_001003789\t0\t-\t49497347\t49510866\t0\t9\t1383,84,98,112,80,80,30,164,159,\t0,1549,1963,2413,8280,9178,10460,14696,16009,\n+chr22\t49496078\t49512162\tBC075856\t0\t-\t49497347\t49510866\t0\t10\t1368,84,125,112,80,80,30,164,155,90,\t0,1534,1918,2398,8265,9163,10445,14681,15384,15994,\n+chr22\t49499795\t49512202\tBC020495\t0\t-\t49501678\t49510866\t0\t6\t1886,80,80,30,160,130,\t0,4548,5446,6728,10964,12277,\n+chr22\t49512368\t49517925\tAL365511\t0\t+\t49513809\t49517553\t0\t4\t225,121,49,462,\t0,1376,4953,5095,\n+chr22\t49512383\t49517744\tBC019348\t0\t+\t49513809\t49517553\t0\t4\t210,121,49,278,\t0,1361,4938,5083,\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/histogram_in1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/histogram_in1.tabular Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,10 @@
+1 68 4.1
+2 71 4.6
+3 62 3.8
+4 75 4.4
+5 58 3.2
+6 60 3.1
+7 67 3.8
+8 68 4.1
+9 71 4.3
+10 69 3.7

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/histogram_out1.pdf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/histogram_out1.pdf Sat Feb 21 16:33:42 2015 +0100

[

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diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/html_file.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/html_file.txt Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,74 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN">
+<HTML>
+<HEAD>
+
+
+ <META HTTP-EQUIV="Content-Type" CONTENT="text/html;CHARSET=iso-8859-1">
+ <META http-equiv="Content-Script-Type" content="text/javascript">
+ <META HTTP-EQUIV="Pragma" CONTENT="no-cache">
+ <META HTTP-EQUIV="Expires" CONTENT="-1">
+ <TITLE>
+Hyperlinks to Genome Browser </TITLE>
+ <LINK REL="STYLESHEET" HREF="/style/HGStyle.css">
+
+</HEAD>
+<BODY BGCOLOR="#FFF9D2" LINK="0000CC" VLINK="#330066" ALINK="#6600FF">
+<A NAME="TOP"></A>
+
+<TABLE BORDER=0 CELLPADDING=0 CELLSPACING=0 WIDTH="100%">
+
+
+<TR><TD COLSPAN=3 HEIGHT=40 >
+<table bgcolor="#000000" cellpadding="1" cellspacing="1" width="100%%" height="27">
+<tr bgcolor="#2636D1"><td valign="middle">
+ <table BORDER=0 CELLSPACING=0 CELLPADDING=0 bgcolor="#2636D1" height="24"><TR>
+ <TD VALIGN="middle"><font color="#89A1DE"> 
+
+ <A HREF="/index.html?org=Bushbaby&db=otoGar1&hgsid=1118408" class="topbar">
+           Home</A>    
+       <A HREF="/cgi-bin/hgGateway?org=Bushbaby&db=otoGar1&hgsid=1118408" class="topbar">
+           Genomes</A>    
+       <A HREF="/cgi-bin/hgTracks?org=Bushbaby&db=otoGar1&hgsid=1118408" class="topbar">
+           Genome Browser</A>    
+       <A HREF="/cgi-bin/hgBlat?command=start&org=Bushbaby&db=otoGar1&hgsid=1118408" class="topbar">           Blat</A>    
+       <A HREF="/cgi-bin/hgTables?org=Bushbaby&db=otoGar1&hgsid=1118408&hgta_doMainPage=1" class="topbar">
+           Tables</A>    
+       <A HREF="/cgi-bin/hgNear?org=Bushbaby&db=otoGar1&hgsid=1118408" class="topbar">
+           Gene Sorter</A>    
+<A HREF="/cgi-bin/hgSession?org=Bushbaby&db=otoGar1&hgsid=1118408&hgS_doMainPage=1" class="topbar">Session</A>   
+       <A HREF="/FAQ/" class="topbar">
+           FAQ</A>    
+
+       <A HREF="/goldenPath/help/hgTablesHelp.html"
+       class="topbar">
+           Help</A>
+ </font></TD>
+       </TR></TABLE>
+</TD></TR></TABLE>
+</TD></TR>
+
+
+
+<TR><TD COLSPAN=3>
+   
+   <TABLE WIDTH="100%" BGCOLOR="#888888" BORDER="0" CELLSPACING="0" CELLPADDING="1"><TR><TD>
+    <TABLE BGCOLOR="#FFFEE8" WIDTH="100%"  BORDER="0" CELLSPACING="0" CELLPADDING="0"><TR><TD>
+ <TABLE BGCOLOR="#D9E4F8" BACKGROUND="/images/hr.gif" WIDTH="100%"><TR><TD>
+ <FONT SIZE="4"><b> 
+Hyperlinks to Genome Browser</b></FONT></TD></TR></TABLE>
+ <TABLE BGCOLOR="#FFFEE8" WIDTH="100%" CELLPADDING=0><TR><TH HEIGHT=10></TH></TR>
+ <TR><TD WIDTH=10> </TD><TD>
+
+
+<A HREF="http://hgwdev.cse.ucsc.edu/cgi-bin/hgTracks?db=otoGar1&position=scaffold_0.1-193456:96554-98437&gold=pack" TARGET=_blank>scaffold_0.1-193456_25 at scaffold_0.1-193456:96554-98437</A><BR>
+<A HREF="http://hgwdev.cse.ucsc.edu/cgi-bin/hgTracks?db=otoGar1&position=scaffold_0.1-193456:100227-101729&gold=pack" TARGET=_blank>scaffold_0.1-193456_26 at scaffold_0.1-193456:100227-101729</A><BR>
+<A HREF="http://hgwdev.cse.ucsc.edu/cgi-bin/hgTracks?db=otoGar1&position=scaffold_0.1-193456:101830-103994&gold=pack" TARGET=_blank>scaffold_0.1-193456_27 at scaffold_0.1-193456:101830-103994</A><BR>
+<A HREF="http://hgwdev.cse.ucsc.edu/cgi-bin/hgTracks?db=otoGar1&position=scaffold_0.1-193456:105267-107614&gold=pack" TARGET=_blank>scaffold_0.1-193456_28 at scaffold_0.1-193456:105267-107614</A><BR>
+
+ </TD><TD WIDTH=15></TD></TR></TABLE>
+ <br></TD></TR></TABLE>
+ </TD></TR></TABLE>
+
+</TD></TR></TABLE>
+
+</BODY></HTML>

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/interval2maf_3from28way.maf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/interval2maf_3from28way.maf Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,1301 @@\n+##maf version=1\n+a score=378218.0\n+s hg18.chr1 99287304 223 - 247249719 TCCTCTATGCAAGAGTACACTAGCTATTCTGTGGACAGGAGCCAGACAATGTGAGCTGTACATAAGAATTATTTTTGCAGTGTCAAAAGCCATTCTAGGTGGAATCCAAATCACCACTTGCCTTAGACAGACACCCCCTCAGCTTCACTGCAGGTCCAGAGTCAGCCGAGGCCAGAGAGAGAACCACCAGGAGTGGAAGCAACACTCTCTAGGTTCTCTGCAC \n+s panTro2.chr1 101234886 223 - 229974691 TCCTCTATGCAAGAGTACACTAGCTATTCTATGGACAGGAGCCAGACAATGTGAGCTGTACATAAGAATTATTTTTGCAGTGTCAAAAGCCATTCTAGGTGGAATCCAAATCACCACTTGCCTTAGACAGACACCCCCTCAGCTTCACTGCAGGTCCAGAGTCAGCCGAGGCCACAGAGAGAACCACCAGGAGTGGAAGCAACACTCTCTAGGTTCTCTGCAC \n+\n+a score=10640.0\n+s hg18.chr1 99287270 34 - 247249719 GCTGTAAGATGCCATGTATTTTGTGATTCTACAA \n+s panTro2.chr1 101234852 34 - 229974691 GCTGTAAGATGCCATGTATTTTGTGATTCTACAA \n+\n+a score=43023.0\n+s hg18.chr1 99287229 41 - 247249719 AGGGCCCAGAGGATCTGGCCATGTTCTCATGGCATCATTGA \n+s panTro2.chr1 101234811 41 - 229974691 AGGGCCCAGAGGATCTGGCCATGTTCTCATGGCATCATTGA \n+\n+a score=120618.0\n+s hg18.chr1 99287139 90 - 247249719 TCCTTGAAAGGGAAAGACTCTAAAACTTTTCTCTGAATTATGGCCCTGCCACCCCAGCTGGGTTTTTCTCTCAAAGGGAGACAGTAATGA \n+s panTro2.chr1 101234721 90 - 229974691 TCCTTGAAAGGGAAAGACTCTAAAACTTTTCTCTGAATTACGGCCCTGCCACCCCAGCTGGGTTTTTCTCTCAAAGGGAGACAGTAATGA \n+\n+a score=39239.0\n+s hg18.chr1 147984545 50 + 247249719 AGAAAAACTTTAGTGGAAACAACCAGTACTTAAAGACCATTTTATGAGGC \n+s panTro2.chr1 128764240 50 + 229974691 AGAAAAACTTTAGTGGAAACAACCAGTACTTAAAGACCATTTTATGAGGC \n+i panTro2.chr1 C 0 C 0 \n+\n+a score=93901.0\n+s hg18.chr1 147984595 35 + 247249719 TGTCATTTACGTATTATCTCTTTTGCTGTTTTTGT \n+s panTro2.chr1 128764290 35 + 229974691 TGTCATTTACATATTATCTCTTTTGCTGTTTTTGT \n+i panTro2.chr1 C 0 C 0 \n+\n+a score=-5867.0\n+s hg18.chr1 99171300 19 - 247249719 CGTGGGGAGAACTGCGCTG \n+s panTro2.chr1 101114588 19 - 229974691 CGGGGGGAGAACTGCGCTG \n+\n+a score=-4312.0\n+s hg18.chr1 99171258 42 - 247249719 GGGAAATGACCACCTCGGCCTCGCCGGGGTTCTGCGGACAAA \n+s panTro2.chr1 101114546 42 - 229974691 GGGAAATGACCACCTCGGCCTCGCCGGGGTTCTGCGGGCAAA \n+\n+a score=-5717.0\n+s hg18.chr1 99171247 11 - 247249719 CCGGCTAGGGA \n+s panTro2.chr1 101114535 11 - 229974691 CCGGCTAGGGA \n+\n+a score=-26975.0\n+s hg18.chr1 99171193 54 - 247249719 GAGCGCCACACGCCCGTGCTTCGCGCCCAAACCGGCCTCACCCGGCGCGGCCAT \n+s panTro2.chr1 101114481 54 - 229974691 GAGCGCCACACGCCCGTGCTTCGCGCCCAAACCGGCCTCACCCGGCGCGGCCAT \n+\n+a score=-60785.0\n+s hg18.chr1 99171137 56 - 247249719 ACTAGGGGGACGCTCAGGGCTCGCGGTCCTGAGCGCGGCTGGCCTTTGCGGAAGTG \n+s panTro2.chr1 101114425 56 - 229974691 ACTAGGGGGACGCTCAGGGCTCGCGGTCCTGAGCGCGGCTGGCCTTTGCGGAAGTG \n+\n+a score=151634.0\n+s hg18.chr1 148185136 140 + 247249719 acgtctgtaatcccagctactcgtgaggctgatgcaggagaatcacttgaacctgggaagtggaggttgctgtgagccaagattgtgccactgcatttcagcctggctgacagagcaagacttcctctgaaaaaaaaaaa \n+s panTro2.chr1 128947445 139 + 229974691 acgtctgtaatcccagctactcgtgaggctaatgcaggagaatcacttgaacctgggaagtggaggttgctgtgagccaagattgtgccactgcatttcagcctgggtgacagagcaagacttcctctg-gaaaaaaaaa \n+i panTro2.chr1 C 0 C 0 \n+\n+a score=518150.0\n+s hg18.chr10 80123058 56 - 135374737 ACAATATTGTCGAGGGAACTGAAAAACAATCTCACAGTCAATCTACTTCACTGTAA \n+s mm8.chr10 74075614 56 + 129959148 TTAGAGTTGTTGAGGGAATTGACGTGCAACCTCACAGTCAATCAACATCTTTGTAA \n+s panTro2.chr10 82310642 56 - 135001995 ACAATATTGTCGAGGGAACTGAAAAACAATCTCACAGTCAATCTACTTCACTGTAA \n+\n+a score=200210.0\n+s hg18.chr10 80122998 60 - 135374737 TGTGCCCTTCAGAAGTAACAAATATGGAAATCACATCTGAACAAAACAAGGGGAGTTTGA \n+s panTro2.chr10 82310582 60 - 135001995 TGTGCCCTTCGGAAGTAACAAATATGGAAATCACATTTGAACAAAACAAGGAGAATTTGA \n+s mm8.chr10 74075554 60 + 129959148 TTTGCCCTGCAGAGAAAACAGGCATGAAAATCACACATGACCAGAGCCAGGAAACGTTGG \n+\n+a score=136193.0\n+s hg18.chr10 80122957 41 - 135374737 AAAAAACTATCTACGCACAAATGTTTCAGAACTTCAAACTA \n+'..b'gcaagctccgcctcccaggttcacgccattctcctgcctcagcctcccgagtagctgggactacaggcgcctgccaccacgcccagctaattttttgtatttttagtagagatggggtttcaccgtgttagccaggatggtctcgatctcctgacctcttgatctgcccaccttggcctcccaaagtgctgggattacaggtgagagccaccacgcccagccaaaaaaaaaagcccaattttcaaaaaggggcaaagggg \n+\n+a score=17937.0\n+s hg18.chrX 122745548 189 + 154913754 ccgggcacggtggctcacgcctgtaatctcagcactttgggaggccaaggcagggggatcaggaggtcaggagttcgagaccagcctggccaaagcgaccagcctggccaacatggtgaaaccctgtctctactaaaaatacaaaaattagccgggcatggtggcagtacctgtaatcccagctactcg \n+s panTro2.chrX 123191640 189 + 155361357 ccgggcacggtggctcacgcctgtaatctcagcactttgggaggccaaggcagggggatcaggaggtcaggagttcgagaccagcctggccaaagggaccagcctggccaacatggtgaaaccctgtctctactaaaaatacaaaaattagccgggcatggtggcagtacctgtaatcccagctactcg \n+i panTro2.chrX I 759 C 0 \n+\n+a score=88563.0\n+s hg18.chrX 122745737 187 + 154913754 ggaggctgaggcaggagaattgcttgaacccaggaggcagaggttgcagtaagctgagattgccccattgcactccagcctgggcaacagagtgagactcctactcaaaaaaaaaaaaaaaaaaaa-gttggcggatgcggggacagcaaagggcttaagtagacatttcttcaaagaagatatacaa \n+s panTro2.chrX 123191829 188 + 155361357 ggaggctgaggcaggagaattgcttgaacccaggaggcagaggttgcagtaagctgagattgccccattgcactccagcctgggcaacagagtgagactcctactcaaaaaaaaaaaaaaaaaaaaaGTTGGCAGATGCGGGGACAgcaaagggcttaagtagacatttcttcaaagaagatatacaa \n+i panTro2.chrX C 0 C 0 \n+\n+a score=60355.0\n+s hg18.chrX 2264558 232 - 154913754 ctatctgggctcactgccagctccgcctcccgggttcacgccattcttctgcctcagcgtcccgagtagctgggactataggcgcccgccaccgcgcccggctaaatttttgtatttttagtagagatggggtttcaccctgttagccaggatggtctcgacctcctgacctcgtgatctgcccgcctcaccctcccaaagtgctgggatgccaggcgggagcccccgcgcc \n+s panTro2.chrX 2180049 232 - 155361357 ctctctgggctcactgccagctctgcctcccgggttcatgccattcttctgcctcagcgtcccgagtagctgggactacaggcgcccgcccccgcgcccggctaaatttttgtatttttagtagagatggggtttcaccctgttagccaggatggtctcgacctcctgacctcgtgatctgcccgcctcaccctcccaaagtgctgggattacaggcgtgagccaccgtgcc \n+\n+a score=-54866.0\n+s hg18.chrX 152691446 7 + 154913754 TCAGAAC \n+s panTro2.chrX 153225439 7 + 155361357 TCAGAAC \n+i panTro2.chrX C 0 C 0 \n+s mm8.chrX 70018668 2 + 165556469 -----GC \n+i mm8.chrX C 0 C 0 \n+\n+a score=-88144.0\n+s hg18.chrX 152691453 18 + 154913754 CGGAGGGCCTTGGGCATG \n+s mm8.chrX 70018670 18 + 165556469 TGGAGGGTCTTGAGGATG \n+i mm8.chrX C 0 C 0 \n+s panTro2.chrX 153225446 18 + 155361357 CGGAGGGCCTTGGGCATG \n+i panTro2.chrX C 0 C 0 \n+\n+a score=2270241.0\n+s hg18.chrX 2219694 31 - 154913754 AGGCCAACCTGCGTAGCATGAGCTTGGGGTT \n+s panTro2.chrX 2133314 5 - 155361357 --------------------------GGGTT \n+s mm8.chrX 95535223 31 - 165556469 AGGCCAACCTGCGTAACATGAGCTTGGGGTT \n+\n+a score=-439513.0\n+s hg18.chrX 2219662 32 - 154913754 AAGCCCTCACCCCCGCCACCGGGTCCAGGTCA \n+s mm8.chrX 95535191 32 - 165556469 AAGCCCCTGCCCCTGCCCCCACATTCAGGTCA \n+\n+a score=-528572.0\n+s hg18.chrX 2219603 59 - 154913754 TGGCCCCACCCGCCCCTGGACAGAGCCCGCCCAGGGTGCGATGGGGGCAGGTCTGTGGC \n+s mm8.chrX 95535133 58 - 165556469 TGGCTCCTGAC-CTCAGGGCCTGATCCCACACCACCTGTATTAGCAATGGGTCAGAGGT \n+\n+a score=-746000.0\n+s hg18.chrX 2219540 63 - 154913754 CTTTGTGCCTGTGTCCCTGCTGAGGACATCTCACTTTCCTTCCC--CCCACCTGCTGGGGCTTCC \n+s mm8.chrX 95535080 53 - 165556469 ------------GGCCCTGGTGAGGATAGTCCTCAGATCTTCTCTGAGCCCACTCCTGGAGTTCC \n+\n+a score=-199075.0\n+s hg18.chrX 2219515 25 - 154913754 CGGGGAGCCGGCCACAGGGTCAGGC \n+s mm8.chrX 95535063 17 - 165556469 TATGGAAGAAGCCCCAA-------- \n+\n+a score=1368003.0\n+s hg18.chrX 2219491 24 - 154913754 TTCTCCACCATGGTCTCTGTCCTG \n+s mm8.chrX 95535039 24 - 165556469 TTCTCTACCATGGTCTCCGTCCTG \n+\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/interval_maf_to_merged_fasta_out.dat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/interval_maf_to_merged_fasta_out.dat Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,715 @@\n+>hg17.chr1(-):147962192-147962580\n+ACTTGATCCTGCTCCCTCGGTGTCTGCATTGACTCCTCATGCTGGGACTGGACCCGTCAACCCCCCTGCTCGCTGCTCACGTACCTTCATCACTTTTAGTGATGATGCAACTTTCGAGGAATGGTTCCCCCAAGGGCGGCCCCCAAAAGTCCCTGTTCGTGAGGTCTGTCCAGTGACCCATCGTCCAGCCCTATACCGGGACCCTGTTACAGACATACCCTATGCCACTGCTCGAGCCTTCAAGATCATTCGTGAGGCTTACAAGAAGTACATTACTGCCCATGGACTGCCGCCCACTGCCTCAGCCCTGGGCCCCGGCCCGCCACCTCCTGAGCCCCTCCCTGGCTCTGGGCCCCGAGCCTTGCGCCAGAAAATTGTCATTAAATGA\n+>canFam1\n+GCTGGATCCTACTCCCACAGCTTCTGCACTGACTCCCCATGCCGGCACTGGACCCGTTGTCCCTCCACCTCGCTGCTCGCGTACTTTCATCACTTTTAGTGATGATGCAACATTTGAGGAATGGTTTCCCCAAGGCCGGCCCCCAAAGGTCCCTGTTCGGGAGGTCTGCCCCGTGACCCATCGCCCAGCCCTGTACCGGGACCCTGTCACAGACATCCCCTACGCCACTGCTCGAGCCTTCAAGATCATCCGTGAGGCCTACAAGAAGTACATCACTGCCCACGGACTGCCGCCCACTGCCTCAGCCCTGGGCCCTGGCCCACCACCTCCCGAGCCCCTCCCTGGTTCTGGGCCCCGAGCCTTGCGCCAGAAAATTGTCATCAAATAA\n+>mm5\n+CCTTGATCCTGCTCCTACAGCCTCTGCACTGGCTCCACATGCTGGGACCGGGACTGCCACCCCTCCTGCTCACTGCTCTCGCACCTTCATCACGTTCAGTGATGATGCAACGTTTGAAGAGTGGTTCCCCCAGGGGCGACCCCCGAAGGTCCCGGTGCGGGAGGTCTGCCCAGTGACCCACCGTCCAGCTTTGTACCGGGACCCTGTTACAGACATACCCTATGCCACTGCTAGAGCCTTCAAGATCATCCGTGAGGCGTACAAGAAGTACATCACTGCCCACGGACTTCCACCCACCGCCTCGGCGCTGGGCCCCGGGCCCCCACCCCCCGAGCCACTACCTGGCTCTGGGCCTCGAGCCTTGCGTCAGAAGATTGTCATCAAAT--\n+>panTro1\n+ACTTGATCCTGCTCCCTCCCCTTCTGCATTGACTCCTCATGCTGGGACTGGACCCGTCAACCCCCCTGCTCGCTGCTCACGTACCTTCATCACTTTTAGTGATGATGCAACTTTCGAGGAATGGTTCCCCCAAGGGCGGCCCCCAAAAGTCCCTGTTCGTGAGGTTTGTCCAGTGACCCATCGTCCAGCCCTATACCGGGACCCTGTTACAGACATACCCTATGCCACTGCTCGAGCCTTCAAGATCATTCGTGAGGCTTACAAGAAGTACATTACTGCCCATGGACTGCCGCCCACTGCCTCAGCCCTGGGCCCTGGCCCGCCACCTCCTGAGCCCCTCCCTGGCTCTGGGCCCCGAGCCTTGCGCCAGAAAATTGTCATTAAATGA\n+>rn3\n+ACTTGATCCTGCTCCTACGTCCTCTGCACTGACTGCACATGCTGGCACTGGACCTGCCGTCCCTCCTCCTCACTGCTCACGTACCTTCATCACATTCAGTGATGATGCCACGTTTGAAGAATGGTTCCCCCAAGGGCGACCACCAAAGGTCCCTGTTCGGGAGGTCTGCCCAGTGACCCACCGTCCAGCTTTGTACCGGGACCCTGTTACAGACATACCCTATGCCACTGCTAGAGCCTTCAAGATCATCCGTGAGGCGTACAAGAAGTACATCACTGCCCACGGACTACCACCCACTGCCTCAGCGCTGGGCCCCGGGCCCCCACCCCCCGAGCCACTCCCTGGCGCTGGGCCCCGAGCCTTGCGTCAGAAGATTGTCATCAAAT--\n+\n+>hg17.chr1(+):147984545-147984630\n+ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG\n+>canFam1\n+ATGGCGTCGGCCTCCTCTGGGCCGTCG---GCGGCTGGGGTTTCATCCTTTGATCCCGGGGTCCCTTCCTGTGCTTCGGCTTCAG\n+>mm5\n+ATGGCGTCCGCCTCCTCAGGGCCAGCG---GCGGCCGGGTTTTCATCCCTTGATGCCGGGGCCCCTGCTGGTA------CCGCAG\n+>panTro1\n+ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG\n+>rn3\n+ATGGCGTCCGCCTCCTCAGGGCCAGCG---GCGGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTA------CCGCAG\n+\n+>hg17.chr1(-):148078400-148078582\n+GTTCTCAGCTTCCTTGCTTCCATGGCTCCAGCACCATTCGAAACCTCAAAGAGAGGTTCCACATGAGCATGACTGAGGAGCAGCTGCAGCTGCTGGTGGAGCAGATGGTGGATGGCAGTATGCGGTCTATCACCACCAAACTCTATGACGGCTTCCAGTACCTCACCAACGGCATCATGTGA\n+>canFam1\n+GTTCTCAGCTTCCTTGCTTCCATGGCTCCAGCACCATCCGCAACCTCAAAGAGCGGTTCCACATGAGCATGACTGAGGAGCAGCTCCAGCTGCTGGTGGAGCAGATGGTAGATGGCAGCATGCGGTCTATCACCACCAAACTCTATGACGGCTTCCAGTACCTCACCAATGGCATCATGTGA\n+>mm5\n+GTTCTCAGCTTCCTTGCTTCCATGGCTCCAGCACCATTCGCAACCTCAAAGAGAGGTTCCACATGAGCATGACTGAGGAGCAGCTGCAGCTGCTGGTGGAGCAGATGGTGGACGGCAGCATGAGGTCCATCACCACCAAACTCTACGATGGCTTCCAGTACCTCACCAATGGCATCATGTGA\n+>panTro1\n+GTTCTCAGCTTCCTTGCTTCCATGGCTCCAGCACCATTCGAAACCTCAAAGAGAGGTTCCACATGAGCATGACTGAGGAGCAGCTGCAGCTGCTGGTGGAGCAGATGGTGGATGGCAGTATGCGGTCTATCACCACCAAACTCTATGACGGCTTCCAGTACCTCACCAACGGCATCATGTGA\n+>rn3\n+GTTCTCAGCTTCCTTGCTTCCATGGCTCCAGCACCATTCGCAACCTCAAAGAGAGGTTCCACATGAGCATGACTGAGGAGCAGCTGCAGCTGCTGGTGGAGCAGATGGTGGACGGCAGCATGAGGTCCATCACCACCAAACTCTACGATGGCTTCCAGTACCTCACCAATGGCATCATGTGA\n+\n+>hg17.chr1(+):148185136-148185276\n+ATGGAAGCGTTTTTGGGGTCGCGGTCCGGACTTTGGGCGGGGGGTCCGGCCCCAGGACAGTTTTACCGCATTCCGTCCACTCCCGATTCCTTCATGGATCCGGCGTCTGCACTTTACAGAGGTCCAATCACGCGGACCCA\n+>canFam1\n+ATGGAAGCCTTTCTGGAGTCGCGGTCCAGAGTTTGGGCCGGTGGTCCCGCCCCGGGGCAGTTTTACCACATCCCGCCTAGTTCCGTCGCCTCCGTGGAGCCGGCGTTTTCTCCTTACGGGGGTCCGGTTACGCGCACGCA\n+>mm5\n+ATGGAAGCGTTTTGGGAGTCACGGGCTGGCCACTGGGCCGGGGGTCCGGCTCCAGGGCAGTTTTACCGCATCCCGGCCACCCCCAGCGGCCTCATGGACCCGGCGTCGGCGCCCTGCGAGGGTCCCATCACTC'..b'ATACCCGAGGAACCCTGCCATGTATAGTGAAGAAGCTAGATTAAAGTCCTTTCAGAACTGGCCAGACTATGCTCACCTAACCCCAAGAGAGTTAGCAAGTGCTGGACTCTACTACACAGGTATTGGTGACCAAGTGCAGTGCTTTTGTTGTGGTGGAAAACTGAAAAATTGGGAACCTTGTGATCGTGCCTGGTCAGAACACAGGCGACACTTTCCTAATTGCTTCTTTGTTTTGGGCCGGAATCTTAATATTCGAAGTGAATCTGATGCTGTGAGTTCTGATAGGAATTTCCCAAATTCAACAAATCTTCCAAGAAATCCATCCATGGCAGATTATGAAGCACGGATCTTTACTTTTGGGACATGGATATACTCAGTTAACAAGGAGCAGCTTGCAAGAGCTGGATTTTATGCTTTAG\n+>rn3\n+ATGACTTTTAACAGTTTTGAAGGATCTAGAACTGTTGTACCTGCAGACACCAATAAGGATGAAGAATTTGTAGAAGAGTTTAATAGATTAAAAACATTTGCTAACTTCCCAAGCAGCAGTCCTGTTTCAGCATCAACATTGGCGCGAGCGGGGTTTCTCTACACTGGTGAAGGAGACACCGTGCAGTGTTTCAGTTGTCACGCGGCAGTAGATAGATGGCAGTATGGAGACTCAGCTGTTGGAAGACACAGGAGAATATCCCCAAATTGCAGATTTATCAATGGTTTTTATTTTGAAAACGGTGCCACACAGTCTACATCTCCTGGCATCCAAAATGGCCAGTACAAATCTGAAAACTGTGTGGGAAACAGAAATCATTTTGCTCTTGACAGGCCGTCGGAGACTCATGCAGATTATCTCCTGAGAACTGGACAGGTTGTAGATATTTCAGATACCATATACCCGAGGAACCCGGCCATGTGTAGTGAAGAAGCCAGACTGAAGACGTTTCAGAACTGGCCAGACTATGCCCATTTAAGCCCCAGAGAGTTAGCTAGTGCTGGACTCTACTACACGGGGATTGATGATCAAGTGCAATGCTTTTGTTGTGGTGGAAAACTGAAAAATTGGGAACCCTGTGACCGTGCCTGGTCAGAGCACAGGAGACACTTTCCCAACTGCTTCTTCGTTTTGGGCCGGAATGTTAATGTTCGAAGTGAGTCTGG---TGTGAGTTCAGATAGGAATTTCCCAAATTCAACAAATTCTCCAAGAAATCCAGCCATGGCAGAATATGACGCACGGATCGTTACTTTTGGAACATGGCTATACTCAGTTAACAAGGAGCAGCTTGCAAGAGCTGGATTTTATGCTTTAG\n+\n+>hg17.chrX(-):152648964-152649196\n+TGACAACGAGGAGAAGGCCTTTGGCAGCAGCCAGCCATCGCTCAACGGGGACATCAAGCCCCTGGGCAGTGACGACAGCCTGGCCGATTATGGGGGCAGCGTGGATGTTCAGTTCAACGAGGATGGTTCGTTCATTGGCCAGTACAGTGGCAAGAAGGAGAAGGAGGCGGCAGGGGGCAATGACAGCTCAGGGGCCACTTCCCCCATCAACCCTGCCGTGGCCCTAGAATAG\n+>canFam1\n+TGACAACGAGGAGAAGGCCTTTGGCAGCAGCCAGCCGTCCCTCAATGGGGACATCAAGCCCCTGGGCAGTGACGACAGCCTGGCCGACTACGGGGGCAGCGTGGACGTGCAGTTCAACGAGGACGGCTCCTTCATCGGCCAGTACAGCGGCAAGAAGGAGAAGGAGGCAGCAGGCGGCAACGACAGCTCAGGGGCCGCCTCCCCCATCAACCCTGCCGGGGCCCTAGAGTAG\n+>mm5\n+TGACAATGAAGAGAAGGCCTTTGGCAGCAGCCAGCCATCTCTCAACGGAGACATCAAACCCCTAGGCAGTGATGACAGCCTGGCTGATTATGGGGGCAGTGTGGACGTCCAGTTCAATGAGGATGGCTCTTTCATCGGCCAGTACAGTGGCAAGAAAGAGAAGGAGGCAGCAGGAGGCAATGACAGTTCAGGGGCTACCTCTCCTATCAATCCTGCAGTAGCCCTAGAATAG\n+>panTro1\n+TGACAACGAGGAGAAGGCCTTTGGCAGCAGCCAGCCATCGCTCAACGGGGACATCAAGCCCCTGGGCAGTGACGACAGCCTGGCCGATTATGGGGGCAGCGTGGATGTTCAGTTCAACGAGGATGGTTCGTTCATTGGCCAGTACAGTGGCAAGAAGGAGAAGGAGGCGGCAGGGGGCAATGACAGCTCAGGGGCCACCTCCCCCATCAACCCTGCCGTGGCCCTAGAATAG\n+>rn3\n+TGACAATGAAGAGAAGGCCTTCGGCAGCAGCCAGCCATCTCTCAATGGAGACATCAAACCCCTAGGCAGTGATGACAGTCTGGCTGATTATGGGGGCAGTGTGGATGTCCAGTTCAATGAGGATGGCTCTTTCATCGGCCAATACAGTGGCAAAAAAGAGAAGGAGGCAGCGGGAGGCAATGACAGCTCAGGGGCTACCTCTCCTATCAATCCTGCAGTAGCCCTAGAATAG\n+\n+>hg17.chrX(+):152691446-152691471\n+ATGCTCATGGCGTCCACCACTTCCG\n+>canFam1\n+ATGCTCCTGGCATCCACCACCTCGG\n+>mm5\n+ATGATCCTGGTGTCTACCACGTCTG\n+>panTro1\n+-------------------------\n+>rn3\n+ATGCTCCTGGTGTCTACCGTGTCCG\n+\n+>hg17.chrX(-):152694029-152694263\n+GCTGTGGCACAGAACATGGACTCTGTGTTTAAGGAGCTCTTGGGAAAGACCTCTGTCCGCCAGGGCCTTGGGCCAGCATCTACCACCTCTCCCAGTCCTGGGCCCCGAAGCCCAAAGGCCCCGCCCAGCAGCCGCCTGGGCAGGAACAAAGGCTTCTCCCGGGGCCCTGGGGCCCCAGCCTCACCCTCAGCTTCCCACCCCCAGGGCCTAGACACGACCCCCAAGCCACACTGA\n+>canFam1\n+GCTGTGGCACAGACCATGGATTCCGTGTTTAAGGAGCTCCTGGGAAAGACCTccgcccgccagggcgcggggcccgcgtccaccggctcccccggccccgggcccTGCAGCCTGAAGCCTCCGGCCTCCGGCCGCCTGGGTAGGAGCAAAGGCTTCTCCCGCGGCTCCGGGGCCCCGGCGTCCCCCTCGGCGTCCCATCCCCAGGGCCTGGACTCTCCACTTAAGC---ACTGA\n+>mm5\n+GCTGTGGCACAGAACATGAATTCTGTGTTTAAGGAGCTCTTGGGAAAGACTGCTGTCCGCCAGGGCCATGGGTTAGCATCTACAGCCTCCCCGAGTCTAGG------AACTCTGACGCCCCTGGCCTGCAGCAGCATCAGCAAAAACAAAGTCTTCTCCCGGGGACCTGGGGCTCCAATTTCCCCCTCAACCTCCCATCCCCAGGGTCCAGATTCAACTCGCAAGCCAGTCTGA\n+>panTro1\n+GCTGTGGCACAGAACATGGACTCTGTGTTTAAGGAGCTCTTGGGAAAGACCTCTGTCCGCCAGGGCCTTGGGCCAGCATCTACCACCTCTCCCAGTCCTGGGCCCCGAAGCCCAAAGGCCCCGCCCAGCAGCCGCCTGGGCAGGAACAAAGGCTTCTCCCGGGGCCCTGGGGCCCCAGCCTCACCCTCAGCTTCCCACCCCCAGGGCCTAGACACGACCCCCAAGCCACACTGA\n+>rn3\n+GCTGTGGCGCAGAACATGGATTCTGTGTTTAAGGAGCTCTTGGGAAAGGCTGCTGTCCGCCAGGGCCATGGGCTAGCATCTACAGCCTCCCCCAGTCTAGGAACTCGAAACCTGAAGCCCCTGGCCTGCAGCAGCTTCAGCAAAAACAAAGTCTTCTCCCGGGGACCTGGGGCTCCAGTTTCCCCCTCAGTTTCCCATCCCCAGGGTCCAGATTCAACTCGCAAGCCAGTCTGA\n+\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/interval_maf_to_merged_fasta_out3.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/interval_maf_to_merged_fasta_out3.fasta Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,480 @@\n+>hg18.chr16(+):20682314-20682813\n+ctgtggatcagaggaccctgtgccagatcatacaactccttgcagttcatgtaaggactcggattttacctggagtggaaaaagaagcactgaaagatttgagcaggggagtaacctgatagcgtttatgtttAGTCCTGCCACTTCGACAGATAAACGCACCAATGGGCTTGATGAGATTTAGGCCAACCCATAACCGCCCCTCAACTTCTTTCCTTTCAATTTCAAAACTCCTCTATGGCTTCCTCCATCTGTTCTTCCTTCTGAGAAGTGCTCTCTCTGCCCCTTTACAGAACTAACCACTTCGGCAACTCCTTGGACACTTTCCTTCTTGTTAATAATTTGCTTTCTCCGCCCCTCAAAAGCTTGCTGTTTCTGTAAATCATTACCTGTAAGAGGAACCGCTGGGAGTCCTGTAAACTTTAGCCCAGAGCTTGGCTCCTCCTCCAGAATGTCTCCACCAATCAAGGAAAGTGTTTTGGGCCAGTCTTGCTCCTCC\n+>mm8\n+GTCTGGGTCAGAGGACA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTTCCCTCCTAGTAACGCACTGCCTTCCCAGCCTACTAAAACTCTGCTGTGTGTACAGATCATTACCTGTAATAAGACAGGCCAGGGTT-ATGTAAACAT----------TCACGCTCCTCCCACCAA-TATATCCACCAATTAAGGAAAGCACTGCCGGCCAGTCTGACTCCTCC\n+\n+>hg18.chrX(+):123339504-123340003\n+CTACTGATTAGTAGTTTTGTTTTTTTTTTCTTTCCTCCCTCAAGCTTTAGGAGTTGTAAAAAGAATAATAATAGTTCAAGGCAGTATTAAAACCACAGCTGTAAGTAATAAAAAGTGCATTTCCTGAATATAATACAAATGTAACTTTAACAAACTAAAGGCACGAACCAACCAAATACGTATTACAAACTAGAAATGCACAGTTCAAGGTAATCACTATTAAGTAAAAGCTTCAAATATTTGTTTCTAATGGATATTTAAAGCAGTTTGAAAATGATACATCATCAATGAATTGCAAAAACGTATAATTGCTTAAAATATAAGCAAAATAGACTCTAATATTGACATTTTGGATTTGTGATAAAATACATAATCACATTTATGAATGCACTCTCTATATACAGTTCACAAATTATTTTTCCATTAATTTAAAAGAACATCAGAGGTTCTAGGAACTTAAGGTCCATTTTTAGGTTGGTGTGGAGGTATTCAAATTTTC\n+>mm8\n+CAACTTGTTA-TACCTTTTTTTTTTTTTCTTTTCCTCCTCAAAACTTTAGGAGTTGTAAAGAGAACAATAATATTTCAAGGCAGTATTAAAACCACAGTTGTAAGTGATAAAAAGTGCATTTCCTGAATATAATACAAATATAACTTTAGGTAACCAAAGGCACAAACTAACTAAATACATATTACAAACTAGAATTGCACAGTTCAAGGTAATTACTATTAAGGAATAGTTCCAAATATTTCTTCCTAATGAATATTTAAATCGGTTTGAAAATGATACATCACTAGTGAGTTGCAAAAGAGCGCAATCACTTAAAATAGAAGCAAAATAGGCTCCAAGATTGACACATTGGGTTAGTGATAAAATAC---ACCACATTTAAGAATGCACT-TTTATGTACAGTTAACAAATTATTTTCCTATTGACTTCAAAGAATGTCAGAGGTTCTAGGAACTTAAGATCTATTTTTAGGTTGGTGTGGAGGTATTCAAATTTTC\n+\n+>hg18.chr3(+):52503897-52504396\n+CGGGCAGGACCAGCGGCTCAGGAGTGGCTGGGGCTAGTGAGGGGATGTGGGTCTGGTGGGCTAGCAGGGTGCCTGTAGCGAGTCAGAGCCCCATGAGCGCCCTGGAGTTGGAAAGGTGGAGGCAGGAACAGACAGACCCATTCAGGGGCTGCCCTGCCTTCCGCCGACCAGCACCCCAGGAGCCTCTGAATGAAACACACTGGGCTCGCAGGCGGGGGACTCGTTCACGTGTGCCTTTGGATTTGCTTCAGAACCTCTGATAGAGCCCAGGTCCCGGGGCTCATGGTGGCCTGGACTTCCAGGTTGTGATGCCAGGAGGGTCCCAGCCGGGAAGCCCCGAGCAGGGCTCAGGCCGCCCATGGGGGGTCAGTGGCCAGCACCTTCCCTTCCGCCTGCAGGCTGCTGATATGCAGGAGGAAATCCTGGCGGGTTCCTGTGGGGGTGAGCTGGCGGGGCCTCCGGGCTGCTTTTAAGGCCACTGCCCGCCCCGTCCCGCCTG\n+>mm8\n+--------------GGCTCAGGAAGGCCTGAGGCTGGT-AGGGGAGACCAGTCTGAGGGGCTAGCATGGTGTTTCCACC------------------TCTACTGGTGTCTGAAAGACTGAGGCAGCTGGGGGCCAGCCAGCCCAGGGGCTGTCCAACCTCCTAGGCACCAGAACCCCGA-AGCTTCTGAATG-AAAAAGCCAGCTTGACAGATGGGAAAATTATTTATTGGTGC--TTAAATTTGCTTTAGAATCTCCCCTAGACCCCAGG-CAGGTGGCTAATGGTGGTCTGGACCTCTAGACTATGGTGCCAGGGAGGTCCTGGCCAGGAAGCCCTGAACAGGGCCCAGGTCGTCCATGGGGGGTCACTGGCCAGCGTCTTCCCTTCCGCCTGCAGGCTGCTGATACGCAGGAGGAAATCCTGGTGGGTTCCTGTGGGGGTGAGCTGA---------CGGATAGCTTTTAAAGCGGCTGCCCACCCTGTCCTGCCT-\n+\n+>hg18.chr6(+):112089190-112089689\n+AAACATGAAAAAAAATTTTATTGTTTTAGACAAAGAGGCCACTTTTGGAAAATAATACTTTTTTTTTTTTAGTTGAATCAGGTGAAGACAGAGTTAAAATCACATAGGATTTGCATTTTTAAAAAAGGAAAGCACTAGGATTGTTGGCACTGGAGTAACTATTTACACTGAACAGAGGTTTGGCCTTTTACATAACATCGATACAATGCATTTTCCAAAGTCTGAGAAATAACAAGGTTCTGTCTCGAATGCTTCACAGAGGAGGTTCGGATTTGGGGACAAGTGTCATTAATGAGGGCCATGGAAGTTCGTCAGCTTCAGAGTCACATGCAATCTGATCCTGGGCGGTTCCGCTGCTGGGGAGCAGCTGGCTACGGAATTGAAAGCTAATGGGGAGGGGTGGGGCAGCCTCTGGGACAAGGCCTCTCTCCGCAGACCCGGGCCTTACAGGTTTTCACCAGGTTGGTACTGGGGCTCTGTCGCGGTAAAGTAGTCTTCC\n+>mm8\n+AAACATGAAAAAAAATTTTATTGTTTTAGACAAAGAGGCCACTTTTGGAAAATAATACTTTTTTTTTTTTAGTTGAATCAGGTGAAGACAGAGTTAAAATCACATAGGATTTGCTTTTTTAAAAAAGGAAAGCACTGGGATTGTTGGCACAGGAGCAGCTATTTACACTGAACAGAGGTTTGGCCTTTGACATAACATCGATACAATGCATTTCC--AAGTCTGAGAAATAACACGCTTCTGTCTCAGATGGTTCACAGAGGAGGTTCGGACTGGGGGACAAGTGTCATTAATGAGGGCCGTGGAA'..b'GGGGAAGCGGGGAAGAAGCAGGAAGCCCAGAGCCTCCTGGAAACACTGGCCAAAAAGCCCATGCATCCCTTCTTGGAAGCCAAGCAGATCTGACACATAGGAAATACTGGCTTTCCTGGCTTCCCCAAGAAACCTTCAGCTTTGCCCTGGAGGTTTCCATCAGCGAGCAGGAGGTGAAGAGCAGAAGCCTCAGAAAGCAGGTTAGAAGAGGAAGAGGGTGCTGGGTTGGCAAGAAGTGACAGCCCCATATTGTACGGGAACATATTTTGTATCATGTGCACAAGATAAAGAACAGCTAAAGCTGTTTTAAAAGTATAGCCGGGGGACATAGGGGTAAAAGGACCCAAACGCTACAAT\n+>mm8\n+GC---CAC----TCCT---------CTCCTTGGGA-TGAACTGCCTGCGGTTCTGGGTTGCACATACAAGAGCAACCAGCATGTTTGTGCTCAGGTTTGCAGGGATGTCCACCCACTGAGACT------CTTGTGAGCCCAGGGAGAGGTGGGGACAAGGTAGGAGCTTGCAAGCCTCCTGAACGCAGCGGCTAGAACCTCCATGCACACCTACCTAGGAACAAATCAAGTCAGACTCGTGGGATACACAT-GTGGCCCGAAAG-CTCCGGAAACCTTCTGCTGTGTTCTGGAGGCTTCCATCTGAGAGCAAGG-GGGAGGAGTGCACACTGCAGAGAGCAGCTCAGAAGAGGAAGCAGCTGCTGGGTTGGCAGGAGGTGACAACCCTGTGTTCTATAGGAACATGGTTTGTGTCACGTGCACATGATAGAGGACAGCCAAAGCCATTTTGCTAGTA-ATCTAGGGGCTTCGTGAGTAAAAAGACCCAAAAACTCCACT\n+\n+>hg18.chr10(+):94822723-94823222\n+ccttcctcttataccgtctctttatcctgccaGGGCTAAGGACCCCCTTCCCTGCTGTCCAGCTGGGGCGCCAAGCAGCAGGGCCCTCCGAATAGGCGAGCTGTGCTTGGATCTCAGAGACGGGCACCGACTGCCGAGCCCCAGACGAAGTGCCCCAGGGTCGGGGATCAGGCTTGTGCAGGGTAGCACCTGGGGACCTGAGGGACCTGGAGGCCTTCTTGTATCCTGAAGTAGGACCTTCTAAGACTTCATGAGTCCTGGCCCCCTTGCAGGGGTTGGGGAGCTGGGGATCCCAGATCTGCCTATTGCGCCCGATGCCCCGAGGCTCTCTCTTGGACTCTGGCCCTGAGTTCTTCTGCGCGATCCTTCGGAGACGTCTGGAGGCCTGCTTTATGcatctctcttggacctcagtttccccacacgtgggaggaggcagctggacgattcctgaaaggactttccCTTGCTTCCTCATCACGTGGAAGAGAGCCCACCC\n+>mm8\n+CTCCCTGTATTC-----CTCCCCATTCTGCCTGGACTGGGGGCCCTCTTCCCGGCCGCTTGGCTGAGGTTGCAAGCCCCAGGGCTATAGGAATGGGCCGGCTTGGCGGTATTACTACAGTGGAG-GTTGACTTTGGAGCCTCTGGTACCAGGGCTTAGAGAAGGGAGTCAGGCATGTGCAAGGCTGCACCTGGGGGCCC-AGAGACCTGGAGGCTTCTTTGAACTCGAAAGCAGGATTTTCCAAGTCTTCATGCGC-TGGCTCGCCTGTGGGGCCCTGGAAAGCTAGCG-TCCACGATCCGCCAGTCATACTTGACCTCCGAGACCG---GCTAGGACCCTCGCCCTGGGATCTTCTT-GGGATCCTCCAGA----TCAGGAAGCGT---------------TTGGAATCTCATTTACTCAACCGGTGGGTCAAGTCCATTGGATGATTCTTGAACGC----------GCTTTCCAAGCCAATGGAAAAGAGCCCACGA\n+\n+>hg18.chr10(+):94823138-94823637\n+ttccccacacgtgggaggaggcagctggacgattcctgaaaggactttccCTTGCTTCCTCATCACGTGGAAGAGAGCCCACCCGGCACCTGGAAATGGAAAGCCAGTGAAGGCTGCTTTGGGCCGGGGCAGCGGGTGGGACCGGGCGGGAGGGATTCCAAAGAGACCGCCGGGAAGGCTAGAGCTTGGAATTCCGGCTCCTCGGAGTCCTGGCCCTCCCCCACCGCCGCCTCGGAGCTCAGCACACCTTGGATGGGGGAGGCGGGCAGCTCCTAGCCCCGCACCCCAGGAGGCGCGCTCGGAGGGAAGCCGCCACCGCGCCGCCTCTGCCTCGGCGCGGAACAAACGGTTAAAGATTTTGGGCAGCGCCTCGCGGGGGGAGGAGCCAGGGGCCCAATCCGCAATTAAAGATGAACTTTGGGTGAACTAATTGTCTGACCAAGGTAACGTGGGCAGCAACCTGGGCCGCCTATAAAGCGGCAGCGCCGTGGGGTTTGAA\n+>mm8\n+TACTCAACCGGTGGGTCAAGTCCATTGGATGATTCTTGAACGC----------GCTTTCCAAGCCAATGGAAAAGAGCCCACGAGGCGCCTGTGAATGGTGAGCTGG----GAAGGCTTCGGGCTCGGGCAGCTGGTTCGACCCGGCTCGAGGGACAGCAGAGAGACAGCTAGGAAACCCAGGACTCCAAATTCCCACTTCTTGGAACCCCGACTCCCCCCCCCCGCCGCCTCGGAGCTCTGCACACCTAGGACAAGGAAAGAGGTG--TTCCTAGTCCCGCACCCCAGGAGGCGCGCTCAGAGGGAAGCCGCCAGTGCGCCGCCTCTGCCTCGGCGCGGAACAAACGGTTAAAGATTTTGGGCAGCGCCTCGAGGGGGGAGGAGCCAGGGGCCCGATCCGCAATTAAAGATGAACTTTGGGTGAACTAATTGTCTGACCAAGGTAACGTGGGCAGTAACCTGGGCGGCCTATAAAGAGGGCGCGCGGCGGGGTTCGGA\n+\n+>hg18.chr10(+):29005931-29006430\n+CCGCCTCCCCCGGGCTCCCACCCGAACCCTCCTCCGCCACCTGCACAGGCCGGGGCATTGTCACTCGCCCCTGGGGGTTCCAGAAAACGCAGTGCGGCCGGGGAGGACGACCACACGGACCCCCTGCGTGTTTCGGGGGGCACCCAAAAGAAGCCCCGCGCTGGGGAACGCTGACCACCCGAGGCTGAGCCGTCAGGGTCTCGGAGGCGGGTTCCCGAGCCGGTCCCGGGGCTGGGCTCCCCCGGCGCCTCGCGAAGGTCACTGACGCGCAGGCCTCCGCAAGGGGGAGCGCGGGAGACGGCAGCGCACCAGCCGGGCGCCCCAGCCGGGCGCCCCAGACGCCGGCGCCGCTCGGAGCCGCCGGGCAGGTCCCCCAGCGCTCGCGTCTGGGCCCGCCCCCCGCTGCGGGGCGGATTGACAGGAGCCCGGCGGCCAATCGGACGCCGTggggcggggcgaggcggggcggtgcaggccggCTCCCGGCGCGGGGCGCTAT\n+>mm8\n+CTGCCCCTTCTTGACTATCACCCTACTCCTCCTCGGCCA--CGCGCGGGCGGGCGTATTGTTACATGGCCCTGGTGGTTTCGGCAACCGAAGTATGGCCGAGGATGATGACTACTGAGATCCCTTGCAGGTTTCAGGTGGGACAAAAGCGAAGCCACGTGCTGGAGGCCGCTGACCA---GAGACTGAGCAGTGAGGGTCTCGTAGCAAA--CTCCGAACCTATCTAGAAGAGGGGCT-CTGCGACGCATAT--GAGGCTGT--TCGCGCAGGCGTTCGCTAGGGGGAGTGCT-----------------------GCGGCCGTGTCCACAGTGCTACTTGCCAGCGCCAGCGGGAGCCCGGCGGCTTGTCTGCCTTAGCCCGCGTCTGGCCCCGCCCCCTGCGGCTGGGCCCTGGGGCTAGAG-GCGTCCGCCAATCGGAGAGTG-GAGGCGGGGCAGGGCGGGGCCGCGCTGGCCCACTCTGGGCGCCGGGCGCTAT\n+\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/interval_maf_to_merged_fasta_user_out.dat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/interval_maf_to_merged_fasta_user_out.dat Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,715 @@\n+>hg17.chr1(-):147962192-147962580\n+ACTTGATCCTGCTCCCTCGGTGTCTGCATTGACTCCTCATGCTGGGACTGGACCCGTCAACCCCCCTGCTCGCTGCTCACGTACCTTCATCACTTTTAGTGATGATGCAACTTTCGAGGAATGGTTCCCCCAAGGGCGGCCCCCAAAAGTCCCTGTTCGTGAGGTCTGTCCAGTGACCCATCGTCCAGCCCTATACCGGGACCCTGTTACAGACATACCCTATGCCACTGCTCGAGCCTTCAAGATCATTCGTGAGGCTTACAAGAAGTACATTACTGCCCATGGACTGCCGCCCACTGCCTCAGCCCTGGGCCCCGGCCCGCCACCTCCTGAGCCCCTCCCTGGCTCTGGGCCCCGAGCCTTGCGCCAGAAAATTGTCATTAAATGA\n+>panTro1\n+ACTTGATCCTGCTCCCTCCCCTTCTGCATTGACTCCTCATGCTGGGACTGGACCCGTCAACCCCCCTGCTCGCTGCTCACGTACCTTCATCACTTTTAGTGATGATGCAACTTTCGAGGAATGGTTCCCCCAAGGGCGGCCCCCAAAAGTCCCTGTTCGTGAGGTTTGTCCAGTGACCCATCGTCCAGCCCTATACCGGGACCCTGTTACAGACATACCCTATGCCACTGCTCGAGCCTTCAAGATCATTCGTGAGGCTTACAAGAAGTACATTACTGCCCATGGACTGCCGCCCACTGCCTCAGCCCTGGGCCCTGGCCCGCCACCTCCTGAGCCCCTCCCTGGCTCTGGGCCCCGAGCCTTGCGCCAGAAAATTGTCATTAAATGA\n+>mm5\n+CCTTGATCCTGCTCCTACAGCCTCTGCACTGGCTCCACATGCTGGGACCGGGACTGCCACCCCTCCTGCTCACTGCTCTCGCACCTTCATCACGTTCAGTGATGATGCAACGTTTGAAGAGTGGTTCCCCCAGGGGCGACCCCCGAAGGTCCCGGTGCGGGAGGTCTGCCCAGTGACCCACCGTCCAGCTTTGTACCGGGACCCTGTTACAGACATACCCTATGCCACTGCTAGAGCCTTCAAGATCATCCGTGAGGCGTACAAGAAGTACATCACTGCCCACGGACTTCCACCCACCGCCTCGGCGCTGGGCCCCGGGCCCCCACCCCCCGAGCCACTACCTGGCTCTGGGCCTCGAGCCTTGCGTCAGAAGATTGTCATCAAAT--\n+>rn3\n+ACTTGATCCTGCTCCTACGTCCTCTGCACTGACTGCACATGCTGGCACTGGACCTGCCGTCCCTCCTCCTCACTGCTCACGTACCTTCATCACATTCAGTGATGATGCCACGTTTGAAGAATGGTTCCCCCAAGGGCGACCACCAAAGGTCCCTGTTCGGGAGGTCTGCCCAGTGACCCACCGTCCAGCTTTGTACCGGGACCCTGTTACAGACATACCCTATGCCACTGCTAGAGCCTTCAAGATCATCCGTGAGGCGTACAAGAAGTACATCACTGCCCACGGACTACCACCCACTGCCTCAGCGCTGGGCCCCGGGCCCCCACCCCCCGAGCCACTCCCTGGCGCTGGGCCCCGAGCCTTGCGTCAGAAGATTGTCATCAAAT--\n+>canFam1\n+GCTGGATCCTACTCCCACAGCTTCTGCACTGACTCCCCATGCCGGCACTGGACCCGTTGTCCCTCCACCTCGCTGCTCGCGTACTTTCATCACTTTTAGTGATGATGCAACATTTGAGGAATGGTTTCCCCAAGGCCGGCCCCCAAAGGTCCCTGTTCGGGAGGTCTGCCCCGTGACCCATCGCCCAGCCCTGTACCGGGACCCTGTCACAGACATCCCCTACGCCACTGCTCGAGCCTTCAAGATCATCCGTGAGGCCTACAAGAAGTACATCACTGCCCACGGACTGCCGCCCACTGCCTCAGCCCTGGGCCCTGGCCCACCACCTCCCGAGCCCCTCCCTGGTTCTGGGCCCCGAGCCTTGCGCCAGAAAATTGTCATCAAATAA\n+\n+>hg17.chr1(+):147984545-147984630\n+ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG\n+>panTro1\n+ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG\n+>mm5\n+ATGGCGTCCGCCTCCTCAGGGCCAGCG---GCGGCCGGGTTTTCATCCCTTGATGCCGGGGCCCCTGCTGGTA------CCGCAG\n+>rn3\n+ATGGCGTCCGCCTCCTCAGGGCCAGCG---GCGGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTA------CCGCAG\n+>canFam1\n+ATGGCGTCGGCCTCCTCTGGGCCGTCG---GCGGCTGGGGTTTCATCCTTTGATCCCGGGGTCCCTTCCTGTGCTTCGGCTTCAG\n+\n+>hg17.chr1(-):148078400-148078582\n+GTTCTCAGCTTCCTTGCTTCCATGGCTCCAGCACCATTCGAAACCTCAAAGAGAGGTTCCACATGAGCATGACTGAGGAGCAGCTGCAGCTGCTGGTGGAGCAGATGGTGGATGGCAGTATGCGGTCTATCACCACCAAACTCTATGACGGCTTCCAGTACCTCACCAACGGCATCATGTGA\n+>panTro1\n+GTTCTCAGCTTCCTTGCTTCCATGGCTCCAGCACCATTCGAAACCTCAAAGAGAGGTTCCACATGAGCATGACTGAGGAGCAGCTGCAGCTGCTGGTGGAGCAGATGGTGGATGGCAGTATGCGGTCTATCACCACCAAACTCTATGACGGCTTCCAGTACCTCACCAACGGCATCATGTGA\n+>mm5\n+GTTCTCAGCTTCCTTGCTTCCATGGCTCCAGCACCATTCGCAACCTCAAAGAGAGGTTCCACATGAGCATGACTGAGGAGCAGCTGCAGCTGCTGGTGGAGCAGATGGTGGACGGCAGCATGAGGTCCATCACCACCAAACTCTACGATGGCTTCCAGTACCTCACCAATGGCATCATGTGA\n+>rn3\n+GTTCTCAGCTTCCTTGCTTCCATGGCTCCAGCACCATTCGCAACCTCAAAGAGAGGTTCCACATGAGCATGACTGAGGAGCAGCTGCAGCTGCTGGTGGAGCAGATGGTGGACGGCAGCATGAGGTCCATCACCACCAAACTCTACGATGGCTTCCAGTACCTCACCAATGGCATCATGTGA\n+>canFam1\n+GTTCTCAGCTTCCTTGCTTCCATGGCTCCAGCACCATCCGCAACCTCAAAGAGCGGTTCCACATGAGCATGACTGAGGAGCAGCTCCAGCTGCTGGTGGAGCAGATGGTAGATGGCAGCATGCGGTCTATCACCACCAAACTCTATGACGGCTTCCAGTACCTCACCAATGGCATCATGTGA\n+\n+>hg17.chr1(+):148185136-148185276\n+ATGGAAGCGTTTTTGGGGTCGCGGTCCGGACTTTGGGCGGGGGGTCCGGCCCCAGGACAGTTTTACCGCATTCCGTCCACTCCCGATTCCTTCATGGATCCGGCGTCTGCACTTTACAGAGGTCCAATCACGCGGACCCA\n+>panTro1\n+ATGGAGGCGTTTTTGGGGTCGCGGTCCGGACTTTGGGCGGGGTGTCCGGCCCCAGGACAGTTTTACCGCATTCCGTCCACTCCCGATTCCTTCATGGATCCGGCGTCTGCACTTTACAGAGGTCCAATCACGCGGACCCA\n+>mm5\n+ATGGAAGCGTTTTGGGAGTCACGGGCTGGCCACTGGGCCGGGGGTCCGGCTCCAGGGCAGTTTTACCGCATCCCGGCCACCCCCAGCGGCCTCATGGACCCGGCGTCGGCGCCCTGCGAGGGTCCCATCACTC'..b'CCGAGGAACCCGGCCATGTGTAGTGAAGAAGCCAGACTGAAGACGTTTCAGAACTGGCCAGACTATGCCCATTTAAGCCCCAGAGAGTTAGCTAGTGCTGGACTCTACTACACGGGGATTGATGATCAAGTGCAATGCTTTTGTTGTGGTGGAAAACTGAAAAATTGGGAACCCTGTGACCGTGCCTGGTCAGAGCACAGGAGACACTTTCCCAACTGCTTCTTCGTTTTGGGCCGGAATGTTAATGTTCGAAGTGAGTCTGG---TGTGAGTTCAGATAGGAATTTCCCAAATTCAACAAATTCTCCAAGAAATCCAGCCATGGCAGAATATGACGCACGGATCGTTACTTTTGGAACATGGCTATACTCAGTTAACAAGGAGCAGCTTGCAAGAGCTGGATTTTATGCTTTAG\n+>canFam1\n+ATGACTTTTAACAGTTTTGAAGGAGCTAAAACTTGTGTACCTGCAGGCATCAATAAGGATGAAGAATTTGTAGAAGAGTTTAATAGATTAAAAACTTTTGCTAATTTTCCAAGTAGCAGTCCTGTTTCAGCATCAACGTTAGCACGAGCTGGTTTTCTGTATACTGGTGAAGGAGATACTGTGCGGTGCTTTAGTTGTCATGCATCAATAGATAGATGGCAATATGGAGACTCAGCAGTTGGAAGACACAGGAAAGTATCCCCAAATTGCAGATTTATCAATGGCTTTTATTTTGAAAACACTGCTGCACAACCTACAAATCCAGGTATCCAAAATGGTCAATATAATGCAGAAAACTATCTGAGAAACAGAGATCATTTTGTTTTAGACAGACCATCTGAGACTCATGCAGATTATCTTTTGAGAACTGGACAGGTCGTAGATATATCAGACACCACATACCCGGAGAACCCTGCCATGTATAGTGAAGAAGCTAGATTAAACTCATTTCAGAACTGGCCAGACTATGTCCACTTGACCCCAAGAGAGTTAGCTAGTGCTGGATTCTACTACACAGGTATTGACGATCAAGTGCAGTGCTTTTGTTGTGGTGGAAAACTGAAAAATTGGGAACCGTGTGATAATGCATGGTCAGAACACAGGCGACACTTTCCTAATTGCTTCTTTGTTCTGGGCCGGAATGTTAATATTCGAAGTGAATCTGATGTTGCGAGTACTGATAGGAACGTCCCAAATTCAACAAGTATTCCAGAAAATCCAGCCATGGCAGATTATGAAGCACGGATCGTTACTTTTCGGATGTGGATGTGTTCAATTAACAAGGAGCAACTTGCAAGAGCTGGATTTTATTCTTTAG\n+\n+>hg17.chrX(-):152648964-152649196\n+TGACAACGAGGAGAAGGCCTTTGGCAGCAGCCAGCCATCGCTCAACGGGGACATCAAGCCCCTGGGCAGTGACGACAGCCTGGCCGATTATGGGGGCAGCGTGGATGTTCAGTTCAACGAGGATGGTTCGTTCATTGGCCAGTACAGTGGCAAGAAGGAGAAGGAGGCGGCAGGGGGCAATGACAGCTCAGGGGCCACTTCCCCCATCAACCCTGCCGTGGCCCTAGAATAG\n+>panTro1\n+TGACAACGAGGAGAAGGCCTTTGGCAGCAGCCAGCCATCGCTCAACGGGGACATCAAGCCCCTGGGCAGTGACGACAGCCTGGCCGATTATGGGGGCAGCGTGGATGTTCAGTTCAACGAGGATGGTTCGTTCATTGGCCAGTACAGTGGCAAGAAGGAGAAGGAGGCGGCAGGGGGCAATGACAGCTCAGGGGCCACCTCCCCCATCAACCCTGCCGTGGCCCTAGAATAG\n+>mm5\n+TGACAATGAAGAGAAGGCCTTTGGCAGCAGCCAGCCATCTCTCAACGGAGACATCAAACCCCTAGGCAGTGATGACAGCCTGGCTGATTATGGGGGCAGTGTGGACGTCCAGTTCAATGAGGATGGCTCTTTCATCGGCCAGTACAGTGGCAAGAAAGAGAAGGAGGCAGCAGGAGGCAATGACAGTTCAGGGGCTACCTCTCCTATCAATCCTGCAGTAGCCCTAGAATAG\n+>rn3\n+TGACAATGAAGAGAAGGCCTTCGGCAGCAGCCAGCCATCTCTCAATGGAGACATCAAACCCCTAGGCAGTGATGACAGTCTGGCTGATTATGGGGGCAGTGTGGATGTCCAGTTCAATGAGGATGGCTCTTTCATCGGCCAATACAGTGGCAAAAAAGAGAAGGAGGCAGCGGGAGGCAATGACAGCTCAGGGGCTACCTCTCCTATCAATCCTGCAGTAGCCCTAGAATAG\n+>canFam1\n+TGACAACGAGGAGAAGGCCTTTGGCAGCAGCCAGCCGTCCCTCAATGGGGACATCAAGCCCCTGGGCAGTGACGACAGCCTGGCCGACTACGGGGGCAGCGTGGACGTGCAGTTCAACGAGGACGGCTCCTTCATCGGCCAGTACAGCGGCAAGAAGGAGAAGGAGGCAGCAGGCGGCAACGACAGCTCAGGGGCCGCCTCCCCCATCAACCCTGCCGGGGCCCTAGAGTAG\n+\n+>hg17.chrX(+):152691446-152691471\n+ATGCTCATGGCGTCCACCACTTCCG\n+>panTro1\n+-------------------------\n+>mm5\n+ATGATCCTGGTGTCTACCACGTCTG\n+>rn3\n+ATGCTCCTGGTGTCTACCGTGTCCG\n+>canFam1\n+ATGCTCCTGGCATCCACCACCTCGG\n+\n+>hg17.chrX(-):152694029-152694263\n+GCTGTGGCACAGAACATGGACTCTGTGTTTAAGGAGCTCTTGGGAAAGACCTCTGTCCGCCAGGGCCTTGGGCCAGCATCTACCACCTCTCCCAGTCCTGGGCCCCGAAGCCCAAAGGCCCCGCCCAGCAGCCGCCTGGGCAGGAACAAAGGCTTCTCCCGGGGCCCTGGGGCCCCAGCCTCACCCTCAGCTTCCCACCCCCAGGGCCTAGACACGACCCCCAAGCCACACTGA\n+>panTro1\n+GCTGTGGCACAGAACATGGACTCTGTGTTTAAGGAGCTCTTGGGAAAGACCTCTGTCCGCCAGGGCCTTGGGCCAGCATCTACCACCTCTCCCAGTCCTGGGCCCCGAAGCCCAAAGGCCCCGCCCAGCAGCCGCCTGGGCAGGAACAAAGGCTTCTCCCGGGGCCCTGGGGCCCCAGCCTCACCCTCAGCTTCCCACCCCCAGGGCCTAGACACGACCCCCAAGCCACACTGA\n+>mm5\n+GCTGTGGCACAGAACATGAATTCTGTGTTTAAGGAGCTCTTGGGAAAGACTGCTGTCCGCCAGGGCCATGGGTTAGCATCTACAGCCTCCCCGAGTCTAGG------AACTCTGACGCCCCTGGCCTGCAGCAGCATCAGCAAAAACAAAGTCTTCTCCCGGGGACCTGGGGCTCCAATTTCCCCCTCAACCTCCCATCCCCAGGGTCCAGATTCAACTCGCAAGCCAGTCTGA\n+>rn3\n+GCTGTGGCGCAGAACATGGATTCTGTGTTTAAGGAGCTCTTGGGAAAGGCTGCTGTCCGCCAGGGCCATGGGCTAGCATCTACAGCCTCCCCCAGTCTAGGAACTCGAAACCTGAAGCCCCTGGCCTGCAGCAGCTTCAGCAAAAACAAAGTCTTCTCCCGGGGACCTGGGGCTCCAGTTTCCCCCTCAGTTTCCCATCCCCAGGGTCCAGATTCAACTCGCAAGCCAGTCTGA\n+>canFam1\n+GCTGTGGCACAGACCATGGATTCCGTGTTTAAGGAGCTCCTGGGAAAGACCTccgcccgccagggcgcggggcccgcgtccaccggctcccccggccccgggcccTGCAGCCTGAAGCCTCCGGCCTCCGGCCGCCTGGGTAGGAGCAAAGGCTTCTCCCGCGGCTCCGGGGCCCCGGCGTCCCCCTCGGCGTCCCATCCCCAGGGCCTGGACTCTCCACTTAAGC---ACTGA\n+\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/iris.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/iris.tabular Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,151 @@
+5.1 3.5 1.4 0.2 Iris-setosa
+4.9 3.0 1.4 0.2 Iris-setosa
+4.7 3.2 1.3 0.2 Iris-setosa
+4.6 3.1 1.5 0.2 Iris-setosa
+5.0 3.6 1.4 0.2 Iris-setosa
+5.4 3.9 1.7 0.4 Iris-setosa
+4.6 3.4 1.4 0.3 Iris-setosa
+5.0 3.4 1.5 0.2 Iris-setosa
+4.4 2.9 1.4 0.2 Iris-setosa
+4.9 3.1 1.5 0.1 Iris-setosa
+5.4 3.7 1.5 0.2 Iris-setosa
+4.8 3.4 1.6 0.2 Iris-setosa
+4.8 3.0 1.4 0.1 Iris-setosa
+4.3 3.0 1.1 0.1 Iris-setosa
+5.8 4.0 1.2 0.2 Iris-setosa
+5.7 4.4 1.5 0.4 Iris-setosa
+5.4 3.9 1.3 0.4 Iris-setosa
+5.1 3.5 1.4 0.3 Iris-setosa
+5.7 3.8 1.7 0.3 Iris-setosa
+5.1 3.8 1.5 0.3 Iris-setosa
+5.4 3.4 1.7 0.2 Iris-setosa
+5.1 3.7 1.5 0.4 Iris-setosa
+4.6 3.6 1.0 0.2 Iris-setosa
+5.1 3.3 1.7 0.5 Iris-setosa
+4.8 3.4 1.9 0.2 Iris-setosa
+5.0 3.0 1.6 0.2 Iris-setosa
+5.0 3.4 1.6 0.4 Iris-setosa
+5.2 3.5 1.5 0.2 Iris-setosa
+5.2 3.4 1.4 0.2 Iris-setosa
+4.7 3.2 1.6 0.2 Iris-setosa
+4.8 3.1 1.6 0.2 Iris-setosa
+5.4 3.4 1.5 0.4 Iris-setosa
+5.2 4.1 1.5 0.1 Iris-setosa
+5.5 4.2 1.4 0.2 Iris-setosa
+4.9 3.1 1.5 0.1 Iris-setosa
+5.0 3.2 1.2 0.2 Iris-setosa
+5.5 3.5 1.3 0.2 Iris-setosa
+4.9 3.1 1.5 0.1 Iris-setosa
+4.4 3.0 1.3 0.2 Iris-setosa
+5.1 3.4 1.5 0.2 Iris-setosa
+5.0 3.5 1.3 0.3 Iris-setosa
+4.5 2.3 1.3 0.3 Iris-setosa
+4.4 3.2 1.3 0.2 Iris-setosa
+5.0 3.5 1.6 0.6 Iris-setosa
+5.1 3.8 1.9 0.4 Iris-setosa
+4.8 3.0 1.4 0.3 Iris-setosa
+5.1 3.8 1.6 0.2 Iris-setosa
+4.6 3.2 1.4 0.2 Iris-setosa
+5.3 3.7 1.5 0.2 Iris-setosa
+5.0 3.3 1.4 0.2 Iris-setosa
+7.0 3.2 4.7 1.4 Iris-versicolor
+6.4 3.2 4.5 1.5 Iris-versicolor
+6.9 3.1 4.9 1.5 Iris-versicolor
+5.5 2.3 4.0 1.3 Iris-versicolor
+6.5 2.8 4.6 1.5 Iris-versicolor
+5.7 2.8 4.5 1.3 Iris-versicolor
+6.3 3.3 4.7 1.6 Iris-versicolor
+4.9 2.4 3.3 1.0 Iris-versicolor
+6.6 2.9 4.6 1.3 Iris-versicolor
+5.2 2.7 3.9 1.4 Iris-versicolor
+5.0 2.0 3.5 1.0 Iris-versicolor
+5.9 3.0 4.2 1.5 Iris-versicolor
+6.0 2.2 4.0 1.0 Iris-versicolor
+6.1 2.9 4.7 1.4 Iris-versicolor
+5.6 2.9 3.6 1.3 Iris-versicolor
+6.7 3.1 4.4 1.4 Iris-versicolor
+5.6 3.0 4.5 1.5 Iris-versicolor
+5.8 2.7 4.1 1.0 Iris-versicolor
+6.2 2.2 4.5 1.5 Iris-versicolor
+5.6 2.5 3.9 1.1 Iris-versicolor
+5.9 3.2 4.8 1.8 Iris-versicolor
+6.1 2.8 4.0 1.3 Iris-versicolor
+6.3 2.5 4.9 1.5 Iris-versicolor
+6.1 2.8 4.7 1.2 Iris-versicolor
+6.4 2.9 4.3 1.3 Iris-versicolor
+6.6 3.0 4.4 1.4 Iris-versicolor
+6.8 2.8 4.8 1.4 Iris-versicolor
+6.7 3.0 5.0 1.7 Iris-versicolor
+6.0 2.9 4.5 1.5 Iris-versicolor
+5.7 2.6 3.5 1.0 Iris-versicolor
+5.5 2.4 3.8 1.1 Iris-versicolor
+5.5 2.4 3.7 1.0 Iris-versicolor
+5.8 2.7 3.9 1.2 Iris-versicolor
+6.0 2.7 5.1 1.6 Iris-versicolor
+5.4 3.0 4.5 1.5 Iris-versicolor
+6.0 3.4 4.5 1.6 Iris-versicolor
+6.7 3.1 4.7 1.5 Iris-versicolor
+6.3 2.3 4.4 1.3 Iris-versicolor
+5.6 3.0 4.1 1.3 Iris-versicolor
+5.5 2.5 4.0 1.3 Iris-versicolor
+5.5 2.6 4.4 1.2 Iris-versicolor
+6.1 3.0 4.6 1.4 Iris-versicolor
+5.8 2.6 4.0 1.2 Iris-versicolor
+5.0 2.3 3.3 1.0 Iris-versicolor
+5.6 2.7 4.2 1.3 Iris-versicolor
+5.7 3.0 4.2 1.2 Iris-versicolor
+5.7 2.9 4.2 1.3 Iris-versicolor
+6.2 2.9 4.3 1.3 Iris-versicolor
+5.1 2.5 3.0 1.1 Iris-versicolor
+5.7 2.8 4.1 1.3 Iris-versicolor
+6.3 3.3 6.0 2.5 Iris-virginica
+5.8 2.7 5.1 1.9 Iris-virginica
+7.1 3.0 5.9 2.1 Iris-virginica
+6.3 2.9 5.6 1.8 Iris-virginica
+6.5 3.0 5.8 2.2 Iris-virginica
+7.6 3.0 6.6 2.1 Iris-virginica
+4.9 2.5 4.5 1.7 Iris-virginica
+7.3 2.9 6.3 1.8 Iris-virginica
+6.7 2.5 5.8 1.8 Iris-virginica
+7.2 3.6 6.1 2.5 Iris-virginica
+6.5 3.2 5.1 2.0 Iris-virginica
+6.4 2.7 5.3 1.9 Iris-virginica
+6.8 3.0 5.5 2.1 Iris-virginica
+5.7 2.5 5.0 2.0 Iris-virginica
+5.8 2.8 5.1 2.4 Iris-virginica
+6.4 3.2 5.3 2.3 Iris-virginica
+6.5 3.0 5.5 1.8 Iris-virginica
+7.7 3.8 6.7 2.2 Iris-virginica
+7.7 2.6 6.9 2.3 Iris-virginica
+6.0 2.2 5.0 1.5 Iris-virginica
+6.9 3.2 5.7 2.3 Iris-virginica
+5.6 2.8 4.9 2.0 Iris-virginica
+7.7 2.8 6.7 2.0 Iris-virginica
+6.3 2.7 4.9 1.8 Iris-virginica
+6.7 3.3 5.7 2.1 Iris-virginica
+7.2 3.2 6.0 1.8 Iris-virginica
+6.2 2.8 4.8 1.8 Iris-virginica
+6.1 3.0 4.9 1.8 Iris-virginica
+6.4 2.8 5.6 2.1 Iris-virginica
+7.2 3.0 5.8 1.6 Iris-virginica
+7.4 2.8 6.1 1.9 Iris-virginica
+7.9 3.8 6.4 2.0 Iris-virginica
+6.4 2.8 5.6 2.2 Iris-virginica
+6.3 2.8 5.1 1.5 Iris-virginica
+6.1 2.6 5.6 1.4 Iris-virginica
+7.7 3.0 6.1 2.3 Iris-virginica
+6.3 3.4 5.6 2.4 Iris-virginica
+6.4 3.1 5.5 1.8 Iris-virginica
+6.0 3.0 4.8 1.8 Iris-virginica
+6.9 3.1 5.4 2.1 Iris-virginica
+6.7 3.1 5.6 2.4 Iris-virginica
+6.9 3.1 5.1 2.3 Iris-virginica
+5.8 2.7 5.1 1.9 Iris-virginica
+6.8 3.2 5.9 2.3 Iris-virginica
+6.7 3.3 5.7 2.5 Iris-virginica
+6.7 3.0 5.2 2.3 Iris-virginica
+6.3 2.5 5.0 1.9 Iris-virginica
+6.5 3.0 5.2 2.0 Iris-virginica
+6.2 3.4 5.4 2.3 Iris-virginica
+5.9 3.0 5.1 1.8 Iris-virginica
+

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/joiner_out1.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/joiner_out1.bed Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,49 @@
+chr1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 - chr1 147962192 147962580 NM_005997_cds_0_0_chr1_147962193_r 0 -
+chr1 147984545 147984630 CCDS990.1_cds_0_0_chr1_147984546_f 0 + chr1 147984545 147984630 BC007833_cds_0_0_chr1_147984546_f 0 +
+chr1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 - chr1 148078400 148078582 AJ011123_cds_0_0_chr1_148078401_r 0 -
+chr1 148185136 148185276 CCDS996.1_cds_0_0_chr1_148185137_f 0 + chr1 148185136 148185276 NM_002796_cds_0_0_chr1_148185137_f 0 +
+chr10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 - chr10 55251623 55253124 AY029205_cds_0_0_chr10_55251624_r 0 -
+chr11 116124407 116124501 CCDS8374.1_cds_0_0_chr11_116124408_r 0 - chr11 116124407 116124501 AK057832_cds_0_0_chr11_116124408_r 0 -
+chr11 116206508 116206563 CCDS8377.1_cds_0_0_chr11_116206509_f 0 + chr11 116206508 116206563 NM_000040_cds_1_0_chr11_116206509_f 0 +
+chr11 116211733 116212337 CCDS8378.1_cds_0_0_chr11_116211734_r 0 - chr11 116211733 116212337 BC005380_cds_0_0_chr11_116211734_r 0 -
+chr12 38440094 38440321 CCDS8736.1_cds_0_0_chr12_38440095_r 0 - chr12 38440094 38440321 NM_052885_cds_0_0_chr12_38440095_r 0 -
+chr13 112381694 112381953 CCDS9526.1_cds_0_0_chr13_112381695_f 0 + chr13 112381694 112381953 NM_207440_cds_1_0_chr13_112381695_f 0 +
+chr14 98710240 98712285 CCDS9949.1_cds_0_0_chr14_98710241_r 0 - chr14 98710240 98712285 NM_022898_cds_0_0_chr14_98710241_r 0 -
+chr15 41486872 41487060 CCDS10096.1_cds_0_0_chr15_41486873_r 0 - chr15 41486872 41487060 BX537418_cds_0_0_chr15_41486873_r 0 -
+chr15 41673708 41673857 CCDS10097.1_cds_0_0_chr15_41673709_f 0 + chr15 41673708 41673857 AK223365_cds_0_0_chr15_41673709_f 0 +
+chr15 41679161 41679250 CCDS10098.1_cds_0_0_chr15_41679162_r 0 - chr15 41679161 41679250 NM_153700_cds_0_0_chr15_41679162_r 0 -
+chr16 142908 143003 CCDS10397.1_cds_0_0_chr16_142909_f 0 + chr16 142908 143003 NM_005332_cds_0_0_chr16_142909_f 0 +
+chr16 244413 244681 CCDS10402.1_cds_0_0_chr16_244414_f 0 + chr16 244413 244681 AK057165_cds_2_0_chr16_244414_f 0 +
+chr16 259268 259383 CCDS10403.1_cds_0_0_chr16_259269_r 0 - chr16 259268 259383 AB016929_cds_0_0_chr16_259269_r 0 -
+chr18 23786114 23786321 CCDS11891.1_cds_0_0_chr18_23786115_r 0 - chr18 23786114 23786321 NM_001792_cds_0_0_chr18_23786115_r 0 -
+chr18 59406881 59407046 CCDS11985.1_cds_0_0_chr18_59406882_f 0 + chr18 59406881 59407046 NM_012397_cds_1_0_chr18_59406882_f 0 +
+chr18 59455932 59456337 CCDS11986.1_cds_0_0_chr18_59455933_r 0 - chr18 59455932 59456337 AB046400_cds_0_0_chr18_59455933_r 0 -
+chr19 59068595 59069564 CCDS12866.1_cds_0_0_chr19_59068596_f 0 + chr19 59068595 59069564 BC013995_cds_1_0_chr19_59068596_f 0 +
+chr19 59236026 59236146 CCDS12872.1_cds_0_0_chr19_59236027_r 0 - chr19 59236026 59236146 NM_198481_cds_0_0_chr19_59236027_r 0 -
+chr19 59297998 59298008 CCDS12877.1_cds_0_0_chr19_59297999_f 0 + chr19 59297998 59298008 NM_004542_cds_0_0_chr19_59297999_f 0 +
+chr2 118288583 118288668 CCDS2120.1_cds_0_0_chr2_118288584_f 0 + chr2 118288583 118288668 NM_006773_cds_0_0_chr2_118288584_f 0 +
+chr2 220229609 220230869 CCDS2443.1_cds_0_0_chr2_220229610_r 0 - chr2 220229609 220230869 NM_024536_cds_0_0_chr2_220229610_r 0 -
+chr20 33330413 33330423 CCDS13249.1_cds_0_0_chr20_33330414_r 0 - chr20 33330413 33330423 NM_181466_cds_0_0_chr20_33330414_r 0 -
+chr20 33513606 33513792 CCDS13255.1_cds_0_0_chr20_33513607_f 0 + chr20 33513606 33513792 AF022655_cds_1_0_chr20_33513607_f 0 +
+chr21 32869641 32870022 CCDS13615.1_cds_0_0_chr21_32869642_r 0 - chr21 32869641 32870022 NM_018277_cds_3_0_chr21_32869642_r 0 -
+chr21 33321040 33322012 CCDS13620.1_cds_0_0_chr21_33321041_f 0 + chr21 33321040 33322012 NM_005806_cds_1_0_chr21_33321041_f 0 +
+chr22 30120223 30120265 CCDS13897.1_cds_0_0_chr22_30120224_f 0 + chr22 30120223 30120265 NM_004147_cds_0_0_chr22_30120224_f 0 +
+chr22 30160419 30160661 CCDS13898.1_cds_0_0_chr22_30160420_r 0 - chr22 30160419 30160661 BC032941_cds_0_0_chr22_30160420_r 0 -
+chr5 131424298 131424460 CCDS4149.1_cds_0_0_chr5_131424299_f 0 + chr5 131424298 131424460 NM_000588_cds_0_0_chr5_131424299_f 0 +
+chr5 131556601 131556672 CCDS4151.1_cds_0_0_chr5_131556602_r 0 - chr5 131556601 131556672 BC035813_cds_0_0_chr5_131556602_r 0 -
+chr5 131621326 131621419 CCDS4152.1_cds_0_0_chr5_131621327_f 0 + chr5 131621326 131621419 BC003096_cds_0_0_chr5_131621327_f 0 +
+chr6 108299600 108299744 CCDS5061.1_cds_0_0_chr6_108299601_r 0 - chr6 108299600 108299744 NM_007214_cds_0_0_chr6_108299601_r 0 -
+chr6 108594662 108594687 CCDS5063.1_cds_0_0_chr6_108594663_f 0 + chr6 108594662 108594687 NM_003269_cds_0_0_chr6_108594663_f 0 +
+chr6 108640045 108640151 CCDS5064.1_cds_0_0_chr6_108640046_r 0 - chr6 108640045 108640151 NM_003795_cds_0_0_chr6_108640046_r 0 -
+chr6 108722976 108723115 CCDS5067.1_cds_0_0_chr6_108722977_f 0 + chr6 108722976 108723115 NM_145315_cds_0_0_chr6_108722977_f 0 +
+chr7 113660517 113660685 CCDS5760.1_cds_0_0_chr7_113660518_f 0 + chr7 113660517 113660685 AF467257_cds_1_0_chr7_113660518_f 0 +
+chr7 116512159 116512389 CCDS5771.1_cds_0_0_chr7_116512160_r 0 - chr7 116512159 116512389 NM_003391_cds_0_0_chr7_116512160_r 0 -
+chr7 116714099 116714152 CCDS5773.1_cds_0_0_chr7_116714100_f 0 + chr7 116714099 116714152 NM_000492_cds_0_0_chr7_116714100_f 0 +
+chr7 116945541 116945787 CCDS5774.1_cds_0_0_chr7_116945542_r 0 - chr7 116945541 116945787 AF377960_cds_0_0_chr7_116945542_r 0 -
+chr8 118881131 118881317 CCDS6324.1_cds_0_0_chr8_118881132_r 0 - chr8 118881131 118881317 NM_000127_cds_0_0_chr8_118881132_r 0 -
+chr9 128764156 128764189 CCDS6914.1_cds_0_0_chr9_128764157_f 0 + chr9 128764156 128764189 BC051300_cds_0_0_chr9_128764157_f 0 +
+chr9 128787519 128789136 CCDS6915.1_cds_0_0_chr9_128787520_r 0 - chr9 128787519 128789136 NM_014908_cds_0_0_chr9_128787520_r 0 -
+chrX 122745047 122745924 CCDS14606.1_cds_0_0_chrX_122745048_f 0 + chrX 122745047 122745924 NM_001167_cds_1_0_chrX_122745048_f 0 +
+chrX 152648964 152649196 CCDS14733.1_cds_0_0_chrX_152648965_r 0 - chrX 152648964 152649196 NM_000425_cds_0_0_chrX_152648965_r 0 -
+chrX 152691446 152691471 CCDS14735.1_cds_0_0_chrX_152691447_f 0 + chrX 152691446 152691471 AF101728_cds_0_0_chrX_152691447_f 0 +
+chrX 152694029 152694263 CCDS14736.1_cds_0_0_chrX_152694030_r 0 - chrX 152694029 152694263 BC052303_cds_0_0_chrX_152694030_r 0 -
\ No newline at end of file

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/joiner_out2.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/joiner_out2.bed Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,65 @@
+chr1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 - chr1 147962192 147962580 NM_005997_cds_0_0_chr1_147962193_r 0 -
+chr1 147984545 147984630 CCDS990.1_cds_0_0_chr1_147984546_f 0 + chr1 147984545 147984630 BC007833_cds_0_0_chr1_147984546_f 0 +
+chr1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 - chr1 148078400 148078582 AJ011123_cds_0_0_chr1_148078401_r 0 -
+chr1 148185136 148185276 CCDS996.1_cds_0_0_chr1_148185137_f 0 + chr1 148185136 148185276 NM_002796_cds_0_0_chr1_148185137_f 0 +
+chr10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 - chr10 55251623 55253124 AY029205_cds_0_0_chr10_55251624_r 0 -
+chr11 116124407 116124501 CCDS8374.1_cds_0_0_chr11_116124408_r 0 - chr11 116124407 116124501 AK057832_cds_0_0_chr11_116124408_r 0 -
+chr11 116206508 116206563 CCDS8377.1_cds_0_0_chr11_116206509_f 0 + chr11 116206508 116206563 NM_000040_cds_1_0_chr11_116206509_f 0 +
+chr11 116211733 116212337 CCDS8378.1_cds_0_0_chr11_116211734_r 0 - chr11 116211733 116212337 BC005380_cds_0_0_chr11_116211734_r 0 -
+chr11 1812377 1812407 CCDS7726.1_cds_0_0_chr11_1812378_f 0 +
+chr12 38440094 38440321 CCDS8736.1_cds_0_0_chr12_38440095_r 0 - chr12 38440094 38440321 NM_052885_cds_0_0_chr12_38440095_r 0 -
+chr13 112381694 112381953 CCDS9526.1_cds_0_0_chr13_112381695_f 0 + chr13 112381694 112381953 NM_207440_cds_1_0_chr13_112381695_f 0 +
+chr14 98710240 98712285 CCDS9949.1_cds_0_0_chr14_98710241_r 0 - chr14 98710240 98712285 NM_022898_cds_0_0_chr14_98710241_r 0 -
+chr15 41486872 41487060 CCDS10096.1_cds_0_0_chr15_41486873_r 0 - chr15 41486872 41487060 BX537418_cds_0_0_chr15_41486873_r 0 -
+chr15 41673708 41673857 CCDS10097.1_cds_0_0_chr15_41673709_f 0 + chr15 41673708 41673857 AK223365_cds_0_0_chr15_41673709_f 0 +
+chr15 41679161 41679250 CCDS10098.1_cds_0_0_chr15_41679162_r 0 - chr15 41679161 41679250 NM_153700_cds_0_0_chr15_41679162_r 0 -
+chr15 41826029 41826196 CCDS10101.1_cds_0_0_chr15_41826030_f 0 +
+chr16 142908 143003 CCDS10397.1_cds_0_0_chr16_142909_f 0 + chr16 142908 143003 NM_005332_cds_0_0_chr16_142909_f 0 +
+chr16 179963 180135 CCDS10401.1_cds_0_0_chr16_179964_r 0 -
+chr16 244413 244681 CCDS10402.1_cds_0_0_chr16_244414_f 0 + chr16 244413 244681 AK057165_cds_2_0_chr16_244414_f 0 +
+chr16 259268 259383 CCDS10403.1_cds_0_0_chr16_259269_r 0 - chr16 259268 259383 AB016929_cds_0_0_chr16_259269_r 0 -
+chr18 23786114 23786321 CCDS11891.1_cds_0_0_chr18_23786115_r 0 - chr18 23786114 23786321 NM_001792_cds_0_0_chr18_23786115_r 0 -
+chr18 59406881 59407046 CCDS11985.1_cds_0_0_chr18_59406882_f 0 + chr18 59406881 59407046 NM_012397_cds_1_0_chr18_59406882_f 0 +
+chr18 59455932 59456337 CCDS11986.1_cds_0_0_chr18_59455933_r 0 - chr18 59455932 59456337 AB046400_cds_0_0_chr18_59455933_r 0 -
+chr18 59600586 59600754 CCDS11988.1_cds_0_0_chr18_59600587_f 0 +
+chr19 59068595 59069564 CCDS12866.1_cds_0_0_chr19_59068596_f 0 + chr19 59068595 59069564 BC013995_cds_1_0_chr19_59068596_f 0 +
+chr19 59236026 59236146 CCDS12872.1_cds_0_0_chr19_59236027_r 0 - chr19 59236026 59236146 NM_198481_cds_0_0_chr19_59236027_r 0 -
+chr19 59297998 59298008 CCDS12877.1_cds_0_0_chr19_59297999_f 0 + chr19 59297998 59298008 NM_004542_cds_0_0_chr19_59297999_f 0 +
+chr19 59302168 59302288 CCDS12878.1_cds_0_0_chr19_59302169_r 0 -
+chr2 118288583 118288668 CCDS2120.1_cds_0_0_chr2_118288584_f 0 + chr2 118288583 118288668 NM_006773_cds_0_0_chr2_118288584_f 0 +
+chr2 118394148 118394202 CCDS2121.1_cds_0_0_chr2_118394149_r 0 -
+chr2 220190202 220190242 CCDS2441.1_cds_0_0_chr2_220190203_f 0 +
+chr2 220229609 220230869 CCDS2443.1_cds_0_0_chr2_220229610_r 0 - chr2 220229609 220230869 NM_024536_cds_0_0_chr2_220229610_r 0 -
+chr20 33330413 33330423 CCDS13249.1_cds_0_0_chr20_33330414_r 0 - chr20 33330413 33330423 NM_181466_cds_0_0_chr20_33330414_r 0 -
+chr20 33513606 33513792 CCDS13255.1_cds_0_0_chr20_33513607_f 0 + chr20 33513606 33513792 AF022655_cds_1_0_chr20_33513607_f 0 +
+chr20 33579500 33579527 CCDS13256.1_cds_0_0_chr20_33579501_r 0 -
+chr20 33593260 33593348 CCDS13257.1_cds_0_0_chr20_33593261_f 0 +
+chr21 32707032 32707192 CCDS13614.1_cds_0_0_chr21_32707033_f 0 +
+chr21 32869641 32870022 CCDS13615.1_cds_0_0_chr21_32869642_r 0 - chr21 32869641 32870022 NM_018277_cds_3_0_chr21_32869642_r 0 -
+chr21 33321040 33322012 CCDS13620.1_cds_0_0_chr21_33321041_f 0 + chr21 33321040 33322012 NM_005806_cds_1_0_chr21_33321041_f 0 +
+chr21 33744994 33745040 CCDS13625.1_cds_0_0_chr21_33744995_r 0 -
+chr22 30120223 30120265 CCDS13897.1_cds_0_0_chr22_30120224_f 0 + chr22 30120223 30120265 NM_004147_cds_0_0_chr22_30120224_f 0 +
+chr22 30160419 30160661 CCDS13898.1_cds_0_0_chr22_30160420_r 0 - chr22 30160419 30160661 BC032941_cds_0_0_chr22_30160420_r 0 -
+chr22 30665273 30665360 CCDS13901.1_cds_0_0_chr22_30665274_f 0 +
+chr22 30939054 30939266 CCDS13903.1_cds_0_0_chr22_30939055_r 0 -
+chr5 131424298 131424460 CCDS4149.1_cds_0_0_chr5_131424299_f 0 + chr5 131424298 131424460 NM_000588_cds_0_0_chr5_131424299_f 0 +
+chr5 131556601 131556672 CCDS4151.1_cds_0_0_chr5_131556602_r 0 - chr5 131556601 131556672 BC035813_cds_0_0_chr5_131556602_r 0 -
+chr5 131621326 131621419 CCDS4152.1_cds_0_0_chr5_131621327_f 0 + chr5 131621326 131621419 BC003096_cds_0_0_chr5_131621327_f 0 +
+chr5 131847541 131847666 CCDS4155.1_cds_0_0_chr5_131847542_r 0 -
+chr6 108299600 108299744 CCDS5061.1_cds_0_0_chr6_108299601_r 0 - chr6 108299600 108299744 NM_007214_cds_0_0_chr6_108299601_r 0 -
+chr6 108594662 108594687 CCDS5063.1_cds_0_0_chr6_108594663_f 0 + chr6 108594662 108594687 NM_003269_cds_0_0_chr6_108594663_f 0 +
+chr6 108640045 108640151 CCDS5064.1_cds_0_0_chr6_108640046_r 0 - chr6 108640045 108640151 NM_003795_cds_0_0_chr6_108640046_r 0 -
+chr6 108722976 108723115 CCDS5067.1_cds_0_0_chr6_108722977_f 0 + chr6 108722976 108723115 NM_145315_cds_0_0_chr6_108722977_f 0 +
+chr7 113660517 113660685 CCDS5760.1_cds_0_0_chr7_113660518_f 0 + chr7 113660517 113660685 AF467257_cds_1_0_chr7_113660518_f 0 +
+chr7 116512159 116512389 CCDS5771.1_cds_0_0_chr7_116512160_r 0 - chr7 116512159 116512389 NM_003391_cds_0_0_chr7_116512160_r 0 -
+chr7 116714099 116714152 CCDS5773.1_cds_0_0_chr7_116714100_f 0 + chr7 116714099 116714152 NM_000492_cds_0_0_chr7_116714100_f 0 +
+chr7 116945541 116945787 CCDS5774.1_cds_0_0_chr7_116945542_r 0 - chr7 116945541 116945787 AF377960_cds_0_0_chr7_116945542_r 0 -
+chr8 118881131 118881317 CCDS6324.1_cds_0_0_chr8_118881132_r 0 - chr8 118881131 118881317 NM_000127_cds_0_0_chr8_118881132_r 0 -
+chr9 128764156 128764189 CCDS6914.1_cds_0_0_chr9_128764157_f 0 + chr9 128764156 128764189 BC051300_cds_0_0_chr9_128764157_f 0 +
+chr9 128787519 128789136 CCDS6915.1_cds_0_0_chr9_128787520_r 0 - chr9 128787519 128789136 NM_014908_cds_0_0_chr9_128787520_r 0 -
+chr9 128882427 128882523 CCDS6917.1_cds_0_0_chr9_128882428_f 0 +
+chr9 128937229 128937445 CCDS6919.1_cds_0_0_chr9_128937230_r 0 -
+chrX 122745047 122745924 CCDS14606.1_cds_0_0_chrX_122745048_f 0 + chrX 122745047 122745924 NM_001167_cds_1_0_chrX_122745048_f 0 +
+chrX 152648964 152649196 CCDS14733.1_cds_0_0_chrX_152648965_r 0 - chrX 152648964 152649196 NM_000425_cds_0_0_chrX_152648965_r 0 -
+chrX 152691446 152691471 CCDS14735.1_cds_0_0_chrX_152691447_f 0 + chrX 152691446 152691471 AF101728_cds_0_0_chrX_152691447_f 0 +
+chrX 152694029 152694263 CCDS14736.1_cds_0_0_chrX_152694030_r 0 - chrX 152694029 152694263 BC052303_cds_0_0_chrX_152694030_r 0 -
\ No newline at end of file

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/joiner_out3.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/joiner_out3.bed Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,65 @@
+chr1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 - chr1 147962192 147962580 NM_005997_cds_0_0_chr1_147962193_r 0 -
+chr1 147984545 147984630 CCDS990.1_cds_0_0_chr1_147984546_f 0 + chr1 147984545 147984630 BC007833_cds_0_0_chr1_147984546_f 0 +
+chr1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 - chr1 148078400 148078582 AJ011123_cds_0_0_chr1_148078401_r 0 -
+chr1 148185136 148185276 CCDS996.1_cds_0_0_chr1_148185137_f 0 + chr1 148185136 148185276 NM_002796_cds_0_0_chr1_148185137_f 0 +
+chr10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 - chr10 55251623 55253124 AY029205_cds_0_0_chr10_55251624_r 0 -
+chr11 116124407 116124501 CCDS8374.1_cds_0_0_chr11_116124408_r 0 - chr11 116124407 116124501 AK057832_cds_0_0_chr11_116124408_r 0 -
+chr11 116206508 116206563 CCDS8377.1_cds_0_0_chr11_116206509_f 0 + chr11 116206508 116206563 NM_000040_cds_1_0_chr11_116206509_f 0 +
+chr11 116211733 116212337 CCDS8378.1_cds_0_0_chr11_116211734_r 0 - chr11 116211733 116212337 BC005380_cds_0_0_chr11_116211734_r 0 -
+chr11 1812377 1812407 CCDS7726.1_cds_0_0_chr11_1812378_f 0 + ~ ~ ~ ~ ~ ~
+chr12 38440094 38440321 CCDS8736.1_cds_0_0_chr12_38440095_r 0 - chr12 38440094 38440321 NM_052885_cds_0_0_chr12_38440095_r 0 -
+chr13 112381694 112381953 CCDS9526.1_cds_0_0_chr13_112381695_f 0 + chr13 112381694 112381953 NM_207440_cds_1_0_chr13_112381695_f 0 +
+chr14 98710240 98712285 CCDS9949.1_cds_0_0_chr14_98710241_r 0 - chr14 98710240 98712285 NM_022898_cds_0_0_chr14_98710241_r 0 -
+chr15 41486872 41487060 CCDS10096.1_cds_0_0_chr15_41486873_r 0 - chr15 41486872 41487060 BX537418_cds_0_0_chr15_41486873_r 0 -
+chr15 41673708 41673857 CCDS10097.1_cds_0_0_chr15_41673709_f 0 + chr15 41673708 41673857 AK223365_cds_0_0_chr15_41673709_f 0 +
+chr15 41679161 41679250 CCDS10098.1_cds_0_0_chr15_41679162_r 0 - chr15 41679161 41679250 NM_153700_cds_0_0_chr15_41679162_r 0 -
+chr15 41826029 41826196 CCDS10101.1_cds_0_0_chr15_41826030_f 0 + ~ ~ ~ ~ ~ ~
+chr16 142908 143003 CCDS10397.1_cds_0_0_chr16_142909_f 0 + chr16 142908 143003 NM_005332_cds_0_0_chr16_142909_f 0 +
+chr16 179963 180135 CCDS10401.1_cds_0_0_chr16_179964_r 0 - ~ ~ ~ ~ ~ ~
+chr16 244413 244681 CCDS10402.1_cds_0_0_chr16_244414_f 0 + chr16 244413 244681 AK057165_cds_2_0_chr16_244414_f 0 +
+chr16 259268 259383 CCDS10403.1_cds_0_0_chr16_259269_r 0 - chr16 259268 259383 AB016929_cds_0_0_chr16_259269_r 0 -
+chr18 23786114 23786321 CCDS11891.1_cds_0_0_chr18_23786115_r 0 - chr18 23786114 23786321 NM_001792_cds_0_0_chr18_23786115_r 0 -
+chr18 59406881 59407046 CCDS11985.1_cds_0_0_chr18_59406882_f 0 + chr18 59406881 59407046 NM_012397_cds_1_0_chr18_59406882_f 0 +
+chr18 59455932 59456337 CCDS11986.1_cds_0_0_chr18_59455933_r 0 - chr18 59455932 59456337 AB046400_cds_0_0_chr18_59455933_r 0 -
+chr18 59600586 59600754 CCDS11988.1_cds_0_0_chr18_59600587_f 0 + ~ ~ ~ ~ ~ ~
+chr19 59068595 59069564 CCDS12866.1_cds_0_0_chr19_59068596_f 0 + chr19 59068595 59069564 BC013995_cds_1_0_chr19_59068596_f 0 +
+chr19 59236026 59236146 CCDS12872.1_cds_0_0_chr19_59236027_r 0 - chr19 59236026 59236146 NM_198481_cds_0_0_chr19_59236027_r 0 -
+chr19 59297998 59298008 CCDS12877.1_cds_0_0_chr19_59297999_f 0 + chr19 59297998 59298008 NM_004542_cds_0_0_chr19_59297999_f 0 +
+chr19 59302168 59302288 CCDS12878.1_cds_0_0_chr19_59302169_r 0 - ~ ~ ~ ~ ~ ~
+chr2 118288583 118288668 CCDS2120.1_cds_0_0_chr2_118288584_f 0 + chr2 118288583 118288668 NM_006773_cds_0_0_chr2_118288584_f 0 +
+chr2 118394148 118394202 CCDS2121.1_cds_0_0_chr2_118394149_r 0 - ~ ~ ~ ~ ~ ~
+chr2 220190202 220190242 CCDS2441.1_cds_0_0_chr2_220190203_f 0 + ~ ~ ~ ~ ~ ~
+chr2 220229609 220230869 CCDS2443.1_cds_0_0_chr2_220229610_r 0 - chr2 220229609 220230869 NM_024536_cds_0_0_chr2_220229610_r 0 -
+chr20 33330413 33330423 CCDS13249.1_cds_0_0_chr20_33330414_r 0 - chr20 33330413 33330423 NM_181466_cds_0_0_chr20_33330414_r 0 -
+chr20 33513606 33513792 CCDS13255.1_cds_0_0_chr20_33513607_f 0 + chr20 33513606 33513792 AF022655_cds_1_0_chr20_33513607_f 0 +
+chr20 33579500 33579527 CCDS13256.1_cds_0_0_chr20_33579501_r 0 - ~ ~ ~ ~ ~ ~
+chr20 33593260 33593348 CCDS13257.1_cds_0_0_chr20_33593261_f 0 + ~ ~ ~ ~ ~ ~
+chr21 32707032 32707192 CCDS13614.1_cds_0_0_chr21_32707033_f 0 + ~ ~ ~ ~ ~ ~
+chr21 32869641 32870022 CCDS13615.1_cds_0_0_chr21_32869642_r 0 - chr21 32869641 32870022 NM_018277_cds_3_0_chr21_32869642_r 0 -
+chr21 33321040 33322012 CCDS13620.1_cds_0_0_chr21_33321041_f 0 + chr21 33321040 33322012 NM_005806_cds_1_0_chr21_33321041_f 0 +
+chr21 33744994 33745040 CCDS13625.1_cds_0_0_chr21_33744995_r 0 - ~ ~ ~ ~ ~ ~
+chr22 30120223 30120265 CCDS13897.1_cds_0_0_chr22_30120224_f 0 + chr22 30120223 30120265 NM_004147_cds_0_0_chr22_30120224_f 0 +
+chr22 30160419 30160661 CCDS13898.1_cds_0_0_chr22_30160420_r 0 - chr22 30160419 30160661 BC032941_cds_0_0_chr22_30160420_r 0 -
+chr22 30665273 30665360 CCDS13901.1_cds_0_0_chr22_30665274_f 0 + ~ ~ ~ ~ ~ ~
+chr22 30939054 30939266 CCDS13903.1_cds_0_0_chr22_30939055_r 0 - ~ ~ ~ ~ ~ ~
+chr5 131424298 131424460 CCDS4149.1_cds_0_0_chr5_131424299_f 0 + chr5 131424298 131424460 NM_000588_cds_0_0_chr5_131424299_f 0 +
+chr5 131556601 131556672 CCDS4151.1_cds_0_0_chr5_131556602_r 0 - chr5 131556601 131556672 BC035813_cds_0_0_chr5_131556602_r 0 -
+chr5 131621326 131621419 CCDS4152.1_cds_0_0_chr5_131621327_f 0 + chr5 131621326 131621419 BC003096_cds_0_0_chr5_131621327_f 0 +
+chr5 131847541 131847666 CCDS4155.1_cds_0_0_chr5_131847542_r 0 - ~ ~ ~ ~ ~ ~
+chr6 108299600 108299744 CCDS5061.1_cds_0_0_chr6_108299601_r 0 - chr6 108299600 108299744 NM_007214_cds_0_0_chr6_108299601_r 0 -
+chr6 108594662 108594687 CCDS5063.1_cds_0_0_chr6_108594663_f 0 + chr6 108594662 108594687 NM_003269_cds_0_0_chr6_108594663_f 0 +
+chr6 108640045 108640151 CCDS5064.1_cds_0_0_chr6_108640046_r 0 - chr6 108640045 108640151 NM_003795_cds_0_0_chr6_108640046_r 0 -
+chr6 108722976 108723115 CCDS5067.1_cds_0_0_chr6_108722977_f 0 + chr6 108722976 108723115 NM_145315_cds_0_0_chr6_108722977_f 0 +
+chr7 113660517 113660685 CCDS5760.1_cds_0_0_chr7_113660518_f 0 + chr7 113660517 113660685 AF467257_cds_1_0_chr7_113660518_f 0 +
+chr7 116512159 116512389 CCDS5771.1_cds_0_0_chr7_116512160_r 0 - chr7 116512159 116512389 NM_003391_cds_0_0_chr7_116512160_r 0 -
+chr7 116714099 116714152 CCDS5773.1_cds_0_0_chr7_116714100_f 0 + chr7 116714099 116714152 NM_000492_cds_0_0_chr7_116714100_f 0 +
+chr7 116945541 116945787 CCDS5774.1_cds_0_0_chr7_116945542_r 0 - chr7 116945541 116945787 AF377960_cds_0_0_chr7_116945542_r 0 -
+chr8 118881131 118881317 CCDS6324.1_cds_0_0_chr8_118881132_r 0 - chr8 118881131 118881317 NM_000127_cds_0_0_chr8_118881132_r 0 -
+chr9 128764156 128764189 CCDS6914.1_cds_0_0_chr9_128764157_f 0 + chr9 128764156 128764189 BC051300_cds_0_0_chr9_128764157_f 0 +
+chr9 128787519 128789136 CCDS6915.1_cds_0_0_chr9_128787520_r 0 - chr9 128787519 128789136 NM_014908_cds_0_0_chr9_128787520_r 0 -
+chr9 128882427 128882523 CCDS6917.1_cds_0_0_chr9_128882428_f 0 + ~ ~ ~ ~ ~ ~
+chr9 128937229 128937445 CCDS6919.1_cds_0_0_chr9_128937230_r 0 - ~ ~ ~ ~ ~ ~
+chrX 122745047 122745924 CCDS14606.1_cds_0_0_chrX_122745048_f 0 + chrX 122745047 122745924 NM_001167_cds_1_0_chrX_122745048_f 0 +
+chrX 152648964 152649196 CCDS14733.1_cds_0_0_chrX_152648965_r 0 - chrX 152648964 152649196 NM_000425_cds_0_0_chrX_152648965_r 0 -
+chrX 152691446 152691471 CCDS14735.1_cds_0_0_chrX_152691447_f 0 + chrX 152691446 152691471 AF101728_cds_0_0_chrX_152691447_f 0 +
+chrX 152694029 152694263 CCDS14736.1_cds_0_0_chrX_152694030_r 0 - chrX 152694029 152694263 BC052303_cds_0_0_chrX_152694030_r 0 -

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/joiner_out4.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/joiner_out4.bed Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,65 @@
+chr1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 - chr1 147962192 147962580 NM_005997_cds_0_0_chr1_147962193_r 0 -
+chr1 147984545 147984630 CCDS990.1_cds_0_0_chr1_147984546_f 0 + chr1 147984545 147984630 BC007833_cds_0_0_chr1_147984546_f 0 +
+chr1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 - chr1 148078400 148078582 AJ011123_cds_0_0_chr1_148078401_r 0 -
+chr1 148185136 148185276 CCDS996.1_cds_0_0_chr1_148185137_f 0 + chr1 148185136 148185276 NM_002796_cds_0_0_chr1_148185137_f 0 +
+chr10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 - chr10 55251623 55253124 AY029205_cds_0_0_chr10_55251624_r 0 -
+chr11 116124407 116124501 CCDS8374.1_cds_0_0_chr11_116124408_r 0 - chr11 116124407 116124501 AK057832_cds_0_0_chr11_116124408_r 0 -
+chr11 116206508 116206563 CCDS8377.1_cds_0_0_chr11_116206509_f 0 + chr11 116206508 116206563 NM_000040_cds_1_0_chr11_116206509_f 0 +
+chr11 116211733 116212337 CCDS8378.1_cds_0_0_chr11_116211734_r 0 - chr11 116211733 116212337 BC005380_cds_0_0_chr11_116211734_r 0 -
+chr11 1812377 1812407 CCDS7726.1_cds_0_0_chr11_1812378_f 0 + NoChrom
+chr12 38440094 38440321 CCDS8736.1_cds_0_0_chr12_38440095_r 0 - chr12 38440094 38440321 NM_052885_cds_0_0_chr12_38440095_r 0 -
+chr13 112381694 112381953 CCDS9526.1_cds_0_0_chr13_112381695_f 0 + chr13 112381694 112381953 NM_207440_cds_1_0_chr13_112381695_f 0 +
+chr14 98710240 98712285 CCDS9949.1_cds_0_0_chr14_98710241_r 0 - chr14 98710240 98712285 NM_022898_cds_0_0_chr14_98710241_r 0 -
+chr15 41486872 41487060 CCDS10096.1_cds_0_0_chr15_41486873_r 0 - chr15 41486872 41487060 BX537418_cds_0_0_chr15_41486873_r 0 -
+chr15 41673708 41673857 CCDS10097.1_cds_0_0_chr15_41673709_f 0 + chr15 41673708 41673857 AK223365_cds_0_0_chr15_41673709_f 0 +
+chr15 41679161 41679250 CCDS10098.1_cds_0_0_chr15_41679162_r 0 - chr15 41679161 41679250 NM_153700_cds_0_0_chr15_41679162_r 0 -
+chr15 41826029 41826196 CCDS10101.1_cds_0_0_chr15_41826030_f 0 + NoChrom
+chr16 142908 143003 CCDS10397.1_cds_0_0_chr16_142909_f 0 + chr16 142908 143003 NM_005332_cds_0_0_chr16_142909_f 0 +
+chr16 179963 180135 CCDS10401.1_cds_0_0_chr16_179964_r 0 - NoChrom
+chr16 244413 244681 CCDS10402.1_cds_0_0_chr16_244414_f 0 + chr16 244413 244681 AK057165_cds_2_0_chr16_244414_f 0 +
+chr16 259268 259383 CCDS10403.1_cds_0_0_chr16_259269_r 0 - chr16 259268 259383 AB016929_cds_0_0_chr16_259269_r 0 -
+chr18 23786114 23786321 CCDS11891.1_cds_0_0_chr18_23786115_r 0 - chr18 23786114 23786321 NM_001792_cds_0_0_chr18_23786115_r 0 -
+chr18 59406881 59407046 CCDS11985.1_cds_0_0_chr18_59406882_f 0 + chr18 59406881 59407046 NM_012397_cds_1_0_chr18_59406882_f 0 +
+chr18 59455932 59456337 CCDS11986.1_cds_0_0_chr18_59455933_r 0 - chr18 59455932 59456337 AB046400_cds_0_0_chr18_59455933_r 0 -
+chr18 59600586 59600754 CCDS11988.1_cds_0_0_chr18_59600587_f 0 + NoChrom
+chr19 59068595 59069564 CCDS12866.1_cds_0_0_chr19_59068596_f 0 + chr19 59068595 59069564 BC013995_cds_1_0_chr19_59068596_f 0 +
+chr19 59236026 59236146 CCDS12872.1_cds_0_0_chr19_59236027_r 0 - chr19 59236026 59236146 NM_198481_cds_0_0_chr19_59236027_r 0 -
+chr19 59297998 59298008 CCDS12877.1_cds_0_0_chr19_59297999_f 0 + chr19 59297998 59298008 NM_004542_cds_0_0_chr19_59297999_f 0 +
+chr19 59302168 59302288 CCDS12878.1_cds_0_0_chr19_59302169_r 0 - NoChrom
+chr2 118288583 118288668 CCDS2120.1_cds_0_0_chr2_118288584_f 0 + chr2 118288583 118288668 NM_006773_cds_0_0_chr2_118288584_f 0 +
+chr2 118394148 118394202 CCDS2121.1_cds_0_0_chr2_118394149_r 0 - NoChrom
+chr2 220190202 220190242 CCDS2441.1_cds_0_0_chr2_220190203_f 0 + NoChrom
+chr2 220229609 220230869 CCDS2443.1_cds_0_0_chr2_220229610_r 0 - chr2 220229609 220230869 NM_024536_cds_0_0_chr2_220229610_r 0 -
+chr20 33330413 33330423 CCDS13249.1_cds_0_0_chr20_33330414_r 0 - chr20 33330413 33330423 NM_181466_cds_0_0_chr20_33330414_r 0 -
+chr20 33513606 33513792 CCDS13255.1_cds_0_0_chr20_33513607_f 0 + chr20 33513606 33513792 AF022655_cds_1_0_chr20_33513607_f 0 +
+chr20 33579500 33579527 CCDS13256.1_cds_0_0_chr20_33579501_r 0 - NoChrom
+chr20 33593260 33593348 CCDS13257.1_cds_0_0_chr20_33593261_f 0 + NoChrom
+chr21 32707032 32707192 CCDS13614.1_cds_0_0_chr21_32707033_f 0 + NoChrom
+chr21 32869641 32870022 CCDS13615.1_cds_0_0_chr21_32869642_r 0 - chr21 32869641 32870022 NM_018277_cds_3_0_chr21_32869642_r 0 -
+chr21 33321040 33322012 CCDS13620.1_cds_0_0_chr21_33321041_f 0 + chr21 33321040 33322012 NM_005806_cds_1_0_chr21_33321041_f 0 +
+chr21 33744994 33745040 CCDS13625.1_cds_0_0_chr21_33744995_r 0 - NoChrom
+chr22 30120223 30120265 CCDS13897.1_cds_0_0_chr22_30120224_f 0 + chr22 30120223 30120265 NM_004147_cds_0_0_chr22_30120224_f 0 +
+chr22 30160419 30160661 CCDS13898.1_cds_0_0_chr22_30160420_r 0 - chr22 30160419 30160661 BC032941_cds_0_0_chr22_30160420_r 0 -
+chr22 30665273 30665360 CCDS13901.1_cds_0_0_chr22_30665274_f 0 + NoChrom
+chr22 30939054 30939266 CCDS13903.1_cds_0_0_chr22_30939055_r 0 - NoChrom
+chr5 131424298 131424460 CCDS4149.1_cds_0_0_chr5_131424299_f 0 + chr5 131424298 131424460 NM_000588_cds_0_0_chr5_131424299_f 0 +
+chr5 131556601 131556672 CCDS4151.1_cds_0_0_chr5_131556602_r 0 - chr5 131556601 131556672 BC035813_cds_0_0_chr5_131556602_r 0 -
+chr5 131621326 131621419 CCDS4152.1_cds_0_0_chr5_131621327_f 0 + chr5 131621326 131621419 BC003096_cds_0_0_chr5_131621327_f 0 +
+chr5 131847541 131847666 CCDS4155.1_cds_0_0_chr5_131847542_r 0 - NoChrom
+chr6 108299600 108299744 CCDS5061.1_cds_0_0_chr6_108299601_r 0 - chr6 108299600 108299744 NM_007214_cds_0_0_chr6_108299601_r 0 -
+chr6 108594662 108594687 CCDS5063.1_cds_0_0_chr6_108594663_f 0 + chr6 108594662 108594687 NM_003269_cds_0_0_chr6_108594663_f 0 +
+chr6 108640045 108640151 CCDS5064.1_cds_0_0_chr6_108640046_r 0 - chr6 108640045 108640151 NM_003795_cds_0_0_chr6_108640046_r 0 -
+chr6 108722976 108723115 CCDS5067.1_cds_0_0_chr6_108722977_f 0 + chr6 108722976 108723115 NM_145315_cds_0_0_chr6_108722977_f 0 +
+chr7 113660517 113660685 CCDS5760.1_cds_0_0_chr7_113660518_f 0 + chr7 113660517 113660685 AF467257_cds_1_0_chr7_113660518_f 0 +
+chr7 116512159 116512389 CCDS5771.1_cds_0_0_chr7_116512160_r 0 - chr7 116512159 116512389 NM_003391_cds_0_0_chr7_116512160_r 0 -
+chr7 116714099 116714152 CCDS5773.1_cds_0_0_chr7_116714100_f 0 + chr7 116714099 116714152 NM_000492_cds_0_0_chr7_116714100_f 0 +
+chr7 116945541 116945787 CCDS5774.1_cds_0_0_chr7_116945542_r 0 - chr7 116945541 116945787 AF377960_cds_0_0_chr7_116945542_r 0 -
+chr8 118881131 118881317 CCDS6324.1_cds_0_0_chr8_118881132_r 0 - chr8 118881131 118881317 NM_000127_cds_0_0_chr8_118881132_r 0 -
+chr9 128764156 128764189 CCDS6914.1_cds_0_0_chr9_128764157_f 0 + chr9 128764156 128764189 BC051300_cds_0_0_chr9_128764157_f 0 +
+chr9 128787519 128789136 CCDS6915.1_cds_0_0_chr9_128787520_r 0 - chr9 128787519 128789136 NM_014908_cds_0_0_chr9_128787520_r 0 -
+chr9 128882427 128882523 CCDS6917.1_cds_0_0_chr9_128882428_f 0 + NoChrom
+chr9 128937229 128937445 CCDS6919.1_cds_0_0_chr9_128937230_r 0 - NoChrom
+chrX 122745047 122745924 CCDS14606.1_cds_0_0_chrX_122745048_f 0 + chrX 122745047 122745924 NM_001167_cds_1_0_chrX_122745048_f 0 +
+chrX 152648964 152649196 CCDS14733.1_cds_0_0_chrX_152648965_r 0 - chrX 152648964 152649196 NM_000425_cds_0_0_chrX_152648965_r 0 -
+chrX 152691446 152691471 CCDS14735.1_cds_0_0_chrX_152691447_f 0 + chrX 152691446 152691471 AF101728_cds_0_0_chrX_152691447_f 0 +
+chrX 152694029 152694263 CCDS14736.1_cds_0_0_chrX_152694030_r 0 - chrX 152694029 152694263 BC052303_cds_0_0_chrX_152694030_r 0 -

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/kcca_out1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/kcca_out1.tabular Sat Feb 21 16:33:42 2015 +0100

[

b'@@ -0,0 +1,304 @@\n+\\#Component\\\t1\\\t2\\\t3\\\t4\n+\\#Correlation\\\t\\-?0\\.99\\d*\\\t\\-?0\\.99\\d*\\\t\\-?0\\.93\\d*\\\t\\-?0\\.93\\d*\n+\\#Estimated\\ 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\d*\\\t\\-?0\\.0015\\d*\\\t\\-?0\\.010\\d*\\\t\\-?0\\.010\\d*\n+1\\d*\\\t\\-?0\\.0081\\d*\\\t\\-?0\\.0081\\d*\\\t\\-?0\\.020\\d*\\\t\\-?0\\.020\\d*\n+1\\d*\\\t\\-?0\\.0037\\d*\\\t\\-?0\\.0037\\d*\\\t\\-?0\\.00065\\d*\\\t\\-?0\\.00065\\d*\n+1\\d*\\\t\\-?0\\.0010\\d*\\\t\\-?0\\.0010\\d*\\\t\\-?0\\.022\\d*\\\t\\-?0\\.022\\d*\n+1\\d*\\\t\\-?0\\.00063\\d*\\\t\\-?0\\.00063\\d*\\\t\\-?0\\.0048\\d*\\\t\\-?0\\.0048\\d*\n+1\\d*\\\t\\-?0\\.0033\\d*\\\t\\-?0\\.0033\\d*\\\t\\-?0\\.0096\\d*\\\t\\-?0\\.0096\\d*\n+1\\d*\\\t\\-?0\\.0014\\d*\\\t\\-?0\\.0014\\d*\\\t\\-?0\\.010\\d*\\\t\\-?0\\.010\\d*\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/kcca_out2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/kcca_out2.tabular Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,304 @@\n+\\#Component\\\t1\\\t2\n+\\#Correlation\\\t\\-?0\\.99\\d*\\\t\\-?0\\.99\\d*\n+\\#Estimated\\ 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diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/knownGeneUpstream500Flanks.dat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/knownGeneUpstream500Flanks.dat Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,964 @@\n+chr22\t14538299\t14538799\tBC066547\t0\t-\t14537305\t14537938\t0\t1\t2759,\t0,\n+chr22\t14572995\t14573495\tBX248778\t0\t-\t14538811\t14539138\t0\t8\t599,91,136,114,112,148,111,90,\t0,3606,28020,28374,30241,30473,31890,34115,\n+chr22\t14824358\t14824858\tNM_001005239\t0\t-\t14823377\t14824358\t0\t1\t981,\t0,\n+chr22\t15341946\t15342446\tAY026350\t0\t+\t15342479\t15343061\t0\t1\t1320,\t0,\n+chr22\t15448254\t15448754\tNM_014406\t0\t-\t15446320\t15447994\t0\t1\t2051,\t0,\n+chr22\t15503751\t15504251\tAK095032\t0\t+\t15504572\t15504974\t0\t1\t2133,\t0,\n+chr22\t15677136\t15677636\tBC045548\t0\t-\t15639062\t15663517\t0\t4\t930,254,345,86,\t0,16291,24259,38127,\n+chr22\t15939911\t15940411\tNM_014339\t0\t+\t15940535\t15965264\t0\t13\t262,25,147,113,127,48,164,84,85,12,102,42,2191,\t0,12094,12829,13807,15387,17028,17171,18526,19758,20623,20885,22759,23339,\n+chr22\t15976697\t15977197\tNM_031890\t0\t-\t15974834\t15976571\t0\t1\t4954,\t0,\n+chr22\t16014723\t16015223\tNM_033070\t0\t-\t15993464\t16014695\t0\t8\t837,189,175,34,94,113,204,154,\t0,1029,3538,5577,7503,10927,12021,21605,\n+chr22\t16020731\t16021231\tNM_017829\t0\t-\t15993464\t16020688\t0\t8\t837,189,175,34,94,113,204,79,\t0,1029,3538,5577,7503,10927,12021,27688,\n+chr22\t16055099\t16055599\tNM_177405\t0\t-\t16036926\t16055022\t0\t7\t2275,203,158,109,91,128,107,\t0,2518,3302,9037,10640,12381,20247,\n+chr22\t16065333\t16065833\tNM_017424\t0\t-\t16036926\t16065121\t0\t9\t2273,203,158,109,91,128,211,220,534,\t0,2516,3300,9035,10638,12379,24259,27767,30052,\n+chr22\t16053967\t16054467\tAK130623\t0\t-\t16053157\t16053556\t0\t2\t33,1379,\t0,9814,\n+chr22\t16330681\t16331181\tAL832377\t0\t+\t16353079\t16407094\t0\t18\t97,184,140,105,50,170,84,154,130,38,92,127,389,129,847,1417,112,498,\t0,19807,21814,23035,25486,27251,34217,46516,60164,61581,61701,62054,63473,64900,65218,71210,75088,75907,\n+chr22\t16330681\t16331181\tAF336133\t0\t+\t16353079\t16407094\t0\t18\t97,184,140,105,50,170,84,210,134,38,92,127,389,129,847,1417,112,1311,\t0,19807,21814,23035,25486,27251,34217,46516,60160,61581,61701,62054,63473,64900,65218,71210,75088,75907,\n+chr22\t16402742\t16403242\tAK091754\t0\t+\t16403257\t16404572\t0\t4\t566,167,112,1299,\t0,1239,3027,3846,\n+chr22\t16417236\t16417736\tNM_031481\t0\t+\t16437264\t16447556\t0\t11\t231,63,220,123,56,91,119,166,155,76,787,\t0,6806,19328,20620,20941,22146,22999,26719,27508,29173,29678,\n+chr22\t16486089\t16486589\tNM_001696\t0\t-\t16449993\t16485955\t0\t9\t578,88,95,69,90,67,110,66,167,\t0,2370,6035,7868,8933,20653,21052,27302,36444,\n+chr22\t16495538\t16496038\tNM_015367\t0\t+\t16513031\t16584854\t0\t7\t168,171,108,157,70,144,2545,\t0,16943,44495,50267,57422,63524,87958,\n+chr22\t16495591\t16496091\tCR608603\t0\t+\t16513031\t16559712\t0\t6\t115,171,108,157,70,1491,\t0,16890,44442,50214,57369,63471,\n+chr22\t16495630\t16496130\tAL831982\t0\t+\t16513031\t16584126\t0\t5\t76,171,108,157,3941,\t0,16851,44403,50175,87866,\n+chr22\t16495644\t16496144\tBC007658\t0\t+\t16559592\t16584854\t0\t7\t62,171,108,157,70,144,2027,\t0,16837,44389,50161,57316,63418,87852,\n+chr22\t16512531\t16513031\tAF539453\t0\t+\t16513031\t16542014\t0\t5\t121,108,98,157,858,\t0,27502,28897,33274,70965,\n+chr22\t16545803\t16546303\tAF146568\t0\t+\t16546373\t16584854\t0\t4\t159,70,144,2545,\t0,7157,13259,37693,\n+chr22\t16631812\t16632312\tNM_001196\t0\t-\t16592899\t16607436\t0\t6\t1452,213,140,211,70,112,\t0,3877,5209,9663,15965,40241,\n+chr22\t16631333\t16631833\tNM_197966\t0\t-\t16592899\t16631009\t0\t6\t1452,213,140,211,70,404,\t0,3877,5209,9663,15965,39470,\n+chr22\t16631732\t16632232\tAY005151\t0\t-\t16596712\t16607436\t0\t7\t93,213,140,95,211,70,32,\t0,2518,3850,4583,8304,14606,38882,\n+chr22\t16634141\t16634641\tAK097861\t0\t+\t16634856\t16635369\t0\t1\t2160,\t0,\n+chr22\t16764147\t16764647\tCR456364\t0\t-\t16699095\t16764132\t0\t19\t343,88,89,187,174,63,113,197,148,97,127,116,258,101,156,102,117,208,279,\t0,23224,24249,30162,44203,45495,45648,47359,49810,52133,53609,54571,55049,57773,59167,60203,60956,62957,64874,\n+chr22\t16721799\t16722299\tAK124853\t0\t-\t16720930\t16721356\t0\t1\t2038,\t0,\n+chr22\t16818604\t16819104\tAK094477\t0\t-\t16817923\t16818349\t0\t1\t2251,\t0,\n+chr22\t16886204\t16886704\tAK123935\t0\t+\t16894400\t16894982\t0\t2\t170,2209,\t0,6375,\n+chr22\t16936204\t16936704\tAK000085\t0\t-\t16935437\t16936076\t0\t1\t1699,\t0,\n+chr22\t16934742\t1693524'..b'102,1491,2256,2444,2613,2748,2964,\n+chr22\t49236257\t49236757\tNM_033200\t0\t-\t49231963\t49235627\t0\t14\t749,97,112,169,183,97,106,135,142,179,218,29,339,103,\t0,857,1389,1608,1851,2106,2278,2452,2723,3084,3334,3687,3831,4631,\n+chr22\t49236253\t49236753\tBC002942\t0\t-\t49231963\t49236248\t0\t14\t745,97,112,169,183,97,106,135,142,179,218,29,254,99,\t0,853,1385,1604,1847,2102,2274,2448,2719,3080,3330,3683,3827,4627,\n+chr22\t49236315\t49236815\tNM_014551\t0\t+\t49245061\t49247932\t0\t9\t203,102,56,85,69,80,146,84,562,\t0,8204,9184,9334,9498,9730,9890,10406,10947,\n+chr22\t49236316\t49236816\tBC001298\t0\t+\t49245061\t49251832\t0\t19\t202,102,56,85,69,80,146,84,131,72,67,108,54,71,73,69,50,102,455,\t0,8203,9183,9333,9497,9729,9889,10405,10946,12721,13299,13497,13742,13937,14099,14257,14427,14577,14773,\n+chr22\t49236331\t49236831\tNM_152299\t0\t+\t49245061\t49251948\t0\t20\t187,102,56,85,69,80,146,84,131,72,67,108,54,71,73,69,50,102,150,237,\t0,8188,9168,9318,9482,9714,9874,10390,10931,12706,13284,13482,13727,13922,14084,14242,14412,14562,14758,14976,\n+chr22\t49236331\t49236831\tBC001937\t0\t+\t49236910\t49251948\t0\t20\t187,102,56,85,69,80,146,84,131,72,67,108,54,71,73,69,50,102,150,237,\t0,8188,9168,9318,9482,9714,9874,10390,10931,12706,13284,13482,13727,13922,14084,14242,14412,14562,14758,14976,\n+chr22\t49236332\t49236832\tBC009441\t0\t+\t49236910\t49251948\t0\t20\t186,102,56,85,69,80,146,84,131,72,67,108,54,71,73,72,50,102,150,236,\t0,8187,9167,9317,9481,9713,9873,10389,10930,12705,13283,13481,13726,13921,14083,14238,14411,14561,14757,14975,\n+chr22\t49236332\t49236832\tBC009441\t0\t+\t49245061\t49251948\t0\t20\t186,102,56,85,69,80,146,84,131,72,67,108,54,71,73,72,50,102,150,236,\t0,8187,9167,9317,9481,9713,9873,10389,10930,12705,13283,13481,13726,13921,14083,14238,14411,14561,14757,14975,\n+chr22\t49254116\t49254616\tNM_005138\t0\t-\t49252183\t49252984\t0\t2\t855,72,\t0,1902,\n+chr22\t49258599\t49259099\tNM_001953\t0\t-\t49254342\t49258282\t0\t10\t167,141,231,163,119,130,99,203,224,123,\t0,249,494,824,1413,1836,2760,3384,3744,4152,\n+chr22\t49260395\t49260895\tS72487\t0\t-\t49260065\t49260230\t0\t4\t851,117,122,632,\t0,1002,1227,1481,\n+chr22\t49276105\t49276605\tNM_138433\t0\t+\t49277036\t49278524\t0\t1\t2080,\t0,\n+chr22\t49307022\t49307522\tNM_004377\t0\t-\t49297910\t49306488\t0\t19\t561,93,114,153,135,165,117,106,186,196,85,108,78,138,102,178,140,160,64,\t0,715,1432,2030,2297,2514,3145,3342,4014,4659,5474,5632,7174,7337,7675,7996,8463,8914,9525,\n+chr22\t49311538\t49312038\tNM_005198\t0\t-\t49307753\t49311354\t0\t11\t298,82,104,109,82,59,96,134,114,109,408,\t0,468,769,1016,1232,1400,1607,2462,2791,3291,3600,\n+chr22\t49311098\t49311598\tCR456603\t0\t+\t49311602\t49311719\t0\t2\t298,140,\t0,572,\n+chr22\t49328774\t49329274\tNM_139124\t0\t+\t49329391\t49339351\t0\t11\t182,106,93,358,76,173,110,108,71,99,842,\t0,1087,2521,4004,4665,4859,5122,5955,6218,9509,10004,\n+chr22\t49356720\t49357220\tNM_000487\t0\t-\t49353716\t49356345\t0\t8\t437,103,128,125,170,219,241,593,\t0,551,908,1126,1563,1806,2138,2528,\n+chr22\t49356715\t49357215\tBC014210\t0\t-\t49353716\t49356351\t0\t8\t436,103,128,125,170,219,241,588,\t0,550,907,1125,1562,1805,2137,2527,\n+chr22\t49386505\t49387005\tAK127606\t0\t-\t49384128\t49384557\t0\t1\t2720,\t0,\n+chr22\t49466290\t49466790\tNM_001097\t0\t+\t49466807\t49473779\t0\t5\t94,204,284,146,646,\t0,1052,1475,5842,6434,\n+chr22\t49485157\t49485657\tNM_203477\t0\t+\t49527348\t49527714\t0\t4\t241,175,121,852,\t0,26034,28087,41569,\n+chr22\t49512231\t49512731\tNM_007081\t0\t-\t49497347\t49510866\t0\t9\t1383,84,95,112,80,80,30,160,159,\t0,1549,1963,2413,8280,9178,10460,14696,16009,\n+chr22\t49512231\t49512731\tNM_001003789\t0\t-\t49497347\t49510866\t0\t9\t1383,84,98,112,80,80,30,164,159,\t0,1549,1963,2413,8280,9178,10460,14696,16009,\n+chr22\t49512162\t49512662\tBC075856\t0\t-\t49497347\t49510866\t0\t10\t1368,84,125,112,80,80,30,164,155,90,\t0,1534,1918,2398,8265,9163,10445,14681,15384,15994,\n+chr22\t49512202\t49512702\tBC020495\t0\t-\t49501678\t49510866\t0\t6\t1886,80,80,30,160,130,\t0,4548,5446,6728,10964,12277,\n+chr22\t49511868\t49512368\tAL365511\t0\t+\t49513809\t49517553\t0\t4\t225,121,49,462,\t0,1376,4953,5095,\n+chr22\t49511883\t49512383\tBC019348\t0\t+\t49513809\t49517553\t0\t4\t210,121,49,278,\t0,1361,4938,5083,\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/kpca_out1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/kpca_out1.tabular Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,304 @@
+#Component 1 2
+#Eigenvalue 748.5 31.76
+#Principal component vectors 1 2
+1 -0.003553 0.0108
+2 -0.003722 -0.003192
+3 -0.003887 -0.003062
+4 -0.0038 -0.007509
+5 -0.0036 0.01068
+6 -0.002995 0.02441
+7 -0.003814 -0.001828
+8 -0.00354 0.006305
+9 -0.004002 -0.01452
+10 -0.003663 -0.001368
+11 -0.003267 0.02134
+12 -0.003575 0.001815
+13 -0.003807 -0.004912
+14 -0.004281 -0.01352
+15 -0.003251 0.03864
+16 -0.002922 0.04394
+17 -0.003349 0.02585
+18 -0.003521 0.01053
+19 -0.002847 0.02952
+20 -0.003403 0.01643
+21 -0.003128 0.01419
+22 -0.003382 0.01406
+23 -0.004124 0.003402
+24 -0.003227 0.004863
+25 -0.003329 0.0007417
+26 -0.003506 -0.001891
+27 -0.003393 0.005424
+28 -0.003411 0.01263
+29 -0.003506 0.01091
+30 -0.003655 -0.004034
+31 -0.00361 -0.003953
+32 -0.003234 0.01438
+33 -0.003377 0.02573
+34 -0.003236 0.0352
+35 -0.003663 -0.001368
+36 -0.003801 0.003321
+37 -0.003401 0.01999
+38 -0.003663 -0.001368
+39 -0.004064 -0.01246
+40 -0.003482 0.008422
+41 -0.00366 0.008718
+42 -0.004057 -0.02284
+43 -0.004044 -0.008892
+44 -0.003315 0.006892
+45 -0.003022 0.01469
+46 -0.003747 -0.005408
+47 -0.003352 0.01636
+48 -0.003865 -0.00534
+49 -0.003328 0.01907
+50 -0.003632 0.004649
+51 0.002131 0.02353
+52 0.001268 0.01077
+53 0.00232 0.0165
+54 -0.0005446 -0.02218
+55 0.001391 0.002863
+56 0.0003522 -0.01197
+57 0.001503 0.008832
+58 -0.001879 -0.02529
+59 0.001425 0.008304
+60 -0.000784 -0.0196
+61 -0.001688 -0.03188
+62 0.000332 -0.002273
+63 -0.0002401 -0.01364
+64 0.001079 -0.003714
+65 -0.0007557 -0.005543
+66 0.001375 0.01646
+67 0.0004002 -0.01059
+68 -0.0001866 -0.007917
+69 0.0007813 -0.01567
+70 -0.0006023 -0.01492
+71 0.001281 -0.003829
+72 0.0001411 -0.0001777
+73 0.00148 -0.01053
+74 0.0009533 -0.005025
+75 0.0008315 0.006252
+76 0.001242 0.01179
+77 0.001929 0.008282
+78 0.002309 0.007654
+79 0.000773 -0.00466
+80 -0.0009729 -0.007942
+81 -0.0008252 -0.01809
+82 -0.0009752 -0.01705
+83 -0.0003282 -0.007332
+84 0.001528 -0.01434
+85 0.0002046 -0.0145
+86 0.0009586 0.006116
+87 0.001825 0.01357
+88 0.0006918 -0.009912
+89 -0.0001648 -0.006837
+90 -0.0004951 -0.01827
+91 -5.753e-05 -0.01874
+92 0.00098 -0.0006915
+93 -0.0002379 -0.01011
+94 -0.001821 -0.02537
+95 -0.0001244 -0.01378
+96 1.283e-06 -0.005116
+97 2.13e-05 -0.007654
+98 0.0006301 0.001939
+99 -0.001958 -0.01857
+100 -0.000121 -0.00904
+101 0.003803 -0.00735
+102 0.001462 -0.01964
+103 0.004318 0.006231
+104 0.002705 -0.009198
+105 0.003481 -0.006612
+106 0.006089 0.01059
+107 -0.0003162 -0.03404
+108 0.004981 0.005895
+109 0.003329 -0.01195
+110 0.005217 0.01984
+111 0.002443 0.005619
+112 0.002393 -0.009436
+113 0.003352 0.003334
+114 0.001216 -0.02527
+115 0.001742 -0.01987
+116 0.002768 0.0001267
+117 0.002831 -0.001715
+118 0.006776 0.03336
+119 0.006694 -0.002136
+120 0.0012 -0.02356
+121 0.003951 0.00754
+122 0.001074 -0.02014
+123 0.006251 0.00718
+124 0.001691 -0.007518
+125 0.003625 0.006525
+126 0.004493 0.01431
+127 0.001482 -0.006514
+128 0.001565 -0.004955
+129 0.002951 -0.01093
+130 0.004001 0.01226
+131 0.004821 0.00717
+132 0.006416 0.04314
+133 0.003005 -0.01144
+134 0.001834 -0.005554
+135 0.002168 -0.01795
+136 0.005535 0.01723
+137 0.003198 -0.000593
+138 0.002747 -0.001526
+139 0.001328 -0.006202
+140 0.00336 0.008984
+141 0.003579 0.001004
+142 0.003037 0.01072
+143 0.001462 -0.01964
+144 0.004127 0.003295
+145 0.003853 0.004392
+146 0.002912 0.002869
+147 0.001813 -0.01327
+148 0.002518 -2.875e-06
+149 0.002741 -0.0004153
+150 0.001611 -0.01074
+#Rotated values 1 2
+1 -398.9 51.44
+2 -417.9 -15.21
+3 -436.4 -14.59
+4 -426.6 -35.77
+5 -404.2 50.89
+6 -336.3 116.3
+7 -428.2 -8.706
+8 -397.5 30.04
+9 -449.3 -69.17
+10 -411.3 -6.517
+11 -366.8 101.6
+12 -401.4 8.645
+13 -427.5 -23.4
+14 -480.6 -64.4
+15 -365 184
+16 -328.1 209.3
+17 -376 123.1
+18 -395.3 50.18
+19 -319.7 140.6
+20 -382.1 78.28
+21 -351.3 67.61
+22 -379.7 66.98
+23 -463.1 16.21
+24 -362.3 23.16
+25 -373.8 3.533
+26 -393.6 -9.008
+27 -381 25.84
+28 -383 60.16
+29 -393.6 51.96
+30 -410.4 -19.22
+31 -405.3 -18.83
+32 -363.1 68.48
+33 -379.2 122.6
+34 -363.4 167.7
+35 -411.3 -6.517
+36 -426.8 15.82
+37 -381.9 95.23
+38 -411.3 -6.517
+39 -456.3 -59.36
+40 -391 40.12
+41 -410.9 41.53
+42 -455.5 -108.8
+43 -454.1 -42.36
+44 -372.2 32.83
+45 -339.3 69.98
+46 -420.7 -25.76
+47 -376.4 77.94
+48 -433.9 -25.44
+49 -373.7 90.82
+50 -407.8 22.14
+51 239.3 112.1
+52 142.4 51.31
+53 260.5 78.62
+54 -61.14 -105.7
+55 156.2 13.64
+56 39.54 -57.03
+57 168.7 42.07
+58 -210.9 -120.5
+59 160 39.56
+60 -88.03 -93.36
+61 -189.5 -151.8
+62 37.28 -10.83
+63 -26.96 -64.96
+64 121.1 -17.69
+65 -84.85 -26.41
+66 154.4 78.39
+67 44.94 -50.46
+68 -20.95 -37.71
+69 87.72 -74.64
+70 -67.63 -71.05
+71 143.8 -18.24
+72 15.84 -0.8465
+73 166.2 -50.16
+74 107 -23.94
+75 93.36 29.78
+76 139.5 56.16
+77 216.6 39.45
+78 259.2 36.46
+79 86.79 -22.2
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diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/kpca_out2.pdf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/kpca_out2.pdf Sat Feb 21 16:33:42 2015 +0100

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diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/lav_to_bed_out_1.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/lav_to_bed_out_1.bed Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,2 @@
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diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/lav_to_bed_out_2.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/lav_to_bed_out_2.bed Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,2 @@
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diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/ldInput1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/ldInput1.txt Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,5000 @@\n+rs11186873\t06984\tC\tC\n+rs11186873\t06985\tC\tC\n+rs11186873\t06986\tC\tC\n+rs11186873\t06989\tC\tC\n+rs11186873\t06991\tC\tC\n+rs11186873\t06993\tC\tC\n+rs11186873\t06994\tC\tC\n+rs11186873\t06995\tC\tC\n+rs11186873\t06997\tC\tC\n+rs11186873\t07000\tC\tC\n+rs11186873\t07014\tC\tC\n+rs11186873\t07019\tN\tN\n+rs11186873\t07022\tC\tC\n+rs11186873\t07029\tC\tC\n+rs11186873\t07031\tC\tC\n+rs11186873\t07034\tN\tN\n+rs11186873\t07037\tC\tC\n+rs11186873\t07045\tC\tC\n+rs11186873\t07048\tN\tN\n+rs11186873\t07051\tC\tC\n+rs11186873\t07055\tC\tC\n+rs11186873\t07056\tC\tC\n+rs11186873\t07345\tC\tC\n+rs11186873\t07346\tC\tC\n+rs11186873\t07347\tC\tC\n+rs11186873\t07348\tC\tC\n+rs11186873\t07349\tC\tC\n+rs11186873\t07357\tC\tC\n+rs11186873\t07435\tC\tC\n+rs11186873\t10830\tC\tC\n+rs11186873\t10831\tC\tC\n+rs11186873\t10835\tC\tC\n+rs11186873\t10836\tC\tC\n+rs11186873\t10837\tC\tC\n+rs11186873\t10838\tC\tC\n+rs11186873\t10839\tC\tC\n+rs11186873\t10840\tC\tC\n+rs11186873\t10843\tC\tC\n+rs11186873\t10845\tC\tC\n+rs11186873\t10846\tC\tC\n+rs11186873\t10847\tC\tC\n+rs11186873\t10850\tC\tC\n+rs11186873\t10851\tN\tN\n+rs11186873\t10852\tC\tC\n+rs11186873\t10853\tC\tC\n+rs11186873\t10854\tC\tC\n+rs11186873\t10855\tC\tC\n+rs11186873\t10856\tC\tC\n+rs11186873\t10857\tN\tN\n+rs11186873\t10859\tC\tC\n+rs11186873\t10860\tN\tN\n+rs11186873\t10861\tC\tC\n+rs11186873\t10863\tC\tC\n+rs11186873\t10864\tC\tC\n+rs11186873\t10865\tC\tC\n+rs11186873\t11829\tC\tC\n+rs11186873\t11830\tC\tC\n+rs11186873\t11831\tC\tC\n+rs11186873\t11832\tC\tC\n+rs11186873\t11839\tC\tC\n+rs11186873\t11840\tC\tC\n+rs11186873\t11843\tC\tC\n+rs11186873\t11881\tC\tC\n+rs11186873\t11882\tC\tC\n+rs11186873\t11891\tC\tC\n+rs11186873\t11892\tC\tC\n+rs11186873\t11893\tC\tC\n+rs11186873\t11894\tC\tC\n+rs11186873\t11917\tC\tT\n+rs11186873\t11918\tC\tC\n+rs11186873\t11919\tC\tC\n+rs11186873\t11920\tC\tC\n+rs11186873\t11930\tC\tC\n+rs11186873\t11931\tC\tC\n+rs11186873\t11992\tC\tC\n+rs11186873\t11993\tC\tC\n+rs11186873\t11994\tC\tC\n+rs11186873\t11995\tC\tC\n+rs11186873\t12003\tC\tC\n+rs11186873\t12004\tN\tN\n+rs11186873\t12005\tC\tC\n+rs11186873\t12006\tC\tC\n+rs11186873\t12043\tC\tC\n+rs11186873\t12044\tC\tC\n+rs11186873\t12045\tC\tC\n+rs11186873\t12056\tC\tC\n+rs11186873\t12057\tC\tC\n+rs11186873\t12144\tC\tC\n+rs11186873\t12145\tC\tC\n+rs11186873\t12146\tC\tC\n+rs11186873\t12154\tC\tC\n+rs11186873\t12155\tC\tC\n+rs11186873\t12156\tC\tC\n+rs11186873\t12234\tC\tC\n+rs11186873\t12236\tN\tN\n+rs11186873\t12239\tC\tC\n+rs11186873\t12248\tC\tC\n+rs11186873\t12249\tC\tC\n+rs11186873\t12264\tC\tC\n+rs11186873\t12272\tC\tC\n+rs11186873\t12273\tC\tC\n+rs11186873\t12275\tC\tC\n+rs11186873\t12282\tC\tC\n+rs11186873\t12283\tC\tC\n+rs11186873\t12286\tC\tC\n+rs11186873\t12287\tC\tC\n+rs11186873\t12335\tC\tC\n+rs11186873\t12336\tC\tC\n+rs11186873\t12340\tC\tC\n+rs11186873\t12341\tC\tC\n+rs11186873\t12342\tC\tC\n+rs11186873\t12343\tC\tC\n+rs11186873\t12344\tC\tC\n+rs11186873\t12347\tC\tC\n+rs11186873\t12348\tC\tC\n+rs11186873\t12375\tC\tC\n+rs11186873\t12376\tC\tC\n+rs11186873\t12383\tC\tC\n+rs11186873\t12386\tC\tC\n+rs11186873\t12399\tC\tC\n+rs11186873\t12400\tC\tC\n+rs11186873\t12413\tC\tC\n+rs11186873\t12489\tC\tC\n+rs11186873\t12546\tC\tC\n+rs11186873\t12707\tC\tC\n+rs11186873\t12708\tC\tC\n+rs11186873\t12716\tC\tC\n+rs11186873\t12717\tN\tN\n+rs11186873\t12718\tC\tC\n+rs11186873\t12739\tC\tC\n+rs11186873\t12740\tC\tC\n+rs11186873\t12748\tC\tC\n+rs11186873\t12749\tC\tC\n+rs11186873\t12750\tC\tC\n+rs11186873\t12751\tC\tC\n+rs11186873\t12752\tC\tC\n+rs11186873\t12753\tC\tC\n+rs11186873\t12760\tC\tC\n+rs11186873\t12761\tC\tC\n+rs11186873\t12762\tC\tC\n+rs11186873\t12763\tC\tC\n+rs11186873\t12766\tC\tC\n+rs11186873\t12767\tC\tC\n+rs11186873\t12775\tC\tC\n+rs11186873\t12776\tC\tC\n+rs11186873\t12777\tC\tC\n+rs11186873\t12778\tC\tC\n+rs11186873\t12801\tC\tC\n+rs11186873\t12802\tC\tC\n+rs11186873\t12812\tC\tC\n+rs11186873\t12813\tC\tC\n+rs11186873\t12814\tC\tC\n+rs11186873\t12815\tC\tC\n+rs11186873\t12817\tC\tC\n+rs11186873\t12818\tC\tC\n+rs11186873\t12827\tC\tC\n+rs11186873\t12828\tC\tC\n+rs11186873\t12829\tC\tC\n+rs11186873\t12830\tC\tC\n+rs11186873\t12832\tC\tC\n+rs11186873\t12842\tC\tC\n+rs11186873\t12843\tC\tC\n+rs11186873\t12864\tC\tC\n+rs11186873\t12865\tC\tC\n+rs11186873\t12872\tC\tC\n+rs11186873\t12873\tC\tC\n+rs11186873\t12874\tC\tC\n+rs11186873\t12875\tC\tC\n+rs11186873\t12877\tC\tC\n+rs11186873\t12878\tC\tC\n+rs11186873\t12889\tC\tC\n+rs11186873\t12890\tC\tC\n+rs11186873\t12891\tC\tC\n+rs11186873\t12892\tC\tC\n+rs11186874\t06984\tN\tN\n+rs11186874\t06985\tC\tC\n+rs11186874\t06986\tN\tN\n+rs11186874\t06989\tN\tN\n+rs11186874\t06991\tC\tC\n+rs11186874\t06993\tC\tC\n+rs11186874\t06994\tC\t'..b'2343\tN\tN\n+rs4339951\t12344\tN\tN\n+rs4339951\t12347\tN\tN\n+rs4339951\t12348\tN\tN\n+rs4339951\t12375\tN\tN\n+rs4339951\t12376\tN\tN\n+rs4339951\t12383\tN\tN\n+rs4339951\t12386\tN\tN\n+rs4339951\t12399\tN\tN\n+rs4339951\t12400\tN\tN\n+rs4339951\t12413\tN\tN\n+rs4339951\t12489\tN\tN\n+rs4339951\t12546\tN\tN\n+rs4339951\t12707\tC\tC\n+rs4339951\t12708\tN\tN\n+rs4339951\t12716\tC\tC\n+rs4339951\t12717\tC\tC\n+rs4339951\t12718\tN\tN\n+rs4339951\t12739\tN\tN\n+rs4339951\t12740\tC\tC\n+rs4339951\t12748\tN\tN\n+rs4339951\t12749\tN\tN\n+rs4339951\t12750\tC\tC\n+rs4339951\t12751\tC\tC\n+rs4339951\t12752\tC\tC\n+rs4339951\t12753\tC\tC\n+rs4339951\t12760\tC\tC\n+rs4339951\t12761\tC\tC\n+rs4339951\t12762\tC\tC\n+rs4339951\t12763\tC\tC\n+rs4339951\t12766\tN\tN\n+rs4339951\t12767\tN\tN\n+rs4339951\t12775\tN\tN\n+rs4339951\t12776\tN\tN\n+rs4339951\t12777\tN\tN\n+rs4339951\t12778\tN\tN\n+rs4339951\t12801\tC\tC\n+rs4339951\t12802\tC\tC\n+rs4339951\t12812\tC\tC\n+rs4339951\t12813\tC\tC\n+rs4339951\t12814\tC\tC\n+rs4339951\t12815\tC\tC\n+rs4339951\t12817\tN\tN\n+rs4339951\t12818\tN\tN\n+rs4339951\t12827\tN\tN\n+rs4339951\t12828\tN\tN\n+rs4339951\t12829\tN\tN\n+rs4339951\t12830\tN\tN\n+rs4339951\t12832\tN\tN\n+rs4339951\t12842\tN\tN\n+rs4339951\t12843\tN\tN\n+rs4339951\t12864\tC\tC\n+rs4339951\t12865\tC\tC\n+rs4339951\t12872\tC\tC\n+rs4339951\t12873\tC\tC\n+rs4339951\t12874\tC\tC\n+rs4339951\t12875\tC\tC\n+rs4339951\t12877\tN\tN\n+rs4339951\t12878\tC\tC\n+rs4339951\t12889\tN\tN\n+rs4339951\t12890\tN\tN\n+rs4339951\t12891\tC\tC\n+rs4339951\t12892\tC\tC\n+rs7906870\t06984\tN\tN\n+rs7906870\t06985\tG\tG\n+rs7906870\t06986\tN\tN\n+rs7906870\t06989\tN\tN\n+rs7906870\t06991\tG\tG\n+rs7906870\t06993\tG\tG\n+rs7906870\t06994\tG\tG\n+rs7906870\t06995\tN\tN\n+rs7906870\t06997\tN\tN\n+rs7906870\t07000\tG\tG\n+rs7906870\t07014\tN\tN\n+rs7906870\t07019\tG\tG\n+rs7906870\t07022\tG\tG\n+rs7906870\t07029\tG\tG\n+rs7906870\t07031\tN\tN\n+rs7906870\t07034\tG\tG\n+rs7906870\t07037\tN\tN\n+rs7906870\t07045\tN\tN\n+rs7906870\t07048\tG\tG\n+rs7906870\t07051\tN\tN\n+rs7906870\t07055\tG\tG\n+rs7906870\t07056\tG\tG\n+rs7906870\t07345\tG\tG\n+rs7906870\t07346\tN\tN\n+rs7906870\t07347\tN\tN\n+rs7906870\t07348\tG\tG\n+rs7906870\t07349\tN\tN\n+rs7906870\t07357\tG\tG\n+rs7906870\t07435\tN\tN\n+rs7906870\t10830\tG\tG\n+rs7906870\t10831\tG\tG\n+rs7906870\t10835\tG\tG\n+rs7906870\t10836\tN\tN\n+rs7906870\t10837\tN\tN\n+rs7906870\t10838\tG\tG\n+rs7906870\t10839\tG\tG\n+rs7906870\t10840\tN\tN\n+rs7906870\t10843\tN\tN\n+rs7906870\t10845\tN\tN\n+rs7906870\t10846\tG\tG\n+rs7906870\t10847\tG\tG\n+rs7906870\t10850\tN\tN\n+rs7906870\t10851\tG\tG\n+rs7906870\t10852\tN\tN\n+rs7906870\t10853\tN\tN\n+rs7906870\t10854\tG\tG\n+rs7906870\t10855\tG\tG\n+rs7906870\t10856\tG\tG\n+rs7906870\t10857\tG\tG\n+rs7906870\t10859\tG\tG\n+rs7906870\t10860\tG\tG\n+rs7906870\t10861\tG\tG\n+rs7906870\t10863\tG\tG\n+rs7906870\t10864\tN\tN\n+rs7906870\t10865\tN\tN\n+rs7906870\t11829\tG\tG\n+rs7906870\t11830\tG\tG\n+rs7906870\t11831\tG\tG\n+rs7906870\t11832\tG\tG\n+rs7906870\t11839\tG\tG\n+rs7906870\t11840\tG\tG\n+rs7906870\t11843\tN\tN\n+rs7906870\t11881\tG\tG\n+rs7906870\t11882\tG\tG\n+rs7906870\t11891\tN\tN\n+rs7906870\t11892\tN\tN\n+rs7906870\t11893\tN\tN\n+rs7906870\t11894\tN\tN\n+rs7906870\t11917\tN\tN\n+rs7906870\t11918\tN\tN\n+rs7906870\t11919\tN\tN\n+rs7906870\t11920\tN\tN\n+rs7906870\t11930\tN\tN\n+rs7906870\t11931\tN\tN\n+rs7906870\t11992\tN\tN\n+rs7906870\t11993\tG\tG\n+rs7906870\t11994\tG\tG\n+rs7906870\t11995\tG\tG\n+rs7906870\t12003\tG\tG\n+rs7906870\t12004\tG\tG\n+rs7906870\t12005\tG\tG\n+rs7906870\t12006\tG\tG\n+rs7906870\t12043\tG\tG\n+rs7906870\t12044\tG\tG\n+rs7906870\t12045\tN\tN\n+rs7906870\t12056\tG\tG\n+rs7906870\t12057\tG\tG\n+rs7906870\t12144\tG\tG\n+rs7906870\t12145\tG\tG\n+rs7906870\t12146\tG\tG\n+rs7906870\t12154\tG\tG\n+rs7906870\t12155\tG\tG\n+rs7906870\t12156\tG\tG\n+rs7906870\t12234\tG\tG\n+rs7906870\t12236\tN\tN\n+rs7906870\t12239\tG\tG\n+rs7906870\t12248\tG\tG\n+rs7906870\t12249\tG\tG\n+rs7906870\t12264\tG\tG\n+rs7906870\t12272\tN\tN\n+rs7906870\t12273\tN\tN\n+rs7906870\t12275\tN\tN\n+rs7906870\t12282\tN\tN\n+rs7906870\t12283\tN\tN\n+rs7906870\t12286\tN\tN\n+rs7906870\t12287\tN\tN\n+rs7906870\t12335\tN\tN\n+rs7906870\t12336\tN\tN\n+rs7906870\t12340\tN\tN\n+rs7906870\t12341\tN\tN\n+rs7906870\t12342\tN\tN\n+rs7906870\t12343\tN\tN\n+rs7906870\t12344\tN\tN\n+rs7906870\t12347\tN\tN\n+rs7906870\t12348\tN\tN\n+rs7906870\t12375\tN\tN\n+rs7906870\t12376\tN\tN\n+rs7906870\t12383\tN\tN\n+rs7906870\t12386\tN\tN\n+rs7906870\t12399\tN\tN\n+rs7906870\t12400\tN\tN\n+rs7906870\t12413\tN\tN\n+rs7906870\t12489\tN\tN\n+rs7906870\t12546\tN\tN\n+rs7906870\t12707\tG\tG\n+rs7906870\t12708\tN\tN\n+rs7906870\t12716\tG\tG\n+rs7906870\t12717\tG\tG\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/ldOutput1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/ldOutput1.txt Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,9 @@
+rs746842 rs7088903,rs17107517,rs11186879,rs11186895,rs11186894,rs11186884,rs11186888,rs11186875,rs11186898
+rs9804247 rs7917088,rs7098170
+rs11186873 rs12767296
+rs10882042 rs4933228
+rs730075
+rs10882041
+rs12411618
+rs11186874
+rs11186882

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/lda_analy_output.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/lda_analy_output.txt Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,134 @@\n+structure(c(37.9310344827586, 23.6363636363636, 62.5, 37.9310344827586, \n+23.6363636363636, 62.5, 37.9310344827586, 23.6363636363636, 62.5, \n+37.9310344827586, 23.6363636363636, 62.5, 37.9310344827586, 23.6363636363636, \n+62.5, 37.9310344827586, 23.6363636363636, 62.5, 37.9310344827586, \n+23.6363636363636, 62.5, 37.9310344827586, 23.6363636363636, 62.5, \n+37.9310344827586, 23.6363636363636, 62.5, 37.9310344827586, 23.6363636363636, \n+62.5, 37.9310344827586, 23.6363636363636, 62.5, 37.9310344827586, \n+23.6363636363636, 62.5, 37.9310344827586, 23.6363636363636, 62.5, \n+37.9310344827586, 23.6363636363636, 62.5, 37.9310344827586, 23.6363636363636, \n+62.5, 37.9310344827586, 23.6363636363636, 62.5, 37.9310344827586, \n+23.6363636363636, 62.5, 37.9310344827586, 23.6363636363636, 62.5, \n+37.9310344827586, 23.6363636363636, 62.5, 37.9310344827586, 23.6363636363636, \n+62.5, 37.9310344827586, 23.6363636363636, 62.5, 39.0804597701149, \n+23.6363636363636, 65.625, 39.0804597701149, 23.6363636363636, \n+65.625, 39.0804597701149, 23.6363636363636, 65.625, 39.0804597701149, \n+23.6363636363636, 65.625, 39.0804597701149, 23.6363636363636, \n+65.625, 39.0804597701149, 23.6363636363636, 65.625, 39.0804597701149, \n+23.6363636363636, 65.625, 39.0804597701149, 23.6363636363636, \n+65.625, 39.0804597701149, 23.6363636363636, 65.625, 39.0804597701149, \n+23.6363636363636, 65.625, 39.0804597701149, 23.6363636363636, \n+65.625, 39.0804597701149, 23.6363636363636, 65.625, 39.0804597701149, \n+23.6363636363636, 65.625, 39.0804597701149, 23.6363636363636, \n+65.625, 39.0804597701149, 23.6363636363636, 65.625, 39.0804597701149, \n+23.6363636363636, 65.625, 39.0804597701149, 23.6363636363636, \n+65.625, 39.0804597701149, 23.6363636363636, 65.625, 39.0804597701149, \n+23.6363636363636, 65.625, 39.0804597701149, 23.6363636363636, \n+65.625, 39.0804597701149, 23.6363636363636, 65.625, 39.0804597701149, \n+23.6363636363636, 65.625, 40.2298850574713, 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43.6781609195402, 21.8181818181818, 81.25, 43.6781609195402, \n+21.8181818181818, 81.25, 43.6781609195402, 21.8181818181818, \n+81.25, 56.3218390804598, 78.1818181818182, 18.75), .Dim = c(3L, \n+201L))\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/library/3.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/library/3.bed Sat Feb 21 16:33:42 2015 +0100

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/library/4.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/library/4.bed Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,1 @@
+chr22 30128507 31828507 uc003bnx.1_cds_2_0_chr22_29227_f 0 +

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/library/5.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/library/5.bed Sat Feb 21 16:33:42 2015 +0100

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/linkToDavid.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/linkToDavid.tabular Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,10 @@
+10188
+10457
+10628
+1080
+1116
+11200
+1452
+1474
+1499
+1589

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/linkToDavid_1.out
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/linkToDavid_1.out Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,3 @@
+<html><head><title>DAVID link</title></head><body>
+<A TARGET=_BLANK HREF="http://david.abcc.ncifcrf.gov/api.jsp?type=ENTREZ_GENE_ID&ids=10188,10457,10628,1080,1116,11200,1452,1474,1499,1589&tool=summary">click here to send of identifiers to DAVID</A>
+</body></html>

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/linkToGProfile.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/linkToGProfile.tabular Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,10 @@
+1 10188
+2 10457
+3 10628
+4 1080
+5 1116
+6 11200
+7 1452
+8 1474
+9 1499
+10 1589

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/linkToGProfile_1.out
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/linkToGProfile_1.out Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,3 @@
+<html><head><title>g:Profiler link</title></head><body>
+<A TARGET=_BLANK HREF="http://biit.cs.ut.ee/gprofiler/index.cgi?organism=hsapiens&query=10188+10457+10628+1080+1116+11200+1452+1474+1499+1589&r_chr=1&r_start=start&r_end=end&analytical=1&domain_size_type=annotated&term=&significant=1&sort_by_structure=1&user_thr=1.00&output=png&prefix=ENTREZGENE_ACC">click here to send list of identifiers to g:Profiler</A>
+</body></html>

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/lps_arrhythmia.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/lps_arrhythmia.tabular Sat Feb 21 16:33:42 2015 +0100

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diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/lps_arrhythmia_beta.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/lps_arrhythmia_beta.tabular Sat Feb 21 16:33:42 2015 +0100

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+-0.16854 -0.16854 -0.16854 -0.16854 -0.16854 -0.16854 -0.16854 -0.16854 -0.16854 -0.16854 -0.16854

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/lps_arrhythmia_log.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/lps_arrhythmia_log.txt Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,197 @@\n+Data set has 452 vectors with 279 features.\n+ Sampled 452 points out of 452\n+ calculateLambdaMax: n=279, m=452, m+=245, m-=207\n+ computed value of lambda_max: 1.8231e+02\n+\n+ **** Initial point: nz=0, f= 0.69314718056, lambda= 1.641e+02\n+iter 1, gpnorm=4.2035e-02, nonzero= 1 ( 0.4%), function=6.931471805599e-01, alpha=1.0000e+00\n+iter 2, gpnorm=1.9781e-02, nonzero= 1 ( 0.4%), function=6.903943411116e-01, alpha=8.0000e-01\n+iter 3, gpnorm=6.0325e-03, nonzero= 1 ( 0.4%), function=6.896822613633e-01, alpha=6.4000e-01\n+iter 4, gpnorm=7.2193e-04, nonzero= 1 ( 0.4%), function=6.896101060279e-01, alpha=5.1200e-01\n+iter 5, gpnorm=1.0530e-05, nonzero= 1 ( 0.4%), function=6.896090566277e-01, alpha=4.0960e-01\n+iter 6, gpnorm=1.7618e-09, nonzero= 1 ( 0.4%), function=6.896090564044e-01, alpha=3.2768e-01\n+ Function evals = 12, Gradient evals = 6.0\n+\n+ **** Initial point: nz=1, f= 0.689609056404, lambda= 1.168e+02\n+iter 1, gpnorm=1.7618e-09, nonzero= 1 ( 0.4%), function=6.896090564044e-01, alpha=3.2768e-01\n+ Function evals = 2, Gradient evals = 1.0\n+\n+ **** Initial point: nz=1, f= 0.689609056404, lambda= 8.310e+01\n+iter 1, gpnorm=1.7618e-09, nonzero= 1 ( 0.4%), function=6.896090564044e-01, alpha=3.2768e-01\n+ Function evals = 2, Gradient evals = 1.0\n+\n+ **** Initial point: nz=1, f= 0.689609056404, lambda= 5.914e+01\n+iter 1, gpnorm=1.7618e-09, nonzero= 1 ( 0.4%), function=6.896090564044e-01, alpha=3.2768e-01\n+ Function evals = 2, Gradient evals = 1.0\n+\n+ **** Initial point: nz=1, f= 0.689609056404, lambda= 4.209e+01\n+iter 1, gpnorm=1.7618e-09, nonzero= 1 ( 0.4%), function=6.896090564044e-01, alpha=3.2768e-01\n+ Function evals = 2, Gradient evals = 1.0\n+\n+ **** Initial point: nz=1, f= 0.689609056404, lambda= 2.996e+01\n+iter 1, gpnorm=1.7618e-09, nonzero= 1 ( 0.4%), function=6.896090564044e-01, alpha=3.2768e-01\n+ Function evals = 2, Gradient evals = 1.0\n+\n+ **** Initial point: nz=1, f= 0.689609056404, lambda= 2.132e+01\n+iter 1, gpnorm=1.7618e-09, nonzero= 1 ( 0.4%), function=6.896090564044e-01, alpha=3.2768e-01\n+ Function evals = 2, Gradient evals = 1.0\n+\n+ **** Initial point: nz=1, f= 0.689609056404, lambda= 1.517e+01\n+iter 1, gpnorm=1.7618e-09, nonzero= 1 ( 0.4%), function=6.896090564044e-01, alpha=3.2768e-01\n+ Function evals = 2, Gradient evals = 1.0\n+\n+ **** Initial point: nz=1, f= 0.689609056404, lambda= 1.080e+01\n+iter 1, gpnorm=1.7618e-09, nonzero= 1 ( 0.4%), function=6.896090564044e-01, alpha=3.2768e-01\n+ Function evals = 2, Gradient evals = 1.0\n+\n+ **** Initial point: nz=1, f= 0.689609056404, lambda= 7.685e+00\n+iter 1, gpnorm=1.7618e-09, nonzero= 1 ( 0.4%), function=6.896090564044e-01, alpha=3.2768e-01\n+ Function evals = 2, Gradient evals = 1.0\n+\n+ **** Initial point: nz=1, f= 0.689609056404, lambda= 5.469e+00\n+iter 1, gpnorm=1.7618e-09, nonzero= 1 ( 0.4%), function=6.896090564044e-01, alpha=3.2768e-01\n+ Function evals = 2, Gradient evals = 1.0\n+\n+lambda=1.64e+02 solution:\n+ optimal log-likelihood function value: 6.90e-01\n+ optimal *regularized* log-likelihood function value: 6.90e-01\n+ number of non-zeros at the optimum: 1\n+ number of iterations required: 6\n+ prediction using this solution:\n+ 54.20% of vectors were correctly predicted.\n+ 245 correctly predicted.\n+ 207 in +1 predicted to be in -1.\n+ 0 in -1 predicted to be in +1.\n+ 0 in +1 with 50/50 chance.\n+ 0 in -1 with 50/50 chance.\n+\n+lambda=1.17e+02 solution:\n+ optimal log-likelihood function value: 6.90e-01\n+ optimal *regularized* log-likelihood function value: 6.90e-01\n+ number of non-zeros at the optimum: 1\n+ number of iterations required: 1\n+ prediction using this solution:\n+ 54.20% of vectors were correctly predicted.\n+ 245 correctly predicted.\n+ 207 in +1 predicted to be in -1.\n+ 0 in -1 predicted to be in '..b'1 predicted to be in -1.\n+ 0 in -1 predicted to be in +1.\n+ 0 in +1 with 50/50 chance.\n+ 0 in -1 with 50/50 chance.\n+\n+lambda=5.91e+01 solution:\n+ optimal log-likelihood function value: 6.90e-01\n+ optimal *regularized* log-likelihood function value: 6.90e-01\n+ number of non-zeros at the optimum: 1\n+ number of iterations required: 1\n+ prediction using this solution:\n+ 54.20% of vectors were correctly predicted.\n+ 245 correctly predicted.\n+ 207 in +1 predicted to be in -1.\n+ 0 in -1 predicted to be in +1.\n+ 0 in +1 with 50/50 chance.\n+ 0 in -1 with 50/50 chance.\n+\n+lambda=4.21e+01 solution:\n+ optimal log-likelihood function value: 6.90e-01\n+ optimal *regularized* log-likelihood function value: 6.90e-01\n+ number of non-zeros at the optimum: 1\n+ number of iterations required: 1\n+ prediction using this solution:\n+ 54.20% of vectors were correctly predicted.\n+ 245 correctly predicted.\n+ 207 in +1 predicted to be in -1.\n+ 0 in -1 predicted to be in +1.\n+ 0 in +1 with 50/50 chance.\n+ 0 in -1 with 50/50 chance.\n+\n+lambda=3.00e+01 solution:\n+ optimal log-likelihood function value: 6.90e-01\n+ optimal *regularized* log-likelihood function value: 6.90e-01\n+ number of non-zeros at the optimum: 1\n+ number of iterations required: 1\n+ prediction using this solution:\n+ 54.20% of vectors were correctly predicted.\n+ 245 correctly predicted.\n+ 207 in +1 predicted to be in -1.\n+ 0 in -1 predicted to be in +1.\n+ 0 in +1 with 50/50 chance.\n+ 0 in -1 with 50/50 chance.\n+\n+lambda=2.13e+01 solution:\n+ optimal log-likelihood function value: 6.90e-01\n+ optimal *regularized* log-likelihood function value: 6.90e-01\n+ number of non-zeros at the optimum: 1\n+ number of iterations required: 1\n+ prediction using this solution:\n+ 54.20% of vectors were correctly predicted.\n+ 245 correctly predicted.\n+ 207 in +1 predicted to be in -1.\n+ 0 in -1 predicted to be in +1.\n+ 0 in +1 with 50/50 chance.\n+ 0 in -1 with 50/50 chance.\n+\n+lambda=1.52e+01 solution:\n+ optimal log-likelihood function value: 6.90e-01\n+ optimal *regularized* log-likelihood function value: 6.90e-01\n+ number of non-zeros at the optimum: 1\n+ number of iterations required: 1\n+ prediction using this solution:\n+ 54.20% of vectors were correctly predicted.\n+ 245 correctly predicted.\n+ 207 in +1 predicted to be in -1.\n+ 0 in -1 predicted to be in +1.\n+ 0 in +1 with 50/50 chance.\n+ 0 in -1 with 50/50 chance.\n+\n+lambda=1.08e+01 solution:\n+ optimal log-likelihood function value: 6.90e-01\n+ optimal *regularized* log-likelihood function value: 6.90e-01\n+ number of non-zeros at the optimum: 1\n+ number of iterations required: 1\n+ prediction using this solution:\n+ 54.20% of vectors were correctly predicted.\n+ 245 correctly predicted.\n+ 207 in +1 predicted to be in -1.\n+ 0 in -1 predicted to be in +1.\n+ 0 in +1 with 50/50 chance.\n+ 0 in -1 with 50/50 chance.\n+\n+lambda=7.68e+00 solution:\n+ optimal log-likelihood function value: 6.90e-01\n+ optimal *regularized* log-likelihood function value: 6.90e-01\n+ number of non-zeros at the optimum: 1\n+ number of iterations required: 1\n+ prediction using this solution:\n+ 54.20% of vectors were correctly predicted.\n+ 245 correctly predicted.\n+ 207 in +1 predicted to be in -1.\n+ 0 in -1 predicted to be in +1.\n+ 0 in +1 with 50/50 chance.\n+ 0 in -1 with 50/50 chance.\n+\n+lambda=5.47e+00 solution:\n+ optimal log-likelihood function value: 6.90e-01\n+ optimal *regularized* log-likelihood function value: 6.90e-01\n+ number of non-zeros at the optimum: 1\n+ number of iterations required: 1\n+ prediction using this solution:\n+ 54.20% of vectors were correctly predicted.\n+ 245 correctly predicted.\n+ 207 in +1 predicted to be in -1.\n+ 0 in -1 predicted to be in +1.\n+ 0 in +1 with 50/50 chance.\n+ 0 in -1 with 50/50 chance.\n+\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/maf_by_block_number_out.dat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/maf_by_block_number_out.dat Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,25 @@
+##maf version=1
+a score=60426.0
+s hg17.chr7    127471195 331 + 158628139 gtttgccatcttttgctgctctagggaatccagcagctgtcaccatgtaaacaagcccaggctagaccaGTTACCCTCATCATCTTAGCTGATAGCCAGCCAGCCACCACAGGCAtgagtcaggccatattgctggacccacagaattatgagctaaataaatagtcttgggttaagccactaagttttaggcatagtgtgttatgtaTCTCACAAACATATAAGACTGTGTGTTTGTTGACTGGAGGAAGAGATGCTATAAAGACCACCTTTTAAAACTTCCC-------------------------------AAATACT-GCCACTGATGTCCTG-----ATGGAGGTA-------TGAA-------------------AACATCCACTAA
+s panTro1.chr6 129885076 331 + 161576975 gtttgccatcttttgctgctcttgggaatccagcagctgtcaccatgtaaacaagcccaggctagaccaGTTACCCTCATCATCTTAGCTGATAGCCAGCCAGCCACCACAGGCAtgagtcaggccatattgctggacccacagaattatgagctaaataaatagtcttgggttaagccactaagttttaggcatagtgtgttatgtaTCTCACAAACATATAAGACTGTGTGTTTGTTGACTGGAGGAAGAGATGCTATAAAGACCACCTTTTGAAACTTCCC-------------------------------AAATACT-GCCACTGATGTCCTG-----ATGGAGGTA-------TGAA-------------------AACATCCACTAA
+s mm5.chr6      28904571 357 + 149721531 CTCCACTCTCGTTTGCTGTT----------------CTGTCACCATGGAAACAAA-CGAGGGTGGTCCAGTTACTATCTTGACTGCAGCTGGCAGTCAGTT-GCCACT-----CAGGAATAAGGCTATGCCATT-GATCCACTGAACCGTGATCTGGAAACCTGGCTGTTGTTT-------CAAGCCTTGGGGCCAGTTTGCGGTGTTACTCATGA--CTCTAAGATCGTGTGCTTG----CTGCAGGAAGAGACAGCAAGGGGGTTACATTTAAAAAGCCCCCAGTTTAGCTATAGGCAGGCCAACAGGTGTAAAAATACTCACTAGTAATGGGCTGAACTCATGGAGGTAGCATTAGTGAGACACTGTAACTGTTTTTTTAAAAATCACTAA
+s rn3.chr4      56178191 282 + 187371129 CTTCACTCTCATTTGCTGTT----------------CTGTCACTATGGAGACAAACACAGGCTAGCCCAGTTACTATCTTGATCACAGCAGCT-GTCAGCTAGCTGCCACTCACAGGAATAAGGCCATACCATT-GATCCACTGAACCTTGATCTAGGAATTTGGC----------------------TGGGGCCAGTTTGCGGTGTCACTCATGA--CTCTAAGATTGTGTGTTTG----CTCCAGGAAGAGACGGCAAGAGGATTACCTTTAAAAGGTTC---------------------------------GGAGTCTAGCTGTAGACAGCCCA-----ATG--GGTA-------TAAC-------------------AATACTCACTAA
+
+a score=43613.0
+s hg17.chr7     127471584 104 + 158628139 GAGATATTTGGggaaatt---ttgtatagactagctttcacgatgttagggaattattattgtgtgataatggtcttgcagttaca-cagaaattcttccttattttt
+s panTro1.chr6  129885465 104 + 161576975 GAGACATTTGGggaaatt---ttgtatagactagctttcacgatgttagggagttattattgtgtgataatggtcttgcagttaca-cagaaattcttccttattttt
+s mm5.chr6       28909125 102 + 149721531 GAGACATTTGGGGGAAATACGATGTATA------CTTTCATGATCTTAAAGAATTGCTATTGTTTGATAGTGATATTATGGTTAAATTAAAAAAAAACCCTTACTTTT
+s rn3.chr4       56182196  99 + 187371129 GAGATATTTGGGGGAAATATGATGTGCA------CTTCCATGATCTTAAAGAATTGCTACTGTTTGATAGTGATCTTATGGTTAAA-TAAAAAAAAT--CTTAGTTGT
+s canFam1.chr14  52864846 108 -  63549963 GAGATATTTGGGGGAATTTGAATGTAGTGTTGCTCTTTTGTGATGCTAAGAAATTATAATTGTCTGATGATAGTCTCGTGGTTATGGGGGAAATGCTTCCTTATTTTT
+
+a score=60426.0
+s hg17.chr7    127471195 331 + 158628139 gtttgccatcttttgctgctctagggaatccagcagctgtcaccatgtaaacaagcccaggctagaccaGTTACCCTCATCATCTTAGCTGATAGCCAGCCAGCCACCACAGGCAtgagtcaggccatattgctggacccacagaattatgagctaaataaatagtcttgggttaagccactaagttttaggcatagtgtgttatgtaTCTCACAAACATATAAGACTGTGTGTTTGTTGACTGGAGGAAGAGATGCTATAAAGACCACCTTTTAAAACTTCCC-------------------------------AAATACT-GCCACTGATGTCCTG-----ATGGAGGTA-------TGAA-------------------AACATCCACTAA
+s panTro1.chr6 129885076 331 + 161576975 gtttgccatcttttgctgctcttgggaatccagcagctgtcaccatgtaaacaagcccaggctagaccaGTTACCCTCATCATCTTAGCTGATAGCCAGCCAGCCACCACAGGCAtgagtcaggccatattgctggacccacagaattatgagctaaataaatagtcttgggttaagccactaagttttaggcatagtgtgttatgtaTCTCACAAACATATAAGACTGTGTGTTTGTTGACTGGAGGAAGAGATGCTATAAAGACCACCTTTTGAAACTTCCC-------------------------------AAATACT-GCCACTGATGTCCTG-----ATGGAGGTA-------TGAA-------------------AACATCCACTAA
+s mm5.chr6      28904571 357 + 149721531 CTCCACTCTCGTTTGCTGTT----------------CTGTCACCATGGAAACAAA-CGAGGGTGGTCCAGTTACTATCTTGACTGCAGCTGGCAGTCAGTT-GCCACT-----CAGGAATAAGGCTATGCCATT-GATCCACTGAACCGTGATCTGGAAACCTGGCTGTTGTTT-------CAAGCCTTGGGGCCAGTTTGCGGTGTTACTCATGA--CTCTAAGATCGTGTGCTTG----CTGCAGGAAGAGACAGCAAGGGGGTTACATTTAAAAAGCCCCCAGTTTAGCTATAGGCAGGCCAACAGGTGTAAAAATACTCACTAGTAATGGGCTGAACTCATGGAGGTAGCATTAGTGAGACACTGTAACTGTTTTTTTAAAAATCACTAA
+s rn3.chr4      56178191 282 + 187371129 CTTCACTCTCATTTGCTGTT----------------CTGTCACTATGGAGACAAACACAGGCTAGCCCAGTTACTATCTTGATCACAGCAGCT-GTCAGCTAGCTGCCACTCACAGGAATAAGGCCATACCATT-GATCCACTGAACCTTGATCTAGGAATTTGGC----------------------TGGGGCCAGTTTGCGGTGTCACTCATGA--CTCTAAGATTGTGTGTTTG----CTCCAGGAAGAGACGGCAAGAGGATTACCTTTAAAAGGTTC---------------------------------GGAGTCTAGCTGTAGACAGCCCA-----ATG--GGTA-------TAAC-------------------AATACTCACTAA
+
+a score=8157.0
+s hg17.chr7    127471526 58 + 158628139 AATTTGTGGTTTATTCATTTTTCATTATTTTGTTTAAGGAGGTCTATAGTGGAAGAGG
+s panTro1.chr6 129885407 58 + 161576975 AATTTGTGGTTTATTCGTTTTTCATTATTTTGTTTAAGGAGGTCTATAGTGGAAGAGG
+s mm5.chr6      28904928 54 + 149721531 AA----CGTTTCATTGATTGCTCATCATTTAAAAAAAGAAATTCCTCAGTGGAAGAGG
+

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/maf_by_block_numbers.dat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/maf_by_block_numbers.dat Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,4 @@
+0
+2
+0
+1

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/maf_limit_size1_out.maf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/maf_limit_size1_out.maf Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,55 @@\n+##maf version=1\n+a score=60426.0\n+s hg17.chr7 127471195 331 + 158628139 gtttgccatcttttgctgctctagggaatccagcagctgtcaccatgtaaacaagcccaggctagaccaGTTACCCTCATCATCTTAGCTGATAGCCAGCCAGCCACCACAGGCAtgagtcaggccatattgctggacccacagaattatgagctaaataaatagtcttgggttaagccactaagttttaggcatagtgtgttatgtaTCTCACAAACATATAAGACTGTGTGTTTGTTGACTGGAGGAAGAGATGCTATAAAGACCACCTTTTAAAACTTCCC-------------------------------AAATACT-GCCACTGATGTCCTG-----ATGGAGGTA-------TGAA-------------------AACATCCACTAA \n+s panTro1.chr6 129885076 331 + 161576975 gtttgccatcttttgctgctcttgggaatccagcagctgtcaccatgtaaacaagcccaggctagaccaGTTACCCTCATCATCTTAGCTGATAGCCAGCCAGCCACCACAGGCAtgagtcaggccatattgctggacccacagaattatgagctaaataaatagtcttgggttaagccactaagttttaggcatagtgtgttatgtaTCTCACAAACATATAAGACTGTGTGTTTGTTGACTGGAGGAAGAGATGCTATAAAGACCACCTTTTGAAACTTCCC-------------------------------AAATACT-GCCACTGATGTCCTG-----ATGGAGGTA-------TGAA-------------------AACATCCACTAA \n+s mm5.chr6 28904571 357 + 149721531 CTCCACTCTCGTTTGCTGTT----------------CTGTCACCATGGAAACAAA-CGAGGGTGGTCCAGTTACTATCTTGACTGCAGCTGGCAGTCAGTT-GCCACT-----CAGGAATAAGGCTATGCCATT-GATCCACTGAACCGTGATCTGGAAACCTGGCTGTTGTTT-------CAAGCCTTGGGGCCAGTTTGCGGTGTTACTCATGA--CTCTAAGATCGTGTGCTTG----CTGCAGGAAGAGACAGCAAGGGGGTTACATTTAAAAAGCCCCCAGTTTAGCTATAGGCAGGCCAACAGGTGTAAAAATACTCACTAGTAATGGGCTGAACTCATGGAGGTAGCATTAGTGAGACACTGTAACTGTTTTTTTAAAAATCACTAA \n+s rn3.chr4 56178191 282 + 187371129 CTTCACTCTCATTTGCTGTT----------------CTGTCACTATGGAGACAAACACAGGCTAGCCCAGTTACTATCTTGATCACAGCAGCT-GTCAGCTAGCTGCCACTCACAGGAATAAGGCCATACCATT-GATCCACTGAACCTTGATCTAGGAATTTGGC----------------------TGGGGCCAGTTTGCGGTGTCACTCATGA--CTCTAAGATTGTGTGTTTG----CTCCAGGAAGAGACGGCAAGAGGATTACCTTTAAAAGGTTC---------------------------------GGAGTCTAGCTGTAGACAGCCCA-----ATG--GGTA-------TAAC-------------------AATACTCACTAA \n+\n+a score=8157.0\n+s hg17.chr7 127471526 58 + 158628139 AATTTGTGGTTTATTCATTTTTCATTATTTTGTTTAAGGAGGTCTATAGTGGAAGAGG \n+s panTro1.chr6 129885407 58 + 161576975 AATTTGTGGTTTATTCGTTTTTCATTATTTTGTTTAAGGAGGTCTATAGTGGAAGAGG \n+s mm5.chr6 28904928 54 + 149721531 AA----CGTTTCATTGATTGCTCATCATTTAAAAAAAGAAATTCCTCAGTGGAAGAGG \n+\n+a score=43613.0\n+s hg17.chr7 127471584 104 + 158628139 GAGATATTTGGggaaatt---ttgtatagactagctttcacgatgttagggaattattattgtgtgataatggtcttgcagttaca-cagaaattcttccttattttt \n+s panTro1.chr6 129885465 104 + 161576975 GAGACATTTGGggaaatt---ttgtatagactagctttcacgatgttagggagttattattgtgtgataatggtcttgcagttaca-cagaaattcttccttattttt \n+s mm5.chr6 28909125 102 + 149721531 GAGACATTTGGGGGAAATACGATGTATA------CTTTCATGATCTTAAAGAATTGCTATTGTTTGATAGTGATATTATGGTTAAATTAAAAAAAAACCCTTACTTTT \n+s rn3.chr4 56182196 99 + 187371129 GAGATATTTGGGGGAAATATGATGTGCA------CTTCCATGATCTTAAAGAATTGCTACTGTTTGATAGTGATCTTATGGTTAAA-TAAAAAAAAT--CTTAGTTGT \n+s canFam1.chr14 52864846 108 - 63549963 GAGATATTTGGGGGAATTTGAATGTAGTGTTGCTCTTTTGTGATGCTAAGAAATTATAATTGTCTGATGATAGTCTCGTGGTTATGGGGGAAATGCTTCCTTATTTTT \n+\n+a score=63217.0\n+s hg17.chr7 127471688 183 + 158628139 tgggaa---gcaccaaag----tagggat---aaaatgtcatgatgtgtgcaatacactttaaaatgtttttg-----ccaaaataatt----------------aatgaagc--aaatatggaaa-ataataattattaaatctaggtgatgggtatattgtagttcactatagtattgcacacttttctgtatgtttaaatttttcatttaaaaa \n+s panTro1.chr6 129885569 183 + 161576975 tgggaa---acaccaaag----tagggat---aaaatgtcatgatgtgtgcaatacgctttaaaatatttttg-----ccaaaataatt----------------aatgaagc--aaatatggaaa-ataataattattaaatctaggtgatgggtatattgtagttcactatagtattgcacacttttctgtatgtttaaaattttcatttaaaaa \n+s mm5.chr6 28909227 176 + 149721531 CATAAA---ATACTCAAATATTTAGGGGTATGACAATGTCATAGTGTCTGCAATTTGCTTTAAAATAATTTTG-------AAAAC---------------------CTGAGGCTAAACTATGGGAA-ATAGCAATTATTACATATGGGTAATAAGTA-----TAACTCACTATATTATTTTTCACTAT----TGTGTTTGAAATTTTCATTTTAAAA \n+s rn3.chr4 56182295 194 + 187371129 TAGAAA---ATACTCAAATATTTAGGGGCGTGACAATGTCACAGTGTCTGCAATTTGCTTTAAAG-ATTTTTAAATATTTAAAAAAGTTTTAATAATTTTGAAAAACTGAAGCTACACTATGGGAA-GTGGTAATTGTTACATATGGGTAATAAGTA-----TAATTCGTTATATTATT-------------TTTCTTAGAATTTTTCATTTGAAAA \n+s canFam1.chr14 528651'..b'TCTCCAATGTGATCTGATGGT-GCCGCCAGGACCTA-TGTCAGCCTACCGTTCCATGTCCCCTCCACACCATCATCACTGCAGGTGTGTTTTCCCACATTTTAAATATCTG-------CTTCCCGGTGGCCTTGAGTCTAGAGGAGTCCCCCCACTATGGTGGCACTAATACTGAAGGTCAGAAATAATCAGTTCTGTGGTGCATGTTGCCCCTGAGGTTCTGTTCGGGAAACTTCTTCTG-AGCAC----ATGCACCTGGCACTGCAAACGTACCAGGA \n+\n+a score=82819.0\n+s hg17.chr7 127472258 423 + 158628139 gatggccca-atccctgtcctct---taaaacctaagggaggagaTGGAAAGGGG-CACCCAACCCAGACTGAGAGACAGGAATTAGCTGCAAGGGGAACTAGGAAAAGCTTCTTTA---AGGATGGAGAGGCCCTAGTGGAAT-GGGGAGATTCTTCCGGGAGAAGCGATGGATGCACAGTTGGGCATCCCCACAGACGGACTGGAAAGAAAAAAGGCCTGGAGGAATCAATGTG-------CAATGTATGTGTGTTCCCTGGTTcaagggctgg-gaactttctcta-aagggccaggtagaaaacattttaggctttctaagccaag--gcaaaat-tgaggatattacatgggtacttatacaacaagaataaacaatt---tacacaattttttgttgacagaattcaaaactttat----agacacagaaatgcaaatttcctgt \n+s panTro1.chr6 129886139 423 + 161576975 gatggccca-atccctgtcctct---taaaacctaagggaggagaTGGAAAGGGG-CACCCAACCCAGACTGAGAGACAGGAATTAGCTGCAAGGGGAACTAGGAAAAGCTTCTTTA---AGGATGGAGAGACCCTAGTGGAAT-GGGGAGATTCTTCCGGGAGAAGCGATGGATGCGCAGTTGGGCATCCCCACAGACGGACTGGAAAGAAAAAAGGCCTGGAGGAATCAATGTG-------CAATGTATGTGTGTTCCCTGGTTcaagggctgg-gaactttctcta-aagggccaggtagaaaacattttaggctttctaagccaag--gcaaaat-tgaggatattacatgggtacttatacaacaagaataaacaatt---tacacaattttttgttgacagaattcaaaactttat----agacacagaaatgtaaatttcctgt \n+s mm5.chr6 28911067 334 + 149721531 AATGGCAGAGGGCTCTGTTCTCT----------------------------------GTCCA---TAGACAAGGAAGC---------CTGCCAGTGG-----------------------TGGAGAGCAGGGCCTATGCAAAACAGGGGGGGTTCTGTGGGCAGAAGGGATGGACCTGACTCCAGGAACGCCCATA-AGAGACGGGCAGGACTGGGAGCCAGGAGCAGCCAGCGCA--------GGTGTGTGTAGGTTTCATAGTTT---------------------------GCAGGTTAGCAAACAATTCTCGCTTGGCAGGCCAAGA-GGGAAAT-AAAGGTTACCCCGTGGGTACTTAT---ACAAGAGAAAACAAG-------ACAATTTTTGGTTGACCAAATTCAGAACTTTATTTGAGGATGCTAAAGTTTTAATTTCTTAA \n+s rn3.chr4 56183879 340 + 187371129 AATGGCAGAGGCCCCTGTTCTCT----------------------------------GTCCA---TAGTCAAAGAAGC---------CTCTCAG----------------------A---TGGAGAGCAGGGCCTATGCAAAAG-AGGGGGCTTCTGTAGGCAGAAGGGATGGACTAGCCTCCGGACATAGCCATAGAGAGGCTGGCAGGACTGAGACCCAGGAGAAGCCAGCGCAGGTGTGCGGGCGTGTGTATATTTCATAGTTT---------------------------GCAGGTTGGCAAACAATTCCTGCTTTGCAGGCCAAGA-GGAAACT-GAAGGTGACCCCGTGAGTGCTTAC---ACAAGAGAAAACAAG-------ACAATTTTTGGTTGACCAAATTCAGAACTTTATTTGAGGATGCTAAAGTTTAAATTTCTTTT \n+s canFam1.chr14 52866108 405 - 63549963 GGAGACTTG-ATGCCTGCCTTCCACTTACAGCCTGTGGGCAGAGGTGGGAAGAGGTCACGCAAGCCAGTTGGAATGAGGGGAGTTGGCTGGAAAGGTGACCAGGACAAGCTACTTCAACCAGGAAGAAGAGACCCC---------GG--------TGCTTGGAGAAGGCCTGATTGAGCAGTCCTGCATGCCCGCCCAC-GACTGGCAGGAATAAAGACCCAGAAGAGCTAACGTG-------CAATGTA------TTTTCTAGTTCCAgggttggcaaactttctctctaagggtgggatgataaacattttaggcttttcagaccaagaggcgacatcagagggtat---gtaggt---------acaagagggaaaagttgcccccggaattttttg--gataaaattcaaaactttacttagggatgccaaaatgtaaacttcatat \n+\n+a score=15522.0\n+s hg17.chr7 127473809 97 + 158628139 tttttttttcaaacttttacaaatgtagaaaccattcttagcttttgggcattaccaaacccggcagtgg-caggctcggttcaccaacgtcatttgc \n+s panTro1.chr6 129887686 97 + 161576975 tttttttttcaaacttttacaaatgtagaaaccattcttagcttttgggcattaccaaacccggcagtgg-AAGGCTCGGTTCACCAACATCATTTGC \n+s canFam1.chr14 52866548 97 - 63549963 tatatttttcaactctttaaaaatgcaaaaaccattcctagc-tcggggccatggtggtcctggtggtggtcggatttggctcacccacataacttgc \n+\n+a score=28088.0\n+s hg17.chr7 127473906 331 + 158628139 agttccccgCTTTATGTTATGGgttttgttttgttttgtttttttt-attgagacagagtttcactcttgttgcccaggctgtagtgcaatggtctgatcttggctcactgcaacctccacttcccaggttcaagccattctcctgcctcagcctctcaagtagctgggattacagacactcaccaccacacctggctaattttgtatttttagtagagatgaggtttcaccatgttggccaggctggtctcgaaatcctgacctcaggtgatccacccaccttggcctcccaaagtgctgggattacaggcttgagctaccacgcctggct \n+s panTro1.chr6 129887783 318 + 161576975 AGTTCCCCGCTTTATATTATGGGttttttttttttttttttttttttattgagacagagtttcactcttgttgcccaggctgtagtg--------------tggctcactgcaacctccacttcccaggttcaagccattctcctgcctcagcctctcaagtagctgggattacagacactcaccaccacacctggctaattttgtatttttagtagagatgaggtttcatcatgttggccaggctggtctcgaaatcctgacctcaggtgatccacccaccttggcctcccaaagtgctgggattacaggcttgagctaccacgcctggct \n+\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/maf_reverse_complement_out.dat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/maf_reverse_complement_out.dat Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,55 @@\n+##maf version=1\n+a score=60426.0\n+s hg17.chr7 31156613 331 - 158628139 TTAGTGGATGTT-------------------TTCA-------TACCTCCAT-----CAGGACATCAGTGGC-AGTATTT-------------------------------GGGAAGTTTTAAAAGGTGGTCTTTATAGCATCTCTTCCTCCAGTCAACAAACACACAGTCTTATATGTTTGTGAGAtacataacacactatgcctaaaacttagtggcttaacccaagactatttatttagctcataattctgtgggtccagcaatatggcctgactcaTGCCTGTGGTGGCTGGCTGGCTATCAGCTAAGATGATGAGGGTAACtggtctagcctgggcttgtttacatggtgacagctgctggattccctagagcagcaaaagatggcaaac \n+s panTro1.chr6 31691568 331 - 161576975 TTAGTGGATGTT-------------------TTCA-------TACCTCCAT-----CAGGACATCAGTGGC-AGTATTT-------------------------------GGGAAGTTTCAAAAGGTGGTCTTTATAGCATCTCTTCCTCCAGTCAACAAACACACAGTCTTATATGTTTGTGAGAtacataacacactatgcctaaaacttagtggcttaacccaagactatttatttagctcataattctgtgggtccagcaatatggcctgactcaTGCCTGTGGTGGCTGGCTGGCTATCAGCTAAGATGATGAGGGTAACtggtctagcctgggcttgtttacatggtgacagctgctggattcccaagagcagcaaaagatggcaaac \n+s mm5.chr6 120816603 357 - 149721531 TTAGTGATTTTTAAAAAAACAGTTACAGTGTCTCACTAATGCTACCTCCATGAGTTCAGCCCATTACTAGTGAGTATTTTTACACCTGTTGGCCTGCCTATAGCTAAACTGGGGGCTTTTTAAATGTAACCCCCTTGCTGTCTCTTCCTGCAG----CAAGCACACGATCTTAGAG--TCATGAGTAACACCGCAAACTGGCCCCAAGGCTTG-------AAACAACAGCCAGGTTTCCAGATCACGGTTCAGTGGATC-AATGGCATAGCCTTATTCCTG-----AGTGGC-AACTGACTGCCAGCTGCAGTCAAGATAGTAACTGGACCACCCTCG-TTTGTTTCCATGGTGACAG----------------AACAGCAAACGAGAGTGGAG \n+s rn3.chr4 131192656 282 - 187371129 TTAGTGAGTATT-------------------GTTA-------TACC--CAT-----TGGGCTGTCTACAGCTAGACTCC---------------------------------GAACCTTTTAAAGGTAATCCTCTTGCCGTCTCTTCCTGGAG----CAAACACACAATCTTAGAG--TCATGAGTGACACCGCAAACTGGCCCCA----------------------GCCAAATTCCTAGATCAAGGTTCAGTGGATC-AATGGTATGGCCTTATTCCTGTGAGTGGCAGCTAGCTGAC-AGCTGCTGTGATCAAGATAGTAACTGGGCTAGCCTGTGTTTGTCTCCATAGTGACAG----------------AACAGCAAATGAGAGTGAAG \n+\n+a score=8157.0\n+s hg17.chr7 31156555 58 - 158628139 CCTCTTCCACTATAGACCTCCTTAAACAAAATAATGAAAAATGAATAAACCACAAATT \n+s panTro1.chr6 31691510 58 - 161576975 CCTCTTCCACTATAGACCTCCTTAAACAAAATAATGAAAAACGAATAAACCACAAATT \n+s mm5.chr6 120816549 54 - 149721531 CCTCTTCCACTGAGGAATTTCTTTTTTTAAATGATGAGCAATCAATGAAACG----TT \n+\n+a score=43613.0\n+s hg17.chr7 31156451 104 - 158628139 aaaaataaggaagaatttctg-tgtaactgcaagaccattatcacacaataataattccctaacatcgtgaaagctagtctatacaa---aatttccCCAAATATCTC \n+s panTro1.chr6 31691406 104 - 161576975 aaaaataaggaagaatttctg-tgtaactgcaagaccattatcacacaataataactccctaacatcgtgaaagctagtctatacaa---aatttccCCAAATGTCTC \n+s mm5.chr6 120812304 102 - 149721531 AAAAGTAAGGGTTTTTTTTTAATTTAACCATAATATCACTATCAAACAATAGCAATTCTTTAAGATCATGAAAG------TATACATCGTATTTCCCCCAAATGTCTC \n+s rn3.chr4 131188834 99 - 187371129 ACAACTAAG--ATTTTTTTTA-TTTAACCATAAGATCACTATCAAACAGTAGCAATTCTTTAAGATCATGGAAG------TGCACATCATATTTCCCCCAAATATCTC \n+s canFam1.chr14 10685009 108 + 63549963 AAAAATAAGGAAGCATTTCCCCCATAACCACGAGACTATCATCAGACAATTATAATTTCTTAGCATCACAAAAGAGCAACACTACATTCAAATTCCCCCAAATATCTC \n+\n+a score=63217.0\n+s hg17.chr7 31156268 183 - 158628139 tttttaaatgaaaaatttaaacatacagaaaagtgtgcaatactatagtgaactacaatatacccatcacctagatttaataattattat-tttccatattt--gcttcatt----------------aattattttgg-----caaaaacattttaaagtgtattgcacacatcatgacatttt---atcccta----ctttggtgc---ttccca \n+s panTro1.chr6 31691223 183 - 161576975 tttttaaatgaaaattttaaacatacagaaaagtgtgcaatactatagtgaactacaatatacccatcacctagatttaataattattat-tttccatattt--gcttcatt----------------aattattttgg-----caaaaatattttaaagcgtattgcacacatcatgacatttt---atcccta----ctttggtgt---ttccca \n+s mm5.chr6 120812128 176 - 149721531 TTTTAAAATGAAAATTTCAAACACA----ATAGTGAAAAATAATATAGTGAGTTA-----TACTTATTACCCATATGTAATAATTGCTAT-TTCCCATAGTTTAGCCTCAG---------------------GTTTT-------CAAAATTATTTTAAAGCAAATTGCAGACACTATGACATTGTCATACCCCTAAATATTTGAGTAT---TTTATG \n+s rn3.chr4 131188640 194 - 187371129 TTTTCAAATGAAAAATTCTAAGAAA-------------AATAATATAACGAATTA-----TACTTATTACCCATATGTAACAATTACCAC-TTCCCATAGTGTAGCTTCAGTTTTTCAAAATTATTAAAACTTTTTTAAATATTTAAAAAT-CTTTAAAGCAAATTGCAGACACTGTGACATTGTCACGCCCCTAAATATTTGAGTAT---TTTCTA \n+s canFam1.chr14 106846'..b'ATGGTGTGGAGGGGACATGGAACGGTAGGCTGACA-TAGGTCCTGGCGGC-ACCATCAGATCACATTGGAGACTTTCTTATGGAAACATGTTCCCCAAAGGTtgtgtgctccatcaag--------------------------------------------------actgcagggctctgtt---------------------------------------------------------------------------------------------ttgttcac \n+\n+a score=82819.0\n+s hg17.chr7 31155458 423 - 158628139 acaggaaatttgcatttctgtgtct----ataaagttttgaattctgtcaacaaaaaattgtgta---aattgtttattcttgttgtataagtacccatgtaatatcctca-attttgc--cttggcttagaaagcctaaaatgttttctacctggccctt-tagagaaagttc-ccagcccttgAACCAGGGAACACACATACATTG-------CACATTGATTCCTCCAGGCCTTTTTTCTTTCCAGTCCGTCTGTGGGGATGCCCAACTGTGCATCCATCGCTTCTCCCGGAAGAATCTCCCC-ATTCCACTAGGGCCTCTCCATCCT---TAAAGAAGCTTTTCCTAGTTCCCCTTGCAGCTAATTCCTGTCTCTCAGTCTGGGTTGGGTG-CCCCTTTCCAtctcctcccttaggtttta---agaggacagggat-tgggccatc \n+s panTro1.chr6 31690413 423 - 161576975 acaggaaatttacatttctgtgtct----ataaagttttgaattctgtcaacaaaaaattgtgta---aattgtttattcttgttgtataagtacccatgtaatatcctca-attttgc--cttggcttagaaagcctaaaatgttttctacctggccctt-tagagaaagttc-ccagcccttgAACCAGGGAACACACATACATTG-------CACATTGATTCCTCCAGGCCTTTTTTCTTTCCAGTCCGTCTGTGGGGATGCCCAACTGCGCATCCATCGCTTCTCCCGGAAGAATCTCCCC-ATTCCACTAGGGTCTCTCCATCCT---TAAAGAAGCTTTTCCTAGTTCCCCTTGCAGCTAATTCCTGTCTCTCAGTCTGGGTTGGGTG-CCCCTTTCCAtctcctcccttaggtttta---agaggacagggat-tgggccatc \n+s mm5.chr6 120810130 334 - 149721531 TTAAGAAATTAAAACTTTAGCATCCTCAAATAAAGTTCTGAATTTGGTCAACCAAAAATTGT-------CTTGTTTTCTCTTGT---ATAAGTACCCACGGGGTAACCTTT-ATTTCCC-TCTTGGCCTGCCAAGCGAGAATTGTTTGCTAACCTGC---------------------------AAACTATGAAACCTACACACACC--------TGCGCTGGCTGCTCCTGGCTCCCAGTCCTGCCCGTCTCT-TATGGGCGTTCCTGGAGTCAGGTCCATCCCTTCTGCCCACAGAACCCCCCCTGTTTTGCATAGGCCCTGCTCTCCA-----------------------CCACTGGCAG---------GCTTCCTTGTCTA---TGGAC----------------------------------AGAGAACAGAGCCCTCTGCCATT \n+s rn3.chr4 131186910 340 - 187371129 AAAAGAAATTTAAACTTTAGCATCCTCAAATAAAGTTCTGAATTTGGTCAACCAAAAATTGT-------CTTGTTTTCTCTTGT---GTAAGCACTCACGGGGTCACCTTC-AGTTTCC-TCTTGGCCTGCAAAGCAGGAATTGTTTGCCAACCTGC---------------------------AAACTATGAAATATACACACGCCCGCACACCTGCGCTGGCTTCTCCTGGGTCTCAGTCCTGCCAGCCTCTCTATGGCTATGTCCGGAGGCTAGTCCATCCCTTCTGCCTACAGAAGCCCCCT-CTTTTGCATAGGCCCTGCTCTCCA---T----------------------CTGAGAG---------GCTTCTTTGACTA---TGGAC----------------------------------AGAGAACAGGGGCCTCTGCCATT \n+s canFam1.chr14 10683450 405 + 63549963 atatgaagtttacattttggcatccctaagtaaagttttgaattttatc--caaaaaattccgggggcaacttttccctcttgt---------acctac---ataccctctgatgtcgcctcttggtctgaaaagcctaaaatgtttatcatcccacccttagagagaaagtttgccaacccTGGAACTAGAAAA------TACATTG-------CACGTTAGCTCTTCTGGGTCTTTATTCCTGCCAGTC-GTGGGCGGGCATGCAGGACTGCTCAATCAGGCCTTCTCCAAGCA--------CC---------GGGGTCTCTTCTTCCTGGTTGAAGTAGCTTGTCCTGGTCACCTTTCCAGCCAACTCCCCTCATTCCAACTGGCTTGCGTGACCTCTTCCCACCTCTGCCCACAGGCTGTAAGTGGAAGGCAGGCAT-CAAGTCTCC \n+\n+a score=15522.0\n+s hg17.chr7 31154233 97 - 158628139 gcaaatgacgttggtgaaccgagcctg-ccactgccgggtttggtaatgcccaaaagctaagaatggtttctacatttgtaaaagtttgaaaaaaaaa \n+s panTro1.chr6 31689192 97 - 161576975 GCAAATGATGTTGGTGAACCGAGCCTT-ccactgccgggtttggtaatgcccaaaagctaagaatggtttctacatttgtaaaagtttgaaaaaaaaa \n+s canFam1.chr14 10683318 97 + 63549963 gcaagttatgtgggtgagccaaatccgaccaccaccaggaccaccatggccccga-gctaggaatggtttttgcatttttaaagagttgaaaaatata \n+\n+a score=28088.0\n+s hg17.chr7 31153902 331 - 158628139 agccaggcgtggtagctcaagcctgtaatcccagcactttgggaggccaaggtgggtggatcacctgaggtcaggatttcgagaccagcctggccaacatggtgaaacctcatctctactaaaaatacaaaattagccaggtgtggtggtgagtgtctgtaatcccagctacttgagaggctgaggcaggagaatggcttgaacctgggaagtggaggttgcagtgagccaagatcagaccattgcactacagcctgggcaacaagagtgaaactctgtctcaat-aaaaaaaacaaaacaaaacaaaacCCATAACATAAAGcggggaact \n+s panTro1.chr6 31688874 318 - 161576975 agccaggcgtggtagctcaagcctgtaatcccagcactttgggaggccaaggtgggtggatcacctgaggtcaggatttcgagaccagcctggccaacatgatgaaacctcatctctactaaaaatacaaaattagccaggtgtggtggtgagtgtctgtaatcccagctacttgagaggctgaggcaggagaatggcttgaacctgggaagtggaggttgcagtgagcca--------------cactacagcctgggcaacaagagtgaaactctgtctcaataaaaaaaaaaaaaaaaaaaaaaaaCCCATAATATAAAGCGGGGAACT \n+\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/maf_split_by_species_collapsed_out.maf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/maf_split_by_species_collapsed_out.maf Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,61 @@
+##maf version=1
+a score=2047408.0
+s species1.chr1 147984545 85 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG
+s species2.chr1 129723125 85 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG
+s species3.chr3  68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
+
+a score=2047408.0
+s species1.chr1 147984545 83 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTT--GTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG
+s species2.chr1 129723125 85 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG
+s species3.chr3  68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
+
+a score=2047408.0
+s species1.chr1 147984645 79 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTT------AG
+s species2.chr1 129723125 85 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG
+s species3.chr3  68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
+
+a score=2047408.0
+s species1.chr1 147984645 79 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTC---GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTC---AG
+s species2.chr1 129723125 85 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG
+s species3.chr3  68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
+
+a score=2047408.0
+s species1.chr1 147984545 85 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG
+s species2.chr1 129723125 83 - 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCT--GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG
+s species3.chr3  68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
+
+a score=2047408.0
+s species1.chr1 147984545 83 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTT-GTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG
+s species2.chr1 129723125 83 - 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCT-GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG
+s species3.chr3  68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC--GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
+
+a score=2047408.0
+s species1.chr1 147984645 79 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTT------AG
+s species2.chr1 129723125 83 - 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCT--GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG
+s species3.chr3  68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
+
+a score=2047408.0
+s species1.chr1 147984645 79 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTC-GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTC---AG
+s species2.chr1 129723125 83 - 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG
+s species3.chr3  68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC-GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
+
+a score=2047408.0
+s species1.chr1 147984545 85 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG
+s species2.chr1 129723925 79 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTC------AG
+s species3.chr3  68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
+
+a score=2047408.0
+s species1.chr1 147984545 83 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTT--GTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG
+s species2.chr1 129723925 79 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTC------AG
+s species3.chr3  68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
+
+a score=2047408.0
+s species1.chr1 147984645 79 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTAG
+s species2.chr1 129723925 79 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCAG
+s species3.chr3  68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGCAG
+
+a score=2047408.0
+s species1.chr1 147984645 79 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTC---GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCAG
+s species2.chr1 129723925 79 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTC---AG
+s species3.chr3  68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC---AG
+

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/maf_split_by_species_in.maf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/maf_split_by_species_in.maf Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,11 @@
+##maf version=1
+a score=2047408.0
+s species1.chr1          147984545 85 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG
+s species1.chr1          147984545 83 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTT--GTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG
+s species1.chr1          147984645 79 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTT------AG
+s species1.chr1          147984645 79 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTC---GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTC---AG
+s species2.chr1          129723125 85 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG
+s species2.chr1          129723125 83 - 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCT--GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG
+s species2.chr1          129723925 79 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTC------AG
+s species3.chr3           68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
+

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/maf_split_by_species_not_collapsed_out.maf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/maf_split_by_species_not_collapsed_out.maf Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,61 @@
+##maf version=1
+a score=2047408.0
+s species1.chr1 147984545 85 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG
+s species2.chr1 129723125 85 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG
+s species3.chr3  68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
+
+a score=2047408.0
+s species1.chr1 147984545 83 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTT--GTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG
+s species2.chr1 129723125 85 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG
+s species3.chr3  68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
+
+a score=2047408.0
+s species1.chr1 147984645 79 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTT------AG
+s species2.chr1 129723125 85 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG
+s species3.chr3  68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
+
+a score=2047408.0
+s species1.chr1 147984645 79 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTC---GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTC---AG
+s species2.chr1 129723125 85 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG
+s species3.chr3  68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
+
+a score=2047408.0
+s species1.chr1 147984545 85 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG
+s species2.chr1 129723125 83 - 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCT--GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG
+s species3.chr3  68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
+
+a score=2047408.0
+s species1.chr1 147984545 83 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTT--GTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG
+s species2.chr1 129723125 83 - 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCT--GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG
+s species3.chr3  68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
+
+a score=2047408.0
+s species1.chr1 147984645 79 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTT------AG
+s species2.chr1 129723125 83 - 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCT--GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG
+s species3.chr3  68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
+
+a score=2047408.0
+s species1.chr1 147984645 79 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTC---GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTC---AG
+s species2.chr1 129723125 83 - 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCT--GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG
+s species3.chr3  68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
+
+a score=2047408.0
+s species1.chr1 147984545 85 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG
+s species2.chr1 129723925 79 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTC------AG
+s species3.chr3  68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
+
+a score=2047408.0
+s species1.chr1 147984545 83 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTT--GTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG
+s species2.chr1 129723925 79 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTC------AG
+s species3.chr3  68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
+
+a score=2047408.0
+s species1.chr1 147984645 79 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTT------AG
+s species2.chr1 129723925 79 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTC------AG
+s species3.chr3  68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
+
+a score=2047408.0
+s species1.chr1 147984645 79 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTC---GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTC---AG
+s species2.chr1 129723925 79 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTC------AG
+s species3.chr3  68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
+

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/maf_stats_interval_out.dat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/maf_stats_interval_out.dat Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,426 @@\n+chr1\t147962192\t147962580\tCCDS989.1_cds_0_0_chr1_147962193_r\t0\t-\thg17\t388\t0\n+chr1\t147962192\t147962580\tCCDS989.1_cds_0_0_chr1_147962193_r\t0\t-\tcanFam1\t388\t0\n+chr1\t147962192\t147962580\tCCDS989.1_cds_0_0_chr1_147962193_r\t0\t-\tdanRer1\t366\t22\n+chr1\t147962192\t147962580\tCCDS989.1_cds_0_0_chr1_147962193_r\t0\t-\tfr1\t260\t128\n+chr1\t147962192\t147962580\tCCDS989.1_cds_0_0_chr1_147962193_r\t0\t-\tgalGal2\t129\t259\n+chr1\t147962192\t147962580\tCCDS989.1_cds_0_0_chr1_147962193_r\t0\t-\tmm5\t386\t2\n+chr1\t147962192\t147962580\tCCDS989.1_cds_0_0_chr1_147962193_r\t0\t-\tpanTro1\t388\t0\n+chr1\t147962192\t147962580\tCCDS989.1_cds_0_0_chr1_147962193_r\t0\t-\trn3\t386\t2\n+chr1\t147984545\t147984630\tCCDS990.1_cds_0_0_chr1_147984546_f\t0\t+\thg17\t85\t0\n+chr1\t147984545\t147984630\tCCDS990.1_cds_0_0_chr1_147984546_f\t0\t+\tcanFam1\t82\t3\n+chr1\t147984545\t147984630\tCCDS990.1_cds_0_0_chr1_147984546_f\t0\t+\tmm5\t76\t9\n+chr1\t147984545\t147984630\tCCDS990.1_cds_0_0_chr1_147984546_f\t0\t+\tpanTro1\t85\t0\n+chr1\t147984545\t147984630\tCCDS990.1_cds_0_0_chr1_147984546_f\t0\t+\trn3\t76\t9\n+chr1\t148078400\t148078582\tCCDS993.1_cds_0_0_chr1_148078401_r\t0\t-\thg17\t182\t0\n+chr1\t148078400\t148078582\tCCDS993.1_cds_0_0_chr1_148078401_r\t0\t-\tcanFam1\t182\t0\n+chr1\t148078400\t148078582\tCCDS993.1_cds_0_0_chr1_148078401_r\t0\t-\tdanRer1\t182\t0\n+chr1\t148078400\t148078582\tCCDS993.1_cds_0_0_chr1_148078401_r\t0\t-\tfr1\t182\t0\n+chr1\t148078400\t148078582\tCCDS993.1_cds_0_0_chr1_148078401_r\t0\t-\tgalGal2\t182\t0\n+chr1\t148078400\t148078582\tCCDS993.1_cds_0_0_chr1_148078401_r\t0\t-\tmm5\t182\t0\n+chr1\t148078400\t148078582\tCCDS993.1_cds_0_0_chr1_148078401_r\t0\t-\tpanTro1\t182\t0\n+chr1\t148078400\t148078582\tCCDS993.1_cds_0_0_chr1_148078401_r\t0\t-\trn3\t182\t0\n+chr1\t148185136\t148185276\tCCDS996.1_cds_0_0_chr1_148185137_f\t0\t+\thg17\t140\t0\n+chr1\t148185136\t148185276\tCCDS996.1_cds_0_0_chr1_148185137_f\t0\t+\tcanFam1\t140\t0\n+chr1\t148185136\t148185276\tCCDS996.1_cds_0_0_chr1_148185137_f\t0\t+\tmm5\t140\t0\n+chr1\t148185136\t148185276\tCCDS996.1_cds_0_0_chr1_148185137_f\t0\t+\tpanTro1\t140\t0\n+chr1\t148185136\t148185276\tCCDS996.1_cds_0_0_chr1_148185137_f\t0\t+\trn3\t140\t0\n+chr10\t55251623\t55253124\tCCDS7248.1_cds_0_0_chr10_55251624_r\t0\t-\thg17\t1501\t0\n+chr10\t55251623\t55253124\tCCDS7248.1_cds_0_0_chr10_55251624_r\t0\t-\tcanFam1\t1396\t105\n+chr10\t55251623\t55253124\tCCDS7248.1_cds_0_0_chr10_55251624_r\t0\t-\tdanRer1\t809\t692\n+chr10\t55251623\t55253124\tCCDS7248.1_cds_0_0_chr10_55251624_r\t0\t-\tfr1\t200\t1301\n+chr10\t55251623\t55253124\tCCDS7248.1_cds_0_0_chr10_55251624_r\t0\t-\tgalGal2\t1139\t362\n+chr10\t55251623\t55253124\tCCDS7248.1_cds_0_0_chr10_55251624_r\t0\t-\tmm5\t1435\t66\n+chr10\t55251623\t55253124\tCCDS7248.1_cds_0_0_chr10_55251624_r\t0\t-\tpanTro1\t1411\t90\n+chr10\t55251623\t55253124\tCCDS7248.1_cds_0_0_chr10_55251624_r\t0\t-\trn3\t1432\t69\n+chr11\t116124407\t116124501\tCCDS8374.1_cds_0_0_chr11_116124408_r\t0\t-\thg17\t94\t0\n+chr11\t116124407\t116124501\tCCDS8374.1_cds_0_0_chr11_116124408_r\t0\t-\tcanFam1\t94\t0\n+chr11\t116124407\t116124501\tCCDS8374.1_cds_0_0_chr11_116124408_r\t0\t-\tfr1\t94\t0\n+chr11\t116124407\t116124501\tCCDS8374.1_cds_0_0_chr11_116124408_r\t0\t-\tgalGal2\t94\t0\n+chr11\t116124407\t116124501\tCCDS8374.1_cds_0_0_chr11_116124408_r\t0\t-\tmm5\t94\t0\n+chr11\t116124407\t116124501\tCCDS8374.1_cds_0_0_chr11_116124408_r\t0\t-\tpanTro1\t94\t0\n+chr11\t116124407\t116124501\tCCDS8374.1_cds_0_0_chr11_116124408_r\t0\t-\trn3\t94\t0\n+chr11\t116206508\t116206563\tCCDS8377.1_cds_0_0_chr11_116206509_f\t0\t+\thg17\t55\t0\n+chr11\t116206508\t116206563\tCCDS8377.1_cds_0_0_chr11_116206509_f\t0\t+\tcanFam1\t55\t0\n+chr11\t116206508\t116206563\tCCDS8377.1_cds_0_0_chr11_116206509_f\t0\t+\tmm5\t55\t0\n+chr11\t116206508\t116206563\tCCDS8377.1_cds_0_0_chr11_116206509_f\t0\t+\tpanTro1\t55\t0\n+chr11\t116211733\t116212337\tCCDS8378.1_cds_0_0_chr11_116211734_r\t0\t-\thg17\t604\t0\n+chr11\t116211733\t116212337\tCCDS8378.1_cds_0_0_chr11_116211734_r\t0\t-\tcanFam1\t604\t0\n+chr11\t116211733\t116212337\tCCDS8378.1_cds_0_0_chr11_116211734_r\t0\t-\tgalGal2\t579\t25\n+chr11\t116211733\t116212337\tCCDS8378.1_cds_0_0_chr11_116211734_r\t0\t-\tmm5\t598\t6\n+chr11\t116211733\t116212337\tCCDS8378.1_cds_0_0_chr11_116211734_r\t0\t-\tpanTro1\t604\t0\n+chr11\t116211733\t116212337\tCCDS8378.1_cds_0_0_chr11_116211734_r\t0\t-\trn3'..b'89136\tCCDS6915.1_cds_0_0_chr9_128787520_r\t0\t-\thg17\t1617\t0\n+chr9\t128787519\t128789136\tCCDS6915.1_cds_0_0_chr9_128787520_r\t0\t-\tcanFam1\t1610\t7\n+chr9\t128787519\t128789136\tCCDS6915.1_cds_0_0_chr9_128787520_r\t0\t-\tdanRer1\t1574\t43\n+chr9\t128787519\t128789136\tCCDS6915.1_cds_0_0_chr9_128787520_r\t0\t-\tfr1\t1581\t36\n+chr9\t128787519\t128789136\tCCDS6915.1_cds_0_0_chr9_128787520_r\t0\t-\tgalGal2\t1582\t35\n+chr9\t128787519\t128789136\tCCDS6915.1_cds_0_0_chr9_128787520_r\t0\t-\tmm5\t1604\t13\n+chr9\t128787519\t128789136\tCCDS6915.1_cds_0_0_chr9_128787520_r\t0\t-\tpanTro1\t1546\t71\n+chr9\t128787519\t128789136\tCCDS6915.1_cds_0_0_chr9_128787520_r\t0\t-\trn3\t1610\t7\n+chr9\t128882427\t128882523\tCCDS6917.1_cds_0_0_chr9_128882428_f\t0\t+\thg17\t96\t0\n+chr9\t128882427\t128882523\tCCDS6917.1_cds_0_0_chr9_128882428_f\t0\t+\tcanFam1\t96\t0\n+chr9\t128882427\t128882523\tCCDS6917.1_cds_0_0_chr9_128882428_f\t0\t+\tdanRer1\t96\t0\n+chr9\t128882427\t128882523\tCCDS6917.1_cds_0_0_chr9_128882428_f\t0\t+\tfr1\t96\t0\n+chr9\t128882427\t128882523\tCCDS6917.1_cds_0_0_chr9_128882428_f\t0\t+\tmm5\t96\t0\n+chr9\t128882427\t128882523\tCCDS6917.1_cds_0_0_chr9_128882428_f\t0\t+\tpanTro1\t96\t0\n+chr9\t128882427\t128882523\tCCDS6917.1_cds_0_0_chr9_128882428_f\t0\t+\trn3\t96\t0\n+chr9\t128937229\t128937445\tCCDS6919.1_cds_0_0_chr9_128937230_r\t0\t-\thg17\t216\t0\n+chr9\t128937229\t128937445\tCCDS6919.1_cds_0_0_chr9_128937230_r\t0\t-\tcanFam1\t216\t0\n+chr9\t128937229\t128937445\tCCDS6919.1_cds_0_0_chr9_128937230_r\t0\t-\tdanRer1\t216\t0\n+chr9\t128937229\t128937445\tCCDS6919.1_cds_0_0_chr9_128937230_r\t0\t-\tfr1\t216\t0\n+chr9\t128937229\t128937445\tCCDS6919.1_cds_0_0_chr9_128937230_r\t0\t-\tgalGal2\t216\t0\n+chr9\t128937229\t128937445\tCCDS6919.1_cds_0_0_chr9_128937230_r\t0\t-\tmm5\t216\t0\n+chr9\t128937229\t128937445\tCCDS6919.1_cds_0_0_chr9_128937230_r\t0\t-\tpanTro1\t216\t0\n+chr9\t128937229\t128937445\tCCDS6919.1_cds_0_0_chr9_128937230_r\t0\t-\trn3\t216\t0\n+chrX\t122745047\t122745924\tCCDS14606.1_cds_0_0_chrX_122745048_f\t0\t+\thg17\t877\t0\n+chrX\t122745047\t122745924\tCCDS14606.1_cds_0_0_chrX_122745048_f\t0\t+\tcanFam1\t877\t0\n+chrX\t122745047\t122745924\tCCDS14606.1_cds_0_0_chrX_122745048_f\t0\t+\tdanRer1\t774\t103\n+chrX\t122745047\t122745924\tCCDS14606.1_cds_0_0_chrX_122745048_f\t0\t+\tfr1\t619\t258\n+chrX\t122745047\t122745924\tCCDS14606.1_cds_0_0_chrX_122745048_f\t0\t+\tgalGal2\t857\t20\n+chrX\t122745047\t122745924\tCCDS14606.1_cds_0_0_chrX_122745048_f\t0\t+\tmm5\t874\t3\n+chrX\t122745047\t122745924\tCCDS14606.1_cds_0_0_chrX_122745048_f\t0\t+\tpanTro1\t877\t0\n+chrX\t122745047\t122745924\tCCDS14606.1_cds_0_0_chrX_122745048_f\t0\t+\trn3\t874\t3\n+chrX\t152648964\t152649196\tCCDS14733.1_cds_0_0_chrX_152648965_r\t0\t-\thg17\t232\t0\n+chrX\t152648964\t152649196\tCCDS14733.1_cds_0_0_chrX_152648965_r\t0\t-\tcanFam1\t232\t0\n+chrX\t152648964\t152649196\tCCDS14733.1_cds_0_0_chrX_152648965_r\t0\t-\tdanRer1\t212\t20\n+chrX\t152648964\t152649196\tCCDS14733.1_cds_0_0_chrX_152648965_r\t0\t-\tfr1\t218\t14\n+chrX\t152648964\t152649196\tCCDS14733.1_cds_0_0_chrX_152648965_r\t0\t-\tgalGal2\t232\t0\n+chrX\t152648964\t152649196\tCCDS14733.1_cds_0_0_chrX_152648965_r\t0\t-\tmm5\t232\t0\n+chrX\t152648964\t152649196\tCCDS14733.1_cds_0_0_chrX_152648965_r\t0\t-\tpanTro1\t232\t0\n+chrX\t152648964\t152649196\tCCDS14733.1_cds_0_0_chrX_152648965_r\t0\t-\trn3\t232\t0\n+chrX\t152691446\t152691471\tCCDS14735.1_cds_0_0_chrX_152691447_f\t0\t+\thg17\t25\t0\n+chrX\t152691446\t152691471\tCCDS14735.1_cds_0_0_chrX_152691447_f\t0\t+\tcanFam1\t25\t0\n+chrX\t152691446\t152691471\tCCDS14735.1_cds_0_0_chrX_152691447_f\t0\t+\tmm5\t25\t0\n+chrX\t152691446\t152691471\tCCDS14735.1_cds_0_0_chrX_152691447_f\t0\t+\trn3\t25\t0\n+chrX\t152694029\t152694263\tCCDS14736.1_cds_0_0_chrX_152694030_r\t0\t-\thg17\t234\t0\n+chrX\t152694029\t152694263\tCCDS14736.1_cds_0_0_chrX_152694030_r\t0\t-\tcanFam1\t231\t3\n+chrX\t152694029\t152694263\tCCDS14736.1_cds_0_0_chrX_152694030_r\t0\t-\tdanRer1\t67\t167\n+chrX\t152694029\t152694263\tCCDS14736.1_cds_0_0_chrX_152694030_r\t0\t-\tfr1\t61\t173\n+chrX\t152694029\t152694263\tCCDS14736.1_cds_0_0_chrX_152694030_r\t0\t-\tgalGal2\t149\t85\n+chrX\t152694029\t152694263\tCCDS14736.1_cds_0_0_chrX_152694030_r\t0\t-\tmm5\t228\t6\n+chrX\t152694029\t152694263\tCCDS14736.1_cds_0_0_chrX_152694030_r\t0\t-\tpanTro1\t234\t0\n+chrX\t152694029\t152694263\tCCDS14736.1_cds_0_0_chrX_152694030_r\t0\t-\trn3\t234\t0\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/maf_stats_summary_out.dat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/maf_stats_summary_out.dat Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,9 @@
+#species nucleotides coverage
+mm5 17186 0.9555
+panTro1 17732 0.9858
+danRer1 12263 0.6818
+canFam1 17034 0.9470
+fr1 11318 0.6292
+galGal2 13522 0.7518
+hg17 17987 1.0000
+rn3 16410 0.9123

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/maf_thread_for_species.dat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/maf_thread_for_species.dat Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,17 @@
+##maf version=1
+a score=0.0
+s hg17.chr7    127471195 676 + 158628139 gtttgccatcttttgctgctctagggaatccagcagctgtcaccatgtaaacaagcccaggctagaccaGTTACCCTCATCATCTTAGCTGATAGCCAGCCAGCCACCACAGGCAtgagtcaggccatattgctggacccacagaattatgagctaaataaatagtcttgggttaagccactaagttttaggcatagtgtgttatgtaTCTCACAAACATATAAGACTGTGTGTTTGTTGACTGGAGGAAGAGATGCTATAAAGACCACCTTTTAAAACTTCCCAAATACTGCCACTGATGTCCTGATGGAGGTATGAAAACATCCACTAAAATTTGTGGTTTATTCATTTTTCATTATTTTGTTTAAGGAGGTCTATAGTGGAAGAGGGAGATATTTGGggaaattttgtatagactagctttcacgatgttagggaattattattgtgtgataatggtcttgcagttacacagaaattcttccttattttttgggaagcaccaaagtagggataaaatgtcatgatgtgtgcaatacactttaaaatgtttttgccaaaataattaatgaagcaaatatggaaaataataattattaaatctaggtgatgggtatattgtagttcactatagtattgcacacttttctgtatgtttaaatttttcatttaaaaa
+s panTro1.chr6 129885076 676 + 161576975 gtttgccatcttttgctgctcttgggaatccagcagctgtcaccatgtaaacaagcccaggctagaccaGTTACCCTCATCATCTTAGCTGATAGCCAGCCAGCCACCACAGGCAtgagtcaggccatattgctggacccacagaattatgagctaaataaatagtcttgggttaagccactaagttttaggcatagtgtgttatgtaTCTCACAAACATATAAGACTGTGTGTTTGTTGACTGGAGGAAGAGATGCTATAAAGACCACCTTTTGAAACTTCCCAAATACTGCCACTGATGTCCTGATGGAGGTATGAAAACATCCACTAAAATTTGTGGTTTATTCGTTTTTCATTATTTTGTTTAAGGAGGTCTATAGTGGAAGAGGGAGACATTTGGggaaattttgtatagactagctttcacgatgttagggagttattattgtgtgataatggtcttgcagttacacagaaattcttccttattttttgggaaacaccaaagtagggataaaatgtcatgatgtgtgcaatacgctttaaaatatttttgccaaaataattaatgaagcaaatatggaaaataataattattaaatctaggtgatgggtatattgtagttcactatagtattgcacacttttctgtatgtttaaaattttcatttaaaaa
+
+a score=0.0
+s hg17.chr7    127471872 375 + 158628139 ctttgagctagacaccaggctatgagctaggagcatagcaatgaccaaatagactcctaccaactcaaagaatgcacattctCTGGGAAACATGTTTCCATTAGGAAGCCTCGAATGCAATGTGACTGTGGTCTCCAGGACCTGTGTGATCCTGGCTTTTCCTGTTCCCTCCGCATCATCACTGCAGGTGTGTTTTCCCAAGTTTTAAACATTTACCTTCCCAGTGGCCTTGCGTCTAGAGGAATCCCTGTATAGTGGTACATGAATATAACACATAACAAAAATCATCTCTATGGTGTGTGTTGTTCCTGGGGTTCAattcagcaaattttccctgggcacccatgtgttcttggcactggaaaagtaccggga
+s panTro1.chr6 129885753 375 + 161576975 ctttgagctagacaccaggctatgagctaggagcatagcaatgaccaaatagactcctaccaactcaaagaatgcacattctCTGGGAAACATGTTTCCATTAGGAAGCCTCGAATGCAATGTGACTGTGGTCTCCAGGACATGTGTGATCCTGGCTTTTCCTGTTCCCTCTGCATCATCACTGCAGGTGTATTTTCCCAAGTTTTAAACATTTACCTTCCCAGTGGCCTTGCGTCTAGAGGAATCCCTGTATAGTGGTACATGAATATAACACATAACAAAAATCATCTCTATGGTGTGTGTTGTTCCTGGGGTTCAattcagcaaatttttcctgggcacccatgtgttcttggcactggaaaagtaccggga
+
+a score=0.0
+s hg17.chr7    127472258 423 + 158628139 gatggcccaatccctgtcctcttaaaacctaagggaggagaTGGAAAGGGGCACCCAACCCAGACTGAGAGACAGGAATTAGCTGCAAGGGGAACTAGGAAAAGCTTCTTTAAGGATGGAGAGGCCCTAGTGGAATGGGGAGATTCTTCCGGGAGAAGCGATGGATGCACAGTTGGGCATCCCCACAGACGGACTGGAAAGAAAAAAGGCCTGGAGGAATCAATGTGCAATGTATGTGTGTTCCCTGGTTcaagggctgggaactttctctaaagggccaggtagaaaacattttaggctttctaagccaaggcaaaattgaggatattacatgggtacttatacaacaagaataaacaatttacacaattttttgttgacagaattcaaaactttatagacacagaaatgcaaatttcctgt
+s panTro1.chr6 129886139 423 + 161576975 gatggcccaatccctgtcctcttaaaacctaagggaggagaTGGAAAGGGGCACCCAACCCAGACTGAGAGACAGGAATTAGCTGCAAGGGGAACTAGGAAAAGCTTCTTTAAGGATGGAGAGACCCTAGTGGAATGGGGAGATTCTTCCGGGAGAAGCGATGGATGCGCAGTTGGGCATCCCCACAGACGGACTGGAAAGAAAAAAGGCCTGGAGGAATCAATGTGCAATGTATGTGTGTTCCCTGGTTcaagggctgggaactttctctaaagggccaggtagaaaacattttaggctttctaagccaaggcaaaattgaggatattacatgggtacttatacaacaagaataaacaatttacacaattttttgttgacagaattcaaaactttatagacacagaaatgtaaatttcctgt
+
+a score=0.0
+s hg17.chr7    127473809 428 + 158628139 tttttttttcaaacttttacaaatgtagaaaccattcttagcttttgggcattaccaaacccggcagtggcaggctcggttcaccaacgtcatttgcagttccccgCTTTATGTTATGGgttttgttttgttttgtttttttt-attgagacagagtttcactcttgttgcccaggctgtagtgcaatggtctgatcttggctcactgcaacctccacttcccaggttcaagccattctcctgcctcagcctctcaagtagctgggattacagacactcaccaccacacctggctaattttgtatttttagtagagatgaggtttcaccatgttggccaggctggtctcgaaatcctgacctcaggtgatccacccaccttggcctcccaaagtgctgggattacaggcttgagctaccacgcctggct
+s panTro1.chr6 129887686 415 + 161576975 tttttttttcaaacttttacaaatgtagaaaccattcttagcttttgggcattaccaaacccggcagtggAAGGCTCGGTTCACCAACATCATTTGCAGTTCCCCGCTTTATATTATGGGttttttttttttttttttttttttattgagacagagtttcactcttgttgcccaggctgtagtg--------------tggctcactgcaacctccacttcccaggttcaagccattctcctgcctcagcctctcaagtagctgggattacagacactcaccaccacacctggctaattttgtatttttagtagagatgaggtttcatcatgttggccaggctggtctcgaaatcctgacctcaggtgatccacccaccttggcctcccaaagtgctgggattacaggcttgagctaccacgcctggct
+

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/maf_to_interval_out_hg17.interval
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/maf_to_interval_out_hg17.interval Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,2 @@
+#chrom start end strand score name bosTau2 canFam2 dasNov1 hg17 mm7 panTro1 rheMac2 rn3
+chr7 127471910 127472074 + 94204.0 hg17_5_0 atgtgaacaa---------------------------------------------------------------------------------------------aacggacccgtgtgggactcggcggagcacacagattttgcgggagCACGTTCCCGTTAGGAAGTCTCTGATGCAATACGACCGGTGCCTTCAGGACCTG-TG--AGGCTGACTTTCCTTA-CCCCTCCACACCATCATCAAGGCAGGTGTGATTTTCCAGG cagtgaacaa---------------------------------------------------------------------------------------------aacagagccctgcagt-cttgatggagcacacaacctttg-gggaaCATGTTTCCATAAGAAAGTCTCCAATGTGATCTGA-TGGTGCCGCCAGGACCTA-TGTCAGCCTACCGTTCCATGTCCCCTCCACACCATCATCACTGCAGGTGTGTTTTCCCACA CAGTGAGCAA-----------------------------------------------------------------------------------------------CAGCCTGGCTCCGT-CC--GGGGGCCGCTCAGCAGCTC-GGGAGCGTGGAGACG---GGAAGTCTGTCACGCGATGCG-----------CTGGGCCCG------------CTGTTCCCGCCCCCCTCC---CCCC----------------TTTCCCAAG caatgaccaa----------------------------------------------------------------------------------------------atagactcctaccaa-ctc-aaagaatgcacattctCTG-GGAAACATGTTTCCATTAGGAAGCCTCGAATGCAATGTGACTGTGGTCTCCAGGACCTG-TGTGATCCTGGCTTTTCCTGTTCCCTCCG---CATCATCACTGCAGGTGTGTTTTCCCAAG caaaaaccaa------------------------------------------------------------------------------------------------aaaaACCTATAGC-CTC-ACAGGGTGGGTTGTCTTTG-AGGAACATGCATCCGCTAGAAAGTCCCAAGTACACTATGACAGTTG--CCCAGGCCCCGCCTTAAACCTGGTTTTCCTGGTTTCTTTCA---CATCATTACCACGAATATATTTCCTCAAG caatgaccaa----------------------------------------------------------------------------------------------atagactcctaccaa-ctc-aaagaatgcacattctCTG-GGAAACATGTTTCCATTAGGAAGCCTCGAATGCAATGTGACTGTGGTCTCCAGGACATG-TGTGATCCTGGCTTTTCCTGTTCCCTCTG---CATCATCACTGCAGGTGTATTTTCCCAAG caatgaccaa----------------------------------------------------------------------------------------------atagacccctaccga-ctc-aaagaatgtacattctTTG-GGAAACATGTTTCCATCAGAAAATCTCAAATGCAATGTGACTGGGGTCTCCAGGACCTG-TGTGAGCCTGGCTTTTCCTGTTCCCTCCA---CATCATCACTGCAGGTGTATTTTCCC--G --ATGACCAATATACACTGTTTACATGTATAGCATTGTGAATGGAGACATAAAAAGATAATCTAGCTTTGTGCTAGGTAGGTGCTGAGCTCTTAACAGTGCTGGGCAGAAACCTATAAC-CTC-ACAGGGTGGGTTGTCTTTG-AGGAGCGTGCTAACCCTAGGAAGTCTCAAATACAATGTGATGGTTGCCCCCAGGCACCACCTTGAACCTGGTCTTCCTGGTTTCTTTCA---CACCATTACCACAAATACATTTTCTCAGG

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/maf_to_interval_out_panTro1.interval
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/maf_to_interval_out_panTro1.interval Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,2 @@
+#chrom start end strand score name bosTau2 canFam2 dasNov1 hg17 mm7 panTro1 rheMac2 rn3
+chr6 129885791 129885955 + 94204.0 panTro1_5_0 atgtgaacaa---------------------------------------------------------------------------------------------aacggacccgtgtgggactcggcggagcacacagattttgcgggagCACGTTCCCGTTAGGAAGTCTCTGATGCAATACGACCGGTGCCTTCAGGACCTG-TG--AGGCTGACTTTCCTTA-CCCCTCCACACCATCATCAAGGCAGGTGTGATTTTCCAGG cagtgaacaa---------------------------------------------------------------------------------------------aacagagccctgcagt-cttgatggagcacacaacctttg-gggaaCATGTTTCCATAAGAAAGTCTCCAATGTGATCTGA-TGGTGCCGCCAGGACCTA-TGTCAGCCTACCGTTCCATGTCCCCTCCACACCATCATCACTGCAGGTGTGTTTTCCCACA CAGTGAGCAA-----------------------------------------------------------------------------------------------CAGCCTGGCTCCGT-CC--GGGGGCCGCTCAGCAGCTC-GGGAGCGTGGAGACG---GGAAGTCTGTCACGCGATGCG-----------CTGGGCCCG------------CTGTTCCCGCCCCCCTCC---CCCC----------------TTTCCCAAG caatgaccaa----------------------------------------------------------------------------------------------atagactcctaccaa-ctc-aaagaatgcacattctCTG-GGAAACATGTTTCCATTAGGAAGCCTCGAATGCAATGTGACTGTGGTCTCCAGGACCTG-TGTGATCCTGGCTTTTCCTGTTCCCTCCG---CATCATCACTGCAGGTGTGTTTTCCCAAG caaaaaccaa------------------------------------------------------------------------------------------------aaaaACCTATAGC-CTC-ACAGGGTGGGTTGTCTTTG-AGGAACATGCATCCGCTAGAAAGTCCCAAGTACACTATGACAGTTG--CCCAGGCCCCGCCTTAAACCTGGTTTTCCTGGTTTCTTTCA---CATCATTACCACGAATATATTTCCTCAAG caatgaccaa----------------------------------------------------------------------------------------------atagactcctaccaa-ctc-aaagaatgcacattctCTG-GGAAACATGTTTCCATTAGGAAGCCTCGAATGCAATGTGACTGTGGTCTCCAGGACATG-TGTGATCCTGGCTTTTCCTGTTCCCTCTG---CATCATCACTGCAGGTGTATTTTCCCAAG caatgaccaa----------------------------------------------------------------------------------------------atagacccctaccga-ctc-aaagaatgtacattctTTG-GGAAACATGTTTCCATCAGAAAATCTCAAATGCAATGTGACTGGGGTCTCCAGGACCTG-TGTGAGCCTGGCTTTTCCTGTTCCCTCCA---CATCATCACTGCAGGTGTATTTTCCC--G --ATGACCAATATACACTGTTTACATGTATAGCATTGTGAATGGAGACATAAAAAGATAATCTAGCTTTGTGCTAGGTAGGTGCTGAGCTCTTAACAGTGCTGGGCAGAAACCTATAAC-CTC-ACAGGGTGGGTTGTCTTTG-AGGAGCGTGCTAACCCTAGGAAGTCTCAAATACAATGTGATGGTTGCCCCCAGGCACCACCTTGAACCTGGTCTTCCTGGTTTCTTTCA---CACCATTACCACAAATACATTTTCTCAGG

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/master2snp_output.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/master2snp_output.txt Sat Feb 21 16:33:42 2015 +0100

[

@@ -0,0 +1,30 @@
+#{"column_names":["chr","pos","A","B","Q","1A","1B","1G","1Q"],
+#"individuals":[["na",6]],
+#"dbkey":"hg19","pos":2,"rPos":2,"ref":1,"scaffold":1,"species":"hg19"}
+chr1 41980 A G -1 0 1 0 76
+chr1 51672 T C -1 0 1 0 53
+chr1 52237 T G -1 0 7 0 63
+chr1 53205 G C -1 30 7 1 93
+chr1 54042 C T -1 10 3 1 66
+chr1 54585 T C -1 19 9 1 94
+chr1 55163 C A -1 0 9 0 76
+chr1 55301 C T -1 19 15 1 87
+chr1 55321 C T -1 12 12 1 95
+chr1 55325 T C -1 11 12 1 95
+chr1 55925 T C -1 0 12 0 66
+chr1 57951 A C -1 0 2 0 72
+chr1 58210 A G -1 0 11 0 98
+chr1 59050 A G -1 21 6 1 66
+chr1 59343 C T -1 23 25 1 57
+chr1 59497 T C -1 15 12 1 74
+chr1 60828 C T -1 11 1 1 60
+chr1 61441 A G -1 0 8 0 23
+chr1 68305 C T -1 20 27 1 44
+chr1 68315 T C -1 20 27 1 44
+chr1 69452 G A -1 37 6 1 61
+chr1 69510 A G -1 0 3 0 123
+chr1 69551 G C -1 27 4 1 98
+chr1 69568 T C -1 29 3 1 98
+chr1 77461 G A -1 0 4 0 26
+chr1 82733 T C -1 17 18 1 42
+chr1 233472 C G -1 42 21 1 118

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/masterVarTest.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/masterVarTest.txt Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,5000 @@\n+#ASSEMBLY_ID\tGS19026-1100-37-ASM\n+#CNV_WINDOW_WIDTH\t2000\n+#COSMIC\tCOSMIC v48\n+#DBSNP_BUILD\tdbSNP build 131\n+#DGV_VERSION\t9\n+#FORMAT_VERSION\t1.5\n+#GENERATED_AT\t2011-Feb-18 17:35:36.151072\n+#GENERATED_BY\tcgatools\n+#GENE_ANNOTATIONS\tNCBI build 37.1\n+#GENOME_REFERENCE\tNCBI build 37\n+#MIRBASE_VERSION\tmiRBase version 15\n+#PFAM_DATE\tAugust 13, 2010\n+#REPMASK_GENERATED_AT\t2010-Dec-03 14:38\n+#SAMPLE\tGS00392-DNA_F04\n+#SEGDUP_GENERATED_AT\t2010-Dec-01 13:40\n+#SOFTWARE_VERSION\t1.3.0\n+#SRC_SOFTWARE_VERSION\t1.10.0.26\n+#TYPE\tVAR-OLPL\n+\n+>locus\tploidy\tchromosome\tbegin\tend\tzygosity\tvarType\treference\tallele1Seq\tallele2Seq\tallele1Score\tallele2Score\tallele1HapLink\tallele2HapLink\txRef\tevidenceIntervalId\tallele1ReadCount\tallele2ReadCount\tneitherAlleleReadCount\ttotalReadCount\tminReferenceScore\tallele1Gene\tallele2Gene\tmiRBaseId\trepeatMasker\tsegDupOverlap\trelativeCoverage\tcalledPloidy\n+1\t2\tchr1\t0\t10000\tno-call\tcomplex\t=\t?\t?\t\t\t\t\t\t\t\t\t\t\t-16\t\t\t\t\t\t\t\n+2\t2\tchr1\t10000\t11093\tno-call\tcomplex\t=\t?\t?\t\t\t\t\t\t\t\t\t\t\t-172\t\t\t\t\t\t1.17\tN\n+3\t2\tchr1\t11093\t11108\thom\tref\t=\t=\t=\t\t\t\t\t\t\t\t\t\t\t15\t\t\t\t\t\t1.17\tN\n+4\t2\tchr1\t11108\t11135\tno-call\tcomplex\t=\t?\t?\t\t\t\t\t\t\t\t\t\t\t-15\t\t\t\t\t\t1.17\tN\n+5\t2\tchr1\t11135\t11145\thom\tref\t=\t=\t=\t\t\t\t\t\t\t\t\t\t\t13\t\t\t\t\t\t1.17\tN\n+6\t2\tchr1\t11145\t11170\tno-call\tcomplex\t=\t?\t?\t\t\t\t\t\t\t\t\t\t\t-15\t\t\t\t\t\t1.17\tN\n+7\t2\tchr1\t11170\t11177\thom\tref\t=\t=\t=\t\t\t\t\t\t\t\t\t\t\t12\t\t\t\t\t\t1.17\tN\n+8\t2\tchr1\t11177\t11204\tno-call\tcomplex\t=\t?\t?\t\t\t\t\t\t\t\t\t\t\t-111\t\t\t\t\t\t1.17\tN\n+9\t2\tchr1\t11204\t11214\thom\tref\t=\t=\t=\t\t\t\t\t\t\t\t\t\t\t17\t\t\t\t\t\t1.17\tN\n+10\t2\tchr1\t11214\t11236\tno-call\tcomplex\t=\t?\t?\t\t\t\t\t\t\t\t\t\t\t-10\t\t\t\t\t\t1.17\tN\n+11\t2\tchr1\t11236\t11269\thom\tref\t=\t=\t=\t\t\t\t\t\t\t\t\t\t\t10\t\t\t\t\t\t1.17\tN\n+12\t2\tchr1\t11269\t11276\tno-call\tcomplex\t=\t?\t?\t\t\t\t\t\t\t\t\t\t\t-82\t100287102:XM_002342010.1:LOC100287102::::TSS-UPSTREAM:UNKNOWN-INC\t100287102:XM_002342010.1:LOC100287102::::TSS-UPSTREAM:UNKNOWN-INC\t\t\t\t1.17\tN\n+13\t2\tchr1\t11276\t11287\thom\tref\t=\t=\t=\t\t\t\t\t\t\t\t\t\t\t16\t\t\t\t\t\t1.17\tN\n+14\t2\tchr1\t11287\t11321\tno-call\tcomplex\t=\t?\t?\t\t\t\t\t\t\t\t\t\t\t-53\t\t\t\t\t\t1.17\tN\n+15\t2\tchr1\t11321\t11339\thom\tref\t=\t=\t=\t\t\t\t\t\t\t\t\t\t\t10\t\t\t\t\t\t1.17\tN\n+16\t2\tchr1\t11339\t11350\tno-call\tcomplex\t=\t?\t?\t\t\t\t\t\t\t\t\t\t\t-22\t\t\t\t\t\t1.17\tN\n+17\t2\tchr1\t11350\t11364\thom\tref\t=\t=\t=\t\t\t\t\t\t\t\t\t\t\t17\t\t\t\t\t\t1.17\tN\n+18\t2\tchr1\t11364\t11395\tno-call\tcomplex\t=\t?\t?\t\t\t\t\t\t\t\t\t\t\t-186\t\t\t\t\t\t1.17\tN\n+19\t2\tchr1\t11395\t11405\thom\tref\t=\t=\t=\t\t\t\t\t\t\t\t\t\t\t23\t\t\t\t\t\t1.17\tN\n+20\t2\tchr1\t11405\t11436\tno-call\tcomplex\t=\t?\t?\t\t\t\t\t\t\t\t\t\t\t-93\t\t\t\t\t\t1.17\tN\n+21\t2\tchr1\t11436\t11453\thom\tref\t=\t=\t=\t\t\t\t\t\t\t\t\t\t\t49\t\t\t\t\t\t1.17\tN\n+22\t2\tchr1\t11453\t11481\tno-call\tcomplex\t=\t?\t?\t\t\t\t\t\t\t\t\t\t\t-329\t\t\t\t\t\t1.17\tN\n+23\t2\tchr1\t11481\t11504\thom\tref\t=\t=\t=\t\t\t\t\t\t\t\t\t\t\t60\t\t\t\t\t\t1.17\tN\n+24\t2\tchr1\t11504\t11511\tno-call\tcomplex\t=\t?\t?\t\t\t\t\t\t\t\t\t\t\t-215\t100287102:XM_002342010.1:LOC100287102::::TSS-UPSTREAM:UNKNOWN-INC\t100287102:XM_002342010.1:LOC100287102::::TSS-UPSTREAM:UNKNOWN-INC\t\t\t\t1.17\tN\n+25\t2\tchr1\t11511\t11527\thom\tref\t=\t=\t=\t\t\t\t\t\t\t\t\t\t\t88\t\t\t\t\t\t1.17\tN\n+26\t2\tchr1\t11527\t11579\tno-call\tcomplex\t=\t?\t?\t\t\t\t\t\t\t\t\t\t\t-1562\t\t\t\t\t\t1.17\tN\n+27\t2\tchr1\t11579\t11637\thom\tref\t=\t=\t=\t\t\t\t\t\t\t\t\t\t\t86\t\t\t\t\t\t1.17\tN\n+28\t2\tchr1\t11637\t11677\tno-call\tcomplex\t=\t?\t?\t\t\t\t\t\t\t\t\t\t\t-427\t\t\t\t\t\t1.17\tN\n+29\t2\tchr1\t11677\t11706\thom\tref\t=\t=\t=\t\t\t\t\t\t\t\t\t\t\t41\t\t\t\t\t\t1.17\tN\n+30\t2\tchr1\t11706\t11713\tno-call\tcomplex\t=\t?\t?\t\t\t\t\t\t\t\t\t\t\t-44\t100287102:XM_002342010.1:LOC100287102::::TSS-UPSTREAM:UNKNOWN-INC\t100287102:XM_002342010.1:LOC100287102::::TSS-UPSTREAM:UNKNOWN-INC\t\t\t\t1.17\tN\n+31\t2\tchr1\t11713\t11777\thom\tref\t=\t=\t=\t\t\t\t\t\t\t\t\t\t\t21\t\t\t\t\t\t1.17\tN\n+32\t2\tchr1\t11777\t11816\tno-call\tcomplex\t=\t?\t?\t\t\t\t\t\t\t\t\t\t\t-272\t\t\t\t\t\t1.17\tN\n+33\t2\tchr1\t11816\t11859\thom\tref\t=\t=\t=\t\t\t\t\t\t\t\t\t\t\t18\t\t\t\t\t\t1.17\tN\n+34\t2\tchr1\t11859\t11866\tno-call\tcomplex\t=\t?\t?\t\t\t\t\t\t\t\t\t\t\t-288\t100287102:XM_002342010.1:LOC100287102::::TSS-UPSTREAM:UNKNOWN-INC\t100287102:XM_002342010.1:LOC100287102::::TSS-UPSTREAM:UNKNOWN-INC\t\t\t\t1.17\tN\n+35\t2\tchr1\t11866\t11903\thom\tref\t=\t=\t=\t\t\t\t\t\t\t\t\t\t\t76\t\t\t\t\t\t1.17\tN\n+36\t2\tchr1\t11903\t11925\tno-call\tcomplex\t=\t?\t?\t\t\t\t\t\t\t\t\t\t\t-490\t\t\t\t\t\t1.17\tN\n+37\t2\tchr1\t11925\t11956\thom\tref\t=\t=\t=\t\t\t\t\t\t\t\t\t\t\t53\t\t\t\t\t\t1.17\tN\n+38\t2\tchr1\t11956\t11973\tno-call\tcomplex\t=\t?\t?\t\t\t\t\t\t\t\t\t\t\t-166\t\t\t\t\t\t1.17\tN\n+39\t2\tchr1\t11973\t12006\thom\tref\t=\t=\t=\t\t\t\t\t\t\t\t\t\t\t41\t\t\t\t\t\t1.'..b'\t\t\t\t\t\t\t\t\t\t\t-946\t\t\t\t\t\t1.17\tN\n+4925\t2\tchr1\t251441\t251492\thom\tref\t=\t=\t=\t\t\t\t\t\t\t\t\t\t\t30\t\t\t\t\t\t1.17\tN\n+4926\t2\tchr1\t251492\t251513\tno-call\tcomplex\t=\t?\t?\t\t\t\t\t\t\t\t\t\t\t-341\t\t\t\t\t\t1.17\tN\n+4927\t2\tchr1\t251513\t251524\thom\tref\t=\t=\t=\t\t\t\t\t\t\t\t\t\t\t45\t\t\t\t\t\t1.17\tN\n+4928\t2\tchr1\t251524\t251539\tno-call\tcomplex\t=\t?\t?\t\t\t\t\t\t\t\t\t\t\t-118\t\t\t\t\t\t1.17\tN\n+4929\t2\tchr1\t251539\t251590\thom\tref\t=\t=\t=\t\t\t\t\t\t\t\t\t\t\t25\t\t\t\t\t\t1.17\tN\n+4930\t2\tchr1\t251590\t251597\tno-call\tcomplex\t=\t?\t?\t\t\t\t\t\t\t\t\t\t\t-372\t\t\t\t\t\t1.17\tN\n+4931\t2\tchr1\t251597\t251624\thom\tref\t=\t=\t=\t\t\t\t\t\t\t\t\t\t\t60\t\t\t\t\t\t1.17\tN\n+4932\t2\tchr1\t251624\t251666\tno-call\tcomplex\t=\t?\t?\t\t\t\t\t\t\t\t\t\t\t-251\t\t\t\t\t\t1.17\tN\n+4933\t2\tchr1\t251666\t251747\thom\tref\t=\t=\t=\t\t\t\t\t\t\t\t\t\t\t47\t\t\t\t\t\t1.17\tN\n+4934\t2\tchr1\t251747\t251763\tno-call\tcomplex\t=\t?\t?\t\t\t\t\t\t\t\t\t\t\t-104\t\t\t\t\t\t1.17\tN\n+4935\t2\tchr1\t251763\t251790\thom\tref\t=\t=\t=\t\t\t\t\t\t\t\t\t\t\t47\t\t\t\t\t\t1.17\tN\n+4936\t2\tchr1\t251790\t251807\tno-call\tcomplex\t=\t?\t?\t\t\t\t\t\t\t\t\t\t\t-1220\t\t\t\t\t\t1.17\tN\n+4937\t2\tchr1\t251807\t251925\thom\tref\t=\t=\t=\t\t\t\t\t\t\t\t\t\t\t11\t\t\t\t\t\t1.17\tN\n+4938\t2\tchr1\t251925\t251952\tno-call\tcomplex\t=\t?\t?\t\t\t\t\t\t\t\t\t\t\t-286\t\t\t\t\t\t1.17\tN\n+4939\t2\tchr1\t251952\t252011\thom\tref\t=\t=\t=\t\t\t\t\t\t\t\t\t\t\t22\t\t\t\t\t\t1.17\tN\n+4940\t2\tchr1\t252011\t252034\tno-call\tcomplex\t=\t?\t?\t\t\t\t\t\t\t\t\t\t\t-554\t\t\t\t\t\t1.17\tN\n+4941\t2\tchr1\t252034\t252043\thom\tref\t=\t=\t=\t\t\t\t\t\t\t\t\t\t\t32\t\t\t\t\t\t1.17\tN\n+4942\t2\tchr1\t252043\t252055\tno-call\tcomplex\t=\t?\t?\t\t\t\t\t\t\t\t\t\t\t-117\t\t\t\t\t\t1.17\tN\n+4943\t2\tchr1\t252055\t252088\thom\tref\t=\t=\t=\t\t\t\t\t\t\t\t\t\t\t18\t\t\t\t\t\t1.17\tN\n+4944\t2\tchr1\t252088\t252109\tno-call\tcomplex\t=\t?\t?\t\t\t\t\t\t\t\t\t\t\t-336\t\t\t\t\t\t1.17\tN\n+4945\t2\tchr1\t252109\t252178\thom\tref\t=\t=\t=\t\t\t\t\t\t\t\t\t\t\t41\t\t\t\t\t\t1.17\tN\n+4946\t2\tchr1\t252178\t252208\tno-call\tcomplex\t=\t?\t?\t\t\t\t\t\t\t\t\t\t\t-173\t\t\t\t\t\t1.17\tN\n+4947\t2\tchr1\t252208\t252288\thom\tref\t=\t=\t=\t\t\t\t\t\t\t\t\t\t\t-16\t\t\t\t\t\t1.17\tN\n+4948\t2\tchr1\t252288\t252306\tno-call\tcomplex\t=\t?\t?\t\t\t\t\t\t\t\t\t\t\t-65\t\t\t\t\t\t1.17\tN\n+4949\t2\tchr1\t252306\t252329\thom\tref\t=\t=\t=\t\t\t\t\t\t\t\t\t\t\t14\t\t\t\t\t\t1.17\tN\n+4950\t2\tchr1\t252329\t252374\tno-call\tcomplex\t=\t?\t?\t\t\t\t\t\t\t\t\t\t\t-323\t\t\t\t\t\t1.17\tN\n+4951\t2\tchr1\t252374\t252468\thom\tref\t=\t=\t=\t\t\t\t\t\t\t\t\t\t\t0\t\t\t\t\t\t1.17\tN\n+4952\t2\tchr1\t252468\t252482\tno-call\tcomplex\t=\t?\t?\t\t\t\t\t\t\t\t\t\t\t-203\t\t\t\t\t\t1.17\tN\n+4953\t2\tchr1\t252482\t252635\thom\tref\t=\t=\t=\t\t\t\t\t\t\t\t\t\t\t23\t\t\t\t\t\t1.17\tN\n+4954\t2\tchr1\t252635\t252662\tno-call\tcomplex\t=\t?\t?\t\t\t\t\t\t\t\t\t\t\t-295\t\t\t\t\t\t1.17\tN\n+4955\t2\tchr1\t252662\t252675\thom\tref\t=\t=\t=\t\t\t\t\t\t\t\t\t\t\t38\t\t\t\t\t\t1.17\tN\n+4956\t2\tchr1\t252675\t252682\tno-call\tcomplex\t=\t?\t?\t\t\t\t\t\t\t\t\t\t\t-13\t\t\t\t\t\t1.17\tN\n+4957\t2\tchr1\t252682\t252721\thom\tref\t=\t=\t=\t\t\t\t\t\t\t\t\t\t\t11\t\t\t\t\t\t1.17\tN\n+4958\t2\tchr1\t252721\t252752\tno-call\tcomplex\t=\t?\t?\t\t\t\t\t\t\t\t\t\t\t-257\t\t\t\t\t\t1.17\tN\n+4959\t2\tchr1\t252752\t252792\thom\tref\t=\t=\t=\t\t\t\t\t\t\t\t\t\t\t31\t\t\t\t\t\t1.17\tN\n+4960\t2\tchr1\t252792\t252806\tno-call\tcomplex\t=\t?\t?\t\t\t\t\t\t\t\t\t\t\t-362\t\t\t\t\t\t1.17\tN\n+4961\t2\tchr1\t252806\t252849\thom\tref\t=\t=\t=\t\t\t\t\t\t\t\t\t\t\t31\t\t\t\t\t\t1.17\tN\n+4962\t2\tchr1\t252849\t252882\tno-call\tcomplex\t=\t?\t?\t\t\t\t\t\t\t\t\t\t\t-193\t\t\t\t\t\t1.17\tN\n+4963\t2\tchr1\t252882\t252915\thom\tref\t=\t=\t=\t\t\t\t\t\t\t\t\t\t\t-60\t\t\t\t\t\t1.17\tN\n+4964\t2\tchr1\t252915\t252915\thalf\tref\t\t\t?\t61\t0\t\t\t\t\t\t\t\t\t-59\t\t\t\t\t10\t1.17\tN\n+4965\t2\tchr1\t252915\t252952\thom\tref\t=\t=\t=\t\t\t\t\t\t\t\t\t\t\t-59\t\t\t\t\t\t1.17\tN\n+4966\t2\tchr1\t252952\t252991\tno-call\tcomplex\t=\t?\t?\t\t\t\t\t\t\t\t\t\t\t-373\t\t\t\t\t\t1.17\tN\n+4967\t2\tchr1\t252991\t253167\thom\tref\t=\t=\t=\t\t\t\t\t\t\t\t\t\t\t18\t\t\t\t\t\t1.17\tN\n+4968\t2\tchr1\t253167\t253203\tno-call\tcomplex\t=\t?\t?\t\t\t\t\t\t\t\t\t\t\t-108\t\t\t\t\t\t1.17\tN\n+4969\t2\tchr1\t253203\t253224\thom\tref\t=\t=\t=\t\t\t\t\t\t\t\t\t\t\t73\t\t\t\t\t\t1.17\tN\n+4970\t2\tchr1\t253224\t253270\tno-call\tcomplex\t=\t?\t?\t\t\t\t\t\t\t\t\t\t\t-1017\t\t\t\t\t\t1.17\tN\n+4971\t2\tchr1\t253270\t253281\thom\tref\t=\t=\t=\t\t\t\t\t\t\t\t\t\t\t51\t\t\t\t\t\t1.17\tN\n+4972\t2\tchr1\t253281\t253288\tno-call\tcomplex\t=\t?\t?\t\t\t\t\t\t\t\t\t\t\t-32\t\t\t\t\t\t1.17\tN\n+4973\t2\tchr1\t253288\t253470\thom\tref\t=\t=\t=\t\t\t\t\t\t\t\t\t\t\t-37\t\t\t\t\t\t1.17\tN\n+4974\t2\tchr1\t253470\t253471\thalf\tref\tC\tC\tN\t76\t120\t\t\t\t\t\t\t\t\t35\t\t\t\t\t10\t1.17\tN\n+4975\t2\tchr1\t253471\t253546\thom\tref\t=\t=\t=\t\t\t\t\t\t\t\t\t\t\t35\t\t\t\t\t\t1.17\tN\n+4976\t2\tchr1\t253546\t253590\tno-call\tcomplex\t=\t?\t?\t\t\t\t\t\t\t\t\t\t\t-235\t\t\t\t\t\t1.17\tN\n+4977\t2\tchr1\t253590\t253663\thom\tref\t=\t=\t=\t\t\t\t\t\t\t\t\t\t\t52\t\t\t\t\t\t1.17\tN\n+4978\t2\tchr1\t253663\t253670\tno-call\tcomplex\t=\t?\t?\t\t\t\t\t\t\t\t\t\t\t-287\t\t\t\t\t\t1.17\tN\n+4979\t2\tchr1\t253670\t253775\thom\tref\t=\t=\t=\t\t\t\t\t\t\t\t\t\t\t23\t\t\t\t\t\t1.17\tN\n+4980\t2\tchr1\t253775\t253782\tno-call\tcomplex\t=\t?\t?\t\t\t\t\t\t\t\t\t\t\t-207\t\t\t\t\t\t1.17\tN\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/masterVar_output.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/masterVar_output.txt Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,27 @@
+chr1 41980 41981 G 1 1 76
+chr1 51672 51673 C 1 1 53
+chr1 52237 52238 G 1 7 63
+chr1 53205 53206 C/G 2 7,30 93,127
+chr1 54042 54043 T/C 2 3,10 66,84
+chr1 54585 54586 C/T 2 9,19 94,94
+chr1 55163 55164 A 1 9 76
+chr1 55301 55302 T/C 2 15,19 87,95
+chr1 55321 55322 T/C 2 12,12 95,95
+chr1 55325 55326 C/T 2 12,11 95,95
+chr1 55925 55926 C 1 12 66
+chr1 57951 57952 C 1 2 72
+chr1 58210 58211 G 1 11 98
+chr1 59050 59051 G/A 2 6,21 66,91
+chr1 59343 59344 T/C 2 25,23 57,120
+chr1 59497 59498 C/T 2 12,15 74,120
+chr1 60828 60829 T/C 2 1,11 60,97
+chr1 61441 61442 G 1 8 23
+chr1 68305 68306 T/C 2 27,20 44,44
+chr1 68315 68316 C/T 2 27,20 44,44
+chr1 69452 69453 A/G 2 6,37 61,121
+chr1 69510 69511 G 1 3 123
+chr1 69551 69552 C/G 2 4,27 98,98
+chr1 69568 69569 C/T 2 3,29 98,98
+chr1 77461 77462 A 1 4 26
+chr1 82733 82734 C/T 2 18,17 42,118
+chr1 233472 233473 G/C 2 21,42 118,118

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/matrix_generator_for_pc_and_lda_input_1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/matrix_generator_for_pc_and_lda_input_1.tabular Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,88 @@\n+\tCTCAGAAAAAAA \tCCATCCATCCATCCATCC \tAGAGGGAGAGGG \tATCTGTTGATGG \tAGGGGTGACAGA \tATCCCATTTACA \tAAGGGTATCAGT \tATAATATATACA \tTATTATATGTATA \tCATCATCATCATCA \tCCCCATGATCCA \tTGATTCCTTAAAGAA \tAACACTTGGACA \tTATTAATATAATTTATAAA \tATGTTTATTTTA \tTATCCAGGAGAA \tCAATTCTCCTGCC \tACCATAAAAATGAGAAC \tCTCAGCCATAAAAA \tATGAGTGAGAATAT \tACTGTGAGTCAA \tTAAACTAAAGAGCTTCTGCACAGCA \tTCCTTTGGGTATAT \tATGCTGCTATAAAGACACATGCACAC \tTGCTGGAGAGGATGTGGAGAAATAGGAACACTTTTACACTG \tTCCACAATGGTTGAA \tTTGGCTGCATAAAT \tCAATGGAACAGAACAGAGCCCTCAGAAATAA \tGAACTAGAAATACCATTTGACCCAGC \tTCAAAGATCAGAT \tGACCCATCTCACACCAGTTAGAATG \tCAAAGAGAATAAAATACCTAGGTATTTTATTCTTTTT \tAAAATGGCCATACTGCCCAAG \tAAATTTTTCCAATTCTGTGAAGAAA \tTTCACAATAGCAAAGAC \tTAGGAAGAATCAATA \tCTGGGTATATACCCAGTAATGG \tTTGGAAGTTCTGGCCAGGGCAA \tTGAAGGACCTCTTCAAGGAGAACTACAAACCACTGCTCAA \tCTCTCACCACTCCTATTCAACATA \tACACACACATAT \tCCATGAGCATGGAATGTTCT \tAACCCAAATGTCC \tTTTACAAGAAAAAAACAAACAACCCCA \tAGTTCTAGATCC \tCTGGAAGCATTCCCTTT \tGATCCCATTTGTC \tGATATGAACAGACA \tTGGGTTTGTCATA \tAGTTTCTTTTGC \tAATTACCCAGTCT \tTCATGTCATCTGCAAACA \tAAAACTCTCAAT \tCAACTTCAGCAA \tATTGGCTGTGGGTTT \tAATTAGATCCCA \tGACCTAAAACCA \tAGAATCTACAAT \tAAACCAAACACC \tGGAGTTCCAGACCAGCCT \tCCTTGCCCATGCC \tATCATACTGAAT \tAGGAAGTCAAATT \tAGCAAACCACCA \tAGCATGATTTATA \tGAGAGCCAAATCATGAGTG \tAAAGAGCCAAAT \tAGCAATTGTGAATGG \tCACTATTCACAATTGC \tTCAGGATACAAAATCAATG \tCAATGAACTCAAACAAATT \tTCCAACAAAGGACATGAACTCATC \tAATTGAACAATGAGAACATGTGGTAT \tAACCACAATGAGAACA \tGTGTATATATATACAT \tACATATATATAT \tGTCAGATGGATA \tTCATCTGACAAAGGGCTAATATCCAG \tTTTGTCAGGTTTGTCAAAG \tTTCTTAATCCAGTCTATCATT \tTTTAATCCATCTTGA \tAAACTACCATCAGAGTGAACAGGCA \tGCCATCAGAGAAAT \tACAGGCAACCTACA \tGCAACCTACTCA \tTAGAAAACCCCAT \n+ARHGEF9 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diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/matrix_generator_for_pc_and_lda_input_2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/matrix_generator_for_pc_and_lda_input_2.tabular Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,87 @@
+ARHGEF9 XLMR
+KIAA2022 XLMR
+ZDHHC15 XLMR
+PGK1 XLMR
+BRWD3 XLMR
+PAK3 XLMR
+AGTR2 XLMR
+GRIA3 XLMR
+ZDHHC9 XLMR
+GPC3 XLMR
+PHF6 XLMR
+SOX3 XLMR
+FMR1 XLMR
+MTM1 XLMR
+SHROOM4 XLMR
+KLF8 XLMR
+UXT XLMR
+PCSK1N XLMR
+PAGE1 XLMR
+PAGE4 XLMR
+CLCN5 XLMR
+NUDT10 XLMR
+NUDT11 XLMR
+GSPT2 XLMR
+TMEM29 XLMR
+GPR173 XLMR
+HUWE1 XLMR
+TSR2 XLMR
+TRO XLMR
+MAGEH1 XLMR
+USP51 XLMR
+RRAGB XLMR
+UBQLN2 CONTROL
+SPIN3 CONTROL
+SPIN2A CONTROL
+ZXDA CONTROL
+SPIN4 CONTROL
+MTMR8 CONTROL
+KIAA1166 CONTROL
+LAS1L CONTROL
+MSN CONTROL
+HEPH CONTROL
+AR CONTROL
+STARD8 CONTROL
+TMEM28 CONTROL
+EDA CONTROL
+SLC7A3 CONTROL
+CXCR3 CONTROL
+NAP1L2 CONTROL
+CHIC1 CONTROL
+FXYD8 CONTROL
+RNF12 CONTROL
+UPRT CONTROL
+MAGEE2 CONTROL
+CXorf26 CONTROL
+MAGEE1 CONTROL
+FGF16 CONTROL
+TAF9B CONTROL
+CYSLTR1 CONTROL
+ZCCHC5 CONTROL
+GPR23 CONTROL
+P2RY10 CONTROL
+ITM2A CONTROL
+TBX22 CONTROL
+NSBP1 CONTROL
+RPS6KA6 CONTROL
+HDX CONTROL
+APOOL CONTROL
+ZNF711 CONTROL
+POF1B CONTROL
+CHM CONTROL
+DACH2 CONTROL
+KLHL4 CONTROL
+CPXCR1 CONTROL
+PABPC5 CONTROL
+DIAPH2 CONTROL
+SYTL4 CONTROL
+CSTF2 CONTROL
+DRP2 CONTROL
+TCEAL2 CONTROL
+BEX5 CONTROL
+NXF3 CONTROL
+BEX4 CONTROL
+TCEAL4 CONTROL
+ESX1 CONTROL
+IL1RAPL2 CONTROL
+NRK CONTROL

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/matrix_generator_for_pc_and_lda_output.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/matrix_generator_for_pc_and_lda_output.tabular Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,88 @@\n+ \tAGTR2 \tARHGEF9 \tBRWD3 \tCLCN5 \tFMR1 \tGPC3 \tGPR173 \tGRIA3 \tGSPT2 \tHUWE1 \tKIAA2022 \tKLF8 \tMAGEH1 \tMTM1 \tNUDT10 \tNUDT11 \tPAGE1 \tPAGE4 \tPAK3 \tPCSK1N \tPGK1 \tPHF6 \tRRAGB \tSHROOM4 \tSOX3 \tTMEM29 \tTRO \tTSR2 \tUSP51 \tUXT \tZDHHC15 \tZDHHC9 \tX(SUM) \tAPOOL \tAR \tBEX4 \tBEX5 \tCHIC1 \tCHM \tCPXCR1 \tCSTF2 \tCXCR3 \tCXorf26 \tCYSLTR1 \tDACH2 \tDIAPH2 \tDRP2 \tEDA \tESX1 \tFGF16 \tFXYD8 \tGPR23 \tHDX \tHEPH \tIL1RAPL2 \tITM2A \tKIAA1166 \tKLHL4 \tLAS1L \tMAGEE1 \tMAGEE2 \tMSN \tMTMR8 \tNAP1L2 \tNRK \tNSBP1 \tNXF3 \tP2RY10 \tPABPC5 \tPOF1B \tRNF12 \tRPS6KA6 \tSLC7A3 \tSPIN2A \tSPIN3 \tSPIN4 \tSTARD8 \tSYTL4 \tTAF9B \tTBX22 \tTCEAL2 \tTCEAL4 \tTMEM28 \tUBQLN2 \tUPRT \tZCCHC5 \tZNF711 \tZXDA \tY(SUM) \t\n+CTCAGAAAAAAA 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\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t2\t1\t0\t0\t0\t0\t0\t0\t0\t0\t1\t1\t0\t0\t0\t2\t0\t0\t1\t0\t0\t3\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t12\tEOL\n+AACCACAATGAGAACA \t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t1\t4\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t3\tEOL\n+GTGTATATATATACAT \t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t1\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t3\tEOL\n+ACATATATATAT \t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t5\tEOL\n+GTCAGATGGATA \t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t1\t0\t0\t0\t1\t0\t0\t0\t0\t0\t1\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t3\t1\t0\t0\t0\t0\t0\t0\t1\t0\t0\t10\tEOL\n+TCATCTGACAAAGGGCTAATATCCAG \t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t3\tEOL\n+TTTGTCAGGTTTGTCAAAG \t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\tEOL\n+TTCTTAATCCAGTCTATCATT \t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t1\t0\t0\t0\t0\t0\t0\t0\t0\t2\t0\t0\t0\t0\t0\t0\t0\t1\t0\t1\t1\t0\t0\t0\t1\t0\t1\t3\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t1\t0\t0\t0\t0\t0\t0\t3\t0\t0\t15\tEOL\n+TTTAATCCATCTTGA \t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t2\t0\t0\t0\t0\t0\t0\t1\t0\t0\t3\t1\t0\t0\t0\t3\t0\t0\t1\t0\t0\t0\t0\t3\t0\t0\t0\t0\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t2\t0\t0\t0\t0\t0\t0\t4\t0\t0\t20\tEOL\n+AAACTACCATCAGAGTGAACAGGCA \t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t2\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t5\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t1\t0\t0\t0\t1\t0\t1\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t1\t0\t0\t8\tEOL\n+GCCATCAGAGAAAT \t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t3\t1\t0\t0\t0\t0\t0\t0\t1\t0\t0\t8\tEOL\n+ACAGGCAACCTACA \t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t2\t0\t0\t0\t0\t0\t0\t0\t1\t4\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t2\t0\t0\t7\tEOL\n+GCAACCTACTCA \t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t7\tEOL\n+TAGAAAACCCCAT \t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t1\t0\t0\t3\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t1\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t2\t0\t0\t8\tEOL\n+ \tX \tX \tX \tX \tX \tX \tX \tX \tX \tX \tX \tX \tX \tX \tX \tX \tX \tX \tX \tX \tX \tX \tX \tX \tX \tX \tX \tX \tX \tX \tX \tX \t \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \tY \t \t\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/megablast_wrapper_test1.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/megablast_wrapper_test1.fa Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,40 @@
+>0_0.666667
+GAGTTTTATCGCTTCCATGACGCAGAAGTT
+>1_0.600000
+AACACTTTCGGATATTTCTGATGAGTCGAA
+>2_0.400000
+AGCAGGAATTACTACTGCTTGTTTACGAAT
+>3_0.566667
+TAAATCGAAGTGGACTGCTGGCGGAAAATG
+>4_0.766667
+TCCTTGCGCAGCTCGAGAAGCTCTTACTTT
+>5_0.533333
+GCGACCTTTCGCCATCAACTAACGATTCTG
+>6_0.533333
+TTGGATGAGGAGAAGTGGCTTAATATGCTT
+>7_0.400000
+GGCACGTTCGTCAAGGACTGGTTTAGATAT
+>8_0.500000
+CATGGTAGAGATTCTCTTGTTGACATTTTA
+>9_0.400000
+AAAGAGCGTGGATTACTATCTGAGTCCGAT
+>10_0.500000
+ATAGGTAAGAAATCATGAGTCAAGTTACTG
+>11_0.533333
+AACAATCCGTACGTTTCCAGACCGCTTTGG
+>12_0.700000
+TTCAGGCTTCTGCCGTTTTGGATTTAACCG
+>13_0.533333
+AAGATGATTTCGATTTTCTGACGAGTAACA
+>14_0.666667
+CTGACCGCTCTCGTGCTCGTCGCTGCGTTG
+>15_0.666667
+AGGCTTGCGTTTATGGTACGCTGGACTTTG
+>16_0.566667
+TTCCTGCTCCTGTTGAGTTTATTGCTGCCG
+>17_0.533333
+TCATTGCTTATTATGTTCATCCCGTCAACA
+>18_0.566667
+TCATCATGGAAGGCGCTGAATTTACGGAAA
+>19_0.566667
+ACATTATTAATGGCGTCGAGCGTCCGGTTA
\ No newline at end of file

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/megablast_wrapper_test1.out
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/megablast_wrapper_test1.out Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,20 @@
+0_0.666667 phiX174 5386 100.00 30 0 0 1 30 1 30 1e-13 60.0
+1_0.600000 phiX174 5386 100.00 30 0 0 1 30 31 60 1e-13 60.0
+2_0.400000 phiX174 5386 100.00 30 0 0 1 30 76 105 1e-13 60.0
+3_0.566667 phiX174 5386 100.00 30 0 0 1 30 106 135 1e-13 60.0
+4_0.766667 phiX174 5386 100.00 30 0 0 1 30 151 180 1e-13 60.0
+5_0.533333 phiX174 5386 100.00 30 0 0 1 30 181 210 1e-13 60.0
+6_0.533333 phiX174 5386 100.00 30 0 0 1 30 226 255 1e-13 60.0
+7_0.400000 phiX174 5386 100.00 30 0 0 1 30 256 285 1e-13 60.0
+8_0.500000 phiX174 5386 100.00 30 0 0 1 30 301 330 1e-13 60.0
+9_0.400000 phiX174 5386 100.00 30 0 0 1 30 331 360 1e-13 60.0
+10_0.500000 phiX174 5386 100.00 30 0 0 1 30 376 405 1e-13 60.0
+11_0.533333 phiX174 5386 100.00 30 0 0 1 30 406 435 1e-13 60.0
+12_0.700000 phiX174 5386 100.00 30 0 0 1 30 451 480 1e-13 60.0
+13_0.533333 phiX174 5386 100.00 30 0 0 1 30 481 510 1e-13 60.0
+14_0.666667 phiX174 5386 100.00 30 0 0 1 30 526 555 1e-13 60.0
+15_0.666667 phiX174 5386 100.00 30 0 0 1 30 556 585 1e-13 60.0
+16_0.566667 phiX174 5386 100.00 30 0 0 1 30 601 630 1e-13 60.0
+17_0.533333 phiX174 5386 100.00 30 0 0 1 30 631 660 1e-13 60.0
+18_0.566667 phiX174 5386 100.00 30 0 0 1 30 676 705 1e-13 60.0
+19_0.566667 phiX174 5386 100.00 30 0 0 1 30 706 735 1e-13 60.0

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/megablast_xml_parser_test1.gz

Binary file rnaseq/cutadapt/test-data/megablast_xml_parser_test1.gz has changed

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/megablast_xml_parser_test1_out.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/megablast_xml_parser_test1_out.tabular Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,103 @@\n+0_0.666667\t30\tgnl|BL_ORD_ID|0\t5528445\t59.96\t8.38112e-11\t1\t30\t5436010\t5436039\t1\t1\t30\t30\tCGGACAGCGCCGCCACCAACAAAGCCACCA\tCGGACAGCGCCGCCACCAACAAAGCCACCA\t||||||||||||||||||||||||||||||\n+1_0.600000\t30\tgnl|BL_ORD_ID|0\t5528445\t59.96\t8.38112e-11\t1\t30\t696993\t697022\t1\t1\t30\t30\tAAAACACCGGATGCTCCGGCGCTGGCAGAT\tAAAACACCGGATGCTCCGGCGCTGGCAGAT\t||||||||||||||||||||||||||||||\n+2_0.400000\t30\tgnl|BL_ORD_ID|0\t5528445\t59.96\t8.38112e-11\t1\t30\t4100018\t4100047\t1\t1\t30\t30\tTTTGCTTTTAGTACACCGGATTCAGAACCA\tTTTGCTTTTAGTACACCGGATTCAGAACCA\t||||||||||||||||||||||||||||||\n+3_0.566667\t30\tgnl|BL_ORD_ID|0\t5528445\t59.96\t8.38112e-11\t30\t1\t2305844\t2305873\t1\t-1\t30\t30\tCCGTCCAGAAAGGTGTATTCATGGGGACGG\tCCGTCCAGAAAGGTGTATTCATGGGGACGG\t||||||||||||||||||||||||||||||\n+4_0.766667\t30\tgnl|BL_ORD_ID|0\t5528445\t59.96\t8.38112e-11\t1\t30\t3457901\t3457930\t1\t1\t30\t30\tCACGCTACGTGCGCCCCCGCCCAGAAGGCG\tCACGCTACGTGCGCCCCCGCCCAGAAGGCG\t||||||||||||||||||||||||||||||\n+5_0.533333\t30\tgnl|BL_ORD_ID|0\t5528445\t59.96\t8.38112e-11\t30\t1\t1264131\t1264160\t1\t-1\t30\t30\tGCACTTAACCCGCTTCGGCGGGTTTTGTTT\tGCACTTAACCCGCTTCGGCGGGTTTTGTTT\t||||||||||||||||||||||||||||||\n+5_0.533333\t30\tgnl|BL_ORD_ID|0\t5528445\t59.96\t8.38112e-11\t30\t1\t1636485\t1636514\t1\t-1\t30\t30\tGCACTTAACCCGCTTCGGCGGGTTTTGTTT\tGCACTTAACCCGCTTCGGCGGGTTTTGTTT\t||||||||||||||||||||||||||||||\n+5_0.533333\t30\tgnl|BL_ORD_ID|0\t5528445\t59.96\t8.38112e-11\t1\t30\t2318694\t2318723\t1\t1\t30\t30\tAAACAAAACCCGCCGAAGCGGGTTAAGTGC\tAAACAAAACCCGCCGAAGCGGGTTAAGTGC\t||||||||||||||||||||||||||||||\n+5_0.533333\t30\tgnl|BL_ORD_ID|0\t5528445\t59.96\t8.38112e-11\t1\t30\t2777043\t2777072\t1\t1\t30\t30\tAAACAAAACCCGCCGAAGCGGGTTAAGTGC\tAAACAAAACCCGCCGAAGCGGGTTAAGTGC\t||||||||||||||||||||||||||||||\n+6_0.533333\t30\tgnl|BL_ORD_ID|0\t5528445\t59.96\t8.38112e-11\t1\t30\t1185124\t1185153\t1\t1\t30\t30\tTAAGCCGTTACTGGCAGCAAGTGCAGGCAA\tTAAGCCGTTACTGGCAGCAAGTGCAGGCAA\t||||||||||||||||||||||||||||||\n+7_0.400000\t30\tgnl|BL_ORD_ID|0\t5528445\t59.96\t8.38112e-11\t1\t30\t2458203\t2458232\t1\t1\t30\t30\tTGAATTTACCGTTATCTATCTTGCCTGCCT\tTGAATTTACCGTTATCTATCTTGCCTGCCT\t||||||||||||||||||||||||||||||\n+9_0.400000\t30\tgnl|BL_ORD_ID|0\t5528445\t59.96\t8.38112e-11\t1\t30\t5286666\t5286695\t1\t1\t30\t30\tGCGTTTTGCTAAACTTCTGCCGGAATATAA\tGCGTTTTGCTAAACTTCTGCCGGAATATAA\t||||||||||||||||||||||||||||||\n+10_0.500000\t30\tgnl|BL_ORD_ID|0\t5528445\t59.96\t8.38112e-11\t1\t30\t2787672\t2787701\t1\t1\t30\t30\tAAAGAGGCGAGCAGAGTAAAACGCAGGCAA\tAAAGAGGCGAGCAGAGTAAAACGCAGGCAA\t||||||||||||||||||||||||||||||\n+12_0.700000\t30\tgnl|BL_ORD_ID|0\t5528445\t59.96\t8.38112e-11\t1\t30\t4116145\t4116174\t1\t1\t30\t30\tGCGGACGATCTTCACGGTCGCCACGCGGAC\tGCGGACGATCTTCACGGTCGCCACGCGGAC\t||||||||||||||||||||||||||||||\n+13_0.533333\t30\tgnl|BL_ORD_ID|0\t5528445\t59.96\t8.38112e-11\t1\t30\t5442351\t5442380\t1\t1\t30\t30\tTTCTTGTTGGATGGCATACTCCGGCAGCCA\tTTCTTGTTGGATGGCATACTCCGGCAGCCA\t||||||||||||||||||||||||||||||\n+14_0.666667\t30\tgnl|BL_ORD_ID|0\t5528445\t59.96\t8.38112e-11\t1\t30\t4626492\t4626521\t1\t1\t30\t30\tACCCCGATATCGTCGCAGGCGTTGCCGCAC\tACCCCGATATCGTCGCAGGCGTTGCCGCAC\t||||||||||||||||||||||||||||||\n+15_0.666667\t30\tgnl|BL_ORD_ID|0\t5528445\t59.96\t8.38112e-11\t1\t30\t346897\t346926\t1\t1\t30\t30\tGGCTGCTGTCTCCGCTGGAAGAGGCGCTTC\tGGCTGCTGTCTCCGCTGGAAGAGGCGCTTC\t||||||||||||||||||||||||||||||\n+15_0.666667\t30\tgnl|BL_ORD_ID|0\t5528445\t59.96\t8.38112e-11\t30\t1\t1466536\t1466565\t1\t-1\t30\t30\tGAAGCGCCTCTTCCAGCGGAGACAGCAGCC\tGAAGCGCCTCTTCCAGCGGAGACAGCAGCC\t||||||||||||||||||||||||||||||\n+15_0.666667\t30\tgnl|BL_ORD_ID|0\t5528445\t59.96\t8.38112e-11\t1\t30\t1750132\t1750161\t1\t1\t30\t30\tGGCTGCTGTCTCCGCTGGAAGAGGCGCTTC\tGGCTGCTGTCTCCGCTGGAAGAGGCGCTTC\t||||||||||||||||||||||||||||||\n+15_0.666667\t30\tgnl|BL_ORD_ID|0\t5528445\t59.96\t8.38112e-11\t1\t30\t1908046\t1908075\t1\t1\t30\t30\tGGCTGCTGTCTCCGCTGGAAGAGGCGCTTC\tGGCTGCTGTCTCCGCTGGAAGAGGCGCTTC\t||||||||||||||||||||||||||||||\n+15_0.666667\t30\tgnl|BL_ORD_ID|0\t5528445\t59.96\t8.38112e-11\t1\t30\t2279107\t2279136\t1\t1\t30\t30\tGGCTGCTGTCTCCGCTGGAAGAGGCGCTTC\tGGCTGCTGTCTCCGCTGGAAGAGGCGCTTC\t||||||||||||||||||||||||||||||\n+15_0.666667\t30\tgnl|BL_ORD_ID|0\t5528445\t59.96\t8.38112e-11\t1\t30\t2813407\t2813436\t1\t1\t30\t30\tGGCTGCTGTCTCCGCTGGAAGAGGCGCTTC\tGGCTGCTGTCTCCGCTGGAAGAGGCGCTTC\t||||||||||||||||||||'..b'||||\n+70_0.466667\t30\tgnl|BL_ORD_ID|0\t5528445\t59.96\t8.38112e-11\t1\t30\t1317239\t1317268\t1\t1\t30\t30\tTGGTGTTCAGCATCTCAACGGTAATTCGCT\tTGGTGTTCAGCATCTCAACGGTAATTCGCT\t||||||||||||||||||||||||||||||\n+71_0.533333\t30\tgnl|BL_ORD_ID|0\t5528445\t59.96\t8.38112e-11\t1\t30\t5080463\t5080492\t1\t1\t30\t30\tCAGGATGCAAACTGCCGGGAGATCCAGTTA\tCAGGATGCAAACTGCCGGGAGATCCAGTTA\t||||||||||||||||||||||||||||||\n+72_0.533333\t30\tgnl|BL_ORD_ID|0\t5528445\t59.96\t8.38112e-11\t1\t30\t3605409\t3605438\t1\t1\t30\t30\tAACTGGAAGGGCTTGGGATGACACAACAGC\tAACTGGAAGGGCTTGGGATGACACAACAGC\t||||||||||||||||||||||||||||||\n+73_0.500000\t30\tgnl|BL_ORD_ID|0\t5528445\t59.96\t8.38112e-11\t1\t30\t3280815\t3280844\t1\t1\t30\t30\tTTTAAGCGCCAACCAGGCTTCTTTGGTTGC\tTTTAAGCGCCAACCAGGCTTCTTTGGTTGC\t||||||||||||||||||||||||||||||\n+75_0.533333\t30\tgnl|BL_ORD_ID|0\t5528445\t59.96\t8.38112e-11\t1\t30\t2230266\t2230295\t1\t1\t30\t30\tATAACCCTCTGCAACCGCCGCTTCAGCAAA\tATAACCCTCTGCAACCGCCGCTTCAGCAAA\t||||||||||||||||||||||||||||||\n+76_0.600000\t30\tgnl|BL_ORD_ID|0\t5528445\t59.96\t8.38112e-11\t1\t30\t462631\t462660\t1\t1\t30\t30\tTGAAGCCGTACAACGGGCGCTGGAATTCGC\tTGAAGCCGTACAACGGGCGCTGGAATTCGC\t||||||||||||||||||||||||||||||\n+77_0.700000\t30\tgnl|BL_ORD_ID|0\t5528445\t59.96\t8.38112e-11\t1\t30\t2939076\t2939105\t1\t1\t30\t30\tGAGCTGCAACGCGGTCAGCCAGCTGGCGGT\tGAGCTGCAACGCGGTCAGCCAGCTGGCGGT\t||||||||||||||||||||||||||||||\n+78_0.566667\t30\tgnl|BL_ORD_ID|0\t5528445\t59.96\t8.38112e-11\t1\t30\t5422053\t5422082\t1\t1\t30\t30\tCGGAGTATCCGTTCCCCAACGACAAGCATC\tCGGAGTATCCGTTCCCCAACGACAAGCATC\t||||||||||||||||||||||||||||||\n+79_0.500000\t30\tgnl|BL_ORD_ID|0\t5528445\t59.96\t8.38112e-11\t1\t30\t4387420\t4387449\t1\t1\t30\t30\tAATACCGGGAAGAGACAACGGGGTCTCTTT\tAATACCGGGAAGAGACAACGGGGTCTCTTT\t||||||||||||||||||||||||||||||\n+81_0.433333\t30\tgnl|BL_ORD_ID|0\t5528445\t59.96\t8.38112e-11\t1\t30\t1037150\t1037179\t1\t1\t30\t30\tATTAATGTTGCCGGCACAACATAATAGGGC\tATTAATGTTGCCGGCACAACATAATAGGGC\t||||||||||||||||||||||||||||||\n+82_0.500000\t30\tgnl|BL_ORD_ID|0\t5528445\t59.96\t8.38112e-11\t1\t30\t1182188\t1182217\t1\t1\t30\t30\tACTGGGTTGCTCTGAACAAGAAAGGCGCTA\tACTGGGTTGCTCTGAACAAGAAAGGCGCTA\t||||||||||||||||||||||||||||||\n+83_0.533333\t30\tgnl|BL_ORD_ID|0\t5528445\t59.96\t8.38112e-11\t1\t30\t5430210\t5430239\t1\t1\t30\t30\tCGCCAGGGACGTATCGCGTCGATATCTATT\tCGCCAGGGACGTATCGCGTCGATATCTATT\t||||||||||||||||||||||||||||||\n+84_0.533333\t30\tgnl|BL_ORD_ID|0\t5528445\t59.96\t8.38112e-11\t1\t30\t310995\t311024\t1\t1\t30\t30\tTGCTCGTTCCCGTCGTGATGAAGCTCGAAA\tTGCTCGTTCCCGTCGTGATGAAGCTCGAAA\t||||||||||||||||||||||||||||||\n+85_0.500000\t30\tgnl|BL_ORD_ID|0\t5528445\t59.96\t8.38112e-11\t1\t30\t4174173\t4174202\t1\t1\t30\t30\tAGGAAAGCAAACAACACGACCACCATCAGC\tAGGAAAGCAAACAACACGACCACCATCAGC\t||||||||||||||||||||||||||||||\n+86_0.566667\t30\tgnl|BL_ORD_ID|0\t5528445\t59.96\t8.38112e-11\t1\t30\t163690\t163719\t1\t1\t30\t30\tGGCAACGCAGGCGCATGATTCTGCTTGGAA\tGGCAACGCAGGCGCATGATTCTGCTTGGAA\t||||||||||||||||||||||||||||||\n+88_0.533333\t30\tgnl|BL_ORD_ID|0\t5528445\t59.96\t8.38112e-11\t1\t30\t3071785\t3071814\t1\t1\t30\t30\tCGTACCGGGCTGAAAGTAGAAGAGCGTTTC\tCGTACCGGGCTGAAAGTAGAAGAGCGTTTC\t||||||||||||||||||||||||||||||\n+90_0.466667\t30\tgnl|BL_ORD_ID|0\t5528445\t59.96\t8.38112e-11\t1\t30\t692131\t692160\t1\t1\t30\t30\tATCACCGTTTCGCTAACCGGTACGTTTAAC\tATCACCGTTTCGCTAACCGGTACGTTTAAC\t||||||||||||||||||||||||||||||\n+91_0.566667\t30\tgnl|BL_ORD_ID|0\t5528445\t59.96\t8.38112e-11\t1\t30\t3307050\t3307079\t1\t1\t30\t30\tTTCGCCCGGCAAGCTTACCCAACGCTTATC\tTTCGCCCGGCAAGCTTACCCAACGCTTATC\t||||||||||||||||||||||||||||||\n+94_0.466667\t30\tgnl|BL_ORD_ID|0\t5528445\t59.96\t8.38112e-11\t1\t30\t1813009\t1813038\t1\t1\t30\t30\tCCACGGTGATATCTGGTGCCATACTGATAA\tCCACGGTGATATCTGGTGCCATACTGATAA\t||||||||||||||||||||||||||||||\n+96_0.533333\t30\tgnl|BL_ORD_ID|0\t5528445\t59.96\t8.38112e-11\t1\t30\t573782\t573811\t1\t1\t30\t30\tTTGCCGGGAAGAGAGATATCAATGGCAGGC\tTTGCCGGGAAGAGAGATATCAATGGCAGGC\t||||||||||||||||||||||||||||||\n+97_0.566667\t30\tgnl|BL_ORD_ID|0\t5528445\t59.96\t8.38112e-11\t1\t30\t3570563\t3570592\t1\t1\t30\t30\tTGCGCCGCCGGATTGTTGCTCAACATGCTT\tTGCGCCGCCGGATTGTTGCTCAACATGCTT\t||||||||||||||||||||||||||||||\n+98_0.366667\t30\tgnl|BL_ORD_ID|0\t5528445\t59.96\t8.38112e-11\t1\t30\t4545136\t4545165\t1\t1\t30\t30\tAACGCGCTAACCGCCAATAATAACAAAATT\tAACGCGCTAACCGCCAATAATAACAAAATT\t||||||||||||||||||||||||||||||\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/meme/fimo/fimo_output_almost-gff_1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/meme/fimo/fimo_output_almost-gff_1.txt Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,1924 @@\n+##gff-version 3\n+phiX174\tfimo\tpolypeptide_motif\t1388\t1398\t29.2484\t+\t.\tmotif_name=1;pvalue=6.3e-11;qvalue=1.22e-09;sequence=AATATCTATAA\n+phiX174\tfimo\tpolypeptide_motif\t847\t857\t29.0063\t+\t.\tmotif_name=1;pvalue=6.85e-11;qvalue=1.22e-09;sequence=AATGTCTAAAG\n+phiX174\tfimo\tpolypeptide_motif\t2301\t2311\t27.4326\t+\t.\tmotif_name=1;pvalue=1.09e-10;qvalue=1.3e-09;sequence=AGGTTATAACG\n+phiX174\tfimo\tpolypeptide_motif\t5063\t5073\t25.2537\t+\t.\tmotif_name=1;pvalue=3.01e-10;qvalue=2.45e-09;sequence=AGGAGCTAAAG\n+phiX174\tfimo\tpolypeptide_motif\t989\t999\t25.0116\t+\t.\tmotif_name=1;pvalue=3.42e-10;qvalue=2.45e-09;sequence=TGAGGATAAAT\n+phiX174\tfimo\tpolypeptide_motif\t4713\t4723\t23.4379\t+\t.\tmotif_name=1;pvalue=7.83e-10;qvalue=3.64e-09;sequence=GACTGCTATCA\n+phiX174\tfimo\tpolypeptide_motif\t855\t865\t23.1958\t+\t.\tmotif_name=1;pvalue=8.56e-10;qvalue=3.64e-09;sequence=AAGGTAAAAAA\n+phiX174\tfimo\tpolypeptide_motif\t5048\t5058\t23.0748\t+\t.\tmotif_name=1;pvalue=9.01e-10;qvalue=3.64e-09;sequence=TGCTGCTAAAG\n+phiX174\tfimo\tpolypeptide_motif\t3155\t3165\t22.8327\t+\t.\tmotif_name=1;pvalue=1.02e-09;qvalue=3.64e-09;sequence=TATGGCTAAAG\n+phiX174\tfimo\tpolypeptide_motif\t5009\t5019\t22.8327\t+\t.\tmotif_name=1;pvalue=1.02e-09;qvalue=3.64e-09;sequence=TGTGGCTAAAT\n+phiX174\tfimo\tpolypeptide_motif\t814\t824\t22.4695\t+\t.\tmotif_name=1;pvalue=1.25e-09;qvalue=4.07e-09;sequence=TGCGTCAAAAA\n+phiX174\tfimo\tpolypeptide_motif\t2832\t2842\t22.1064\t+\t.\tmotif_name=1;pvalue=1.47e-09;qvalue=4.38e-09;sequence=TTGGTCTAACT\n+phiX174\tfimo\tpolypeptide_motif\t3830\t3840\t21.6222\t+\t.\tmotif_name=1;pvalue=1.75e-09;qvalue=4.81e-09;sequence=TATTGATAAAG\n+phiX174\tfimo\tpolypeptide_motif\t3560\t3570\t21.3801\t+\t.\tmotif_name=1;pvalue=1.96e-09;qvalue=5e-09;sequence=TGCGTCTATTA\n+phiX174\tfimo\tpolypeptide_motif\t2882\t2892\t21.0169\t+\t.\tmotif_name=1;pvalue=2.32e-09;qvalue=5.53e-09;sequence=AGGTTATTAAA\n+phiX174\tfimo\tpolypeptide_motif\t4453\t4463\t20.6537\t+\t.\tmotif_name=1;pvalue=2.65e-09;qvalue=5.91e-09;sequence=AAGGTATTAAG\n+phiX174\tfimo\tpolypeptide_motif\t2493\t2503\t20.1695\t+\t.\tmotif_name=1;pvalue=3.09e-09;qvalue=6.08e-09;sequence=GACACCTAAAG\n+phiX174\tfimo\tpolypeptide_motif\t4104\t4114\t20.1695\t+\t.\tmotif_name=1;pvalue=3.09e-09;qvalue=6.08e-09;sequence=GGCTTCCATAA\n+phiX174\tfimo\tpolypeptide_motif\t4955\t4965\t20.0485\t+\t.\tmotif_name=1;pvalue=3.24e-09;qvalue=6.08e-09;sequence=TGATGCTAAAG\n+phiX174\tfimo\tpolypeptide_motif\t1885\t1895\t19.6853\t+\t.\tmotif_name=1;pvalue=3.72e-09;qvalue=6.32e-09;sequence=TGCGACTAAAG\n+phiX174\tfimo\tpolypeptide_motif\t3376\t3386\t19.6853\t+\t.\tmotif_name=1;pvalue=3.72e-09;qvalue=6.32e-09;sequence=AGAATCAAAAA\n+phiX174\tfimo\tpolypeptide_motif\t52\t62\t19.4432\t+\t.\tmotif_name=1;pvalue=4.01e-09;qvalue=6.45e-09;sequence=TGAGTCGAAAA\n+phiX174\tfimo\tpolypeptide_motif\t1390\t1400\t19.3222\t+\t.\tmotif_name=1;pvalue=4.15e-09;qvalue=6.45e-09;sequence=TATCTATAACA\n+phiX174\tfimo\tpolypeptide_motif\t2017\t2027\t18.959\t+\t.\tmotif_name=1;pvalue=4.57e-09;qvalue=6.75e-09;sequence=TTCGTCTAAGA\n+phiX174\tfimo\tpolypeptide_motif\t1000\t1010\t18.838\t+\t.\tmotif_name=1;pvalue=4.73e-09;qvalue=6.75e-09;sequence=TATGTCTAATA\n+phiX174\tfimo\tpolypeptide_motif\t1555\t1565\t18.3538\t+\t.\tmotif_name=1;pvalue=5.47e-09;qvalue=7.4e-09;sequence=GACTTCTACCA\n+phiX174\tfimo\tpolypeptide_motif\t4430\t4440\t18.2327\t+\t.\tmotif_name=1;pvalue=5.66e-09;qvalue=7.4e-09;sequence=TGAGTATAATT\n+phiX174\tfimo\tpolypeptide_motif\t1927\t1937\t18.1117\t+\t.\tmotif_name=1;pvalue=5.84e-09;qvalue=7.4e-09;sequence=GACTTATACCG\n+phiX174\tfimo\tpolypeptide_motif\t2981\t2991\t17.9906\t+\t.\tmotif_name=1;pvalue=6.01e-09;qvalue=7.4e-09;sequence=CATGTCTAAAT\n+phiX174\tfimo\tpolypeptide_motif\t4203\t4213\t17.7485\t+\t.\tmotif_name=1;pvalue=6.35e-09;qvalue=7.52e-09;sequence=GACGGCCATAA\n+phiX174\tfimo\tpolypeptide_motif\t1669\t1679\t17.6275\t+\t.\tmotif_name=1;pvalue=6.52e-09;qvalue=7.52e-09;sequence=TGGAGGTAAAA\n+phiX174\tfimo\tpolypeptide_motif\t3260\t3270\t17.2643\t+\t.\tmotif_name=1;pvalue=7.15e-09;qvalue=7.78e-09;sequence=CGCTGATAAAG\n+phiX174\tfimo\tpolypeptide_motif\t3047\t3057\t17.1433\t+\t.\tmotif_name=1;pvalue=7.38e-09;qvalue=7.78e-09;sequence=TACCGATAACA\n+phiX174\tfimo\tpolypeptide_'..b'e-06;sequence=AGGATACTCGT\n+phiX174\tfimo\tpolypeptide_motif\t3363\t3373\t-15.4195\t+\t.\tmotif_name=1;pvalue=9.64e-05;qvalue=1.81e-06;sequence=GACGCCGGATT\n+phiX174\tfimo\tpolypeptide_motif\t4599\t4609\t-15.4195\t+\t.\tmotif_name=1;pvalue=9.64e-05;qvalue=1.81e-06;sequence=GACGACCGATT\n+phiX174\tfimo\tpolypeptide_motif\t4600\t4610\t-15.4195\t+\t.\tmotif_name=1;pvalue=9.64e-05;qvalue=1.81e-06;sequence=ACGACCGATTA\n+phiX174\tfimo\tpolypeptide_motif\t4758\t4768\t-15.4195\t+\t.\tmotif_name=1;pvalue=9.64e-05;qvalue=1.81e-06;sequence=GGCCGTCTTCA\n+phiX174\tfimo\tpolypeptide_motif\t4875\t4885\t-15.4195\t+\t.\tmotif_name=1;pvalue=9.64e-05;qvalue=1.81e-06;sequence=TGGCCTTATGG\n+phiX174\tfimo\tpolypeptide_motif\t4953\t4963\t-15.4195\t+\t.\tmotif_name=1;pvalue=9.64e-05;qvalue=1.81e-06;sequence=GTTGATGCTAA\n+phiX174\tfimo\tpolypeptide_motif\t4978\t4988\t-15.4195\t+\t.\tmotif_name=1;pvalue=9.64e-05;qvalue=1.81e-06;sequence=AAGCTACCAGT\n+phiX174\tfimo\tpolypeptide_motif\t5265\t5275\t-15.4195\t+\t.\tmotif_name=1;pvalue=9.64e-05;qvalue=1.81e-06;sequence=GAGATGAGATT\n+phiX174\tfimo\tpolypeptide_motif\t160\t170\t-15.5405\t+\t.\tmotif_name=1;pvalue=9.87e-05;qvalue=1.83e-06;sequence=AGCTCGAGAAG\n+phiX174\tfimo\tpolypeptide_motif\t201\t211\t-15.5405\t+\t.\tmotif_name=1;pvalue=9.87e-05;qvalue=1.83e-06;sequence=AACGATTCTGT\n+phiX174\tfimo\tpolypeptide_motif\t274\t284\t-15.5405\t+\t.\tmotif_name=1;pvalue=9.87e-05;qvalue=1.83e-06;sequence=TGGTTTAGATA\n+phiX174\tfimo\tpolypeptide_motif\t333\t343\t-15.5405\t+\t.\tmotif_name=1;pvalue=9.87e-05;qvalue=1.83e-06;sequence=AGAGCGTGGAT\n+phiX174\tfimo\tpolypeptide_motif\t371\t381\t-15.5405\t+\t.\tmotif_name=1;pvalue=9.87e-05;qvalue=1.83e-06;sequence=CACTAATAGGT\n+phiX174\tfimo\tpolypeptide_motif\t468\t478\t-15.5405\t+\t.\tmotif_name=1;pvalue=9.87e-05;qvalue=1.83e-06;sequence=TTGGATTTAAC\n+phiX174\tfimo\tpolypeptide_motif\t777\t787\t-15.5405\t+\t.\tmotif_name=1;pvalue=9.87e-05;qvalue=1.83e-06;sequence=GGAAACACTGA\n+phiX174\tfimo\tpolypeptide_motif\t804\t814\t-15.5405\t+\t.\tmotif_name=1;pvalue=9.87e-05;qvalue=1.83e-06;sequence=GAAGAAAACGT\n+phiX174\tfimo\tpolypeptide_motif\t926\t936\t-15.5405\t+\t.\tmotif_name=1;pvalue=9.87e-05;qvalue=1.83e-06;sequence=GGCGCTCGTCT\n+phiX174\tfimo\tpolypeptide_motif\t972\t982\t-15.5405\t+\t.\tmotif_name=1;pvalue=9.87e-05;qvalue=1.83e-06;sequence=GGCTTCGGCCC\n+phiX174\tfimo\tpolypeptide_motif\t1133\t1143\t-15.5405\t+\t.\tmotif_name=1;pvalue=9.87e-05;qvalue=1.83e-06;sequence=GACGCCGTTGG\n+phiX174\tfimo\tpolypeptide_motif\t1330\t1340\t-15.5405\t+\t.\tmotif_name=1;pvalue=9.87e-05;qvalue=1.83e-06;sequence=TGGCACGATTA\n+phiX174\tfimo\tpolypeptide_motif\t1946\t1956\t-15.5405\t+\t.\tmotif_name=1;pvalue=9.87e-05;qvalue=1.83e-06;sequence=GGCGACCCTGT\n+phiX174\tfimo\tpolypeptide_motif\t2195\t2205\t-15.5405\t+\t.\tmotif_name=1;pvalue=9.87e-05;qvalue=1.83e-06;sequence=CAGTTGTTGCA\n+phiX174\tfimo\tpolypeptide_motif\t2254\t2264\t-15.5405\t+\t.\tmotif_name=1;pvalue=9.87e-05;qvalue=1.83e-06;sequence=GACCACTCGCG\n+phiX174\tfimo\tpolypeptide_motif\t2893\t2903\t-15.5405\t+\t.\tmotif_name=1;pvalue=9.87e-05;qvalue=1.83e-06;sequence=GAGATTATTTG\n+phiX174\tfimo\tpolypeptide_motif\t2957\t2967\t-15.5405\t+\t.\tmotif_name=1;pvalue=9.87e-05;qvalue=1.83e-06;sequence=TGCTTCTGCTC\n+phiX174\tfimo\tpolypeptide_motif\t3404\t3414\t-15.5405\t+\t.\tmotif_name=1;pvalue=9.87e-05;qvalue=1.83e-06;sequence=ACTGGACAATC\n+phiX174\tfimo\tpolypeptide_motif\t3425\t3435\t-15.5405\t+\t.\tmotif_name=1;pvalue=9.87e-05;qvalue=1.83e-06;sequence=TGCCGAGATGC\n+phiX174\tfimo\tpolypeptide_motif\t3432\t3442\t-15.5405\t+\t.\tmotif_name=1;pvalue=9.87e-05;qvalue=1.83e-06;sequence=ATGCAAAATGA\n+phiX174\tfimo\tpolypeptide_motif\t3453\t3463\t-15.5405\t+\t.\tmotif_name=1;pvalue=9.87e-05;qvalue=1.83e-06;sequence=GAGATTGCTGG\n+phiX174\tfimo\tpolypeptide_motif\t3827\t3837\t-15.5405\t+\t.\tmotif_name=1;pvalue=9.87e-05;qvalue=1.83e-06;sequence=TGGTATTGATA\n+phiX174\tfimo\tpolypeptide_motif\t3973\t3983\t-15.5405\t+\t.\tmotif_name=1;pvalue=9.87e-05;qvalue=1.83e-06;sequence=GCTTTTTTATG\n+phiX174\tfimo\tpolypeptide_motif\t4018\t4028\t-15.5405\t+\t.\tmotif_name=1;pvalue=9.87e-05;qvalue=1.83e-06;sequence=ATTATTTTGAC\n+phiX174\tfimo\tpolypeptide_motif\t5243\t5253\t-15.5405\t+\t.\tmotif_name=1;pvalue=9.87e-05;qvalue=1.83e-06;sequence=ATTGAAGCAGA\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/meme/fimo/fimo_output_html_1.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/meme/fimo/fimo_output_html_1.html Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,17464 @@\n+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\n+<html xmlns:cis="http://zlab.bu.edu/schema/cisml" xmlns:fimo="http://noble.gs.washington.edu/schema/cisml" xmlns:mem="http://noble.gs.washington.edu/meme">\n+<head>\n+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">\n+<title>FIMO Results</title>\n+<style type="text/css">\n+ td.left {text-align: left;}\n+ td.right {text-align: right; padding-right: 1cm;}\n+ </style>\n+</head>\n+<body bgcolor="#D5F0FF">\n+<a name="top_buttons"></a><hr>\n+<table summary="buttons" align="left" cellspacing="0"><tr>\n+<td bgcolor="#00FFFF"><a href="#database_and_motifs"><b>Database and Motifs</b></a></td>\n+<td bgcolor="#DDFFDD"><a href="#sec_i"><b>High-scoring Motif Occurences</b></a></td>\n+<td bgcolor="#DDDDFF"><a href="#debugging_information"><b>Debugging Information</b></a></td>\n+</tr></table>\n+<br><br><hr>\n+<center><big><b>FIMO - Motif search tool</b></big></center>\n+<hr>\n+<p>\n+ FIMO version 4.6.0, \n+ (Release date: 8 PST 20)\n+ </p>\n+<p>\n+ For further information on how to interpret these results\n+ or to get a copy of the FIMO software please access\n+ <a href="http://meme.nbcr.net">http://meme.nbcr.net</a></p>\n+<hr>\n+<center><big><b><a name="database_and_motifs">DATABASE AND MOTIFS</a></b></big></center>\n+<hr>\n+<div style="padding-left: 0.75in; line-height: 1em; font-family: monospace;">\n+<p>\n+ DATABASE \n+ /path/to/dataset_?.dat<br>\n+ Database contains \n+ 1\n+ sequences,\n+ 5386\n+ residues\n+ </p>\n+<p>\n+ MOTIFS \n+ /path/to/dataset_?.dat \n+ (protein)\n+ <table>\n+<thead><tr>\n+<th style="border-bottom: 1px dashed;">MOTIF</th>\n+<th style="border-bottom: 1px dashed; padding-left: 1em;">WIDTH</th>\n+<th style="border-bottom: 1px dashed; padding-left: 1em;" align="left">\n+ BEST POSSIBLE MATCH\n+ </th>\n+</tr></thead>\n+<tbody><tr>\n+<td align="right">1</td>\n+<td align="right" style="padding-left: 1em;">11</td>\n+<td align="left" style="padding-left: 1em;">GGGGTATAAAA</td>\n+</tr></tbody>\n+</table></p>\n+<p>\n+ Random model letter frequencies \n+ (from non-redundant database):\n+ <br>A 0.073 C 0.018 D 0.052 E 0.062 F 0.040 G 0.069 H 0.022 I 0.056 K 0.058 \n+<br>\n+L 0.092 M 0.023 N 0.046 P 0.051 Q 0.041 R 0.052 S 0.074 T 0.059 V 0.064 \n+<br>\n+W 0.013 Y 0.033 </p>\n+</div>\n+<hr>\n+<center><big><b><a name="sec_i">SECTION I: HIGH-SCORING MOTIF OCCURENCES</a></b></big></center>\n+<hr>\n+<ul>\n+<li> Each of the following \n+ 1923\n+ motif occurrences has \n+ \n+ p-value less than \n+ 0.0001</li>\n+<li> The p-value of a motif occurrence is defined as the\n+ probability of a random sequence of the same length as the motif\n+ matching that position of the sequence with as good or better a score.\n+ </li>\n+<li> The score for the match of a position in a sequence to a motif\n+ is computed by summing the appropriate entries from each column of\n+ the position-dependent scoring matrix that represents the motif.\n+ </li>\n+<li> The q-value of a motif occurrence is defined as the\n+ false discovery rate if the occurrence is accepted as significant.\n+ </li>\n+<li>The table is sorted by increasing p-value.</li>\n+<li>If the start position is larger than the end position,\n+ the motif occurrence is on the reverse strand.\n+ </li>\n+</ul>\n+<table border="1">\n+<thead><tr>\n+<th>Motif</th>\n+<th>Sequence Name</th>\n+<th>Start</th>\n+<th>End</th>\n+<th>p-value</th>\n+<th>q-value</th>\n+<th>Matched Sequence</th>\n+</tr></thead>\n+<tbody>\n+<tr>\n+<td align="left"><a name="occurrences_phiX174">1</a></td>\n+<td align="left">phiX174</td>\n+<td align="left">1388</td>\n+<td align="left">1398</td>\n+<td align="left">6.3e-11</td>\n+<td align="left">1.22e-09</td>\n+<td align="left"><code style="font-size: x-large;">AATATCTATAA</code></td>\n+</tr>\n+<tr>\n+<td align="left"><a name="occurren'..b'd>\n+<td align="left">phiX174</td>\n+<td align="left">3425</td>\n+<td align="left">3435</td>\n+<td align="left">9.87e-05</td>\n+<td align="left">1.83e-06</td>\n+<td align="left"><code style="font-size: x-large;">TGCCGAGATGC</code></td>\n+</tr>\n+<tr>\n+<td align="left"><a name="occurrences_phiX174">1</a></td>\n+<td align="left">phiX174</td>\n+<td align="left">3432</td>\n+<td align="left">3442</td>\n+<td align="left">9.87e-05</td>\n+<td align="left">1.83e-06</td>\n+<td align="left"><code style="font-size: x-large;">ATGCAAAATGA</code></td>\n+</tr>\n+<tr>\n+<td align="left"><a name="occurrences_phiX174">1</a></td>\n+<td align="left">phiX174</td>\n+<td align="left">3453</td>\n+<td align="left">3463</td>\n+<td align="left">9.87e-05</td>\n+<td align="left">1.83e-06</td>\n+<td align="left"><code style="font-size: x-large;">GAGATTGCTGG</code></td>\n+</tr>\n+<tr>\n+<td align="left"><a name="occurrences_phiX174">1</a></td>\n+<td align="left">phiX174</td>\n+<td align="left">3827</td>\n+<td align="left">3837</td>\n+<td align="left">9.87e-05</td>\n+<td align="left">1.83e-06</td>\n+<td align="left"><code style="font-size: x-large;">TGGTATTGATA</code></td>\n+</tr>\n+<tr>\n+<td align="left"><a name="occurrences_phiX174">1</a></td>\n+<td align="left">phiX174</td>\n+<td align="left">3973</td>\n+<td align="left">3983</td>\n+<td align="left">9.87e-05</td>\n+<td align="left">1.83e-06</td>\n+<td align="left"><code style="font-size: x-large;">GCTTTTTTATG</code></td>\n+</tr>\n+<tr>\n+<td align="left"><a name="occurrences_phiX174">1</a></td>\n+<td align="left">phiX174</td>\n+<td align="left">4018</td>\n+<td align="left">4028</td>\n+<td align="left">9.87e-05</td>\n+<td align="left">1.83e-06</td>\n+<td align="left"><code style="font-size: x-large;">ATTATTTTGAC</code></td>\n+</tr>\n+<tr>\n+<td align="left"><a name="occurrences_phiX174">1</a></td>\n+<td align="left">phiX174</td>\n+<td align="left">5243</td>\n+<td align="left">5253</td>\n+<td align="left">9.87e-05</td>\n+<td align="left">1.83e-06</td>\n+<td align="left"><code style="font-size: x-large;">ATTGAAGCAGA</code></td>\n+</tr>\n+</tbody>\n+</table>\n+<hr>\n+<center><big><b><a name="debugging_information">DEBUGGING INFORMATION</a></b></big></center>\n+<hr>\n+<p>\n+ Command line:\n+ </p>\n+<pre>fimo --o /path/to/dataset_?_files --verbosity 1 /path/to/dataset_?.dat /path/to/dataset_?.dat</pre>\n+<p>\n+ Settings:\n+ </p>\n+<pre><table>\n+<tr>\n+<td style="padding-right: 2em">output directory = /path/to/dataset_?_files</td>\n+<td style="padding-left: 5em; padding-right: 2em">MEME file name = /path/to/dataset_?.dat</td>\n+<td style="padding-left: 5em; padding-right: 2em">sequence file name = /path/to/dataset_?.dat</td>\n+</tr>\n+<tr>\n+<td style="padding-right: 2em">background file name = (null)</td>\n+<td style="padding-left: 5em; padding-right: 2em">motif name = motif</td>\n+<td style="padding-left: 5em; padding-right: 2em">allow clobber = false</td>\n+</tr>\n+<tr>\n+<td style="padding-right: 2em">compute q-values = true</td>\n+<td style="padding-left: 5em; padding-right: 2em">output p-threshold set = false</td>\n+<td style="padding-left: 5em; padding-right: 2em">output q-threshold set = false</td>\n+</tr>\n+<tr>\n+<td style="padding-right: 2em">text only = false</td>\n+<td style="padding-left: 5em; padding-right: 2em">scan both strands = false</td>\n+<td style="padding-left: 5em; padding-right: 2em">max sequence length = 250000000</td>\n+</tr>\n+<tr>\n+<td style="padding-right: 2em">output q-value threshold = 1</td>\n+<td style="padding-left: 5em; padding-right: 2em">output p-value threshold = 0.0001</td>\n+<td style="padding-left: 5em; padding-right: 2em">pseudocount = 0.1</td>\n+</tr>\n+<tr>\n+<td style="padding-right: 2em">verbosity = 1</td>\n+<td style="padding-left: 5em; padding-right: 2em"></td>\n+<td align="right"></td>\n+</tr>\n+</table></pre>\n+<p>\n+ This information can be useful in the event you wish to report a\n+ problem with the FIMO software.\n+ </p>\n+<hr>\n+<span style="background-color: #DDDDFF"><a href="#top_buttons"><b>Go to top</b></a></span>\n+</body>\n+</html>\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/meme/fimo/fimo_output_interval_1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/meme/fimo/fimo_output_interval_1.txt Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,1924 @@\n+#chr\tstart\tend\tpattern name\tscore\tstrand\tmatched sequence\tp-value\tq-value\n+phiX174\t1387\t1398\t1\t29.2484\t+\tAATATCTATAA\t6.3e-11\t1.22e-09\n+phiX174\t846\t857\t1\t29.0063\t+\tAATGTCTAAAG\t6.85e-11\t1.22e-09\n+phiX174\t2300\t2311\t1\t27.4326\t+\tAGGTTATAACG\t1.09e-10\t1.3e-09\n+phiX174\t5062\t5073\t1\t25.2537\t+\tAGGAGCTAAAG\t3.01e-10\t2.45e-09\n+phiX174\t988\t999\t1\t25.0116\t+\tTGAGGATAAAT\t3.42e-10\t2.45e-09\n+phiX174\t4712\t4723\t1\t23.4379\t+\tGACTGCTATCA\t7.83e-10\t3.64e-09\n+phiX174\t854\t865\t1\t23.1958\t+\tAAGGTAAAAAA\t8.56e-10\t3.64e-09\n+phiX174\t5047\t5058\t1\t23.0748\t+\tTGCTGCTAAAG\t9.01e-10\t3.64e-09\n+phiX174\t3154\t3165\t1\t22.8327\t+\tTATGGCTAAAG\t1.02e-09\t3.64e-09\n+phiX174\t5008\t5019\t1\t22.8327\t+\tTGTGGCTAAAT\t1.02e-09\t3.64e-09\n+phiX174\t813\t824\t1\t22.4695\t+\tTGCGTCAAAAA\t1.25e-09\t4.07e-09\n+phiX174\t2831\t2842\t1\t22.1064\t+\tTTGGTCTAACT\t1.47e-09\t4.38e-09\n+phiX174\t3829\t3840\t1\t21.6222\t+\tTATTGATAAAG\t1.75e-09\t4.81e-09\n+phiX174\t3559\t3570\t1\t21.3801\t+\tTGCGTCTATTA\t1.96e-09\t5e-09\n+phiX174\t2881\t2892\t1\t21.0169\t+\tAGGTTATTAAA\t2.32e-09\t5.53e-09\n+phiX174\t4452\t4463\t1\t20.6537\t+\tAAGGTATTAAG\t2.65e-09\t5.91e-09\n+phiX174\t2492\t2503\t1\t20.1695\t+\tGACACCTAAAG\t3.09e-09\t6.08e-09\n+phiX174\t4103\t4114\t1\t20.1695\t+\tGGCTTCCATAA\t3.09e-09\t6.08e-09\n+phiX174\t4954\t4965\t1\t20.0485\t+\tTGATGCTAAAG\t3.24e-09\t6.08e-09\n+phiX174\t1884\t1895\t1\t19.6853\t+\tTGCGACTAAAG\t3.72e-09\t6.32e-09\n+phiX174\t3375\t3386\t1\t19.6853\t+\tAGAATCAAAAA\t3.72e-09\t6.32e-09\n+phiX174\t51\t62\t1\t19.4432\t+\tTGAGTCGAAAA\t4.01e-09\t6.45e-09\n+phiX174\t1389\t1400\t1\t19.3222\t+\tTATCTATAACA\t4.15e-09\t6.45e-09\n+phiX174\t2016\t2027\t1\t18.959\t+\tTTCGTCTAAGA\t4.57e-09\t6.75e-09\n+phiX174\t999\t1010\t1\t18.838\t+\tTATGTCTAATA\t4.73e-09\t6.75e-09\n+phiX174\t1554\t1565\t1\t18.3538\t+\tGACTTCTACCA\t5.47e-09\t7.4e-09\n+phiX174\t4429\t4440\t1\t18.2327\t+\tTGAGTATAATT\t5.66e-09\t7.4e-09\n+phiX174\t1926\t1937\t1\t18.1117\t+\tGACTTATACCG\t5.84e-09\t7.4e-09\n+phiX174\t2980\t2991\t1\t17.9906\t+\tCATGTCTAAAT\t6.01e-09\t7.4e-09\n+phiX174\t4202\t4213\t1\t17.7485\t+\tGACGGCCATAA\t6.35e-09\t7.52e-09\n+phiX174\t1668\t1679\t1\t17.6275\t+\tTGGAGGTAAAA\t6.52e-09\t7.52e-09\n+phiX174\t3259\t3270\t1\t17.2643\t+\tCGCTGATAAAG\t7.15e-09\t7.78e-09\n+phiX174\t3046\t3057\t1\t17.1433\t+\tTACCGATAACA\t7.38e-09\t7.78e-09\n+phiX174\t4117\t4128\t1\t17.0222\t+\tGATGGATAACC\t7.62e-09\t7.78e-09\n+phiX174\t4175\t4186\t1\t17.0222\t+\tGAGTTCGATAA\t7.62e-09\t7.78e-09\n+phiX174\t5369\t5380\t1\t16.7801\t+\tGGCGTATCCAA\t8.08e-09\t8.02e-09\n+phiX174\t697\t708\t1\t16.2959\t+\tTACGGAAAACA\t9.08e-09\t8.07e-09\n+phiX174\t1241\t1252\t1\t16.2959\t+\tAGTGGATTAAG\t9.08e-09\t8.07e-09\n+phiX174\t2582\t2593\t1\t16.2959\t+\tTACATCTGTCA\t9.08e-09\t8.07e-09\n+phiX174\t2298\t2309\t1\t16.0538\t+\tTGAGGTTATAA\t9.63e-09\t8.07e-09\n+phiX174\t274\t285\t1\t15.9328\t+\tGGTTTAGATAT\t9.9e-09\t8.07e-09\n+phiX174\t1800\t1811\t1\t15.9328\t+\tGACCTATAAAC\t9.9e-09\t8.07e-09\n+phiX174\t1287\t1298\t1\t15.8117\t+\tGACTGTTAACA\t1.02e-08\t8.07e-09\n+phiX174\t4188\t4199\t1\t15.8117\t+\tGTGATATGTAT\t1.02e-08\t8.07e-09\n+phiX174\t1302\t1313\t1\t15.5696\t+\tTGGTTATATTG\t1.09e-08\t8.07e-09\n+phiX174\t1385\t1396\t1\t15.5696\t+\tTGAATATCTAT\t1.09e-08\t8.07e-09\n+phiX174\t2576\t2587\t1\t15.5696\t+\tGATGGATACAT\t1.09e-08\t8.07e-09\n+phiX174\t3771\t3782\t1\t15.5696\t+\tAGGATATTTCT\t1.09e-08\t8.07e-09\n+phiX174\t903\t914\t1\t15.4486\t+\tAGGTACTAAAG\t1.13e-08\t8.07e-09\n+phiX174\t936\t947\t1\t15.3275\t+\tTTGGTATGTAG\t1.18e-08\t8.07e-09\n+phiX174\t2278\t2289\t1\t15.3275\t+\tTCGTGATAAAA\t1.18e-08\t8.07e-09\n+phiX174\t3163\t3174\t1\t15.3275\t+\tAGCTGGTAAAG\t1.18e-08\t8.07e-09\n+phiX174\t23\t34\t1\t15.2064\t+\tAGAAGTTAACA\t1.23e-08\t8.29e-09\n+phiX174\t852\t863\t1\t15.0854\t+\tTAAAGGTAAAA\t1.28e-08\t8.47e-09\n+phiX174\t837\t848\t1\t14.9643\t+\tGAGTGATGTAA\t1.33e-08\t8.48e-09\n+phiX174\t1983\t1994\t1\t14.9643\t+\tAATTTCTATGA\t1.33e-08\t8.48e-09\n+phiX174\t4306\t4317\t1\t14.7222\t+\tTATTAATAACA\t1.45e-08\t9.07e-09\n+phiX174\t0\t11\t1\t14.6012\t+\tGAGTTTTATCG\t1.49e-08\t9.2e-09\n+phiX174\t4302\t4313\t1\t14.3591\t+\tTTGATATTAAT\t1.63e-08\t9.84e-09\n+phiX174\t5032\t5043\t1\t14.238\t+\tGTCAGATATGG\t1.69e-08\t1.01e-08\n+phiX174\t321\t332\t1\t14.117\t+\tGACATTTTAAA\t1.78e-08\t1.04e-08\n+phiX174\t2578\t2589\t1\t13.9959\t+\tTGGATACATCT\t1.88e-08\t1.08e-08\n+phiX174\t5000\t5011\t1\t13.7538\t+\tGGTTTCTATGT\t2.1e-08\t1.19e-08\n+phiX174\t3568\t3579\t1\t13.6328\t+\tTATGGAAAACA\t2.22e-08\t1.2e-08\n+phiX174\t4216\t4227\t1\t13.6328\t+\tTGCTTCTGACG\t2.22e-08\t1.2'..b'76e-06\n+phiX174\t3591\t3602\t1\t-15.1774\t+\tAGCAACAGCAG\t9.18e-05\t1.76e-06\n+phiX174\t3634\t3645\t1\t-15.1774\t+\tAGCTCAAACGG\t9.18e-05\t1.76e-06\n+phiX174\t3682\t3693\t1\t-15.1774\t+\tGACTCGCAAGG\t9.18e-05\t1.76e-06\n+phiX174\t3726\t3737\t1\t-15.1774\t+\tCGCAGAATCAG\t9.18e-05\t1.76e-06\n+phiX174\t4110\t4121\t1\t-15.1774\t+\tATAAGCAGATG\t9.18e-05\t1.76e-06\n+phiX174\t4346\t4357\t1\t-15.1774\t+\tAAATGGTTTTT\t9.18e-05\t1.76e-06\n+phiX174\t4425\t4436\t1\t-15.1774\t+\tGCGATGAGTAT\t9.18e-05\t1.76e-06\n+phiX174\t5046\t5057\t1\t-15.1774\t+\tTTGCTGCTAAA\t9.18e-05\t1.76e-06\n+phiX174\t70\t81\t1\t-15.2984\t+\tGATAAAGCAGG\t9.41e-05\t1.79e-06\n+phiX174\t934\t945\t1\t-15.2984\t+\tCTTTGGTATGT\t9.41e-05\t1.79e-06\n+phiX174\t1227\t1238\t1\t-15.2984\t+\tCGTTTATGGTG\t9.41e-05\t1.79e-06\n+phiX174\t1556\t1567\t1\t-15.2984\t+\tCTTCTACCACA\t9.41e-05\t1.79e-06\n+phiX174\t1934\t1945\t1\t-15.2984\t+\tCCGATATTGCT\t9.41e-05\t1.79e-06\n+phiX174\t2217\t2228\t1\t-15.2984\t+\tGGTTAAATTTA\t9.41e-05\t1.79e-06\n+phiX174\t2287\t2298\t1\t-15.2984\t+\tAAGATTGAGTG\t9.41e-05\t1.79e-06\n+phiX174\t2368\t2379\t1\t-15.2984\t+\tTAGGTTTTCTG\t9.41e-05\t1.79e-06\n+phiX174\t2933\t2944\t1\t-15.2984\t+\tTTTGGTGCTAT\t9.41e-05\t1.79e-06\n+phiX174\t3781\t3792\t1\t-15.2984\t+\tTAATGTCGTCA\t9.41e-05\t1.79e-06\n+phiX174\t4256\t4267\t1\t-15.2984\t+\tAAGTTAATGGA\t9.41e-05\t1.79e-06\n+phiX174\t4575\t4586\t1\t-15.2984\t+\tTTTTTGACACT\t9.41e-05\t1.79e-06\n+phiX174\t4857\t4868\t1\t-15.2984\t+\tATAGCTTGCAA\t9.41e-05\t1.79e-06\n+phiX174\t5167\t5178\t1\t-15.2984\t+\tAATGACAAATC\t9.41e-05\t1.79e-06\n+phiX174\t5286\t5297\t1\t-15.2984\t+\tAAGTTACTGTA\t9.41e-05\t1.79e-06\n+phiX174\t5372\t5383\t1\t-15.2984\t+\tGTATCCAACCT\t9.41e-05\t1.79e-06\n+phiX174\t16\t27\t1\t-15.4195\t+\tATGACGCAGAA\t9.64e-05\t1.81e-06\n+phiX174\t226\t237\t1\t-15.4195\t+\tTGGATGAGGAG\t9.64e-05\t1.81e-06\n+phiX174\t271\t282\t1\t-15.4195\t+\tACTGGTTTAGA\t9.64e-05\t1.81e-06\n+phiX174\t357\t368\t1\t-15.4195\t+\tGATGCTGTTCA\t9.64e-05\t1.81e-06\n+phiX174\t840\t851\t1\t-15.4195\t+\tTGATGTAATGT\t9.64e-05\t1.81e-06\n+phiX174\t1346\t1357\t1\t-15.4195\t+\tATACCAATAAA\t9.64e-05\t1.81e-06\n+phiX174\t1527\t1538\t1\t-15.4195\t+\tTGAGACTGAGC\t9.64e-05\t1.81e-06\n+phiX174\t3273\t3284\t1\t-15.4195\t+\tAGGATACTCGT\t9.64e-05\t1.81e-06\n+phiX174\t3362\t3373\t1\t-15.4195\t+\tGACGCCGGATT\t9.64e-05\t1.81e-06\n+phiX174\t4598\t4609\t1\t-15.4195\t+\tGACGACCGATT\t9.64e-05\t1.81e-06\n+phiX174\t4599\t4610\t1\t-15.4195\t+\tACGACCGATTA\t9.64e-05\t1.81e-06\n+phiX174\t4757\t4768\t1\t-15.4195\t+\tGGCCGTCTTCA\t9.64e-05\t1.81e-06\n+phiX174\t4874\t4885\t1\t-15.4195\t+\tTGGCCTTATGG\t9.64e-05\t1.81e-06\n+phiX174\t4952\t4963\t1\t-15.4195\t+\tGTTGATGCTAA\t9.64e-05\t1.81e-06\n+phiX174\t4977\t4988\t1\t-15.4195\t+\tAAGCTACCAGT\t9.64e-05\t1.81e-06\n+phiX174\t5264\t5275\t1\t-15.4195\t+\tGAGATGAGATT\t9.64e-05\t1.81e-06\n+phiX174\t159\t170\t1\t-15.5405\t+\tAGCTCGAGAAG\t9.87e-05\t1.83e-06\n+phiX174\t200\t211\t1\t-15.5405\t+\tAACGATTCTGT\t9.87e-05\t1.83e-06\n+phiX174\t273\t284\t1\t-15.5405\t+\tTGGTTTAGATA\t9.87e-05\t1.83e-06\n+phiX174\t332\t343\t1\t-15.5405\t+\tAGAGCGTGGAT\t9.87e-05\t1.83e-06\n+phiX174\t370\t381\t1\t-15.5405\t+\tCACTAATAGGT\t9.87e-05\t1.83e-06\n+phiX174\t467\t478\t1\t-15.5405\t+\tTTGGATTTAAC\t9.87e-05\t1.83e-06\n+phiX174\t776\t787\t1\t-15.5405\t+\tGGAAACACTGA\t9.87e-05\t1.83e-06\n+phiX174\t803\t814\t1\t-15.5405\t+\tGAAGAAAACGT\t9.87e-05\t1.83e-06\n+phiX174\t925\t936\t1\t-15.5405\t+\tGGCGCTCGTCT\t9.87e-05\t1.83e-06\n+phiX174\t971\t982\t1\t-15.5405\t+\tGGCTTCGGCCC\t9.87e-05\t1.83e-06\n+phiX174\t1132\t1143\t1\t-15.5405\t+\tGACGCCGTTGG\t9.87e-05\t1.83e-06\n+phiX174\t1329\t1340\t1\t-15.5405\t+\tTGGCACGATTA\t9.87e-05\t1.83e-06\n+phiX174\t1945\t1956\t1\t-15.5405\t+\tGGCGACCCTGT\t9.87e-05\t1.83e-06\n+phiX174\t2194\t2205\t1\t-15.5405\t+\tCAGTTGTTGCA\t9.87e-05\t1.83e-06\n+phiX174\t2253\t2264\t1\t-15.5405\t+\tGACCACTCGCG\t9.87e-05\t1.83e-06\n+phiX174\t2892\t2903\t1\t-15.5405\t+\tGAGATTATTTG\t9.87e-05\t1.83e-06\n+phiX174\t2956\t2967\t1\t-15.5405\t+\tTGCTTCTGCTC\t9.87e-05\t1.83e-06\n+phiX174\t3403\t3414\t1\t-15.5405\t+\tACTGGACAATC\t9.87e-05\t1.83e-06\n+phiX174\t3424\t3435\t1\t-15.5405\t+\tTGCCGAGATGC\t9.87e-05\t1.83e-06\n+phiX174\t3431\t3442\t1\t-15.5405\t+\tATGCAAAATGA\t9.87e-05\t1.83e-06\n+phiX174\t3452\t3463\t1\t-15.5405\t+\tGAGATTGCTGG\t9.87e-05\t1.83e-06\n+phiX174\t3826\t3837\t1\t-15.5405\t+\tTGGTATTGATA\t9.87e-05\t1.83e-06\n+phiX174\t3972\t3983\t1\t-15.5405\t+\tGCTTTTTTATG\t9.87e-05\t1.83e-06\n+phiX174\t4017\t4028\t1\t-15.5405\t+\tATTATTTTGAC\t9.87e-05\t1.83e-06\n+phiX174\t5242\t5253\t1\t-15.5405\t+\tATTGAAGCAGA\t9.87e-05\t1.83e-06\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/meme/fimo/fimo_output_txt_1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/meme/fimo/fimo_output_txt_1.txt Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,1924 @@\n+#pattern name\tsequence name\tstart\tstop\tscore\tp-value\tq-value\tmatched sequence\n+1\tphiX174\t1388\t1398\t29.2484\t6.3e-11\t1.22e-09\tAATATCTATAA\n+1\tphiX174\t847\t857\t29.0063\t6.85e-11\t1.22e-09\tAATGTCTAAAG\n+1\tphiX174\t2301\t2311\t27.4326\t1.09e-10\t1.3e-09\tAGGTTATAACG\n+1\tphiX174\t5063\t5073\t25.2537\t3.01e-10\t2.45e-09\tAGGAGCTAAAG\n+1\tphiX174\t989\t999\t25.0116\t3.42e-10\t2.45e-09\tTGAGGATAAAT\n+1\tphiX174\t4713\t4723\t23.4379\t7.83e-10\t3.64e-09\tGACTGCTATCA\n+1\tphiX174\t855\t865\t23.1958\t8.56e-10\t3.64e-09\tAAGGTAAAAAA\n+1\tphiX174\t5048\t5058\t23.0748\t9.01e-10\t3.64e-09\tTGCTGCTAAAG\n+1\tphiX174\t3155\t3165\t22.8327\t1.02e-09\t3.64e-09\tTATGGCTAAAG\n+1\tphiX174\t5009\t5019\t22.8327\t1.02e-09\t3.64e-09\tTGTGGCTAAAT\n+1\tphiX174\t814\t824\t22.4695\t1.25e-09\t4.07e-09\tTGCGTCAAAAA\n+1\tphiX174\t2832\t2842\t22.1064\t1.47e-09\t4.38e-09\tTTGGTCTAACT\n+1\tphiX174\t3830\t3840\t21.6222\t1.75e-09\t4.81e-09\tTATTGATAAAG\n+1\tphiX174\t3560\t3570\t21.3801\t1.96e-09\t5e-09\tTGCGTCTATTA\n+1\tphiX174\t2882\t2892\t21.0169\t2.32e-09\t5.53e-09\tAGGTTATTAAA\n+1\tphiX174\t4453\t4463\t20.6537\t2.65e-09\t5.91e-09\tAAGGTATTAAG\n+1\tphiX174\t2493\t2503\t20.1695\t3.09e-09\t6.08e-09\tGACACCTAAAG\n+1\tphiX174\t4104\t4114\t20.1695\t3.09e-09\t6.08e-09\tGGCTTCCATAA\n+1\tphiX174\t4955\t4965\t20.0485\t3.24e-09\t6.08e-09\tTGATGCTAAAG\n+1\tphiX174\t1885\t1895\t19.6853\t3.72e-09\t6.32e-09\tTGCGACTAAAG\n+1\tphiX174\t3376\t3386\t19.6853\t3.72e-09\t6.32e-09\tAGAATCAAAAA\n+1\tphiX174\t52\t62\t19.4432\t4.01e-09\t6.45e-09\tTGAGTCGAAAA\n+1\tphiX174\t1390\t1400\t19.3222\t4.15e-09\t6.45e-09\tTATCTATAACA\n+1\tphiX174\t2017\t2027\t18.959\t4.57e-09\t6.75e-09\tTTCGTCTAAGA\n+1\tphiX174\t1000\t1010\t18.838\t4.73e-09\t6.75e-09\tTATGTCTAATA\n+1\tphiX174\t1555\t1565\t18.3538\t5.47e-09\t7.4e-09\tGACTTCTACCA\n+1\tphiX174\t4430\t4440\t18.2327\t5.66e-09\t7.4e-09\tTGAGTATAATT\n+1\tphiX174\t1927\t1937\t18.1117\t5.84e-09\t7.4e-09\tGACTTATACCG\n+1\tphiX174\t2981\t2991\t17.9906\t6.01e-09\t7.4e-09\tCATGTCTAAAT\n+1\tphiX174\t4203\t4213\t17.7485\t6.35e-09\t7.52e-09\tGACGGCCATAA\n+1\tphiX174\t1669\t1679\t17.6275\t6.52e-09\t7.52e-09\tTGGAGGTAAAA\n+1\tphiX174\t3260\t3270\t17.2643\t7.15e-09\t7.78e-09\tCGCTGATAAAG\n+1\tphiX174\t3047\t3057\t17.1433\t7.38e-09\t7.78e-09\tTACCGATAACA\n+1\tphiX174\t4118\t4128\t17.0222\t7.62e-09\t7.78e-09\tGATGGATAACC\n+1\tphiX174\t4176\t4186\t17.0222\t7.62e-09\t7.78e-09\tGAGTTCGATAA\n+1\tphiX174\t5370\t5380\t16.7801\t8.08e-09\t8.02e-09\tGGCGTATCCAA\n+1\tphiX174\t698\t708\t16.2959\t9.08e-09\t8.07e-09\tTACGGAAAACA\n+1\tphiX174\t1242\t1252\t16.2959\t9.08e-09\t8.07e-09\tAGTGGATTAAG\n+1\tphiX174\t2583\t2593\t16.2959\t9.08e-09\t8.07e-09\tTACATCTGTCA\n+1\tphiX174\t2299\t2309\t16.0538\t9.63e-09\t8.07e-09\tTGAGGTTATAA\n+1\tphiX174\t275\t285\t15.9328\t9.9e-09\t8.07e-09\tGGTTTAGATAT\n+1\tphiX174\t1801\t1811\t15.9328\t9.9e-09\t8.07e-09\tGACCTATAAAC\n+1\tphiX174\t1288\t1298\t15.8117\t1.02e-08\t8.07e-09\tGACTGTTAACA\n+1\tphiX174\t4189\t4199\t15.8117\t1.02e-08\t8.07e-09\tGTGATATGTAT\n+1\tphiX174\t1303\t1313\t15.5696\t1.09e-08\t8.07e-09\tTGGTTATATTG\n+1\tphiX174\t1386\t1396\t15.5696\t1.09e-08\t8.07e-09\tTGAATATCTAT\n+1\tphiX174\t2577\t2587\t15.5696\t1.09e-08\t8.07e-09\tGATGGATACAT\n+1\tphiX174\t3772\t3782\t15.5696\t1.09e-08\t8.07e-09\tAGGATATTTCT\n+1\tphiX174\t904\t914\t15.4486\t1.13e-08\t8.07e-09\tAGGTACTAAAG\n+1\tphiX174\t937\t947\t15.3275\t1.18e-08\t8.07e-09\tTTGGTATGTAG\n+1\tphiX174\t2279\t2289\t15.3275\t1.18e-08\t8.07e-09\tTCGTGATAAAA\n+1\tphiX174\t3164\t3174\t15.3275\t1.18e-08\t8.07e-09\tAGCTGGTAAAG\n+1\tphiX174\t24\t34\t15.2064\t1.23e-08\t8.29e-09\tAGAAGTTAACA\n+1\tphiX174\t853\t863\t15.0854\t1.28e-08\t8.47e-09\tTAAAGGTAAAA\n+1\tphiX174\t838\t848\t14.9643\t1.33e-08\t8.48e-09\tGAGTGATGTAA\n+1\tphiX174\t1984\t1994\t14.9643\t1.33e-08\t8.48e-09\tAATTTCTATGA\n+1\tphiX174\t4307\t4317\t14.7222\t1.45e-08\t9.07e-09\tTATTAATAACA\n+1\tphiX174\t1\t11\t14.6012\t1.49e-08\t9.2e-09\tGAGTTTTATCG\n+1\tphiX174\t4303\t4313\t14.3591\t1.63e-08\t9.84e-09\tTTGATATTAAT\n+1\tphiX174\t5033\t5043\t14.238\t1.69e-08\t1.01e-08\tGTCAGATATGG\n+1\tphiX174\t322\t332\t14.117\t1.78e-08\t1.04e-08\tGACATTTTAAA\n+1\tphiX174\t2579\t2589\t13.9959\t1.88e-08\t1.08e-08\tTGGATACATCT\n+1\tphiX174\t5001\t5011\t13.7538\t2.1e-08\t1.19e-08\tGGTTTCTATGT\n+1\tphiX174\t3569\t3579\t13.6328\t2.22e-08\t1.2e-08\tTATGGAAAACA\n+1\tphiX174\t4217\t4227\t13.6328\t2.22e-08\t1.2e-08\tTGCTTCTGACG\n+1\tphiX174\t4262\t4272\t13.6328\t2.22e-08\t1.2e-08\tAATGGATGAAT\n+1\tphiX174\t194\t204\t13.5117\t2.33e-08\t1.24e-08\tATCAACTAACG\n+1\tph'..b'e-06\tTCGCGATTCAA\n+1\tphiX174\t2370\t2380\t-15.1774\t9.18e-05\t1.76e-06\tAGGTTTTCTGC\n+1\tphiX174\t3573\t3583\t-15.1774\t9.18e-05\t1.76e-06\tGAAAACACCAA\n+1\tphiX174\t3592\t3602\t-15.1774\t9.18e-05\t1.76e-06\tAGCAACAGCAG\n+1\tphiX174\t3635\t3645\t-15.1774\t9.18e-05\t1.76e-06\tAGCTCAAACGG\n+1\tphiX174\t3683\t3693\t-15.1774\t9.18e-05\t1.76e-06\tGACTCGCAAGG\n+1\tphiX174\t3727\t3737\t-15.1774\t9.18e-05\t1.76e-06\tCGCAGAATCAG\n+1\tphiX174\t4111\t4121\t-15.1774\t9.18e-05\t1.76e-06\tATAAGCAGATG\n+1\tphiX174\t4347\t4357\t-15.1774\t9.18e-05\t1.76e-06\tAAATGGTTTTT\n+1\tphiX174\t4426\t4436\t-15.1774\t9.18e-05\t1.76e-06\tGCGATGAGTAT\n+1\tphiX174\t5047\t5057\t-15.1774\t9.18e-05\t1.76e-06\tTTGCTGCTAAA\n+1\tphiX174\t71\t81\t-15.2984\t9.41e-05\t1.79e-06\tGATAAAGCAGG\n+1\tphiX174\t935\t945\t-15.2984\t9.41e-05\t1.79e-06\tCTTTGGTATGT\n+1\tphiX174\t1228\t1238\t-15.2984\t9.41e-05\t1.79e-06\tCGTTTATGGTG\n+1\tphiX174\t1557\t1567\t-15.2984\t9.41e-05\t1.79e-06\tCTTCTACCACA\n+1\tphiX174\t1935\t1945\t-15.2984\t9.41e-05\t1.79e-06\tCCGATATTGCT\n+1\tphiX174\t2218\t2228\t-15.2984\t9.41e-05\t1.79e-06\tGGTTAAATTTA\n+1\tphiX174\t2288\t2298\t-15.2984\t9.41e-05\t1.79e-06\tAAGATTGAGTG\n+1\tphiX174\t2369\t2379\t-15.2984\t9.41e-05\t1.79e-06\tTAGGTTTTCTG\n+1\tphiX174\t2934\t2944\t-15.2984\t9.41e-05\t1.79e-06\tTTTGGTGCTAT\n+1\tphiX174\t3782\t3792\t-15.2984\t9.41e-05\t1.79e-06\tTAATGTCGTCA\n+1\tphiX174\t4257\t4267\t-15.2984\t9.41e-05\t1.79e-06\tAAGTTAATGGA\n+1\tphiX174\t4576\t4586\t-15.2984\t9.41e-05\t1.79e-06\tTTTTTGACACT\n+1\tphiX174\t4858\t4868\t-15.2984\t9.41e-05\t1.79e-06\tATAGCTTGCAA\n+1\tphiX174\t5168\t5178\t-15.2984\t9.41e-05\t1.79e-06\tAATGACAAATC\n+1\tphiX174\t5287\t5297\t-15.2984\t9.41e-05\t1.79e-06\tAAGTTACTGTA\n+1\tphiX174\t5373\t5383\t-15.2984\t9.41e-05\t1.79e-06\tGTATCCAACCT\n+1\tphiX174\t17\t27\t-15.4195\t9.64e-05\t1.81e-06\tATGACGCAGAA\n+1\tphiX174\t227\t237\t-15.4195\t9.64e-05\t1.81e-06\tTGGATGAGGAG\n+1\tphiX174\t272\t282\t-15.4195\t9.64e-05\t1.81e-06\tACTGGTTTAGA\n+1\tphiX174\t358\t368\t-15.4195\t9.64e-05\t1.81e-06\tGATGCTGTTCA\n+1\tphiX174\t841\t851\t-15.4195\t9.64e-05\t1.81e-06\tTGATGTAATGT\n+1\tphiX174\t1347\t1357\t-15.4195\t9.64e-05\t1.81e-06\tATACCAATAAA\n+1\tphiX174\t1528\t1538\t-15.4195\t9.64e-05\t1.81e-06\tTGAGACTGAGC\n+1\tphiX174\t3274\t3284\t-15.4195\t9.64e-05\t1.81e-06\tAGGATACTCGT\n+1\tphiX174\t3363\t3373\t-15.4195\t9.64e-05\t1.81e-06\tGACGCCGGATT\n+1\tphiX174\t4599\t4609\t-15.4195\t9.64e-05\t1.81e-06\tGACGACCGATT\n+1\tphiX174\t4600\t4610\t-15.4195\t9.64e-05\t1.81e-06\tACGACCGATTA\n+1\tphiX174\t4758\t4768\t-15.4195\t9.64e-05\t1.81e-06\tGGCCGTCTTCA\n+1\tphiX174\t4875\t4885\t-15.4195\t9.64e-05\t1.81e-06\tTGGCCTTATGG\n+1\tphiX174\t4953\t4963\t-15.4195\t9.64e-05\t1.81e-06\tGTTGATGCTAA\n+1\tphiX174\t4978\t4988\t-15.4195\t9.64e-05\t1.81e-06\tAAGCTACCAGT\n+1\tphiX174\t5265\t5275\t-15.4195\t9.64e-05\t1.81e-06\tGAGATGAGATT\n+1\tphiX174\t160\t170\t-15.5405\t9.87e-05\t1.83e-06\tAGCTCGAGAAG\n+1\tphiX174\t201\t211\t-15.5405\t9.87e-05\t1.83e-06\tAACGATTCTGT\n+1\tphiX174\t274\t284\t-15.5405\t9.87e-05\t1.83e-06\tTGGTTTAGATA\n+1\tphiX174\t333\t343\t-15.5405\t9.87e-05\t1.83e-06\tAGAGCGTGGAT\n+1\tphiX174\t371\t381\t-15.5405\t9.87e-05\t1.83e-06\tCACTAATAGGT\n+1\tphiX174\t468\t478\t-15.5405\t9.87e-05\t1.83e-06\tTTGGATTTAAC\n+1\tphiX174\t777\t787\t-15.5405\t9.87e-05\t1.83e-06\tGGAAACACTGA\n+1\tphiX174\t804\t814\t-15.5405\t9.87e-05\t1.83e-06\tGAAGAAAACGT\n+1\tphiX174\t926\t936\t-15.5405\t9.87e-05\t1.83e-06\tGGCGCTCGTCT\n+1\tphiX174\t972\t982\t-15.5405\t9.87e-05\t1.83e-06\tGGCTTCGGCCC\n+1\tphiX174\t1133\t1143\t-15.5405\t9.87e-05\t1.83e-06\tGACGCCGTTGG\n+1\tphiX174\t1330\t1340\t-15.5405\t9.87e-05\t1.83e-06\tTGGCACGATTA\n+1\tphiX174\t1946\t1956\t-15.5405\t9.87e-05\t1.83e-06\tGGCGACCCTGT\n+1\tphiX174\t2195\t2205\t-15.5405\t9.87e-05\t1.83e-06\tCAGTTGTTGCA\n+1\tphiX174\t2254\t2264\t-15.5405\t9.87e-05\t1.83e-06\tGACCACTCGCG\n+1\tphiX174\t2893\t2903\t-15.5405\t9.87e-05\t1.83e-06\tGAGATTATTTG\n+1\tphiX174\t2957\t2967\t-15.5405\t9.87e-05\t1.83e-06\tTGCTTCTGCTC\n+1\tphiX174\t3404\t3414\t-15.5405\t9.87e-05\t1.83e-06\tACTGGACAATC\n+1\tphiX174\t3425\t3435\t-15.5405\t9.87e-05\t1.83e-06\tTGCCGAGATGC\n+1\tphiX174\t3432\t3442\t-15.5405\t9.87e-05\t1.83e-06\tATGCAAAATGA\n+1\tphiX174\t3453\t3463\t-15.5405\t9.87e-05\t1.83e-06\tGAGATTGCTGG\n+1\tphiX174\t3827\t3837\t-15.5405\t9.87e-05\t1.83e-06\tTGGTATTGATA\n+1\tphiX174\t3973\t3983\t-15.5405\t9.87e-05\t1.83e-06\tGCTTTTTTATG\n+1\tphiX174\t4018\t4028\t-15.5405\t9.87e-05\t1.83e-06\tATTATTTTGAC\n+1\tphiX174\t5243\t5253\t-15.5405\t9.87e-05\t1.83e-06\tATTGAAGCAGA\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/meme/fimo/fimo_output_xml_1.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/meme/fimo/fimo_output_xml_1.xml Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,53 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<?xml-stylesheet type="text/xsl" href="fimo-to-html.xsl"?>
+
+<fimo version="4.6.0" release="8 PST 20">
+  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+  xsi:schemaLocation=  xmlns:fimo="http://noble.gs.washington.edu/schema/fimo"
+>
+<command-line>fimo --o /path/to/dataset_?_files --verbosity 1 /path/to/dataset_?.dat /path/to/dataset_?.dat</command-line>
+<settings>
+<setting name="output directory">/path/to/dataset_?_files</setting>
+<setting name="MEME file name">/path/to/dataset_?.dat</setting>
+<setting name="sequence file name">/path/to/dataset_?.dat</setting>
+<setting name="background file name">(null)</setting>
+<setting name="motif name">motif</setting>
+<setting name="allow clobber">false</setting>
+<setting name="compute q-values">true</setting>
+<setting name="output p-threshold set">false</setting>
+<setting name="output q-threshold set">false</setting>
+<setting name="text only">false</setting>
+<setting name="scan both strands">false</setting>
+<setting name="max sequence length">250000000</setting>
+<setting name="output q-value threshold">  1</setting>
+<setting name="output p-value threshold">0.0001</setting>
+<setting name="pseudocount">0.1</setting>
+<setting name="verbosity">1</setting>
+</settings>
+<sequence-data num-sequences="1" num-residues="5386" />
+<alphabet>protein</alphabet>
+<motif name="1" width="11" best-possible-match="GGGGTATAAAA"/>
+<background source="non-redundant database">
+<value letter="A">0.073</value>
+<value letter="C">0.018</value>
+<value letter="D">0.052</value>
+<value letter="E">0.062</value>
+<value letter="F">0.040</value>
+<value letter="G">0.069</value>
+<value letter="H">0.022</value>
+<value letter="I">0.056</value>
+<value letter="K">0.058</value>
+<value letter="L">0.092</value>
+<value letter="M">0.023</value>
+<value letter="N">0.046</value>
+<value letter="P">0.051</value>
+<value letter="Q">0.041</value>
+<value letter="R">0.052</value>
+<value letter="S">0.074</value>
+<value letter="T">0.059</value>
+<value letter="V">0.064</value>
+<value letter="W">0.013</value>
+<value letter="Y">0.033</value>
+</background>
+<cisml-file>cisml.xml</cisml-file>
+</fimo>

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/meme/meme/meme_input_1.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/meme/meme/meme_input_1.fasta Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,66 @@
+>chr21_19617074_19617124_+
+AAAAATTATTACTAGGGAGGGGGCCGGAACCTCGGGACGTGGGTATATAA
+>chr21_26934381_26934431_+
+GCGCCTGGTCGGTTATGAGTCACAAGTGAGTTATAAAAGGGTCGCACGTT
+>chr21_28217753_28217803_-
+CAAAGGGGAGGAGTGGGGTGGGGGTGGGGGTTTCACTGGTCCACTATAAA
+>chr21_31710037_31710087_-
+AACACCCAGGTTTCTGAGTATATAATCGCCGCACCAAAGAATTTAATTTT
+>chr21_31744582_31744632_-
+CCCAGGTCTAAGAGCATATATAACTTGGAGTCCAGACTATGACATTCAAA
+>chr21_31768316_31768366_+
+AACGTATATAAATGGTCCTGTCCAGATGTGGCATGCAAACTCAGAATCTT
+>chr21_31914206_31914256_-
+TGACACCCACTACTTAGAGTATAAAATCATTCTGAGAAGTTAGAGACACC
+>chr21_31933633_31933683_-
+TCAGAGTATATATAAATGTTCCTGTCCAGTCACAGTCACCAAACTGACCT
+>chr21_31962741_31962791_-
+ACATATAACTCAGGTTGGATAAAATAATTTGTACAAATCAGGAGAGTCAA
+>chr21_31964683_31964733_+
+TCTGATTCACTGAGGCATATAAAAGGCCCTCTGCGGAGAAGTGTCCATAC
+>chr21_31973364_31973414_+
+aaacttaaaactctataaacttaaaactCTAGAATCTGATCCTGCTATAC
+>chr21_31992870_31992920_+
+CTCATACACTATTGAAGATGTATAAAATTTCATTTGCAGATGGTGACATT
+>chr21_32185595_32185645_-
+TCACCACCCACCAGAGCTGGGATATATAAAGAAGGTTCTGAGACTAGGAA
+>chr21_32202076_32202126_-
+TGCCCACCAGCTTGAGGTATAAAAAGCCCTGTACGGGAAGAGACCTTCAT
+>chr21_32253899_32253949_-
+AGCCCCACCCACCAGCAAGGATATATAAAAGCTCAGGAGTCTGGAGTGAC
+>chr21_32410820_32410870_-
+TCTACCCCACTAATCACTGAGGATGTATAAAAGTCCCAGGGAAGCTGGTG
+>chr21_36411748_36411798_-
+ATAGTTCTGTATAGTTTCAGTTGGCATCtaaaaattatataactttattt
+>chr21_37838750_37838800_-
+gatggttttataaggggcctcaccctcggctcagccctcattcttctcct
+>chr21_45705687_45705737_+
+CCGGGGCGGAGCGGCCTTTGCTCTTTGCGTGGTCGCGGGGGTATAACAGC
+>chr21_45971413_45971463_-
+CAGGCCCTGGGCATATAAAAGCCCCAGCAGCCAACAGGctcacacacaca
+>chr21_45978668_45978718_-
+CAGAGGGGTATAAAGGTTCCGACCACTCAGAGGCCTGGCACGAtcactca
+>chr21_45993530_45993580_+
+CCAAGGAGGAGTATAAAAGCCCCACAAACCCGAGCACCTCACTCACTCGC
+>chr21_46020421_46020471_+
+GAGACATATAAAAGCCAACATCCCTGAGCACCTAACACACGGactcactc
+>chr21_46031920_46031970_+
+GGAAAATACCCAGGGAGGGTATAAAACCTCAGCAGCCAGGGCACACAAAC
+>chr21_46046964_46047014_+
+ACAAGGCCAGGAGGGGTATAAAAGCCTGAGAGCCCCAAGAACctcacaca
+>chr21_46057197_46057247_+
+ATTGCTGAGTCTCCTGCTGGGAAAACACAGGCCCTGGGCATATAAAAGCC
+>chr21_46086869_46086919_-
+GACAGGTGTGCTTCTGTGCTGTGGGGATGCCTGGGCCCAGGTATAAAGGC
+>chr21_46102103_46102153_-
+AGGTGTGTGCTTCTGTGCTGTGGGGATGCCTGGGTCCAGGTATAAAGGCT
+>chr21_47517957_47518007_+
+CCTGGCGGCGGGGCGGGTCAGGCCGGCGGGGCGGGGTATAAAGGGGGCGG
+>chr21_47517957_47518007_+
+CCTGGCGGCGGGGCGGGTCAGGCCGGCGGGGCGGGGTATAAAGGGGGCGG
+>chr21_47517957_47518007_+
+CCTGGCGGCGGGGCGGGTCAGGCCGGCGGGGCGGGGTATAAAGGGGGCGG
+>chr21_47575506_47575556_-
+TGAGAAGCCGGTGGGGAGGTGCTGCCGGTGAGCGTATAAAGGCCCTGGCG
+>chr21_47575506_47575556_-
+TGAGAAGCCGGTGGGGAGGTGCTGCCGGTGAGCGTATAAAGGCCCTGGCG

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/meme/meme/meme_output_html_1.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/meme/meme/meme_output_html_1.html Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,2904 @@\n+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\n+<html>\n+<head>\n+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">\n+<title>MEME</title>\n+<style type="text/css">\n+ \n+ /* START INCLUDED FILE "meme.css" */\n+ /* The following is the content of meme.css */\n+ body { background-color:white; font-size: 12px; font-family: Verdana, Arial, Helvetica, sans-serif;}\n+\n+ div.help {\n+ display: inline-block;\n+ margin: 0px;\n+ padding: 0px;\n+ width: 12px;\n+ height: 13px;\n+ cursor: pointer;\n+ background-image: url("help.gif");\n+ background-image: url("data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAAwAAAANAQMAAACn5x0BAAAAAXNSR0IArs4c6QAAAAZQTFRFAAAAnp6eqp814gAAAAF0Uk5TAEDm2GYAAAABYktHRACIBR1IAAAACXBIWXMAAAsTAAALEwEAmpwYAAAAB3RJTUUH2gMJBQgGYqhNZQAAACZJREFUCNdj+P+BoUGAoV+AYeYEEGoWYGgTYGgRAAm2gRGQ8f8DAOnhC2lYnqs6AAAAAElFTkSuQmCC");\n+ }\n+ \n+ p.spaced { line-height: 1.8em;}\n+ \n+ p.pad { padding-left: 30px; padding-top: 5px; padding-bottom: 10px;}\n+\n+ td.jump { font-size: 13px; color: #ffffff; background-color: #00666a;\n+ font-family: Georgia, "Times New Roman", Times, serif;}\n+\n+ a.jump { margin: 15px 0 0; font-style: normal; font-variant: small-caps;\n+ font-weight: bolder; font-family: Georgia, "Times New Roman", Times, serif;}\n+\n+ h2.mainh {font-size: 1.5em; font-style: normal; margin: 15px 0 0;\n+ font-variant: small-caps; font-family: Georgia, "Times New Roman", Times, serif;}\n+\n+ h2.line {border-bottom: 1px solid #CCCCCC; font-size: 1.5em; font-style: normal;\n+ margin: 15px 0 0; padding-bottom: 3px; font-variant: small-caps;\n+ font-family: Georgia, "Times New Roman", Times, serif;}\n+\n+ h4 {border-bottom: 1px solid #CCCCCC; font-size: 1.2em; font-style: normal;\n+ margin: 10px 0 0; padding-bottom: 3px; font-family: Georgia, "Times New Roman", Times, serif;}\n+\n+ h5 {margin: 0px}\n+\n+ a.help { font-size: 9px; font-style: normal; text-transform: uppercase;\n+ font-family: Georgia, "Times New Roman", Times, serif;}\n+\n+ div.pad { padding-left: 30px; padding-top: 5px; padding-bottom: 10px;}\n+ \n+ div.pad1 { margin: 10px 5px;}\n+\n+ div.pad2 { margin: 25px 5px 5px;}\n+ h2.pad2 { padding: 25px 5px 5px;}\n+\n+ div.pad3 { padding: 5px 0px 10px 30px;}\n+\n+ div.box { border: 2px solid #CCCCCC; padding:10px;}\n+\n+ div.bar { border-left: 7px solid #00666a; padding:5px; margin-top:25px; }\n+\n+ div.subsection {margin:25px 0px;}\n+\n+ img {border:0px none;}\n+\n+ th.majorth {text-align:left;}\n+ th.minorth {font-weight:normal; text-align:left; width:8em; padding: 3px 0px;}\n+ th.actionth {font-weight:normal; text-align:left;}\n+\n+ .strand_name {text-align:left;}\n+ .strand_side {padding:0px 10px;}\n+ .strand_start {padding:0px 10px;}\n+ .strand_pvalue {text-align:center; padding:0px 10px;}\n+ .strand_lflank {text-align:right; padding-right:5px; font-weight:bold; font-size:large; font-family: \'Courier New\', Courier, monospace; color:gray;}\n+ .strand_seq {text-align:center; font-weight:bold; font-size:large; font-family: \'Courier New\', Courier, monospace;}\n+ .strand_rflank {text-align:left; padding-left:5px; font-weight:bold; font-size:large; font-family: \'Courier New\', Courier, monospace; color:gray;}\n+\n+ .block_td {height:25px;}\n+ .block_container {position:relative; width:99%; height:25px; padding:0px; margin:0px;}\n+ .block_motif {position:absolute; z-index:3; height:12px; top:0px; text-align:center; vertical-align:middle; background-color:cyan;}\n+ .block_rule {position:absolute; z-index:2; width:100%; height:1px; top:12px; left:0px; background-color:gray;}\n+ .block_plus_sym {positi'..b'ncies of letters in the motif sites.\n+ </dd>\n+<dt>\n+<a name="format_BLOCKS_doc"></a>BLOCKS Format</dt>\n+<dd>\n+ For use with <a href="http://blocks.fhcrc.org/blocks">BLOCKS tools</a>.\n+ </dd>\n+<dt>\n+<a name="format_FASTA_doc"></a>FASTA Format</dt>\n+<dd>\n+ The FASTA format as described <a href="http://meme.nbcr.net/meme/doc/fasta-format.html">here</a>.\n+ </dd>\n+<dt>\n+<a name="format_raw_doc"></a>Raw Format</dt>\n+<dd>\n+ Just the sites of the sequences that contributed to the motif. One site per line.\n+ </dd>\n+</dl>\n+</div>\n+<a name="sites_doc"></a><h5 class="doc">Sites</h5>\n+<div class="doc"><p>\n+ MEME displays the occurrences (sites) of the motif in the training set. The sites are shown aligned with each other, and the ten sequence\n+ positions preceding and following each site are also shown. Each site is identified by the name of the sequence where it occurs,\n+ the strand (if both strands of DNA sequences are being used), and the position in the sequence where the site begins. When the DNA strand\n+ is specified, \'+\' means the sequence in the training set, and \'-\' means the reverse complement of the training set sequence.\n+ (For \'-\' strands, the \'start\' position is actually the position on the <b>positive</b> strand where the site ends.) The sites are <b>listed \n+ in order of increasing statistical significance</b> (<i>p</i>-value). The <i>p</i>-value of a site is computed from the the match score of \n+ the site with the <a href="#format_PSSM_doc">position specific scoring matrix</a> for the motif. The <i>p</i>-value gives the probability of a \n+ random string (generated from the background letter frequencies) having the same match score or higher. (This is referred to as the \n+ <b>position <i>p</i>-value</b> by the MAST algorithm.)\n+ </p></div>\n+<a name="diagrams_doc"></a><h5 class="doc">Block Diagrams</h5>\n+<div class="doc"><p>\n+ The occurrences of the motif in the training set sequences are shown as coloured blocks on a line. One diagram is printed for each\n+ sequence showing all the sites contributating to that motif in that sequence. The sequences are <b>listed in the same order as in the input</b> \n+ to make it easier to compare multiple block diagrams. Additionally the best <i>p</i>-value for the sequence/motif combination is\n+ listed though this may not be in ascending order as with the sites. The <i>p</i>-value of an occurrence is the probability of a single\n+ random subsequence the length of the motif, generated according to the 0-order background model, having a score at least as high as \n+ the score of the occurrence. When the DNA strand is specified \'+\', it means the motif appears from left to right on the sequence, and \'-\' \n+ means the motif appears from right to left on the complementary strand. A sequence position scale is shown at the end of each table of \n+ block diagrams. \n+ </p></div>\n+<a name="combined_doc"></a><h5>Combined Block Diagrams</h5>\n+<div class="doc">\n+<p>\n+ The motif occurrences shown in the motif summary <b>may not be exactly the same as those reported in each motif section</b> because \n+ only motifs with a position <em>p</em>-value of 0.0001 that don\'t overlap other, more significant motif occurrences are shown. \n+ </p>\n+<p>\n+ See the documentation for <a href="http://meme.nbcr.net/meme/mast-output.html">MAST output</a> for the definition of position and\n+ combined <em>p</em>-values.\n+ </p>\n+</div>\n+</div></span><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br>\n+</form></body>\n+</html>\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/meme/meme/meme_output_txt_1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/meme/meme/meme_output_txt_1.txt Sat Feb 21 16:33:42 2015 +0100

[

b'@@ -0,0 +1,325 @@\n+********************************************************************************\n+MEME - Motif discovery tool\n+********************************************************************************\n+MEME version 4.6.0 (Release date: Thu Jan 20 14:06:48 PST 2011)\n+\n+For further information on how to interpret these results or to get\n+a copy of the MEME software please access http://meme.nbcr.net.\n+\n+This file may be used as input to the MAST algorithm for searching\n+sequence databases for matches to groups of motifs. MAST is available\n+for interactive use and downloading at http://meme.nbcr.net.\n+********************************************************************************\n+\n+\n+********************************************************************************\n+REFERENCE\n+********************************************************************************\n+If you use this program in your research, please cite:\n+\n+Timothy L. Bailey and Charles Elkan,\n+"Fitting a mixture model by expectation maximization to discover\n+motifs in biopolymers", Proceedings of the Second International\n+Conference on Intelligent Systems for Molecular Biology, pp. 28-36,\n+AAAI Press, Menlo Park, California, 1994.\n+********************************************************************************\n+\n+\n+********************************************************************************\n+TRAINING SET\n+********************************************************************************\n+DATAFILE= dataset_3.dat\n+ALPHABET= ACDEFGHIKLMNPQRSTVWY\n+Sequence name Weight Length Sequence name Weight Length \n+------------- ------ ------ ------------- ------ ------ \n+chr21_19617074_19617124_ 1.0000 50 chr21_26934381_26934431_ 1.0000 50 \n+chr21_28217753_28217803_ 1.0000 50 chr21_31710037_31710087_ 1.0000 50 \n+chr21_31744582_31744632_ 1.0000 50 chr21_31768316_31768366_ 1.0000 50 \n+chr21_31914206_31914256_ 1.0000 50 chr21_31933633_31933683_ 1.0000 50 \n+chr21_31962741_31962791_ 1.0000 50 chr21_31964683_31964733_ 1.0000 50 \n+chr21_31973364_31973414_ 1.0000 50 chr21_31992870_31992920_ 1.0000 50 \n+chr21_32185595_32185645_ 1.0000 50 chr21_32202076_32202126_ 1.0000 50 \n+chr21_32253899_32253949_ 1.0000 50 chr21_32410820_32410870_ 1.0000 50 \n+chr21_36411748_36411798_ 1.0000 50 chr21_37838750_37838800_ 1.0000 50 \n+chr21_45705687_45705737_ 1.0000 50 chr21_45971413_45971463_ 1.0000 50 \n+chr21_45978668_45978718_ 1.0000 50 chr21_45993530_45993580_ 1.0000 50 \n+chr21_46020421_46020471_ 1.0000 50 chr21_46031920_46031970_ 1.0000 50 \n+chr21_46046964_46047014_ 1.0000 50 chr21_46057197_46057247_ 1.0000 50 \n+chr21_46086869_46086919_ 1.0000 50 chr21_46102103_46102153_ 1.0000 50 \n+chr21_47517957_47518007_ 1.0000 50 chr21_47575506_47575556_ 1.0000 50 \n+********************************************************************************\n+\n+********************************************************************************\n+COMMAND LINE SUMMARY\n+********************************************************************************\n+This information can also be useful in the event you wish to report a\n+problem with the MEME software.\n+\n+command: meme dataset_3.dat -o dataset_4_files -nostatus \n+\n+model: mod= zoops nmotifs= 1 evt= inf\n+object function= E-value of product of p-values\n+width: minw= 8 maxw= 50 minic= 0.00\n+width: wg= 11 ws= 1 endgaps= yes\n+nsites: minsites= 2 maxsites= 30 wnsites= 0.8\n+theta: prob= 1 spmap= pam spfuzz= 120\n+global: substring= yes branching= no wbranch= no\n+em: prior= megap b= 7500 maxiter= 50\n+ distance= 1e-05\n+data: n= 1500 N= 30'..b'0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 \n+ 0.760000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.240000 0.000000 0.000000 0.000000 \n+ 0.960000 0.040000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 \n+ 0.840000 0.000000 0.000000 0.000000 0.000000 0.120000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.040000 0.000000 0.000000 0.000000 \n+--------------------------------------------------------------------------------\n+\n+--------------------------------------------------------------------------------\n+\tMotif 1 regular expression\n+--------------------------------------------------------------------------------\n+[GA][GA][GC][GA]TATA[AT]AA\n+--------------------------------------------------------------------------------\n+\n+\n+\n+\n+Time 2.13 secs.\n+\n+********************************************************************************\n+\n+\n+********************************************************************************\n+SUMMARY OF MOTIFS\n+********************************************************************************\n+\n+--------------------------------------------------------------------------------\n+\tCombined block diagrams: non-overlapping sites with p-value < 0.0001\n+--------------------------------------------------------------------------------\n+SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM\n+------------- ---------------- -------------\n+chr21_19617074_19617124_ 1.22e-03 39_[1(3.06e-05)]\n+chr21_26934381_26934431_ 2.21e-03 27_[1(5.52e-05)]_12\n+chr21_28217753_28217803_ 7.29e-01 50\n+chr21_31710037_31710087_ 2.37e-03 14_[1(5.94e-05)]_25\n+chr21_31744582_31744632_ 1.22e-03 12_[1(3.06e-05)]_27\n+chr21_31768316_31768366_ 1.53e-03 [1(3.82e-05)]_39\n+chr21_31914206_31914256_ 6.70e-04 15_[1(1.68e-05)]_24\n+chr21_31933633_31933683_ 1.81e-03 4_[1(4.54e-05)]_35\n+chr21_31962741_31962791_ 1.61e-02 50\n+chr21_31964683_31964733_ 1.36e-04 13_[1(3.41e-06)]_26\n+chr21_31973364_31973414_ 1.99e-01 50\n+chr21_31992870_31992920_ 3.47e-04 16_[1(8.67e-06)]_23\n+chr21_32185595_32185645_ 3.47e-04 18_[1(8.67e-06)]_21\n+chr21_32202076_32202126_ 2.01e-04 13_[1(5.01e-06)]_26\n+chr21_32253899_32253949_ 8.11e-04 19_[1(2.03e-05)]_20\n+chr21_32410820_32410870_ 3.47e-04 21_[1(8.67e-06)]_18\n+chr21_36411748_36411798_ 2.71e-03 22_[1(6.78e-05)]_17\n+chr21_37838750_37838800_ 8.23e-02 50\n+chr21_45705687_45705737_ 1.53e-03 37_[1(3.82e-05)]_2\n+chr21_45971413_45971463_ 1.36e-04 9_[1(3.41e-06)]_30\n+chr21_45978668_45978718_ 6.37e-04 4_[1(1.59e-05)]_35\n+chr21_45993530_45993580_ 1.60e-04 7_[1(4.00e-06)]_32\n+chr21_46020421_46020471_ 4.83e-04 2_[1(1.21e-05)]_37\n+chr21_46031920_46031970_ 2.43e-04 15_[1(6.06e-06)]_24\n+chr21_46046964_46047014_ 4.26e-05 12_[1(1.06e-06)]_27\n+chr21_46057197_46057247_ 1.36e-04 36_[1(3.41e-06)]_3\n+chr21_46086869_46086919_ 4.30e-02 50\n+chr21_46102103_46102153_ 4.30e-02 50\n+chr21_47517957_47518007_ 6.37e-04 32_[1(1.59e-05)]_7\n+chr21_47575506_47575556_ 1.61e-03 30_[1(4.02e-05)]_9\n+--------------------------------------------------------------------------------\n+\n+********************************************************************************\n+\n+\n+********************************************************************************\n+Stopped because nmotifs = 1 reached.\n+********************************************************************************\n+\n+CPU: scofield\n+\n+********************************************************************************\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/meme/meme/meme_output_xml_1.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/meme/meme/meme_output_xml_1.xml Sat Feb 21 16:33:42 2015 +0100

[

b'@@ -0,0 +1,1286 @@\n+<?xml version=\'1.0\' encoding=\'UTF-8\' standalone=\'yes\'?>\n+\n+<!DOCTYPE MEME[\n+<!ELEMENT MEME (\n+ training_set,\n+ model, \n+ motifs, \n+ scanned_sites_summary?\n+)>\n+<!ATTLIST MEME \n+ version CDATA #REQUIRED\n+ release CDATA #REQUIRED\n+>\n+\n+<!ELEMENT training_set (alphabet, ambigs, sequence+, letter_frequencies)>\n+<!ATTLIST training_set datafile CDATA #REQUIRED length CDATA #REQUIRED>\n+<!ELEMENT alphabet (letter+)>\n+<!ATTLIST alphabet id (amino-acid|nucleotide) #REQUIRED\n+ length CDATA #REQUIRED>\n+<!ELEMENT ambigs (letter+)>\n+<!ELEMENT letter EMPTY>\n+<!ATTLIST letter id ID #REQUIRED>\n+<!ATTLIST letter symbol CDATA #REQUIRED>\n+<!ELEMENT sequence EMPTY>\n+<!ATTLIST sequence id ID #REQUIRED\n+ name CDATA #REQUIRED\n+ length CDATA #REQUIRED\n+ weight CDATA #REQUIRED\n+>\n+<!ELEMENT letter_frequencies (alphabet_array)>\n+\n+\n+<!ELEMENT model (\n+ command_line,\n+ host,\n+ type,\n+ nmotifs,\n+ evalue_threshold,\n+ object_function,\n+ min_width,\n+ max_width,\n+ minic,\n+ wg,\n+ ws,\n+ endgaps,\n+ minsites,\n+ maxsites,\n+ wnsites,\n+ prob,\n+ spmap,\n+ spfuzz,\n+ prior,\n+ beta,\n+ maxiter,\n+ distance,\n+ num_sequences,\n+ num_positions,\n+ seed,\n+ seqfrac,\n+ strands,\n+ priors_file,\n+ reason_for_stopping,\n+ background_frequencies\n+)>\n+<!ELEMENT command_line (#PCDATA)*>\n+<!ELEMENT host (#PCDATA)*>\n+<!ELEMENT type (#PCDATA)*>\n+<!ELEMENT nmotifs (#PCDATA)*>\n+<!ELEMENT evalue_threshold (#PCDATA)*>\n+<!ELEMENT object_function (#PCDATA)*>\n+<!ELEMENT min_width (#PCDATA)*>\n+<!ELEMENT max_width (#PCDATA)*>\n+<!ELEMENT minic (#PCDATA)*>\n+<!ELEMENT wg (#PCDATA)*>\n+<!ELEMENT ws (#PCDATA)*>\n+<!ELEMENT endgaps (#PCDATA)*>\n+<!ELEMENT minsites (#PCDATA)*>\n+<!ELEMENT maxsites (#PCDATA)*>\n+<!ELEMENT wnsites (#PCDATA)*>\n+<!ELEMENT prob (#PCDATA)*>\n+<!ELEMENT spmap (#PCDATA)*>\n+<!ELEMENT spfuzz (#PCDATA)*>\n+<!ELEMENT prior (#PCDATA)*>\n+<!ELEMENT beta (#PCDATA)*>\n+<!ELEMENT maxiter (#PCDATA)*>\n+<!ELEMENT distance (#PCDATA)*>\n+<!ELEMENT num_sequences (#PCDATA)*>\n+<!ELEMENT num_positions (#PCDATA)*>\n+<!ELEMENT seed (#PCDATA)*>\n+<!ELEMENT seqfrac (#PCDATA)*>\n+<!ELEMENT strands (#PCDATA)*>\n+<!ELEMENT priors_file (#PCDATA)*>\n+<!ELEMENT reason_for_stopping (#PCDATA)*>\n+<!ELEMENT background_frequencies (alphabet_array)>\n+<!ATTLIST background_frequencies source CDATA #REQUIRED>\n+\n+\n+<!ELEMENT motifs (motif+)>\n+<!ELEMENT motif (scores, probabilities, regular_expression?, contributing_sites)>\n+<!ATTLIST motif id ID #REQUIRED\n+ name CDATA #REQUIRED\n+ width CDATA #REQUIRED\n+ sites CDATA #REQUIRED\n+ llr CDATA #REQUIRED\n+ ic CDATA #REQUIRED\n+ re CDATA #REQUIRED\n+ bayes_threshold CDATA #REQUIRED\n+ e_value CDATA #REQUIRED\n+ elapsed_time CDATA #REQUIRED\n+ url CDATA ""\n+>\n+<!ELEMENT scores (alphabet_matrix)>\n+<!ELEMENT probabilities (alphabet_matrix)>\n+<!ELEMENT regular_expression (#PCDATA)*>\n+\n+\n+\n+<!ELEMENT contributing_sites (contributing_site+)>\n+<!ELEMENT contributing_site (left_flank, site, right_flank)>\n+<!ATTLIST contributing_site sequence_id IDREF #REQUIRED\n+ position CDATA #REQUIRED\n+ strand (plus|minus|none) \'none\'\n+ pvalue CDATA #REQUIRED\n+>\n+\n+<!ELEMENT left_flank (#PCDATA)>\n+\n+<!ELEMENT site (letter_ref+)>\n+\n+<!ELEMENT right_flank (#PCDATA)>\n+\n+\n+<!-- Scanned site'..b'="none" position="12" pvalue="3.06e-05"/>\n+</scanned_sites>\n+<scanned_sites sequence_id="sequence_5" pvalue="1.53e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="0" pvalue="3.82e-05"/>\n+</scanned_sites>\n+<scanned_sites sequence_id="sequence_6" pvalue="6.70e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="15" pvalue="1.68e-05"/>\n+</scanned_sites>\n+<scanned_sites sequence_id="sequence_7" pvalue="1.81e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="4" pvalue="4.54e-05"/>\n+</scanned_sites>\n+<scanned_sites sequence_id="sequence_8" pvalue="1.61e-02" num_sites="0"></scanned_sites>\n+<scanned_sites sequence_id="sequence_9" pvalue="1.36e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="13" pvalue="3.41e-06"/>\n+</scanned_sites>\n+<scanned_sites sequence_id="sequence_10" pvalue="1.99e-01" num_sites="0"></scanned_sites>\n+<scanned_sites sequence_id="sequence_11" pvalue="3.47e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="16" pvalue="8.67e-06"/>\n+</scanned_sites>\n+<scanned_sites sequence_id="sequence_12" pvalue="3.47e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="18" pvalue="8.67e-06"/>\n+</scanned_sites>\n+<scanned_sites sequence_id="sequence_13" pvalue="2.01e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="13" pvalue="5.01e-06"/>\n+</scanned_sites>\n+<scanned_sites sequence_id="sequence_14" pvalue="8.11e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="19" pvalue="2.03e-05"/>\n+</scanned_sites>\n+<scanned_sites sequence_id="sequence_15" pvalue="3.47e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="21" pvalue="8.67e-06"/>\n+</scanned_sites>\n+<scanned_sites sequence_id="sequence_16" pvalue="2.71e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="22" pvalue="6.78e-05"/>\n+</scanned_sites>\n+<scanned_sites sequence_id="sequence_17" pvalue="8.23e-02" num_sites="0"></scanned_sites>\n+<scanned_sites sequence_id="sequence_18" pvalue="1.53e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="37" pvalue="3.82e-05"/>\n+</scanned_sites>\n+<scanned_sites sequence_id="sequence_19" pvalue="1.36e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="9" pvalue="3.41e-06"/>\n+</scanned_sites>\n+<scanned_sites sequence_id="sequence_20" pvalue="6.37e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="4" pvalue="1.59e-05"/>\n+</scanned_sites>\n+<scanned_sites sequence_id="sequence_21" pvalue="1.60e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="7" pvalue="4.00e-06"/>\n+</scanned_sites>\n+<scanned_sites sequence_id="sequence_22" pvalue="4.83e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="2" pvalue="1.21e-05"/>\n+</scanned_sites>\n+<scanned_sites sequence_id="sequence_23" pvalue="2.43e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="15" pvalue="6.06e-06"/>\n+</scanned_sites>\n+<scanned_sites sequence_id="sequence_24" pvalue="4.26e-05" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="12" pvalue="1.06e-06"/>\n+</scanned_sites>\n+<scanned_sites sequence_id="sequence_25" pvalue="1.36e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="36" pvalue="3.41e-06"/>\n+</scanned_sites>\n+<scanned_sites sequence_id="sequence_26" pvalue="4.30e-02" num_sites="0"></scanned_sites>\n+<scanned_sites sequence_id="sequence_27" pvalue="4.30e-02" num_sites="0"></scanned_sites>\n+<scanned_sites sequence_id="sequence_28" pvalue="6.37e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="32" pvalue="1.59e-05"/>\n+</scanned_sites>\n+<scanned_sites sequence_id="sequence_29" pvalue="1.61e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="30" pvalue="4.02e-05"/>\n+</scanned_sites>\n+</scanned_sites_summary>\n+</MEME>\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/mergeCols.dat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/mergeCols.dat Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,65 @@
+chr1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 - CCDS989.1_cds_0_0_chr1_147962193_rchr1-
+chr1 147984545 147984630 CCDS990.1_cds_0_0_chr1_147984546_f 0 + CCDS990.1_cds_0_0_chr1_147984546_fchr1+
+chr1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 - CCDS993.1_cds_0_0_chr1_148078401_rchr1-
+chr1 148185136 148185276 CCDS996.1_cds_0_0_chr1_148185137_f 0 + CCDS996.1_cds_0_0_chr1_148185137_fchr1+
+chr10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 - CCDS7248.1_cds_0_0_chr10_55251624_rchr10-
+chr11 116124407 116124501 CCDS8374.1_cds_0_0_chr11_116124408_r 0 - CCDS8374.1_cds_0_0_chr11_116124408_rchr11-
+chr11 116206508 116206563 CCDS8377.1_cds_0_0_chr11_116206509_f 0 + CCDS8377.1_cds_0_0_chr11_116206509_fchr11+
+chr11 116211733 116212337 CCDS8378.1_cds_0_0_chr11_116211734_r 0 - CCDS8378.1_cds_0_0_chr11_116211734_rchr11-
+chr11 1812377 1812407 CCDS7726.1_cds_0_0_chr11_1812378_f 0 + CCDS7726.1_cds_0_0_chr11_1812378_fchr11+
+chr12 38440094 38440321 CCDS8736.1_cds_0_0_chr12_38440095_r 0 - CCDS8736.1_cds_0_0_chr12_38440095_rchr12-
+chr13 112381694 112381953 CCDS9526.1_cds_0_0_chr13_112381695_f 0 + CCDS9526.1_cds_0_0_chr13_112381695_fchr13+
+chr14 98710240 98712285 CCDS9949.1_cds_0_0_chr14_98710241_r 0 - CCDS9949.1_cds_0_0_chr14_98710241_rchr14-
+chr15 41486872 41487060 CCDS10096.1_cds_0_0_chr15_41486873_r 0 - CCDS10096.1_cds_0_0_chr15_41486873_rchr15-
+chr15 41673708 41673857 CCDS10097.1_cds_0_0_chr15_41673709_f 0 + CCDS10097.1_cds_0_0_chr15_41673709_fchr15+
+chr15 41679161 41679250 CCDS10098.1_cds_0_0_chr15_41679162_r 0 - CCDS10098.1_cds_0_0_chr15_41679162_rchr15-
+chr15 41826029 41826196 CCDS10101.1_cds_0_0_chr15_41826030_f 0 + CCDS10101.1_cds_0_0_chr15_41826030_fchr15+
+chr16 142908 143003 CCDS10397.1_cds_0_0_chr16_142909_f 0 + CCDS10397.1_cds_0_0_chr16_142909_fchr16+
+chr16 179963 180135 CCDS10401.1_cds_0_0_chr16_179964_r 0 - CCDS10401.1_cds_0_0_chr16_179964_rchr16-
+chr16 244413 244681 CCDS10402.1_cds_0_0_chr16_244414_f 0 + CCDS10402.1_cds_0_0_chr16_244414_fchr16+
+chr16 259268 259383 CCDS10403.1_cds_0_0_chr16_259269_r 0 - CCDS10403.1_cds_0_0_chr16_259269_rchr16-
+chr18 23786114 23786321 CCDS11891.1_cds_0_0_chr18_23786115_r 0 - CCDS11891.1_cds_0_0_chr18_23786115_rchr18-
+chr18 59406881 59407046 CCDS11985.1_cds_0_0_chr18_59406882_f 0 + CCDS11985.1_cds_0_0_chr18_59406882_fchr18+
+chr18 59455932 59456337 CCDS11986.1_cds_0_0_chr18_59455933_r 0 - CCDS11986.1_cds_0_0_chr18_59455933_rchr18-
+chr18 59600586 59600754 CCDS11988.1_cds_0_0_chr18_59600587_f 0 + CCDS11988.1_cds_0_0_chr18_59600587_fchr18+
+chr19 59068595 59069564 CCDS12866.1_cds_0_0_chr19_59068596_f 0 + CCDS12866.1_cds_0_0_chr19_59068596_fchr19+
+chr19 59236026 59236146 CCDS12872.1_cds_0_0_chr19_59236027_r 0 - CCDS12872.1_cds_0_0_chr19_59236027_rchr19-
+chr19 59297998 59298008 CCDS12877.1_cds_0_0_chr19_59297999_f 0 + CCDS12877.1_cds_0_0_chr19_59297999_fchr19+
+chr19 59302168 59302288 CCDS12878.1_cds_0_0_chr19_59302169_r 0 - CCDS12878.1_cds_0_0_chr19_59302169_rchr19-
+chr2 118288583 118288668 CCDS2120.1_cds_0_0_chr2_118288584_f 0 + CCDS2120.1_cds_0_0_chr2_118288584_fchr2+
+chr2 118394148 118394202 CCDS2121.1_cds_0_0_chr2_118394149_r 0 - CCDS2121.1_cds_0_0_chr2_118394149_rchr2-
+chr2 220190202 220190242 CCDS2441.1_cds_0_0_chr2_220190203_f 0 + CCDS2441.1_cds_0_0_chr2_220190203_fchr2+
+chr2 220229609 220230869 CCDS2443.1_cds_0_0_chr2_220229610_r 0 - CCDS2443.1_cds_0_0_chr2_220229610_rchr2-
+chr20 33330413 33330423 CCDS13249.1_cds_0_0_chr20_33330414_r 0 - CCDS13249.1_cds_0_0_chr20_33330414_rchr20-
+chr20 33513606 33513792 CCDS13255.1_cds_0_0_chr20_33513607_f 0 + CCDS13255.1_cds_0_0_chr20_33513607_fchr20+
+chr20 33579500 33579527 CCDS13256.1_cds_0_0_chr20_33579501_r 0 - CCDS13256.1_cds_0_0_chr20_33579501_rchr20-
+chr20 33593260 33593348 CCDS13257.1_cds_0_0_chr20_33593261_f 0 + CCDS13257.1_cds_0_0_chr20_33593261_fchr20+
+chr21 32707032 32707192 CCDS13614.1_cds_0_0_chr21_32707033_f 0 + CCDS13614.1_cds_0_0_chr21_32707033_fchr21+
+chr21 32869641 32870022 CCDS13615.1_cds_0_0_chr21_32869642_r 0 - CCDS13615.1_cds_0_0_chr21_32869642_rchr21-
+chr21 33321040 33322012 CCDS13620.1_cds_0_0_chr21_33321041_f 0 + CCDS13620.1_cds_0_0_chr21_33321041_fchr21+
+chr21 33744994 33745040 CCDS13625.1_cds_0_0_chr21_33744995_r 0 - CCDS13625.1_cds_0_0_chr21_33744995_rchr21-
+chr22 30120223 30120265 CCDS13897.1_cds_0_0_chr22_30120224_f 0 + CCDS13897.1_cds_0_0_chr22_30120224_fchr22+
+chr22 30160419 30160661 CCDS13898.1_cds_0_0_chr22_30160420_r 0 - CCDS13898.1_cds_0_0_chr22_30160420_rchr22-
+chr22 30665273 30665360 CCDS13901.1_cds_0_0_chr22_30665274_f 0 + CCDS13901.1_cds_0_0_chr22_30665274_fchr22+
+chr22 30939054 30939266 CCDS13903.1_cds_0_0_chr22_30939055_r 0 - CCDS13903.1_cds_0_0_chr22_30939055_rchr22-
+chr5 131424298 131424460 CCDS4149.1_cds_0_0_chr5_131424299_f 0 + CCDS4149.1_cds_0_0_chr5_131424299_fchr5+
+chr5 131556601 131556672 CCDS4151.1_cds_0_0_chr5_131556602_r 0 - CCDS4151.1_cds_0_0_chr5_131556602_rchr5-
+chr5 131621326 131621419 CCDS4152.1_cds_0_0_chr5_131621327_f 0 + CCDS4152.1_cds_0_0_chr5_131621327_fchr5+
+chr5 131847541 131847666 CCDS4155.1_cds_0_0_chr5_131847542_r 0 - CCDS4155.1_cds_0_0_chr5_131847542_rchr5-
+chr6 108299600 108299744 CCDS5061.1_cds_0_0_chr6_108299601_r 0 - CCDS5061.1_cds_0_0_chr6_108299601_rchr6-
+chr6 108594662 108594687 CCDS5063.1_cds_0_0_chr6_108594663_f 0 + CCDS5063.1_cds_0_0_chr6_108594663_fchr6+
+chr6 108640045 108640151 CCDS5064.1_cds_0_0_chr6_108640046_r 0 - CCDS5064.1_cds_0_0_chr6_108640046_rchr6-
+chr6 108722976 108723115 CCDS5067.1_cds_0_0_chr6_108722977_f 0 + CCDS5067.1_cds_0_0_chr6_108722977_fchr6+
+chr7 113660517 113660685 CCDS5760.1_cds_0_0_chr7_113660518_f 0 + CCDS5760.1_cds_0_0_chr7_113660518_fchr7+
+chr7 116512159 116512389 CCDS5771.1_cds_0_0_chr7_116512160_r 0 - CCDS5771.1_cds_0_0_chr7_116512160_rchr7-
+chr7 116714099 116714152 CCDS5773.1_cds_0_0_chr7_116714100_f 0 + CCDS5773.1_cds_0_0_chr7_116714100_fchr7+
+chr7 116945541 116945787 CCDS5774.1_cds_0_0_chr7_116945542_r 0 - CCDS5774.1_cds_0_0_chr7_116945542_rchr7-
+chr8 118881131 118881317 CCDS6324.1_cds_0_0_chr8_118881132_r 0 - CCDS6324.1_cds_0_0_chr8_118881132_rchr8-
+chr9 128764156 128764189 CCDS6914.1_cds_0_0_chr9_128764157_f 0 + CCDS6914.1_cds_0_0_chr9_128764157_fchr9+
+chr9 128787519 128789136 CCDS6915.1_cds_0_0_chr9_128787520_r 0 - CCDS6915.1_cds_0_0_chr9_128787520_rchr9-
+chr9 128882427 128882523 CCDS6917.1_cds_0_0_chr9_128882428_f 0 + CCDS6917.1_cds_0_0_chr9_128882428_fchr9+
+chr9 128937229 128937445 CCDS6919.1_cds_0_0_chr9_128937230_r 0 - CCDS6919.1_cds_0_0_chr9_128937230_rchr9-
+chrX 122745047 122745924 CCDS14606.1_cds_0_0_chrX_122745048_f 0 + CCDS14606.1_cds_0_0_chrX_122745048_fchrX+
+chrX 152648964 152649196 CCDS14733.1_cds_0_0_chrX_152648965_r 0 - CCDS14733.1_cds_0_0_chrX_152648965_rchrX-
+chrX 152691446 152691471 CCDS14735.1_cds_0_0_chrX_152691447_f 0 + CCDS14735.1_cds_0_0_chrX_152691447_fchrX+
+chrX 152694029 152694263 CCDS14736.1_cds_0_0_chrX_152694030_r 0 - CCDS14736.1_cds_0_0_chrX_152694030_rchrX-

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/mosaik_test_input.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/mosaik_test_input.fastq Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,996 @@\n+@178508read3065:10\n+ATTCTTTTAATTTAATATCTTTTCTGTAGCCTGACGAATTTGTGAAAGAAAAACGGAAGATCAGGGAAAAAGGACCGAGATTCGGTCATGACAGCGATC\n++\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+@albumin_SNPread1768:15\n+TTTAATTTAATATCTTTTCTGTAGCCTGACGAATTTGTGAAAGAAAAACGGAAGATCAGGGAAAAAGGACCGAGATTCGGTCATGACAGCGATCCACCTG\n++\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+@178508read936:35\n+GTAGCCTGACGAATTTGTGAAAGAAAAACGGAAGATCAGGGAAAAAGGACCGAGATTCGGTCATGACAGCGATCCACCTGTAAGTAAATTAACAAATTA\n++\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+@178508read4161:42\n+GACGAATTTGTGAAAGAAAAACGGAAGATCAGGGAAAAAGGACCGAGATTCGGTCATGACAGCGATCCACCTGTAAGTAAATTAACAAATTATTGATTT\n++\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+@albumin_SNPread3935:46\n+AATTTGTGAAAGAAAAACGGAAGATCAGGGAAAAAGGACCGAGATTCGGTCATGACAGCGATCCACCTGTAAGTAAATTAACAAATTATTGATTTATAT\n++\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+@178508read1854:72\n+AGGGAAAAAGGACCGAGATTCGGTCATGACAGCGATCCACCTGTAAGTAAATTAACAAATTATTGATTTATATCTTAAGTTTCTTATTTTTTAAAATTCT\n++\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+@albumin_SNPread4016:77\n+AAAAGGACCGAGATTCGGTCATGACAGCGATCCACCTGTAAGTAAATTAACAAATTATTGATTTATATCTTAAGTTTCTTATTTTTTAAAATTCTGTTCT\n++\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+@albumin_SNPread1172:81\n+GGACCGAGATTCGGTCATGACAGCGATCCACCTGTAAGTAAATTAACAAATTATTGATTTATATCTTAAGTTTCTTATTTTTTAAAATTCTGTTCTCAT\n++\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+@albumin_SNPread2933:93\n+GGTCATGACAGCGATCCACCTGTAAGTAAATTAACAAATTATTGATTTATATCTTAAGTTTCTTATTTTTTAAAATTCTGTTCTCATGATTTTTGTTAT\n++\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+@178508read3498:99\n+GACAGCGATCCACCTGTAAGTAAATTAACAAATTATTGATTTATATCTTAAGTTTCTTATTTTTTAAAATTCTGTTCTCATGATTTTTGTTATCCTCTAA\n++\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+@albumin_SNPread2322:102\n+AGCGATCCACCTGTAAGTAAATTAACAAATTATTGATTTATATCTTAAGTTTCTTATTTTTTAAAATTCTGTTCTCATGATTTTTGTTATCCTCTAACAT\n++\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+@albumin_SNPread2079:108\n+CCACCTGTAAGTAAATTAACAAATTATTGATTTATATCTTAAGTTTCTTATTTTTTAAAATTCTGTTCTCATGATTTTTGTTATCCTCTAACATGTTTT\n++\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+@178508read1649:114\n+GTAAGTAAATTAACAAATTATTGATTTATATCTTAAGTTTCTTATTTTTTAAAATTCTGTTCTCATGATTTTTGTTATCCTCTAACATGTTTTCAATTTT\n++\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+@178508read1863:121\n+AATTAACAAATTATTGATTTATATCTTAAGTTTCTTATTTTTTAAAATTCTGTTCTCATGATTTTTGTTATCCTCTAACATGTTTTCAATTTTAGGCAT\n++\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+@178508read1206:129\n+AATTATTGATTTATATCTTAAGTTTCTTATTTTTTAAAATTCTGTTCTCATGATTTTTGTTATCCTCTAACATGTTTTCAATTTTAGGCATTCCTTTTT\n++\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+@albumin_SNPread1177:154\n+CTTATTTTTTAAAATTCTGTTCTCATGATTTTTGTTATCCTCTAACATGTTTTCAATTTTAGGCATTCCTTTTTTTTCCTCTATTGCTTTATTCTTTAT\n++\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+@178508read1581:160\n+TTTTAAAATTCTGTTCTCATGATTTTTGTTATCCTCTAACATGTTTTCAATTTTAGGCATTCCTTTTTTTTCCTCTATTGCTTTATTCTTTATTTATTT\n++\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+@albumin_SNPread3940:164\n+AAAATTCTGTTCTCATGATTTTTGTTATCCTCTAACATGTTTTCAATTTTAGGCATTCCTTTTTTTTCCTC'..b'AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+@178508read4247:2174\n+AATTTATATAAATTATTCTATATTTCCTTATCCATCTAATTAGCTGTTTTCCTGTTTGGTAAAAATTGCATGCAATGTATATTTTTTGAGGACCACTGTA\n++\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+@178508read4172:2181\n+ATAAATTATTCTATATTTCCTTATCCATCTAATTAGCTGTTTTCCTGTTTGGTAAAAATTGCATGCAATGTATATTTTTTGAGGACCACTGTATACGTGT\n++\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+@albumin_SNPread1269:2186\n+TTATTCTATATTTCCTTATCCATCTAATTAGCTGTTTTCCTGTTTGGTAAAAATTGCATGCAATGTATATTTTTTGAGGACCACTGTATACGTGTCAGAA\n++\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+@178508read2879:2197\n+TTCCTTATCCATCTAATTAGCTGTTTTCCTGTTTGGTAAAAATTGCATGCAATGTATATTTTTTGAGGACCACTGTATACGTGTCAGAAAAGTTTTTTTC\n++\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+@178508read1032:2219\n+GTTTTCCTGTTTGGTAAAAATTGCATGCAATGTATATTTTTTGAGGACCACTGTATACGTGTCAGAAAAGTTTTTTTCCATTCATTATTCACATTAATTC\n++\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+@albumin_SNPread4090:2260\n+TGAGGACCACTGTATACGTGTCAGAAAAGTTTTTTTCCATTCATTATTCACATTAATTCAAATTATTCCTAATAATGTTACTTTCATCACTAATTAATC\n++\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+@albumin_SNPread1282:2263\n+GGACCACTGTATACGTGTCAGAAAAGTTTTTTTCCATTCATTATTCACATTAATTCAAATTATTCCTAATAATGTTACTTTCATCACTAATTAATCCAT\n++\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+@178508read1101:2276\n+CGTGTCAGAAAAGTTTTTTTCCATTCATTATTCACATTAATTCAAATTATTCCTAATAATGTTACTTTCATCACTAATTAATCCATTTTTGAGGGAGAAA\n++\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+@178508read3397:2281\n+CAGAAAAGTTTTTTTCCATTCATTATTCACATTAATTCAAATTATTCCTAATAATGTTACTTTCATCACTAATTAATCCATTTTTGAGGGAGAAAAAAA\n++\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+@178508read146:2310\n+CATTAATTCAAATTATTCCTAATAATGTTACTTTCATCACTAATTAATCCATTTTTGAGGGAGAAAAAAAATCATTTGAATTGATAATAAGTCATTAAA\n++\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+@albumin_SNPread2523:2318\n+CAAATTATTCCTAATAATGTTACTTTCATCACTAATTAATCCATTTTTGAGGGAGAAAAAAAATCATTTGAATTGATAATAAGTCATTAAATTCATAGCG\n++\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+@albumin_SNPread3432:2342\n+TTCATCACTAATTAATCCATTTTTGAGGGAGAAAAAAAATCATTTGAATTGATAATAAGTCATTAAATTCATAGCGAAATGTCTTGTTTTCGCCCAAACG\n++\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+@albumin_SNPread4285:2343\n+TCATCACTAATTAATCCATTTTTGAGGGAGAAAAAAAATCATTTGAATTGATAATAAGTCATTAAATTCATAGCGAAATGTCTTGTTTTCGCCCAAACG\n++\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+@albumin_SNPread2604:2344\n+CATCACTAATTAATCCATTTTTGAGGGAGAAAAAAAATCATTTGAATTGATAATAAGTCATTAAATTCATAGCGAAATGTCTTGTTTTCGCCCAAACGAT\n++\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+@albumin_SNPread1672:2356\n+ATCCATTTTTGAGGGAGAAAAAAAATCATTTGAATTGATAATAAGTCATTAAATTCATAGCGAAATGTCTTGTTTTCGCCCAAACGATTATATCATGTGG\n++\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+@178508read540:2377\n+AAAATCATTTGAATTGATAATAAGTCATTAAATTCATAGCGAAATGTCTTGTTTTCGCCCAAACGATTATATCATGTGGGTACTTCAAACTGAATGCTGT\n++\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+@178508read2561:2379\n+AATCATTTGAATTGATAATAAGTCATTAAATTCATAGCGAAATGTCTTGTTTTCGCCCAAACGATTATATCATGTGGGTACTTCAAACTGAATGCTGTGG\n++\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/mosaik_test_out.sam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/mosaik_test_out.sam Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,252 @@\n+@HD\tVN:1.0\tSO:unsorted\n+@SQ\tSN:178508\tLN:92940\tM5:5AD42BE00D3601103159A8EB2F8A3ED0\n+@RG\tID:ZEFJ6FJUOOY\tSM:unknown\tPL:454\n+albumin_SNPread1768:15\t0\t178508\t16\t69\t100M\t*\t0\t0\tTTTAATTTAATATCTTTTCTGTAGCCTGACGAATTTGTGAAAGAAAAACGGAAGATCAGGGAAAAAGGACCGAGATTCGGTCATGACAGCGATCCACCTG\tAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\tRG:Z:ZEFJ6FJUOOY\tNM:i:0\tMD:Z:100\n+178508read3065:10\t0\t178508\t11\t69\t99M\t*\t0\t0\tATTCTTTTAATTTAATATCTTTTCTGTAGCCTGACGAATTTGTGAAAGAAAAACGGAAGATCAGGGAAAAAGGACCGAGATTCGGTCATGACAGCGATC\tAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\tRG:Z:ZEFJ6FJUOOY\tNM:i:0\tMD:Z:99\n+178508read936:35\t0\t178508\t36\t67\t99M\t*\t0\t0\tGTAGCCTGACGAATTTGTGAAAGAAAAACGGAAGATCAGGGAAAAAGGACCGAGATTCGGTCATGACAGCGATCCACCTGTAAGTAAATTAACAAATTA\tAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\tRG:Z:ZEFJ6FJUOOY\tNM:i:0\tMD:Z:99\n+178508read4161:42\t0\t178508\t43\t67\t99M\t*\t0\t0\tGACGAATTTGTGAAAGAAAAACGGAAGATCAGGGAAAAAGGACCGAGATTCGGTCATGACAGCGATCCACCTGTAAGTAAATTAACAAATTATTGATTT\tAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\tRG:Z:ZEFJ6FJUOOY\tNM:i:0\tMD:Z:99\n+albumin_SNPread3935:46\t0\t178508\t47\t66\t99M\t*\t0\t0\tAATTTGTGAAAGAAAAACGGAAGATCAGGGAAAAAGGACCGAGATTCGGTCATGACAGCGATCCACCTGTAAGTAAATTAACAAATTATTGATTTATAT\tAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\tRG:Z:ZEFJ6FJUOOY\tNM:i:0\tMD:Z:99\n+178508read1854:72\t0\t178508\t73\t66\t100M\t*\t0\t0\tAGGGAAAAAGGACCGAGATTCGGTCATGACAGCGATCCACCTGTAAGTAAATTAACAAATTATTGATTTATATCTTAAGTTTCTTATTTTTTAAAATTCT\tAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\tRG:Z:ZEFJ6FJUOOY\tNM:i:0\tMD:Z:100\n+albumin_SNPread1172:81\t0\t178508\t82\t65\t99M\t*\t0\t0\tGGACCGAGATTCGGTCATGACAGCGATCCACCTGTAAGTAAATTAACAAATTATTGATTTATATCTTAAGTTTCTTATTTTTTAAAATTCTGTTCTCAT\tAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\tRG:Z:ZEFJ6FJUOOY\tNM:i:0\tMD:Z:99\n+albumin_SNPread4016:77\t0\t178508\t78\t65\t100M\t*\t0\t0\tAAAAGGACCGAGATTCGGTCATGACAGCGATCCACCTGTAAGTAAATTAACAAATTATTGATTTATATCTTAAGTTTCTTATTTTTTAAAATTCTGTTCT\tAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\tRG:Z:ZEFJ6FJUOOY\tNM:i:0\tMD:Z:100\n+albumin_SNPread2933:93\t0\t178508\t94\t59\t99M\t*\t0\t0\tGGTCATGACAGCGATCCACCTGTAAGTAAATTAACAAATTATTGATTTATATCTTAAGTTTCTTATTTTTTAAAATTCTGTTCTCATGATTTTTGTTAT\tAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\tRG:Z:ZEFJ6FJUOOY\tNM:i:0\tMD:Z:99\n+178508read3498:99\t0\t178508\t100\t59\t100M\t*\t0\t0\tGACAGCGATCCACCTGTAAGTAAATTAACAAATTATTGATTTATATCTTAAGTTTCTTATTTTTTAAAATTCTGTTCTCATGATTTTTGTTATCCTCTAA\tAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\tRG:Z:ZEFJ6FJUOOY\tNM:i:0\tMD:Z:100\n+albumin_SNPread2079:108\t0\t178508\t109\t55\t99M\t*\t0\t0\tCCACCTGTAAGTAAATTAACAAATTATTGATTTATATCTTAAGTTTCTTATTTTTTAAAATTCTGTTCTCATGATTTTTGTTATCCTCTAACATGTTTT\tAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\tRG:Z:ZEFJ6FJUOOY\tNM:i:0\tMD:Z:99\n+albumin_SNPread2322:102\t0\t178508\t103\t57\t100M\t*\t0\t0\tAGCGATCCACCTGTAAGTAAATTAACAAATTATTGATTTATATCTTAAGTTTCTTATTTTTTAAAATTCTGTTCTCATGATTTTTGTTATCCTCTAACAT\tAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\tRG:Z:ZEFJ6FJUOOY\tNM:i:0\tMD:Z:100\n+178508read1649:114\t0\t178508\t115\t52\t100M\t*\t0\t0\tGTAAGTAAATTAACAAATTATTGATTTATATCTTAAGTTTCTTATTTTTTAAAATTCTGTTCTCATGATTTTTGTTATCCTCTAACATGTTTTCAATTTT\tAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\tRG:Z:ZEFJ6FJUOOY\tNM:i:0\tMD:Z:100\n+178508read1863:121\t0\t178508\t122\t53\t99M\t*\t0\t0\tAATTAACAAATTATTGATTTATATCTTAAGTTTCTTATTTTTTAAAATTCTGTTCTCATGATTTTTGTTATCCTCTAACATGTTTTCAATTTTAGGCAT\tAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA'..b':100\n+albumin_SNPread1269:2186\t0\t178508\t2187\t64\t100M\t*\t0\t0\tTTATTCTATATTTCCTTATCCATCTAATTAGCTGTTTTCCTGTTTGGTAAAAATTGCATGCAATGTATATTTTTTGAGGACCACTGTATACGTGTCAGAA\tAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\tRG:Z:ZEFJ6FJUOOY\tNM:i:0\tMD:Z:100\n+178508read1032:2219\t0\t178508\t2220\t64\t100M\t*\t0\t0\tGTTTTCCTGTTTGGTAAAAATTGCATGCAATGTATATTTTTTGAGGACCACTGTATACGTGTCAGAAAAGTTTTTTTCCATTCATTATTCACATTAATTC\tAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\tRG:Z:ZEFJ6FJUOOY\tNM:i:0\tMD:Z:100\n+albumin_SNPread4090:2260\t0\t178508\t2261\t61\t99M\t*\t0\t0\tTGAGGACCACTGTATACGTGTCAGAAAAGTTTTTTTCCATTCATTATTCACATTAATTCAAATTATTCCTAATAATGTTACTTTCATCACTAATTAATC\tAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\tRG:Z:ZEFJ6FJUOOY\tNM:i:0\tMD:Z:99\n+albumin_SNPread1282:2263\t0\t178508\t2264\t60\t99M\t*\t0\t0\tGGACCACTGTATACGTGTCAGAAAAGTTTTTTTCCATTCATTATTCACATTAATTCAAATTATTCCTAATAATGTTACTTTCATCACTAATTAATCCAT\tAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\tRG:Z:ZEFJ6FJUOOY\tNM:i:0\tMD:Z:99\n+178508read1101:2276\t0\t178508\t2277\t61\t100M\t*\t0\t0\tCGTGTCAGAAAAGTTTTTTTCCATTCATTATTCACATTAATTCAAATTATTCCTAATAATGTTACTTTCATCACTAATTAATCCATTTTTGAGGGAGAAA\tAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\tRG:Z:ZEFJ6FJUOOY\tNM:i:0\tMD:Z:100\n+178508read3397:2281\t0\t178508\t2282\t58\t99M\t*\t0\t0\tCAGAAAAGTTTTTTTCCATTCATTATTCACATTAATTCAAATTATTCCTAATAATGTTACTTTCATCACTAATTAATCCATTTTTGAGGGAGAAAAAAA\tAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\tRG:Z:ZEFJ6FJUOOY\tNM:i:0\tMD:Z:99\n+178508read146:2310\t0\t178508\t2311\t56\t99M\t*\t0\t0\tCATTAATTCAAATTATTCCTAATAATGTTACTTTCATCACTAATTAATCCATTTTTGAGGGAGAAAAAAAATCATTTGAATTGATAATAAGTCATTAAA\tAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\tRG:Z:ZEFJ6FJUOOY\tNM:i:0\tMD:Z:99\n+albumin_SNPread2523:2318\t0\t178508\t2319\t59\t100M\t*\t0\t0\tCAAATTATTCCTAATAATGTTACTTTCATCACTAATTAATCCATTTTTGAGGGAGAAAAAAAATCATTTGAATTGATAATAAGTCATTAAATTCATAGCG\tAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\tRG:Z:ZEFJ6FJUOOY\tNM:i:0\tMD:Z:100\n+albumin_SNPread3432:2342\t0\t178508\t2343\t65\t100M\t*\t0\t0\tTTCATCACTAATTAATCCATTTTTGAGGGAGAAAAAAAATCATTTGAATTGATAATAAGTCATTAAATTCATAGCGAAATGTCTTGTTTTCGCCCAAACG\tAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\tRG:Z:ZEFJ6FJUOOY\tNM:i:0\tMD:Z:100\n+albumin_SNPread4285:2343\t0\t178508\t2344\t65\t99M\t*\t0\t0\tTCATCACTAATTAATCCATTTTTGAGGGAGAAAAAAAATCATTTGAATTGATAATAAGTCATTAAATTCATAGCGAAATGTCTTGTTTTCGCCCAAACG\tAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\tRG:Z:ZEFJ6FJUOOY\tNM:i:0\tMD:Z:99\n+albumin_SNPread2604:2344\t0\t178508\t2345\t65\t100M\t*\t0\t0\tCATCACTAATTAATCCATTTTTGAGGGAGAAAAAAAATCATTTGAATTGATAATAAGTCATTAAATTCATAGCGAAATGTCTTGTTTTCGCCCAAACGAT\tAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\tRG:Z:ZEFJ6FJUOOY\tNM:i:0\tMD:Z:100\n+albumin_SNPread1672:2356\t0\t178508\t2357\t65\t100M\t*\t0\t0\tATCCATTTTTGAGGGAGAAAAAAAATCATTTGAATTGATAATAAGTCATTAAATTCATAGCGAAATGTCTTGTTTTCGCCCAAACGATTATATCATGTGG\tAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\tRG:Z:ZEFJ6FJUOOY\tNM:i:0\tMD:Z:100\n+178508read540:2377\t0\t178508\t2378\t66\t100M\t*\t0\t0\tAAAATCATTTGAATTGATAATAAGTCATTAAATTCATAGCGAAATGTCTTGTTTTCGCCCAAACGATTATATCATGTGGGTACTTCAAACTGAATGCTGT\tAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\tRG:Z:ZEFJ6FJUOOY\tNM:i:0\tMD:Z:100\n+178508read2561:2379\t0\t178508\t2380\t68\t100M\t*\t0\t0\tAATCATTTGAATTGATAATAAGTCATTAAATTCATAGCGAAATGTCTTGTTTTCGCCCAAACGATTATATCATGTGGGTACTTCAAACTGAATGCTGTGG\tAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\tRG:Z:ZEFJ6FJUOOY\tNM:i:0\tMD:Z:100\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/mosaik_test_ref.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/mosaik_test_ref.fasta Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,1550 @@\n+>178508\n+GATCCGCGGAATTCTTTTAATTTAATATCTTTTCTGTAGCCTGACGAATTTGTGAAAGAA\n+AAACGGAAGATCAGGGAAAAAGGACCGAGATTCGGTCATGACAGCGATCCACCTGTAAGT\n+AAATTAACAAATTATTGATTTATATCTTAAGTTTCTTATTTTTTAAAATTCTGTTCTCAT\n+GATTTTTGTTATCCTCTAACATGTTTTCAATTTTAGGCATTCCTTTTTTTTCCTCTATTG\n+CTTTATTCTTTATTTATTTTTTCTCAATCCAATCCTGTATTCTGATTTTTACTTCTTCTT\n+TCTTTCTACCCTTTTTCTCTTCTATTTACGGCCTGTTGATTTTTTTTCTTTGTTTTCTTA\n+GCCCTTGTTTTAGTTTTATTCTCTTCATAAAAGTTGCCATTTTCATCCCCAAAGATGTTT\n+GCTCCAGTGGAGAGACACGTATAGGAATATGGAATTATATTTGCAGTGGTGTGAGATTGA\n+AAGTGCATTTTTGTTAAACCTTTTCTTTGCATCTTTTCCTTTCCTATCTACTTTTTCCTC\n+CTTTTTCACAATTTCTGGTCAAATTCAATATACATTCTTTTTTTTCAGTGATATATTTGT\n+TTAATTAAATAGAATTATAGAAAATTGGCTATGGTGTGAGATTGAAATTATAATTTGCAA\n+TTGTTTGCAAGATGATCTGAATCTAGTGATTGAAGTGCATTTTTTTGTTATATTCACTTT\n+CCTTTTCCCATCAATGCATCCTACCAGCTTTTTATCACAAACCGCATGAAAAAAGATATG\n+TATTAGCCACCATTAGTATAGAAAACATCATAGTTGTAGCAATATATTTGCATATTTTCA\n+AGCCAATATAAAGGTATATATTTCATAGCTTCTTTTCTGCAGTTATTAGATGATCGTATA\n+GATTTTCTGTATATTTCATTTTGTTCTATCCGTTATTTTATTCACGTATTCTTACCTGCC\n+AAGAGCATTTTAAAACAATGACACCCCCATATTTAGTAGGTAGTCATAATCCAGAGTAAT\n+TCTTACGTGGGTCTGATCTTGGGTCATGTAATATTTTGGATGATGTGTTTCTCAAATTTG\n+TTTAAACTAAAGAAAAAGAAGAAGGTGAAGAAGGTGGTGAGGATTCTATCCCCCTATCCT\n+ACCTCCTCTCCCCCATCCCGAATCCAAAAGATTCGTAAAACAAAGGTGAGATAGAAAACC\n+GACTAACTCCAAAGATTTTTAACCCAGATGTGTGCACGTGTATTGTCATGAATAACATGG\n+TGTTGTCAGGAACCTTGTCTCGGCAATCTAGGCATCCTTAACAGGCTTCACTTCAAATTA\n+CAGGGGGTTGTTTGCTATTAATGTTTGTCATTTATTTAGTTATTTTTTATTAGGATTATA\n+ACATGGATACTGTCATATATGTTTAATGGTGGTTGGCATTCACTCTGTGTTTAACTCCAT\n+TTTCATCAGCTTCAAGCTTTCAATCATCAAATCTATATAATTGACCATACTTAAAAGTAA\n+AGTAAAGCCCTTGAATCTGGTATATGTTGTGTACAAAGTTCTACCTAATCAAAACGTTCA\n+TGCATTAACCCTTTATCATTCACAGAGGTATAGGGCACAGTAGTCATCATTAACCTTGCC\n+GATAACATATCTATGATGAATTTAACTTTATATTACATGTTTTTTGTTCCATTTATAATT\n+GAAATACTATAATACACAAAGATGAATCTTTTTGTGATAATGAGACTCATAGGCTTTGAC\n+CTACATGTATACATGTTACTTTACAGTTGAGGGTAGGTATTTATGGCTTGAATCAGTGAA\n+AAGAATTACTTTGATGAGGGAGCATTCTATTTCCACTTAAAATTATTGGAACAGTAGGAA\n+CGAAAACAATTGCTGTTTCTTATTACAGATAGTAGATCAGTAATATGTTAACTTTTTATC\n+TACTGTACTACGGATTGAAATCCGATAGACTGCCACATCATATTATGGCATACATTTTAC\n+AACTGCATTGCTTGTGCAATTAAAGTTGACAATGATGGGCTACTGTTTGTTTTTGTTTCA\n+TACGTTGATTGTAGGAGATTTTCTTTAGTCATGGATTCACTAATTTGTTCATTTTATCTA\n+CATTTATGTATCTATGTGTCTATTACTACTGGATTTTCATACATCTATTTATTCATCCAT\n+GCAGGTAACTGATCAATTTATATAAATTATTCTATATTTCCTTATCCATCTAATTAGCTG\n+TTTTCCTGTTTGGTAAAAATTGCATGCAATGTATATTTTTTGAGGACCACTGTATACGTG\n+TCAGAAAAGTTTTTTTCCATTCATTATTCACATTAATTCAAATTATTCCTAATAATGTTA\n+CTTTCATCACTAATTAATCCATTTTTGAGGGAGAAAAAAAATCATTTGAATTGATAATAA\n+GTCATTAAATTCATAGCGAAATGTCTTGTTTTCGCCCAAACGATTATATCATGTGGGTAC\n+TTCAAACTGAATGCTGTGGTACAGTGAGGGTTTGATCTGTGAGTTTTGGCAGTGGAGGAA\n+AATGACATCTCACCAAATGAAATTAAACTTACATTCAATTTCAAGTTTACAAATAAATAA\n+AGAAATGATGTGTTCCCAAAAATTTGCGGTTTAAAATGTACAACACCTAAAAACCTTTAA\n+AAAAAAAAGTAATTTGTGAAGACTATTATTTGAATTTGAATATATCAAAATGTCCCTTTA\n+TTCCATGTTATGTGGGGCGTAGGTCAATAGCTGAACTCATGGAATAATCTTTGTTTCAGC\n+TCTCTCACCTGGTAAAATTTTTAAAGAAAGAGAAGAGGGGATAATATATTATAACATTTA\n+AGATTATCAACCTATTTCTTCAATATTTTTCCTGCATCTGTTAATCTTTTTTAGCCGGAG\n+CCAGAAAAGAAAAAGAAGCGACCGAAGGGACCTCATTTCCATGCTGAAAAGGAACCTGAA\n+CCGGTAAGTCCTTTTTTATTCCTGAAGGTTCTAATTAATTTAACTTTTTTTTGACGAGTA\n+TGGAGCATCAAGATAGATATAAGTTACGACAACATATACCAAATGGAAAAGAATATCTCA\n+AAAAGAGGACTTTGTACCATATTTTTTGCATTTCTTGTCAAAAAGTGCTTTTGATACACC\n+CTGATGGATAAATGAAAGACATTACACTAAAGTTTCTTCTTTTTGACTCTATTTTCTGAT\n+ATGTTTGTTCACGGCAGTTAGTTGGAAATGGATCAATGCACTGTCCAACCGCTTCTATGT\n+ATGAGTAAAAGTTTTGAAAATGAATCATTTTTTGTTCAACTACTATGCAAGAAGGATCAT\n+ATAACAACGCTTATCGGAGTATGGCAGACTTTAGAGTAAGTTGCCCAAAAAGTACTATAC\n+ATATGTATGTATTTCAGGACACATTCACTTAACAGTTACATACATAAGTAGAAAATATAT\n+GTTATTAAAGTAGAGTGTGCTATGTTTCATTAATTTTATCTTTGTATGTTTAGTCATAAT\n+GACAAATAGTTTGATAATCTTAAATGTCATCATAATATAATATTTCCCCTCTTATATGTT\n+TTTTATAAATTTTACCAGGTGAGAGAGCTGAAACAAAGATTATTCCATGAGTTCAGCTAT\n+TGATCTACGTCCCAGATGCTTGGACTTCAACCAACTTCTTCATTGAGCTGATCTCCCGGA\n+ATCCTTTCTGTATCTTTCCATGTGGTGCATTGCTGTATTTATCACAAATACCCATGAAAA\n+TTCATCTATTCAAAGCCAGAATGGTGTTAACTCTGTGTTAGAGTATTTGAGTTAATGTCC\n+TTCTAGTTCTAGATGACCTCTCCTTTCCTTTCTCTCTTTTTCTAGGTATTACAATGTAGA\n+AA'..b'GGATATGCAAGAAGACATGGATCAATGCCT\n+ACTTAAAGCTTGATGATGATGATCCTGCCATTATCTGCTTCAAAGAACTGGGTGAGGGTT\n+CCATTCCAACTGAGCTTAGCAATGGAGAGCTTCCAACACAGGTGAAGGCACTAGAGCATT\n+TTATATGTCGTGTATACTGTTCATCAGGTCCAACAACCCTACCATCGCTCAGATGGGAAC\n+TGTTCCGATCAAAGAACCTGGAAGGTGAGATGTTACCTCCAACTCGTGCCGCATTACTAC\n+CTCACATCCTCCGTGCCAATTACATCACGATGAGAGATAAATCATACAAGACTAACTACC\n+CAGTGCTTCCTCCTATCGAAGAGAATGGATGGTATTCAGATAATCGAGGATGTCTTCCAG\n+TCAAGTGTCTAGCGCTCCCTGCACCACGGGCAGTACTTGAACTCATCAAATGTGGCTGCA\n+AATCAGGATGCAAGGGACGGTGTAGCTGCTCCAACAACGATTTGCCCTGCACTCCTCTCT\n+GTAAATGCTATAGTGGAGACTGTGAAAACCGGACAAGGGAGGATGCTCCATATAGTGACA\n+GCGATTGACTTTAACTGGAAGTCTGATTAACTTTCCTGTTGTCATGGTAACCACGAAGTA\n+GGTGGTTACCCCTTTTCCGATTTTATTTTATGTTTTGTTTATAACTGGAAAATATTTCCA\n+AATTTTTTTGATTTAGATCAAGATTGTGCCATATTTACAAGTATTTCGGCACAAAATAGC\n+TCAATTTGTTTCTGTTGTTTTTTTTTTCTCCGGGGCGGGGGGACCATATCAACATTTTCG\n+TATTATTTTGCATTTGAAAAAAAATATTACATATATAATTTGTCAACTTTCTGATTGACT\n+GATGCAATTACAGTGCCTAGAAGTTGATATTTGAGAATTTTGTTATATTATCATCTGAAG\n+GTGTTTGGCGCCATCTGGTGTTTAAGTAAGTTCTTCATTTGATAGAATACTAAAATAGGG\n+TTGATTTTTATATTAACAGCCTAAAATAACAGTGTTAATGACATGTGATAGGTTTCACAA\n+TTATTCCACTGTATAATAACACACAACACACAATAATGCCATTTCCACTTATTATTTCAA\n+AATTCTAGCCCAAAAGAAAGAAGAAGGGCACATTTTTTAGGAAATATTTCCCAGTTTTTC\n+ACAATTTTTCGCAAATTGCGCCCCCATAAGGTCAAAGTGAAAAAGTTTTATGACGCGATA\n+TCATTAAAAATGAATCCGTATATACCTCAGACAACTTCACAGTGAAATTGGCGAAAAAAT\n+ATATGAATTAGGGTGGAAGACACCAAATTTCCCTATTGCGCTTTATGCAATTTTGGCGCC\n+CAAAATGGACCCCCCAGGAAGTGAAGGAGGGGTCTCAAAATTTGAACCCCATCATTTTTG\n+GCCAATTGGGACCCTTTTGAAGCCAAAACAGCCCCCCCCCCCCCCTAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATCAATTTTGGCAAAAAAATCCTACGG\n+GATTACATACCATACCGCACTATGACCCATAATCGTTCGGTCAGCCTAAACCTGGTACAA\n+GGCGACTTTGACCAAACTTTCAAAAGACCCTTATTGTGCCCAGTCACCCGTGGCAGAAAT\n+GTTATGAATAGGGTATCATTGGACAGAAGAGATGTTACTCGCCATCATGAAATAAATTTC\n+AAAGTCATATTGTTTGTGATATTCTAATAAAGAGCTACCAAAGTTGGGTACATTTTTTTG\n+TAAACTCACTGTATACATAGAGAGAGAGAGAGTGGGGGAGGAGAAAAGGGAAGAGGGGGG\n+GGGGGGGAGAGAGAGAGAGAGATCCTGCTACTACTACTGTCGCTAGATTACTGCTATAAA\n+AACTACTATTTCTTAAAAGGCAAGTACACTCCAAAAATACCTTACTTTCAATAGAAATCA\n+GACAATATGTAATCAGACAATTATTTCCCTCACTTTCACTATTATATAAAATTTCTTTTG\n+TCTATCTTCTTCTTCTCTCTCTCCCCCCCTCTCTCTCTCTCTCTCTCTCTCACACACACA\n+CACACAAACGTACACACTCACACACACACTCTCTCTCTCTCCCTCTCTCCATCTCACTCT\n+CATCTCTGTCTTTGTCTCTTTGTCTCTCCCTCCCCCCCCCCTCTCTCTCTCTCTCTATAT\n+ATAATCAGACAATATATAATACCTATATCCCTCACTCTCACTTTCTCACTCCCTCTCGTT\n+TTTTTTTCTTTCTCTCTCTCTCTCTCTCTCTCTCTTATCTCAATCGATCAATATCGTGAT\n+CAATCCAGCTGCATAAGGAAAACAATTATTAGGGGCTATAATATTGAACGCTTCACAAGT\n+ATTAGTATGAGTTCAGTTATATATTTTTATTTGACAAAGTCTTGACAAATTCAGTATCAA\n+TAAGAGTTTAACAATTCGTCAACATTTCATGCACCTTTCACTGGCTAAGAGTCTCCTGTA\n+TCTGAATTTTAGACACAATAATGTTTTAGTCTCTGGTAAGATATGCATTCTGTCCAAGGA\n+AAGACATTAGTGACTATTAGTATATTTACACAAGCAATCTTTTTTTATACAAATTGTACA\n+CCTCGGCGACCACATTGACGTCTTCTTCATTGACTGCGATCTCAACCACTTCAGGTGGTG\n+AAGATGTCGTTACGCTTTCCGTCGTTGGATGCTCCTTCTCCTCACTTTCATTCTCACCCC\n+AACGTCCTCGGTTACCATAGGGATGACGGTGGCCATCACGCCTGGGAGATCCTTCTTCGG\n+TTCTGTTGCGTCTGCCGAAGGGACGGTCTCCGAAAGGCTTTCTACCGAAGGGGTTGACCC\n+AGAAGGGCCTCATCTCAAACATTGGTCTGTCCTGATCTCCATCTCCGGTCTTGTTGTGAT\n+GACGATGGGGGTGATCTCCCGTCTCATTATGACCCTGGTGACCTTCTGTGTGGTTGCGTC\n+TGCCGAAGTGGTTGAACCGGAAGGGCCTCGTATCATTTGGTTTGTCCTGATCTTGATCTC\n+CCGTCTCATTATGTCCTTGGTGACCCTCTGTCTGGTTATGATGACGGTGGTGGTGGCCTT\n+GGTGGCCATGGTGGCCATGATGGTGAGGGTGAGGACGGCCATCCTCCTCGTTGCGTTCAT\n+TGCGCTGACCGAACGGTTGTTCCTCTGGTCGGTCCTGAGGTGGACCTTGACGGTGACCAT\n+GATGACGACGTCCATGACCATCAAACTGACCGCGCCCTCCTAGACCATCACCAATTTGTT\n+GGGAAGCATCAGTTTCTTCTTCTCCATCACCACGTCTTCCTCCTTGGCCGAAGAAAGGTC\n+TTCCTCCAGCACCATCTGGTCTGGAGCCACCAAATCCAGGTCCGTCGAATCTCCTACCAC\n+CCATCGGACCGCCATTTTGTCTGCGTCCATCCATATGTGGGGCACCAAATCCAGGTCCAT\n+CGAACCTCCTTCCACCCATTGGTCCACCATCTTGCCTAGATCCACCCATCTGCATTCCAC\n+CAGGCCTTCCTCCAAAGCGACCTTGTCCTCTCTCTCTGCCATTCTCATTTCCTCGCCGTT\n+CATTGAAATCTCTTCGTGCGTGAGCTGTAAGGGTTAATGAAATAATCGAATTAATTAAGT\n+AATCACATTCTGCATTATTATATTTGGCTCTACATTGGTTTATAGCAGGTGACAAATAAG\n+AATGGTAACTCGCCTTCTTATATTTTTTTCCCTTTATGTTTAATCCTAATCCGTAAGTGC\n+GGTTCGATATTCAAAACGCCTAATTCTGACTGAATTAAATTTGATTACCAGATTGAACGT\n+AAACATAATACACATCCTTTGTCATTCAGAAAACGGATTGGTGTAGGCTTAATAAATACA\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/mutation_data1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/mutation_data1.txt Sat Feb 21 16:33:42 2015 +0100

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diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/mutation_data1_interactive.svg
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/mutation_data1_interactive.svg Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,868 @@\n+<?xml version="1.0" standalone="no"?>\n+<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">\n+\n+<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" version="1.1">\n+<script type="text/javascript">\n+/**\n+ * SVGPan library 1.2\n+ * ====================\n+ *\n+ * Given an unique existing element with id "viewport", including the\n+ * the library into any SVG adds the following capabilities:\n+ *\n+ * - Mouse panning\n+ * - Mouse zooming (using the wheel)\n+ * - Object dargging\n+ *\n+ * Known issues:\n+ *\n+ * - Zooming (while panning) on Safari has still some issues\n+ *\n+ * Releases:\n+ *\n+ * 1.2, Sat Mar 20 08:42:50 GMT 2010, Zeng Xiaohui\n+ * Fixed a bug with browser mouse handler interaction\n+ *\n+ * 1.1, Wed Feb 3 17:39:33 GMT 2010, Zeng Xiaohui\n+ * Updated the zoom code to support the mouse wheel on Safari/Chrome\n+ *\n+ * 1.0, Andrea Leofreddi\n+ * First release\n+ *\n+ * This code is licensed under the following BSD license:\n+ *\n+ * Copyright 2009-2010 Andrea Leofreddi (a.leofreddi@itcharm.com). All rights reserved.\n+ *\n+ * Redistribution and use in source and binary forms, with or without modification, are\n+ * permitted provided that the following conditions are met:\n+ *\n+ * 1. Redistributions of source code must retain the above copyright notice, this list of\n+ * conditions and the following disclaimer.\n+ *\n+ * 2. Redistributions in binary form must reproduce the above copyright notice, this list\n+ * of conditions and the following disclaimer in the documentation and/or other materials\n+ * provided with the distribution.\n+ *\n+ * THIS SOFTWARE IS PROVIDED BY Andrea Leofreddi ``AS IS\'\' AND ANY EXPRESS OR IMPLIED\n+ * WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND\n+ * FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL Andrea Leofreddi OR\n+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR\n+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR\n+ * SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON\n+ * ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING\n+ * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF\n+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.\n+ *\n+ * The views and conclusions contained in the software and documentation are those of the\n+ * authors and should not be interpreted as representing official policies, either expressed\n+ * or implied, of Andrea Leofreddi.\n+ */\n+\n+var root = document.documentElement;\n+\n+var state = \'none\', stateTarget, stateOrigin, stateTf;\n+\n+setupHandlers(root);\n+\n+/**\n+ * Register handlers\n+ */\n+function setupHandlers(root){\n+ setAttributes(root, {\n+ "onmouseup" : "add(evt)",\n+ "onmousedown" : "handleMouseDown(evt)",\n+ "onmousemove" : "handleMouseMove(evt)",\n+ "onmouseup" : "handleMouseUp(evt)",\n+ //"onmouseout" : "handleMouseUp(evt)", // Decomment this to stop the pan functionality when dragging out of the SVG element\n+ });\n+\n+ if(navigator.userAgent.toLowerCase().indexOf(\'webkit\') >= 0)\n+ window.addEventListener(\'mousewheel\', handleMouseWheel, false); 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diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/mutation_data1_zoom3x.svg
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/ngs_simulation_in1.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/ngs_simulation_in1.fasta Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,41 @@
+>gi|209210|gb|L09136.1|SYNPUC18CV pUC18c cloning vector (beta-galactosidase mRNA on complementary strand)
+TCGCGCGTTTCGGTGATGACGGTGAAAACCTCTGACACATGCAGCTCCCGGAGACGGTCACAGCTTGTCT
+GTAAGCGGATGCCGGGAGCAGACAAGCCCGTCAGGGCGCGTCAGCGGGTGTTGGCGGGTGTCGGGGCTGG
+CTTAACTATGCGGCATCAGAGCAGATTGTACTGAGAGTGCACCATATGCGGTGTGAAATACCGCACAGAT
+GCGTAAGGAGAAAATACCGCATCAGGCGCCATTCGCCATTCAGGCTGCGCAACTGTTGGGAAGGGCGATC
+GGTGCGGGCCTCTTCGCTATTACGCCAGCTGGCGAAAGGGGGATGTGCTGCAAGGCGATTAAGTTGGGTA
+ACGCCAGGGTTTTCCCAGTCACGACGTTGTAAAACGACGGCCAGTGCCAAGCTTGCATGCCTGCAGGTCG
+ACTCTAGAGGATCCCCGGGTACCGAGCTCGAATTCGTAATCATGGTCATAGCTGTTTCCTGTGTGAAATT
+GTTATCCGCTCACAATTCCACACAACATACGAGCCGGAAGCATAAAGTGTAAAGCCTGGGGTGCCTAATG
+AGTGAGCTAACTCACATTAATTGCGTTGCGCTCACTGCCCGCTTTCCAGTCGGGAAACCTGTCGTGCCAG
+CTGCATTAATGAATCGGCCAACGCGCGGGGAGAGGCGGTTTGCGTATTGGGCGCTCTTCCGCTTCCTCGC
+TCACTGACTCGCTGCGCTCGGTCGTTCGGCTGCGGCGAGCGGTATCAGCTCACTCAAAGGCGGTAATACG
+GTTATCCACAGAATCAGGGGATAACGCAGGAAAGAACATGTGAGCAAAAGGCCAGCAAAAGGCCAGGAAC
+CGTAAAAAGGCCGCGTTGCTGGCGTTTTTCCATAGGCTCCGCCCCCCTGACGAGCATCACAAAAATCGAC
+GCTCAAGTCAGAGGTGGCGAAACCCGACAGGACTATAAAGATACCAGGCGTTTCCCCCTGGAAGCTCCCT
+CGTGCGCTCTCCTGTTCCGACCCTGCCGCTTACCGGATACCTGTCCGCCTTTCTCCCTTCGGGAAGCGTG
+GCGCTTTCTCATAGCTCACGCTGTAGGTATCTCAGTTCGGTGTAGGTCGTTCGCTCCAAGCTGGGCTGTG
+TGCACGAACCCCCCGTTCAGCCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTGAGTCCAACCCGGT
+AAGACACGACTTATCGCCACTGGCAGCAGCCACTGGTAACAGGATTAGCAGAGCGAGGTATGTAGGCGGT
+GCTACAGAGTTCTTGAAGTGGTGGCCTAACTACGGCTACACTAGAAGGACAGTATTTGGTATCTGCGCTC
+TGCTGAAGCCAGTTACCTTCGGAAAAAGAGTTGGTAGCTCTTGATCCGGCAAACAAACCACCGCTGGTAG
+CGGTGGTTTTTTTGTTTGCAAGCAGCAGATTACGCGCAGAAAAAAAGGATCTCAAGAAGATCCTTTGATC
+TTTTCTACGGGGTCTGACGCTCAGTGGAACGAAAACTCACGTTAAGGGATTTTGGTCATGAGATTATCAA
+AAAGGATCTTCACCTAGATCCTTTTAAATTAAAAATGAAGTTTTAAATCAATCTAAAGTATATATGAGTA
+AACTTGGTCTGACAGTTACCAATGCTTAATCAGTGAGGCACCTATCTCAGCGATCTGTCTATTTCGTTCA
+TCCATAGTTGCCTGACTCCCCGTCGTGTAGATAACTACGATACGGGAGGGCTTACCATCTGGCCCCAGTG
+CTGCAATGATACCGCGAGACCCACGCTCACCGGCTCCAGATTTATCAGCAATAAACCAGCCAGCCGGAAG
+GGCCGAGCGCAGAAGTGGTCCTGCAACTTTATCCGCCTCCATCCAGTCTATTAATTGTTGCCGGGAAGCT
+AGAGTAAGTAGTTCGCCAGTTAATAGTTTGCGCAACGTTGTTGCCATTGCTACAGGCATCGTGGTGTCAC
+GCTCGTCGTTTGGTATGGCTTCATTCAGCTCCGGTTCCCAACGATCAAGGCGAGTTACATGATCCCCCAT
+GTTGTGCAAAAAAGCGGTTAGCTCCTTCGGTCCTCCGATCGTTGTCAGAAGTAAGTTGGCCGCAGTGTTA
+TCACTCATGGTTATGGCAGCACTGCATAATTCTCTTACTGTCATGCCATCCGTAAGATGCTTTTCTGTGA
+CTGGTGAGTACTCAACCAAGTCATTCTGAGAATAGTGTATGCGGCGACCGAGTTGCTCTTGCCCGGCGTC
+AATACGGGATAATACCGCGCCACATAGCAGAACTTTAAAAGTGCTCATCATTGGAAAACGTTCTTCGGGG
+CGAAAACTCTCAAGGATCTTACCGCTGTTGAGATCCAGTTCGATGTAACCCACTCGTGCACCCAACTGAT
+CTTCAGCATCTTTTACTTTCACCAGCGTTTCTGGGTGAGCAAAAACAGGAAGGCAAAATGCCGCAAAAAA
+GGGAATAAGGGCGACACGGAAATGTTGAATACTCATACTCTTCCTTTTTCAATATTATTGAAGCATTTAT
+CAGGGTTATTGTCTCATGAGCGGATACATATTTGAATGTATTTAGAAAAATAAACAAATAGGGGTTCCGC
+GCACATTTCCCCGAAAAGTGCCACCTGACGTCTAAGAAACCATTATTATCATGACATTAACCTATAAAAA
+TAGGCGTATCACGAGGCCCTTTCGTC
+

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/ngs_simulation_out1.png

Binary file rnaseq/cutadapt/test-data/ngs_simulation_out1.png has changed

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/ngs_simulation_out2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/ngs_simulation_out2.tabular Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,19 @@
+      FP       FN GENOMESIZE.2686     fprate     hetcol     errcol
+Min.   :0.00   Min.   :0   Mode:logical   Min.   :0.000e+00   Min.   :0.1   Min.   :0.02
+1st Qu.:0.00   1st Qu.:0   NA's:25        1st Qu.:0.000e+00   1st Qu.:0.1   1st Qu.:0.02
+Median :0.00   Median :0   NA Median :0.000e+00   Median :0.1   Median :0.02
+Mean   :0.04   Mean   :0   NA Mean   :1.489e-05   Mean   :0.1   Mean   :0.02
+3rd Qu.:0.00   3rd Qu.:0   NA 3rd Qu.:0.000e+00   3rd Qu.:0.1   3rd Qu.:0.02
+Max.   :1.00   Max.   :0   NA Max.   :3.723e-04   Max.   :0.1   Max.   :0.02
+
+False Positive Rate Summary
+ 0.01 0.02
+0.02 9.710e-03 4.468e-05
+0.04 9.680e-03 1.489e-05
+0.1 9.695e-03 1.489e-05
+
+False Negative Rate Summary
+ 0.01 0.02
+0.02 0.16 0.52
+0.04 0.00 0.04
+0.1 0.00 0.00

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/ngs_simulation_out3.png

Binary file rnaseq/cutadapt/test-data/ngs_simulation_out3.png has changed

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/pass_input.gff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/pass_input.gff Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,100 @@
+chr7 Nimblegen ID 40307603 40307652 1.668944
+chr7 Nimblegen ID 40307703 40307752 0.8041307
+chr7 Nimblegen ID 40307808 40307865 -1.089931
+chr7 Nimblegen ID 40307920 40307969 1.055044
+chr7 Nimblegen ID 40308005 40308068 2.447853
+chr7 Nimblegen ID 40308125 40308174 0.1638694
+chr7 Nimblegen ID 40308223 40308275 -0.04796628
+chr7 Nimblegen ID 40308318 40308367 0.9335709
+chr7 Nimblegen ID 40308526 40308584 0.5143972
+chr7 Nimblegen ID 40308611 40308660 -1.089931
+chr7 Nimblegen ID 40308721 40308770 0.5143972
+chr7 Nimblegen ID 40308821 40308875 0.1638694
+chr7 Nimblegen ID 40308946 40308996 0.3488488
+chr7 Nimblegen ID 40309026 40309075 -0.2999181
+chr7 Nimblegen ID 40309151 40309200 0.9335709
+chr7 Nimblegen ID 40309251 40309300 0.66513
+chr7 Nimblegen ID 40309351 40309401 -0.04796628
+chr7 Nimblegen ID 40309426 40309482 0.8041307
+chr7 Nimblegen ID 40309526 40309576 0.1638694
+chr7 Nimblegen ID 40309626 40309686 0.66513
+chr7 Nimblegen ID 40309726 40309775 0.8041307
+chr7 Nimblegen ID 40309851 40309900 1.926153
+chr7 Nimblegen ID 40309951 40310000 1.382456
+chr7 Nimblegen ID 40310036 40310085 1.169756
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+chr7 Nimblegen ID 40311151 40311202 0.8041307
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+chr7 Nimblegen ID 40311346 40311397 0.8041307
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+chr7 Nimblegen ID 40311551 40311600 1.055044
+chr7 Nimblegen ID 40311641 40311690 0.9335709
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+chr7 Nimblegen ID 40311826 40311875 0.3488488
+chr7 Nimblegen ID 40311951 40312010 0.9335709
+chr7 Nimblegen ID 40312046 40312095 1.169756
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+chr7 Nimblegen ID 40314127 40314176 1.382456
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+chr7 Nimblegen ID 40314472 40314521 1.481793
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+chr7 Nimblegen ID 40314852 40314909 -1.089931
+chr7 Nimblegen ID 40314957 40315007 1.278645
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+chr7 Nimblegen ID 40317452 40317501 1.169756
+chr7 Nimblegen ID 40317567 40317616 -0.2999181
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+chr7 Nimblegen ID 40317752 40317801 0.1638694

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/pass_output.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/pass_output.tab Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,2 @@
+ID Chr Start End WinSz PeakValue # of FPs FDR
+1 chr7 40310931 40311266 4 1.663446 0.299144 0.299144

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/pca_out1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/pca_out1.tabular Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,159 @@
+#Component 1 2 3 4
+#Std. deviation 1.706 0.9598 0.3839 0.1436
+#Proportion of variance explained 0.7277 0.2303 0.03684 0.005152
+#Loadings 1 2 3 4
+c1 0.5224 -0.3723 0.721 0.262
+c2 -0.2634 -0.9256 -0.242 -0.1241
+c3 0.5813 -0.02109 -0.1409 -0.8012
+c4 0.5656 -0.06542 -0.6338 0.5235
+#Scores 1 2 3 4
+1 -2.265 -0.5057 0.1219 0.02307
+2 -2.086 0.6554 0.2273 0.1032
+3 -2.368 0.3185 -0.05148 0.02783
+4 -2.304 0.5754 -0.09886 -0.06631
+5 -2.389 -0.6748 -0.02143 -0.0374
+6 -2.071 -1.519 -0.03068 0.004399
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+8 -2.234 -0.2476 0.08257 -0.02551
+9 -2.342 1.095 -0.1536 -0.02679
+10 -2.189 0.4486 0.2466 -0.03991
+11 -2.163 -1.071 0.264 0.0153
+12 -2.327 -0.1586 -0.1002 -0.1346
+13 -2.224 0.7091 0.2232 0.002631
+14 -2.64 0.9383 -0.1896 -0.01942
+15 -2.192 -1.89 0.4695 0.1928
+16 -2.251 -2.722 -0.0326 0.04713
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+52 0.7325 -0.5986 0.09407 0.004454
+53 1.242 -0.6148 0.5548 0.009673
+54 0.3973 1.758 0.01857 0.0674
+55 1.073 0.2118 0.3974 0.1055
+56 0.3845 0.5911 -0.1268 -0.2405
+57 0.7487 -0.7787 -0.1487 -0.0783
+58 -0.4979 1.849 -0.2556 -0.03939
+59 0.9262 -0.03033 0.5955 -0.0291
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+61 -0.1247 2.658 0.03981 0.01614
+62 0.4387 0.05888 -0.2067 0.03985
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+65 -0.03726 0.4328 -0.1981 0.109
+66 0.8759 -0.51 0.5035 0.1051
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+69 1.215 1.633 0.4794 0.2282
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+86 0.4318 -0.8551 -0.4507 -0.1111
+87 1.049 -0.5222 0.3961 0.0373
+88 1.036 1.392 0.6854 0.1391
+89 0.06707 0.2126 -0.2941 -0.1475
+90 0.2754 1.33 -0.09344 0.009948
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+98 0.5739 0.1537 0.27 -0.01941
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+101 1.848 -0.8717 -1.003 -0.05107
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+104 1.439 0.05001 -0.1634 -0.2358
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+106 2.754 -0.7884 0.5862 -0.1009
+107 0.3584 1.56 -0.991 -0.133
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+109 2.002 0.7239 0.3941 -0.08499
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+112 1.599 0.4282 -0.0233 0.05894
+113 1.884 -0.4143 -0.02455 0.1463
+114 1.253 1.167 -0.5821 0.09968
+115 1.464 0.4441 -1.004 0.275
+116 1.592 -0.677 -0.6367 0.1906
+117 1.471 -0.2532 -0.03666 -0.1554
+118 2.437 -2.557 0.1342 -0.2757
+119 3.309 0.002361 0.7069 0.04676
+120 1.254 1.718 0.2646 -0.06307
+121 2.04 -0.9074 -0.2319 0.1671
+122 0.9739 0.5712 -0.8295 0.02732
+123 2.898 -0.3978 0.8609 -0.1261
+124 1.329 0.4868 0.004707 0.1406
+125 1.704 -1.014 -0.296 -0.06274
+126 1.958 -1.003 0.4228 -0.2185
+127 1.172 0.3189 -0.1307 0.1257
+128 1.02 -0.06554 -0.338 -0.009069
+129 1.786 0.1933 -0.27 0.03121
+130 1.865 -0.5554 0.7175 -0.2076
+131 2.435 -0.2467 0.7302 -0.01679
+132 2.316 -2.626 0.4996 -0.2132
+133 1.86 0.1847 -0.3533 0.1
+134 1.111 0.296 0.1827 -0.1857
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+136 2.801 -0.8447 0.547 0.2963
+137 1.58 -1.072 -0.9434 0.03361
+138 1.347 -0.4223 -0.18 -0.2159
+139 0.9234 -0.01923 -0.4174 0.004744
+140 1.854 -0.6724 0.01482 0.1949
+141 2.016 -0.6104 -0.4259 0.2468
+142 1.903 -0.686 -0.1278 0.4692
+143 1.153 0.7013 -0.5315 -0.04041
+144 2.043 -0.8647 -0.3353 0.04428
+145 2.002 -1.049 -0.6293 0.2126
+146 1.871 -0.3828 -0.2545 0.3889
+147 1.558 0.9053 0.02538 0.2213
+148 1.521 -0.2668 -0.1793 0.1189
+149 1.376 -1.016 -0.9314 0.02415
+150 0.9593 0.02228 -0.5288 -0.1637

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/pca_out2.pdf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/pca_out2.pdf Sat Feb 21 16:33:42 2015 +0100

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diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/pca_out3.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/pca_out3.tabular Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,159 @@
+#Component 1 2 3 4
+#Std. deviation 2.049 0.4905 0.2793 0.1534
+#Proportion of variance explained 0.9246 0.05302 0.01719 0.005183
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diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/pca_out4.pdf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/pca_out4.pdf Sat Feb 21 16:33:42 2015 +0100

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diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/pca_out5.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/pca_out5.tabular Sat Feb 21 16:33:42 2015 +0100

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+#Component 1 2 3 4
+#Std. deviation 1.706 0.9598 0.3839 0.1436
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+#Loadings 1 2 3 4
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diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/pca_out6.pdf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/pca_out6.pdf Sat Feb 21 16:33:42 2015 +0100

[

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diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/perm_in1.fastqsanger
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/perm_in1.fastqsanger Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,76 @@
+@HWI-EAS91_1_30788AAXX:1:1:1761:343/1
+TTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGA
++
+IIIIIII""IIIIIIIIIII?I0IIIIHIIIGIIIII0II?I""IIIIII
+@HWI-EAS91_1_30788AAXX:1:1:1578:331/1
+TGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGC
++
+IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII
+@HWI-EAS91_1_30788AAXX:1:1:1647:512/1
+TACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCA
++
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+@HWI-EAS91_1_30788AAXX:1:1:1570:620/1
+GAGTAACAAAGTaaaGTTTGGAccGTTTTTGTCTCGTGCTCGTCGCTGCG
++
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+@HWI-EAS91_1_30788AAXX:1:1:1599:330/1
+AGAAGAAAACGTGCGTCAAAAATTACGTGCaGAAGGAGTGATGTAATGTC
++
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++
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+@HWI-EAS91_1_30788AAXX:1:1:1746:351/1
+CTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGT
++
+IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII
+@HWI-EAS91_1_30788AAXX:1:1:1582:633/1
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++
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++
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++
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+@HWI-EAS91_1_30788AAXX:1:1:1749:466/1
+TTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCT
++
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++
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++
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++
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++
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+@HWI-EAS91_1_30788AAXX:1:1:1572:270/1
+TGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTA
++
+IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII
+@HWI-EAS91_1_30788AAXX:1:1:1785:1272/1
+TATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCT
++
+III""""""IIIIIIIII""FI"IIII""II+ICI"IIIIIII000IIII
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++
+IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIII1"IIIIIII000IIII
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++
+IIIIIII""IIIIIIIIIIIIIIIIIIIIIII8II"IIIIIII000IIII

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/perm_in2.fastqsanger
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/perm_in2.fastqsanger Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,76 @@
+@HWI-EAS91_1_30788AAXX:1:1:1761:343/2
+TTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGG
++
+IIIIIII""IIIIIII0II?I""IIIIIIIIIIII?I0IIIIHIIIGIII
+@HWI-EAS91_1_30788AAXX:1:1:1578:331/2
+AAGGACTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTCT
++
+IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII
+@HWI-EAS91_1_30788AAXX:1:1:1647:512/2
+TTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTG
++
+IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII
+@HWI-EAS91_1_30788AAXX:1:1:1570:620/2
+CTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCT
++
+IIIIIII""IIIIIIIIIIIIIBIIIIIIIIIIII?I0IIIIHIIIGIII
+@HWI-EAS91_1_30788AAXX:1:1:1599:330/2
+TTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCA
++
+IIIIIII""IIIIIIIIIIIIIIIIIII<III@II?I0IIIIHIIIGIII
+@HWI-EAS91_1_30788AAXX:1:1:1652:270/2
+GCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCG
++
+IIIIIII""IIIIIIIIIIIIIIIIIIIIIII6II?I0IIIIHIIIGIII
+@HWI-EAS91_1_30788AAXX:1:1:1746:351/2
+CCACTCCTCTCCCGACTGTGTGTGTGTGTGTTTATATTGACCATGCCGCT
++
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+@HWI-EAS91_1_30788AAXX:1:1:1582:633/2
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++
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+@HWI-EAS91_1_30788AAXX:1:1:1598:534/2
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++
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+@HWI-EAS91_1_30788AAXX:1:1:1572:324/2
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++
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++
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++
+IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII
+@HWI-EAS91_1_30788AAXX:1:1:1763:587/2
+CATTGCATTCAGATGGATACATCTGTCAACGCCGCTAATCAGGTTGTTTC
++
+IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII
+@HWI-EAS91_1_30788AAXX:1:1:1616:363/2
+GTGACTATTGACGTCCTTCCCCGTACGCCGGGCAATAAtGTTTATGTTGG
++
+IIIIIII""IIIIIIIIIIIIIIIIIIIIIIDIII?I0IIIIHIIIGIII
+@HWI-EAS91_1_30788AAXX:1:1:1768:715/2
+AGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATA
++
+IIIIIII""IIIIIIIIIIIIIDIIIIIIIIIIII?I0IIIIHIIIGIII
+@HWI-EAS91_1_30788AAXX:1:1:1572:270/2
+ACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATG
++
+IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII
+@HWI-EAS91_1_30788AAXX:1:1:1785:1272/2
+GACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCGTC
++
+III""""""IIIIIIIII""FI"IIII""II+ICI?I0IIIIHIIIGIII
+@HWI-EAS91_1_30788AAXX:1:1:1673:514/2
+GCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATG
++
+IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIII1?I0IIIIHIIIGIII
+@HWI-EAS91_1_30788AAXX:1:1:1634:330/2
+TCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTaCTAT
++
+IIIIIII""IIIIIIIIIIIIIIIIIIIIIII8II?I0IIIIHIIIGIII

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/perm_in3.fastqsanger
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/perm_in3.fastqsanger Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,396 @@\n+@HWI-EAS91_1_30788AAXX:1:1:1513:715/1\n+GTTTTTTGGGCATAGATGTTTAGTTGTGGTAGTCAG\n++\n+IIIIIII""IIIIIIIIIIIIIIIIIIIDI?II-+I\n+@HWI-EAS91_1_30788AAXX:1:1:1698:516/1\n+GTTGTTAGGGAGAGGAGTTGAACCTCTGAGTGTAAA\n++\n+IIIIIII""IIIIIIIIIIIIIIIIIII5IIIII9I\n+@HWI-EAS91_1_30788AAXX:1:1:1491:637/1\n+GCTAGCAGGATGGATCCGGCAATTGGGGCTTCTACA\n++\n+IIIIIII""IIIIIIIIIIIIFIIIIIIIIIIIABD\n+@HWI-EAS91_1_30788AAXX:1:1:1711:249/1\n+GGAAGTAGGGGCCTGCGTTCAGGCGTTCTGTTTGGT\n++\n+IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-EAS91_1_30788AAXX:1:1:1634:211/1\n+GAAGCAGGGGCTTGATACTGACACTTCGTCGACGTA\n++\n+IIIIIII""IIIIIIIIIIIIIIIIIIIIII9IIDF\n+@HWI-EAS91_1_30788AAXX:1:1:1218:141/1\n+GTTAAATATTGGGAGTGGGGGGGGGGGGGAGTTTTG\n++\n+IIIIIII""IIIIIIIIIIIIIIIIIIII1IIII+I\n+@HWI-EAS91_1_30788AAXX:1:1:1398:854/1\n+GTGAAGAGGAGGGGATTTATTAGTACGGGAAGGGTG\n++\n+IIIIIII""IIIIIBIIIIIIIIIIIIIIA=IIIII\n+@HWI-EAS91_1_30788AAXX:1:1:1310:991/1\n+GAATAGTGGTAGTATTATTCCTTCTAGGCATAGGAG\n++\n+IIIIIII""IIIIIIIIII4IIIIIIDII:IEI2:I\n+@HWI-EAS91_1_30788AAXX:1:1:1716:413/1\n+GATCCAAGGCTTTATCAACACCTATTCTGATTCTTC\n++\n+IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-EAS91_1_30788AAXX:1:1:1630:59/1\n+GGAGCGGGGGGTTGGTAAGGTTGGGGTCGAGTATGA\n++\n+IIIIIII""IIIIIIIIIIIIIIIIIIII;IIHIIF\n+@HWI-EAS91_1_30788AAXX:1:1:1601:805/1\n+GAAAACAGGAAAACAATCCAGTCACTTACCCTATGC\n++\n+IIIIIII""IIIIIIIIIIIIIIIIIIIIIII@III\n+@HWI-EAS91_1_30788AAXX:1:1:1663:724/1\n+GTTTGCCGGCGCCATCCTACGCTCCATTCCCAACAA\n++\n+IIIIIII""IIII8IIIIIIHIIII6IIIII1CI=3\n+@HWI-EAS91_1_30788AAXX:1:1:1454:975/1\n+GCTAGGCGGGAGTGGTAAAAGGCTCAGAAGAAGCCA\n++\n+IIIIIII""IIIIIIIIIIIIIIIIEIG;IIIIIII\n+@HWI-EAS91_1_30788AAXX:1:1:1461:255/1\n+GTACACCGGCGCCTGAGCCCTACTAATAACTCTCAT\n++\n+IIIIIII""IIIIII9IIIIIIEI(II9.I4III,I\n+@HWI-EAS91_1_30788AAXX:1:1:1775:764/1\n+GCATCCCGGTAGATCTAATTTTCTAAATCTGTCAAC\n++\n+IIIIIII""III@IIII+IIIIII8H8IIIIIIICI\n+@HWI-EAS91_1_30788AAXX:1:1:1269:520/1\n+GGAGTATGGAATAAGTGATTTTAGATCGGTTTGTCG\n++\n+IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-EAS91_1_30788AAXX:1:1:1303:1162/1\n+GAGCAAGGGCAGGAGGAGGAGTCCTAGGATGTCTTT\n++\n+IIIIIII""IIIIFII4*IGIAI(IAII49\',3I6I\n+@HWI-EAS91_1_30788AAXX:1:1:1090:409/1\n+GTTTGTTGGGAATGGAGCGTAGGATGGCGTAGGCAA\n++\n+IIIIIII""IIIIIIIIIIIIIIIIIIIII:IIA8I\n+@HWI-EAS91_1_30788AAXX:1:1:1336:1000/1\n+GGTAAATGGGAAATATTAAGTTTCTGTTTCTAGATC\n++\n+IIIIIII""IIIIIIIIIIIIIIIIIIIIIIII9II\n+@HWI-EAS91_1_30788AAXX:1:1:1199:1376/1\n+GTTTTCTGGAAAACCTTCACCTATTTATGGGGGTTT\n++\n+IIIIIII""IIIIIIIIIIIII;III3IIG&:/III\n+@HWI-EAS91_1_30788AAXX:1:1:1598:1148/1\n+GATCAATGGTTTGGATCAATAAGTGATTATATATTT\n++\n+IIIIIII""IIIIIDIIIIII?IIICII=IHIIIII\n+@HWI-EAS91_1_30788AAXX:1:1:1723:1459/1\n+GAAACCCGGACGTTTGGATGGGCCCGGAGCGAGGAT\n++\n+IIIIIII""IIIIIIIIDIIIIIIIII9HII-II=I\n+@HWI-EAS91_1_30788AAXX:1:1:1442:1346/1\n+TATCAAGGGGCTGCTTCGAATCCGAAGTGGTGGCTG\n++\n+IIIIIII""IIIIIDIIIII1I(I4II<?<-II*,&\n+@HWI-EAS91_1_30788AAXX:1:1:850:117/1\n+GTATGACGGTAAAGAAAATTATTACGAATGCATGGG\n++\n+IIIIIII""IIIIIIEIEIIIIIIIIEBIDD9I;:?\n+@HWI-EAS91_1_30788AAXX:1:1:795:325/1\n+GGGTACTGGGAAGTGGAATGGTGTGAGTCCAAGTTT\n++\n+IIIIIII""IIIIIIIIIIIIIIIIIIIII65IIII\n+@HWI-EAS91_1_30788AAXX:1:1:873:453/1\n+GAGTAGGGGGATTGCTAGAGTTACTTCGTATGAGAT\n++\n+IIIIIII""IIIIIIIIIIIIIIIII@IIIIIII=I\n+@HWI-EAS91_1_30788AAXX:1:1:1285:1334/1\n+GATATGGGGTCTGGAATAGGATTGCGCTGTTATCCC\n++\n+IIIIIII""IIIIIBIIGIIIIIIIIII8IIIII8I\n+@HWI-EAS91_1_30788AAXX:1:1:905:406/1\n+GAAAAGTGGTAGGCTATATGCAACTTCGCAAAGGAC\n++\n+IIIIIII""IIIIIIIIBIIIIBIIII=I@96D2*I\n+@HWI-EAS91_1_30788AAXX:1:1:1774:595/1\n+TTTAGGTGGGATGTGGGGATCATGTAGGAGTCAAAG\n++\n+IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIEI\n+@HWI-EAS91_1_30788AAXX:1:1:1694:931/1\n+TTAAATTGGCATTAGAATTGAGTAGTTTTTAGGTAA\n++\n+IIIIIII""IIIIIIIIIIIIIIIIIIIIIIH,III\n+@HWI-EAS91_1_30788AAXX:1:1:1092:1151/1\n+GAGAGTTGGCTGATTTAGGCGCCCAGGGATAGCGTC\n++\n+IIIIIII""IIIIIIIIIII5III>IIIII6@III5\n+@HWI-EAS91_1_30788AAXX:1:1:803:557/1\n+GGTGTGTGGGCGCTTCATGGCCTGATTCAATTAAGC\n++\n+IIIIIII""IIIIIIIIIIIIIII<IIII?III406\n+@HWI-EAS91_1_30788AAXX:1:1:1315:1200/1\n+TAGTTTTGGGGGGTTTTCTTCAAAACCTTCACCTAT\n++\n+IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIII;I\n+@HWI-EAS91_1_30788AAXX:1:1:765:358/1\n+GGTGTTTGGATGAGGACGGCTACGATTACTAGGGCT\n++\n+IIII'..b'_30788AAXX:1:1:843:504/1\n+ACAACATGGAATACCATCTCATCCATAGGATCTTTT\n++\n+IIIIIII""IIIIIIIIAIIIIII>IIHI=IIIIII\n+@HWI-EAS91_1_30788AAXX:1:1:942:318/1\n+TTCATACGGGCCATGTCCAGCCTAGCTGTCTACTCA\n++\n+IIIIIII""IIIIIIIIIIHIIIIIIIIIII<IIIF\n+@HWI-EAS91_1_30788AAXX:1:1:1719:283/1\n+TTTTGTTGGCCGAGGTCACCCCAACCGAAATTGCTG\n++\n+IIIIIII""IIIIIIIIIIIIIIIIII3=2IGIIII\n+@HWI-EAS91_1_30788AAXX:1:1:1517:961/1\n+TGTCACTGGTCCATATTAATATCTTCCTAGCATTCA\n++\n+IIIIIII""IIIII=III9I@IIIIIIIBIIEIII>\n+@HWI-EAS91_1_30788AAXX:1:1:1482:345/1\n+AGGATGTGGGTTAATAGCCCTATAGCTAGAAGTAAG\n++\n+IIIIIII""IIIIIIIIIIIIIIIIII?IAHIIAAI\n+@HWI-EAS91_1_30788AAXX:1:1:1697:533/1\n+ATGAGGTGGATTAGGAGGTGTCCGGCGGTAATGTTA\n++\n+IIIIIII""IIIIIIIIIIIIIIIIIIII1>IIIII\n+@HWI-EAS91_1_30788AAXX:1:1:1159:1225/1\n+TTTCTACGGCAAGGGACGCCCATTTTCCTCATCCCC\n++\n+IIIIIII""IIIII=I7IIII3IIIIIIII/ID@II\n+@HWI-EAS91_1_30788AAXX:1:1:982:332/1\n+AAGGATTGGATCCCCTCCTCCTGCGGGGTCGAAGAA\n++\n+IIIIIII""IIIIIIIIIIIIIIIIIIIIII?<I7@\n+@HWI-EAS91_1_30788AAXX:1:1:1073:668/1\n+AGCATTTGGCAACCCCTACCTGCCAGAACTCTACTC\n++\n+IIIIIII""IIIIIIIIIIIIIII>I4@IIIIIIII\n+@HWI-EAS91_1_30788AAXX:1:1:1386:1163/1\n+AGTTGGCGGAAAAGCAGCCATCAATTAAGAAAGCGT\n++\n+IIIIIII""IIIIIIIIIICII=GIIIII@IGIIII\n+@HWI-EAS91_1_30788AAXX:1:1:1196:344/1\n+ATTGAAGGGAGTTGATTAGGGTATTTAGCTGTTAAC\n++\n+IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII7\n+@HWI-EAS91_1_30788AAXX:1:1:1551:1269/1\n+ATTACCAGGATCCTAATAGGAGCCAATATCACCATC\n++\n+IIIIIII""IIIIIIIIGIIIIIIIIIIII@II4II\n+@HWI-EAS91_1_30788AAXX:1:1:928:468/1\n+AGGAGATGGAAATTTTAACTTGGCGCTATAGAGAAA\n++\n+IIIIIII""IIIIIIIIIIIIIIIIIIIIC<IHIII\n+@HWI-EAS91_1_30788AAXX:1:1:763:835/1\n+GCTCAGAGGAAGCCAGAGAAGAAGAAGACTTCTGAG\n++\n+IIIIIII""IIIIIIIHIEFIIFI<IIIIIIDII:I\n+@HWI-EAS91_1_30788AAXX:1:1:1363:330/1\n+TAGCCTCGGAGTTTTAGTAGAATGGCTGCTAGCACT\n++\n+IIIIIII""IIIIIIII@IIIIIIIIII5I,5C-75\n+@HWI-EAS91_1_30788AAXX:1:1:1001:837/1\n+ATACTATGGCTGTGAGGAATAATCATAACTAGTTCC\n++\n+IIIIIII""IIIII2IIIIIIIIIIIFIII:IIIII\n+@HWI-EAS91_1_30788AAXX:1:1:1189:616/1\n+TTTGATAGGGTAAAACATAGAGGCTCAAACCCTCTT\n++\n+IIIIIII""IIIIIIIIIIIIIIIIICIIIIIIIII\n+@HWI-EAS91_1_30788AAXX:1:1:1212:634/1\n+ATCAACAGGTATTCTGATTCTTCGGACACCCCGAAG\n++\n+IIIIIII""IIIIIIIIIIIIIIIIIIAIIIIF(.I\n+@HWI-EAS91_1_30788AAXX:1:1:1271:421/1\n+ACACGACGGCACCTAATGACCCACCAAACCCACGCT\n++\n+IIIIIII""IIIIIIIIIIIIIIII>C:IIIDI<II\n+@HWI-EAS91_1_30788AAXX:1:1:1582:328/1\n+AGCATTAGGCTTTTAAGTTAAAGATTGAGGGTTCAA\n++\n+IIIIIII""IIIIII,IIIB;BI<IIIIII+IIIBI\n+@HWI-EAS91_1_30788AAXX:1:1:1133:687/1\n+AGAGAGCGGATTAGGAATACGATTATTAGTGTGTGG\n++\n+IIIIIII""IIIIIIIIIIIIIIIIIIIIIII4III\n+@HWI-EAS91_1_30788AAXX:1:1:1231:662/1\n+TCACTCTGGAGAACATATAAAACCAACATAACCTCC\n++\n+IIIIIII""IIIIIIIIIIIIIIIIII?ICCIIIII\n+@HWI-EAS91_1_30788AAXX:1:1:1693:1140/1\n+ATTGATAGGATGGGGGTTAGGGGGAGGAGTAGGGAG\n++\n+IIIIIII""IIIIIIIIIIIIIII:II5II7IIA-I\n+@HWI-EAS91_1_30788AAXX:1:1:867:279/1\n+AAGCATTGGACTGTAAATCTAAAGACAGGGGTTGGA\n++\n+IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-EAS91_1_30788AAXX:1:1:1095:605/1\n+AAGCAAGGGACTGAAAATGCCTAGATGAGTATTCTT\n++\n+IIIIIII""IIIIIIIIIIIIIIIEIIIIIIIIIII\n+@HWI-EAS91_1_30788AAXX:1:1:1650:1185/1\n+ACCCCAGGGAACCCTCTCAGCACTCCCCCTCATATT\n++\n+IIIIIII""IIIIIIIIIIII6IIIIIIIII5I-II\n+@HWI-EAS91_1_30788AAXX:1:1:799:192/1\n+AATGTTAGGGGTTAGCCGCACGGCTAGGGCTACAGG\n++\n+IIIIIII""IIIIIIIIII8IIIEIIIII<I::%II\n+@HWI-EAS91_1_30788AAXX:1:1:1082:719/1\n+TCTTGAGGGTCTATGGTGCTGGTATGGGTTAATTTA\n++\n+IIIIIII""IIIIIIA8III>I92I3+3IIE0III<\n+@HWI-EAS91_1_30788AAXX:1:1:1746:1180/1\n+AAAATTAGGGAGAAGTAATCTAGTTTGAAGCTTAGG\n++\n+IIIIIII""IIIIIIIIIIIIIIIIIIFIIIIIIII\n+@HWI-EAS91_1_30788AAXX:1:1:606:460/1\n+TTAATTTGGATTATAATAACACTCACAATATTCATA\n++\n+IIIIIII""IIIIIIIIIIIIIIIIII?I6IIIII6\n+@HWI-EAS91_1_30788AAXX:1:1:1059:362/1\n+ATCGGTAGGCTCGTAGCTTCAGTATCATTGGTGGCC\n++\n+IIIIIII""IIIIIIIIIIIIIIIIIIIII2)</II\n+@HWI-EAS91_1_30788AAXX:1:1:1483:1161/1\n+ATATGTGGGGGGTGGGGATGAGTGCTAGGATCAGGA\n++\n+IIIIIII""IIIIIIIIIIIIIIIHIAIIFIIIIIH\n+@HWI-EAS91_1_30788AAXX:1:1:1273:600/1\n+TACTGAGGGGTATCCTGAGGTATGGGTGTCTAATAC\n++\n+IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII\n+@HWI-EAS91_1_30788AAXX:1:1:1190:1283/1\n+TTTCTGGGGTACAAGACCAGGGTAATGTGCGATATA\n++\n+IIIIIII""IIIIIIIIIIIIIIIAIIIII-?IIIE\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/perm_in4.fastqcssanger
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/perm_in4.fastqcssanger Sat Feb 21 16:33:42 2015 +0100

b"@@ -0,0 +1,576 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diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/perm_in5.fastqcssanger
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/perm_in5.fastqcssanger Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,48 @@
+@853_60_741/1
+G31030031122312021111010130200021003210121320000223
++
+==9:>>=;><9;=<<>;><>>;?<=?:>?><=>?9<>=<9=;<?=>>><9
+@853_111_1583/1
+G21011211200202112131111130201231220231231220200322
++
+:A<A>>>;=<;=<@A;?<<@<>?@><99A=<7=;=:6;<<:9::<;89=<
+@853_111_1628/1
+G10102021032020010121032020232110130223102122302200
++
+?;<<>;=<=>?8;>9>;<><=9;<;=<5<><;8=>?978<=8;;8<8:;:
+@853_276_1541/1
+G03222011023120123332203020012312001121123311001231
++
+=<><;A<<>@<@<<?:<:<>=:<==;?<<<<:>=A?;==;==;<@;;8:<
+@853_394_432/1
+G13312311132110330003300222221112131200021120330332
++
+@=>@A<?>>==?A?<??=@?>?=?><?=?=:@?=?==A=<;<<@=<<>=5
+@853_460_1442/1
+G02101122101002202021313212112232110310010223211122
++
+>??:?>@>A=?=:>A>>9?><==A>>>=?>;==:>>>;:;==:<;>;9<=
+@865_1106_310/1
+G01222230300213322221202031001001030210000110220102
++
+;6?;=>=:9>:=<:<>:<;<>;?;>>;<<<>9><>:9===?<6<::5:;;
+@869_1532_1255/1
+G21022233110003122233210021301222000112122113330022
++
+=;8:?@=?;;9:8;=>;5A?;<8><<=:9><;9<=8;96>8<5==:<98;
+@889_1337_1562/1
+G32320230101133233031203331023110123123110321101011
++
+==?@=@??@?=@>==;?=>=;;?>=<;==<=:A;<<<=7=8:;==6<>=;
+@891_252_1590/1
+G21001002321200302231203001233020201230020220002300
++
+<A>9<=9A;A><>>>;>@?A>9=;@>@>?<><@>@@<;=;8:7>:;:5=<
+@892_582_183/1
+G01101032230201131100203303123121133333011110033000
++
+;><:><=>;<<>:=>?>>;<=;:9><<:=:>;:;>;:=9;;=799<7699
+@932_1836_1806/1
+G32331100031222332100213012220001121221133300220331
++
+;:<;<;<><;>9@=<=<:>A:8<<=<=?<:@?<=?<;>9;<6<><<::5>

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/perm_in6.fastqcssanger
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/perm_in6.fastqcssanger Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,48 @@
+@853_60_741/2
+T30321031112011000112320211202221320221313213231311
++
+99?;>=;?>:>=>:<>>?85>=<;:><995@::<7@<=88==>;=?>>9<
+@853_111_1583/2
+T10022103103000201030021103111120021021121130210022
++
+?;<<>;=<=>?8;>9>;<><=9;<;=<5<><;8=>?978<=8;;8<8:;:
+@853_111_1628/2
+T33002021100103231100332001320020101002002311222011
++
+><@A>=>;>?A<A:<;???@==>;?>>?8?<8;:@?=<;6>6<;;9=?<5
+@853_276_1541/2
+T30303002200001133331103221321130031333013232132322
++
+A?:5A<?:=A>A8@8AA:@:<@97<@@@>A7?@6?@;8?A7@986;5;?=
+@853_394_432/2
+T30030000333322020222202211233333002103312202000110
++
+:<:=>:?><==>=><<=><:;>=;:;9;><9<><@8;:;>=;:7:>7:7=
+@853_460_1442/2
+T11130211103112102212221200202022130303003210122101
++
+>A=:>@@==>@>=<<>?9>>=;9<<==:<<;>8;;;<<<:<:7=95>:;9
+@865_1106_310/2
+T33223200002331021122331020030003301230300213231311
++
+?@@=?A>A>==:=;=????A<;;>A<<?=>?<@<=@9:>9>:56A<;;9;
+@869_1532_1255/2
+T03103330303100300112231121121003120312113022230331
++
+@A=><>9=<@>;<;<==?;?<A=?<=<<:A>7>9:;:<=7:8@6><>96<
+@889_1337_1562/2
+T10031203121130222303312100203132322201123110000101
++
+=A;A@>AA@>?>A@>A:>@:<>>=5;;=;<;88?=>5=;899:9<<;>98
+@891_252_1590/2
+T03210330303300030311113131021332033110001211222031
++
+8;8?;><::;9;:>;><:>9=8;68:<?<;=@===<=>9=:>A9=89;==
+@892_582_183/2
+T20322002021213100112021203203010031223003101212213
++
+@?=?@>A?>>>??>A;@>?==>>@<>??><<>>::=?:=?=;6<>=<>=<
+@932_1836_1806/2
+T03233010131101303202311220122201011323220123130010
++
+AA<?A@AAAA>?A>A@=>@>A>??A@?>>@>@=>A9?>:?>8@@=>>=>@

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/perm_out1.sam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/perm_out1.sam Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,33 @@
+HWI-EAS91_1_30788AAXX:1:1:1761:343/1 65 phiX174 5 255 50M = 69 64 TTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGA IIIIIII""IIIIIIIIIII?I0IIIIHIIIGIIIII0II?I""IIIIII NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1761:343/1 129 phiX174 69 255 50M = 5 64 TTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGG IIIIIII""IIIIIII0II?I""IIIIIIIIIIII?I0IIIIHIIIGIII NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1578:331/1 65 phiX174 209 255 50M = 268 59 TGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1578:331/1 129 phiX174 268 255 50M = 209 59 AAGGACTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTCT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1647:512/1 65 phiX174 401 255 50M = 451 50 TACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCA IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1647:512/1 129 phiX174 451 255 50M = 401 50 TTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTG IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1570:620/2 0 phiX174 559 255 50M * 0 0 CTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCT IIIIIII""IIIIIIIIIIIIIBIIIIIIIIIIII?I0IIIIHIIIGIII NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1599:330/1 65 phiX174 803 255 50M = 868 65 AGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAGTGATGTAATGTC IIIIIII""IIIIIIIIIIIIIIIIIII<III@II"IIIIIII000IIII NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1599:330/1 129 phiX174 868 255 50M = 803 65 TTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCA IIIIIII""IIIIIIIIIIIIIIIIIII<III@II?I0IIIIHIIIGIII NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1652:270/2 0 phiX174 973 255 50M * 0 0 GCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCG IIIIIII""IIIIIIIIIIIIIIIIIIIIIII6II?I0IIIIHIIIGIII NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1746:351/1 0 phiX174 1218 255 50M * 0 0 CTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1582:633/1 0 phiX174 1517 255 50M * 0 0 CCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCAC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1598:534/1 65 phiX174 1717 255 50M = 1772 55 GCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAA IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1598:534/1 129 phiX174 1772 255 50M = 1717 55 TTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1572:324/2 0 phiX174 1972 255 50M * 0 0 GCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGT IIIIIII""IIIIIIIIIIIIIIIIIIII+7I05I?I0IIIIHIIIGIII NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1749:466/1 65 phiX174 2201 255 50M = 2251 50 TTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1749:466/1 129 phiX174 2251 255 50M = 2201 50 GCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTG IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1629:446/1 65 phiX174 2301 255 50M = 2355 54 AGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1629:446/1 129 phiX174 2355 255 50M = 2301 54 CAAGCGAAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCAGA IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1763:587/1 65 phiX174 2501 255 50M = 2566 65 AAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1763:587/1 129 phiX174 2566 255 50M = 2501 65 CATTGCATTCAGATGGATACATCTGTCAACGCCGCTAATCAGGTTGTTTC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1616:363/1 65 phiX174 2718 255 50M = 2773 55 TGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGG IIIIIII""IIIIIIIIIIIIIIIIIIIIIIDIII"IIIIIII000IIII NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1616:363/1 129 phiX174 2773 255 50M = 2718 55 GTGACTATTGACGTCCTTCCCCGTACGCCGGGCAATAATGTTTATGTTGG IIIIIII""IIIIIIIIIIIIIIIIIIIIIIDIII?I0IIIIHIIIGIII NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1768:715/1 65 phiX174 3118 255 50M = 3173 55 ACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCT IIIIIII""IIIIIIIIIIIIIDIIIIIIIIIIII"IIIIIII000IIII NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1768:715/1 129 phiX174 3173 255 50M = 3118 55 AGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATA IIIIIII""IIIIIIIIIIIIIDIIIIIIIIIIII?I0IIIIHIIIGIII NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1572:270/1 65 phiX174 3518 255 50M = 3577 59 TGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTA IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1572:270/1 129 phiX174 3577 255 50M = 3518 59 ACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATG IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1785:1272/1 65 phiX174 3818 255 50M = 3873 55 TATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCT III""""""IIIIIIIII""FI"IIII""II+ICI"IIIIIII000IIII NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1785:1272/1 129 phiX174 3873 255 50M = 3818 55 GACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCGTC III""""""IIIIIIIII""FI"IIII""II+ICI?I0IIIIHIIIGIII NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1673:514/1 65 phiX174 4018 255 50M = 4072 54 ATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIII1"IIIIIII000IIII NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1673:514/1 129 phiX174 4072 255 50M = 4018 54 GCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATG IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIII1?I0IIIIHIIIGIII NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1634:330/1 65 phiX174 4418 255 50M = 4473 55 GGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATG IIIIIII""IIIIIIIIIIIIIIIIIIIIIII8II"IIIIIII000IIII NM:i:0
+HWI-EAS91_1_30788AAXX:1:1:1634:330/1 129 phiX174 4473 255 50M = 4418 55 TCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTACTAT IIIIIII""IIIIIIIIIIIIIIIIIIIIIII8II?I0IIIIHIIIGIII NM:i:0

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/perm_out2.sam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/perm_out2.sam Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,98 @@\n+HWI-EAS91_1_30788AAXX:1:1:1513:715/1\t16\tchrM\t9563\t255\t36M\t*\t0\t0\tCTGACTACCACAACTAAACATCTATGCCCAAAAAAC\tI+-II?IDIIIIIIIIIIIIIIIIIII""IIIIIII\tNM:i:2\n+HWI-EAS91_1_30788AAXX:1:1:1698:516/1\t16\tchrM\t2735\t255\t36M\t*\t0\t0\tTTTACACTCAGAGGTTCAACTCCTCTCCCTAACAAC\tI9IIIII5IIIIIIIIIIIIIIIIIII""IIIIIII\tNM:i:0\n+HWI-EAS91_1_30788AAXX:1:1:1491:637/1\t16\tchrM\t10864\t255\t36M\t*\t0\t0\tTGTAGAAGCCCCAATTGCCGGATCCATCCTGCTAGC\tDBAIIIIIIIIIIIFIIIIIIIIIIII""IIIIIII\tNM:i:2\n+HWI-EAS91_1_30788AAXX:1:1:1711:249/1\t16\tchrM\t10617\t255\t36M\t*\t0\t0\tACCAAACAGAACGCCTGAACGCAGGCCCCTACTTCC\tIIIIIIIIIIIIIIIIIIIIIIIIIII""IIIIIII\tNM:i:1\n+HWI-EAS91_1_30788AAXX:1:1:1634:211/1\t0\tchrM\t9350\t255\t36M\t*\t0\t0\tGAAGCAGGGGCTTGATACTGACACTTCGTCGACGTA\tIIIIIII""IIIIIIIIIIIIIIIIIIIIII9IIDF\tNM:i:2\n+HWI-EAS91_1_30788AAXX:1:1:1398:854/1\t16\tchrM\t3921\t255\t36M\t*\t0\t0\tCACCCTTCCCGTACTAATAAATCCCCTCCTCTTCAC\tIIIII=AIIIIIIIIIIIIIIBIIIII""IIIIIII\tNM:i:2\n+HWI-EAS91_1_30788AAXX:1:1:1310:991/1\t16\tchrM\t10002\t255\t36M\t*\t0\t0\tCTCCTATGCCTAGAAGGAATAATACTACCACTATTC\tI:2IEI:IIDIIIIII4IIIIIIIIII""IIIIIII\tNM:i:1\n+HWI-EAS91_1_30788AAXX:1:1:1716:413/1\t0\tchrM\t6040\t255\t36M\t*\t0\t0\tGATCCAAGGCTTTATCAACACCTATTCTGATTCTTC\tIIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII\tNM:i:2\n+HWI-EAS91_1_30788AAXX:1:1:1630:59/1\t16\tchrM\t12387\t255\t36M\t*\t0\t0\tTCATACTCGACCCCAACCTTACCAACCCCCCGCTCC\tFIIHII;IIIIIIIIIIIIIIIIIIII""IIIIIII\tNM:i:1\n+HWI-EAS91_1_30788AAXX:1:1:1601:805/1\t0\tchrM\t12584\t255\t36M\t*\t0\t0\tGAAAACAGGAAAACAATCCAGTCACTTACCCTATGC\tIIIIIII""IIIIIIIIIIIIIIIIIIIIIII@III\tNM:i:2\n+HWI-EAS91_1_30788AAXX:1:1:1663:724/1\t0\tchrM\t15012\t255\t36M\t*\t0\t0\tGTTTGCCGGCGCCATCCTACGCTCCATTCCCAACAA\tIIIIIII""IIII8IIIIIIHIIII6IIIII1CI=3\tNM:i:2\n+HWI-EAS91_1_30788AAXX:1:1:1454:975/1\t16\tchrM\t8929\t255\t36M\t*\t0\t0\tTGGCTTCTTCTGAGCCTTTTACCACTCCCGCCTAGC\tIIIIIII;GIEIIIIIIIIIIIIIIII""IIIIIII\tNM:i:2\n+HWI-EAS91_1_30788AAXX:1:1:1461:255/1\t0\tchrM\t12988\t255\t36M\t*\t0\t0\tGTACACCGGCGCCTGAGCCCTACTAATAACTCTCAT\tIIIIIII""IIIIII9IIIIIIEI(II9.I4III,I\tNM:i:2\n+HWI-EAS91_1_30788AAXX:1:1:1775:764/1\t0\tchrM\t16613\t255\t36M\t*\t0\t0\tGCATCCCGGTAGATCTAATTTTCTAAATCTGTCAAC\tIIIIIII""III@IIII+IIIIII8H8IIIIIIICI\tNM:i:2\n+HWI-EAS91_1_30788AAXX:1:1:1269:520/1\t16\tchrM\t11036\t255\t36M\t*\t0\t0\tCGACAAACCGATCTAAAATCACTTATTCCATACTCC\tIIIIIIIIIIIIIIIIIIIIIIIIIII""IIIIIII\tNM:i:1\n+HWI-EAS91_1_30788AAXX:1:1:1303:1162/1\t16\tchrM\t14866\t255\t36M\t*\t0\t0\tAAAGACATCCTAGGACTCCTCCTCCTGCCCTTGCTC\tI6I3,\'94IIAI(IAIGI*4IIFIIII""IIIIIII\tNM:i:2\n+HWI-EAS91_1_30788AAXX:1:1:1090:409/1\t16\tchrM\t15014\t255\t36M\t*\t0\t0\tTTGCCTACGCCATCCTACGCTCCATTCCCAACAAAC\tI8AII:IIIIIIIIIIIIIIIIIIIII""IIIIIII\tNM:i:0\n+HWI-EAS91_1_30788AAXX:1:1:1336:1000/1\t16\tchrM\t11616\t255\t36M\t*\t0\t0\tGATCTAGAAACAGAAACTTAATATTTCCCATTTACC\tII9IIIIIIIIIIIIIIIIIIIIIIII""IIIIIII\tNM:i:2\n+HWI-EAS91_1_30788AAXX:1:1:1199:1376/1\t16\tchrM\t14023\t255\t36M\t*\t0\t0\tAAACCCCCATAAATAGGTGAAGGTTTTCCAGAAAAC\tIII/:&GII3III;IIIIIIIIIIIII""IIIIIII\tNM:i:2\n+HWI-EAS91_1_30788AAXX:1:1:1598:1148/1\t16\tchrM\t2334\t255\t36M\t*\t0\t0\tAAATATATAATCACTTATTGATCCAAACCATTGATC\tIIIIIHI=IICIII?IIIIIIDIIIII""IIIIIII\tNM:i:0\n+HWI-EAS91_1_30788AAXX:1:1:1723:1459/1\t16\tchrM\t15787\t255\t36M\t*\t0\t0\tATCCTCGCTCCGGGCCCATCCAAACGTCCGGGTTTC\tI=II-IIH9IIIIIIIIIDIIIIIIII""IIIIIII\tNM:i:2\n+HWI-EAS91_1_30788AAXX:1:1:1442:1346/1\t16\tchrM\t9331\t255\t36M\t*\t0\t0\tCAGCCACCACTTCGGATTCGAAGCAGCCCCTTGATA\t&,*II-<?<II4I(I1IIIIIDIIIII""IIIIIII\tNM:i:1\n+HWI-EAS91_1_30788AAXX:1:1:850:117/1\t16\tchrM\t5540\t255\t36M\t*\t0\t0\tCCCATGCATTCGTAATAATTTTCTTTACCGTCATAC\t?:;I9DDIBEIIIIIIIIEIEIIIIII""IIIIIII\tNM:i:2\n+HWI-EAS91_1_30788AAXX:1:1:795:325/1\t16\tchrM\t4249\t255\t36M\t*\t0\t0\tAAACTTGGACTCACACCATTCCACTTCCCAGTACCC\tIIII56IIIIIIIIIIIIIIIIIIIII""IIIIIII\tNM:i:2\n+HWI-EAS91_1_30788AAXX:1:1:873:453/1\t16\tchrM\t3188\t255\t36M\t*\t0\t0\tATCTCATACGAAGTAACTCTAGCAATCCCCCTACTC\tI=IIIIIII@IIIIIIIIIIIIIIIII""IIIIIII\tNM:i:2\n+HWI-EAS91_1_30788AAXX:1:1:1285:1334/1\t16\tchrM\t2389\t255\t36M\t*\t0\t0\tGGGATAACAGCGCAATCCTATTCCAGACCCCATATC\tI8IIIII8IIIIIIIIIIGIIBIIIII""IIIIIII\tNM:i:2\n+HWI-EAS91_1_30788AAXX:1:1:905:406/1\t0\tchrM\t2844\t255\t36M\t*\t0\t0\tGAAAAGTGGTAGGCTATATGCAACTTCGCAAAGGAC\tIIIIIII""IIIIIIIIBIIIIBIIII=I@96D2*I\tNM:i:2\n+HWI-EAS91_1_30788AAXX:1:1:1774'..b'CCATTTTCCTCATCCCC\tIIIIIII""IIIII=I7IIII3IIIIIIII/ID@II\tNM:i:2\n+HWI-EAS91_1_30788AAXX:1:1:982:332/1\t16\tchrM\t6016\t255\t36M\t*\t0\t0\tTTCTTCGACCCCGCAGGAGGAGGGGATCCAATCCTT\t@7I<?IIIIIIIIIIIIIIIIIIIIII""IIIIIII\tNM:i:0\n+HWI-EAS91_1_30788AAXX:1:1:1073:668/1\t0\tchrM\t3502\t255\t36M\t*\t0\t0\tAGCATTTGGCAACCCCTACCTGCCAGAACTCTACTC\tIIIIIII""IIIIIIIIIIIIIII>I4@IIIIIIII\tNM:i:2\n+HWI-EAS91_1_30788AAXX:1:1:1386:1163/1\t0\tchrM\t1616\t255\t36M\t*\t0\t0\tAGTTGGCGGAAAAGCAGCCATCAATTAAGAAAGCGT\tIIIIIII""IIIIIIIIIICII=GIIIII@IGIIII\tNM:i:2\n+HWI-EAS91_1_30788AAXX:1:1:1196:344/1\t16\tchrM\t5155\t255\t36M\t*\t0\t0\tGTTAACAGCTAAATACCCTAATCAACTCCCTTCAAT\t7IIIIIIIIIIIIIIIIIIIIIIIIII""IIIIIII\tNM:i:2\n+HWI-EAS91_1_30788AAXX:1:1:1551:1269/1\t0\tchrM\t11375\t255\t36M\t*\t0\t0\tATTACCAGGATCCTAATAGGAGCCAATATCACCATC\tIIIIIII""IIIIIIIIGIIIIIIIIIIII@II4II\tNM:i:2\n+HWI-EAS91_1_30788AAXX:1:1:928:468/1\t0\tchrM\t1192\t255\t36M\t*\t0\t0\tAGGAGATGGAAATTTTAACTTGGCGCTATAGAGAAA\tIIIIIII""IIIIIIIIIIIIIIIIIIIIC<IHIII\tNM:i:1\n+HWI-EAS91_1_30788AAXX:1:1:763:835/1\t16\tchrM\t8908\t255\t36M\t*\t0\t0\tCTCAGAAGTCTTCTTCTTCTCTGGCTTCCTCTGAGC\tI:IIDIIIIII<IFIIFEIHIIIIIII""IIIIIII\tNM:i:1\n+HWI-EAS91_1_30788AAXX:1:1:1363:330/1\t16\tchrM\t10891\t255\t36M\t*\t0\t0\tAGTGCTAGCAGCCATTCTACTAAAACTCCGAGGCTA\t57-C5,I5IIIIIIIIII@IIIIIIII""IIIIIII\tNM:i:2\n+HWI-EAS91_1_30788AAXX:1:1:1001:837/1\t0\tchrM\t10991\t255\t36M\t*\t0\t0\tATACTATGGCTGTGAGGAATAATCATAACTAGTTCC\tIIIIIII""IIIII2IIIIIIIIIIIFIII:IIIII\tNM:i:2\n+HWI-EAS91_1_30788AAXX:1:1:1189:616/1\t0\tchrM\t3753\t255\t36M\t*\t0\t0\tTTTGATAGGGTAAAACATAGAGGCTCAAACCCTCTT\tIIIIIII""IIIIIIIIIIIIIIIIICIIIIIIIII\tNM:i:1\n+HWI-EAS91_1_30788AAXX:1:1:1212:634/1\t0\tchrM\t6053\t255\t36M\t*\t0\t0\tATCAACAGGTATTCTGATTCTTCGGACACCCCGAAG\tIIIIIII""IIIIIIIIIIIIIIIIIIAIIIIF(.I\tNM:i:2\n+HWI-EAS91_1_30788AAXX:1:1:1271:421/1\t0\tchrM\t8630\t255\t36M\t*\t0\t0\tACACGACGGCACCTAATGACCCACCAAACCCACGCT\tIIIIIII""IIIIIIIIIIIIIIII>C:IIIDI<II\tNM:i:2\n+HWI-EAS91_1_30788AAXX:1:1:1582:328/1\t0\tchrM\t7752\t255\t36M\t*\t0\t0\tAGCATTAGGCTTTTAAGTTAAAGATTGAGGGTTCAA\tIIIIIII""IIIIII,IIIB;BI<IIIIII+IIIBI\tNM:i:2\n+HWI-EAS91_1_30788AAXX:1:1:1133:687/1\t16\tchrM\t7122\t255\t36M\t*\t0\t0\tCCACACACTAATAATCGTATTCCTAATCCGCTCTCT\tIII4IIIIIIIIIIIIIIIIIIIIIII""IIIIIII\tNM:i:2\n+HWI-EAS91_1_30788AAXX:1:1:1231:662/1\t0\tchrM\t13783\t255\t36M\t*\t0\t0\tTCACTCTGGAGAACATATAAAACCAACATAACCTCC\tIIIIIII""IIIIIIIIIIIIIIIIII?ICCIIIII\tNM:i:2\n+HWI-EAS91_1_30788AAXX:1:1:1693:1140/1\t16\tchrM\t4932\t255\t36M\t*\t0\t0\tCTCCCTACTCCTCCCCCTAACCCCCATCCTATCAAT\tI-AII7II5II:IIIIIIIIIIIIIII""IIIIIII\tNM:i:1\n+HWI-EAS91_1_30788AAXX:1:1:867:279/1\t16\tchrM\t5309\t255\t36M\t*\t0\t0\tTCCAACCCCTGTCTTTAGATTTACAGTCCAATGCTT\tIIIIIIIIIIIIIIIIIIIIIIIIIII""IIIIIII\tNM:i:1\n+HWI-EAS91_1_30788AAXX:1:1:1095:605/1\t0\tchrM\t23\t255\t36M\t*\t0\t0\tAAGCAAGGGACTGAAAATGCCTAGATGAGTATTCTT\tIIIIIII""IIIIIIIIIIIIIIIEIIIIIIIIIII\tNM:i:1\n+HWI-EAS91_1_30788AAXX:1:1:1650:1185/1\t0\tchrM\t14956\t255\t36M\t*\t0\t0\tACCCCAGGGAACCCTCTCAGCACTCCCCCTCATATT\tIIIIIII""IIIIIIIIIIII6IIIIIIIII5I-II\tNM:i:2\n+HWI-EAS91_1_30788AAXX:1:1:799:192/1\t16\tchrM\t8421\t255\t36M\t*\t0\t0\tCCTGTAGCCCTAGCCGTGCGGCTAACCCCTAACATT\tII%::I<IIIIIEIII8IIIIIIIIII""IIIIIII\tNM:i:1\n+HWI-EAS91_1_30788AAXX:1:1:1082:719/1\t16\tchrM\t7191\t255\t36M\t*\t0\t0\tTAAATTAACCCATACCAGCACCATAGACCCTCAAGA\t<III0EII3+3I29I>III8AIIIIII""IIIIIII\tNM:i:2\n+HWI-EAS91_1_30788AAXX:1:1:1746:1180/1\t16\tchrM\t12013\t255\t36M\t*\t0\t0\tCCTAAGCTTCAAACTAGATTACTTCTCCCTAATTTT\tIIIIIIIIFIIIIIIIIIIIIIIIIII""IIIIIII\tNM:i:2\n+HWI-EAS91_1_30788AAXX:1:1:606:460/1\t0\tchrM\t4552\t255\t36M\t*\t0\t0\tTTAATTTGGATTATAATAACACTCACAATATTCATA\tIIIIIII""IIIIIIIIIIIIIIIIII?I6IIIII6\tNM:i:2\n+HWI-EAS91_1_30788AAXX:1:1:1059:362/1\t16\tchrM\t7348\t255\t36M\t*\t0\t0\tGGCCACCAATGATACTGAAGCTACGAGCCTACCGAT\tII/<)2IIIIIIIIIIIIIIIIIIIII""IIIIIII\tNM:i:2\n+HWI-EAS91_1_30788AAXX:1:1:1483:1161/1\t16\tchrM\t15080\t255\t36M\t*\t0\t0\tTCCTGATCCTAGCACTCATCCCCACCCCCCACATAT\tHIIIIIFIIAIHIIIIIIIIIIIIIII""IIIIIII\tNM:i:1\n+HWI-EAS91_1_30788AAXX:1:1:1273:600/1\t16\tchrM\t13855\t255\t36M\t*\t0\t0\tGTATTAGACACCCATACCTCAGGATACCCCTCAGTA\tIIIIIIIIIIIIIIIIIIIIIIIIIII""IIIIIII\tNM:i:2\n+HWI-EAS91_1_30788AAXX:1:1:1190:1283/1\t16\tchrM\t15338\t255\t36M\t*\t0\t0\tTATATCGCACATTACCCTGGTCTTGTACCCCAGAAA\tEIII?-IIIIIAIIIIIIIIIIIIIII""IIIIIII\tNM:i:2\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/perm_out3.fastqsanger
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/perm_out3.fastqsanger Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,4 @@
+@HWI-EAS91_1_30788AAXX:1:1:1218:141/1
+GTTAAATATTGGGAGTGGGGGGGGGGGGGAGTTTTG
++
+IIIIIII""IIIIIIIIIIIIIIIIIIII1IIII+I

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/perm_out4.sam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/perm_out4.sam Sat Feb 21 16:33:42 2015 +0100

[

b'@@ -0,0 +1,55 @@\n+1831_573_1219\t16\tphiX174\t2201\t255\t35M\t*\t0\t0\tTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGAC\t-A@EE>NVA7FQZSC8GRJK<EVGC<==39BP\\__\tNM:i:0\tCS:Z:G1211130300300301021212330201121310\tCQ:Z:@@@=4/+)5)408?\'665>*/5?<61\';<3,:,5-\n+1831_573_1242\t0\tphiX174\t647\t255\t35M\t*\t0\t0\tTCATCCCGTCAACATTCAAACGGCCTGTCTCATCA\t[[WSWNGS]US^_\\WQW]WL?CEMUIMSTSJ*1U;\tNM:i:1\tCS:Z:T2132003121011302100130302112221121\tCQ:Z:>>>::>17=A5?@@=;7A=;2.60>82<8=74+;;\n+1831_573_1647\t16\tphiX174\t1117\t255\t35M\t*\t0\t0\tCGACTCCTTCGAGATGGACGCCGTTGGCGCTCTCC\t4NIKVOPIBACPWOQ^^WSZ_\\Y][Y]]^_[[_^[\tNM:i:0\tCS:Z:G0222233301013033120132223202022123\tCQ:Z:=?@@<@@???;A==@@;9?@?3=;6.4/;6:=/;4\n+1831_573_1684\t16\tphiX174\t3695\t255\t35M\t*\t0\t0\tTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGC\t?\\VWTLTTUZVV[_^\\Y[_ZWUW]^_XKR[SQJNT\tNM:i:0\tCS:Z:G3310013212312012302121010221231123\tCQ:Z:7>1:8<@39@@??9=;@@<>?@@<;<?7>76?9>?\n+1831_574_109\t0\tphiX174\t3728\t255\t35M\t*\t0\t0\tGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCG\t07651#4817>@65<2:84716=788<1995.7?6\tNM:i:1\tCS:Z:G3122332123301331032220222133301033\tCQ:Z:07651#4817>@65<2:84716=788<1995.7?6\n+1831_574_148\t16\tphiX174\t2368\t255\t35M\t*\t0\t0\tGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCA\t;NEGQTTTJAMH9B@@PHHSQUJML=LPMUMPJGV\tNM:i:0\tCS:Z:T1200113123030012202302312200010231\tCQ:Z:<;->3;;3>//>0;;7=,=4-4/+>029<9<624;\n+1831_574_575\t16\tphiX174\t4005\t255\t35M\t*\t0\t0\tGAATGTCACGCTGATTATTTTGACTTTGAGCGTAT\t<JC>=PXK;2BW[T;CXA"&?U\\\\__WU]^[Z]^U\tNM:i:1\tCS:Z:A3313322100212102033032123311211302\tCQ:Z:7?@>=?@>8@@@=@6*%&<=\'5@<<\',0<=4*5/<\n+1831_574_592\t16\tphiX174\t2949\t255\t35M\t*\t0\t0\tGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCAT\t2BBLI?LTSPIFFIMD:?MRLECQ][G7DI9=A?I\tNM:i:0\tCS:Z:A3103330110123102223122023103310330\tCQ:Z:73-5)19,,<@>4067<2.-864346;9<1/;212\n+1831_574_824\t16\tphiX174\t3996\t255\t35M\t*\t0\t0\tTACCCTTCTGAATGTCACGCTGATTATTTTGACTT\t?VRCD\\ZK5?ZWJ7D]WP=AVQRHH[J64CUZ__Z\tNM:i:0\tCS:Z:A0212100033032123311211302122020013\tCQ:Z:;@@@;;),+@<-<7;<&89??&29?<$2:A<);8?\n+1831_574_1194\t0\tphiX174\t1135\t255\t35M\t*\t0\t0\tCGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTC\tNRXFJ]WXXX^^PP_\\\\RO\\]]SR^_XLRUKC:A6\tNM:i:0\tCS:Z:C3303101033322220312200222013013312\tCQ:Z::5>;,??9@9@?@1@@=@3=@>@4?@@94?75/,6\n+1831_574_1591\t16\tphiX174\t5117\t255\t35M\t*\t0\t0\tGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCG\t9CB??UTRA!7YIJXQUSUEEZWX[WNV^ZY^\\XY\tNM:i:1\tCS:Z:C3202101330322130221230222201123202\tCQ:Z:==<A><?@78@<=;@&@6>8:?,><&&<7>8(8+9\n+1831_574_1624\t16\tphiX174\t4057\t255\t35M\t*\t0\t0\tCTATTGAGGCTTGTGGCATTTCTACTCTTTCTCAA\t)5?C6:LSC5DHJA6@FNI54;D?137CB3-3CQ:\tNM:i:1\tCS:Z:C0122200222132200313011102302210332\tCQ:Z:#<6.&(,7-+))7..\'/;43.)927.(<85&13-)\n+1831_574_1903\t0\tphiX174\t5208\t255\t35M\t*\t0\t0\tAAGCTGGGTTACGACGCGACGCCGTTCAACCAGAC\tTMJT^]XQV__WQY]UUYXUVVV]QNSGOOJOPI/\tNM:i:1\tCS:Z:A0232100103132133321330310210101221\tCQ:Z:<956?@>;7@@@8:@>8><=9>9>@2=71?1:6;/\n+1831_575_54\t16\tphiX174\t3586\t255\t35M\t*\t0\t0\tTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGC\t8ST4/MPK:7HONA7BTVCHY[^YRSVLMSMU_\\Z\tNM:i:1\tCS:Z:G3331330322230200102132110132013200\tCQ:Z:>=@@68<2;<8;?@<>+9>7,,6972&57:4&9<8\n+1831_575_197\t16\tphiX174\t4860\t255\t35M\t*\t0\t0\tAGCTTGCAAAATACGTGGCCTTATGGTTACAGTAT\t,=.<SADLUZH>67?JXRIFRTTVOQZ`RHIRXF8\tNM:i:1\tCS:Z:A3312113010133020301131330001310032\tCQ:Z:,-:?463@A:88?6?437<=.2&1.;@67.4@%2,\n+1831_575_444\t16\tphiX174\t5097\t255\t35M\t*\t0\t0\tAAGCTGTCGCTACTTCCCAAGAAGCTGTTCAGAAT\t>XO0/QUSCCY]]LJWZ^[W\\ZVGF[^[JIVZ_QM\tNM:i:1\tCS:Z:A3022120112320220100202132332113320\tCQ:Z:<2@@;<.=?@<+=:A<<@?<</>@><(<8>4&5;>\n+1831_575_622\t0\tphiX174\t2484\t255\t35M\t*\t0\t0\tTGTTTTACAGACACCTAAAGCTACATCGTCAACGT\t`XY^\\_^Z[^ZY[Z[WNQOLO?DOBJB@M>EQ$!+\tNM:i:1\tCS:Z:T1100031122111023002323113231210111\tCQ:Z:@A8B=@@?<@?<>>=?96<497)<4/<\':4+;74+\n+1831_575_938\t16\tphiX174\t1132\t255\t35M\t*\t0\t0\tGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGC\t7N@<NSTMKOQVHAONKTXVTUWZXRTWZ^XY_YT\tNM:i:0\tCS:Z:G3103102220022130222233301013033120\tCQ:Z:;:@@:?@;=8;>=;;:=<93<4.;<6:2<9;4)87\n+1831_575_970\t16\tphiX174\t231\t255\t35M\t*\t0\t0\tTGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCG\t5PXYYNKY^\\[VW[\\]XY[VUTRY_[Y]_ZW\\\\\\\\\tNM:i:0\tCS:Z:C3201311301023133303023011202220221\tCQ:Z:=@=@=;@@><@@:9<:=?;>@=?9>>?@:2===<5\n+1831_575_1138\t0\tphiX174\t1912\t255\t35M\t*\t0\t0\tCGCTAAAGGTGCTTTGACTTATACCGATATTGCTG\tXLJ7-IK'..b"]][ZWKFQPA?FSTQPKD.\tNM:i:0\tCS:Z:C3022113203032010120310102321001031\tCQ:Z:<3>@?9>@?B=>=;>A???=>:25=4.25?6<57.\n+1831_576_882\t0\tphiX174\t5052\t255\t35M\t*\t0\t0\tGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTC\tPGTVV^YMQ]]VNT]ZWXQ;7LYVPKIRXTTLNU8\tNM:i:0\tCS:Z:G3230020122320223230022031020110122\tCQ:Z:?26?8?@:4>@>96??<<=5'1<>9846=<9<1>8\n+1831_576_898\t0\tphiX174\t517\t255\t35M\t*\t0\t0\tGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGC\t\\_bTPa`\\ZY]WOMW`YYLL]VNS^]SSLES][J.\tNM:i:0\tCS:Z:G0230132312121033222231132231233213\tCQ:Z:=@@C2?C>?<>@886B?;?.??87=B<8<15??=.\n+1831_576_923\t0\tphiX174\t1049\t255\t35M\t*\t0\t0\tCATCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCT\tLCBEMWHCNQTTNSXUNLTVUKAKV[TMRRURIJ7\tNM:i:0\tCS:Z:C1322010320202013210121223010123122\tCQ:Z:76.51=;.699<96>;;49<;;11;<@59:9=647\n+1831_576_1131\t16\tphiX174\t4060\t255\t35M\t*\t0\t0\tTTGAGGCTTGTGGCATTTCTACTCTTTCTCAATCC\t<MJBDSMK>BWZI2FPGKEOI<PWVQ?KNN>>SC@\tNM:i:1\tCS:Z:G0233122200222132200313011102302210\tCQ:Z:104@#@/@,4>9?2+?1571@',>=;(759;*92<\n+1831_576_1289\t16\tphiX174\t1898\t255\t35M\t*\t0\t0\tATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTA\t0DBK[ONJ9GWSQ@;@CINYOHKU_VQZ_aRNYTX\tNM:i:0\tCS:Z:T3021210023110200323310302013121203\tCQ:Z:@9<>1B@@;7@@663==28,5':8<<,.=2>>.50\n+1831_576_1367\t0\tphiX174\t1838\t255\t35M\t*\t0\t0\tGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCG\t]^_[Y]_\\\\[[[X\\]]^]WRXZXZZXSROMXVNN7\tNM:i:0\tCS:Z:G2231310311233110031222013332011023\tCQ:Z:??@@<>@@=@<@<=@>@??9:?<=>=<8;59@787\n+1831_576_1416\t0\tphiX174\t4521\t255\t35M\t*\t0\t0\tATTCAGCGTTTGATGAATGCAATGCGACAGGCTCA\t1AYL;>>I[F4JG@CBSURK<KUQB,AZRJCFPW@\tNM:i:0\tCS:Z:A3021233100123120313103133211203221\tCQ:Z:+';?..1.<@'.=+6.5?7<0-?7;(%=>56.98@\n+1831_576_1605\t0\tphiX174\t5208\t255\t35M\t*\t0\t0\tAAGCTGGGTTACGACGCGACGCCGTTCAACCAGAC\tQ[bb_]NKZYTVW[_XX^]]WTNQSA>BMPKNMB,\tNM:i:1\tCS:Z:A0232100103132133321330310210101221\tCQ:Z:6<@C@@>1;@:;<<@@9@???9<3?5-21=4877,\n+1831_576_1729\t16\tphiX174\t5193\t255\t35M\t*\t0\t0\tTTAATCCAACTTACCAAGCTGGGTTACGACGCGAC\t>ZL:FYXSQV]^ZSW^\\TU\\\\[YKM_^][ZZZ^^^\tNM:i:0\tCS:Z:G1233312313010012320101302101023030\tCQ:Z:@?@?<?<@>A?/==?>?7>?@8<?@>99;><+0=>\n+1831_576_1982\t16\tphiX174\t5023\t255\t35M\t*\t0\t0\tTTAACAAAAAGTCAGATATGGACCTTGCTGCTAAA\t@JFRDK\\_\\MQUU_UQST^ZX^[\\XX[Y^LK^^_K\tNM:i:0\tCS:Z:T0032312310201201333221212000011030\tCQ:Z:,@@?@,A><@9@=?@9B=8<6@@6@2<A?>.7<+@\n+1831_577_133\t16\tphiX174\t1713\t255\t35M\t*\t0\t0\tTCATGCGCTCTAATCTCTGGGCATCTGGCTATGAT\t)&/8<NA=EPP;FEI]YY]_VFO]HDXOM[\\[]SB\tNM:i:1\tCS:Z:A3213323012231300122223032223331322\tCQ:Z:/4@>>?=1?:+>@07@@><>@*<+1@15)96'2$)\n+1831_577_281\t16\tphiX174\t4576\t255\t35M\t*\t0\t0\tTTTTTGACACTCTCACGTTGGCTGACGACCGATTA\t?XWE?WXSYURPOYWMJ@I[[RQ]VTXW\\WR\\[FC\tNM:i:0\tCS:Z:T3032301231212301013112222111210000\tCQ:Z:7-:B;8@=;>7@>4?=?+659?;5<7?;9@8(>:?\n+1831_577_322\t16\tphiX174\t457\t255\t35M\t*\t0\t0\tCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTC\t/E?@MNMJTZM79LI;A5:H@IIHIFLPEDHQXWU\tNM:i:1\tCS:Z:G2003213220230103303201000130312202\tCQ:Z:9=;>4506;255464-<#7+194&2<?65968)7/\n+1831_577_362\t0\tphiX174\t2152\t255\t35M\t*\t0\t0\tACTTATTCGCCACCATGATTATGACCAGTGTTTCC\tGS`XY^^[ZWMLTH>LEDHI?,3EQDAQPB5%(@6\tNM:i:1\tCS:Z:A1203302330110131230331210121110220\tCQ:Z:62B?:@?@<?958=,3:,90:&'-99,6<5.($+6\n+1831_577_382\t16\tphiX174\t4685\t255\t35M\t*\t0\t0\tGGGTCGCAAGGCTAATGATTCACACGCCGACTGCT\t*>C@NMMI2333IUD=>FNE;1=LSE19JHEKMJB\tNM:i:0\tCS:Z:A2312123033111120321303230201332100\tCQ:Z:12957/:1))=76(*24;,3+:<.&.&-=1=2/5*\n+1831_577_488\t16\tphiX174\t4947\t255\t35M\t*\t0\t0\tTGGCCTGTTGATGCTAAAGGTGAGCCGCTTAAAGC\t@SEJPW]VUWXQLSPSOMXXXTVZQKJJSG59EKM\tNM:i:0\tCS:Z:G3200302330322110200323132101120301\tCQ:Z::48.,*>6566<?8=<=<2>6;94>;=9>@8924@\n+1831_577_545\t0\tphiX174\t1710\t255\t35M\t*\t0\t0\tTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTAT\t[YWTWZY\\_\\OKHP[[WTY\\VLDDFLTMBBMPOD-\tNM:i:0\tCS:Z:T0112131333222303222210031322103233\tCQ:Z:>><<9?<>?A<481@<@8==@76/61<95.5988-\n+1831_577_637\t0\tphiX174\t4246\t255\t35M\t*\t0\t0\tCTGTTACTGAGAAGTTAATGGATGAATTGGCACAA\tD8?2<WFB@DQC1-<OMOLMTSRM=6?G>,EYN?,\tNM:i:1\tCS:Z:C2113312122202103031023120301031110\tCQ:Z:8-,4#>:-6+:8,&(5;3=0>7=68&1/9&'?;4,\n+1831_577_692\t0\tphiX174\t3904\t255\t35M\t*\t0\t0\tTGTCTAGGAAATAACCGTCAGGATTGACACCCTCC\taMK^^aIG`_^JJ_]]JI[Z]FCX[[XXTU[UKP<\tNM:i:0\tCS:Z:T1122320200330103121202301211100220\tCQ:Z:@B,@?@B(@A?@+@@>@+?=>@'=<@<=<9=?75<\n"

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/perm_out5.sam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/perm_out5.sam Sat Feb 21 16:33:42 2015 +0100

[

@@ -0,0 +1,9 @@
+865_1106_310/2 16 chrM 16577 255 50M * 0 0 ACATGCTACTTTAATCAATAAAATTTCCATAGACAGGTATCCCCCTAGAT ;SSUV\VJNWVVWRX\X[[Z\Z[ZW\^XUV\_]]][WWVVYZ^^^_[\_^ NM:i:2 CS:Z:A3223200002331021122331020030003301230300213231311 CQ:Z:?@@=?A>A>==:=;=????A<;;>A<<?=>?<@<=@9:>9>:56A<;;9;
+869_1532_1255/1 113 chrM 3727 255 50M = 1979 1748 AGAAATATGTCTGACAAAAGAGTTACTTTGATAGAGTAAAACATAGAGGT ;RPTUVYQPSUSNSRTXTSVYVRVXWYUSVY_UOXZWRQRSUY[\^XQRW NM:i:3 CS:Z:A1022233110003122233210021301222000112122113330022 CQ:Z:=;8:?@=?;;9:8;=>;5A?;<8><<=:9><;9<=8;96>8<5==:<98;
+869_1532_1255/1 177 chrM 1979 255 50M = 3727 1748 GTATTAGAGGCACTGCCTGCCCAGTGACATCTGTTTAAACGGCCGCGGTA <QNVYYSUWQPSXUTTRVTT^ZUWXXZ[]\ZYY[YXVVVX][XUVYYZ]` NM:i:0 CS:Z:T3103330303100300112231121121003120312113022230331 CQ:Z:@A=><>9=<@>;<;<==?;?<A=?<=<<:A>7>9:;:<=7:8@6><>96<
+889_1337_1562/2 16 chrM 1951 255 50M * 0 0 ACCAAAAACATCACCTCTAGCATTCCCAGTATTAGAGGCACTGCCTGCCC 8PVXVWTRRQPRWQRZ[VORVVWWUOQZ[YUY]WZ^]`^\\]`a^]`[[] NM:i:2 CS:Z:G0031203121130222303312100203132322201123110000101 CQ:Z:=A;A@>AA@>?>A@>A:>@:<>>=5;;=;<;88?=>5=;899:9<<;>98
+891_252_1590/1 65 chrM 15434 255 50M = 97 15337 ACCCAAAGCTGAAATTCTACTTAAACTATTCCTTGATTTCCTCCCCTAAA \^VTXUY[[^YY[[XX]^_^VUWZ]]]\ZYY[]]_[VWWRQPTWTTNQX< NM:i:2 CS:Z:A1001002321200302231203001233020201230020220002300 CQ:Z:<A>9<=9A;A><>>>;>@?A>9=;@>@>?<><@>@@<;=;8:7>:;:5=<
+891_252_1590/1 129 chrM 97 255 50M = 15434 15337 TAGTTATTAATAAAATTACACATGCAAGTATCCGCACCCCAGTGAGAATG RRVYXYUSTSSTWXXYUWVUTRPMQUZZVW\\YYXXZVUVW^YUTPSWY= NM:i:2 CS:Z:T3210330303300030311113131021332033110001211222031 CQ:Z:8;8?;><::;9;:>;><:>9=8;68:<?<;=@===<=>9=:>A9=89;==
+892_582_183/1 16 chrM 14089 255 50M * 0 0 AAAATAAACACAATATATGTCATCATTATTCCCACGTGGAATCTAACCAC 9QNLRTQOSWUSUVTXXTTXWVVUWYVRTWXVX[\\ZVWYWVXZXYWUYX NM:i:0 CS:Z:G1101032230201131100203303123121133333011110033000 CQ:Z:;><:><=>;<<>:=>?>>;<=;:9><<:=:>;:;>;:=9;;=799<7699
+932_1836_1806/1 113 chrM 3723 255 50M = 2434 1289 CATAAGAAATATGTCTGACAAAAGAGTTACTTTGATAGAGTAAAACATAG >RNSUWYYQQVSVXVZ[XZ^YUZ[XXXWSQZ^WUXXX\XVXVYYVVVVUT NM:i:2 CS:Z:C2331100031222332100213012220001121221133300220331 CQ:Z:;:<;<;<><;>9@=<=<:>A:8<<=<=?<:@?<=?<;>9;<6<><<::5>
+932_1836_1806/1 177 chrM 2434 255 50M = 3723 1289 GGTTTACGACCTCGATGTTGGATCAAGACATCCTAATGGTGCAACCGCTA @]ZZ[Z\_WU\XW\WY^Z\]]#!\^`_]\^^]]Z\`^^_\^aaa``_Z\a NM:i:1 CS:Z:T3233010131101303202311220122201011323220123130010 CQ:Z:AA<?A@AAAA>?A>A@=>@>A>??A@?>>@>@=>A9?>:?>8@@=>>=>@

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/pgSnp2snp_output.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/pgSnp2snp_output.txt Sat Feb 21 16:33:42 2015 +0100

[

b'@@ -0,0 +1,10002 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diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/pgSnpTest.ref.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/pgSnpTest.ref.txt Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,10000 @@\n+chr1\t1888681\t1888682\tC/T\t2\t4,3\t0.8893,0.8453\tT\n+chr1\t3118325\t3118326\tT\t1\t8\t0.8796\tC\n+chr1\t3211457\t3211458\tA/C\t2\t17,10\t0.8610,0.8576\tA\n+chr1\t3222692\t3222693\tA/G\t2\t14,10\t0.8694,0.8619\tG\n+chr1\t3281273\t3281274\tA/G\t2\t4,5\t0.8210,0.8427\tG\n+chr1\t3630475\t3630476\tC/T\t2\t12,12\t0.8589,0.8430\tC\n+chr1\t4599834\t4599835\tT\t1\t18\t0.8797\tC\n+chr1\t5287107\t5287108\tG\t1\t6\t0.8443\tT\n+chr1\t5307765\t5307766\tC/T\t2\t22,12\t0.8485,0.8505\tC\n+chr1\t5341621\t5341622\tA/C\t2\t5,3\t0.8741,0.9001\tA\n+chr1\t5478586\t5478587\tG\t1\t11\t0.8997\tA\n+chr1\t5680961\t5680962\tA/C\t2\t16,10\t0.8671,0.8135\tA\n+chr1\t5736051\t5736052\tA/G\t2\t57,34\t0.8655,0.8676\tG\n+chr1\t5831207\t5831208\tC/T\t2\t5,10\t0.8978,0.8575\tC\n+chr1\t6200884\t6200885\tC\t1\t13\t0.8346\tA\n+chr1\t6307254\t6307255\tC\t1\t11\t0.8723\tT\n+chr1\t6621228\t6621229\tG/T\t2\t10,11\t0.8405,0.8336\tG\n+chr1\t7094424\t7094425\tA\t1\t4\t0.8578\tG\n+chr1\t7392593\t7392594\tC/T\t2\t15,25\t0.8653,0.8644\tC\n+chr1\t7500089\t7500090\tG\t1\t13\t0.8508\tC\n+chr1\t7911301\t7911302\tC/T\t2\t8,9\t0.9113,0.8736\tC\n+chr1\t7954646\t7954647\tC/T\t2\t12,8\t0.8365,0.8490\tC\n+chr1\t8027386\t8027387\tC/T\t2\t15,21\t0.8669,0.8528\tC\n+chr1\t8549302\t8549303\tC/T\t2\t8,7\t0.8606,0.8633\tC\n+chr1\t8932179\t8932180\tG/T\t2\t13,12\t0.8136,0.8594\tG\n+chr1\t9016389\t9016390\tT\t1\t14\t0.8590\tC\n+chr1\t9494443\t9494444\tT\t1\t6\t0.8567\tC\n+chr1\t10615774\t10615775\tC\t1\t15\t0.8684\tT\n+chr1\t10622975\t10622976\tT\t1\t4\t0.8001\tC\n+chr1\t10782207\t10782208\tT\t1\t3\t0.8402\tC\n+chr1\t12238146\t12238147\tA/G\t2\t4,9\t0.8560,0.8449\tG\n+chr1\t12429037\t12429038\tA/G\t2\t8,6\t0.8692,0.8863\tA\n+chr1\t12669902\t12669903\tC/T\t2\t10,24\t0.8495,0.8653\tT\n+chr1\t13189040\t13189041\tA/T\t2\t8,4\t0.8592,0.8868\tA\n+chr1\t14208570\t14208571\tA/G\t2\t10,8\t0.8646,0.8495\tG\n+chr1\t14501554\t14501555\tA/G\t2\t17,26\t0.8646,0.8663\tG\n+chr1\t15063865\t15063866\tA/G\t2\t9,18\t0.8571,0.8272\tG\n+chr1\t15286095\t15286096\tG\t1\t21\t0.8600\tA\n+chr1\t15441925\t15441926\tT\t1\t17\t0.8402\tC\n+chr1\t15712178\t15712179\tA\t1\t14\t0.8694\tG\n+chr1\t16207687\t16207688\tG\t1\t16\t0.8512\tC\n+chr1\t16314956\t16314957\tA\t1\t31\t0.8639\tT\n+chr1\t16476823\t16476824\tC/T\t2\t5,8\t0.8822,0.8898\tC\n+chr1\t16730581\t16730582\tG\t1\t9\t0.8232\tC\n+chr1\t17053721\t17053722\tT\t1\t66\t0.8916\tG\n+chr1\t17053765\t17053766\tA/G\t2\t19,11\t0.8246,0.8436\tG\n+chr1\t17408311\t17408312\tC\t1\t22\t0.8786\tG\n+chr1\t17498098\t17498099\tC\t1\t3\t0.7863\tT\n+chr1\t17715847\t17715848\tA\t1\t11\t0.8438\tG\n+chr1\t18857430\t18857431\tC/T\t2\t17,14\t0.8834,0.8586\tC\n+chr1\t19092742\t19092743\tG/T\t2\t16,10\t0.8682,0.8678\tG\n+chr1\t19525584\t19525585\tC\t1\t12\t0.8614\tT\n+chr1\t19921477\t19921478\tA/C\t2\t3,4\t0.8781,0.8884\tC\n+chr1\t20044146\t20044147\tC/T\t2\t5,6\t0.8571,0.8847\tC\n+chr1\t20269168\t20269169\tC/T\t2\t5,10\t0.8936,0.8839\tT\n+chr1\t20947809\t20947810\tT\t1\t8\t0.8416\tC\n+chr1\t21135182\t21135183\tA\t1\t13\t0.8384\tC\n+chr1\t21941643\t21941644\tT\t1\t12\t0.8389\tG\n+chr1\t22324976\t22324977\tC/T\t2\t9,6\t0.8524,0.8158\tC\n+chr1\t22708791\t22708792\tA/T\t2\t8,12\t0.8313,0.8557\tT\n+chr1\t22904350\t22904351\tA/G\t2\t10,4\t0.8451,0.8523\tA\n+chr1\t22928348\t22928349\tG\t1\t7\t0.8629\tA\n+chr1\t23039691\t23039692\tC\t1\t13\t0.8484\tG\n+chr1\t24392068\t24392069\tT\t1\t4\t0.8425\tC\n+chr1\t24851230\t24851231\tA/G\t2\t19,15\t0.8794,0.8807\tA\n+chr1\t25158007\t25158008\tA/G\t2\t7,12\t0.8350,0.8625\tA\n+chr1\t25250192\t25250193\tC/T\t2\t5,4\t0.8613,0.8827\tC\n+chr1\t25349613\t25349614\tG\t1\t6\t0.8963\tA\n+chr1\t25891773\t25891774\tC/T\t2\t9,7\t0.8398,0.8869\tC\n+chr1\t25989060\t25989061\tA/G\t2\t14,5\t0.8271,0.8143\tG\n+chr1\t25996483\t25996484\tA/G\t2\t25,17\t0.7803,0.7880\tA\n+chr1\t26172110\t26172111\tA/G\t2\t24,13\t0.8568,0.8740\tA\n+chr1\t26275739\t26275740\tC/T\t2\t10,16\t0.8335,0.8656\tT\n+chr1\t26436230\t26436231\tA/C\t2\t18,14\t0.8299,0.8245\tC\n+chr1\t27081694\t27081695\tA/G\t2\t7,10\t0.8297,0.8288\tG\n+chr1\t27215078\t27215079\tC/T\t2\t9,5\t0.8749,0.8190\tT\n+chr1\t27527485\t27527486\tA/G\t2\t3,5\t0.8697,0.8867\tA\n+chr1\t28266702\t28266703\tC/T\t2\t4,5\t0.8513,0.8812\tC\n+chr1\t28273015\t28273016\tG\t1\t23\t0.7710\tT\n+chr1\t28548057\t28548058\tC\t1\t22\t0.8518\tG\n+chr1\t28817596\t28817597\tG\t1\t17\t0.8790\tA\n+chr1\t28833437\t28833438\tG/T\t2\t3,5\t0.8753,0.8702\tG\n+chr1\t28848587\t28848588\tG/T\t2\t11,17\t0.8629,0.8546\tG\n+chr1\t29140084\t29140085\tA/C\t2\t8,10\t0.8493,0.8580\tC\n+chr1\t29788803\t29788804\tC\t1\t3\t0.8525\tT\n+chr1\t30086425\t30086426\tA/G\t2\t15,14\t0.8973,0.8948\tA\n+chr1\t30214408\t30214409\tA\t1\t36\t0.8861\tG\n+'..b'+chrX\t111720465\t111720466\tA\t1\t14\t0.8430\tG\n+chrX\t112170053\t112170054\tG\t1\t3\t0.9248\tA\n+chrX\t112459169\t112459170\tA\t1\t19\t0.8654\tG\n+chrX\t113279524\t113279525\tT\t1\t20\t0.8246\tA\n+chrX\t113324217\t113324218\tC\t1\t9\t0.8407\tA\n+chrX\t114056797\t114056798\tC\t1\t11\t0.8067\tT\n+chrX\t115018183\t115018184\tG\t1\t13\t0.8356\tA\n+chrX\t115733503\t115733504\tT\t1\t7\t0.8198\tG\n+chrX\t116139363\t116139364\tG\t1\t7\t0.9105\tA\n+chrX\t116488679\t116488680\tG\t1\t14\t0.8564\tA\n+chrX\t117358634\t117358635\tA\t1\t8\t0.8613\tG\n+chrX\t118498954\t118498955\tC\t1\t4\t0.7954\tT\n+chrX\t118648794\t118648795\tT\t1\t14\t0.8734\tG\n+chrX\t118693641\t118693642\tT\t1\t6\t0.8303\tC\n+chrX\t118869589\t118869590\tG\t1\t8\t0.9096\tA\n+chrX\t120306948\t120306949\tG\t1\t12\t0.8546\tA\n+chrX\t120448877\t120448878\tA\t1\t25\t0.8910\tC\n+chrX\t120872985\t120872986\tT\t1\t8\t0.8337\tC\n+chrX\t121680281\t121680282\tC\t1\t12\t0.8836\tT\n+chrX\t122435686\t122435687\tT\t1\t12\t0.7835\tC\n+chrX\t123397991\t123397992\tA\t1\t4\t0.8356\tG\n+chrX\t123907161\t123907162\tC\t1\t7\t0.8753\tT\n+chrX\t124719518\t124719519\tC\t1\t14\t0.8631\tT\n+chrX\t124768222\t124768223\tT\t1\t5\t0.8839\tC\n+chrX\t125632363\t125632364\tC\t1\t10\t0.8800\tT\n+chrX\t126053340\t126053341\tA\t1\t10\t0.8392\tC\n+chrX\t126195634\t126195635\tA\t1\t7\t0.8718\tG\n+chrX\t126716246\t126716247\tC\t1\t6\t0.8763\tT\n+chrX\t127367145\t127367146\tA\t1\t17\t0.8456\tG\n+chrX\t127457582\t127457583\tG\t1\t8\t0.8587\tC\n+chrX\t128605962\t128605963\tT\t1\t20\t0.8591\tC\n+chrX\t129569189\t129569190\tC\t1\t17\t0.8282\tG\n+chrX\t129811001\t129811002\tG\t1\t20\t0.8687\tC\n+chrX\t130409883\t130409884\tT\t1\t17\t0.8126\tA\n+chrX\t132344700\t132344701\tC\t1\t3\t0.8623\tT\n+chrX\t132915772\t132915773\tA\t1\t15\t0.8894\tC\n+chrX\t133907790\t133907791\tA\t1\t12\t0.8533\tC\n+chrX\t134518384\t134518385\tC\t1\t9\t0.8196\tA\n+chrX\t134766489\t134766490\tA/G\t2\t15,9\t0.8509,0.8127\tA\n+chrX\t134985459\t134985460\tG\t1\t3\t0.8540\tA\n+chrX\t135190793\t135190794\tG\t1\t17\t0.8961\tA\n+chrX\t136655716\t136655717\tG\t1\t6\t0.8716\tT\n+chrX\t136733809\t136733810\tC\t1\t15\t0.8669\tT\n+chrX\t137469231\t137469232\tC\t1\t18\t0.8722\tT\n+chrX\t137852981\t137852982\tT\t1\t11\t0.8276\tG\n+chrX\t139003000\t139003001\tA\t1\t13\t0.8526\tG\n+chrX\t139110302\t139110303\tA\t1\t9\t0.8564\tG\n+chrX\t139529487\t139529488\tC\t1\t18\t0.8521\tT\n+chrX\t139531472\t139531473\tT\t1\t11\t0.8682\tC\n+chrX\t139615864\t139615865\tG\t1\t9\t0.8202\tA\n+chrX\t139702889\t139702890\tC\t1\t3\t0.8590\tT\n+chrX\t140485622\t140485623\tG\t1\t3\t0.8489\tC\n+chrX\t140511684\t140511685\tG\t1\t13\t0.8238\tA\n+chrX\t140743414\t140743415\tC\t1\t4\t0.8914\tT\n+chrX\t141082368\t141082369\tC\t1\t12\t0.8648\tT\n+chrX\t141153066\t141153067\tG\t1\t7\t0.8369\tC\n+chrX\t141213396\t141213397\tA\t1\t4\t0.8604\tC\n+chrX\t142194135\t142194136\tA\t1\t10\t0.8411\tG\n+chrX\t142652846\t142652847\tT\t1\t19\t0.8740\tC\n+chrX\t142688444\t142688445\tA\t1\t6\t0.8866\tC\n+chrX\t142756403\t142756404\tC\t1\t18\t0.8646\tT\n+chrX\t144873543\t144873544\tC\t1\t12\t0.8420\tT\n+chrX\t145351956\t145351957\tT\t1\t5\t0.8467\tC\n+chrX\t145881542\t145881543\tG\t1\t3\t0.8178\tT\n+chrX\t145924332\t145924333\tG\t1\t9\t0.8605\tA\n+chrX\t145935548\t145935549\tC\t1\t14\t0.7743\tA\n+chrX\t146079383\t146079384\tC\t1\t3\t0.8542\tA\n+chrX\t146425710\t146425711\tG\t1\t9\t0.8032\tA\n+chrX\t146613499\t146613500\tC\t1\t11\t0.8771\tA\n+chrX\t147002991\t147002992\tG\t1\t4\t0.8704\tT\n+chrX\t149466820\t149466821\tT\t1\t15\t0.8550\tC\n+chrX\t149603761\t149603762\tA\t1\t3\t0.8279\tC\n+chrX\t150053854\t150053855\tC\t1\t11\t0.8358\tA\n+chrX\t150408360\t150408361\tT\t1\t11\t0.8165\tC\n+chrX\t150451895\t150451896\tA\t1\t23\t0.8775\tG\n+chrX\t150777182\t150777183\tT\t1\t16\t0.8623\tC\n+chrX\t150808405\t150808406\tT\t1\t15\t0.8428\tG\n+chrX\t150923430\t150923431\tG/T\t2\t3,3\t0.8295,0.8593\tT\n+chrX\t150989778\t150989779\tC\t1\t8\t0.8441\tG\n+chrX\t152584270\t152584271\tG\t1\t7\t0.8157\tA\n+chrX\t152845290\t152845291\tT\t1\t12\t0.8522\tC\n+chrX\t153055432\t153055433\tA\t1\t17\t0.8461\tG\n+chrX\t153090059\t153090060\tG\t1\t3\t0.8010\tA\n+chrY\t4223441\t4223442\tG\t1\t8\t0.7722\tA\n+chrY\t9939199\t9939200\tC/T\t2\t20,13\t0.8045,0.8191\tC\n+chrY\t9962146\t9962147\tG/T\t2\t3,5\t0.8341,0.8751\tT\n+chrY\t9991556\t9991557\tG/T\t2\t31,22\t0.8248,0.8247\tT\n+chrY\t10050627\t10050628\tC/T\t2\t4,5\t0.8047,0.8279\tT\n+chrY\t10068141\t10068142\tA/T\t2\t15,20\t0.7954,0.8232\tA\n+chrY\t13195465\t13195466\tG/T\t2\t8,8\t0.8124,0.8215\tG\n+chrY\t13295972\t13295973\tC/T\t2\t16,10\t0.8060,0.8173\tC\n+chrY\t13567253\t13567254\tA/C\t2\t5,6\t0.8285,0.8351\tA\n+chrY\t18619115\t18619116\tC\t1\t4\t0.8518\tA\n+chrY\t59026174\t59026175\tA/G\t2\t5,13\t0.8138,0.8404\tA\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/phiX.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/phiX.fasta Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,79 @@
+>phiX174
+GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT
+GATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAA
+ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTG
+TCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTA
+GATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC
+TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTT
+TCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTT
+CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCT
+TGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG
+TCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC
+GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA
+CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAG
+TGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACT
+AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC
+CCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA
+TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGAC
+TCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA
+CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAA
+GGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTT
+GGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA
+ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGC
+TCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT
+TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC
+ATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCGTGATGTTATTTCTTCATTTGGAGGTAAAAC
+CTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTT
+GATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC
+CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGAC
+TAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG
+TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGT
+TTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA
+AGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGAT
+TATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT
+ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAAC
+GCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGC
+TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGT
+TCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTA
+TATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTG
+TCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC
+CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTG
+AATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGC
+CGGGCAATAATGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGT
+TTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTG
+CTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAA
+AGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT
+GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTG
+GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGA
+TAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTAT
+CTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGG
+TTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA
+GATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGAC
+CAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA
+TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCA
+AACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGAC
+TTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTT
+CTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGA
+TACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCG
+TCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT
+CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTAT
+TGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC
+ATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATG
+TTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGA
+ATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGG
+GACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC
+CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATT
+GCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTACTATTCAGCGTTTGATGAATGCAATGCGACAG
+GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTT
+ATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCG
+CAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGC
+CGTCTTCATTTCCATGCGGTGCATTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC
+GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT
+CGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAG
+CCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA
+TGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT
+TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTG
+TCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGC
+AGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACC
+TGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA
+

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/plot_for_lda_output.pdf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/plot_for_lda_output.pdf Sat Feb 21 16:33:42 2015 +0100

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diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/qualscores.qual454
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/qualscores.qual454 Sat Feb 21 16:33:42 2015 +0100

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+>EYKX4VC04I6APD length=156 xy=3645_0543 region=4 run=R_2007_11_07_16_15_57_
+21 12 8 5 4 2 2 1 1 1 1 1 1 28 38 32 11 28 44 36 24 14 5 24 28 28 28 21 27 42 35 21 7 27 28 27 24 26 28 37 28 35 26 28 26 28 27 24 28 28 27 28 44 18 9 5 3 2 1 1
+1 1 1 1 1 1 1 1 1 35 26 41 34 17 25 24 12 28 28 27 38 32 11 28 28 23 28 27 28 27 20 39 32 12 22 26 36 27 27 27 24 36 28 28 36 27 35 26 40 33 18 1 26 34 27 28 24 22 40 34
+15 26 32 22 28 28 28 25 28 28 39 33 13 27 28 32 22 32 23 42 35 21 7 28 43 36 23 10 27 43 36 23 10 36 28 25
+>EYKX4VC04IPT6U length=143 xy=3457_2692 region=4 run=R_2007_11_07_16_15_57_
+30 20 15 11 8 5 3 1 28 19 27 34 24 44 36 23 13 3 28 35 25 28 27 28 28 28 28 27 35 25 28 36 27 27 28 28 28 28 36 27 36 28 28 42 35 21 6 28 28 27 27 44 35 24 15 8 1 27 27 28
+36 27 28 28 27 28 28 35 26 43 36 23 12 2 28 36 27 26 28 28 36 27 28 28 36 27 41 34 16 25 28 41 34 16 36 28 40 34 14 39 33 13 36 27 40 34 18 2 28 40 34 18 2 35 25 28 27 41 34 19
+4 26 27 28 27 28 28 34 25 36 27 28 28 28 36 27 37 28 28 27 28 27 28
+>EYKX4VC04JX6Y2 length=68 xy=3962_3644 region=4 run=R_2007_11_07_16_15_57_
+28 28 28 27 35 28 6 27 28 27 36 27 28 25 37 28 33 26 2 28 27 28 24 28 37 29 28 28 28 28 28 23 28 32 22 28 36 27 28 26 34 25 28 28 35 26 28 28 26 27 25 28 28 24 28 28 27 27 28 28
+28 28 33 23 28 40 34 14
\ No newline at end of file

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/qualscores.qualsolid
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/qualscores.qualsolid Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,48 @@
+>946_21_302_F3
+2 10 2 2 4 2 21 2 2 4 4 17 5 2 5 2 11 4 2 2 2 10 7 3 15 2 2 2 3 19 3 2 6 3 2
+>946_21_659_F3
+3 31 3 2 2 2 34 3 2 2 2 31 2 2 3 4 31 8 3 2 2 30 4 8 3 3 2 2 6 9 4 4 6 2 2
+>946_21_1071_F3
+5 5 2 2 2 8 5 3 2 3 7 7 2 3 4 6 5 2 2 2 5 5 2 2 2 3 8 2 3 3 3 8 2 3 2
+>946_21_1115_F3
+21 5 2 8 13 31 6 2 17 24 10 27 4 21 29 8 20 2 11 21 13 24 5 5 6 24 31 2 13 6 22 17 6 27 10
+>946_21_1218_F3
+11 21 2 13 13 16 27 16 19 27 22 28 14 26 24 23 29 10 15 13 6 4 7 16 26 22 11 6 16 22 21 6 4 7 21
+>946_21_1232_F3
+17 16 2 28 21 31 15 16 10 11 8 20 6 5 18 6 13 23 7 13 4 12 19 8 6 9 10 19 7 10 6 10 20 14 8
+>946_21_1368_F3
+28 30 31 31 31 20 29 24 27 31 31 31 24 26 31 31 26 15 27 31 27 30 29 27 30 27 30 21 23 26 24 31 17 30 19
+>946_21_1406_F3
+4 29 3 2 4 5 34 8 2 2 3 29 4 2 8 2 11 4 2 2 2 28 8 5 3 4 31 2 2 2 2 28 5 2 2
+>946_21_1695_F3
+25 31 8 29 19 31 19 12 16 31 30 13 16 21 31 22 13 13 19 23 32 16 6 14 16 24 13 6 6 14 8 8 5 11 6
+>946_21_1945_F3
+23 27 14 10 17 31 29 31 10 13 31 29 23 8 24 30 31 28 10 20 26 28 31 5 22 31 24 28 9 7 15 7 20 5 4
+>946_21_2013_F3
+2 26 2 2 2 2 2 2 9 2 2 2 2 2 2 2 2 4 2 2 2 2 3 2 2 2 2 2 2 2 2 2 4 2 2
+>946_22_108_F3
+17 14 12 28 12 17 18 28 19 13 14 6 17 5 3 6 2 7 6 12 16 7 13 9 11 8 2 5 5 6 6 7 20 11 19
+>946_22_1241_F3
+16 8 5 20 11 6 13 5 19 13 8 9 17 31 8 17 2 6 31 21 12 11 8 12 5 8 15 8 5 5 7 5 11 6 10
+>946_22_1296_F3
+10 8 33 31 27 31 26 5 17 11 6 23 8 24 6 8 14 14 27 11 16 8 8 29 5 21 8 5 14 8 7 16 4 5 5
+>946_22_1356_F3
+2 31 4 3 2 6 31 4 2 2 4 2 3 8 2 2 2 3 4 8 2 2 3 3 11 2 2 2 4 2 2 2 9 2 2
+>946_22_1520_F3
+8 11 12 21 13 15 16 25 20 21 14 23 31 23 30 18 25 23 27 30 21 30 15 14 25 22 22 21 21 22 16 23 26 13 21
+>946_22_1532_F3
+27 30 34 26 25 29 31 31 24 29 29 33 28 22 24 31 30 30 24 22 25 31 19 9 26 29 23 22 13 28 30 31 24 7 29
+>946_22_1582_F3
+28 19 4 5 6 25 30 4 5 8 15 19 5 9 8 29 27 4 4 2 27 17 2 2 5 30 22 2 11 6 26 16 3 2 2
+>946_22_1598_F3
+23 5 33 6 19 8 13 4 30 17 11 13 6 16 8 8 27 5 24 8 8 26 16 8 17 2 23 25 4 23 10 16 10 7 13
+>946_22_1834_F3
+31 28 30 31 31 34 27 29 31 28 31 29 16 31 31 25 31 11 27 21 26 29 16 18 21 19 29 13 24 24 27 24 8 24 10
+>946_22_1939_F3
+30 29 31 31 25 31 33 24 31 30 25 31 27 33 31 27 31 26 30 19 16 27 29 31 21 25 27 9 26 27 23 15 20 27 27
+>946_23_975_F3
+31 31 3 3 2 32 29 3 3 4 28 27 2 4 4 30 24 3 7 3 28 24 5 7 8 29 22 2 6 6 2 24 2 2 2
+>946_23_1133_F3
+19 28 22 31 25 14 28 30 32 27 10 33 26 31 31 14 30 30 16 30 10 28 23 16 6 14 17 10 6 8 18 5 8 9 5
+>946_23_1221_F3
+30 26 30 32 23 29 29 27 28 20 26 23 14 29 27 29 28 29 23 14 30 27 30 27 8 24 13 26 11 12 20 17 15 5 21
\ No newline at end of file

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/qualsolid.stats
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/qualsolid.stats Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,36 @@
+column count min max sum mean Q1 med Q3 IQR lW rW
+1 24 2 31 413.0 17.2083333333 5 18.0 28 23 2 31
+2 24 5 31 499.0 20.7916666667 10 26.0 30 20 5 31
+3 24 2 34 324.0 13.5 2 6.5 30 28 2 34
+4 24 2 32 397.0 16.5416666667 3 16.5 31 28 2 32
+5 24 2 31 349.0 14.5416666667 4 13.0 25 21 2 31
+6 24 2 34 456.0 19.0 6 18.5 31 25 2 34
+7 24 2 34 545.0 22.7083333333 15 27.0 30 15 2 34
+8 24 2 31 338.0 14.0833333333 3 10.0 27 24 2 31
+9 24 2 32 377.0 15.7083333333 3 17.0 27 24 2 32
+10 24 2 31 373.0 15.5416666667 4 13.0 27 23 2 31
+11 24 2 31 371.0 15.4583333333 6 12.5 28 22 2 31
+12 24 2 33 505.0 21.0416666667 13 23.0 29 16 2 33
+13 24 2 31 302.0 12.5833333333 4 11.0 23 19 2 31
+14 24 2 33 384.0 16.0 4 18.5 26 22 2 33
+15 24 2 31 392.0 16.3333333333 4 13.0 30 26 2 31
+16 24 2 31 380.0 15.8333333333 6 15.5 29 23 2 31
+17 24 2 31 465.0 19.375 11 24.5 30 19 2 31
+18 24 2 30 304.0 12.6666666667 4 9.0 23 19 2 30
+19 24 2 31 350.0 14.5833333333 4 13.0 27 23 2 31
+20 24 2 31 332.0 13.8333333333 2 13.0 21 19 2 31
+21 24 2 32 358.0 14.9166666667 4 14.5 26 22 2 32
+22 24 2 31 456.0 19.0 8 24.0 28 20 2 31
+23 24 2 31 308.0 12.8333333333 5 8.0 19 14 2 31
+24 24 2 31 280.0 11.6666666667 5 8.5 16 11 2 31
+25 24 2 30 300.0 12.5 5 9.5 21 16 2 30
+26 24 2 31 384.0 16.0 3 20.0 25 22 2 31
+27 24 2 31 389.0 16.2083333333 8 16.0 24 16 2 31
+28 24 2 28 242.0 10.0833333333 2 6.0 21 19 2 28
+29 24 2 26 240.0 10.0 4 6.5 14 10 2 26
+30 24 2 28 297.0 12.375 6 8.5 22 16 2 28
+31 24 2 30 304.0 12.6666666667 3 9.0 22 19 2 30
+32 24 2 31 324.0 13.5 5 12.5 23 18 2 31
+33 24 2 26 255.0 10.625 4 8.0 20 16 2 26
+34 24 2 30 226.0 9.41666666667 2 6.5 13 11 2 29.5
+35 24 2 29 244.0 10.1666666667 2 7.0 19 17 2 29

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/random_phiX_1.fastqcssanger
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/random_phiX_1.fastqcssanger Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,80 @@
+@random_phiX_region_0
+G10122032013310033101313321021200111002331002233200
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+@random_phiX_region_1
+G01032113212201012120321021321231001331220321233013
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+@random_phiX_region_2
+G20332013022003213122121021031212011032031313100201
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+@random_phiX_region_3
+G00130020212022012020131310131203210311202213031002
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+@random_phiX_region_4
+G21331000022222231222301220321002000210312113230321
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+@random_phiX_region_5
+G22323002203102011012211230000101023211233231202001
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+@random_phiX_region_6
+G31131003310112011211023030210213120202310111030313
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+@random_phiX_region_7
+G20123122030103323321033212202023222310213303101033
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+@random_phiX_region_8
+G32231132231233213310122032013310033101313321021200
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+@random_phiX_region_9
+G31003210022003121223310201032113212201012120321021
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+@random_phiX_region_10
+G13112133130013233121023323111331202133200002113102
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+@random_phiX_region_11
+G13311003122201333201102310002033023121332123002222
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+@random_phiX_region_12
+G22222302211220002313313120033101221023233031011233
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+@random_phiX_region_13
+G10031222013332011023100020330231213321230022223021
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+@random_phiX_region_14
+G30300310330131003311010100213101001012230120031033
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+@random_phiX_region_15
+G20133230020113200121203331032333013210332100211000
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+@random_phiX_region_16
+G03030230012220321000022232031230003131012102110321
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+@random_phiX_region_17
+G31312303312101211100201212031021210110131211020332
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+@random_phiX_region_18
+G11013323103313330202313311002220213203321102022012
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+@random_phiX_region_19
+G03211233231202001022023211021220321220312230331012
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/random_phiX_1.fastqsanger
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/random_phiX_1.fastqsanger Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,80 @@
+@random_phiX_region_0
+TTGAGGCTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTT
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+@random_phiX_region_1
+GTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTA
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+@random_phiX_region_2
+AATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTTTCCA
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+@random_phiX_region_3
+GGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+@random_phiX_region_4
+ACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGAC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+@random_phiX_region_5
+AGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACTTCCCA
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+@random_phiX_region_6
+CACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGTGTTAATGC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+@random_phiX_region_7
+AACTACTCCGGTTATCGCTGGCGACTCCTTCGAGATGGACGCCGTTGGCG
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+@random_phiX_region_8
+CTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTATGGTACGCTGGACTTT
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+@random_phiX_region_9
+CAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGACTTAGTTCA
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+@random_phiX_region_10
+TACAGTATGCCCATCGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+@random_phiX_region_11
+TATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGA
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+@random_phiX_region_12
+AGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATA
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+@random_phiX_region_13
+TTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCA
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+@random_phiX_region_14
+CCGGGCAATAACGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGC
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+@random_phiX_region_15
+AACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTT
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+@random_phiX_region_16
+GCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCA
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+@random_phiX_region_17
+CATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAG
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+@random_phiX_region_18
+TGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+@random_phiX_region_19
+GCTGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACT
++
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/rgenetics.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/rgenetics.bed Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,1 @@
+l��+�󪿊��ﮨ�"��"��:*��.��:*��.��:*��,��:*��,��+��+�󪿺��m�� (:��(:��(:��(
\ No newline at end of file

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/rgenetics.bim
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/rgenetics.bim Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,25 @@
+22 rs2283802 0 21784722 4 2
+22 rs2267000 0 21785366 4 2
+22 rs16997606 0 21794754 1 3
+22 rs4820537 0 21794810 1 3
+22 rs3788347 0 21797804 3 1
+22 rs756632 0 21799918 4 2
+22 rs4820539 0 21807970 1 3
+22 rs2283804 0 21820335 1 2
+22 rs2267006 0 21820990 3 1
+22 rs4822363 0 21821000 4 2
+22 rs5751592 0 21827674 4 2
+22 rs5759608 0 21832708 2 4
+22 rs5759612 0 21833170 3 1
+22 rs2267009 0 21860168 3 4
+22 rs2267010 0 21864366 3 1
+22 rs5759636 0 21868698 4 2
+22 rs2071436 0 21871488 4 2
+22 rs2267013 0 21875879 3 1
+22 rs6003566 0 21889806 3 1
+22 rs2256725 0 21892891 2 1
+22 rs12160770 0 21892925 1 3
+22 rs5751611 0 21896019 2 4
+22 rs762601 0 21898858 1 3
+22 rs2156921 0 21899063 3 1
+22 rs4822375 0 21905642 1 3

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/rgenetics.fam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/rgenetics.fam Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,40 @@
+101 1 3 2 2 2
+101 2 0 0 2 1
+101 3 0 0 1 1
+105 1 3 2 2 2
+105 2 0 0 2 1
+105 3 0 0 1 1
+112 1 3 2 1 2
+112 2 0 0 2 1
+112 3 0 0 1 1
+117 1 3 2 2 2
+117 2 0 0 2 1
+117 3 0 0 1 1
+12 1 3 2 1 2
+12 2 0 0 2 1
+12 3 0 0 1 1
+13 1 3 2 1 2
+13 2 0 0 2 1
+13 3 0 0 1 1
+1334 1 10 11 1 2
+1334 10 0 0 1 1
+1334 11 0 0 2 1
+1334 12 0 0 1 1
+1334 13 0 0 2 1
+1334 2 12 13 2 2
+1340 1 9 10 1 2
+1340 10 0 0 2 1
+1340 11 0 0 1 1
+1340 12 0 0 2 1
+1340 2 11 12 2 2
+1340 9 0 0 1 1
+1341 1 11 12 1 1
+1341 11 0 0 1 1
+1341 12 0 0 2 1
+1341 13 0 0 1 1
+1341 14 0 0 2 1
+1341 2 13 14 2 1
+1344 1 12 13 1 1
+1344 12 0 0 1 1
+1344 13 0 0 2 1
+1345 12 0 0 1 1

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/rgenetics.map
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/rgenetics.map Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,25 @@
+22 rs2283802 0 21784722
+22 rs2267000 0 21785366
+22 rs16997606 0 21794754
+22 rs4820537 0 21794810
+22 rs3788347 0 21797804
+22 rs756632 0 21799918
+22 rs4820539 0 21807970
+22 rs2283804 0 21820335
+22 rs2267006 0 21820990
+22 rs4822363 0 21821000
+22 rs5751592 0 21827674
+22 rs5759608 0 21832708
+22 rs5759612 0 21833170
+22 rs2267009 0 21860168
+22 rs2267010 0 21864366
+22 rs5759636 0 21868698
+22 rs2071436 0 21871488
+22 rs2267013 0 21875879
+22 rs6003566 0 21889806
+22 rs2256725 0 21892891
+22 rs12160770 0 21892925
+22 rs5751611 0 21896019
+22 rs762601 0 21898858
+22 rs2156921 0 21899063
+22 rs4822375 0 21905642

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/rgenetics.ped
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/rgenetics.ped Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,40 @@
+101 1 3 2 2 2 2 2 4 2 1 3 3 3 3 3 2 2 3 3 1 2 3 1 2 2 2 2 2 4 3 1 4 4 1 1 2 2 2 2 3 1 3 1 2 1 0 0 2 2 1 3 3 1 1 3
+101 2 0 0 2 1 2 2 4 2 1 3 3 3 3 3 2 2 3 3 1 2 3 1 2 2 2 2 2 4 3 1 4 4 1 1 2 2 2 2 3 1 3 1 2 1 3 3 2 2 1 3 3 1 1 3
+101 3 0 0 1 1 2 2 4 4 1 3 3 3 3 3 2 2 3 3 2 2 1 1 2 2 2 2 4 4 1 1 4 4 1 1 2 2 2 2 1 1 3 1 1 1 1 3 2 4 3 3 1 1 3 3
+105 1 3 2 2 2 2 2 4 2 3 3 3 3 3 1 2 2 3 3 1 1 3 3 2 2 2 2 2 2 3 3 4 4 1 1 2 2 2 2 3 1 1 1 2 1 0 0 2 2 1 1 3 3 1 1
+105 2 0 0 2 1 2 2 4 4 3 3 3 3 3 1 2 2 1 3 1 2 3 1 2 2 4 2 2 4 3 1 4 4 1 1 2 2 2 2 1 1 1 1 1 1 3 3 2 4 1 3 3 1 1 3
+105 3 0 0 1 1 4 2 2 2 3 3 3 3 3 1 2 2 3 3 1 2 3 1 2 2 2 2 2 4 3 1 3 4 1 1 2 2 4 2 3 1 1 1 2 1 3 3 2 4 1 3 3 1 1 3
+112 1 3 2 1 2 4 2 2 2 3 3 1 1 1 1 2 2 3 3 1 2 3 1 2 2 2 2 2 4 3 1 3 4 1 1 2 2 4 2 1 1 1 1 1 1 3 3 4 4 3 3 1 1 3 3
+112 2 0 0 2 1 2 2 2 2 3 3 1 1 1 1 2 2 3 3 1 1 3 3 2 2 2 2 2 2 3 3 4 4 1 1 2 2 2 2 1 1 1 1 1 1 3 3 4 4 3 3 1 1 3 3
+112 3 0 0 1 1 4 2 4 2 3 3 1 3 3 1 2 2 1 3 2 2 1 1 2 2 4 2 4 4 1 1 3 4 1 1 2 2 4 2 1 1 1 1 1 1 3 3 2 4 1 3 3 1 1 3
+117 1 3 2 2 2 2 2 4 2 3 3 3 3 3 3 4 2 1 1 2 2 1 1 2 2 4 2 2 4 3 1 4 4 1 1 2 2 2 2 1 1 1 1 1 1 3 3 2 2 1 1 3 3 1 1
+117 2 0 0 2 1 2 2 4 4 1 3 3 3 3 3 2 2 1 3 2 2 1 1 2 2 4 2 4 4 1 1 4 4 1 1 2 2 2 2 1 1 1 1 1 1 3 3 2 4 1 3 3 1 1 3
+117 3 0 0 1 1 2 2 4 2 3 3 3 3 3 3 4 2 1 1 2 2 1 1 2 2 4 2 2 4 3 1 4 4 1 1 2 2 2 2 1 1 1 1 1 1 3 3 2 4 1 3 3 1 1 3
+12 1 3 2 1 2 2 2 4 4 1 3 3 3 3 3 2 2 3 3 2 2 1 1 2 2 2 2 4 4 1 1 4 4 1 1 2 2 2 2 1 1 3 1 1 1 3 3 2 4 3 3 1 1 3 3
+12 2 0 0 2 1 2 2 4 4 1 3 3 3 3 3 2 2 3 3 2 2 1 1 2 2 2 2 4 4 1 1 4 4 1 1 2 2 2 2 1 1 3 1 1 1 3 3 2 4 3 3 1 1 3 3
+12 3 0 0 1 1 2 2 4 2 1 3 1 3 3 1 2 2 3 3 1 2 3 1 2 2 2 2 2 4 3 1 4 4 1 1 2 2 2 2 1 1 3 1 1 1 3 3 2 4 3 3 1 1 3 3
+13 1 3 2 1 2 4 2 4 2 1 3 3 3 3 1 2 2 3 3 2 2 1 1 2 2 2 2 4 4 1 1 3 4 1 1 2 2 4 2 1 1 3 1 1 1 3 3 2 4 3 3 1 1 3 3
+13 2 0 0 2 1 4 2 2 2 3 3 1 3 1 1 2 2 3 3 1 2 3 1 2 2 2 2 2 4 3 1 3 4 1 1 2 2 4 2 1 1 1 1 1 1 0 0 0 0 3 3 1 1 3 3
+13 3 0 0 1 1 2 2 4 4 1 3 3 3 3 3 2 2 1 3 1 2 3 1 2 2 2 2 2 4 3 1 4 4 3 1 2 2 2 2 1 1 3 1 1 1 3 3 2 2 3 3 1 1 3 3
+1334 1 10 11 1 2 2 2 4 2 3 3 1 3 3 1 2 2 1 3 1 2 3 1 4 2 4 2 2 4 3 1 4 4 1 1 2 2 2 2 1 1 1 1 1 1 3 3 4 4 3 3 1 1 3 3
+1334 10 0 0 1 1 4 2 4 2 3 3 1 3 3 1 2 2 1 3 2 2 1 1 4 2 4 2 4 4 1 1 3 4 1 1 2 2 4 2 3 1 1 1 2 1 3 3 2 4 1 3 3 1 1 3
+1334 11 0 0 2 1 2 2 2 2 3 3 1 1 1 1 2 2 3 3 1 1 3 3 2 2 2 2 2 2 3 3 4 4 1 1 2 2 2 2 1 1 1 1 1 1 3 3 4 4 3 3 1 1 3 3
+1334 12 0 0 1 1 4 2 2 2 3 3 1 3 1 1 2 2 3 3 2 2 1 1 2 2 4 2 4 4 1 1 3 4 1 1 2 2 4 2 3 1 1 1 2 1 3 3 2 4 1 3 3 1 1 3
+1334 13 0 0 2 1 4 2 4 2 3 3 1 3 3 1 4 2 1 3 2 2 1 1 2 2 2 2 2 4 3 1 3 4 1 1 2 2 4 2 1 1 1 1 1 1 3 3 2 4 1 3 3 1 1 3
+1334 2 12 13 2 2 4 4 2 2 3 3 1 3 1 1 2 2 3 3 2 2 1 1 2 2 2 2 4 4 1 1 3 3 1 1 2 2 4 4 3 1 1 1 2 1 3 3 2 4 1 3 3 1 1 3
+1340 1 9 10 1 2 4 2 4 2 3 3 1 3 3 1 2 2 1 3 1 2 3 1 2 2 2 2 2 4 3 1 3 4 3 1 2 2 4 2 1 1 1 1 1 1 3 3 4 4 3 3 1 1 3 3
+1340 10 0 0 2 1 4 2 4 2 3 3 1 3 3 1 2 2 1 3 1 2 3 1 2 2 2 2 2 4 3 1 3 4 3 1 2 2 4 2 1 1 1 1 1 1 3 3 4 4 3 3 1 1 3 3
+1340 11 0 0 1 1 4 2 4 2 3 3 1 3 3 1 4 2 1 3 2 2 1 1 2 2 2 2 2 4 3 1 3 4 1 1 2 2 4 2 1 1 1 1 1 1 3 3 2 4 1 3 3 1 1 3
+1340 12 0 0 2 1 2 2 4 2 3 3 1 3 3 1 2 2 1 3 1 2 3 1 4 2 4 2 2 4 3 1 4 4 1 1 4 2 2 2 1 1 1 1 1 1 3 3 2 4 1 3 3 1 1 3
+1340 2 11 12 2 2 2 2 4 2 3 3 1 3 3 1 4 2 1 3 1 2 3 1 2 2 2 2 2 2 3 3 4 4 1 1 2 2 2 2 1 1 1 1 1 1 3 3 2 4 1 3 3 1 1 3
+1340 9 0 0 1 1 4 4 2 2 3 3 1 1 1 1 2 2 3 3 2 2 1 1 2 2 2 2 4 4 1 1 3 3 1 1 2 2 4 4 1 1 1 1 1 1 3 3 4 4 3 3 1 1 3 3
+1341 1 11 12 1 1 2 2 4 2 3 3 1 3 3 1 2 2 1 3 1 2 3 1 4 2 4 2 2 4 3 1 4 4 1 1 0 0 2 2 1 1 1 1 1 1 3 3 2 2 1 1 3 3 1 1
+1341 11 0 0 1 1 2 2 2 2 3 3 1 1 1 1 2 2 3 3 1 1 3 3 2 2 2 2 2 2 3 3 4 4 1 1 4 2 2 2 1 1 1 1 1 1 3 3 2 4 1 3 3 1 1 3
+1341 12 0 0 2 1 4 2 4 2 3 3 1 3 3 1 2 2 1 3 2 2 1 1 4 2 4 2 4 4 1 1 3 4 1 1 4 2 4 2 3 1 1 1 2 1 3 3 2 2 1 1 3 3 1 1
+1341 13 0 0 1 1 4 2 2 2 3 3 1 1 1 1 2 2 3 3 1 2 3 1 2 2 2 2 2 4 3 1 3 4 1 1 2 2 4 2 1 1 1 1 1 1 3 3 4 4 3 3 1 1 3 3
+1341 14 0 0 2 1 4 2 2 2 3 3 1 1 1 1 2 2 3 3 1 2 3 1 2 2 2 2 2 4 3 1 3 4 1 1 2 2 4 2 1 1 1 1 1 1 3 3 4 4 3 3 1 1 3 3
+1341 2 13 14 2 1 4 2 2 2 3 3 1 1 1 1 2 2 3 3 1 2 3 1 2 2 2 2 2 4 3 1 3 4 1 1 2 2 4 2 1 1 1 1 1 1 3 3 4 4 3 3 1 1 3 3
+1344 1 12 13 1 1 2 2 4 4 3 3 3 3 3 3 4 4 1 1 2 2 1 1 2 2 2 2 2 2 3 3 4 4 1 1 2 2 2 2 1 1 1 1 1 1 3 3 2 2 1 1 3 3 1 1
+1344 12 0 0 1 1 2 2 4 2 3 3 1 3 3 1 4 2 1 3 1 2 3 1 2 2 2 2 2 2 3 3 4 4 1 1 2 2 2 2 1 1 1 1 1 1 3 3 2 4 1 3 3 1 1 3
+1344 13 0 0 2 1 2 2 4 2 3 3 1 3 3 1 4 2 1 3 1 2 3 1 2 2 2 2 2 2 3 3 4 4 1 1 2 2 2 2 1 1 1 1 1 1 3 3 2 4 1 3 3 1 1 3
+1345 12 0 0 1 1 4 2 4 2 3 3 3 3 3 1 2 2 1 3 2 2 1 1 4 2 4 2 4 4 1 1 3 4 1 1 4 2 4 2 3 1 1 1 2 1 3 3 2 2 1 1 3 3 1 1

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/rmap_wrapper_test1.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/rmap_wrapper_test1.bed Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,8 @@
+phix 360 396 seq1 1 -
+phix 4188 4224 seq2 1 +
+phix 4908 4944 seq4 0 -
+phix 2811 2847 seq5 2 +
+phix 3847 3883 seq6 0 -
+phix 91 127 seq7 0 +
+phix 2302 2338 seq8 2 +
+phix 2448 2484 seq9 0 +

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/rmap_wrapper_test1.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/rmap_wrapper_test1.fasta Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,20 @@
+>seq1
+GACTCATGATTTCTTACCTATTAGTGGTTGAACATC
+>seq2
+GTGATATGTATGTTGACGGCCATAAGGCTGCTTCTT
+>seq3
+GTTGTCGATAGAACTTCATGTGCCTGTAAAACAAGT
+>seq4
+ACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGC
+>seq5
+GTTTATGTTGGTTTCATGGTTTTGTCTAACTTTATC
+>seq6
+GCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCG
+>seq7
+GCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGC
+>seq8
+GTTATAACGCCGAAGCGGTAAAAATTTTTATTTTTT
+>seq9
+GTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACCT
+>seq10
+GTGGCCTGTTGATTCTAAAGGTTAGTTTCTTCACGC

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/rmapq_wrapper_test1.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/rmapq_wrapper_test1.bed Sat Feb 21 16:33:42 2015 +0100

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/rmapq_wrapper_test1.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/rmapq_wrapper_test1.fasta Sat Feb 21 16:33:42 2015 +0100

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/rmapq_wrapper_test1.qual
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/rmapq_wrapper_test1.qual Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,10 @@
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+ -40  -40   40  -40 -40  -40  -40   40 -40  -40   40  -40 -40  -40   40  -40 -40   40  -40  -40 -40   40  -40  -40 -40  -40  -40   40 -40  -40   40  -40 -40  -40  -40   40 -40  -40  -40   40 -40  -40   40  -40   40  -40  -40  -40 -40  -40  -40   40 -40  -40   -6    6 -40   40  -40  -40 -40  -40  -40   40    3  -40  -40   -3   40  -40  -40  -40   40  -40  -40  -40 -40  -40   40  -40 -40  -40   40  -40   -0  -40  -40    0 -40  -40  -40   40   40  -40  -40  -40 -40  -40   40  -40 -40  -40  -40   40 -40  -40  -40   40 -40  -40  -40   40 -20   20  -40  -40 -40  -40  -40   40 -40  -40  -40   40 -40   40  -40  -40    8  -40  -40   -8 -40   40  -40  -40 -40  -40   40  -40   -4    4  -40  -40

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/rr.csfasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/rr.csfasta Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,1001 @@\n+# Mon Sep 28 22:46:46 2009 /share/apps/corona/bin/filter_fasta.pl --output=/data/results/solid176/solid176_20090923/Somali_Wild_Ass_a/results.01/primary.20090929010043704 --name=solid176_20090923_Somali_Wild_Ass_a --tag=R3 --minlength=50 --mincalls=25 --prefix=G /data/results/solid176/solid176_20090923/Somali_Wild_Ass_a/jobs/postPrimerSetPrimary.849/rawseq \n+# Cwd: /state/partition1/home/pipeline\n+# Title: solid176_20090923_Somali_Wild_Ass_a\n+>853_7_53_R3\n+G..1...12.3.023.22.22.2.2..22..2...2222.222.2.2.22.\n+>853_7_78_R3\n+G..2...02.2.232.22.11.2.2..12..1...2222.222.2.3.22.\n+>853_7_88_R3\n+G..3...22.2.032.13.22.2.1..23..0...2130.132.1.2.30.\n+>853_7_132_R3\n+G..2...21.2.200.21.30.1.1..30..0...2112.202.2.0.22.\n+>853_7_141_R3\n+G..2...13.1.112.22.00.0.0..02..2...2222.200.2.2.22.\n+>853_7_146_R3\n+G..1...12.2.212.20.11.2.1..12..2...1311.223.1.3.21.\n+>853_7_269_R3\n+G..1...21.2.212.02.01.2.1..21..3...2210.113.2.3.32.\n+>853_7_321_R3\n+G..1...01.2.202.10.11.0.2..22..2...0332.111.2.0.22.\n+>853_7_386_R3\n+G..2...31.2.211.11.31.2.0..31..0...2030.312.1.0.22.\n+>853_7_405_R3\n+G..2...00.0.002.31.23.0.2..32..3...1032.120.2.1.22.\n+>853_7_411_R3\n+G..1...00.1.002.02.12.1.2..22..2...1020.312.2.0.21.\n+>853_7_445_R3\n+G..2...33.0.233.03.31.0.1..13..2...0020.222.2.2.22.\n+>853_7_469_R3\n+G..1...10.3.313.33.33.0.3..02..1...2333.230.2.3.32.\n+>853_7_474_R3\n+G..2...03.2.112.23.31.1.2..21..1...2221.322.2.1.21.\n+>853_7_497_R3\n+G..3...02.2.221.22.12.1.2..13..0...0033.230.2.3.21.\n+>853_7_587_R3\n+G..0...23.2.030.01.02.0.3..33..3...2101.030.0.2.20.\n+>853_7_630_R3\n+G..3...01.0.011.10.21.0.3..22..0...2101.020.3.0.01.\n+>853_7_655_R3\n+G..3...33.3.113.10.20.1.1..02..2...3132.200.1.1.21.\n+>853_7_692_R3\n+G..0...30.0.300.12.30.1.1..30..2...1022.320.3.3.33.\n+>853_7_715_R3\n+G..3...22.1.110.22.31.2.2..21..1...1021.330.1.2.31.\n+>853_7_719_R3\n+G..0...00.3.200.02.30.0.1..20..1...0003.301.2.2.33.\n+>853_7_743_R3\n+G..3...00.0.201.11.03.2.3..30..2...1112.300.2.2.31.\n+>853_7_791_R3\n+G..1...00.2.022.02.32.1.3..21..0...0222.120.1.0.22.\n+>853_7_801_R3\n+G..2...11.1.232.31.01.2.1..22..1...2222.122.2.1.22.\n+>853_7_845_R3\n+G..3...23.0.310.12.22.2.2..22..2...3232.303.2.2.33.\n+>853_7_868_R3\n+G..3...21.0.012.11.00.1.2..31..0...0101.022.2.3.03.\n+>853_7_1026_R3\n+G..2...02.1.333.11.10.2.2..21..3...1323.011.1.2.22.\n+>853_7_1057_R3\n+G..1...22.3.333.22.22.3.1..12..2...2122.332.1.3.21.\n+>853_7_1066_R3\n+G..2...22.2.332.12.01.3.0..21..2...0312.122.0.1.02.\n+>853_7_1107_R3\n+G..1...11.0.223.12.23.2.0..11..1...2012.132.0.3.30.\n+>853_7_1179_R3\n+G..3...02.1.133.00.21.1.3..20..1...3000.002.3.2.23.\n+>853_7_1198_R3\n+G..3...21.2.121.00.13.0.3..01..3...1131.330.1.3.01.\n+>853_7_1261_R3\n+G..0...12.3.202.00.03.2.0..22..0...2112.021.2.3.22.\n+>853_7_1321_R3\n+G..1...20.0.021.12.10.2.0..20..1...2002.012.2.1.22.\n+>853_7_1406_R3\n+G..0...11.0.212.11.00.2.0..23..1...2002.102.1.0.30.\n+>853_7_1431_R3\n+G..3...20.3.020.23.22.2.2..22..1...3302.132.0.2.02.\n+>853_7_1439_R3\n+G..3...12.2.013.21.20.2.1..21..2...2001.123.0.2.12.\n+>853_7_1524_R3\n+G..1...22.3.122.01.11.2.3..20..1...3021.103.2.0.32.\n+>853_7_1537_R3\n+G..0...11.1.233.22.22.1.3..22..2...3311.220.1.2.11.\n+>853_7_1592_R3\n+G..0...10.1.033.00.33.2.1..11..3...0031.333.0.3.32.\n+>853_7_1597_R3\n+G..3...00.2.102.11.21.2.1..00..0...0011.000.2.0.00.\n+>853_7_1650_R3\n+G..3...03.3.203.10.12.0.2..20..2...1113.121.2.1.33.\n+>853_7_1790_R3\n+G..2...13.3.311.21.13.1.0..11..3...0212.001.0.2.22.\n+>853_7_1795_R3\n+G..2...02.0.222.13.22.0.1..11..1...1220.213.0.1.20.\n+>853_7_1807_R3\n+G..3...11.3.213.13.02.1.3..20..1...3031.033.2.1.03.\n+>853_7_1872_R3\n+G..0...33.0.231.21.10.0.0..03..1...1323.110.0.2.01.\n+>853_7_1885_R3\n+G..2...33.1.320.12.01.2.0..11..3...1213.332.1.3.20.\n+>853_7_1910_R3\n+G..3...03.1.331.22.00.2.0..22..2...0120.020.1.2.02.\n+>853_8_43_R3\n+G.130..11.3.030.30.00.3.2..11..1...3221.22222.2.22.\n+>853_8_48_R3\n+G.023..11.1.210.22.30.0.0..22..3...2202.22222.2.22.\n+>853_8_57_R3\n+G.312..02.1.302.20.00.0.0..33..2...3313.22022.3.20.\n+>853_8_106_R3\n+G.223..02.3.313.23.03.2.0..02..1.'..b'.223.22.22.2110.200.1122220321300120.20.\n+>853_15_1876_R3\n+G0002..3001.230.01.20.0231.002.1201113121120001.31.\n+>853_15_1915_R3\n+G2112..0210.212.32.13.3112.120.3320203131230023.00.\n+>853_15_1974_R3\n+G2131..0110.331.01.11.1331.123.3323103221332231.11.\n+>853_16_26_R3\n+G2212..1122.321.32.12.2222.222.2221222222222222.22.\n+>853_16_44_R3\n+G0002..1032.201.31.12.2222.023.2222321221222211.22.\n+>853_16_56_R3\n+G1222..0202.222.02.22.0112.203.3022020223320130.01.\n+>853_16_67_R3\n+G1000..3303.012.00.10.1330.230.1130120322111230.22.\n+>853_16_112_R3\n+G0023..0033.320.22.11.1000.113.3012120222222222.22.\n+>853_16_155_R3\n+G0221..1223.122.23.21.3212.222.2222223222302322.22.\n+>853_16_169_R3\n+G0010..0111.132.30.22.1221.211.2000023100110123.22.\n+>853_16_319_R3\n+G2200..2210.221.21.13.2020.130.3222120020311111.22.\n+>853_16_375_R3\n+G2313..3001.121.12.21.3131.113.3333033333033111.32.\n+>853_16_447_R3\n+G0022..1212.320.20.21.0321.211.2221121222221220.31.\n+>853_16_502_R3\n+G2220..2012.210.10.23.1320.033.2200330301303233.30.\n+>853_16_506_R3\n+G2021..1112.110.10.22.1222.111.1212223212232232.20.\n+>853_16_513_R3\n+G3322..1201.302.30.31.2220.323.3120021003322223.20.\n+>853_16_571_R3\n+G2010..0222.100.13.12.3102.023.0013002222130220.01.\n+>853_16_622_R3\n+G1003..3000.300.02.00.1031.101.0000030003310030.01.\n+>853_16_690_R3\n+G2033..2221.210.03.00.0030.201.0000223100312211.00.\n+>853_16_697_R3\n+G2030..0312.310.32.22.3123.022.2011323200003112.20.\n+>853_16_791_R3\n+G2323..1123.122.12.12.3121.122.3111222231112211.22.\n+>853_16_804_R3\n+G3221..3200.121.22.10.0110.232.1313110211000011.20.\n+>853_16_830_R3\n+G2120..2022.333.21.20.0223.223.0313200310121012.21.\n+>853_16_871_R3\n+G1003..1112.300.21.21.3033.033.1310310030223301.12.\n+>853_16_874_R3\n+G0312..1312.131.23.12.2013.130.2302020022222201.02.\n+>853_16_892_R3\n+G2121..2130.122.13.03.1213.213.3203011112122011.33.\n+>853_16_919_R3\n+G0222..2212.000.11.32.2310.033.2010101230012130.21.\n+>853_16_941_R3\n+G2212..2310.011.11.03.2222.211.2222122223222221.22.\n+>853_16_1040_R3\n+G3101..0122.021.10.31.0220.333.1230033132002222.13.\n+>853_16_1049_R3\n+G3132..0121.311.02.13.3012.302.1113200103012221.12.\n+>853_16_1063_R3\n+G3130..2231.130.11.32.0000.002.1130332001003101.32.\n+>853_16_1081_R3\n+G1100..1113.112.21.20.1233.121.0123003133302222.22.\n+>853_16_1142_R3\n+G3220..1323.110.21.21.0222.111.1133122100110022.20.\n+>853_16_1155_R3\n+G1330..0303.013.32.31.0102.120.0122011112122321.03.\n+>853_16_1188_R3\n+G2313..1101.211.13.33.1021.232.2222212122311133.21.\n+>853_16_1231_R3\n+G2301..2211.033.33.00.2210.203.0221100033000010.22.\n+>853_16_1285_R3\n+G1030..1000.311.20.11.2301.310.1201113132331121.12.\n+>853_16_1300_R3\n+G1101..1122.000.12.10.1133.301.1211302223100130.23.\n+>853_16_1391_R3\n+G0101..1330.232.02.00.1100.101.2013133213103321.23.\n+>853_16_1397_R3\n+G0231..0300.303.03.00.1013.132.1322212323121333.23.\n+>853_16_1528_R3\n+G1100..3231.300.03.10.0200.013.1213123210321100.12.\n+>853_16_1574_R3\n+G2123..1133.031.00.23.0212.033.1300001310200300.33.\n+>853_16_1593_R3\n+G3313..2033.201.23.00.1111.120.0322310111121220.22.\n+>853_16_1653_R3\n+G0000..1111.011.02.21.0111.301.3310230303100110.13.\n+>853_16_1698_R3\n+G1022..0220.112.23.02.0003.202.2013020200022202.02.\n+>853_16_1746_R3\n+G1221..2212.330.00.30.1111.021.2013331032213303.10.\n+>853_16_1806_R3\n+G2131..0221.102.21.22.3102.213.1120211103300110.12.\n+>853_16_1821_R3\n+G2020..2233.223.12.21.2223.101.3211322223122222.23.\n+>853_16_1842_R3\n+G0022..0211.010.21.03.1321.102.2020222023112220.22.\n+>853_16_1853_R3\n+G2300..3303.020.11.13.2001.010.0012022112202122.11.\n+>853_16_1871_R3\n+G1012..0221.030.13.01.0100.112.0102100222022222.22.\n+>853_16_1887_R3\n+G2001..3000.203.12.01.3230.213.0220222201230231.31.\n+>853_16_1919_R3\n+G3011..0111.022.22.01.0232.021.3211120120120110.03.\n+>853_16_1924_R3\n+G3132..0213.321.13.32.3122.123.1021002130301210.23.\n+>853_16_1982_R3\n+G3233..2202.022.00.01.2101.020.2312112223233330.10.\n+>853_17_18_R3\n+G3010..2002.023.21.2213211.120.1200222222231222.222\n+>853_17_101_R3\n+G2223..1023.130.20.1212101.112.1021211212022221.221\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/rr.qualsolid
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/rr.qualsolid Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,1001 @@\n+# Mon Sep 28 22:46:46 2009 /share/apps/corona/bin/filter_fasta.pl --output=/data/results/solid176/solid176_20090923/Somali_Wild_Ass_a/results.01/primary.20090929010043704 --name=solid176_20090923_Somali_Wild_Ass_a --tag=R3 --minlength=50 --mincalls=25 --prefix=G /data/results/solid176/solid176_20090923/Somali_Wild_Ass_a/jobs/postPrimerSetPrimary.849/rawseq \n+# Cwd: /state/partition1/home/pipeline\n+# Title: solid176_20090923_Somali_Wild_Ass_a\n+>853_7_53_R3\n+-1 -1 15 -1 -1 -1 16 15 -1 8 -1 8 15 8 -1 11 12 -1 2 2 -1 4 -1 4 -1 -1 2 2 -1 -1 6 -1 -1 -1 4 10 5 8 -1 4 3 14 -1 8 -1 3 -1 14 7 -1 \n+>853_7_78_R3\n+-1 -1 2 -1 -1 -1 20 11 -1 3 -1 20 5 10 -1 2 23 -1 8 2 -1 20 -1 4 -1 -1 18 4 -1 -1 6 -1 -1 -1 3 3 23 10 -1 5 8 4 -1 8 -1 7 -1 9 2 -1 \n+>853_7_88_R3\n+-1 -1 16 -1 -1 -1 19 17 -1 20 -1 11 17 20 -1 17 19 -1 22 22 -1 19 -1 18 -1 -1 23 16 -1 -1 11 -1 -1 -1 20 16 19 22 -1 8 14 21 -1 11 -1 11 -1 16 5 -1 \n+>853_7_132_R3\n+-1 -1 5 -1 -1 -1 20 2 -1 8 -1 8 5 10 -1 17 5 -1 6 11 -1 5 -1 6 -1 -1 16 8 -1 -1 16 -1 -1 -1 19 7 8 3 -1 14 5 11 -1 6 -1 6 -1 15 3 -1 \n+>853_7_141_R3\n+-1 -1 11 -1 -1 -1 8 11 -1 20 -1 18 8 10 -1 14 14 -1 8 11 -1 18 -1 24 -1 -1 5 14 -1 -1 10 -1 -1 -1 9 9 2 8 -1 13 8 7 -1 7 -1 7 -1 19 18 -1 \n+>853_7_146_R3\n+-1 -1 16 -1 -1 -1 18 18 -1 19 -1 2 16 20 -1 22 7 -1 20 16 -1 16 -1 18 -1 -1 13 20 -1 -1 20 -1 -1 -1 14 8 14 11 -1 5 12 14 -1 11 -1 13 -1 19 11 -1 \n+>853_7_269_R3\n+-1 -1 18 -1 -1 -1 14 13 -1 10 -1 9 19 11 -1 19 17 -1 8 23 -1 17 -1 18 -1 -1 21 17 -1 -1 15 -1 -1 -1 23 19 26 8 -1 8 22 13 -1 20 -1 14 -1 5 4 -1 \n+>853_7_321_R3\n+-1 -1 3 -1 -1 -1 5 6 -1 13 -1 9 2 2 -1 21 3 -1 2 16 -1 10 -1 2 -1 -1 13 10 -1 -1 8 -1 -1 -1 18 21 7 2 -1 9 20 6 -1 2 -1 19 -1 10 7 -1 \n+>853_7_386_R3\n+-1 -1 26 -1 -1 -1 23 21 -1 28 -1 26 24 28 -1 4 20 -1 20 23 -1 27 -1 17 -1 -1 21 17 -1 -1 5 -1 -1 -1 5 18 25 5 -1 14 14 23 -1 9 -1 22 -1 20 9 -1 \n+>853_7_405_R3\n+-1 -1 28 -1 -1 -1 26 25 -1 29 -1 27 23 28 -1 24 27 -1 25 27 -1 28 -1 29 -1 -1 26 23 -1 -1 26 -1 -1 -1 26 14 14 16 -1 5 7 5 -1 14 -1 6 -1 9 12 -1 \n+>853_7_411_R3\n+-1 -1 3 -1 -1 -1 12 2 -1 2 -1 9 2 10 -1 11 5 -1 17 9 -1 2 -1 2 -1 -1 4 6 -1 -1 8 -1 -1 -1 6 3 8 3 -1 14 12 2 -1 2 -1 6 -1 11 10 -1 \n+>853_7_445_R3\n+-1 -1 5 -1 -1 -1 15 4 -1 2 -1 11 5 6 -1 11 6 -1 3 3 -1 5 -1 11 -1 -1 5 8 -1 -1 6 -1 -1 -1 13 13 9 5 -1 2 11 22 -1 16 -1 13 -1 16 15 -1 \n+>853_7_469_R3\n+-1 -1 2 -1 -1 -1 4 4 -1 3 -1 8 8 10 -1 3 11 -1 9 4 -1 13 -1 7 -1 -1 13 2 -1 -1 2 -1 -1 -1 2 5 2 2 -1 2 2 5 -1 2 -1 2 -1 2 2 -1 \n+>853_7_474_R3\n+-1 -1 24 -1 -1 -1 25 25 -1 25 -1 27 20 23 -1 28 29 -1 29 17 -1 28 -1 22 -1 -1 17 10 -1 -1 3 -1 -1 -1 5 2 13 3 -1 2 4 10 -1 2 -1 6 -1 2 2 -1 \n+>853_7_497_R3\n+-1 -1 21 -1 -1 -1 21 21 -1 11 -1 24 19 6 -1 22 25 -1 24 20 -1 24 -1 20 -1 -1 14 4 -1 -1 19 -1 -1 -1 14 16 8 13 -1 6 3 7 -1 15 -1 3 -1 7 11 -1 \n+>853_7_587_R3\n+-1 -1 14 -1 -1 -1 26 26 -1 5 -1 11 5 8 -1 5 7 -1 7 13 -1 12 -1 8 -1 -1 5 5 -1 -1 20 -1 -1 -1 18 20 7 28 -1 23 16 22 -1 11 -1 5 -1 10 8 -1 \n+>853_7_630_R3\n+-1 -1 24 -1 -1 -1 16 27 -1 26 -1 5 18 14 -1 23 29 -1 16 29 -1 28 -1 20 -1 -1 16 5 -1 -1 26 -1 -1 -1 4 16 5 21 -1 6 23 11 -1 7 -1 23 -1 14 4 -1 \n+>853_7_655_R3\n+-1 -1 5 -1 -1 -1 23 2 -1 24 -1 22 5 8 -1 29 20 -1 2 25 -1 30 -1 2 -1 -1 26 3 -1 -1 27 -1 -1 -1 2 23 23 5 -1 2 27 26 -1 4 -1 23 -1 2 2 -1 \n+>853_7_692_R3\n+-1 -1 24 -1 -1 -1 26 26 -1 24 -1 22 25 27 -1 21 26 -1 27 25 -1 24 -1 24 -1 -1 29 25 -1 -1 27 -1 -1 -1 28 11 29 22 -1 26 14 27 -1 28 -1 27 -1 29 7 -1 \n+>853_7_715_R3\n+-1 -1 25 -1 -1 -1 21 24 -1 24 -1 22 27 26 -1 23 25 -1 28 10 -1 21 -1 21 -1 -1 24 18 -1 -1 20 -1 -1 -1 7 22 15 21 -1 5 25 19 -1 7 -1 11 -1 11 3 -1 \n+>853_7_719_R3\n+-1 -1 11 -1 -1 -1 25 13 -1 8 -1 26 2 6 -1 11 11 -1 2 21 -1 22 -1 2 -1 -1 2 13 -1 -1 2 -1 -1 -1 5 2 5 2 -1 2 3 5 -1 2 -1 2 -1 2 2 -1 \n+>853_7_743_R3\n+-1 -1 29 -1 -1 -1 27 24 -1 22 -1 23 25 29 -1 29 26 -1 25 29 -1 24 -1 27 -1 -1 28 24 -1 -1 20 -1 -1 -1 18 20 28 11 -1 25 16 28 -1 8 -1 14 -1 20 11 -1 \n+>853_7_791_R3\n+-1 -1 14 -1 -1 -1 16 14 -1 29 -1 14 8 30 -1 25 14 -1 22 20 -1 27 -1 26 -1 -1 11 1'..b'15 5 -1 2 20 -1 \n+>853_16_1142_R3\n+29 31 25 26 -1 -1 30 27 28 29 -1 29 26 28 -1 32 29 -1 27 29 -1 29 23 25 24 -1 30 25 27 -1 28 29 24 26 21 28 25 27 28 26 29 26 26 25 27 26 -1 19 24 -1 \n+>853_16_1155_R3\n+19 25 24 17 -1 -1 17 25 16 27 -1 25 16 25 -1 27 29 -1 21 27 -1 16 20 24 25 -1 27 9 23 -1 23 24 23 19 26 23 25 8 13 27 27 23 23 22 27 28 -1 2 3 -1 \n+>853_16_1188_R3\n+24 2 3 8 -1 -1 24 17 11 26 -1 24 2 11 -1 7 23 -1 3 17 -1 14 6 2 7 -1 6 10 2 -1 8 9 3 3 2 3 11 2 2 4 11 8 2 2 8 17 -1 2 5 -1 \n+>853_16_1231_R3\n+22 22 19 20 -1 -1 23 18 24 18 -1 23 11 25 -1 15 17 -1 7 5 -1 11 4 2 2 -1 11 6 11 -1 6 2 3 3 6 7 6 4 3 11 2 7 6 4 8 8 -1 2 5 -1 \n+>853_16_1285_R3\n+7 23 11 12 -1 -1 24 17 17 14 -1 25 15 20 -1 26 32 -1 19 20 -1 25 19 20 23 -1 22 23 18 -1 24 24 21 13 14 23 22 14 15 7 21 22 3 10 14 5 -1 2 2 -1 \n+>853_16_1300_R3\n+4 19 6 4 -1 -1 2 9 2 6 -1 13 10 14 -1 11 2 -1 4 4 -1 8 17 11 9 -1 2 13 11 -1 2 18 3 3 4 6 6 3 10 11 11 12 3 5 10 7 -1 8 3 -1 \n+>853_16_1391_R3\n+28 32 27 32 -1 -1 22 26 28 31 -1 30 28 31 -1 30 28 -1 30 32 -1 27 28 28 29 -1 29 25 29 -1 27 20 21 26 26 28 27 21 22 29 20 20 22 16 11 11 -1 10 6 -1 \n+>853_16_1397_R3\n+3 5 8 8 -1 -1 20 14 7 4 -1 13 5 18 -1 18 22 -1 18 11 -1 5 8 11 6 -1 2 4 13 -1 3 11 3 5 11 2 7 5 3 3 3 3 2 5 11 5 -1 3 10 -1 \n+>853_16_1528_R3\n+32 32 27 27 -1 -1 29 32 28 32 -1 28 28 28 -1 29 29 -1 29 30 -1 28 30 28 30 -1 26 31 27 -1 27 29 28 27 23 23 27 29 26 26 25 23 25 21 27 28 -1 28 16 -1 \n+>853_16_1574_R3\n+28 25 18 23 -1 -1 27 26 20 9 -1 20 18 22 -1 21 21 -1 24 8 -1 29 25 24 7 -1 28 21 15 -1 25 21 24 27 25 27 24 15 18 20 7 21 5 19 8 8 -1 12 5 -1 \n+>853_16_1593_R3\n+15 13 3 8 -1 -1 13 13 15 6 -1 9 2 14 -1 3 15 -1 5 2 -1 12 8 6 9 -1 9 17 2 -1 2 20 7 14 6 9 8 7 10 14 8 6 6 18 26 15 -1 18 21 -1 \n+>853_16_1653_R3\n+28 28 27 27 -1 -1 31 29 32 28 -1 28 27 32 -1 30 29 -1 27 21 -1 27 29 31 29 -1 25 21 29 -1 27 25 27 21 17 26 16 24 23 24 26 30 23 25 26 22 -1 29 21 -1 \n+>853_16_1698_R3\n+28 28 25 30 -1 -1 27 29 25 31 -1 31 32 30 -1 31 28 -1 30 30 -1 29 28 27 29 -1 27 29 24 -1 27 26 28 26 27 27 27 23 25 27 24 25 28 22 25 27 -1 22 25 -1 \n+>853_16_1746_R3\n+32 32 31 32 -1 -1 32 32 32 28 -1 27 27 28 -1 26 28 -1 27 32 -1 31 32 30 30 -1 28 28 29 -1 31 28 27 25 25 27 23 28 27 26 28 31 27 28 25 26 -1 26 18 -1 \n+>853_16_1806_R3\n+27 31 21 30 -1 -1 26 21 26 32 -1 26 11 27 -1 26 28 -1 27 27 -1 11 17 28 25 -1 17 24 20 -1 28 29 18 30 25 28 29 23 29 24 22 28 21 28 30 28 -1 20 25 -1 \n+>853_16_1821_R3\n+14 8 18 25 -1 -1 22 25 29 30 -1 14 14 8 -1 5 14 -1 5 11 -1 15 24 26 27 -1 14 18 16 -1 27 13 8 5 8 10 8 13 12 17 5 19 19 11 7 4 -1 3 19 -1 \n+>853_16_1842_R3\n+25 29 24 27 -1 -1 26 29 29 30 -1 29 29 28 -1 27 28 -1 27 21 -1 23 17 22 19 -1 21 23 22 -1 21 24 15 20 27 25 8 24 21 16 22 23 22 28 16 21 -1 5 20 -1 \n+>853_16_1853_R3\n+3 8 20 18 -1 -1 8 3 2 6 -1 20 6 7 -1 11 12 -1 2 7 -1 2 10 13 19 -1 11 5 20 -1 7 11 2 8 11 6 7 6 15 8 5 5 14 6 21 5 -1 5 14 -1 \n+>853_16_1871_R3\n+26 5 24 8 -1 -1 5 27 11 3 -1 8 6 7 -1 4 5 -1 8 24 -1 6 27 8 22 -1 11 11 22 -1 8 19 24 13 23 18 8 22 18 13 21 11 16 17 8 5 -1 20 23 -1 \n+>853_16_1887_R3\n+30 28 26 31 -1 -1 28 10 28 23 -1 28 19 25 -1 25 28 -1 31 27 -1 23 19 25 24 -1 26 15 25 -1 24 26 20 27 16 26 25 22 28 14 27 20 5 25 13 22 -1 5 29 -1 \n+>853_16_1919_R3\n+15 28 23 26 -1 -1 19 26 22 25 -1 23 25 22 -1 18 24 -1 26 27 -1 20 25 19 19 -1 28 23 25 -1 11 22 25 26 24 10 26 28 12 23 20 5 23 22 24 18 -1 25 11 -1 \n+>853_16_1924_R3\n+19 16 6 18 -1 -1 8 7 4 16 -1 25 17 25 -1 13 13 -1 7 15 -1 19 5 5 6 -1 11 2 3 -1 18 8 11 5 22 26 9 9 11 12 4 13 17 13 11 11 -1 2 2 -1 \n+>853_16_1982_R3\n+23 22 23 24 -1 -1 25 28 28 29 -1 30 26 27 -1 26 29 -1 31 23 -1 24 29 27 27 -1 29 25 26 -1 8 23 25 17 25 21 27 27 25 18 5 21 19 25 16 11 -1 13 13 -1 \n+>853_17_18_R3\n+8 11 16 10 -1 -1 21 14 14 11 -1 11 16 11 -1 6 11 -1 4 11 5 18 19 8 14 -1 11 15 5 -1 6 5 14 5 13 5 17 21 9 20 7 11 5 2 7 7 -1 22 8 5 \n+>853_17_101_R3\n+25 18 17 20 -1 -1 20 6 14 14 -1 22 5 17 -1 18 16 -1 16 13 16 20 11 14 20 -1 20 11 14 -1 23 11 16 8 17 21 16 17 11 18 9 22 8 24 16 21 -1 10 19 11 \n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/s2fq_out1.fastqsanger
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/s2fq_out1.fastqsanger Sat Feb 21 16:33:42 2015 +0100

b"@@ -0,0 +1,576 @@\n+@1831_573_1004/1\n+AATACTTTCGGCGCCCTAAACCAGCTCACTGGGG\n++\n+><C&&9952+C>5<.?<79,=42<292:<(9/-7\n+@1831_573_1050/1\n+TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT\n++\n+;@@17?@=>7??@A8?==@4A?A4)&+.'&+'1,\n+@1831_573_1067/1\n+AAGTATGAGTCATTTACCGGGATGCGAAGAAAAG\n++\n+++#%(',%/$,+&1#&),)&+'*'*%#$&#%('$\n+@1831_573_1219/1\n+CGCCCTATAATAATACAGCGCGTTAGACCGCTCA\n++\n+@@=4/+)5)408?'665>*/5?<61';<3,:,5-\n+@1831_573_1242/1\n+GCTGAATCGCACCTAGCAACTATAGCCGGGCCGC\n++\n+>>::>17=A5?@@=;7A=;2.60>82<8=74+;;\n+@1831_573_1333/1\n+AGAATCGTTACCACACACTGCGTCTGGGTATCCG\n++\n+='@#%3=.>)/34*117,,/6-4+.9742456<)\n+@1831_573_1362/1\n+CGATCTCAACCAGGTCCGCGCCCACCCCTGCCTC\n++\n+B@@?@@?@C@BA?@>@<@8A@?@'.8'?17:,+?\n+@1831_573_1448/1\n+TCACGCCGGTCCTTGACTGGCGTTCTCTTCGAGG\n++\n+7=A)?,.@A@@:@@<=/7)@<-#8662%9613&+\n+@1831_573_1490/1\n+CTCGTCATGTTACGCAAAGGCACGTCACAGCACC\n++\n+@@@?,@??@$><=>+%/*>*1,)?26&12'9%7.\n+@1831_573_1523/1\n+ATGGAACGGAACGGGTGAGGAGGGGAACGTAGGG\n++\n+,//*,#8''.6''6'2&27/80)%&#0'%#*,2'\n+@1831_573_1578/1\n+CGAGTAGCAAACAAGACGCCAATCCAGGCGACCC\n++\n+?=@<@C@?@@??=>@;7<<8<694)3511(+1<.\n+@1831_573_1647/1\n+AGGGGTTTACACTATTCGACTGGGTGAGAGGCGT\n++\n+?@@<@@???;A==@@;9?@?3=;6.4/;6:=/;4\n+@1831_573_1684/1\n+TTCAACTGCGTCGACGTAGCGCACAGGCGTCCGT\n++\n+>1:8<@39@@??9=;@@<>?@@<;<?7>76?9>?\n+@1831_573_1769/1\n+TGGACGTATAGTGGCGATGAGCATGTAGGTTCTC\n++\n+54749&&767%/7;3$-7;3#,3//#,45/#&06\n+@1831_573_1853/1\n+CAAAACGCCCGGGGCCTCACATGCGCGGCAGTTC\n++\n+4./B@@72B+/4?@?7?+@9/+99.')2<2&)2&\n+@1831_573_1943/1\n+ATAACGTATGGCAGTGAACGGGCGGAACCTGCCC\n++\n+>/*1,),@-)'0*>5'$/?6@/.&?8/(')A43,\n+@1831_573_1977/1\n+GGCGTAGGGCTCATTGTGCAAGTATCCGACCTCC\n++\n+@?6@8@@9A@=4633A7?9?<3:+7>'@%@?%32\n+@1831_574_109/1\n+TCGGTTGCGTTACTTCATGGGAGGGCTTTACATT\n++\n+7651#4817>@65<2:84716=788<1995.7?6\n+@1831_574_148/1\n+CGAACCTCGTATAACGGAGTAGTCGGAAACAGTC\n++\n+;->3;;3>//>0;;7=,=4-4/+>029<9<624;\n+@1831_574_185/1\n+CCGTTTTGCCTAGTAATGCTCGGCGCAGCGTCGC\n++\n+<4;%%@7>#*>97%6;+8$#<07%1372$%<54#\n+@1831_574_243/1\n+AGGCACCGTAACTCAGGACATTCTCGATTAGTTA\n++\n+@@@95@=9?*><45$<@<4%@9?7#=?>7&>?97\n+@1831_574_257/1\n+ATACCTTCCAAAGCAATAGAATAAAAAACAGTAC\n++\n+>>B>)@?>B@B?@1%*%,#+00.'(+&5&%#$3&\n+@1831_574_293/1\n+TGCTGCAAATAAACATACAGCCTTCTAATGACTA\n++\n+')7'.*%#&$'/.$##$.$&*)+*$#8%&%#&&%\n+@1831_574_389/1\n+CATGGCTATGCACCGGTTTGTAGCGTACTCGAGA\n++\n+)$>/>8):2@:213;;.1)@3%64%+)<7)+$92\n+@1831_574_575/1\n+TTCTTGGCAAGCGCAGATTATGCGTTCCGCCTAG\n++\n+?@>=?@>8@@@=@6*%&<='5@<<',0<=4*5/<\n+@1831_574_592/1\n+TCATTTACCACGTCAGGGTCGGAGTCATTCATTA\n++\n+3-5)19,,<@>4067<2.-864346;9<1/;212\n+@1831_574_617/1\n+AAGCATCGGCGGGAGCGCAAGCTGGGAAGGTGCC\n++\n+>@?;>?=@==@>@=5?@+@:@40@><:0)')64-\n+@1831_574_725/1\n+GACAAGATGGCTATTATTTACAATCCGATCTGCA\n++\n+'>?52+5=;4$6;<8.1<47*9+?7(+5;-).)4\n+@1831_574_734/1\n+CCTGTACGAAAGAACGTAGGCATGGGCTGGGGGG\n++\n+-&.$2&<*(-%):/)%5:)/%7+,9034*A.?70\n+@1831_574_824/1\n+AGCGCAAATTATGCGTTCCGCCTAGCGGAGAACT\n++\n+@@@;;),+@<-<7;<&89??&29?<$2:A<);8?\n+@1831_574_959/1\n+CGCGCTAGGACTCGGCCCCAAGAGACGTTCCGCC\n++\n+A=;+?@9;/<@;<8#&&/*%(%.0$0$2)+1$-1\n+@1831_574_1062/1\n+ACCGGTAATATAAGGCAACATGATTACGGCCACG\n++\n+@821<//:136/8<1/5.427.;>288/0<1$)/\n+@1831_574_1092/1\n+GACTGGCGAAATCATCGCGGAAAAACCCCTATCA\n++\n+8?.,98)03%#,,,(,++$'69'#9'7#';6.%2\n+@1831_574_1103/1\n+ATCTCCTGATTAGACATATCTCCGTAGCTCACGC\n++\n+??>?@=>@@A<>?=@==<:?<;58'&&):+35'1\n+@1831_574_1116/1\n+CACCTCACGTGAGTATAGCAGCCCGAGCGTCACC\n++\n+@++,)/)?./)%<)2>.==:8?&;44&/&,)/*4\n+@1831_574_1194/1\n+TTATCACATTTGGGGATCGGAAGGGACTACTTCG\n++\n+5>;,??9@9@?@1@@=@3=@>@4?@@94?75/,6\n+@1831_574_1204/1\n+CTTACTGGTCTGCTGGACATATAGTGGCGATGAA\n++\n+A5A5B@5:;@@,.9?A1?#.?;3),>82%)='7*\n+@1831_574_1306/1\n+ATTGCTTAGATCCAGTGGCGCTCAATACAACGGA\n++\n+2.7&%''.$&#'%##$#'#%')')$'$%$,)'.1\n+@1831_574_1387/1\n+GTACTTCTCAATGCTGCACTACTATGTACGCCCC\n++\n+?A??:@?@@9?@@?9C;:>&).,,);&'<&7(/'\n+@1831_574_1431/1\n+GACCAGTTTCAGGGCTAACCGTCCCTACTCGACC\n++\n+7?>9BA897;+8*=6#6.+5&-#26$0.,5&'$1\n+@1831_574_1560/1\n+GGCGTCTTAGGATTGAAGAGGGCCTCCCACCCCC\n++\n+))&65<4=>99@:597(1&;+&(%&4#,#&&&*$\n+@1831_574_1591/1\n+TGAGCACTTATGGCTAGGCGTAGGGGACCGTGAG\n++\n+=<A><?@78@<=;@&@6>8:?,><&&<7>8(8+9\n+@1831_574_1624/1\n+ACGGGAAGGGCTGGAATCTACCCAGTAGGCATTG\n++\n+<6.&(,7-+))7..'/;43.)927.(<85&1"..b"(*1%*(%(-2#+)-#.&-#%%$')\n+@1831_576_754/1\n+AGGCGTCCTGCATCGACCGTTCTATCCGCTTAGA\n++\n+4//#(.$)'',>(&#1$<,##%((,#5?#0*%1*\n+@1831_576_815/1\n+TAGGCCTGATATGACACGATCACAGTGCAACATC\n++\n+3>@?9>@?B=>=;>A???=>:25=4.25?6<57.\n+@1831_576_882/1\n+TGTAAGACGGTGAGGTGTAAGGATCAGACCACGG\n++\n+26?8?@:4>@>96??<<=5'1<>9846=<9<1>8\n+@1831_576_898/1\n+AGTACTGTCGCGCATTGGGGTCCTGGTCGTTGCT\n++\n+@@C2?C>?<>@886B?;?.??87=B<8<15??=.\n+@1831_576_923/1\n+CTGGACATGAGAGACTGCACGCGGTACACGTCGG\n++\n+6.51=;.699<96>;;49<;;11;<@59:9=647\n+@1831_576_930/1\n+CTGGCATGTACGTCCATGTCAGACGAGCAGAACT\n++\n+#*0.2&.:((#'14'##-)#%$$2%#$/1&#%/#\n+@1831_576_1019/1\n+GATGCGCGCTGTCATGGCATCGAACCATCGGTCG\n++\n+<$>$,1,&++&@,.)'+/+#9'69/6'2(+-'9-\n+@1831_576_1068/1\n+AAGAGTGACTCACTTACCGGGATGCGATGGAGCC\n++\n+>><=4?;@7=??9?;9>5@9?:8@:=5';7;'#4\n+@1831_576_1131/1\n+AGTTCGGGAAGGGCTGGAATCTACCCAGTAGGCA\n++\n+04@#@/@,4>9?2+?1571@',>=;(759;*92<\n+@1831_576_1168/1\n+CACTTAACTCCGCTGTCGGAAGCCTTACAAGACA\n++\n+@CC6@@2?9=>7?;76<;467@;9,0%26'',4$\n+@1831_576_1207/1\n+CAACCTGACTAAACGGGGATACGCTGGCGCTACA\n++\n+$>2,(&?4?(,@:<&,@>?$&:8A%%=0.%,597\n+@1831_576_1289/1\n+TAGCGCAAGTCCAGAATGTTCATAGACTCGCGAT\n++\n+9<>1B@@;7@@663==28,5':8<<,.=2>>.50\n+@1831_576_1329/1\n+CCAATAGCAGAGACCTAATAGGAAACGAAAGCAA\n++\n+>&0,870/A@@/5.;=;:'&@3'&$$%,+#($&2\n+@1831_576_1367/1\n+GGTCTCATCCGTTCCAATCGGGACTTTGACCAGT\n++\n+?@@<>@@=@<@<=@>@??9:?<=>=<8;59@787\n+@1831_576_1416/1\n+TAGCGTTCAACGTCGATCTCATCTTGCCGATGGC\n++\n+';?..1.<@'.=+6.5?7<0-?7;(%=>56.98@\n+@1831_576_1461/1\n+GAGGGGCGGCCCGGTTCAAGCAGGTAAGCAACAA\n++\n+1&74#(#(&##$#,'###%#%%#*#&%%##%%%'\n+@1831_576_1605/1\n+AGTGCAACATCTGCTTTGCTTATCAGCACACGGC\n++\n+<@C@@>1;@:;<<@@9@???9<3?5-21=4877,\n+@1831_576_1664/1\n+CGCGCACAACTCGCCATGATACGACAAGACCCGA\n++\n+@?>?@=A:@@>@='=<>=).>=9*8)(7#/++;)\n+@1831_576_1671/1\n+GTCTTTGTAAGCCTGGCCTGGTCAGGTCTGGTCT\n++\n+@?@5>@@8&8?25#&)&5&&)15&&,&4%&,&6%\n+@1831_576_1729/1\n+CGTTTCGTCTACAACGTGACACTAGCACAGTATA\n++\n+?@?<?<@>A?/==?>?7>?@8<?@>99;><+0=>\n+@1831_576_1880/1\n+TATGCGCTGTTGAGCTTACAACTCACTAGCGAAT\n++\n+515/792,:,7/%/05,%$):+#8%2(1754))3\n+@1831_576_1982/1\n+AATGTCGTCAGACGACTTTGGCGCGAAAACCATA\n++\n+@@?@,A><@9@=?@9B=8<6@@6@2<A?>.7<+@\n+@1831_576_1987/1\n+AAGGTCTTCTGTCGGCGCTGGACTGAACACCTGA\n++\n+##()(#&##)%)/-#%$11#%3>'##&$,#$$'+\n+@1831_576_2014/1\n+CCGTGACACACAATGCCGGCCCCAGCCTAGCAAT\n++\n+@@9,B29-5>'?,+?79+/A';'2@'5&/9,6&1\n+@1831_576_2028/1\n+ACTCGCCGCATCCCCGAGTGACGCTCGAGACCAA\n++\n+<>9>5'2(&707.8#&&39,0%7/#(#,*%&5*+\n+@1831_577_40/1\n+CCCCGCGTTACGAACGAGAGAAATCTCTTATAAT\n++\n+2/4('.')(<*?#$)%&<,/39<(.2,+<=@611\n+@1831_577_119/1\n+TCCCACAAGCCATTGACATGCTCGCTCTAAACAG\n++\n+>?C11)-1/)#;#/,850*+.+$$5550+%-.40\n+@1831_577_133/1\n+TGCTTGTACGGTCTAACGGGGTATGGGTTTCTGG\n++\n+4@>>?=1?:+>@07@@><>@*<+1@15)96'2$)\n+@1831_577_255/1\n+ATTGAGGCCAAGATAATTGAGGAGAGAGAAGGTG\n++\n+<=87@>69%**#&#-+$.#&&#+$-+%&%.,%5#\n+@1831_577_281/1\n+TATGTACGTCGCGTACACTCCGGGGCCCGCAAAA\n++\n+-:B;8@=;>7@>4?=?+659?;5<7?;9@8(>:?\n+@1831_577_288/1\n+CATCCGAGGCTATCAAGGCGTAAGCACTGACCTA\n++\n+;/79??&=B::298*6.7/+4&21,7,6?.7#'6\n+@1831_577_322/1\n+GAATGCTGGAGTACATTATGACAAACTATCGGAG\n++\n+=;>4506;255464-<#7+194&2<?65968)7/\n+@1831_577_362/1\n+CGATTAGTTACCACTCGTATTCGCACGCCCAGGA\n++\n+2B?:@?@<?958=,3:,90:&'-99,6<5.($+6\n+@1831_577_382/1\n+GTCGCGTATTCCCCGATGCTATGTAGACTTGCAA\n++\n+2957/:1))=76(*24;,3+:<.&.&-=1=2/5*\n+@1831_577_464/1\n+TAGAGGCACCCTAACTCAGGGCTTTCTCGATTAG\n++\n+=<7/<826)>#.'&4204+5#/041.7*91&756\n+@1831_577_488/1\n+TGAATAGTTATGGCCAGAATGTCTGCACCGATAC\n++\n+48.,*>6566<?8=<=<2>6;94>;=9>@8924@\n+@1831_577_511/1\n+GGTGCTTATCAGTTCTTTCTCGGGACTTGTATTT\n++\n+7/+&$:<7%6,$$%'%/+)#$7((&*3>16'0/+\n+@1831_577_545/1\n+ACCGCTCTTTGGGTATGGGGCAATCTGGCATGTT\n++\n+><<9?<>?A<481@<@8==@76/61<95.5988-\n+@1831_577_559/1\n+GTGCCACTATGTTCGACAGACCCTAAGGCGGAAG\n++\n+<@;??@>@?/2<.@1=>12=61/;=?.&2+92)'\n+@1831_577_562/1\n+GTTCCACTACGTTCCACGCAAAGGAATCCGAATC\n++\n+((&*&0%)1%)#($2-,***%/-,,))&,-.1'*\n+@1831_577_637/1\n+GCCTTCGCGGGAGCATATCAGTCGATACATCCCA\n++\n+-,4#>:-6+:8,&(5;3=0>7=68&1/9&'?;4,\n+@1831_577_641/1\n+TATCTACCACCGCGGTGGCGCGAGAATGCTCCCT\n++\n+47;/':A;;5?:72,(=),#*?+.#&7$8#%7/'\n+@1831_577_692/1\n+CCGGTGAGAATTACATCGCGAGTACGCCCAAGGA\n++\n+B,@?@B(@A?@+@@>@+?=>@'=<@<=<9=?75<\n"

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/s2fq_out2.fastqsanger
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/s2fq_out2.fastqsanger Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,192 @@
+@1378_11_329/2
+GTTCGTGGCCGGTGGGTGTTTGGG
++
+###$$#$#$&#####$'$#$###$
+@1378_17_1788/2
+TGGGTGGATGTGTTGTCGTTCATG
++
+#$#$###$#$#######$#$####
+@1378_25_2035/2
+GTGCGTCGGGGAGGGTGCTGTCGG
++
+######%#$%#$$###($###&&%
+@1378_28_770/2
+GGTTGGGAGTTGGCGCGCGTGGTT
++
+###$##%%$####%#%$#%%#($$
+@1378_33_1945/2
+GGGGGGGGGGGGGGGGGGGGGGGG
++
+.6;?;55697>8779457986264
+@1378_34_789/2
+GGGCTTGCGTTAGTGAGAGGTTGT
++
+###%$%$%%###$####$###$#&
+@1378_35_263/2
+GGCGGGGGGGGGGGGGGGGGGGGG
++
+$%%&,)3/)%$-6'$&5&#$''5.
+@1378_43_186/2
+GCTAGGGTTTGGGTTTGCGGTGGG
++
+$%#$########%##%#$###'#'
+@1378_51_1671/2
+GGTGTTGTTCGGATGTAGCGTGGG
++
+##%$$####$########$##0##
+@1378_56_324/2
+GCTGGGTGATCTAAGGAATGTAAT
++
+#$#####$$$#$$$$##%###*(#
+@1378_56_773/2
+TCTGGTCGGTTTCGGGGAGTGGAA
++
+##%%#&$###$#$##%$####%%$
+@1378_62_2027/2
+GTTGGCCTGGCCTGCCGTGCTGCG
++
+*##),/%##$)#%##1$#'%.#&#
+@1378_62_2029/2
+GGCGGTGTGTGGTGCGGCTGTGCG
++
+/$$$=(####%####)$$%$-&%#
+@1378_67_1795/2
+CGTGCCAACGACCGTCCTACGGAG
++
+@@.?7@@@.@:@A<<>>=>70<@7
+@1378_68_466/2
+GTGTCATCTGAGGTAAAGCATTGT
++
+/##$09#$#.=$#$76+$%1'###
+@1378_68_1692/2
+TGTTCGATTTAGGTCTTGCCTCGC
++
+###%%$%%##%$#$##$###$$#$
+@1378_80_664/2
+TGTCTGCGTTGTATCTCTGGTGTA
++
+%##%,%$$#&$$###$#$%##'%#
+@1378_85_1786/2
+CCCTAGGAGCGTATACCGGACGAG
++
+,'&/%/@,&1,&'/)&,6&&1)((
+@1378_86_1011/2
+AGGCGATGGGATATTATTTTACTT
++
+:$###)%##$9$###1$$#$2###
+@1378_86_1789/2
+GGCCAGGTACTAATAAATTCAACA
++
+1.51/&%#'$,*?%#6&0$$5,20
+@1378_91_1596/2
+GCTTTTTCATTCGGTGCCTTTGGA
++
+'>%/3%=()8'#.%?50$&5>%)%
+@1378_94_1595/2
+GCGGGTTAACCCAGTACCTCTGGC
++
+,8@6'>8<76>@@(->9)7'*941
+@1378_95_1039/2
+GTTCTGTGCCAGGTGAGGTACGGA
++
+&##,./#$&)6##+,'#$$0(##$
+@1378_95_1767/2
+CTAATTGACCGGGCAAGCTATTAA
++
+',,2'(10/>:=/7).3&%6&)&6
+@1378_96_1037/2
+CTGCTGGGCCATTTGACTTACTCA
++
+'$#+#(##-%5##+*&###-.$$$
+@1378_96_1764/2
+TCTTTGTAACCCACTTAGTATTTC
++
+4='28>.@4881B807:822>%)1
+@1378_98_1574/2
+AGGCGAGTGTGGGGGTTGTTTGAG
++
++%%$#)##%##$####%###$%$#
+@1378_107_1647/2
+GGTCTGGTTCTATGTTGGTCGACT
++
+###'$$#$$$(#%###(#$##$%#
+@1378_111_829/2
+GGTCTTCTATGGTGCTAAATTAGT
++
+$##'&###$##)#%($#$%#$'%#
+@1378_111_1900/2
+GCACGCCTTTGGGCTAAGCCGTAA
++
+)$)'#%$########$'#&%$#(#
+@1378_112_1483/2
+TGGAGTGGTGTGTTTGCTGAGCCA
++
+#$#)#############$#%#%'%
+@1378_125_1287/2
+TGACGTGGGTTGTCCCGTGAGATT
++
+##$%%#$###$##$$#&%##$(%%
+@1378_126_468/2
+AAAAAACGGGCCGGGCGGACTAGG
++
+@@B@@@>@2>1+?:92)>@8&&<+
+@1378_127_664/2
+TCGCTTTGCCTATGTTTGTTCGGA
++
+#%$%#&##$%#%%###$$###)-'
+@1378_129_463/2
+AAAAAAAAAAAAAAAAAAAAAAAA
++
+,)&20%8'(&35-***1-2&+510
+@1378_129_875/2
+GACCTTTACGTATTGGGGGTTGGC
++
+###)###+###$##$#&%##$,#$
+@1378_140_1251/2
+TTTCCTTCGTGTGCGTGCGGAGTG
++
+#%#%$##$$$######.$$$%#%(
+@1378_141_809/2
+TCTCGTGGTTTCTTTTTTATGTGT
++
+##%)##$$#####%$#$#%%#'##
+@1378_144_983/2
+GTTCGTTCGTGGTGTACGAGGGTG
++
+#(#%#####($#%##$$#%##%#)
+@1378_153_270/2
+GGCCGTGTGCGGGTGTAGATTGGA
++
+%$##($######&##$&$$$$%##
+@1378_155_1689/2
+CGCGTTCGGACAAAGCTAGCACCT
++
+@4@@=6=@@<4:@@681@@@.24.
+@1378_157_1580/2
+GGGATTGAAGGGATGTATGCTAGG
++
+#%$&%#$$'%$%#$##*#%$$$$#
+@1378_161_317/2
+AATCCATACCCACAAAAGCAGGCC
++
+.&%','(@''?7//+&)+2.+)0)
+@1378_177_735/2
+CGAGCCCTAAACCATGAGATCGGA
++
+@@B>@AC9@A<B8@=9>7@5)>,0
+@1378_181_1684/2
+TTTCTGTTGTGGTTTTGTTGGGGT
++
+$##'$%'##%##$%$#$$####$*
+@1378_187_1407/2
+TTGGGTGAAATCTTGTCGAGTGGA
++
+####&##$$###$#####%##%%)
+@1378_203_721/2
+CCTTTACGATCATAAACCATGACC
++
+9<&./1&@;12')?<1',?/)&/.
+@1378_206_2039/2
+CCCCCCCCCCCCCCCCCCCCCCCC
++
+?=>>?=:;<>>4::<=56199(05

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/s2fq_out3.fastqsanger
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/s2fq_out3.fastqsanger Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,192 @@
+@1378_11_329/1
+AGACCGGGCGGGGTGGCGTTCGGT
++
+%##+'#######%###$#$##$(#
+@1378_17_1788/1
+TGCCGTGTCTTGCTAACGCCGATT
++
+#'#$$#$###%%##$$$$######
+@1378_25_2035/1
+CTGCGTGTTGGTGTCTACTGGGGT
++
+#%#'##$#$##&%#%$$$%#%#'#
+@1378_28_770/1
+CTGCTATGCCGGCCGCCTGCCCCT
++
+%##(#$$#%$#$%###$%%$##$#
+@1378_33_1945/1
+GGGGGGGGGGGGGGGGGGGGGGGG
++
++9;64287788752796/576352
+@1378_34_789/1
+ATGGTGGCTGACGCGTTTGACTGT
++
+#$##%#$##$&$#%##$##$###$
+@1378_35_263/1
+GGGCGGGGGGCGGCGGGGGGGGGG
++
+),,#%'$)'-(%&%'%',%%&&(&
+@1378_43_186/1
+ATACTAGTTGGGACGCGTTGTGCT
++
+#$(4%$########$#$###$$$#
+@1378_51_1671/1
+TGGGTAGGTGCGGCTCTTGCGGTC
++
+##$#$%###%%#%#$##$$#####
+@1378_56_324/1
+AGGCTTGGATTGTTGCGCTGACCT
++
+/+#**###%%##%#####$$$#$#
+@1378_56_773/1
+TGTCGTGAGGTCACTTATCCCCAT
++
+&%#%##%%#####&#$%##$%##$
+@1378_62_2027/1
+CTTCCACGATCTGCTCGCTGTGGT
++
+(#&&$##$$#$%#%$$$#$###'#
+@1378_62_2029/1
+TCTGGGCTGTCTTCGGGTCGGTGT
++
+$%$$####$##$$#)##%%#$###
+@1378_67_1795/1
+TAGTGGGCTAGTCCGGGATCTACC
++
+B@C2@@?;-@@1>'A@@91@.@1'
+@1378_68_466/1
+GTGATCGTCGGTGCCAGTCCCTGT
++
+#(%)+##$#$#%#+$%##$#####
+@1378_68_1692/1
+GGTCTTCTGGGCACGGGCCAAGTT
++
+###)%'&%##$###%#######$#
+@1378_80_664/1
+CTGCTTTGATCCCCGGTGGAGCAC
++
+7#%###$$6#######$##$$$##
+@1378_85_1786/1
+ATACTATGTCGATCTGTAAAAAAA
++
+)&.)#3%@$&%-,2#&+.-%0&./
+@1378_86_1011/1
+CTACGTTATTGCTCTGTTTGTCCT
++
+######$%##$$$%###%#$####
+@1378_86_1789/1
+CGAATATCCCCTGGTTTAGAAGTA
++
+61?1;@/>@<=/(.7'(<5@=%$=
+@1378_91_1596/1
+TTAGCGGTTGACTATCTGCTGACA
++
+*&+'#9'(%*'#//,&<),/)'*#
+@1378_94_1595/1
+CGTGCGACAGCCCATGTTTTCAGA
++
+-=..5,3826&*+.+#+#%%6;%#
+@1378_95_1039/1
+CGGCGTCCATCTTCGCCTTGAGAT
++
+$##.#$##$$#%$#$%%$###$)$
+@1378_95_1767/1
+ACACGCACCATCTGGCGGCTAACC
++
+86<65<4<C27/$5+#;-$+#2%$
+@1378_96_1037/1
+ATCCCCCAAGATGCCTGTTGATTG
++
+$#$'##$$$#%$$#%###+##$#$
+@1378_96_1764/1
+TACACCGGAACCTTGCACTAAAGC
++
+6-9'<#+81?+*<8-=69&6;*3)
+@1378_98_1574/1
+GTTCTGCCGGTGTCTGTGGCGGGC
++
+$$#+&$$####%$$$###$%#%%#
+@1378_107_1647/1
+AGGCCTACTACGCGTCATTGATAG
++
+&#$$#$(.#%#$$####&$%##($
+@1378_111_829/1
+TGCGGCACTTGCTTCTTCGTATTT
++
+%#%##%#$%#$#%###$$##&#$$
+@1378_111_1900/1
+TCCCCTCGCTCGGCTCTGTGCTGT
++
+$&%*$#(#)##$#'##%(##$#$%
+@1378_112_1483/1
+TGTCCAGCTATGCGGCTTCCTCCT
++
+%#$+#%#&#$#####%####%$##
+@1378_125_1287/1
+TGTCTCTGGGGGGCCTGGTTAGGT
++
+$##13$'%#$###$$###$$$#&#
+@1378_126_468/1
+TCTCCTGATTAGACATATCTCCGT
++
+7>@318?=,=8@49579?..7,7)
+@1378_127_664/1
+AGAGGTTGGTGTCTTGTCGCAGCT
++
+##'#$######$$%######$$$#
+@1378_129_463/1
+CCTGTGGGCCAAGCCCAATGAAAG
++
+8),,<6(--)<()5&.&/8+;.2+
+@1378_129_875/1
+TTTCTATGGCTTACGCTGTCTGCC
++
+#$($##%####%$#$#####$###
+@1378_140_1251/1
+ATCCTAGCGCGGTGTCTTGGGGAC
++
+#$%1#$$$##$##$#$#$##$%$$
+@1378_141_809/1
+TGTCCTCCAGTGTCTGTTGGGTGT
++
+%&,-##$$#(%###$#$$'###'#
+@1378_144_983/1
+AGCGCCCGGTTGGTGCGGCTCGTC
++
+-$(&%*$#*#))#$$$#%%$#$##
+@1378_153_270/1
+AGTCCTTGTCCCCTGGGTTTTCCC
++
++''$#&%$%#$##&$$($#&#$$#
+@1378_155_1689/1
+TTGGGAGGGAGAGAGACTAGACCG
++
+?4@@4<<??<?-@4@=4<5<?:/>
+@1378_157_1580/1
+TGGGCCTCGGTGCCCTTGGTCTGT
++
+#%)$##'#$$$&#####%#$#$##
+@1378_161_317/1
+TTGGCCGGCAACCCCGGTACCTAA
++
+7<,<'@)@>.)2@/')'&(?/-<(
+@1378_177_735/1
+AGTACGCCATGTATTTGCGACCAG
++
+=?@?C<88@=>:7>@55/.,416,
+@1378_181_1684/1
+CGACTCCCGCATTCACGGTCAAGT
++
+&*#,##$#&$*$$#$#$$$#%$##
+@1378_187_1407/1
+TGGCGTCCACTCGTGGGTCTATCG
++
+$#$'%#$%$%&$%#####$#$#%#
+@1378_203_721/1
+CCTAAATAACCCAGGGTAAAAGAT
++
+9<1+2+1@=259@+;2.71&@+2&
+@1378_206_2039/1
+CCCCCCCCCCCCCCCCCCCCCCCC
++
+9@?8>;>>><<994;=895895-8

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/s2fq_paired_F3.csfasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/s2fq_paired_F3.csfasta Sat Feb 21 16:33:42 2015 +0100

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/s2fq_paired_F3_QV.qualsolid
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/s2fq_paired_F3_QV.qualsolid Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,99 @@
+# Fri Jan 23 21:37:16 2009 /share/apps/corona/bin/filter_fasta.pl --output=/data/results/0176/0176_20090114_1/skmusc_cov_25/results.01/primary.20090124033450140 --name=0176_20090114_1_skmusc_cov_25_ --tag=F3 --minlength=25 --mask=1111111111111111111111111 --prefix=T /data/results/0176/0176_20090114_1/skmusc_cov_25/jobs/postPrimerSetPrimary.1708/rawseq
+# Cwd: /home/pipeline
+# Title: 0176_20090114_1_skmusc_cov_25_
+>1378_11_329_F3
+7 4 2 2 10 6 2 2 2 2 2 2 2 4 2 2 2 3 2 3 2 2 3 7 2
+>1378_17_1788_F3
+6 2 6 2 3 3 2 3 2 2 2 4 4 2 2 3 3 3 3 2 2 2 2 2 2
+>1378_25_2035_F3
+9 2 4 2 6 2 2 3 2 3 2 2 5 4 2 4 3 3 3 4 2 4 2 6 2
+>1378_28_770_F3
+2 4 2 2 7 2 3 3 2 4 3 2 3 4 2 2 2 3 4 4 3 2 2 3 2
+>1378_33_1945_F3
+18 10 24 26 21 19 17 23 22 22 23 23 22 20 17 22 24 21 14 20 22 21 18 20 17
+>1378_34_789_F3
+2 2 3 2 2 4 2 3 2 2 3 5 3 2 4 2 2 3 2 2 3 2 2 2 3
+>1378_35_263_F3
+3 8 11 11 2 4 6 3 8 6 12 7 4 5 4 6 4 6 11 4 4 5 5 7 5
+>1378_43_186_F3
+2 2 3 7 19 4 3 2 2 2 2 2 2 2 2 3 2 3 2 2 2 3 3 3 2
+>1378_51_1671_F3
+2 2 2 3 2 3 4 2 2 2 4 4 2 4 2 3 2 2 3 3 2 2 2 2 2
+>1378_56_324_F3
+3 14 10 2 9 9 2 2 2 4 4 2 2 4 2 2 2 2 2 3 3 3 2 3 2
+>1378_56_773_F3
+9 5 4 2 4 2 2 4 4 2 2 2 2 2 5 2 3 4 2 2 3 4 2 2 3
+>1378_62_2027_F3
+9 7 2 5 5 3 2 2 3 3 2 3 4 2 4 3 3 3 2 3 2 2 2 6 2
+>1378_62_2029_F3
+4 3 4 3 3 2 2 2 2 3 2 2 3 3 2 8 2 2 4 4 2 3 2 2 2
+>1378_67_1795_F3
+33 33 31 34 17 31 31 30 26 12 31 31 16 29 6 32 31 31 24 16 31 13 31 16 6
+>1378_68_466_F3
+4 2 7 4 8 10 2 2 3 2 3 2 4 2 10 3 4 2 2 3 2 2 2 2 2
+>1378_68_1692_F3
+3 2 2 2 8 4 6 5 4 2 2 3 2 2 2 4 2 2 2 2 2 2 2 3 2
+>1378_80_664_F3
+8 22 2 4 2 2 2 3 3 21 2 2 2 2 2 2 2 3 2 2 3 3 3 2 2
+>1378_85_1786_F3
+6 8 5 13 8 2 18 4 31 3 5 4 12 11 17 2 5 10 13 12 4 15 5 13 14
+>1378_86_1011_F3
+2 2 2 2 2 2 2 3 4 2 2 3 3 3 4 2 2 2 4 2 3 2 2 2 2
+>1378_86_1789_F3
+31 21 16 30 16 26 31 14 29 31 27 28 14 7 13 22 6 7 27 20 31 28 4 3 28
+>1378_91_1596_F3
+4 9 5 10 6 2 24 6 7 4 9 6 2 14 14 11 5 27 8 11 14 8 6 9 2
+>1378_94_1595_F3
+8 12 28 13 13 20 11 18 23 17 21 5 9 10 13 10 2 10 2 4 4 21 26 4 2
+>1378_95_1039_F3
+2 3 2 2 13 2 3 2 2 3 3 2 4 3 2 3 4 4 3 2 2 2 3 8 3
+>1378_95_1767_F3
+12 23 21 27 21 20 27 19 27 34 17 22 14 3 20 10 2 26 12 3 10 2 17 4 3
+>1378_96_1037_F3
+2 3 2 3 6 2 2 3 3 3 2 4 3 3 2 4 2 2 2 10 2 2 3 2 3
+>1378_96_1764_F3
+29 21 12 24 6 27 2 10 23 16 30 10 9 27 23 12 28 21 24 5 21 26 9 18 8
+>1378_98_1574_F3
+2 3 3 2 10 5 3 3 2 2 2 2 4 3 3 3 2 2 2 3 4 2 4 4 2
+>1378_107_1647_F3
+2 5 2 3 3 2 3 7 13 2 4 2 3 3 2 2 2 2 5 3 4 2 2 7 3
+>1378_111_829_F3
+2 4 2 4 2 2 4 2 3 4 2 3 2 4 2 2 2 3 3 2 2 5 2 3 3
+>1378_111_1900_F3
+10 3 5 4 9 3 2 7 2 8 2 2 3 2 6 2 2 4 7 2 2 3 2 3 4
+>1378_112_1483_F3
+9 4 2 3 10 2 4 2 5 2 3 2 2 2 2 2 4 2 2 2 2 4 3 2 2
+>1378_125_1287_F3
+4 3 2 2 16 18 3 6 4 2 3 2 2 2 3 3 2 2 2 3 3 3 2 5 2
+>1378_126_468_F3
+23 22 29 31 18 16 23 30 28 11 28 23 31 19 24 20 22 24 30 13 13 22 11 22 8
+>1378_127_664_F3
+9 2 2 6 2 3 2 2 2 2 2 2 3 3 4 2 2 2 2 2 2 3 3 3 2
+>1378_129_463_F3
+4 23 8 11 11 27 21 7 12 12 8 27 7 8 20 5 13 5 14 23 10 26 13 17 10
+>1378_129_875_F3
+2 2 3 7 3 2 2 4 2 2 2 2 4 3 2 3 2 2 2 2 2 3 2 2 2
+>1378_140_1251_F3
+12 2 3 4 16 2 3 3 3 2 2 3 2 2 3 2 3 2 3 2 2 3 4 3 3
+>1378_141_809_F3
+7 4 5 11 12 2 2 3 3 2 7 4 2 2 2 3 2 3 3 6 2 2 2 6 2
+>1378_144_983_F3
+11 12 3 7 5 4 9 3 2 9 2 8 8 2 3 3 3 2 4 4 3 2 3 2 2
+>1378_153_270_F3
+8 10 6 6 3 2 5 4 3 4 2 3 2 2 5 3 3 7 3 2 5 2 3 3 2
+>1378_155_1689_F3
+31 30 19 31 31 19 27 27 30 30 27 30 12 31 19 31 28 19 27 20 27 30 25 14 29
+>1378_157_1580_F3
+3 2 4 8 3 2 2 6 2 3 3 3 5 2 2 2 2 2 4 2 3 2 3 2 2
+>1378_161_317_F3
+8 22 27 11 27 6 31 8 31 29 13 8 17 31 14 6 8 6 5 7 30 14 12 27 7
+>1378_177_735_F3
+31 28 30 31 30 34 27 23 23 31 28 29 25 22 29 31 20 20 14 13 11 19 16 21 11
+>1378_181_1684_F3
+13 5 9 2 11 2 2 3 2 5 3 9 3 3 2 3 2 3 3 3 2 4 3 2 2
+>1378_187_1407_F3
+2 3 2 3 6 4 2 3 4 3 4 5 3 4 2 2 2 2 2 3 2 3 2 4 2
+>1378_203_721_F3
+33 24 27 16 10 17 10 16 31 28 17 20 24 31 10 26 17 13 22 16 5 31 10 17 5
+>1378_206_2039_F3
+26 24 31 30 23 29 26 29 29 29 27 27 24 24 19 26 28 23 24 20 23 24 20 12 23

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/s2fq_paired_R3.csfasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/s2fq_paired_R3.csfasta Sat Feb 21 16:33:42 2015 +0100

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/s2fq_paired_R3_QV.qualsolid
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/s2fq_paired_R3_QV.qualsolid Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,99 @@
+# Mon Jan 19 06:35:55 2009 /share/apps/corona/bin/filter_fasta.pl --output=/data/results/0176/0176_20090114_1/skmusc_cov_25/results.01/primary.20090119120505312 --name=0176_20090114_1_skmusc_cov_25_ --tag=R3 --minlength=25 --mask=1111111111111111111111111 --prefix=G /data/results/0176/0176_20090114_1/skmusc_cov_25/jobs/postPrimerSetPrimary.1512/rawseq
+# Cwd: /home/pipeline
+# Title: 0176_20090114_1_skmusc_cov_25_
+>1378_11_329_R3
+2 2 2 2 3 3 2 3 2 3 5 2 2 2 2 2 3 6 3 2 3 2 2 2 3
+>1378_17_1788_R3
+2 2 3 2 3 2 2 2 3 2 3 2 2 2 2 2 2 2 3 2 3 2 2 2 2
+>1378_25_2035_R3
+2 2 2 2 2 2 2 4 2 3 4 2 3 3 2 2 2 7 3 2 2 2 5 5 4
+>1378_28_770_R3
+2 2 2 2 3 2 2 4 4 3 2 2 2 2 4 2 4 3 2 4 4 2 7 3 3
+>1378_33_1945_R3
+26 13 21 26 30 26 20 20 21 24 22 29 23 22 22 24 19 20 22 24 23 21 17 21 19
+>1378_34_789_R3
+3 2 2 2 4 3 4 3 4 4 2 2 2 3 2 2 2 2 3 2 2 2 3 2 5
+>1378_35_263_R3
+7 3 4 4 5 11 8 18 14 8 4 3 12 21 6 3 5 20 5 2 3 6 6 20 13
+>1378_43_186_R3
+2 3 4 2 3 2 2 2 2 2 2 2 2 4 2 2 4 2 3 2 2 2 6 2 6
+>1378_51_1671_R3
+2 2 2 4 3 3 2 2 2 2 3 2 2 2 2 2 2 2 2 3 2 2 15 2 2
+>1378_56_324_R3
+2 2 3 2 2 2 2 2 3 3 3 2 3 3 3 3 2 2 4 2 2 2 9 7 2
+>1378_56_773_R3
+4 2 2 4 4 2 5 3 2 2 2 3 2 3 2 2 4 3 2 2 2 2 4 4 3
+>1378_62_2027_R3
+10 9 2 2 8 11 14 4 2 2 3 8 2 4 2 2 16 3 2 6 4 13 2 5 2
+>1378_62_2029_R3
+8 14 3 3 3 28 7 2 2 2 2 4 2 2 2 2 8 3 3 4 3 12 5 4 2
+>1378_67_1795_R3
+33 31 31 13 30 22 31 31 31 13 31 25 31 32 27 27 29 29 28 29 22 15 27 31 22
+>1378_68_466_R3
+12 14 2 2 3 15 24 2 3 2 13 28 3 2 3 22 21 10 3 4 16 6 2 2 2
+>1378_68_1692_R3
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diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/s2fq_phiX.csfasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/s2fq_phiX.csfasta Sat Feb 21 16:33:42 2015 +0100

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diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/s2fq_phiX.qualsolid
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/s2fq_phiX.qualsolid Sat Feb 21 16:33:42 2015 +0100

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17 \n+>1831_574_1103_F3\n+31 30 30 29 30 31 28 29 31 31 32 27 29 30 28 31 28 28 2'..b' 17 27 \n+>1831_576_1168_F3\n+29 31 34 34 21 31 31 17 30 24 28 29 22 30 26 22 21 27 26 19 21 22 31 26 24 11 15 4 17 21 6 6 11 19 3 \n+>1831_576_1207_F3\n+4 3 29 17 11 7 5 30 19 30 7 11 31 25 27 5 11 31 29 30 3 5 25 23 32 4 4 28 15 13 4 11 20 24 22 \n+>1831_576_1289_F3\n+31 24 27 29 16 33 31 31 26 22 31 31 21 21 18 28 28 17 23 11 20 6 25 23 27 27 11 13 28 17 29 29 13 20 15 \n+>1831_576_1329_F3\n+27 29 5 15 11 23 22 15 14 32 31 31 14 20 13 26 28 26 25 6 5 31 18 6 5 3 3 4 11 10 2 7 3 5 17 \n+>1831_576_1367_F3\n+30 30 31 31 27 29 31 31 28 31 27 31 27 28 31 29 31 30 30 24 25 30 27 28 29 28 27 23 26 20 24 31 22 23 22 \n+>1831_576_1416_F3\n+10 6 26 30 13 13 16 13 27 31 6 13 28 10 21 13 20 30 22 27 15 12 30 22 26 7 4 28 29 20 21 13 24 23 31 \n+>1831_576_1461_F3\n+2 16 5 22 19 2 7 2 7 5 2 2 3 2 11 6 2 2 2 4 2 4 4 2 9 2 5 4 4 2 2 4 4 4 6 \n+>1831_576_1605_F3\n+21 27 31 34 31 31 29 16 26 31 25 26 27 27 31 31 24 31 30 30 30 24 27 18 30 20 12 17 16 28 19 23 22 22 11 \n+>1831_576_1664_F3\n+31 31 30 29 30 31 28 32 25 31 31 29 31 28 6 28 27 29 28 8 13 29 28 24 9 23 8 7 22 2 14 10 10 26 8 \n+>1831_576_1671_F3\n+31 31 30 31 20 29 31 31 23 5 23 30 17 20 2 5 8 5 20 5 5 8 16 20 5 5 11 5 19 4 5 11 5 21 4 \n+>1831_576_1729_F3\n+31 30 31 30 27 30 27 31 29 32 30 14 28 28 30 29 30 22 29 30 31 23 27 30 31 29 24 24 26 29 27 10 15 28 29 \n+>1831_576_1880_F3\n+15 20 16 20 14 22 24 17 11 25 11 22 14 4 14 15 20 11 4 3 8 25 10 2 23 4 17 7 16 22 20 19 8 8 18 \n+>1831_576_1982_F3\n+11 31 31 30 31 11 32 29 27 31 24 31 28 30 31 24 33 28 23 27 21 31 31 21 31 17 27 32 30 29 13 22 27 10 31 \n+>1831_576_1987_F3\n+8 2 2 7 8 7 2 5 2 2 8 4 8 14 12 2 4 3 16 16 2 4 18 29 6 2 2 5 3 11 2 3 3 6 10 \n+>1831_576_2014_F3\n+31 31 31 24 11 33 17 24 12 20 29 6 30 11 10 30 22 24 10 14 32 6 26 6 17 31 6 20 5 14 24 11 21 5 16 \n+>1831_576_2028_F3\n+20 27 29 24 29 20 6 17 7 5 22 15 22 13 23 2 5 5 18 24 11 15 4 22 14 2 7 2 11 9 4 5 20 9 10 \n+>1831_577_40_F3\n+24 17 14 19 7 6 13 6 8 7 27 9 30 2 3 8 4 5 27 11 14 18 24 27 7 13 17 11 10 27 28 31 21 16 16 \n+>1831_577_119_F3\n+24 29 30 34 16 16 8 12 16 14 8 2 26 2 14 11 23 20 15 9 10 13 10 3 3 20 20 20 15 10 4 12 13 19 15 \n+>1831_577_133_F3\n+14 19 31 29 29 30 28 16 30 25 10 29 31 15 22 31 31 29 27 29 31 9 27 10 16 31 16 20 8 24 21 6 17 3 8 \n+>1831_577_255_F3\n+22 27 28 23 22 31 29 21 24 4 9 9 2 5 2 12 10 3 13 2 5 5 2 10 3 12 10 4 5 4 13 11 4 20 2 \n+>1831_577_281_F3\n+22 12 25 33 26 23 31 28 26 29 22 31 29 19 30 28 30 10 21 20 24 30 26 20 27 22 30 26 24 31 23 7 29 25 30 \n+>1831_577_288_F3\n+20 26 14 22 24 30 30 5 28 33 25 25 17 24 23 9 21 13 22 14 10 19 5 17 16 11 22 11 21 30 13 22 2 6 21 \n+>1831_577_322_F3\n+24 28 26 29 19 20 15 21 26 17 20 20 19 21 19 12 27 2 22 10 16 24 19 5 17 27 30 21 20 24 21 23 8 22 14 \n+>1831_577_362_F3\n+21 17 33 30 25 31 30 31 27 30 24 20 23 28 11 18 25 11 24 15 25 5 6 12 24 24 11 21 27 20 13 7 3 10 21 \n+>1831_577_382_F3\n+16 17 24 20 22 14 25 16 8 8 28 22 21 7 9 17 19 26 11 18 10 25 27 13 5 13 5 12 28 16 28 17 14 20 9 \n+>1831_577_464_F3\n+18 28 27 22 14 27 23 17 21 8 29 2 13 6 5 19 17 15 19 10 20 2 14 15 19 16 13 22 9 24 16 5 22 20 21 \n+>1831_577_488_F3\n+25 19 23 13 11 9 29 21 20 21 21 27 30 23 28 27 28 27 17 29 21 26 24 19 29 26 28 24 29 31 23 24 17 19 31 \n+>1831_577_511_F3\n+2 22 14 10 5 3 25 27 22 4 21 11 3 3 4 6 4 14 10 8 2 3 22 7 7 5 9 18 29 16 21 6 15 14 10 \n+>1831_577_545_F3\n+29 29 27 27 24 30 27 29 30 32 27 19 23 16 31 27 31 23 28 28 31 22 21 14 21 16 27 24 20 13 20 24 23 23 12 \n+>1831_577_559_F3\n+13 27 31 26 30 30 31 29 31 30 14 17 27 13 31 16 28 29 16 17 28 21 16 14 26 28 30 13 5 17 10 24 17 8 6 \n+>1831_577_562_F3\n+2 7 7 5 9 5 15 4 8 16 4 8 2 7 3 17 12 11 9 9 9 4 14 12 11 11 8 8 5 11 12 13 16 6 9 \n+>1831_577_637_F3\n+23 12 11 19 2 29 25 12 21 10 25 23 11 5 7 20 26 18 28 15 29 22 28 21 23 5 16 14 24 5 6 30 26 19 11 \n+>1831_577_641_F3\n+5 19 22 26 14 6 25 32 26 26 20 30 25 22 17 11 7 28 8 11 2 9 30 10 13 2 5 22 3 23 2 4 22 14 6 \n+>1831_577_692_F3\n+31 33 11 31 30 31 33 7 31 32 30 31 10 31 31 29 31 10 30 28 29 31 6 28 27 31 27 28 27 24 28 30 22 20 27\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/scatterplot_in1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/scatterplot_in1.tabular Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,10 @@
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diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/scatterplot_out1.pdf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/secure_hash_message_digest_out1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/secure_hash_message_digest_out1.tabular Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,2 @@
+#md5 sha1 sha224 sha384 sha512
+29e9dd693af0a946e67cd1861b987d13 2d7dcdb10964872752bd6d081725792b3f729ac9 fc28953b6a54a8e2dffce962fa21e3600e91a743eaf3c67164c906e6 957b57a744d074321c475adc134bcf7fa80437f8fb4eb3fcb52971461c5ac24bbda6c3c234ca6614ee1fc4bb6f676a6b 9be59f9dc30bc2b35016dc45f5726a249baef2cdee2eb840665d3cdf4d0a0539c50eea1aa96bfd84f3a619782fc9321e5817e005a8a30c318d45c6759c9601bd

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/sff_converter_fasta.dat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/sff_converter_fasta.dat Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,6 @@
+>GGOQ6K301BJT46
+gactACACGTAGTATAAGCTAAATGTTGGAGAGGATGCTGTAATCAACGTTTTGTGTCTCCTTACAGGACACCAGCTGATTTGGAGGTCATCCAATATAAACCTGGCTGGAACTTGCTATGGTTAGGAGAGCTATGAATGGAAGAGATAATTCCATTATTTAATAAGGCTACAGACAAATTAGGACAAGAAGCAGCTATTAGATTATTTAGTGCTAGCACACCTAAATAGAGAGAGATAAATTCATTAGACTTTTTGCTAttttattgacttttggagagacagtatttaaagtaccaaatcccagaggttgcctatgttggtggtgttgcaagctctattattggcgattgcaatctaccttatccataagttctgcttagagattatttgttattaattttcatctacatcaataaatataggacagtaaggattttgtacaaaatagacaatgggataggtaccagaagaggacagaggaattactggtattttgatatagactacactaacgtacgtacgtaggaattttaaccgggg
+>GGOQ6K301AWPXS
+gactACGTACACACTGGAATAAAATGGAGTTTTCATACTAGAGATTATTATATGGGCTATGTAAAAGAACTAGTAGCAGGATCTAGCACACCAGACAGCCTAAGACTGTATATTTTATATAAGCAACCCGTTATGGCATGGGAAATATCGCCCAGGGTTAAAAAATTTTAACAAGGAATGGCCTTTTTGTAAATATGTGGATAAAAAACAGGGTTCATGTGGGATGATATTGAAAAACAAAAGATTTGCGTAGGAGGAGAAATATCACCAGGATGGGGACCTGGAATGGTTGGCATAGCAAATAAAAGCCTTTAGTTGTGGGGAGAGAAAAATCGAGGCAACTCCTGTTATGATTATAAGAGAAGAGATAGATCCCAAAAAATGGTGTGGAGATTGTTGGAATTTAATGTGTCTTAGAAACTCACCTCCAGGAACGTTGTCAAAGACTCGCTATGTTGGCATGTGGACGGaaagactaaatgttggagaggatgctgtatcaacgttttgttgtcgtccttacacggacaccagctgtagttgtctgtagnttttaccggg
+>GGOQ6K301A8J46
+gactACTATACGAGTCTGCCAATCTTCTTCACTCATCCCCTTCAGGAAGAGTGCAGGGTTCTGGGACTCTCCGTATGTGCCTCCTAGGTACAAGAAAATATCCCCTCTCTTCATCCTTTAATAACACTGATCCTTGTCCCCAATACTCTACTCTCATTGGTCCTTTCCAATTTTTGTCTTTTTTGATCTTTATAGTAAATCCACTGACCTTGCAATTTGCTTGGAATTTGAGAAAAATAATCCTGTATTCTTAATGATTCTTGTTGTGTTAATAATTCATATGGGGGCCATTCCCCCTATTCTACCCCTTTGTTTAAAATTAAGGCAATGCAGAGCGAGAGCCAAAGCATTGTCTAAAGATGTTGTTTCAGGCAAAAACTTCTGAATCCAACACTTTAAAGTATTATTggcattttcaaccaaagcttgagtattgagggttgcctggtattccaaatttatgttttattccctatgtaattgtagtaaaccttcctattttttgattttctaaaatttggtccctattgttctgtttgctagttctgtaactattatgagtccaacctgtttagg

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/sff_converter_fastq.dat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/sff_converter_fastq.dat Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,12 @@
+@GGOQ6K301BJT46
+gactACACGTAGTATAAGCTAAATGTTGGAGAGGATGCTGTAATCAACGTTTTGTGTCTCCTTACAGGACACCAGCTGATTTGGAGGTCATCCAATATAAACCTGGCTGGAACTTGCTATGGTTAGGAGAGCTATGAATGGAAGAGATAATTCCATTATTTAATAAGGCTACAGACAAATTAGGACAAGAAGCAGCTATTAGATTATTTAGTGCTAGCACACCTAAATAGAGAGAGATAAATTCATTAGACTTTTTGCTAttttattgacttttggagagacagtatttaaagtaccaaatcccagaggttgcctatgttggtggtgttgcaagctctattattggcgattgcaatctaccttatccataagttctgcttagagattatttgttattaattttcatctacatcaataaatataggacagtaaggattttgtacaaaatagacaatgggataggtaccagaagaggacagaggaattactggtattttgatatagactacactaacgtacgtacgtaggaattttaaccgggg
++
+FFFFFFFFFFFFFFFIIIIIHHHHHFFBBBFEDDFFFFFHHGFFFFFFF????FFFFFFDDFFFFF<==<ADDDDDDAC8::DCDFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFDDDFFFFFFFFFFFFFFFFFFFFFFA@@FFFFFFDD?????AAAAAB=??ADAACFFFFFDDDFFFFFFFFFDDDD544??8888000<2449=:<<?@841114?>AAAA?:::A???DBBA:::A?A//...::33,,,,------,,,,;;:89=9:9733...2223//9<688<444<AA::::8::BBAA@@>>>43434<4444449??@AA@BBBA:8:<A998<?4448<<<<244<3338<<>:884433822255,,,3--3,,,,,,,,,3774,,,33043///0,,,,,,,,,,,,111,,,,,),0....0),,,.,,,,,,,143.,,,.---86---20787777870206433,,,,,0,,,,,,,0..,,,...3,,,,-44444489965225666----
+@GGOQ6K301AWPXS
+gactACGTACACACTGGAATAAAATGGAGTTTTCATACTAGAGATTATTATATGGGCTATGTAAAAGAACTAGTAGCAGGATCTAGCACACCAGACAGCCTAAGACTGTATATTTTATATAAGCAACCCGTTATGGCATGGGAAATATCGCCCAGGGTTAAAAAATTTTAACAAGGAATGGCCTTTTTGTAAATATGTGGATAAAAAACAGGGTTCATGTGGGATGATATTGAAAAACAAAAGATTTGCGTAGGAGGAGAAATATCACCAGGATGGGGACCTGGAATGGTTGGCATAGCAAATAAAAGCCTTTAGTTGTGGGGAGAGAAAAATCGAGGCAACTCCTGTTATGATTATAAGAGAAGAGATAGATCCCAAAAAATGGTGTGGAGATTGTTGGAATTTAATGTGTCTTAGAAACTCACCTCCAGGAACGTTGTCAAAGACTCGCTATGTTGGCATGTGGACGGaaagactaaatgttggagaggatgctgtatcaacgttttgttgtcgtccttacacggacaccagctgtagttgtctgtagnttttaccggg
++
+FFFFFFFFFFFFFDDDFFD@3333BAA?95558HFFFFFHIIIIIIIHIIIHH?;;A???940000836?AAABDFFFFFFFFFFFFA@@FFFFFFFFFF===?<?????88111119??????ADCCCCAAAAAAAAB555:::?>CFD==;A<9966,,,,,,,,,,,,=887766=;;22-----<466694?ABAAAD666666D7FFFFFFFFFF666FFFF?;;:A;<<75B....D7333<@A@?888<AA==;;<7@><;;<688<00009<>???<<<===<<897==73...3----:99666:>7996/////-<<11202>??AA=:55448BBB===AAADDDDDAA>>===DB@>9723000,,,,,,300004;;><<:99666666.,,,,/7600,,,9922/33000020.00011742---223380220786646770---0331.00..,,,,,,0,,,,,,,..0144330,,,0.0,,,,,,,,,,,)),,,,,,1..,,,,,,,...,,,,,,.,,,,,,,,,,,,!//,--226::
+@GGOQ6K301A8J46
+gactACTATACGAGTCTGCCAATCTTCTTCACTCATCCCCTTCAGGAAGAGTGCAGGGTTCTGGGACTCTCCGTATGTGCCTCCTAGGTACAAGAAAATATCCCCTCTCTTCATCCTTTAATAACACTGATCCTTGTCCCCAATACTCTACTCTCATTGGTCCTTTCCAATTTTTGTCTTTTTTGATCTTTATAGTAAATCCACTGACCTTGCAATTTGCTTGGAATTTGAGAAAAATAATCCTGTATTCTTAATGATTCTTGTTGTGTTAATAATTCATATGGGGGCCATTCCCCCTATTCTACCCCTTTGTTTAAAATTAAGGCAATGCAGAGCGAGAGCCAAAGCATTGTCTAAAGATGTTGTTTCAGGCAAAAACTTCTGAATCCAACACTTTAAAGTATTATTggcattttcaaccaaagcttgagtattgagggttgcctggtattccaaatttatgttttattccctatgtaattgtagtaaaccttcctattttttgattttctaaaatttggtccctattgttctgtttgctagttctgtaactattatgagtccaacctgtttagg
++
+FFFFFFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIFFFFIIIIIIIIIIIIFHFFFFFFFF:::DFFFFFFFFFFFFFDDDFFFFAAABBDD=3333=7B::99?7BBBBBA?4400088/0008??BDDDDFFFFDDBBFFFFFFFFFFFFFFFFFFFFFF???DDB@--,,,=/7,,,,,-::==68<BAFFFFFFFDDDFFFFFFFFFDDD???FFFFDBA>999?94/////>34=;;?>?ABBB5666=BBBB?><=<<986....255---3==8,,,,,--357,,,,-8766=<=2444000977757664400554444<<?@@BDDDDDAAA???AAAAA555:???D<??>DD===DD88833553B443238<76654222....,07/166622///345429:<8888022263,,,.1300,,,00,0034413..,,,,-330-,000207..2220202.344.0.0.00027:----8://22--00,,,,,),,,,,,,00-000.0..00,,,0,,,.0430,,,.2022611...143,,,,,,,,,,000000

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/sff_converter_qual.dat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/sff_converter_qual.dat Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,6 @@
+>GGOQ6K301BJT46
+37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 40 40 40 40 40 39 39 39 39 39 37 37 33 33 33 37 36 35 35 37 37 37 37 37 39 39 38 37 37 37 37 37 37 37 30 30 30 30 37 37 37 37 37 37 35 35 37 37 37 37 37 27 28 28 27 32 35 35 35 35 35 35 32 34 23 25 25 35 34 35 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 35 35 35 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 32 31 31 37 37 37 37 37 37 35 35 30 30 30 30 30 32 32 32 32 32 33 28 30 30 32 35 32 32 34 37 37 37 37 37 35 35 35 37 37 37 37 37 37 37 37 37 35 35 35 35 20 19 19 30 30 23 23 23 23 15 15 15 27 17 19 19 24 28 25 27 27 30 31 23 19 16 16 16 19 30 29 32 32 32 32 30 25 25 25 32 30 30 30 35 33 33 32 25 25 25 32 30 32 14 14 13 13 13 25 25 18 18 11 11 11 11 12 12 12 12 12 12 11 11 11 11 26 26 25 23 24 28 24 25 24 22 18 18 13 13 13 17 17 17 18 14 14 24 27 21 23 23 27 19 19 19 27 32 32 25 25 25 25 23 25 25 33 33 32 32 31 31 29 29 29 19 18 19 18 19 27 19 19 19 19 19 19 24 30 30 31 32 32 31 33 33 33 32 25 23 25 27 32 24 24 23 27 30 19 19 19 23 27 27 27 27 17 19 19 27 18 18 18 23 27 27 29 25 23 23 19 19 18 18 23 17 17 17 20 20 11 11 11 18 12 12 18 11 11 11 11 11 11 11 11 11 18 22 22 19 11 11 11 18 18 15 19 18 14 14 14 15 11 11 11 11 11 11 11 11 11 11 11 11 16 16 16 11 11 11 11 11 8 11 15 13 13 13 13 15 8 11 11 11 13 11 11 11 11 11 11 11 16 19 18 13 11 11 11 13 12 12 12 23 21 12 12 12 17 15 22 23 22 22 22 22 23 22 15 17 15 21 19 18 18 11 11 11 11 11 15 11 11 11 11 11 11 11 15 13 13 11 11 11 13 13 13 18 11 11 11 11 12 19 19 19 19 19 19 23 24 24 21 20 17 17 20 21 21 21 12 12 12 12
+>GGOQ6K301AWPXS
+37 37 37 37 37 37 37 37 37 37 37 37 37 35 35 35 37 37 35 31 18 18 18 18 33 32 32 30 24 20 20 20 23 39 37 37 37 37 37 39 40 40 40 40 40 40 40 39 40 40 40 39 39 30 26 26 32 30 30 30 24 19 15 15 15 15 23 18 21 30 32 32 32 33 35 37 37 37 37 37 37 37 37 37 37 37 37 32 31 31 37 37 37 37 37 37 37 37 37 37 28 28 28 30 27 30 30 30 30 30 23 23 16 16 16 16 16 24 30 30 30 30 30 30 32 35 34 34 34 34 32 32 32 32 32 32 32 32 33 20 20 20 25 25 25 30 29 34 37 35 28 28 26 32 27 24 24 21 21 11 11 11 11 11 11 11 11 11 11 11 11 28 23 23 22 22 21 21 28 26 26 17 17 12 12 12 12 12 27 19 21 21 21 24 19 30 32 33 32 32 32 35 21 21 21 21 21 21 35 22 37 37 37 37 37 37 37 37 37 37 21 21 21 37 37 37 37 30 26 26 25 32 26 27 27 22 20 33 13 13 13 13 35 22 18 18 18 27 31 32 31 30 23 23 23 27 32 32 28 28 26 26 27 22 31 29 27 26 26 27 21 23 23 27 15 15 15 15 24 27 29 30 30 30 27 27 27 28 28 28 27 27 23 24 22 28 28 22 18 13 13 13 18 12 12 12 12 25 24 24 21 21 21 25 29 22 24 24 21 14 14 14 14 14 12 27 27 16 16 17 15 17 29 30 30 32 32 28 25 20 20 19 19 23 33 33 33 28 28 28 32 32 32 35 35 35 35 35 32 32 29 29 28 28 28 35 33 31 29 24 22 17 18 15 15 15 11 11 11 11 11 11 18 15 15 15 15 19 26 26 29 27 27 25 24 24 21 21 21 21 21 21 13 11 11 11 11 14 22 21 15 15 11 11 11 24 24 17 17 14 18 18 15 15 15 15 17 15 13 15 15 15 16 16 22 19 17 12 12 12 17 17 18 18 23 15 17 17 15 22 23 21 21 19 21 22 22 15 12 12 12 15 18 18 16 13 15 15 13 13 11 11 11 11 11 11 15 11 11 11 11 11 11 11 13 13 15 16 19 19 18 18 15 11 11 11 15 13 15 11 11 11 11 11 11 11 11 11 11 11 8 8 11 11 11 11 11 11 16 13 13 11 11 11 11 11 11 11 13 13 13 11 11 11 11 11 11 13 11 11 11 11 11 11 11 11 11 11 11 11 0 14 14 11 12 12 17 17 21 25 25
+>GGOQ6K301A8J46
+37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 37 37 37 37 40 40 40 40 40 40 40 40 40 40 40 40 37 39 37 37 37 37 37 37 37 37 25 25 25 35 37 37 37 37 37 37 37 37 37 37 37 37 37 35 35 35 37 37 37 37 32 32 32 33 33 35 35 28 18 18 18 18 28 22 33 25 25 24 24 30 22 33 33 33 33 33 32 30 19 19 15 15 15 23 23 14 15 15 15 23 30 30 33 35 35 35 35 37 37 37 37 35 35 33 33 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 30 30 30 35 35 33 31 12 12 11 11 11 28 14 22 11 11 11 11 11 12 25 25 28 28 21 23 27 33 32 37 37 37 37 37 37 37 35 35 35 37 37 37 37 37 37 37 37 37 35 35 35 30 30 30 37 37 37 37 35 33 32 29 24 24 24 30 24 19 14 14 14 14 14 29 18 19 28 26 26 30 29 30 32 33 33 33 20 21 21 21 28 33 33 33 33 30 29 27 28 27 27 24 23 21 13 13 13 13 17 20 20 12 12 12 18 28 28 23 11 11 11 11 11 12 12 18 20 22 11 11 11 11 12 23 22 21 21 28 27 28 17 19 19 19 15 15 15 24 22 22 22 20 22 21 21 19 19 15 15 20 20 19 19 19 19 27 27 30 31 31 33 35 35 35 35 35 32 32 32 30 30 30 32 32 32 32 32 20 20 20 25 30 30 30 35 27 30 30 29 35 35 28 28 28 35 35 23 23 23 18 18 20 20 18 33 19 19 18 17 18 23 27 22 21 21 20 19 17 17 17 13 13 13 13 11 15 22 14 16 21 21 21 17 17 14 14 14 18 19 20 19 17 24 25 27 23 23 23 23 15 17 17 17 21 18 11 11 11 13 16 18 15 15 11 11 11 15 15 11 15 15 18 19 19 16 18 13 13 11 11 11 11 12 18 18 15 12 11 15 15 15 17 15 22 13 13 17 17 17 15 17 15 17 13 18 19 19 13 15 13 15 13 15 15 15 17 22 25 12 12 12 12 23 25 14 14 17 17 12 12 15 15 11 11 11 11 11 8 11 11 11 11 11 11 11 15 15 12 15 15 15 13 15 13 13 15 15 11 11 11 15 11 11 11 13 15 19 18 15 11 11 11 13 17 15 17 17 21 16 16 13 13 13 16 19 18 11 11 11 11 11 11 11 11 11 11 15 15 15 15 15 15

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/sff_converter_xml_1.dat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/sff_converter_xml_1.dat Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,18 @@
+<?xml version="1.0"?>
+<trace_volume>
+    <trace>
+        <trace_name>GGOQ6K301BJT46</trace_name>
+        <clip_vector_left>5</clip_vector_left>
+        <clip_vector_right>260</clip_vector_right>
+    </trace>
+    <trace>
+        <trace_name>GGOQ6K301AWPXS</trace_name>
+        <clip_vector_left>5</clip_vector_left>
+        <clip_vector_right>470</clip_vector_right>
+    </trace>
+    <trace>
+        <trace_name>GGOQ6K301A8J46</trace_name>
+        <clip_vector_left>5</clip_vector_left>
+        <clip_vector_right>408</clip_vector_right>
+    </trace>
+</trace_volume>

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/sff_converter_xml_2.dat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/sff_converter_xml_2.dat Sat Feb 21 16:33:42 2015 +0100

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/short_reads_trim_seq_out1.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/short_reads_trim_seq_out1.fasta Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,36 @@
+>EYKX4VC01B65GS length=54 xy=0784_1754 region=1 run=R_2007_11_07_16_15_57_
+TGCCGTGATGAGCGCCACCGGAACGAATTCGACTATGCCGAA
+>EYKX4VC01BNCSP length=187 xy=0558_3831 region=1 run=R_2007_11_07_16_15_57_
+CAGGATTGATCGCCAGATCGGTCGGTGCGTCAGGCGGG
+>EYKX4VC01CD9FT length=115 xy=0865_1719 region=1 run=R_2007_11_07_16_15_57_
+GGCCTGTCGTCCGGCACCTCGCAAGAGCTACAGCAGGCGCGGCTGGCGATCATCGGCGGCACGCCGGCCTATATGTCGCCGGAACACACCACC
+>EYKX4VC01B8FW0 length=95 xy=0799_0514 region=1 run=R_2007_11_07_16_15_57_
+AGAGACCTGAATACGTCAAA
+>EYKX4VC01BCGYW length=115 xy=0434_3926 region=1 run=R_2007_11_07_16_15_57_
+CTGCATGGCGACGAGCTAAA
+>EYKX4VC01AZXC6 length=116 xy=0292_0280 region=1 run=R_2007_11_07_16_15_57_
+GGCCTGTCGTCCGGCACCTCGCAAGAGCTACAGCAGGCGCGGCTGGCGATCATCGGCGGCACGCCGGCCTATATGTCGCCGGAACACACCACC
+>EYKX4VC01CATH5 length=82 xy=0826_0843 region=1 run=R_2007_11_07_16_15_57_
+TTGCACATTCTCGGCCATATCTCTGGACCTACATGACCGATT
+>EYKX4VC01BCEIV length=47 xy=0434_0757 region=1 run=R_2007_11_07_16_15_57_
+TGACGTCGTGCCGAGCTACGACAATGCCGACATG
+>EYKX4VC01BWERM length=83 xy=0662_0304 region=1 run=R_2007_11_07_16_15_57_
+GGCCGAGGTCATGGTGGATCTCGGCCAGG
+>EYKX4VC01BT2O7 length=69 xy=0635_1945 region=1 run=R_2007_11_07_16_15_57_
+GACGCTGTTCAGACCGAACGCGGTAA
+>EYKX4VC01BO0UO length=222 xy=0577_3838 region=1 run=R_2007_11_07_16_15_57_
+CTGCAGTACCGCTTCTGGCTGCACTATGCCGAAGGCTCGCTGATGCCGCTGCTGTTAATGAAGCTGGTGTTCGCCAGCCTGG
+>EYKX4VC01CBCPK length=83 xy=0832_1158 region=1 run=R_2007_11_07_16_15_57_
+GGCCGAGGTCATGGTGGATCTCGGCCAGG
+>EYKX4VC01B474S length=54 xy=0762_2010 region=1 run=R_2007_11_07_16_15_57_
+GAGCGCTGGCGCGCGCGG
+>EYKX4VC01BB4QL length=57 xy=0431_0363 region=1 run=R_2007_11_07_16_15_57_
+AGGAGCTAATTATATGCTCTTGG
+>EYKX4VC01BJ37M length=64 xy=0522_0192 region=1 run=R_2007_11_07_16_15_57_
+TCGAGTATGTATCAAGGACTACATACAA
+>EYKX4VC01BV9R8 length=54 xy=0660_2038 region=1 run=R_2007_11_07_16_15_57_
+CTATTCAGCAGCACTGCGTT
+>EYKX4VC01CEPP8 length=60 xy=0870_2350 region=1 run=R_2007_11_07_16_15_57_
+TCCTCACGTTGTTGTTAGTGTCAG
+>EYKX4VC01BTLME length=78 xy=0630_0292 region=1 run=R_2007_11_07_16_15_57_
+TTATCCACACGCTGTCCGGATCCAGCGCCAGGCGCCGACGCTGGACTTCCGCCGCCTGCGCC

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/short_reads_trim_seq_out2.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/short_reads_trim_seq_out2.fasta Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,62 @@
+>0
+GACTCATGATTTCTTACCTATTAGTGGTTGAACA
+>1
+GTGATATGTATGTTGA
+>2
+GTTGTCGATAGAACTTCATGTG
+>3
+ACCAACCAGAACGTGAAAAAG
+>4
+GTTTATGTTGGTTTCATGGTTT
+>5
+GCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCG
+>6
+GCTTGTTTACGAATTAAATCGAAGTGGACTGCTG
+>7
+GTTATAACGCCGAAGCGGTAAAAATTTTTATTTTTT
+>8
+GTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACCT
+>9
+GTGGCCTGTTGAT
+>10_0
+GTGACCG
+>10_1
+ATAAAGT
+>11
+TCGCTACACGCAGGA
+>12
+GCTCGTTATGGTTTCCGTTGCTGCCATCTCAAAAAC
+>13
+GTTGACGGCCATAAGGCTG
+>14
+GTCAAGGACTGGTTTAGATATGAGTCACATTTTGTT
+>15
+GTGCTGAGTTTTTTTCTGTTACTGTG
+>16
+GACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGG
+>17
+GGAAAATGAGAAAATTCGACCTATCCTTGCGCAGCT
+>18
+GAGTCTCATTTTGCATCTCGGCAATCTCTTTCTGAT
+>19
+GTCATAAGAGGTTTTACCTCCAAATGAAGAAATAAC
+>20
+GCTGGTAATGGTGGTTTTTTTTTTTTTTTTTTT
+>21
+GTTGAGGCTTGCGTTTATGGTACGCTGGACTTT
+>22
+CAAGGT
+>23
+GGCGACTTCACGCCAGAATACGAAA
+>24
+GCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGA
+>25
+GGGATGAACATAATAAGCAATGACG
+>26
+GTATTTTACCAATGACCAAATCAAAGAAATGACTCG
+>27
+GTTTTTAGTGAGTTGTTCCATTCTTTAGCTCCTAGA
+>28
+AAGCTGTTGCCGA
+>29
+GCGTACTTATTCGCCACCATGATTATTAC

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/shrimp_cs_test1.csfasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/shrimp_cs_test1.csfasta Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,5000 @@\n+>2_14_26_F3,-1282216.0\n+T011213122200221123032111221021210131332222101\n+>2_14_192_F3,-1383225.3\n+T110021221100310030120022032222111321022112223\n+>2_14_233_F3,-1082751.1\n+T011001332311121212312022310203312201132111223\n+>2_14_294_F3,-687179.1\n+T213012132300000021323212232103300033102330332\n+>2_14_463_F3\n+T132032030200202202003211302222202230022110222\n+>2_14_578_F3\n+T131013032310120222321211010130110221312110222\n+>2_14_956_F3,-1625621.2,-1625360.0\n+T210213030022120032001012021321220011232201231\n+>2_14_988_F3,1687674.3\n+T221202031310031102033002302330301301010023133\n+>2_14_1028_F3,754444.2\n+T112230301101101120201331111302110031102111321\n+>2_14_1035_F3,-1570954.1\n+T003033103303232110201102100032203301023110332\n+>2_14_1157_F3\n+T330302102023212332202300023010210001331011220\n+>2_14_1185_F3\n+T310110110113210213231123311333112011100111111\n+>2_14_1256_F3\n+T220332330033103230031220313312210032300011103\n+>2_14_1452_F3,408767.1\n+T300032023211022130002011021201330102122112133\n+>2_14_1467_F3,1725735.1\n+T002002011223202300213312213112203002031020300\n+>2_14_1501_F3,-296824.0\n+T232300003200003322211030002010000100202220111\n+>2_15_37_F3,-831611.2\n+T332102232121210322013113212312023121222213322\n+>2_15_85_F3\n+T213021013012303002332212012112221222112212222\n+>2_15_455_F3\n+T021111033122331023012312113232232212010121222\n+>2_15_474_F3,861313.0\n+T301130020200230322222222220200002112323223130\n+>2_15_711_F3\n+T110123132023222210122220013231212001010211310\n+>2_15_728_F3,1727534.3\n+T332301303200212322102330330101032222303230132\n+>2_15_800_F3\n+T311311202021333312003202011210112202323222222\n+>2_15_913_F3,234081.0\n+T000133010220201231210102121030231022310100300\n+>2_15_922_F3\n+T030210011320000021213202010022330022200221332\n+>2_15_1344_F3,1441878.0\n+T332010233223132213021210102102010032012311132\n+>2_15_1457_F3,1814674.3\n+T332130102020103032112122301011033022232300322\n+>2_15_1654_F3,-685937.3\n+T021101123300222011231311001111022223111303310\n+>2_15_1694_F3\n+T223113213133313213321223223222222222232212222\n+>2_15_1870_F3\n+T313131331322312222132123233231312122232212222\n+>2_16_63_F3,1668299.1\n+T303131033120202201213020323120023331033121300\n+>2_16_78_F3\n+T000211121303022003030023222233201120002201132\n+>2_16_134_F3,1731243.3\n+T002111200322221100012320021022112010022102302\n+>2_16_136_F3,273653.2\n+T021302220232322200021321011302020332331011303\n+>2_16_184_F3,906220.1\n+T021113301020231031012202112232212033232211222\n+>2_16_208_F3,1586951.1\n+T200111311132333233203003121211321322021301323\n+>2_16_352_F3,-440913.3\n+T202211102330120210333212230200322113322330322\n+>2_16_384_F3,471462.2\n+T300110020200133020123100133230332231112212222\n+>2_16_388_F3,1736527.0\n+T220113223002202022200002301210332321222212222\n+>2_16_511_F3,-83281.0\n+T302202101020121312112301223021310022302130120\n+>2_16_583_F3\n+T133212213000131222021302012130103231012110221\n+>2_16_603_F3,67584.0\n+T201232013201122131203021002300011313200111220\n+>2_16_718_F3,-1557566.0\n+T001233013301002003323331332031310120010100222\n+>2_16_744_F3,109209.0\n+T003130133013323012321020100123320102233012313\n+>2_16_793_F3\n+T313103331222221002110222203130031231112011222\n+>2_16_902_F3\n+T202223032112020202222023022222010102232022322\n+>2_16_928_F3\n+T313323103333032220021303211002220222200212322\n+>2_16_946_F3,1842581.3\n+T233222200101013032120210120330203220000333321\n+>2_16_1093_F3\n+T333113130033001221231333333130120202212012202\n+>2_16_1165_F3,109943.1\n+T023312020003001203012211213211103301322213233\n+>2_16_1316_F3,-349764.0\n+T323000112000202112010232201023320330213000302\n+>2_16_1408_F3\n+T002000213101010101232032230000200133302000100\n+>2_16_1463_F3,728745.1\n+T223301022333022233202002033100111300311302022\n+>2_16_1563_F3,1967863.0\n+T021302001311233233021200323122211012203011112\n+>2_16_1600_F3,1757811.0\n+T312132320301230220131230021202103230201321111\n+>2_16_1634_F3,1008981.2\n+T010111123102110122103101222312312322112101231\n+>2_16_1659_F3\n+T122221221322213022331311010021111221211312222\n+>2_17_38_F3\n+T1322022221213302220120332123321223212322'..b'30_F3\n+T331003021212202000220022303201020111203132102\n+>2_141_545_F3,-215576.3\n+T010323103203302223002022001332303331020302220\n+>2_141_729_F3,1803810.0\n+T011120100113200102113011300103313303132010211\n+>2_141_748_F3\n+T112323122223222212222303033121210302200012100\n+>2_141_777_F3\n+T331202200212020202321321023101123132322212200\n+>2_141_869_F3\n+T123033213113003132230210112110120001023112222\n+>2_141_976_F3\n+T000100020300210113300023332000313131030201331\n+>2_141_1005_F3\n+T331310113311112332322322331130223312232020232\n+>2_141_1009_F3\n+T210220011211112030222123131102021232212130200\n+>2_141_1110_F3,893659.2\n+T012332032303022103010011201032102222101303300\n+>2_141_1136_F3\n+T030132021311313311001210311121210302132031123\n+>2_141_1246_F3\n+T132021230013201222321300232000230211212022010\n+>2_141_1291_F3\n+T330233121032211211323200333220322102222022220\n+>2_141_1410_F3,-607445.0\n+T033011003110002310332321320210120023013231310\n+>2_141_1549_F3,-866383.0\n+T132012120331102133122013001203012313100101122\n+>2_141_1554_F3,1908928.1\n+T211301211220213213101212011232121230211012020\n+>2_141_1740_F3\n+T201123033022033200233202332230322223232322222\n+>2_141_2020_F3\n+T322223100002320000222002011002110220202030122\n+>2_142_135_F3\n+T300310322222003310022312210031120102332213223\n+>2_142_214_F3,424707.1,330666.1,91385.1,20588.1\n+T032302212011223322222012222330302020122303200\n+>2_142_337_F3,-1191166.2\n+T303121300032022123111020301231111210012311212\n+>2_142_386_F3\n+T331022022102223333223301331030333032230323322\n+>2_142_600_F3,1403023.0\n+T231201031030101112020222220112010012223101202\n+>2_142_676_F3\n+T231313132313002133222321231120211011322312132\n+>2_142_695_F3\n+T003113103311021321201301131112313212233111221\n+>2_142_699_F3\n+T002023222210321321301312101120011320213131222\n+>2_142_733_F3\n+T000210022021103222233322331300223313201012112\n+>2_142_790_F3\n+T222112110020333223232122122230212132121021231\n+>2_142_979_F3,914430.1\n+T333110220011220232310111031211321101331022320\n+>2_142_1031_F3\n+T020010002101012111020122230000320102211000322\n+>2_142_1097_F3\n+T031202101120120300101132333130321032300312230\n+>2_142_1114_F3\n+T002301033312123201220013203030221003201220112\n+>2_142_1163_F3\n+T133321123201201002101022320332213231121011200\n+>2_142_1434_F3,1556197.3\n+T330210023301210321022231112021012311231200112\n+>2_142_1443_F3\n+T002231010211211330023131031103130133130020200\n+>2_142_1487_F3,787594.1\n+T001022200030033230330111000332010013132210222\n+>2_142_1798_F3\n+T233113111311333222323231223222212223332222222\n+>2_142_1928_F3,1106551.0\n+T320120132102100012011212102102202202222022102\n+>2_143_34_F3,-532776.1,-532605.1,-532434.1\n+T230203033223333313323000201013122022112323223\n+>2_143_114_F3,-1137342.0\n+T021302030013132210003302022100331300110233222\n+>2_143_188_F3\n+T003200202032101331313010230120211310110031222\n+>2_143_557_F3,-1543999.1\n+T331103323122201123133212031020202011112130231\n+>2_143_605_F3\n+T122010223013022010031122021232221122220112222\n+>2_143_644_F3,383069.3\n+T330010202301322332222312021321200110122323223\n+>2_143_662_F3\n+T312201203032200232101321112212311023310012223\n+>2_143_760_F3,-706118.0\n+T322002223131023020201101301102111303110000102\n+>2_143_764_F3,-641755.0\n+T231020132132300231032022000123113320331023230\n+>2_143_899_F3\n+T321323110223003320201233222322321021232222222\n+>2_143_1027_F3\n+T322220312202010110020211111030311111112110022\n+>2_143_1139_F3\n+T031032202031103131032330311111211133113033230\n+>2_143_1146_F3,1618968.2\n+T110001012331020133013100312223102231221013302\n+>2_143_1219_F3,437850.1\n+T100022023301021301013000112203220221111211200\n+>2_143_1286_F3\n+T122020220301023310213233333010100010201220122\n+>2_143_1350_F3\n+T300302022223232010321000031021110322112201030\n+>2_143_1363_F3\n+T320301321101010010121023023013211132212312220\n+>2_143_1382_F3,361830.0\n+T000032222230212312312313220012201231321020220\n+>2_143_1602_F3\n+T110000202113021230022113113032310011302113121\n+>2_143_1629_F3\n+T330321123231123230021333132002310001302212312\n+>2_143_1672_F3\n+T023103010032233133012211113002111112010111220\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/shrimp_cs_test1.out
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/shrimp_cs_test1.out Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,1684 @@\n+#FORMAT: readname contigname strand contigstart contigend readstart readend readlength score editstring\n+>2_143_1602_F3\tStreptococcus_suis\t+\t1931110\t1931153\t1\t44\t45\t3140\t13x14x5x1x2x2x1x2x2x2\t\n+>2_143_1382_F3,361830.0\tStreptococcus_suis\t+\t361831\t361875\t1\t45\t45\t4500\t45\t\n+>2_143_1286_F3\tStreptococcus_suis\t+\t1028840\t1028884\t1\t45\t45\t3800\t17x5x5x5x10x3\t\n+>2_143_1219_F3,437850.1\tStreptococcus_suis\t+\t437851\t437895\t1\t45\t45\t4220\t23x12x10\t\n+>2_143_1146_F3,1618968.2\tStreptococcus_suis\t+\t1618969\t1619013\t1\t45\t45\t3940\t25x5x5x5x5\t\n+>2_143_644_F3,383069.3\tStreptococcus_suis\t+\t383070\t383114\t1\t45\t45\t3800\t13x6x9x10x4x3\t\n+>2_142_1928_F3,1106551.0\tStreptococcus_suis\t+\t1106552\t1106596\t1\t45\t45\t4360\t42x3\t\n+>2_142_1487_F3,787594.1\tStreptococcus_suis\t+\t787595\t787639\t1\t45\t45\t4220\t32x10x3\t\n+>2_142_1434_F3,1556197.3\tStreptococcus_suis\t+\t1556198\t1556242\t1\t45\t45\t3940\t12x16x6x8x3\t\n+>2_142_979_F3,914430.1\tStreptococcus_suis\t+\t914431\t914474\t1\t44\t45\t4260\t33x11\t\n+>2_142_600_F3,1403023.0\tStreptococcus_suis\t+\t1403024\t1403068\t1\t45\t45\t4360\t42x3\t\n+>2_142_214_F3,424707.1,330666.1,91385.1,20588.1\tStreptococcus_suis\t+\t20589\t20633\t1\t45\t45\t4220\t28x14x3\t\n+>2_142_214_F3,424707.1,330666.1,91385.1,20588.1\tStreptococcus_suis\t+\t91386\t91430\t1\t45\t45\t4220\t28x14x3\t\n+>2_142_214_F3,424707.1,330666.1,91385.1,20588.1\tStreptococcus_suis\t+\t330667\t330711\t1\t45\t45\t4220\t28x14x3\t\n+>2_142_214_F3,424707.1,330666.1,91385.1,20588.1\tStreptococcus_suis\t+\t424708\t424752\t1\t45\t45\t4220\t28x14x3\t\n+>2_141_1554_F3,1908928.1\tStreptococcus_suis\t+\t1908929\t1908973\t1\t45\t45\t4360\t25x20\t\n+>2_141_1136_F3\tStreptococcus_suis\t+\t27098\t27142\t1\t45\t45\t3660\t2x21x2x6x8x3x3\t\n+>2_141_1110_F3,893659.2\tStreptococcus_suis\t+\t893660\t893704\t1\t45\t45\t4220\t18x3x24\t\n+>2_141_976_F3\tStreptococcus_suis\t+\t1913803\t1913847\t1\t45\t45\t3660\t3x2x15x5x5x12x3\t\n+>2_141_729_F3,1803810.0\tStreptococcus_suis\t+\t1803811\t1803855\t1\t45\t45\t4360\t42x3\t\n+>2_141_459_F3,1327884.2\tStreptococcus_suis\t+\t1327885\t1327928\t1\t44\t45\t3980\t13x16x13x2\t\n+>2_141_451_F3\tStreptococcus_suis\t+\t718702\t718746\t1\t45\t45\t3520\t7x10x10x5x1x4x4x4\t\n+>2_141_430_F3,102506.1\tStreptococcus_suis\t+\t102507\t102551\t1\t45\t45\t4220\t32x10x3\t\n+>2_141_391_F3,1239721.0\tStreptococcus_suis\t+\t1239722\t1239765\t1\t44\t45\t4400\t44\t\n+>2_140_1504_F3,1237582.0\tStreptococcus_suis\t+\t1237583\t1237627\t1\t45\t45\t4360\t42x3\t\n+>2_140_1453_F3,384965.0\tStreptococcus_suis\t+\t384966\t385010\t1\t45\t45\t4500\t45\t\n+>2_140_656_F3,1807373.1\tStreptococcus_suis\t+\t1807374\t1807418\t1\t45\t45\t4080\t28x7x3x7\t\n+>2_140_468_F3,743016.2\tStreptococcus_suis\t+\t743017\t743060\t1\t44\t45\t3840\t31x3x6x1x3\t\n+>2_140_182_F3\tStreptococcus_suis\t+\t125021\t125065\t1\t45\t45\t3660\t12x5x10x5x7x4x2\t\n+>2_140_47_F3,134817.3\tStreptococcus_suis\t+\t134818\t134859\t1\t42\t45\t3640\t8x11x12x8x3\t\n+>2_139_1661_F3,1037315.1\tStreptococcus_suis\t+\t1037316\t1037358\t1\t43\t45\t4020\t33x2x8\t\n+>2_139_364_F3,1717849.1,-1671997.1,-973057.1,-1472365.3\tStreptococcus_suis\t+\t1717850\t1717890\t1\t41\t45\t3820\t31x5x5\t\n+>2_139_247_F3,83667.1\tStreptococcus_suis\t+\t83668\t83704\t1\t37\t45\t3560\t18x19\t\n+>2_139_158_F3,1801682.3\tStreptococcus_suis\t+\t1801683\t1801726\t1\t44\t45\t3590\t8x14x12x2x5G2\t\n+>2_138_766_F3,62383.0\tStreptococcus_suis\t+\t62384\t62428\t1\t45\t45\t4360\t42x3\t\n+>2_138_597_F3,1668250.1\tStreptococcus_suis\t+\t1668251\t1668295\t1\t45\t45\t4360\t27x18\t\n+>2_138_569_F3,1602678.0\tStreptococcus_suis\t+\t1602679\t1602722\t1\t44\t45\t3980\t35x3x4x2\t\n+>2_138_480_F3,357587.1\tStreptococcus_suis\t+\t357588\t357631\t1\t44\t45\t4120\t28x12x4\t\n+>2_138_138_F3,1133969.2\tStreptococcus_suis\t+\t1133970\t1134009\t1\t40\t45\t3440\t31x1x4x2x2\t\n+>2_137_1656_F3,493299.2\tStreptococcus_suis\t+\t493300\t493342\t1\t43\t45\t3460\t12x19x4x1x3x2x2\t\n+>2_137_1606_F3,301958.3\tStreptococcus_suis\t+\t301959\t302003\t1\t45\t45\t3660\t12x17x5x6x2x1x2\t\n+>2_137_1098_F3,498028.2\tStreptococcus_suis\t+\t498029\t498073\t1\t45\t45\t3940\t31x3x3x5x3\t\n+>2_137_535_F3,1717676.0,-1472538.0,-973230.0,-1672170.2,1356192.2\tStreptococcus_suis\t+\t1717677\t1717721\t1\t45\t45\t3970\t38x2x2G2\t\n+>2_137_535_F3,1717676.0,-1472538.0,-973230.0,-1672170.2,1356192.2\tStreptococcus_suis\t+\t1356193\t1356236\t1\t44\t45\t3480\t6A29A1x2x2x2\t\n+>2_137_513_'..b'\t45\t3240\t17x5x10x3x2x1x1x1x1x4\t\n+>2_23_1517_F3,-837837.0\tStreptococcus_suis\t-\t837794\t837838\t1\t45\t45\t4220\t42x1x2\t\n+>2_23_747_F3,-916145.1\tStreptococcus_suis\t-\t916102\t916146\t1\t45\t45\t4220\t34x8x3\t\n+>2_22_1570_F3,-1030692.0\tStreptococcus_suis\t-\t1030649\t1030693\t1\t45\t45\t4220\t40x2x3\t\n+>2_22_1558_F3,-49062.2\tStreptococcus_suis\t-\t49019\t49063\t1\t45\t45\t3940\t18x9x8x7x3\t\n+>2_22_1512_F3\tStreptococcus_suis\t-\t877812\t877856\t1\t45\t45\t3660\t14x15x2x3x2x6x3\t\n+>2_22_1415_F3,-553050.0\tStreptococcus_suis\t-\t553007\t553051\t1\t45\t45\t4500\t45\t\n+>2_22_903_F3\tStreptococcus_suis\t-\t1583412\t1583456\t1\t45\t45\t3380\t20x2x3x3x5x7x2x1x2\t\n+>2_22_727_F3,-1290204.2\tStreptococcus_suis\t-\t1290165\t1290205\t1\t41\t45\t3680\t12x19x8x2\t\n+>2_21_1625_F3,-1640957.2\tStreptococcus_suis\t-\t1640914\t1640958\t1\t45\t45\t3940\t27x5x3x5x5\t\n+>2_21_1397_F3\tStreptococcus_suis\t-\t1387409\t1387450\t1\t42\t45\t3360\t13x12x4x4x2x2x5\t\n+>2_21_767_F3,-890350.1\tStreptococcus_suis\t-\t890312\t890351\t1\t40\t45\t3860\t15x25\t\n+>2_21_678_F3,-102240.0\tStreptococcus_suis\t-\t102197\t102241\t1\t45\t45\t4500\t45\t\n+>2_20_1408_F3,-1310926.3\tStreptococcus_suis\t-\t1310883\t1310927\t1\t45\t45\t3550\t13x10x5x10x2x2A2\t\n+>2_20_1359_F3,-1328721.2\tStreptococcus_suis\t-\t1328678\t1328722\t1\t45\t45\t3830\t11x19x7x2A5\t\n+>2_20_1000_F3,-721404.3\tStreptococcus_suis\t-\t721361\t721405\t1\t45\t45\t3800\t29x3x2x4x4x3\t\n+>2_19_947_F3,-448190.1\tStreptococcus_suis\t-\t448147\t448191\t1\t45\t45\t4220\t18x24x3\t\n+>2_19_361_F3,-1752120.3\tStreptococcus_suis\t-\t1752077\t1752121\t1\t45\t45\t3940\t4x8x17x13x3\t\n+>2_18_1261_F3,-236852.2\tStreptococcus_suis\t-\t236819\t236853\t1\t35\t45\t3220\t27x5x3\t\n+>2_18_896_F3,-727155.0\tStreptococcus_suis\t-\t727112\t727156\t1\t45\t45\t4220\t37x3x5\t\n+>2_18_887_F3,-1294634.0\tStreptococcus_suis\t-\t1294598\t1294635\t1\t38\t45\t3660\t36x2\t\n+>2_18_706_F3,-373364.0\tStreptococcus_suis\t-\t373322\t373365\t1\t44\t45\t4260\t42x2\t\n+>2_18_697_F3,-369193.0\tStreptococcus_suis\t-\t369150\t369194\t1\t45\t45\t3970\t35C6x1x2\t\n+>2_18_45_F3,-472247.0\tStreptococcus_suis\t-\t472205\t472248\t1\t44\t45\t4400\t44\t\n+>2_17_1614_F3,-1674195.0\tStreptococcus_suis\t-\t1674152\t1674196\t1\t45\t45\t4220\t40x3x2\t\n+>2_17_1393_F3,-879512.1\tStreptococcus_suis\t-\t879469\t879513\t1\t45\t45\t4220\t12x30x3\t\n+>2_17_1142_F3,-1903625.0\tStreptococcus_suis\t-\t1903582\t1903626\t1\t45\t45\t4500\t45\t\n+>2_17_1040_F3\tStreptococcus_suis\t-\t275646\t275690\t1\t45\t45\t3660\t7x5x5x5x7x13x3\t\n+>2_17_854_F3,-757864.3\tStreptococcus_suis\t-\t757821\t757865\t1\t45\t45\t3800\t12x13x4x7x6x3\t\n+>2_17_692_F3,-37965.0\tStreptococcus_suis\t-\t37922\t37966\t1\t45\t45\t4110\t40x1C3\t\n+>2_17_422_F3,-674586.3\tStreptococcus_suis\t-\t674545\t674587\t1\t43\t45\t3880\t14x18x2x9\t\n+>2_16_1316_F3,-349764.0\tStreptococcus_suis\t-\t349722\t349765\t1\t44\t45\t3840\t36x3x2x1x2\t\n+>2_16_718_F3,-1557566.0\tStreptococcus_suis\t-\t1557523\t1557567\t1\t45\t45\t4360\t43x2\t\n+>2_16_511_F3,-83281.0\tStreptococcus_suis\t-\t83238\t83282\t1\t45\t45\t4220\t38x4x3\t\n+>2_16_352_F3,-440913.3\tStreptococcus_suis\t-\t440871\t440914\t1\t44\t45\t3730\t3x22x7x8G3\t\n+>2_16_78_F3\tStreptococcus_suis\t-\t1440784\t1440828\t1\t45\t45\t3800\t5x1x2x14x20x3\t\n+>2_16_78_F3\tStreptococcus_suis\t-\t986903\t986947\t1\t45\t45\t3800\t5x1x2x14x20x3\t\n+>2_16_78_F3\tStreptococcus_suis\t-\t593046\t593090\t1\t45\t45\t3800\t5x1x2x14x20x3\t\n+>2_16_78_F3\tStreptococcus_suis\t-\t575660\t575704\t1\t45\t45\t3800\t5x1x2x14x20x3\t\n+>2_15_1654_F3,-685937.3\tStreptococcus_suis\t-\t685894\t685938\t1\t45\t45\t3800\t12x10x5x10x6x2\t\n+>2_15_37_F3,-831611.2\tStreptococcus_suis\t-\t831569\t831612\t1\t44\t45\t3980\t6x17x19x2\t\n+>2_14_1501_F3,-296824.0\tStreptococcus_suis\t-\t296781\t296825\t1\t45\t45\t4220\t35x7x3\t\n+>2_14_1035_F3,-1570954.1\tStreptococcus_suis\t-\t1570911\t1570955\t1\t45\t45\t3970\t12x28x1T3\t\n+>2_14_956_F3,-1625621.2,-1625360.0\tStreptococcus_suis\t-\t1625317\t1625361\t1\t45\t45\t4500\t45\t\n+>2_14_956_F3,-1625621.2,-1625360.0\tStreptococcus_suis\t-\t1625578\t1625622\t1\t45\t45\t4250\t7T37\t\n+>2_14_294_F3,-687179.1\tStreptococcus_suis\t-\t687136\t687180\t1\t45\t45\t4220\t32x10x3\t\n+>2_14_233_F3,-1082751.1\tStreptococcus_suis\t-\t1082708\t1082752\t1\t45\t45\t3520\t32x3x1x2x2x2x1x2\t\n+>2_14_192_F3,-1383225.3\tStreptococcus_suis\t-\t1383182\t1383226\t1\t45\t45\t3800\t13x9x12x6x3x2\t\n+>2_14_26_F3,-1282216.0\tStreptococcus_suis\t-\t1282173\t1282217\t1\t45\t45\t4220\t38x4x3\t\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/shrimp_phix_anc.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/shrimp_phix_anc.fa Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,2 @@
+>PHIX174
+GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAAATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATCTGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCGTCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTACGGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTACGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCaGAAGGAGTGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCATCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGACTCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTACTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTTGGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACAACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGCTCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGCATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCgTGATGTTATTTCTTCATTTGGAGGTAAAACCTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTGTCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGCCTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGCCGGGCAATAAtGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTGCTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAAAGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCTGGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGGTTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGAGATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGACCAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTATGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCAAACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCGTCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTTCTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGCATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGAATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGGGACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCCCTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTaCTATTCAGCGTTTGATGAATGCAATGCGACAGGCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTTATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGCCGTCTTCATTTCCATGCGGTGCAtTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTCGTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCATCGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATATGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGCAGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACCTGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/shrimp_wrapper_test1.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/shrimp_wrapper_test1.fastq Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,40 @@
+@HWI-EAS91_1_306UPAAXX:6:1:959:874
+GCGGGCTGCGACATAAAGCATACCGCCTGGGCGGCG
++HWI-EAS91_1_306UPAAXX:6:1:959:874
+hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh
+@HWI-EAS91_1_306UPAAXX:6:1:1630:1975
+GAAAGAAAATCAGCAACAGTGGCATCGATTTTACGG
++HWI-EAS91_1_306UPAAXX:6:1:1630:1975
+hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh
+@HWI-EAS91_1_306UPAAXX:6:1:770:994
+GCAGGCAGCGTGCTGCGAGTCTTTTCGAATGATAAG
++HWI-EAS91_1_306UPAAXX:6:1:770:994
+hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh
+@HWI-EAS91_1_306UPAAXX:6:1:1274:306
+GTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGC
++HWI-EAS91_1_306UPAAXX:6:1:1274:306
+hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh\h
+@HWI-EAS91_1_306UPAAXX:6:1:1339:209
+GTTTGGTCAGTTCCATCAACATCATAGCCAGATGCC
++HWI-EAS91_1_306UPAAXX:6:1:1339:209
+hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh
+@HWI-EAS91_1_306UPAAXX:6:1:203:1240
+GATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTA
++HWI-EAS91_1_306UPAAXX:6:1:203:1240
+hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh
+@HWI-EAS91_1_306UPAAXX:6:1:869:448
+GCTGGCCATCAGTTCGCGGATACCGGCGGCAAACAT
++HWI-EAS91_1_306UPAAXX:6:1:869:448
+hhhhhhhhhhhhhhhhhhhhhhhhhhhhKhhhhhhh
+@HWI-EAS91_1_306UPAAXX:6:1:939:928
+GGAGGCCTCCAGCAATCTTGAACACTCATCCTTAAT
++HWI-EAS91_1_306UPAAXX:6:1:939:928
+hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh
+@HWI-EAS91_1_306UPAAXX:6:1:1756:1476
+GCGTAGAGGCTTTACTATTCAGCGTTTGATGAATGC
++HWI-EAS91_1_306UPAAXX:6:1:1756:1476
+hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh
+@HWI-EAS91_1_306UPAAXX:6:1:1528:181
+GGCTGGTCAGTATTTTACCAATGACCAAATCAAAGA
++HWI-EAS91_1_306UPAAXX:6:1:1528:181
+hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/shrimp_wrapper_test1.out1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/shrimp_wrapper_test1.out1 Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,7 @@
+#FORMAT: readname contigname strand contigstart contigend readstart readend readlength score editstring
+>HWI-EAS91_1_306UPAAXX:6:1:1528:181 PHIX174 + 3644 3679 1 36 36 3600 36
+>HWI-EAS91_1_306UPAAXX:6:1:1756:1476 PHIX174 + 4505 4540 1 36 36 3600 36
+>HWI-EAS91_1_306UPAAXX:6:1:203:1240 PHIX174 + 310 345 1 36 36 3600 36
+>HWI-EAS91_1_306UPAAXX:6:1:1274:306 PHIX174 + 933 968 1 36 36 3600 36
+>HWI-EAS91_1_306UPAAXX:6:1:939:928 PHIX174 - 4458 4493 1 36 36 3600 36
+>HWI-EAS91_1_306UPAAXX:6:1:1339:209 PHIX174 - 1732 1767 1 36 36 3600 36

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/sift_variants.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/sift_variants.tab Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,20 @@
+chr3 81780819 81780820 + T/C
+chr2 230341629 230341630 + G/A
+chr2 43881516 43881517 + A/T
+chr2 43857513 43857514 + T/C
+chr6 88375601 88375602 + G/A
+chr22 29307352 29307353 - T/A
+chr10 115912481 115912482 - G/T
+chr10 115900917 115900918 - C/T
+chr16 69875501 69875502 + G/T
+chr16 69876077 69876078 + T/C
+chr16 69877146 69877147 + G/A
+chr22 49000824 49000825 - T/A
+chr22 49000550 49000551 - A/C
+chr22 49006738 49006739 - T/G
+chr11 17476317 17476318 - C/G
+chr4 124033757 124033758 - G/T
+chr3 185041095 185041096 - C/G
+chr17 8101873 8101874 + C/T
+chr6 33156519 33156520 + C/T
+chr16 23556916 23556917 - A/G

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/sift_variants_result.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/sift_variants_result.tab Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,21 @@
+#Chrom Position Strand Allele Codons Transcript ID Protein ID Substitution Region dbSNP ID SNP Type Prediction Score Median Info Num seqs at position Gene ID User Comment
+chr3 81780820 + T/C AGA-gGA ENST00000264326 ENSP00000264326 R190G EXON CDS rs2229519:C Nonsynonymous DAMAGING 0.04 3.06 149 ENSG00000114480
+chr2 230341630 + G/T - ENST00000389045 ENSP00000373697 NA EXON CDS rs1803846:A Unknown Not scored NA NA NA ENSG00000153827
+chr2 43881517 + A/T ATA-tTA ENST00000260605 ENSP00000260605 I230L EXON CDS rs11556157:T Nonsynonymous TOLERATED 0.47 3.19 7 ENSG00000138036
+chr2 43857514 + T/C TTT-TcT ENST00000260605 ENSP00000260605 F33S EXON CDS rs2288709:C Nonsynonymous TOLERATED 0.61 3.33 6 ENSG00000138036
+chr6 88375602 + G/A GTT-aTT ENST00000257789 ENSP00000257789 V217I EXON CDS rs2307389:A Nonsynonymous TOLERATED 0.75 3.17 13 ENSG00000135336
+chr22 29307353 + T/A ACC-tCC ENST00000335214 ENSP00000334612 T264S EXON CDS rs42942:A Nonsynonymous TOLERATED 0.4 3.14 23 ENSG00000100029
+chr10 115912482 + C/A CGA-CtA ENST00000369285 ENSP00000358291 R179L EXON CDS rs12782946:T Nonsynonymous TOLERATED 0.06 4.32 2 ENSG00000165813
+chr10 115900918 + G/A CAA-tAA ENST00000369287 ENSP00000358293 Q271* EXON CDS rs7095762:T Nonsynonymous N/A N/A N/A N/A ENSG00000165813
+chr16 69875502 + G/T ACA-AaA ENST00000338099 ENSP00000337512 T608K EXON CDS rs3096381:T Nonsynonymous TOLERATED 0.12 3.41 3 ENSG00000180917
+chr16 69876078 + T/C AAT-AgT ENST00000338099 ENSP00000337512 N416S EXON CDS rs3803704:C Nonsynonymous TOLERATED 1 3.15 26 ENSG00000180917
+chr16 69877147 + G/A CTT-tTT ENST00000338099 ENSP00000337512 L60F EXON CDS rs3096380:A Nonsynonymous TOLERATED 0.31 3.33 31 ENSG00000180917
+chr22 49000825 + T/A AGT-tGT ENST00000248846 ENSP00000248846 S1364C EXON CDS rs5771107:A Nonsynonymous TOLERATED 0.18 3.38 6 ENSG00000128159
+chr22 49000551 + T/G ACT-cCT ENST00000248846 ENSP00000248846 T1377P EXON CDS rs11703226:C Nonsynonymous TOLERATED 0.27 3.38 6 ENSG00000128159
+chr22 49006739 + A/C TTG-TgG ENST00000248846 ENSP00000248846 L567W EXON CDS rs4838865:G Nonsynonymous TOLERATED 0.16 3.15 10 ENSG00000128159
+chr11 17476318 + C/G GAG-GAc ENST00000005226 ENSP00000005226 E819D EXON CDS rs1064074:G Nonsynonymous TOLERATED 0.08 3.95 12 ENSG00000006611
+chr4 124033758 + C/A CGG-CtG ENST00000339154 ENSP00000344011 R40L EXON CDS rs1048201:T Nonsynonymous DAMAGING 0.01 3.14 20 ENSG00000170917
+chr3 185041096 + C/G GTG-cTG ENST00000311101 ENSP00000310676 V212L EXON CDS rs3732581:G Nonsynonymous TOLERATED 0.58 2.94 30 ENSG00000175193
+chr17 8101874 + C/T CCA-CtA ENST00000314666 ENSP00000313490 P367L EXON CDS rs4791641:T Nonsynonymous TOLERATED 0.11 3.02 34 ENSG00000178921
+chr6 33156520 + C/T GCG-GtG ENST00000308461 ENSP00000311794 A65V EXON CDS rs1042121:T Nonsynonymous TOLERATED 1 3.39 397 ENSG00000168383
+chr16 23556917 + T/C TAC-TgC ENST00000261584 ENSP00000261584 Y28C EXON CDS novel Nonsynonymous DAMAGING *Warning! Low confidence. 0 4.32 1 ENSG00000083093

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/simple_line.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/simple_line.txt Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,1 @@
+This is a line of text.

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/simple_line_alternative.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/simple_line_alternative.txt Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,1 @@
+This is a different line of text.
\ No newline at end of file

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/simple_line_x2.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/simple_line_x2.txt Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,2 @@
+This is a line of text.
+This is a line of text.

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/simple_line_x3.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/simple_line_x3.txt Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,3 @@
+This is a line of text.
+This is a line of text.
+This is a line of text.

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/simple_line_x5.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/simple_line_x5.txt Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,5 @@
+This is a line of text.
+This is a line of text.
+This is a line of text.
+This is a line of text.
+This is a line of text.

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/simple_lines_both.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/simple_lines_both.txt Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,2 @@
+This is a line of text.
+This is a different line of text.
\ No newline at end of file

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/simple_lines_interleaved.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/simple_lines_interleaved.txt Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,4 @@
+This is a line of text.
+This is a different line of text.
+This is a line of text.
+This is a different line of text.
\ No newline at end of file

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/snpFreqInput.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/snpFreqInput.txt Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,10 @@
+chr1 210 211 38 4 15 56 0 1 x
+chr1 215 216 53 0 4 5 0 51 x
+chr1 228 229 55 0 2 56 0 1 x
+chr1 230 231 46 0 11 55 0 2 x
+chr1 234 235 43 0 14 55 0 2 x
+chr1 236 237 55 0 2 13 10 34 x
+chr1 437 438 55 0 2 46 0 11 x
+chr1 439 440 56 0 1 55 0 2 x
+chr1 449 450 56 0 1 13 20 24 x
+chr1 518 519 56 0 1 38 4 15 x

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/snpFreqTestOut.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/snpFreqTestOut.txt Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,10 @@
+chr1 210 211 38 4 15 56 0 1 x 47 2 8 47 2 8 1.50219088598917e-05 6.32501425679652e-06
+chr1 215 216 53 0 4 5 0 51 x 29.257 0 27.743 28.743 0 27.257 2.18870370759758e-21 4.60779727915280e-21
+chr1 228 229 55 0 2 56 0 1 x 55.5 0 1.5 55.5 0 1.5 0.999 0.210315789473684
+chr1 230 231 46 0 11 55 0 2 x 50.5 0 6.5 50.5 0 6.5 0.0155644201009862 0.00409590002657532
+chr1 234 235 43 0 14 55 0 2 x 49 0 8 49 0 8 0.00210854461554067 0.000739840215979182
+chr1 236 237 55 0 2 13 10 34 x 34 5 18 34 5 18 6.14613878554783e-17 4.31307984950725e-17
+chr1 437 438 55 0 2 46 0 11 x 50.5 0 6.5 50.5 0 6.5 0.0155644201009862 0.00409590002657532
+chr1 439 440 56 0 1 55 0 2 x 55.5 0 1.5 55.5 0 1.5 0.999 0.210315789473684
+chr1 449 450 56 0 1 13 20 24 x 34.5 10 12.5 34.5 10 12.5 2.25757007974134e-18 2.37638955762246e-18
+chr1 518 519 56 0 1 38 4 15 x 47 2 8 47 2 8 1.50219088598917e-05 6.32501425679652e-06

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/solexa.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/solexa.fasta Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,60 @@
+>0
+GACTCATGATTTCTTACCTATTAGTGGTTGAACATC
+>1
+GTGATATGTATGTTGACGGCCATAAGGCTGCTTCTT
+>2
+GTTGTCGATAGAACTTCATGTGCCTGTAAAACAAGT
+>3
+ACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGC
+>4
+GTTTATGTTGGTTTCATGGTTTTGTCTAACTTTATC
+>5
+GCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCG
+>6
+GCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGC
+>7
+GTTATAACGCCGAAGCGGTAAAAATTTTTATTTTTT
+>8
+GTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACCT
+>9
+GTGGCCTGTTGATTCTAAAGGTTAGTTTCTTCACGC
+>10
+GTGACCGCATAAAGTGCACAACATGGAAATGAGGAC
+>11
+GCAGATCGCTACACGCAGGACGCTTTTTCACGTTCT
+>12
+GCTCGTTATGGTTTCCGTTGCTGCCATCTCAAAAAC
+>13
+GTTGACGGCCATAAGGCTGCTTCTGACGTTCGTGAT
+>14
+GTCAAGGACTGGTTTAGATATGAGTCACATTTTGTT
+>15
+GTGCTGAGTTTTTTTCTGTTACTGTGACATTAATTT
+>16
+GACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGG
+>17
+GGAAAATGAGAAAATTCGACCTATCCTTGCGCAGCT
+>18
+GAGTCTCATTTTGCATCTCGGCAATCTCTTTCTGAT
+>19
+GTCATAAGAGGTTTTACCTCCAAATGAAGAAATAAC
+>20
+GCTGGTAATGGTGGTTTTTTTTTTTTTTTTTTTTTT
+>21
+GTTGAGGCTTGCGTTTATGGTACGCTGGACTTTGTA
+>22
+GAGGAGAGTGCAGGTATTAATATCAAGGTTTGTGAG
+>23
+GGCGACTTCACGCCAGAATACGAAATACCAGGTATT
+>24
+GCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGA
+>25
+GGGATGAACATAATAAGCAATGACGGCAGCAATAAA
+>26
+GTATTTTACCAATGACCAAATCAAAGAAATGACTCG
+>27
+GTTTTTAGTGAGTTGTTCCATTCTTTAGCTCCTAGA
+>28
+GTATTGATAAAGCTGTTGCCGATACTTAGCACTATT
+>29
+GCGTACTTATTCGCCACCATGATTATTACCAGTGTT

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/solexa.qual
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/solexa.qual Sat Feb 21 16:33:42 2015 +0100

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diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/solexa.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/solexa.tabular Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,30 @@
+5 300 902 419 GACTCATGATTTCTTACCTATTAGTGGTTGAACATC
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diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/solexaScore.png

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diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/solexa_high_quality_hist.pdf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/solid2fastq_out_1.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/solid2fastq_out_1.fastq Sat Feb 21 16:33:42 2015 +0100

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diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/solid2fastq_out_2.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/solid2fastq_out_2.fastq Sat Feb 21 16:33:42 2015 +0100

b"@@ -0,0 +1,1988 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diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/solid2fastq_out_3.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/solid2fastq_out_3.fastq Sat Feb 21 16:33:42 2015 +0100

b"@@ -0,0 +1,1988 @@\n+@853_7_53/2\n+G..1...12.3.023.22.22.2.2..22..2...2222.222.2.2.22.\n++\n+!!0!!!10!)!)0)!,-!##!%!%!!##!!'!!!%+&)!%$/!)!$!/(!\n+@853_7_78/2\n+G..2...02.2.232.22.11.2.2..12..1...2222.222.2.3.22.\n++\n+!!#!!!5,!$!5&+!#8!)#!5!%!!3%!!'!!!$$8+!&)%!)!(!*#!\n+@853_7_88/2\n+G..3...22.2.032.13.22.2.1..23..0...2130.132.1.2.30.\n++\n+!!1!!!42!5!,25!24!77!4!3!!81!!,!!!5147!)/6!,!,!1&!\n+@853_7_132/2\n+G..2...21.2.200.21.30.1.1..30..0...2112.202.2.0.22.\n++\n+!!&!!!5#!)!)&+!2&!',!&!'!!1)!!1!!!4()$!/&,!'!'!0$!\n+@853_7_141/2\n+G..2...13.1.112.22.00.0.0..02..2...2222.200.2.2.22.\n++\n+!!,!!!),!5!3)+!//!),!3!9!!&/!!+!!!**#)!.)(!(!(!43!\n+@853_7_146/2\n+G..1...12.2.212.20.11.2.1..12..2...1311.223.1.3.21.\n++\n+!!1!!!33!4!#15!7(!51!1!3!!.5!!5!!!/)/,!&-/!,!.!4,!\n+@853_7_269/2\n+G..1...21.2.212.02.01.2.1..21..3...2210.113.2.3.32.\n++\n+!!3!!!/.!+!*4,!42!)8!2!3!!62!!0!!!84;)!)7.!5!/!&%!\n+@853_7_321/2\n+G..1...01.2.202.10.11.0.2..22..2...0332.111.2.0.22.\n++\n+!!$!!!&'!.!*##!6$!#1!+!#!!.+!!)!!!36(#!*5'!#!4!+(!\n+@853_7_386/2\n+G..2...31.2.211.11.31.2.0..31..0...2030.312.1.0.22.\n++\n+!!;!!!86!=!;9=!%5!58!<!2!!62!!&!!!&3:&!//8!*!7!5*!\n+@853_7_405/2\n+G..2...00.0.002.31.23.0.2..32..3...1032.120.2.1.22.\n++\n+!!=!!!;:!>!<8=!9<!:<!=!>!!;8!!;!!!;//1!&(&!/!'!*-!\n+@853_7_411/2\n+G..1...00.1.002.02.12.1.2..22..2...1020.312.2.0.21.\n++\n+!!$!!!-#!#!*#+!,&!2*!#!#!!%'!!)!!!'$)$!/-#!#!'!,+!\n+@853_7_445/2\n+G..2...33.0.233.03.31.0.1..13..2...0020.222.2.2.22.\n++\n+!!&!!!0%!#!,&'!,'!$$!&!,!!&)!!'!!!..*&!#,7!1!.!10!\n+@853_7_469/2\n+G..1...10.3.313.33.33.0.3..02..1...2333.230.2.3.32.\n++\n+!!#!!!%%!$!))+!$,!*%!.!(!!.#!!#!!!#&##!##&!#!#!##!\n+@853_7_474/2\n+G..2...03.2.112.23.31.1.2..21..1...2221.322.2.1.21.\n++\n+!!9!!!::!:!<58!=>!>2!=!7!!2+!!$!!!&#.$!#%+!#!'!##!\n+@853_7_497/2\n+G..3...02.2.221.22.12.1.2..13..0...0033.230.2.3.21.\n++\n+!!6!!!66!,!94'!7:!95!9!5!!/%!!4!!!/1).!'$(!0!$!(,!\n+@853_7_587/2\n+G..0...23.2.030.01.02.0.3..33..3...2101.030.0.2.20.\n++\n+!!/!!!;;!&!,&)!&(!(.!-!)!!&&!!5!!!35(=!817!,!&!+)!\n+@853_7_630/2\n+G..3...01.0.011.10.21.0.3..22..0...2101.020.3.0.01.\n++\n+!!9!!!1<!;!&3/!8>!1>!=!5!!1&!!;!!!%1&6!'8,!(!8!/%!\n+@853_7_655/2\n+G..3...33.3.113.10.20.1.1..02..2...3132.200.1.1.21.\n++\n+!!&!!!8#!9!7&)!>5!#:!?!#!!;$!!<!!!#88&!#<;!%!8!##!\n+@853_7_692/2\n+G..0...30.0.300.12.30.1.1..30..2...1022.320.3.3.33.\n++\n+!!9!!!;;!9!7:<!6;!<:!9!9!!>:!!<!!!=,>7!;/<!=!<!>(!\n+@853_7_715/2\n+G..3...22.1.110.22.31.2.2..21..1...1021.330.1.2.31.\n++\n+!!:!!!69!9!7<;!8:!=+!6!6!!93!!5!!!(706!&:4!(!,!,$!\n+@853_7_719/2\n+G..0...00.3.200.02.30.0.1..20..1...0003.301.2.2.33.\n++\n+!!,!!!:.!)!;#'!,,!#6!7!#!!#.!!#!!!&#&#!#$&!#!#!##!\n+@853_7_743/2\n+G..3...00.0.201.11.03.2.3..30..2...1112.300.2.2.31.\n++\n+!!>!!!<9!7!8:>!>;!:>!9!<!!=9!!5!!!35=,!:1=!)!/!5,!\n+@853_7_791/2\n+G..1...00.2.022.02.32.1.3..21..0...0222.120.1.0.22.\n++\n+!!/!!!1/!>!/)?!:/!75!<!;!!,/!!=!!!:==1!:9?!7!9!,&!\n+@853_7_801/2\n+G..2...11.1.232.31.01.2.1..22..1...2222.122.2.1.22.\n++\n+!!=!!!>7!=!==9!?=!1=!=!<!!>4!!5!!!)$5)!*'.!&!&!*$!\n+@853_7_845/2\n+G..3...23.0.310.12.22.2.2..22..2...3232.303.2.2.33.\n++\n+!!,!!!<2!<!;20!3)!+'!%!(!!(#!!*!!!,,(#!,#,!#!,!#*!\n+@853_7_868/2\n+G..3...21.0.012.11.00.1.2..31..0...0101.022.2.3.03.\n++\n+!!8!!!@:!<!@;8!<@!:>!@!=!!6<!!<!!!>6;;!?5=!:!7!36!\n+@853_7_1026/2\n+G..2...02.1.333.11.10.2.2..21..3...1323.011.1.2.22.\n++\n+!!'!!!#,!7!'&,!5.!&.!&!*!!8.!!-!!!5.)&!$'(!%!&!4&!\n+@853_7_1057/2\n+G..1...22.3.333.22.22.3.1..12..2...2122.332.1.3.21.\n++\n+!!+!!!55!3!18=!?7!6:!/!7!!?5!!)!!!/)<3!0;,!3!5!+,!\n+@853_7_1066/2\n+G..2...22.2.332.12.01.3.0..21..2...0312.122.0.1.02.\n++\n+!!:!!!;4!<!916!??!:>!5!:!!;,!!/!!!8:8/!/79!/!;!/0!\n+@853_7_1107/2\n+G..1...11.0.223.12.23.2.0..11..1...2012.132.0.3.30.\n++\n+!!8!!!98!0!067!:8!&,!5!,!!.3!!:!!!*5-4!$7/!#!5!4#!\n+@853_7_1179/2\n+G..3...02.1.133.00.21.1.3..20..1...3000.002.3.2.23.\n++\n+!!8!!!69!/!,85!1>!8*!<!8!!)9!!6!!!&78<!3>,!:!7!6&!\n+@853_7_1198/2\n+G..3...21.2.121.00.13.0.3..01..3...1131.330.1.3.01.\n++\n+!!>!!!=;!<!;/7!;;!16!>!1!!<=!!:!!!-4;<!#<>!1!=!3$!\n+@853_7_1261/2\n+G..0...12.3.202.00.03.2.0..22..0...2112.021.2.3.22.\n++\n+!"..b")+!/1!1/1:!38,!)98:3:3/,-&0111<!.+!\n+@853_16_871/2\n+G1003..1112.300.21.21.3033.033.1310310030223301.12.\n++\n+=36>!!7:8:!798!<7!7<!55#2!&=:!/2>.:,.9>+)#>>5,!</!\n+@853_16_874/2\n+G0312..1312.131.23.12.2013.130.2302020022222201.02.\n++\n+&86/!!9585!6::!23!67!:+9=!>#2!7<9::;;78:9=7:3;!'6!\n+@853_16_892/2\n+G2121..2130.122.13.03.1213.213.3203011112122011.33.\n++\n+;<2:!!>82:!=33!?=!94!A479!=8+!5<:*::<48'98#(8;!,#!\n+@853_16_919/2\n+G0222..2212.000.11.32.2310.033.2010101230012130.21.\n++\n+?<::!!=955!<87!9>!4:!;%58!=,4!=-#794/#9:9,#)4:!#-!\n+@853_16_941/2\n+G2212..2310.011.11.03.2222.211.2222122223222221.22.\n++\n+<>:7!!>-9=!>(/!::!1:!9(&*!$#&!*&##&$$##%$&'$#%!#$!\n+@853_16_1040/2\n+G3101..0122.021.10.31.0220.333.1230033132002222.13.\n++\n+713>!!=76@!6/<!75!13!/'&'!,,;!52,38<.'24.,4185!&/!\n+@853_16_1049/2\n+G3132..0121.311.02.13.3012.302.1113200103012221.12.\n++\n+<<:9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diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/sort_in1.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/sort_in1.bed Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,32 @@
+# comment 1 \n\n''" again
+# comment 2 **}"''' special
+# comment 3 @n/n""" characters
+chr6 108298214 108386086 NM_007214 0 - 108299600 108385906 0 21 1530,105,99,102,159,174,60,83,148,155,93,133,95,109,51,59,62,113,115,100,304, 0,2490,6246,10831,12670,23164,23520,27331,31052,32526,34311,36130,36365,38609,41028,42398,43048,51479,54500,59097,87568,
+chr6 108593954 108616704 NM_003269 0 + 108594662 108615360 0 9 733,146,88,236,147,97,150,106,1507, 0,5400,8778,10445,12037,14265,14749,15488,21243,
+chr6 108639410 108689143 NM_152827 0 - 108640045 108688818 0 3 741,125,487, 0,2984,49246,
+chr6 108722790 108950942 NM_145315 0 + 108722976 108950321 0 13 325,224,52,102,131,100,59,83,71,101,141,114,750, 0,28931,52094,60760,61796,71339,107102,152319,181970,182297,215317,224802,227402,
+chr7 113320332 113924911 AK131266 0 + 113862563 113893433 0 20 285,91,178,90,58,75,138,51,201,178,214,105,88,84,77,102,122,70,164,1124, 0,201692,340175,448290,451999,484480,542213,543265,543478,545201,556083,558358,565876,567599,573029,573245,575738,577123,577946,603455,
+chr7 116511232 116557294 NM_003391 0 - 116512159 116556994 0 5 1157,265,278,227,383, 0,20384,37843,43339,45679,
+chr7 116713967 116902666 NM_000492 0 + 116714099 116901113 0 27 185,111,109,216,90,164,126,247,93,183,192,95,87,724,129,38,251,80,151,228,101,249,156,90,173,106,1754, 0,24290,29071,50936,54313,55285,56585,60137,62053,68678,79501,107776,110390,111971,114967,122863,123569,126711,130556,131618,134650,147559,162475,172879,184725,185496,186945,
+chr7 116944658 117107512 AF377960 0 - 116945541 116979926 0 23 1129,102,133,64,186,206,179,188,153,100,87,80,96,276,118,255,151,100,204,1654,225,108,173, 0,7364,8850,10413,13893,14398,17435,24259,24615,35177,35359,45901,47221,49781,56405,66857,69787,72208,73597,80474,100111,150555,162681,
+chr2 118288484 118306183 NM_006773 0 + 118288583 118304530 0 14 184,285,144,136,101,200,115,140,162,153,114,57,178,1796, 0,2765,4970,6482,6971,7183,7468,9890,10261,10768,11590,14270,14610,15903,
+chr2 118389378 118390700 BC005078 0 - 118390395 118390500 0 1 1322, 0,
+chr8 118880786 119193239 NM_000127 0 - 118881131 119192466 0 11 531,172,161,90,96,119,133,120,108,94,1735, 0,5355,7850,13505,19068,20309,23098,30863,36077,37741,310718,
+chrX 122719582 122773357 NM_001167 0 + 122745047 122766566 0 7 96,909,100,79,43,201,6985, 0,25433,28421,31040,32533,40295,46790,
+chr9 128763240 128783870 NM_174933 0 + 128764156 128783586 0 12 261,118,74,159,76,48,56,63,129,117,127,370, 0,522,875,5630,12374,12603,15040,15175,18961,19191,20037,20260,
+chr9 128787362 128789566 NM_014908 0 - 128787519 128789136 0 1 2204, 0,
+chr9 128789530 128848928 NM_015354 0 + 128789552 128848511 0 44 54,55,74,85,81,45,93,120,212,115,201,90,66,120,127,153,127,88,77,115,121,67,129,140,107,207,170,70,68,196,78,86,146,182,201,93,159,138,75,228,132,74,130,594, 0,1491,5075,8652,9254,10312,11104,11317,20808,21702,23060,25462,31564,32908,33566,34851,35204,35595,35776,37202,38860,39111,39891,40349,42422,45499,45827,46675,47158,47621,50453,50840,51474,51926,53831,54186,55119,55619,57449,57605,57947,58352,58541,58804,
+chr9 128849867 128870133 NM_020145 0 - 128850516 128869987 0 11 757,241,101,90,24,63,93,134,129,142,209, 0,1071,1736,2085,2635,4201,6376,6736,13056,14247,20057,
+chr5 131170738 131357870 AF099740 0 - 131311206 131357817 0 31 112,124,120,81,65,40,120,129,61,88,94,79,72,102,144,117,89,73,96,135,135,78,74,52,33,179,100,102,65,115,248, 0,11593,44117,47607,104668,109739,114675,126366,135488,137518,138009,140437,152389,153373,155388,159269,160793,162981,164403,165577,166119,167611,169501,178260,179675,180901,181658,182260,182953,183706,186884,
+chr5 131424245 131426795 NM_000588 0 + 131424298 131426383 0 5 215,42,90,42,535, 0,313,1658,1872,2015,
+chr5 131556201 131590458 NM_004199 0 - 131556601 131582218 0 15 471,97,69,66,54,100,71,177,194,240,138,152,97,100,170, 0,2316,2802,5596,6269,11138,11472,15098,16528,17674,21306,24587,25142,25935,34087,
+chr5 131621285 131637046 NM_003687 0 + 131621326 131635821 0 7 134,152,82,179,164,118,1430, 0,4915,8770,13221,13609,14097,14331,
+chr1 147962006 147975713 NM_005997 0 - 147962192 147975670 0 6 574,145,177,115,153,160, 0,1543,7859,9048,9340,13547,
+chr1 147984101 148035079 BC007833 0 + 147984545 148033414 0 14 529,32,81,131,118,153,300,206,84,49,85,130,46,1668, 0,25695,28767,33118,33695,33998,35644,38005,39629,40577,41402,43885,48367,49310,
+chr1 148077485 148111797 NM_002651 0 - 148078400 148111728 0 12 1097,121,133,266,124,105,110,228,228,45,937,77, 0,2081,2472,6871,9907,10257,11604,14199,15637,18274,23636,34235,
+chr1 148185113 148187485 NM_002796 0 + 148185136 148187378 0 7 163,207,147,82,117,89,120, 0,416,877,1199,1674,1977,2252,
+chrX 152648233 152662158 NM_000425 0 - 152648964 152662138 0 28 963,12,73,135,156,120,174,123,202,116,223,71,198,111,125,157,167,112,144,132,185,112,171,123,203,106,11,100, 0,1436,1545,1951,2390,2653,2889,3156,3367,3772,4717,5122,5424,5868,6066,6370,6629,6909,7588,7871,8124,8456,8858,9125,10220,10660,11296,13825,
+chrX 152691216 152693487 NM_000054 0 + 152691446 152693029 0 3 255,885,664, 0,616,1607,
+chrX 152693677 152712545 NM_001666 0 - 152694029 152712503 0 22 586,100,93,184,74,234,106,135,78,61,103,28,85,192,102,222,129,183,63,163,205,109, 0,1693,2066,2364,2635,2794,3129,3323,3545,3752,5323,5647,5841,6032,6401,11455,11778,13249,13719,13987,14227,18759,
+chr2 220108603 220116964 NM_001927 0 + 220108689 220116217 0 9 664,61,96,162,126,221,44,83,789, 0,1718,1874,2118,2451,2963,5400,7286,7572,
+chr2 220229182 220233943 NM_024536 0 - 220229609 220233765 0 4 1687,180,574,492, 0,1990,2660,4269,

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/sort_in2.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/sort_in2.bed Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,6 @@
+chr10 100 200 feature1 100.01 +
+chr20 800 900 feature2 1.1 +
+chr2 500 600 feature3 1000.1 +
+chr1 300 400 feature4 1.1e-05 +
+chr21 300 500 feature5 1.1e2 +
+chr15 700 800 feature6 1.1e4 +

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/sort_out1.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/sort_out1.bed Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,32 @@
+# comment 1 \n\n''" again
+# comment 2 **}"''' special
+# comment 3 @n/n""" characters
+chr1 148185113 148187485 NM_002796 0 + 148185136 148187378 0 7 163,207,147,82,117,89,120, 0,416,877,1199,1674,1977,2252,
+chr1 148077485 148111797 NM_002651 0 - 148078400 148111728 0 12 1097,121,133,266,124,105,110,228,228,45,937,77, 0,2081,2472,6871,9907,10257,11604,14199,15637,18274,23636,34235,
+chr1 147984101 148035079 BC007833 0 + 147984545 148033414 0 14 529,32,81,131,118,153,300,206,84,49,85,130,46,1668, 0,25695,28767,33118,33695,33998,35644,38005,39629,40577,41402,43885,48367,49310,
+chr1 147962006 147975713 NM_005997 0 - 147962192 147975670 0 6 574,145,177,115,153,160, 0,1543,7859,9048,9340,13547,
+chr2 220229182 220233943 NM_024536 0 - 220229609 220233765 0 4 1687,180,574,492, 0,1990,2660,4269,
+chr2 220108603 220116964 NM_001927 0 + 220108689 220116217 0 9 664,61,96,162,126,221,44,83,789, 0,1718,1874,2118,2451,2963,5400,7286,7572,
+chr2 118389378 118390700 BC005078 0 - 118390395 118390500 0 1 1322, 0,
+chr2 118288484 118306183 NM_006773 0 + 118288583 118304530 0 14 184,285,144,136,101,200,115,140,162,153,114,57,178,1796, 0,2765,4970,6482,6971,7183,7468,9890,10261,10768,11590,14270,14610,15903,
+chr5 131621285 131637046 NM_003687 0 + 131621326 131635821 0 7 134,152,82,179,164,118,1430, 0,4915,8770,13221,13609,14097,14331,
+chr5 131556201 131590458 NM_004199 0 - 131556601 131582218 0 15 471,97,69,66,54,100,71,177,194,240,138,152,97,100,170, 0,2316,2802,5596,6269,11138,11472,15098,16528,17674,21306,24587,25142,25935,34087,
+chr5 131424245 131426795 NM_000588 0 + 131424298 131426383 0 5 215,42,90,42,535, 0,313,1658,1872,2015,
+chr5 131170738 131357870 AF099740 0 - 131311206 131357817 0 31 112,124,120,81,65,40,120,129,61,88,94,79,72,102,144,117,89,73,96,135,135,78,74,52,33,179,100,102,65,115,248, 0,11593,44117,47607,104668,109739,114675,126366,135488,137518,138009,140437,152389,153373,155388,159269,160793,162981,164403,165577,166119,167611,169501,178260,179675,180901,181658,182260,182953,183706,186884,
+chr6 108722790 108950942 NM_145315 0 + 108722976 108950321 0 13 325,224,52,102,131,100,59,83,71,101,141,114,750, 0,28931,52094,60760,61796,71339,107102,152319,181970,182297,215317,224802,227402,
+chr6 108639410 108689143 NM_152827 0 - 108640045 108688818 0 3 741,125,487, 0,2984,49246,
+chr6 108593954 108616704 NM_003269 0 + 108594662 108615360 0 9 733,146,88,236,147,97,150,106,1507, 0,5400,8778,10445,12037,14265,14749,15488,21243,
+chr6 108298214 108386086 NM_007214 0 - 108299600 108385906 0 21 1530,105,99,102,159,174,60,83,148,155,93,133,95,109,51,59,62,113,115,100,304, 0,2490,6246,10831,12670,23164,23520,27331,31052,32526,34311,36130,36365,38609,41028,42398,43048,51479,54500,59097,87568,
+chr7 116944658 117107512 AF377960 0 - 116945541 116979926 0 23 1129,102,133,64,186,206,179,188,153,100,87,80,96,276,118,255,151,100,204,1654,225,108,173, 0,7364,8850,10413,13893,14398,17435,24259,24615,35177,35359,45901,47221,49781,56405,66857,69787,72208,73597,80474,100111,150555,162681,
+chr7 116713967 116902666 NM_000492 0 + 116714099 116901113 0 27 185,111,109,216,90,164,126,247,93,183,192,95,87,724,129,38,251,80,151,228,101,249,156,90,173,106,1754, 0,24290,29071,50936,54313,55285,56585,60137,62053,68678,79501,107776,110390,111971,114967,122863,123569,126711,130556,131618,134650,147559,162475,172879,184725,185496,186945,
+chr7 116511232 116557294 NM_003391 0 - 116512159 116556994 0 5 1157,265,278,227,383, 0,20384,37843,43339,45679,
+chr7 113320332 113924911 AK131266 0 + 113862563 113893433 0 20 285,91,178,90,58,75,138,51,201,178,214,105,88,84,77,102,122,70,164,1124, 0,201692,340175,448290,451999,484480,542213,543265,543478,545201,556083,558358,565876,567599,573029,573245,575738,577123,577946,603455,
+chr8 118880786 119193239 NM_000127 0 - 118881131 119192466 0 11 531,172,161,90,96,119,133,120,108,94,1735, 0,5355,7850,13505,19068,20309,23098,30863,36077,37741,310718,
+chr9 128849867 128870133 NM_020145 0 - 128850516 128869987 0 11 757,241,101,90,24,63,93,134,129,142,209, 0,1071,1736,2085,2635,4201,6376,6736,13056,14247,20057,
+chr9 128789530 128848928 NM_015354 0 + 128789552 128848511 0 44 54,55,74,85,81,45,93,120,212,115,201,90,66,120,127,153,127,88,77,115,121,67,129,140,107,207,170,70,68,196,78,86,146,182,201,93,159,138,75,228,132,74,130,594, 0,1491,5075,8652,9254,10312,11104,11317,20808,21702,23060,25462,31564,32908,33566,34851,35204,35595,35776,37202,38860,39111,39891,40349,42422,45499,45827,46675,47158,47621,50453,50840,51474,51926,53831,54186,55119,55619,57449,57605,57947,58352,58541,58804,
+chr9 128787362 128789566 NM_014908 0 - 128787519 128789136 0 1 2204, 0,
+chr9 128763240 128783870 NM_174933 0 + 128764156 128783586 0 12 261,118,74,159,76,48,56,63,129,117,127,370, 0,522,875,5630,12374,12603,15040,15175,18961,19191,20037,20260,
+chrX 152693677 152712545 NM_001666 0 - 152694029 152712503 0 22 586,100,93,184,74,234,106,135,78,61,103,28,85,192,102,222,129,183,63,163,205,109, 0,1693,2066,2364,2635,2794,3129,3323,3545,3752,5323,5647,5841,6032,6401,11455,11778,13249,13719,13987,14227,18759,
+chrX 152691216 152693487 NM_000054 0 + 152691446 152693029 0 3 255,885,664, 0,616,1607,
+chrX 152648233 152662158 NM_000425 0 - 152648964 152662138 0 28 963,12,73,135,156,120,174,123,202,116,223,71,198,111,125,157,167,112,144,132,185,112,171,123,203,106,11,100, 0,1436,1545,1951,2390,2653,2889,3156,3367,3772,4717,5122,5424,5868,6066,6370,6629,6909,7588,7871,8124,8456,8858,9125,10220,10660,11296,13825,
+chrX 122719582 122773357 NM_001167 0 + 122745047 122766566 0 7 96,909,100,79,43,201,6985, 0,25433,28421,31040,32533,40295,46790,

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/sort_out2.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/sort_out2.bed Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,32 @@
+# comment 1 \n\n''" again
+# comment 2 **}"''' special
+# comment 3 @n/n""" characters
+chr1 147962006 147975713 NM_005997 0 - 147962192 147975670 0 6 574,145,177,115,153,160, 0,1543,7859,9048,9340,13547,
+chr1 147984101 148035079 BC007833 0 + 147984545 148033414 0 14 529,32,81,131,118,153,300,206,84,49,85,130,46,1668, 0,25695,28767,33118,33695,33998,35644,38005,39629,40577,41402,43885,48367,49310,
+chr1 148077485 148111797 NM_002651 0 - 148078400 148111728 0 12 1097,121,133,266,124,105,110,228,228,45,937,77, 0,2081,2472,6871,9907,10257,11604,14199,15637,18274,23636,34235,
+chr1 148185113 148187485 NM_002796 0 + 148185136 148187378 0 7 163,207,147,82,117,89,120, 0,416,877,1199,1674,1977,2252,
+chr2 118288484 118306183 NM_006773 0 + 118288583 118304530 0 14 184,285,144,136,101,200,115,140,162,153,114,57,178,1796, 0,2765,4970,6482,6971,7183,7468,9890,10261,10768,11590,14270,14610,15903,
+chr2 118389378 118390700 BC005078 0 - 118390395 118390500 0 1 1322, 0,
+chr2 220108603 220116964 NM_001927 0 + 220108689 220116217 0 9 664,61,96,162,126,221,44,83,789, 0,1718,1874,2118,2451,2963,5400,7286,7572,
+chr2 220229182 220233943 NM_024536 0 - 220229609 220233765 0 4 1687,180,574,492, 0,1990,2660,4269,
+chr5 131170738 131357870 AF099740 0 - 131311206 131357817 0 31 112,124,120,81,65,40,120,129,61,88,94,79,72,102,144,117,89,73,96,135,135,78,74,52,33,179,100,102,65,115,248, 0,11593,44117,47607,104668,109739,114675,126366,135488,137518,138009,140437,152389,153373,155388,159269,160793,162981,164403,165577,166119,167611,169501,178260,179675,180901,181658,182260,182953,183706,186884,
+chr5 131424245 131426795 NM_000588 0 + 131424298 131426383 0 5 215,42,90,42,535, 0,313,1658,1872,2015,
+chr5 131556201 131590458 NM_004199 0 - 131556601 131582218 0 15 471,97,69,66,54,100,71,177,194,240,138,152,97,100,170, 0,2316,2802,5596,6269,11138,11472,15098,16528,17674,21306,24587,25142,25935,34087,
+chr5 131621285 131637046 NM_003687 0 + 131621326 131635821 0 7 134,152,82,179,164,118,1430, 0,4915,8770,13221,13609,14097,14331,
+chr6 108298214 108386086 NM_007214 0 - 108299600 108385906 0 21 1530,105,99,102,159,174,60,83,148,155,93,133,95,109,51,59,62,113,115,100,304, 0,2490,6246,10831,12670,23164,23520,27331,31052,32526,34311,36130,36365,38609,41028,42398,43048,51479,54500,59097,87568,
+chr6 108593954 108616704 NM_003269 0 + 108594662 108615360 0 9 733,146,88,236,147,97,150,106,1507, 0,5400,8778,10445,12037,14265,14749,15488,21243,
+chr6 108639410 108689143 NM_152827 0 - 108640045 108688818 0 3 741,125,487, 0,2984,49246,
+chr6 108722790 108950942 NM_145315 0 + 108722976 108950321 0 13 325,224,52,102,131,100,59,83,71,101,141,114,750, 0,28931,52094,60760,61796,71339,107102,152319,181970,182297,215317,224802,227402,
+chr7 113320332 113924911 AK131266 0 + 113862563 113893433 0 20 285,91,178,90,58,75,138,51,201,178,214,105,88,84,77,102,122,70,164,1124, 0,201692,340175,448290,451999,484480,542213,543265,543478,545201,556083,558358,565876,567599,573029,573245,575738,577123,577946,603455,
+chr7 116511232 116557294 NM_003391 0 - 116512159 116556994 0 5 1157,265,278,227,383, 0,20384,37843,43339,45679,
+chr7 116713967 116902666 NM_000492 0 + 116714099 116901113 0 27 185,111,109,216,90,164,126,247,93,183,192,95,87,724,129,38,251,80,151,228,101,249,156,90,173,106,1754, 0,24290,29071,50936,54313,55285,56585,60137,62053,68678,79501,107776,110390,111971,114967,122863,123569,126711,130556,131618,134650,147559,162475,172879,184725,185496,186945,
+chr7 116944658 117107512 AF377960 0 - 116945541 116979926 0 23 1129,102,133,64,186,206,179,188,153,100,87,80,96,276,118,255,151,100,204,1654,225,108,173, 0,7364,8850,10413,13893,14398,17435,24259,24615,35177,35359,45901,47221,49781,56405,66857,69787,72208,73597,80474,100111,150555,162681,
+chr8 118880786 119193239 NM_000127 0 - 118881131 119192466 0 11 531,172,161,90,96,119,133,120,108,94,1735, 0,5355,7850,13505,19068,20309,23098,30863,36077,37741,310718,
+chr9 128763240 128783870 NM_174933 0 + 128764156 128783586 0 12 261,118,74,159,76,48,56,63,129,117,127,370, 0,522,875,5630,12374,12603,15040,15175,18961,19191,20037,20260,
+chr9 128787362 128789566 NM_014908 0 - 128787519 128789136 0 1 2204, 0,
+chr9 128789530 128848928 NM_015354 0 + 128789552 128848511 0 44 54,55,74,85,81,45,93,120,212,115,201,90,66,120,127,153,127,88,77,115,121,67,129,140,107,207,170,70,68,196,78,86,146,182,201,93,159,138,75,228,132,74,130,594, 0,1491,5075,8652,9254,10312,11104,11317,20808,21702,23060,25462,31564,32908,33566,34851,35204,35595,35776,37202,38860,39111,39891,40349,42422,45499,45827,46675,47158,47621,50453,50840,51474,51926,53831,54186,55119,55619,57449,57605,57947,58352,58541,58804,
+chr9 128849867 128870133 NM_020145 0 - 128850516 128869987 0 11 757,241,101,90,24,63,93,134,129,142,209, 0,1071,1736,2085,2635,4201,6376,6736,13056,14247,20057,
+chrX 122719582 122773357 NM_001167 0 + 122745047 122766566 0 7 96,909,100,79,43,201,6985, 0,25433,28421,31040,32533,40295,46790,
+chrX 152648233 152662158 NM_000425 0 - 152648964 152662138 0 28 963,12,73,135,156,120,174,123,202,116,223,71,198,111,125,157,167,112,144,132,185,112,171,123,203,106,11,100, 0,1436,1545,1951,2390,2653,2889,3156,3367,3772,4717,5122,5424,5868,6066,6370,6629,6909,7588,7871,8124,8456,8858,9125,10220,10660,11296,13825,
+chrX 152691216 152693487 NM_000054 0 + 152691446 152693029 0 3 255,885,664, 0,616,1607,
+chrX 152693677 152712545 NM_001666 0 - 152694029 152712503 0 22 586,100,93,184,74,234,106,135,78,61,103,28,85,192,102,222,129,183,63,163,205,109, 0,1693,2066,2364,2635,2794,3129,3323,3545,3752,5323,5647,5841,6032,6401,11455,11778,13249,13719,13987,14227,18759,

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/sort_out3.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/sort_out3.bed Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,6 @@
+chr1 300 400 feature4 1.1e-05 +
+chr20 800 900 feature2 1.1 +
+chr10 100 200 feature1 100.01 +
+chr21 300 500 feature5 1.1e2 +
+chr2 500 600 feature3 1000.1 +
+chr15 700 800 feature6 1.1e4 +

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/srma_in1.bam

Binary file rnaseq/cutadapt/test-data/srma_in1.bam has changed

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/srma_in2.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/srma_in2.fa Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,301146 @@\n+>dummy_chr\n+cttgaggtccggagttcaagaccagcctggccaacatggtgaaacctcat\n+ctctactaaaaaaaagaaaaaaatatataaaaattatccaggaatgacgg\n+cgcgtgcctgtaatcccagctactctggaggctgaggcaggagaatcgct\n+tgaacccagaaggcagaggttgcagtgagccaaggttgccccactgcact\n+ccggccccggtaacagagcaagactctatctcaaaaaaaaaaaaaaaaaa\n+aaaaaaaaaaaaaaTTAGCAACAGATTATGGAATAGCTTTTTACCAAAGA\n+GGATCTGTTTTCTGCTGATGGCGACTGCTTTTGCAACTAGCAAACCCCAC\n+CTGTGTTTCCTCAGTTTCCCCATCTGTACAGTCAAAATATTATCTACATT\n+TTAGCCTTATTACGAAGTCATATCATGTGCGAGGGCCAAAATCTCCCAGA\n+ATCTTCAGGAAGGTAGCACATCACCATTAAGGAGACATGTGCTGATATCC\n+TCTGGCTCCTCTGAAATCATCTGGTGATAGCACTAGCGCTCACTAGGGAC\n+CACTAAATTCAGCTGTGCTTTTGCAACAACGATAATAACAAATTATCCCT\n+TCACCAGTAGTTAATAAAACCGCACCATATGTAGAAGAAGAAAATTATAA\n+GACAGAAGGGCTCATCTCCACCCACCACAAGTCAAGACAATACTGTGTAT\n+TGTGATTCACCAAGATGCAGTAAACAAAAAAACACCTTTCCAACCATAAC\n+TGCATTTCTCAGTGTGGGTGATTTCAGACACAGCCAGGGTAAGAAGCCAA\n+GAAATTTCAGTTCTACAGTCTGGAAGAATAAAGGCTAACAACAACAGGCA\n+ATGAAAAATTATTTTTAAAAAAGTTATACAAAACTTTTCTCCTCATAGAT\n+AGAAACAACAACAACAACAAAAAAGCTTAATCTTCCAGAAACCTGTCTCT\n+GGCCAGCTTCCAATCCAGAAAGTCTGCTGATGATGGAAGGAGCTCTCCTT\n+AGGAACTCATATGGCTATGACCTCCCATCTGCATCTGATCCTGCTGATCT\n+GCACCCCCTCCAAAATACACACCCTTCCCTCAAATTCCATGCCtttattt\n+atttatttgtttatttatttatttattgagatggagtctcgctctgtcgc\n+ccaggcgacaacacaatggcgtgatctcggctcactgcaacctccactcc\n+caggttcaagtgattctcctgcctcagcctcctgagtagctgggactgca\n+ggcatgcgctacaacacctggctaatttttgtatttttagttgagaaaga\n+gtttcgccatgttggccaggctggtcttgaactcctgacctcaggtgatc\n+tgcccgccttggcctcccaaagtgctggaattacaggcatgagccaccgt\n+gcccagccGAATTCCATGCCTGTATAACCCTCAGATATTCCTCTTGCCCC\n+AACTGTAGGTTCTGCCCACAGCCTTCTACATGGCTCCATCTAGTTCCTTC\n+CAGACTCTCCTTCTTCAGCACAAATCCCTCTTTCTCACCTCCTGGGATTA\n+TCCTACTGATGATCCACCACTTAGGGTCAAAACCTTTCACCCTTATGAgg\n+gcagcgtgattggtaaatgtaacataggcttaggatctgagagacctgat\n+cctaacctgccattcactgcatctgtgaccttaagccagccacttaatat\n+ccctacgaatcactttctccatctgcaaaacaggatacctgcctgcaggt\n+ttgtgctgggaattaagtgaggcaatgtatgtaaacacactttttcttgg\n+tatttagttggagcttcatgaatattcattTCTTTCTTTCCTCTTGTGTC\n+CTTCTTCCCCTTGTTCTTCCCCGAAGGTCCCTGAAGTATCTTCTACATCT\n+TGTCTCTTCTATTCCTACCCTTCTAATCCAGGTCAGGTCACCTTGCTTTC\n+AAtttccttttttttttttttttgagacagagtcttgctctgtggcctag\n+gctggagtgcagtgatgcgatctcggctcactgcagcctctgcctcccgg\n+gttcaagtgattctcatgcctcagcctcccgagtagctgggattacaagc\n+atgcgccaccaggccaggacaatttttgtatttttagtagagacggagtt\n+tcactatgttggctaggctggtctcaaactcctggcctcaagtgatccac\n+ccgcctcagcctcccaaagtgctgggattacaggcatgagccaccgtgcc\n+tggcACttttttttttttttttaagacaaggtctcactttgttacccagg\n+ctggagtgcaacgcggtgatctcagctcactgcaacctccacctcctggg\n+ttcaagtgattctcatgcctcagccctccaggtagctgggatgacaggtg\n+cgcaccaccacgcctggctaatttttgtatttttagtagagacatggttt\n+caccatgttggccaggctggtctcgaactcctgacctgaaatgatctgcc\n+ctgacctcaggtgatccacctacctcagcttcccaaagtgctgggattac\n+aggcgcccgccaccatgcgcagctCatttttgtatttgtagtagagacgg\n+agtttcgccatgttggccaggatggtcttgagctactgacctcaagtgat\n+ttgcccttctgggcctcccaaagtgttgggactacaggtgtgagccaccg\n+tgcccagccAagatttactttaaagaattggctcatgcatttgcgggggc\n+tgccaagtttgaaatctgcaaggtagggttggagacccagggaaaaaatg\n+atgctgcagtttgagtccaagggcatctggaggcagaacttcttccttct\n+cggggacctcagtcttctgtcttaagatctttgactgattggatgaggcc\n+taccaatgttatgaagggtcatttgctttactcaacccctactgatgtag\n+atgttaattacatccaaacataactgacagcaacatctagacatctagac\n+tggtatttgaccaaacgactaggcaccacaacctaccaagttgacagatc\n+aaatgaaccatcaTTCCCCACACAACAGACTTTTTCTCCAGTGCCTAGTA\n+ATGCCATCAATATTAGCCAAAGGAAGAAAGAGAATAAAATGTATTCCCAC\n+AGAATGTCTACAATGCAATATCCAACAGGTGCTCCTGACAGACTCTCTTC\n+CATCCCACAAGGCCACCTGTCCTGTGCTCTGAAGGGAGGTCAGCTCAGGT\n+GTTCCAGGTAGCCACAGTCTCCGGGGCATGAAGAGGTCGCTGCGAAGAGC\n+GGCAAGTCTTGCAGAATGTCTTCCTTTCCATATATTTCAAGACAATTGCA\n+ACCATCCAAGCTTTTGTCTCTTGGTAGCCAACATCATCAAGAGTGGTGAC\n+TACCTTTTATTTCAACATGGAAAACTGCATTAAAATATATTTACAGATTG\n+GAAAACACACATATCCAGGAACAATGTGGTAGTTTATACCACAGCTTCTG\n+ATTCTTGAAACAGCCGCTACTTTTAACCACCCTCCCTCCCCTCCCAACAA\n+ACATAAATTATGGAGGTCCTGGGTACATAAGCTACCCTGTTGGTGTTATT\n+TCTGCTCTAGTCTTGGATCTGAAATCATCACCCTCTCCCACCTCTAAGCC\n+AAGACTTCAAGCACACAGCATGGTGAGGGTGGGGGGTGTCCCCAGCAAGT\n+CCTCAATTCCAATGCAGCTGGGCTTAAAGTTCAGCATGAAAGGCCAGCAG\n+TGGGGAGGGAGGTTGGAATGATTGTTCAACAGCCTCCCACTCCCTGCTCA\n+TGACTAATGCATC'..b'CCGGTGAGGCCGGGGCCCTGTGGCTAGCGCCCCCGTGTCAGGTGCC\n+TGTGTCGTGCCCTGGGCCTGAGCACGTGGGTCTGAGCACTGCAGGGCTTC\n+TTCCCAAGGCTGTGGTGGCCCGTCTGCTGCCTTGCCTCTGGTTCATCTCC\n+TGCCACAAAGCCTGGCCCACCAGGGAGTGTCGTGACAGGTGGATGTGGGC\n+CCTGGGTGTCCATAGCCTGGCTGGGCTCCCTGCAGGCCCCAGGATTGAAG\n+CTGAGGCTTACCATGGGCCTTGCAGTGGCAGGCGCCTGGCATGCCGGGAG\n+TGGATCTCATGGAGCCCTTTCGCAGGCTCGGGCCAACTTTGTCACTGGGA\n+AATTCTCGTTGTTTCTCTGGGGTCCTCTTTGTTTGCTTTCCTTTCGACAT\n+GGTTAACCCTGCCCTAGTTTCTCACTCTGGTTTGTTTTCTTTCCTTTCAC\n+CCTGGCTCTGCGGTTGTGTGACTCTGCGCCAGCTACCGGCCCTGACCACT\n+CTCCCGGCAGGGCCTAGGCTCTGACGGTGGCGTGAACCCGGCCCTGGTGT\n+GCAGCGGCCCTGCCTCGCCGTGTTGCGTGACGCCCCCTTCGCTGTGTGGT\n+GTTTTGTGGCTCTCTTCAGGTGTTGCCATCTGTCCCTTTTGTTCTCTTTG\n+TCTCCTTGAAAAGTTGATGGGCCTGCAGCCGCACAGGCAGTTGTGGGCAT\n+GGTGGGCGCTGAGTCTGGAGGTTGTTCAAGGCCAGCAGCGTTGCCCAGAG\n+CCCTGCTGCTGACGCTGCCGTCACTGGTTCTAGCTCTCACATTCTCAGCT\n+GCACGTTTCTGTTTCCACCTCAGTAAACGCAAACTCTTGTTCATAGGCAC\n+AGCTGTCACTGCAGCACACAAGGACTCAGGTTTGTAAAGACAAACGATTG\n+ATTTGTGTGTGACGTGCTGTTTGTTTGCACTGGATTTTGCAAATTATTTA\n+CTAAAGAAAAGTACTTCAGACCTTTTGTGGCAAACAATAAATACAGCGAT\n+ACTCTAATCTTCAGTATTCATAAAAATGGGTGGAGTTGTCCCATTTTAAC\n+GCCCCAGCAAAACAGGAGCATTTCTCTAACGGTCTTTACTACAGTGCCTA\n+AGCTACAGTTTGTGCTGCTTTTCAGAAACTGATGTCTTGTGATAGTTACA\n+GCTGTTCTTGGGCTGGGTCCCAGCTCTGGTCTCCAGGGAGGGCCTGGGCC\n+CCCTGGATCCCCTGTGCCTGTTCAGCGTGGGTGTCACCTGCTTCGCCAGC\n+TGGGATTGCGATCCTCGTGTGCCTCCCTGAGTCTGCGTGCATGTCAGCAG\n+GCACCCTGCCCCAGTGCCCCTGGCCCTGAAGATGGTGATGTTCTGGGCCA\n+AGCACAGCCCAGGTCGTGTCCAGGCCCAGGGAGTGCAGTCAGGGGAGCAG\n+CTGCCCTCAGGCCTCGCCGCACGTCTCAGGTTGTGAATGTTACCGCAGCA\n+GCATGTTTACAGCGGACTCGCCGTTAACTGCTGACAGTGGCATCAACATT\n+TATTGAGAATGTTACTTGCATTGGTCATGATAGTTTGTGATAAAAGACTT\n+AACACTTTTACAAATCAAAATGATTTTTTGGAAGCTGGTGAAATGTCAGT\n+TAACATGTATGAATTTAATATTTTAGTTTTTGGGTGGCTTAAAGACTTCA\n+GGATTCAGGCCGGGAGTGGTAGCTCACAGCTGTAATCCCAGAACCAGACT\n+CCATCTCAGAAATAATTATAATAAAATAGAGACTTCGGGACTCAGCAGCA\n+GAGACTCCATCTCAGAAATAATAGTAATAAAATAGAGACTTCAGGACTCA\n+GCAGCAGAGACTCCATCTCAGAAATAATAGTAATAAAATAGAGACTTCAG\n+GACTCAGCAGCAGAGACTCCATCTCAGAAATAATAGTAATAAAATAGAGA\n+CTTCAGGACTCAGCAGCAGAGACTCCATCTCAGAAATAATAATAAAATAG\n+AGACTTCAGGACTCAGCAACAGAGACTCCATCTCAGAAATAATAGTAATA\n+AAATAGAGACTTCAGGATTCAGCAGCAGACACTCCATCTCAGAAATAATA\n+GTAATAAAATAGAGACTTCAGGATTCGGCAGCAGACACTCCATCTCAGAA\n+ATAATAGTAATAAAATAGAGACTTCAGGATTCGGCAGCAGAGACTCCATC\n+TCAGAAATAATAGTAATAAAATGGAGACTTCAGGACTCGGCAGCAGAGAC\n+TCCATCTCAGAAATAATAATAATAAAATGGAGACTTCAGGACTCGGCAGC\n+AGAGACTCCATCTCAGAAATAATAGTAATAAAATAGAGACTTCAGGACTC\n+AGCAGCAGGCACTCCATCTCAGAAATAATAGTAATAAAATAGAGACTTCA\n+GGATTCAGCAGCAGAGACTCCATCTCGGAAATAATAGTAATAAAATAGAG\n+ACTTCAGGATTCAGCAGCAGAGACTCCATCTCAGAAATAATAATAATAAA\n+ATGGAGGCTTCAGGACTTAGCAGCAGAGAGCCCCTTTTTCCAAGACGCTT\n+TTTCATCTGCAGTTTCCACTTGGGCCGGGGCTTCGCACCCCAGgtctcag\n+gctggttttgctgctggaagagaatttttgaggctaggcgatttatcaca\n+gacacacgtttgtgacttacagttctggaggctagaaagcctaaggtcag\n+ggtgccagcaggtttggtgtctggtgaggtacccatctctgcttctaagg\n+cagagccttgcacactgtatcctccggagtggagggctggatcatcctgg\n+ggcagaggcagaagggccgagtgggaggaccactcccaaagccgcttatt\n+gaggcattaaaactgctgtgagggtggagcccttgcggcctcgtcacctt\n+ttcaaggcccttccaataccatcactctggcagttaaatttcaacatgag\n+ttttggaggggacagaaatttaaactgtggtaCCCAGTTAATtttattta\n+tttatttatttatttgaaggagtctcactttgtcacccaggctggagtgc\n+agcaatgcaatctgggctcactgcaacctccatctcccggattcaagtga\n+ttctcctgcctcagcctcccgagtagctgggattacaggcacacgccacc\n+atgtccagctaattttgtatttttagtagagacagggttttaccatgatg\n+gccaggctggtctcaaactcctgacgtcgagtgatccacccgcctcggcc\n+tcccaaagtgctgggattacaggtgtgaaccaccccacccgaccTAGATT\n+CGCTTTTGATTTACCGATGGGGCGTTTGCCTTTCCCCTAGACACGTCACA\n+ACCCCAGGCTCTCAGCACCGTCCGTCGTCTGCTGGGACTGGGCTTAGTCG\n+TGTGTTTCTGTCTGGGAGACTGTACTGAAGGCAGAATTCCTAGAGAATCA\n+CCCACATGTCACTCAGAAGTATTCTTCTCAGGCTTCAGAAATTTGCTTTA\n+GCCAATGTTGTTTTAAAAGATGGGCGTTTTACCCCGAATTGAAGTGACTT\n+CATTTTCGGTGGGTTTTGACTGAATCACCATCAGGAGATGCACGTGTCAT\n+GCACCAGCCTCTGAGGTGCGGGGGTGTCCCCGTGTCTGTCCTGTTTGCAT\n+CCTTAGCTCTCCGGAAGGAAGTGGAGGATCTGACCAAAGAACAGTCGGAG\n+ACCAGGAAGCAGGCTGAGAAGGACCGCTCAGCCCTGCTCTCCCAGATGAA\n+GATTTTGGAGTCTGAGTTAGAAGAACAGCTGTCTCAGCATCGCGGGTGTG\n+CCAAGCAGGCGGAGGCCGTCACTGCCCTGGAACAGCAGGTGGCATCTCTG\n+GACAAGCATTTGCGCAACCAGCGGCAATTCATGGATGTAAGAATTCTGAA\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/srma_in3.bam

Binary file rnaseq/cutadapt/test-data/srma_in3.bam has changed

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/srma_in3.sam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/srma_in3.sam Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,8 @@
+GA5:3:2:1710:1301#0 0 dummy_chr 1279 18 76M * 0 0 GAACTCCTGACCTCAGGTGATCTGCCCGCCTTGGCCTCCCAAAGTGCTGGAATTACAGGCATGAGCCACCGTGCCC 6->;B==?B?AAA??9B<AA?@A==AA9A?<A?<&:A?=<9<?>19;?A=9:?999;=4=6A9/8;4==;1';;3= XT:A:U NM:i:0 X0:i:1 X1:i:3 XM:i:0 XO:i:0 XG:i:0 MD:Z:76 XA:Z:chr14,+56265423,76M,1;chr14,+91530561,76M,1;chr2,+230545178,76M,1;
+GA5:3:24:462:583#0 0 dummy_chr 128882 37 76M * 0 0 TAAAAAAAGGACAGTGACGCACCTTGTATAGCGATGTGTCATCTAAAACATCTATTCAAAGAACAGAAGACTCACC BBABBBB@BBBBBA?BBBBBBAA@AB?BBBA@B=>@?@;@?@?A>=1=?>??><???;;>?;;;?>8999;;9;;< XT:A:U NM:i:3 X0:i:1 X1:i:0 XM:i:3 XO:i:0 XG:i:0 MD:Z:6C21G30G16
+GA5:3:29:1241:1653#0 0 dummy_chr 5591013 37 76M * 0 0 TCATGCACACACAGACAGCTGTCGGGGGATGCATGCCAACCAGAGGGGCCACACATATACCGTGTTGATGGGACAG BBBBBBACBCBBBBBBBBBBBABBABBB@AA>@?@?@>=????<???:?915399<=5=<==5=559545432353 XT:A:U NM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:58T17
+GA5:3:33:1591:303#0 0 dummy_chr 11880048 37 76M * 0 0 CTCGCCTGGGCCCGGTAAAGCCCCCACGTAGCCCCAGCCAGCCTGGAACATGCTTCCTGAGCTCCCAGCTCTTGGT BBBBBBBBBBB@BBB?BBBA@A>B@B?AABB?@>?BA?>AB;??A?6;=AAAAA=>3=9;@;===6,=?;;5==;6 XT:A:U NM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:76
+GA5:3:31:677:1537#0 16 dummy_chr 11880931 37 76M * 0 0 GAGGGTTTGAGAGAGCAGCCAGGAGAGCTTAGGGTCTCAGGGTGTCCCAGACCCCGACACCGGCCAGTGGCGGAAG ###################>9==9=9?>????>>?>8>>??AA?>A??>A4AA?AA?B=ABBBBBBBBBBBBBBBB XT:A:U NM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:76
+GA5:3:49:1480:1116#0 16 dummy_chr 11913868 37 76M * 0 0 GGGAGGAGGCCAGGACTTCAGGGACCCACAGCCATCACCTCCCTCCCCTGCCCCCTACACACCAACTCTCTGGAAA #################################44:4=944==;=???>=?>==??=A=A;ABA?A?AABAAABBB XT:A:U NM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:0T75
+GA5:3:61:213:1812#0 16 dummy_chr 13030396 37 76M * 0 0 GGTCCGGCGGGGTCGGACTGGACCAGCTGTTGGGCTTTGTTTGCTCTTTTTACGAATTGAAAAACTGAAGCCAGGA /=81,5948=485=4,),1;;7:87:6=;;@@AB=C8A@@BAB=>5>BBBB>BBAAA9ABA@B4B;BBBBBBBBCB XT:A:U NM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:0T75
+GA5:3:116:1581:552#0 16 dummy_chr 15055984 37 76M * 0 0 AGAAAGCCTAAGGTCAGGGTGCCAGCAGGTTTGGTGTCTGGTGAGGTACCCATCTCTGCTTCTAAGGCAGAGCCTT 48887429,3=;98<8<8@;<=?8@??98@@@<=AA>@@?B?A@@BA6BA@=@BABBB???B@BBBBBABBCBB?B XT:A:U NM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:76

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/srma_out1.bam

Binary file rnaseq/cutadapt/test-data/srma_out1.bam has changed

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/srma_out2.bam

Binary file rnaseq/cutadapt/test-data/srma_out2.bam has changed

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/tabular_to_fasta_out1.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/tabular_to_fasta_out1.fasta Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,60 @@
+>5_300_902_419
+GACTCATGATTTCTTACCTATTAGTGGTTGAACATC
+>5_300_880_431
+GTGATATGTATGTTGACGGCCATAAGGCTGCTTCTT
+>5_300_896_461
+GTTGTCGATAGAACTTCATGTGCCTGTAAAACAAGT
+>5_300_890_751
+ACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGC
+>5_300_897_443
+GTTTATGTTGGTTTCATGGTTTTGTCTAACTTTATC
+>5_300_906_879
+GCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCG
+>5_300_894_484
+GCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGC
+>5_300_890_811
+GTTATAACGCCGAAGCGGTAAAAATTTTTATTTTTT
+>5_300_889_530
+GTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACCT
+>5_300_898_886
+GTGGCCTGTTGATTCTAAAGGTTAGTTTCTTCACGC
+>5_300_878_205
+GTGACCGCATAAAGTGCACAACATGGAAATGAGGAC
+>5_300_920_381
+GCAGATCGCTACACGCAGGACGCTTTTTCACGTTCT
+>5_300_886_453
+GCTCGTTATGGTTTCCGTTGCTGCCATCTCAAAAAC
+>5_300_893_365
+GTTGACGGCCATAAGGCTGCTTCTGACGTTCGTGAT
+>5_300_892_801
+GTCAAGGACTGGTTTAGATATGAGTCACATTTTGTT
+>5_300_881_945
+GTGCTGAGTTTTTTTCTGTTACTGTGACATTAATTT
+>5_300_883_811
+GACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGG
+>5_300_899_654
+GGAAAATGAGAAAATTCGACCTATCCTTGCGCAGCT
+>5_300_883_644
+GAGTCTCATTTTGCATCTCGGCAATCTCTTTCTGAT
+>5_300_879_877
+GTCATAAGAGGTTTTACCTCCAAATGAAGAAATAAC
+>5_300_900_821
+GCTGGTAATGGTGGTTTTTTTTTTTTTTTTTTTTTT
+>5_300_886_965
+GTTGAGGCTTGCGTTTATGGTACGCTGGACTTTGTA
+>5_300_933_442
+GAGGAGAGTGCAGGTATTAATATCAAGGTTTGTGAG
+>5_300_879_782
+GGCGACTTCACGCCAGAATACGAAATACCAGGTATT
+>5_300_923_441
+GCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGA
+>5_300_877_772
+GGGATGAACATAATAAGCAATGACGGCAGCAATAAA
+>5_300_918_831
+GTATTTTACCAATGACCAAATCAAAGAAATGACTCG
+>5_300_904_940
+GTTTTTAGTGAGTTGTTCCATTCTTTAGCTCCTAGA
+>5_300_956_880
+GTATTGATAAAGCTGTTGCCGATACTTAGCACTATT
+>5_300_883_755
+GCGTACTTATTCGCCACCATGATTATTACCAGTGTT

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/tinywga.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/tinywga.bed Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,1 @@
+l��+�󪿊��ﮨ�"��"��:*��.��:*��.��:*��,��:*��,��+��+�󪿺��m�� (:��(:��(:��(
\ No newline at end of file

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/tinywga.bim
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/tinywga.bim Sat Feb 21 16:33:42 2015 +0100

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/tinywga.fam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/tinywga.fam Sat Feb 21 16:33:42 2015 +0100

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/tinywga.map
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/tinywga.map Sat Feb 21 16:33:42 2015 +0100

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/tinywga.ped
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/tinywga.ped Sat Feb 21 16:33:42 2015 +0100

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/tinywga.ped.space_to_tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/tinywga.ped.space_to_tab Sat Feb 21 16:33:42 2015 +0100

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/tophat_in1.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/tophat_in1.fasta Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,14 @@
+>test_chromosome
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+ACTACTATCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCC
+ACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGC
+AGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCT
+ACGTATTTGGCGCGCGGCGCTACGGCTGAGCGTCGAGCTTGCGATACGCC
+GTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAG
+ACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACT
+GTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAG
+TTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACTTGC
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/trimmer_a_f_c0_s1_e13_i62.dat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/trimmer_a_f_c0_s1_e13_i62.dat Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,5 @@
+12345 abcdef
+67890 ghjkl g
+>assa lljlj ljlj
+sasas hghg hg
+@dgf gfgf gfg

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/trimmer_a_f_c2_s1_e2_i62.dat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/trimmer_a_f_c2_s1_e2_i62.dat Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,5 @@
+12345 ab xyz
+67890 gh ghjt
+>assa lljlj ljlj
+sasas hg hghg
+@dgf gf gfgf

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/trimmer_a_f_c2_s2_e-2_i62.dat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/trimmer_a_f_c2_s2_e-2_i62.dat Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,5 @@
+12345 bcd xyz
+67890 hj ghjt
+>assa lljlj ljlj
+sasas g hghg
+@dgf f gfgf

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/trimmer_tab_delimited.dat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/trimmer_tab_delimited.dat Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,5 @@
+12345 abcdef xyz
+67890 ghjkl ghjt
+>assa lljlj ljlj
+sasas hghg hghg
+@dgf gfgf gfgf

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/uniq_out.dat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/uniq_out.dat Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,20 @@
+4 chr1
+1 chr10
+4 chr11
+1 chr12
+1 chr13
+1 chr14
+4 chr15
+4 chr16
+4 chr18
+4 chr19
+4 chr2
+4 chr20
+4 chr21
+4 chr22
+4 chr5
+4 chr6
+4 chr7
+1 chr8
+4 chr9
+4 chrX
\ No newline at end of file

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/users/test1@bx.psu.edu/1.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/users/test1@bx.psu.edu/1.fasta Sat Feb 21 16:33:42 2015 +0100

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/users/test3@bx.psu.edu/run1/2.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/users/test3@bx.psu.edu/run1/2.fasta Sat Feb 21 16:33:42 2015 +0100

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/vcf2pgSnp_input.vcf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/vcf2pgSnp_input.vcf Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,50 @@\n+##fileformat=VCFv4.1\n+##INFO=<ID=LDAF,Number=1,Type=Float,Description="MLE Allele Frequency Accounting for LD">\n+##INFO=<ID=AVGPOST,Number=1,Type=Float,Description="Average posterior probability from MaCH/Thunder">\n+##INFO=<ID=RSQ,Number=1,Type=Float,Description="Genotype imputation quality from MaCH/Thunder">\n+##INFO=<ID=ERATE,Number=1,Type=Float,Description="Per-marker Mutation rate from MaCH/Thunder">\n+##INFO=<ID=THETA,Number=1,Type=Float,Description="Per-marker Transition rate from MaCH/Thunder">\n+##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants">\n+##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">\n+##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">\n+##INFO=<ID=HOMLEN,Number=.,Type=Integer,Description="Length of base pair identical micro-homology at event breakpoints">\n+##INFO=<ID=HOMSEQ,Number=.,Type=String,Description="Sequence of base pair identical micro-homology at event breakpoints">\n+##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Difference in length between REF and ALT alleles">\n+##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">\n+##INFO=<ID=AC,Number=.,Type=Integer,Description="Alternate Allele Count">\n+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total Allele Count">\n+##ALT=<ID=DEL,Description="Deletion">\n+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n+##FORMAT=<ID=DS,Number=1,Type=Float,Description="Genotype dosage from MaCH/Thunder">\n+##FORMAT=<ID=GL,Number=.,Type=Float,Description="Genotype Likelihoods">\n+##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele, ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/pilot_data/technical/reference/ancestral_alignments/README">\n+##INFO=<ID=AF,Number=1,Type=Float,Description="Global Allele Frequency based on AC/AN">\n+##INFO=<ID=AMR_AF,Number=1,Type=Float,Description="Allele Frequency for samples from AMR based on AC/AN">\n+##INFO=<ID=ASN_AF,Number=1,Type=Float,Description="Allele Frequency for samples from ASN based on AC/AN">\n+##INFO=<ID=AFR_AF,Number=1,Type=Float,Description="Allele Frequency for samples from AFR based on AC/AN">\n+##INFO=<ID=EUR_AF,Number=1,Type=Float,Description="Allele Frequency for samples from EUR based on AC/AN">\n+##INFO=<ID=VT,Number=1,Type=String,Description="indicates what type of variant the line represents">\n+##INFO=<ID=SNPSOURCE,Number=.,Type=String,Description="indicates if a snp was called when analysing the low coverage or exome alignment data">\n+#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tHG00096\tHG00097\tHG00099\tHG00100\n+1\t10523\t.\tTCCG\tT\t152\tPASS\tVT=INDEL;RSQ=0.5246;ERATE=0.0023;AN=2184;AA=.;THETA=0.0172;AC=5;AVGPOST=0.9954;LDAF=0.0045;AF=0.00;AMR_AF=0.00;AFR_AF=0.01\tGT:DS:GL\t0|0:0.000:0.00,-1.50,-34.60\t0|0:0.000:0.00,-0.90,-20.70\t0|0:0.000:0.00,-1.50,-34.50\t0|0:0.000:0.00,-0.30,-6.90\n+1\t10583\trs58108140\tG\tA\t100\tPASS\tVT=SNP;SNPSOURCE=LOWCOV;AN=2184;AC=327;LDAF=0.2363;AVGPOST=0.7630;ERATE=0.0098;AA=.;RSQ=0.4161;THETA=0.0197;SNPSOURCE=LOWCOV;AF=0.15;ASN_AF=0.15;AMR_AF=0.18;AFR_AF=0.04;EUR_AF=0.21\tGT:DS:GL\t0|0:0.250:-0.18,-0.47,-2.42\t0|0:0.200:-0.24,-0.44,-1.16\t0|0:0.250:-0.15,-0.54,-3.12\t0|1:0.750:-0.48,-0.48,-0.48\n+1\t10611\trs189107123\tC\tG\t100\tPASS\tVT=SNP;SNPSOURCE=LOWCOV;THETA=0.0048;RSQ=0.3814;AN=2184;AVGPOST=0.9427;ERATE=0.0024;LDAF=0.0420;AA=.;SNPSOURCE=LOWCOV;AC=39;AF=0.02;ASN_AF=0.02;AMR_AF=0.02;AFR_AF=0.01;EUR_AF=0.02\tGT:DS:GL\t0|0:0.050:-0.48,-0.48,-0.48\t0|0:0.350:-0.24,-0.44,-1.16\t0|0:0.100:-0.22,-0.42,-1.80\t0|0:0.100:-0.48,-0.48,-0.48\n+1\t10616\t.\tCCGCCGTTGCAAAGGCGCGCCG\tC\t2781\tPASS\tVT=INDEL;RSQ=0.1048;AN=2184;LDAF=0.7052;AVGPOST=0.5674;ERATE=0.0146;AA=.;THETA=0.0195;AC=1972;AF=0.90;ASN_AF=0.88;AMR_AF=0.92;AFR_AF=0.89;EUR_AF=0.92\tGT:DS:GL\t1|1:1.450:0,0,0\t1|1:1.750:0,0,0\t1|1:1.200:0,0,0\t0|1:1.150:0,0,0\n+1\t11540\t.\tT\tTA\t263\tPASS\tVT=INDEL;AVGPOST=0.5915;LDAF=0.2676;AN=2184;RSQ=0.0831;AC=93;THETA=0.'..b'7,-0.01,-2.51\t0|0:0.050:-0.01,-1.69,-5.00\t0|0:0.100:-0.48,-0.48,-0.48\n+1\t13417\t.\tC\tCGAGA\t2788\tPASS\tVT=INDEL;AVGPOST=0.7560;THETA=0.0061;AC=52;AN=2184;AA=.;RSQ=0.1970;LDAF=0.1542;ERATE=0.0127;AF=0.02;ASN_AF=0.02;AMR_AF=0.04;AFR_AF=0.01;EUR_AF=0.03\tGT:DS:GL\t0|0:0.050:0.00,-0.30,-5.60\t0|0:0.250:0,0,0\t0|0:0.400:0,0,0\t0|0:0.350:0.00,-0.30,-5.60\n+1\t13957\t.\tTC\tT\t226\tPASS\tVT=INDEL;RSQ=0.2600;AN=2184;AA=.;LDAF=0.0542;THETA=0.0144;AVGPOST=0.9144;ERATE=0.0029;AC=27;AF=0.01;ASN_AF=0.01;AMR_AF=0.01;AFR_AF=0.01;EUR_AF=0.01\tGT:DS:GL\t0|0:0.150:0,0,0\t0|0:0.050:0,0,0\t0|0:0.100:0,0,0\t0|0:0.100:0,0,0\n+1\t13980\trs151276478\tT\tC\t100\tPASS\tVT=SNP;SNPSOURCE=LOWCOV;ERATE=0.0021;THETA=0.0096;RSQ=0.3995;AN=2184;AC=55;LDAF=0.0628;AVGPOST=0.9128;AA=.;SNPSOURCE=LOWCOV;AF=0.03;ASN_AF=0.02;AMR_AF=0.03;AFR_AF=0.01;EUR_AF=0.03\tGT:DS:GL\t0|0:0.100:-0.48,-0.48,-0.48\t0|1:0.950:-0.48,-0.48,-0.48\t0|0:0.050:-0.48,-0.48,-0.48\t0|0:0.050:-0.48,-0.48,-0.48\n+1\t16226\t.\tAG\tA\t104\tPASS\tVT=INDEL;THETA=0.0211;AN=2184;RSQ=0.6096;LDAF=0.0034;AVGPOST=0.9971;AA=A;ERATE=0.0008;AC=4;AF=0.00;AMR_AF=0.00;EUR_AF=0.00\tGT:DS:GL\t0|0:0.000:0.00,-1.50,-24.00\t0|0:0.050:0,0,0\t0|0:0.000:0.00,-0.30,-4.80\t0|0:0.000:0.00,-0.90,-14.40\n+1\t17496\t.\tAC\tA\t209\tPASS\tVT=INDEL;AC=7;AN=2184;ERATE=0.0009;AA=A;RSQ=0.7057;THETA=0.0221;AVGPOST=0.9968;LDAF=0.0045;AF=0.00;AFR_AF=0.01\tGT:DS:GL\t0|0:0.000:0.00,-3.30,-42.90\t0|0:0.000:0,0,0\t0|0:0.000:0,0,0\t0|0:0.000:0,0,0\n+1\t18869\t.\tACC\tA\t126\tPASS\tVT=INDEL;LDAF=0.2562;AC=52;AN=2184;ERATE=0.0162;AVGPOST=0.5962;AA=A;RSQ=0.0889;THETA=0.0107;AF=0.02;ASN_AF=0.04;AMR_AF=0.02;AFR_AF=0.02;EUR_AF=0.01\tGT:DS:GL\t0|0:0.400:0,0,0\t0|0:0.350:0,0,0\t0|0:0.250:0.00,-0.30,-2.90\t0|0:0.550:0,0,0\n+1\t19083\t.\tG\tGCA\t139\tPASS\tVT=INDEL;AVGPOST=0.7121;AN=2184;AC=13;AA=G;THETA=0.0077;ERATE=0.0123;RSQ=0.0826;LDAF=0.1645;AF=0.01;ASN_AF=0.01;AMR_AF=0.01;AFR_AF=0.01;EUR_AF=0.00\tGT:DS:GL\t0|0:0.200:0,0,0\t0|0:0.400:0,0,0\t0|0:0.250:0,0,0\t0|0:0.350:0,0,0\n+1\t19190\t.\tGC\tG\t815\tPASS\tVT=INDEL;AC=131;LDAF=0.2531;AN=2184;AA=G;THETA=0.0161;AVGPOST=0.6408;RSQ=0.1696;ERATE=0.0188;AF=0.06;ASN_AF=0.05;AMR_AF=0.10;AFR_AF=0.07;EUR_AF=0.04\tGT:DS:GL\t0|0:0.650:0,0,0\t0|0:0.200:0,0,0\t0|0:0.650:0,0,0\t0|0:0.500:0,0,0\n+1\t20862\t.\tA\tAG\t78\tPASS\tVT=INDEL;ERATE=0.0067;AVGPOST=0.8007;RSQ=0.0827;LDAF=0.8907;AN=2184;THETA=0.0095;AA=A;AC=2178;AF=1.00;ASN_AF=1.00;AMR_AF=1.00;AFR_AF=0.99;EUR_AF=1.00\tGT:DS:GL\t1|1:1.750:0,0,0\t1|1:1.800:0,0,0\t1|1:1.850:0,0,0\t1|1:1.750:0,0,0\n+1\t30923\trs140337953\tG\tT\t100\tPASS\tVT=SNP;SNPSOURCE=LOWCOV;RSQ=0.5363;LDAF=0.6540;THETA=0.0078;AN=2184;AA=T;ERATE=0.0127;AC=1581;SNPSOURCE=LOWCOV;AVGPOST=0.7309;AF=0.72;ASN_AF=0.88;AMR_AF=0.81;AFR_AF=0.48;EUR_AF=0.72\tGT:DS:GL\t1|1:1.950:-5.00,-0.61,-0.12\t0|0:0.450:-0.10,-0.69,-2.81\t0|0:0.450:-0.11,-0.64,-3.49\t1|1:1.500:-0.48,-0.48,-0.48\n+1\t46402\t.\tC\tCTGT\t104\tPASS\tVT=INDEL;RSQ=0.0943;AA=C;AN=2184;AVGPOST=0.8697;THETA=0.0108;AC=5;LDAF=0.0697;ERATE=0.0056;AF=0.00;ASN_AF=0.00;AMR_AF=0.00;AFR_AF=0.01\tGT:DS:GL\t0|0:0.050:0,0,0\t0|0:0.100:0,0,0\t0|0:0.050:0,0,0\t0|0:0.050:0,0,0\n+1\t47190\t.\tG\tGA\t868\tPASS\tVT=INDEL;LDAF=0.2298;AN=2184;AC=45;AA=G;RSQ=0.1035;AVGPOST=0.6322;THETA=0.0141;ERATE=0.0127;AF=0.02;ASN_AF=0.00;AMR_AF=0.03;AFR_AF=0.05;EUR_AF=0.01\tGT:DS:GL\t0|0:0.350:0,0,0\t0|0:0.500:0,0,0\t0|0:0.550:0,0,0\t0|0:0.400:0,0,0\n+1\t49514\t.\tAG\tA\t449\tPASS\tVT=INDEL;THETA=0.0164;AC=52;AN=2184;RSQ=0.4892;AA=A;LDAF=0.0469;AVGPOST=0.9448;ERATE=0.0053;AF=0.02;ASN_AF=0.02;AMR_AF=0.02;AFR_AF=0.01;EUR_AF=0.03\tGT:DS:GL\t0|0:0.000:0.00,-0.90,-12.40\t0|1:0.800:0,0,0\t0|0:0.150:-0.10,0.00,0.00\t0|0:0.000:0.00,-0.30,-4.20\n+1\t49515\t.\tG\tGA\t44\tPASS\tVT=INDEL;THETA=0.0214;AN=2184;AC=13;AA=A;ERATE=0.0008;AVGPOST=0.9879;LDAF=0.0111;RSQ=0.5361;AF=0.01;ASN_AF=0.02;EUR_AF=0.01\tGT:DS:GL\t0|0:0.050:0.00,-0.90,-9.70\t0|0:0.050:0,0,0\t0|0:0.000:0,0,0\t0|0:0.000:0.00,-0.30,-3.20\n+1\t50481\t.\tGGT\tG\t2370\tPASS\tVT=INDEL;RSQ=0.3702;THETA=0.0038;AN=2184;AA=G;ERATE=0.0177;AVGPOST=0.7981;AC=142;LDAF=0.1660;AF=0.07;ASN_AF=0.05;AMR_AF=0.13;AFR_AF=0.07;EUR_AF=0.04\tGT:DS:GL\t0|0:0.250:0,0,0\t0|0:0.350:0,0,0\t1|0:1.150:-3.00,-0.30,0.00\t0|0:0.250:0,0,0\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/vcf2pgSnp_output.pgSnp
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/vcf2pgSnp_output.pgSnp Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,22 @@
+chr1 10522 10523 TCCG 1 8 0
+chr1 10582 10583 G/A 2 7,1 0,0
+chr1 10610 10611 C 1 8 0
+chr1 10615 10616 CCGCCGTTGCAAAGGCGCGCCG/C 2 1,7 0,0
+chr1 11539 11540 T/T 2 7,1 0,0
+chr1 13301 13302 C/T 2 7,1 0,0
+chr1 13326 13327 G/C 2 7,1 0,0
+chr1 13416 13417 C 1 8 0
+chr1 13956 13957 TC 1 8 0
+chr1 13979 13980 T/C 2 7,1 0,0
+chr1 16225 16226 AG 1 8 0
+chr1 17495 17496 AC 1 8 0
+chr1 18868 18869 ACC 1 8 0
+chr1 19082 19083 G 1 8 0
+chr1 19189 19190 GC 1 8 0
+chr1 20861 20862 A 1 8 0
+chr1 30922 30923 G/T 2 4,4 0,0
+chr1 46401 46402 C 1 8 0
+chr1 47189 47190 G 1 8 0
+chr1 49513 49514 AG/A 2 7,1 0,0
+chr1 49514 49515 G 1 8 0
+chr1 50480 50481 GGT/G 2 7,1 0,0

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/velvet_test_reads.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/velvet_test_reads.fa Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,285716 @@\n+>SEQUENCE_0_length_35\n+GGATATAGGGCCAACCCAACTCAACGGCCTGTCTT\n+>SEQUENCE_1_length_35\n+CGACGAATGACAGGTCACGAATTTGGCGGGGATTA\n+>SEQUENCE_2_length_35\n+CCAAATAGGTCCTTACATCATGAGACGGGCCAAAT\n+>SEQUENCE_3_length_35\n+CGAGATGTATACCTCTAACACTGTGTTCCAAGTAC\n+>SEQUENCE_4_length_35\n+AAGCTCCCGCAATGGATCTTGTGACGGGCTGCTCG\n+>SEQUENCE_5_length_35\n+GCCGGTACAAACAGGAGGCAGGCAGTTCTAGTTCC\n+>SEQUENCE_6_length_35\n+TGCAGGTCAGGGTTCGTCATGCCTAGTGCAACGCC\n+>SEQUENCE_7_length_35\n+GTTCGCTACCAGCTTGTGGACCAGGAGGGTAACCC\n+>SEQUENCE_8_length_35\n+CTTAATACCATGAGTCGAAGAAAATTAACTTGGGG\n+>SEQUENCE_9_length_35\n+CATGGAGTAAGTCCTAGTAGCCTTGTGCATGGCGT\n+>SEQUENCE_10_length_35\n+TGTCCCTGTCACTGGAGTGATCTTTTATTCTCACC\n+>SEQUENCE_11_length_35\n+CTCATGCGTAATTTTAGCCGCCACGGCTATGCGTG\n+>SEQUENCE_12_length_35\n+CTTAGTCCTACAGGTTTTGCTATCCATTAAGCTGC\n+>SEQUENCE_13_length_35\n+ATATCTCGGTGCAGGGATGTTCAACATCATCACAC\n+>SEQUENCE_14_length_35\n+CGTCCATCGCCGATGAAATCCTGCTCAGGAGTGGA\n+>SEQUENCE_15_length_35\n+ACGCGTAGTCCTCTTGCGGCTTCCGCGCCCCGGGA\n+>SEQUENCE_16_length_35\n+CTTGAGCGGTGACCTTCGCGGTTAGCGCACCGTAA\n+>SEQUENCE_17_length_35\n+AGTGGTTTCAGTTCACGCTGCTGGATGTGGTGAGA\n+>SEQUENCE_18_length_35\n+ACTAGTCAACGCCATGAATAAGGGGTCGCAAATTG\n+>SEQUENCE_19_length_35\n+AGGAATTAACTCCTACGGTGAAACTGGTGTGTCAT\n+>SEQUENCE_20_length_35\n+CGCTGAATAAGCAAAATGCGTCGGCTGGGTCGACA\n+>SEQUENCE_21_length_35\n+GGAGACACGCCTGGCACGAGCGGAGGGATAGCTGT\n+>SEQUENCE_22_length_35\n+GAACGTGAGCTTCAATGGTGCCAAAATCGATAAAG\n+>SEQUENCE_23_length_35\n+CAGCACGTGGTTACTAGTCGTAAAGCCCCAAATAG\n+>SEQUENCE_24_length_35\n+TTTCCCTCCGTAGACAAATAGAGGTTAAGGGGCGT\n+>SEQUENCE_25_length_35\n+TTCTCTTCGTGTGAGGCCCTACGCTGTAAGATCCT\n+>SEQUENCE_26_length_35\n+CGGATTGGTCTAGCGTTGGAACTTGTCCGTCATGC\n+>SEQUENCE_27_length_35\n+CGCCTCAGAGCTGTGCTGATGGGTGTCCCCAGTCT\n+>SEQUENCE_28_length_35\n+CCAAGGGGCTCCTGTCGATCCTTGAGTCATTCATC\n+>SEQUENCE_29_length_35\n+AGCTCATTTTGCCGCGCCTGTAAGTCGCATCACAA\n+>SEQUENCE_30_length_35\n+CAGTTGACGAGTTACCGCTTACCCAGACGATTACG\n+>SEQUENCE_31_length_35\n+CCGAAGCGGAGGACAAGAAATTATCCCTATCAATT\n+>SEQUENCE_32_length_35\n+AACGCATTGACCTTGTGTGGGGTCAAACGGCGGAG\n+>SEQUENCE_33_length_35\n+CAGAGTTCCTTCTTCTTCTTGTCGTAGAAACCATC\n+>SEQUENCE_34_length_35\n+GTGGCTTCCCGGTATTGTAACGGGGGGAACCACGG\n+>SEQUENCE_35_length_35\n+CAGCAAGGGGCATACAGCACATCATGTCGCAACTC\n+>SEQUENCE_36_length_35\n+CAACTCGAACGTCTTAGTACTCCACAGATAGAATG\n+>SEQUENCE_37_length_35\n+TTGCGCTCAGCTGTCTGCCGTTGACTTCCTTCAAC\n+>SEQUENCE_38_length_35\n+ACCGTTGCAACTCCACATACCACCCCAGTACCCCA\n+>SEQUENCE_39_length_35\n+CCGGGATAAACCAGAAAAAAAGGCTCGTGACTGTC\n+>SEQUENCE_40_length_35\n+TCAGTTTATCAGCCTCGAGGCCACGATCGAGCCAG\n+>SEQUENCE_41_length_35\n+GCCCACATATTACGACGATGCGGCCCCGCTCTCTA\n+>SEQUENCE_42_length_35\n+GGACTATTCTAAATAAGCGGGTACAACTTACGTAG\n+>SEQUENCE_43_length_35\n+TTCCGCGCCGTCGAGTACAAAACGTCGCAATTTAA\n+>SEQUENCE_44_length_35\n+TATACATGTAGAGACTACGATAAAATTGAAGGGGA\n+>SEQUENCE_45_length_35\n+CCGGTCTATGATCCCTAATGAAAACGTTGATTCCC\n+>SEQUENCE_46_length_35\n+TGGTTTCTCACCGCAATCGGACCTTGCGGGTATGA\n+>SEQUENCE_47_length_35\n+CGTTGCGAGAGCAATCTATCAAGAGGATAAGCGCA\n+>SEQUENCE_48_length_35\n+AGGTAAGGATAGGGGCAAACGCGCGAAGGACACCC\n+>SEQUENCE_49_length_35\n+GACATATAGTCACTTGCTGTCGAATCGTAGTGGCT\n+>SEQUENCE_50_length_35\n+ACCATATAAGGAGTCGGAGCCCCTTGGTCCCCTTC\n+>SEQUENCE_51_length_35\n+GACGTTATTAACACCGTCGTAGCCTTTTCTGAAGC\n+>SEQUENCE_52_length_35\n+GGCTGAGGCCCGCCCCGAAACTTAATAGCCAGAAC\n+>SEQUENCE_53_length_35\n+TTCATACCGAGTCATACGTCGTCTTAGAGCGCATC\n+>SEQUENCE_54_length_35\n+GCTTGCAACTGGTTGATAGTTCAGACGAATGGTCG\n+>SEQUENCE_55_length_35\n+GGAATCAATAGTCGCGTTCAGAGCGCTCACTTTTT\n+>SEQUENCE_56_length_35\n+CGGAACACTAATCACCTTCCTAGTCGGCGGTAACA\n+>SEQUENCE_57_length_35\n+AGTTGGCCACTAAAGCTTACCCTCGAATGACTTCC\n+>SEQUENCE_58_length_35\n+GGCAATTTACTGTATCCCAGAATAACGACTCCCCA\n+>SEQUENCE_59_length_35\n+AGCTTCAGAAAAGGCTACGACGGTGTTAATAACGT\n+>SEQUENCE_60_length_35\n+AGAGTAACGCTAAGCGCAACGATACTCGCCGCGTC\n+>SEQUENCE_61_length_35\n+ATATCGCCCCAGACCTGAGAGTGGCATGCCCGACC\n+>SEQUENCE_62_length_35\n+CACCTGGCCTCATGACCGACACGTTTGGGCCTATT\n+>SEQUENCE_63_length_35\n+ATTTGCAGTTCATCCATCCCAAAGAGCGTGTACGT\n+>SEQUENCE_64_length_35\n+GGTCATACCATTCTGGGACCTCGGGAGCTGGGAGT\n+>SEQUENCE_65_length_35'..b'ACCCCCAAAACGTCACCTATCCGGCCCAGGCGA\n+>SEQUENCE_142797_length_35\n+AACCGCAGAGTCCGGAGCTCCCATAAACGAGGAAT\n+>SEQUENCE_142798_length_35\n+TTCGTCAAGAGATTCCTGTAATCCACCAAAGATTC\n+>SEQUENCE_142799_length_35\n+TTAATGCTCATTGAAAGAGACAGGGGAACGCACCA\n+>SEQUENCE_142800_length_35\n+GACCAGCAATTAAACGTAAACAAACGCGTCGATGT\n+>SEQUENCE_142801_length_35\n+TCCCAAGCCTCAGGAGACCCTCCTGCGGGTCCAGG\n+>SEQUENCE_142802_length_35\n+CCACATCGAACAAGCGATTTATGCCATACGAACCT\n+>SEQUENCE_142803_length_35\n+CGCATGTAACTTCTGAAGGTCACCCGTTGTGTGAT\n+>SEQUENCE_142804_length_35\n+TCCGGGGTCAAATAGACAGCGGAGCCCTCAACCCT\n+>SEQUENCE_142805_length_35\n+ACACCCTGCCCTTGGGCTTAGACGCGTGCCCGTGG\n+>SEQUENCE_142806_length_35\n+AATGACCAGGAACAGGCAGGTTTTTATCTACCTGC\n+>SEQUENCE_142807_length_35\n+CCAGGCGAGCGTCTGCTGGAAGATAACCCTTGATC\n+>SEQUENCE_142808_length_35\n+CGGCCACCGGAGCATAAGGTCAATAGATCGGTCAA\n+>SEQUENCE_142809_length_35\n+TGAACCGTGATATCAGATGACCACCCCTAAGTCGC\n+>SEQUENCE_142810_length_35\n+CCTAGTGCTATCCTGTATCTAAGTTCATCACAGTC\n+>SEQUENCE_142811_length_35\n+TGTGCGCTGCACCTGAGAATTAGAGACAGAGGTGA\n+>SEQUENCE_142812_length_35\n+ATCACCGGTCACCTCGACTGTCCATTAACGGTCTC\n+>SEQUENCE_142813_length_35\n+TCGTCTCAATATGTAAAACATGGTAGTGTGTGAGC\n+>SEQUENCE_142814_length_35\n+GCAGTCTACCCCTGGGGTATGAGCTGCCGCCTCTG\n+>SEQUENCE_142815_length_35\n+AAGATCAGTGCCTTCTCTGTATCAACTGCTCCCTG\n+>SEQUENCE_142816_length_35\n+TCTCGGAGGGCGTAGTAAATGGTAGAATTTACGAA\n+>SEQUENCE_142817_length_35\n+GTATGTAAGTAAACTCCACGTGGCTGCTCTGAGGT\n+>SEQUENCE_142818_length_35\n+CGAACAGTGTACTGGTGCATGTGCCGGAGAGAAAC\n+>SEQUENCE_142819_length_35\n+CGGCGTGCCGCGTAGCTCGCACCCCCGAGCGTTAA\n+>SEQUENCE_142820_length_35\n+GGTGCCCGCCGATACTAATTACGGTCGCTTGACCG\n+>SEQUENCE_142821_length_35\n+GATTAAAACCATGATACCCTGTCCTTCAGACGTGG\n+>SEQUENCE_142822_length_35\n+AAAATGAACGGGCAGAATGCGAGAGCAACATCAAG\n+>SEQUENCE_142823_length_35\n+CAAGACGCGACTGACACTTAATTGATCCGACTTGT\n+>SEQUENCE_142824_length_35\n+GGTCCGTTCTTCGAAGCAGAGCGAAGCGCGCTCAC\n+>SEQUENCE_142825_length_35\n+ATCATCCATGTAGGAGAACAAGTTAGTGGTTTTTG\n+>SEQUENCE_142826_length_35\n+CAGTGCATGGGAGGTAACTGGGCGCAGAGGGCCAG\n+>SEQUENCE_142827_length_35\n+AGCCTAAGATCACGTATCCCATACAGCCCACCGGG\n+>SEQUENCE_142828_length_35\n+ATAGCGTGGTGTCCTTATTATATCTCGCAGGCTGT\n+>SEQUENCE_142829_length_35\n+CCGGGGTATTTGAAATGAGTCGCCAACCGTGGGAG\n+>SEQUENCE_142830_length_35\n+AGCAAGACCTGCAGCTACTGCCTTGGAGGTGGGTG\n+>SEQUENCE_142831_length_35\n+TCCAGTTCCTTCAAAAGGTTATCCACGTTCGTGCA\n+>SEQUENCE_142832_length_35\n+TTTCCGAATGACGCCAACGCGGGAATGACGTGCCA\n+>SEQUENCE_142833_length_35\n+TAATTAGTTGCAAAGTTGAAGGCCAGTCTTGTTGG\n+>SEQUENCE_142834_length_35\n+TGTCTACCTTCAGTTCGTTGGAAGGACAACGATCC\n+>SEQUENCE_142835_length_35\n+CAGGACTACTCGCGGAACCGACAGGATGGGGTAAG\n+>SEQUENCE_142836_length_35\n+GCGCAATGGGAAAAAATACCATGGGTGCCGGTTCA\n+>SEQUENCE_142837_length_35\n+GAGTCAGGATAGCGTCAATCCATCCGGATTTGGCA\n+>SEQUENCE_142838_length_35\n+TATCAAGCCATTGAAGTCTACTAACACCTCAGGTT\n+>SEQUENCE_142839_length_35\n+GGGCTGAGAGCCGGGCCTCTTTGTCCTTAAACGAA\n+>SEQUENCE_142840_length_35\n+ACGTATCAGAGAAAGTCCAAGCTTGATCGTAAAGG\n+>SEQUENCE_142841_length_35\n+CCATTCAACCCTTACCGCTAGACGACGGTCGCGGA\n+>SEQUENCE_142842_length_35\n+CGAAGCTTCTCTCAATCACATACGTGCAAGCGACG\n+>SEQUENCE_142843_length_35\n+TATACGCTGGTGGGATGATAAGCTCAGGGCCTTAG\n+>SEQUENCE_142844_length_35\n+TAAGATATTATAGAGGGACAGACTATGTTGTTGTC\n+>SEQUENCE_142845_length_35\n+ATATCATCAAAGACTCTTTGTGAAGTGGGGCTGTA\n+>SEQUENCE_142846_length_35\n+TGTAAGCCATTATGATTACACGATTCCTCTAACTA\n+>SEQUENCE_142847_length_35\n+CGCTGAGGCTGAATACGCGGTTAAGCAGACCCTAC\n+>SEQUENCE_142848_length_35\n+GAACACACTTAGCCTAGGGTGCACGGGTTCAATGA\n+>SEQUENCE_142849_length_35\n+ATAGAGGAGCCCGATCTTTTGAAATATGCCTCATA\n+>SEQUENCE_142850_length_35\n+GGTCGCGAACTACGGATAATGATTAACCCATTGGA\n+>SEQUENCE_142851_length_35\n+GGATCCAATCCGCGTTGTCACTACACGACGTGAGG\n+>SEQUENCE_142852_length_35\n+CTCTATTCGTCGTATGCCCGCTTTCAAAGCGTATT\n+>SEQUENCE_142853_length_35\n+AACCACTAGCTCGCCCTCCAGCTTCTTACGTTATC\n+>SEQUENCE_142854_length_35\n+GCCCCTCTGGCGTGAGCGGAGATACCCACCATGCC\n+>SEQUENCE_142855_length_35\n+GTATCTTATCTGCCTGGTGACCATCATCGAAGCAT\n+>SEQUENCE_142856_length_35\n+GAGACAGACCACAATACTGTGATGTAAAGCGCGCG\n+>SEQUENCE_142857_length_35\n+TATCTTTTATCGTTTCACAGGGGGCCAGGGGCGCG\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/velvetg_test1/amos.afg
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/velvetg_test1/amos.afg Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,2111232 @@\n+{RED\n+iid:1\n+eid:1\n+seq:\n+GGATATAGGGCCAACCCAACTCAACGGCCTGTCTT\n+.\n+qlt:\n+GGATATAGGGCCAACCCAACTCAACGGCCTGTCTT\n+.\n+}\n+{RED\n+iid:2\n+eid:2\n+seq:\n+CGACGAATGACAGGTCACGAATTTGGCGGGGATTA\n+.\n+qlt:\n+CGACGAATGACAGGTCACGAATTTGGCGGGGATTA\n+.\n+}\n+{RED\n+iid:3\n+eid:3\n+seq:\n+CCAAATAGGTCCTTACATCATGAGACGGGCCAAAT\n+.\n+qlt:\n+CCAAATAGGTCCTTACATCATGAGACGGGCCAAAT\n+.\n+}\n+{RED\n+iid:4\n+eid:4\n+seq:\n+CGAGATGTATACCTCTAACACTGTGTTCCAAGTAC\n+.\n+qlt:\n+CGAGATGTATACCTCTAACACTGTGTTCCAAGTAC\n+.\n+}\n+{RED\n+iid:5\n+eid:5\n+seq:\n+AAGCTCCCGCAATGGATCTTGTGACGGGCTGCTCG\n+.\n+qlt:\n+AAGCTCCCGCAATGGATCTTGTGACGGGCTGCTCG\n+.\n+}\n+{RED\n+iid:6\n+eid:6\n+seq:\n+GCCGGTACAAACAGGAGGCAGGCAGTTCTAGTTCC\n+.\n+qlt:\n+GCCGGTACAAACAGGAGGCAGGCAGTTCTAGTTCC\n+.\n+}\n+{RED\n+iid:7\n+eid:7\n+seq:\n+TGCAGGTCAGGGTTCGTCATGCCTAGTGCAACGCC\n+.\n+qlt:\n+TGCAGGTCAGGGTTCGTCATGCCTAGTGCAACGCC\n+.\n+}\n+{RED\n+iid:8\n+eid:8\n+seq:\n+GTTCGCTACCAGCTTGTGGACCAGGAGGGTAACCC\n+.\n+qlt:\n+GTTCGCTACCAGCTTGTGGACCAGGAGGGTAACCC\n+.\n+}\n+{RED\n+iid:9\n+eid:9\n+seq:\n+CTTAATACCATGAGTCGAAGAAAATTAACTTGGGG\n+.\n+qlt:\n+CTTAATACCATGAGTCGAAGAAAATTAACTTGGGG\n+.\n+}\n+{RED\n+iid:10\n+eid:10\n+seq:\n+CATGGAGTAAGTCCTAGTAGCCTTGTGCATGGCGT\n+.\n+qlt:\n+CATGGAGTAAGTCCTAGTAGCCTTGTGCATGGCGT\n+.\n+}\n+{RED\n+iid:11\n+eid:11\n+seq:\n+TGTCCCTGTCACTGGAGTGATCTTTTATTCTCACC\n+.\n+qlt:\n+TGTCCCTGTCACTGGAGTGATCTTTTATTCTCACC\n+.\n+}\n+{RED\n+iid:12\n+eid:12\n+seq:\n+CTCATGCGTAATTTTAGCCGCCACGGCTATGCGTG\n+.\n+qlt:\n+CTCATGCGTAATTTTAGCCGCCACGGCTATGCGTG\n+.\n+}\n+{RED\n+iid:13\n+eid:13\n+seq:\n+CTTAGTCCTACAGGTTTTGCTATCCATTAAGCTGC\n+.\n+qlt:\n+CTTAGTCCTACAGGTTTTGCTATCCATTAAGCTGC\n+.\n+}\n+{RED\n+iid:14\n+eid:14\n+seq:\n+ATATCTCGGTGCAGGGATGTTCAACATCATCACAC\n+.\n+qlt:\n+ATATCTCGGTGCAGGGATGTTCAACATCATCACAC\n+.\n+}\n+{RED\n+iid:15\n+eid:15\n+seq:\n+CGTCCATCGCCGATGAAATCCTGCTCAGGAGTGGA\n+.\n+qlt:\n+CGTCCATCGCCGATGAAATCCTGCTCAGGAGTGGA\n+.\n+}\n+{RED\n+iid:16\n+eid:16\n+seq:\n+ACGCGTAGTCCTCTTGCGGCTTCCGCGCCCCGGGA\n+.\n+qlt:\n+ACGCGTAGTCCTCTTGCGGCTTCCGCGCCCCGGGA\n+.\n+}\n+{RED\n+iid:17\n+eid:17\n+seq:\n+CTTGAGCGGTGACCTTCGCGGTTAGCGCACCGTAA\n+.\n+qlt:\n+CTTGAGCGGTGACCTTCGCGGTTAGCGCACCGTAA\n+.\n+}\n+{RED\n+iid:18\n+eid:18\n+seq:\n+AGTGGTTTCAGTTCACGCTGCTGGATGTGGTGAGA\n+.\n+qlt:\n+AGTGGTTTCAGTTCACGCTGCTGGATGTGGTGAGA\n+.\n+}\n+{RED\n+iid:19\n+eid:19\n+seq:\n+ACTAGTCAACGCCATGAATAAGGGGTCGCAAATTG\n+.\n+qlt:\n+ACTAGTCAACGCCATGAATAAGGGGTCGCAAATTG\n+.\n+}\n+{RED\n+iid:20\n+eid:20\n+seq:\n+AGGAATTAACTCCTACGGTGAAACTGGTGTGTCAT\n+.\n+qlt:\n+AGGAATTAACTCCTACGGTGAAACTGGTGTGTCAT\n+.\n+}\n+{RED\n+iid:21\n+eid:21\n+seq:\n+CGCTGAATAAGCAAAATGCGTCGGCTGGGTCGACA\n+.\n+qlt:\n+CGCTGAATAAGCAAAATGCGTCGGCTGGGTCGACA\n+.\n+}\n+{RED\n+iid:22\n+eid:22\n+seq:\n+GGAGACACGCCTGGCACGAGCGGAGGGATAGCTGT\n+.\n+qlt:\n+GGAGACACGCCTGGCACGAGCGGAGGGATAGCTGT\n+.\n+}\n+{RED\n+iid:23\n+eid:23\n+seq:\n+GAACGTGAGCTTCAATGGTGCCAAAATCGATAAAG\n+.\n+qlt:\n+GAACGTGAGCTTCAATGGTGCCAAAATCGATAAAG\n+.\n+}\n+{RED\n+iid:24\n+eid:24\n+seq:\n+CAGCACGTGGTTACTAGTCGTAAAGCCCCAAATAG\n+.\n+qlt:\n+CAGCACGTGGTTACTAGTCGTAAAGCCCCAAATAG\n+.\n+}\n+{RED\n+iid:25\n+eid:25\n+seq:\n+TTTCCCTCCGTAGACAAATAGAGGTTAAGGGGCGT\n+.\n+qlt:\n+TTTCCCTCCGTAGACAAATAGAGGTTAAGGGGCGT\n+.\n+}\n+{RED\n+iid:26\n+eid:26\n+seq:\n+TTCTCTTCGTGTGAGGCCCTACGCTGTAAGATCCT\n+.\n+qlt:\n+TTCTCTTCGTGTGAGGCCCTACGCTGTAAGATCCT\n+.\n+}\n+{RED\n+iid:27\n+eid:27\n+seq:\n+CGGATTGGTCTAGCGTTGGAACTTGTCCGTCATGC\n+.\n+qlt:\n+CGGATTGGTCTAGCGTTGGAACTTGTCCGTCATGC\n+.\n+}\n+{RED\n+iid:28\n+eid:28\n+seq:\n+CGCCTCAGAGCTGTGCTGATGGGTGTCCCCAGTCT\n+.\n+qlt:\n+CGCCTCAGAGCTGTGCTGATGGGTGTCCCCAGTCT\n+.\n+}\n+{RED\n+iid:29\n+eid:29\n+seq:\n+CCAAGGGGCTCCTGTCGATCCTTGAGTCATTCATC\n+.\n+qlt:\n+CCAAGGGGCTCCTGTCGATCCTTGAGTCATTCATC\n+.\n+}\n+{RED\n+iid:30\n+eid:30\n+seq:\n+AGCTCATTTTGCCGCGCCTGTAAGTCGCATCACAA\n+.\n+qlt:\n+AGCTCATTTTGCCGCGCCTGTAAGTCGCATCACAA\n+.\n+}\n+{RED\n+iid:31\n+eid:31\n+seq:\n+CAGTTGACGAGTTACCGCTTACCCAGACGATTACG\n+.\n+qlt:\n+CAGTTGACGAGTTACCGCTTACCCAGACGATTACG\n+.\n+}\n+{RED\n+iid:32\n+eid:32\n+seq:\n+CCGAAGCGGAGGACAAGAAATTATCCCTATCAATT\n+.\n+qlt:\n+CCGAAGCGGAGGACAAGAAATTATCCCTATCAATT\n+.\n+}\n+{RED\n+iid:33\n+eid:33\n+seq:\n+AACGCATTGACCTTGTGTGGGGTCAAACGGCGGAG\n+.\n+qlt:\n+AACGCATTGACCTTGTGTGGGGTCAAACGGCGGAG\n+.\n+}\n+{RED\n+iid:34\n+eid:34\n+seq:\n+CAGAGTTCCTTCTTCTTCTTGTCGTAGAAACCATC\n+.\n+qlt:\n+CAGAGTTCCTTCTTCTTCTTGTCGTAGAAACCATC\n+.\n+}\n+{RED\n+iid:35\n+ei'..b'\n+clr:35,0\n+}\n+{TLE\n+src:142658\n+off:98952\n+clr:35,0\n+}\n+{TLE\n+src:142660\n+off:3762\n+clr:35,0\n+}\n+{TLE\n+src:142662\n+off:16375\n+clr:35,0\n+}\n+{TLE\n+src:142663\n+off:77401\n+clr:35,0\n+}\n+{TLE\n+src:142666\n+off:74607\n+clr:35,0\n+}\n+{TLE\n+src:142668\n+off:86458\n+clr:35,0\n+}\n+{TLE\n+src:142670\n+off:91101\n+clr:35,0\n+}\n+{TLE\n+src:142672\n+off:86468\n+clr:35,0\n+}\n+{TLE\n+src:142673\n+off:70818\n+clr:35,0\n+}\n+{TLE\n+src:142676\n+off:55325\n+clr:35,0\n+}\n+{TLE\n+src:142677\n+off:22040\n+clr:35,0\n+}\n+{TLE\n+src:142680\n+off:94965\n+clr:35,0\n+}\n+{TLE\n+src:142681\n+off:81293\n+clr:35,0\n+}\n+{TLE\n+src:142683\n+off:34539\n+clr:35,0\n+}\n+{TLE\n+src:142686\n+off:81635\n+clr:35,0\n+}\n+{TLE\n+src:142687\n+off:3780\n+clr:35,0\n+}\n+{TLE\n+src:142689\n+off:71448\n+clr:35,0\n+}\n+{TLE\n+src:142691\n+off:18630\n+clr:35,0\n+}\n+{TLE\n+src:142693\n+off:648\n+clr:35,0\n+}\n+{TLE\n+src:142696\n+off:60248\n+clr:35,0\n+}\n+{TLE\n+src:142698\n+off:28218\n+clr:35,0\n+}\n+{TLE\n+src:142700\n+off:89465\n+clr:35,0\n+}\n+{TLE\n+src:142701\n+off:21602\n+clr:35,0\n+}\n+{TLE\n+src:142706\n+off:43286\n+clr:35,0\n+}\n+{TLE\n+src:142707\n+off:82581\n+clr:35,0\n+}\n+{TLE\n+src:142709\n+off:29107\n+clr:35,0\n+}\n+{TLE\n+src:142712\n+off:84399\n+clr:35,0\n+}\n+{TLE\n+src:142714\n+off:62132\n+clr:35,0\n+}\n+{TLE\n+src:142715\n+off:18532\n+clr:35,0\n+}\n+{TLE\n+src:142718\n+off:49677\n+clr:35,0\n+}\n+{TLE\n+src:142719\n+off:51720\n+clr:35,0\n+}\n+{TLE\n+src:142721\n+off:64908\n+clr:35,0\n+}\n+{TLE\n+src:142724\n+off:24611\n+clr:35,0\n+}\n+{TLE\n+src:142726\n+off:76052\n+clr:35,0\n+}\n+{TLE\n+src:142727\n+off:30364\n+clr:35,0\n+}\n+{TLE\n+src:142729\n+off:12866\n+clr:35,0\n+}\n+{TLE\n+src:142732\n+off:22496\n+clr:35,0\n+}\n+{TLE\n+src:142734\n+off:14357\n+clr:35,0\n+}\n+{TLE\n+src:142736\n+off:80584\n+clr:35,0\n+}\n+{TLE\n+src:142738\n+off:57514\n+clr:35,0\n+}\n+{TLE\n+src:142739\n+off:99463\n+clr:35,0\n+}\n+{TLE\n+src:142742\n+off:20364\n+clr:35,0\n+}\n+{TLE\n+src:142743\n+off:58743\n+clr:35,0\n+}\n+{TLE\n+src:142748\n+off:1382\n+clr:35,0\n+}\n+{TLE\n+src:142752\n+off:87370\n+clr:35,0\n+}\n+{TLE\n+src:142754\n+off:62439\n+clr:35,0\n+}\n+{TLE\n+src:142756\n+off:71613\n+clr:35,0\n+}\n+{TLE\n+src:142757\n+off:85476\n+clr:35,0\n+}\n+{TLE\n+src:142759\n+off:28266\n+clr:35,0\n+}\n+{TLE\n+src:142764\n+off:24881\n+clr:35,0\n+}\n+{TLE\n+src:142765\n+off:97465\n+clr:35,0\n+}\n+{TLE\n+src:142767\n+off:56708\n+clr:35,0\n+}\n+{TLE\n+src:142769\n+off:43460\n+clr:35,0\n+}\n+{TLE\n+src:142772\n+off:32891\n+clr:35,0\n+}\n+{TLE\n+src:142774\n+off:23266\n+clr:35,0\n+}\n+{TLE\n+src:142775\n+off:53471\n+clr:35,0\n+}\n+{TLE\n+src:142778\n+off:62378\n+clr:35,0\n+}\n+{TLE\n+src:142779\n+off:15038\n+clr:35,0\n+}\n+{TLE\n+src:142783\n+off:93014\n+clr:35,0\n+}\n+{TLE\n+src:142786\n+off:45865\n+clr:35,0\n+}\n+{TLE\n+src:142787\n+off:26323\n+clr:35,0\n+}\n+{TLE\n+src:142789\n+off:64721\n+clr:35,0\n+}\n+{TLE\n+src:142792\n+off:31745\n+clr:35,0\n+}\n+{TLE\n+src:142794\n+off:65985\n+clr:35,0\n+}\n+{TLE\n+src:142798\n+off:66148\n+clr:35,0\n+}\n+{TLE\n+src:142800\n+off:10938\n+clr:35,0\n+}\n+{TLE\n+src:142802\n+off:68975\n+clr:35,0\n+}\n+{TLE\n+src:142804\n+off:3325\n+clr:35,0\n+}\n+{TLE\n+src:142805\n+off:71870\n+clr:35,0\n+}\n+{TLE\n+src:142808\n+off:66342\n+clr:35,0\n+}\n+{TLE\n+src:142809\n+off:51593\n+clr:35,0\n+}\n+{TLE\n+src:142812\n+off:19950\n+clr:35,0\n+}\n+{TLE\n+src:142814\n+off:31364\n+clr:35,0\n+}\n+{TLE\n+src:142816\n+off:49245\n+clr:35,0\n+}\n+{TLE\n+src:142818\n+off:58966\n+clr:35,0\n+}\n+{TLE\n+src:142820\n+off:14409\n+clr:35,0\n+}\n+{TLE\n+src:142821\n+off:39331\n+clr:35,0\n+}\n+{TLE\n+src:142823\n+off:29491\n+clr:35,0\n+}\n+{TLE\n+src:142825\n+off:41291\n+clr:35,0\n+}\n+{TLE\n+src:142828\n+off:4427\n+clr:35,0\n+}\n+{TLE\n+src:142829\n+off:68101\n+clr:35,0\n+}\n+{TLE\n+src:142831\n+off:52388\n+clr:35,0\n+}\n+{TLE\n+src:142834\n+off:26458\n+clr:35,0\n+}\n+{TLE\n+src:142835\n+off:58650\n+clr:35,0\n+}\n+{TLE\n+src:142837\n+off:7217\n+clr:35,0\n+}\n+{TLE\n+src:142839\n+off:64877\n+clr:35,0\n+}\n+{TLE\n+src:142842\n+off:72503\n+clr:35,0\n+}\n+{TLE\n+src:142843\n+off:41891\n+clr:35,0\n+}\n+{TLE\n+src:142845\n+off:81838\n+clr:35,0\n+}\n+{TLE\n+src:142847\n+off:93168\n+clr:35,0\n+}\n+{TLE\n+src:142850\n+off:93821\n+clr:35,0\n+}\n+{TLE\n+src:142851\n+off:86506\n+clr:35,0\n+}\n+{TLE\n+src:142853\n+off:39684\n+clr:35,0\n+}\n+{TLE\n+src:142855\n+off:97754\n+clr:35,0\n+}\n+{TLE\n+src:142858\n+off:26608\n+clr:35,0\n+}\n+}\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/velvetg_test1/contigs.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/velvetg_test1/contigs.fa Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,1668 @@\n+>NODE_1_length_99975_cov_18.672838\n+AGTACCAGCATCATGGATGATGCCAAGAGTCACCTGATGTTTGCGGTTATGCCCTACGGC\n+GAAGATAATGAGATCGGTAGCCCCTACTTCCTTACTTCACCAACCCCTCTAACATTATGT\n+GACTATTGATATGTTCTGGCCTAGTTAACCCGACTCTTCAAATATCTCAGAGTCCGCTGG\n+ATGGGATGGACTACCCAACCGGCATCTTGGTGCGGTCGAGTTGGCAAGGGACTTATTATT\n+CATCATGTGCTACCGGCCCAGAATTTTTTGTTAAGAACTCTCGGTAAAGAATAATAAATT\n+GTCTTACGCCTACCCGCTATTTTATGAAGTCGTACCGTGCTCGGACGCTATTTCTGTAGT\n+ACACCCGCACGAAAAGCCGAACTACGTAACGGTGTTCAGTAGTGGGTCCAATACAACGCC\n+CTGTCGCCATTCTCGAATACTGGTTGGTAGGCCAGTCCCGTGTGAGTGTCTATTATCAAT\n+AGGCGAGTCGGACAGCTCTGGTTTGTGCTGAGTCTGTTAAAGCAAACATTGGATCATTCC\n+GGGAGTGGGCGACAGACCCAGGAATCGGCGGCTGGTCAACACCATAGAGGTGGTCCTTTT\n+GTGACCGTTGTTCCCGCAAATAACTCCTAAAGCACCCTTAAGCGTCGAATTCATTTAAGG\n+GTATGCGCGAGCGTAGAGCGGTCCGGACGGCGATCCGCGAGGCTTCCCTCACAGAAACAT\n+CCATATGCGTTGTTCCGTACACATGTAATGGGAAATATCTTTACACCATGCATATCTCCA\n+CCCCTACATCGGGGTAGGGGGAACACAGATGTCATGCTCAGTGGAACTTGCCTTACAATA\n+CCTGTAAAACGATCAAAGCGGGACGTCATCAGGTCGTGCTGATGACTGTGCCTATCATTA\n+TAATTGATAAATACGCCAAGGCCCTTCTAGATCCGTGTTAAGAGTGCTCGAACGTAGGGA\n+CGCCGGTCTATCTGATAGGACCAATACGCTGTTGCAGTGCAAATCGAAAATAGTTATCTC\n+TTCGTGGCGCACTGGACTAAGTACACCCCTAATGAGTAAACCGGAGTACCTAGGTGACAA\n+TCACGTCGGGCTAAGTAGCAGAATGCCTGTTCGATTAGATCCAATTGATATGCGCGTGTA\n+AGCGACGAATGACAGGTCACGAATTTGGCAGGGATTATGTCCGGAACGGAATAAAACCAG\n+GCGGTTACCAAGACAGGCCGTTGAGTTGGGTTGGCCCTATATCCGTATCCAGAGATACGT\n+TACAACCGTACGACATCTGGACGAGGAACCCTTTGGGAAAATCAACAGGCATGTTCCGGC\n+CGACAGCCTATTTTACGGCTGATCCAGTAACACCTTGCCAATGCCCTGAATAGGGGTCCA\n+GTACTCCCAGCTCCCGAGGTCCCAGAATGGTATGACCGAAATCTAGTCACCCGATGCCTC\n+GAAGCCAAGAGATTTGCCTTGACTGCGTTTCTGGCAGACCATAACCGCTTCGCTAGGTGT\n+AGGCTATCTCAACGCTGTTACGCGACAGGTAGGCGGCCAGACGCACTCCCTTCTCCGACA\n+CTTTTACGATTGAACGAGCCTTCTCCTCGGACTGGCTCGCGGCCAGAGGGAACTTTGCCC\n+GCGCGAGCTTAAGGACAGCCAAAGCCCAGTGAGGGAATCGACTACGTGCCACGGAATCGC\n+CTCCCTTCGTTATAATAGCTGCCGTGCCAGTTGGCTATGCTGTAACCATTGTGGACCTGA\n+TACGCCAGATCGCCGTCGCTATTAAAGCTCGATTCGCAACCTACTTCCCGATGGCTCCGG\n+CGGAGACTGAATTATCGTCCTCCGAAAGTATATCTGCAGGAATCCAAATTTAACGCATTG\n+ACCCTGTGTGGGGTCAAACGGCGGAGGGTCAGCGCATATATTCCGATGGTTTCTACGACA\n+AGAAGAAGAAGGAACTCTGGCTGTATAGTGTTTTTTTATGTCAAGCCGCGTGGGGGTCGT\n+TTATTGTCACCGGGTTTGGTTATAGCTTCTTTTCTGCCTGGTGGGAAATCTGCCAGTTAC\n+TCAATCGTGTTTAGCCAGAATCCGGAGCTGCGGGCTGGTGGACGCGCAGGGATAAAATTA\n+TGAGAGTTTGATTGCATGCCGCAGTAATTCTCCCGAGAGTTCGGGGGCTACACTCTATTG\n+TCGAGCGGCACAGTTAGGATGCGCTCTCTCTGGCGTTCCACCCCCAAGTGACCACCCCGC\n+GCTGCAGTATGTTACGCCGCATTAGTGAGACTATACTGAATGCCGTTTAGCAAACGAGGG\n+TCTGTCCGGCGGTCCTTACTGCGCTGTCGATCGCAATTTTGAATGACTGTAACTGGAGCA\n+GCACCCATAGGGGACGCCGCGACGTTATTTAATGCGACAGAGATGTATTCTTCCGTTAGT\n+TCGCGTCCACCATAGGAGTTTCACCCAAACAGGGTAGTTTCCCCTTGAGCGGTGACCTTC\n+GCGGTTAGCGCACCGTAACACTCGCACTAGGTCTCACCACATCCAGCAGCGTGAACTGAA\n+ATCACTTTAATGGGTATACGGCGAACCGCAGACCACGGTCCAGGGTGACAAGAAGCTATC\n+TATTGCCAAGGTCTTCCCAGTTTGAGCGAGCTCGCCAGCCATTTCCCGCATCTAACCGAA\n+AGGTCGTGCGCACCGGTATAAGACTCAACCGAATTGACAAAAGTCCGTTATTGTAGTGCA\n+AGACTGCTAAGAGAACCCTACTGTTCAGCTTGGGTTCCATCCAATGCATTCCTCGCTCGG\n+ACGGAGGCTTTACCGGGCTCTTGGCCGAAATCAATTGTCTCCCTTAGACTGCCCTCACAT\n+ATCACACGCACCCAAGGTCACCCAACAACACTCATGGAATGCCGCACGCTGAAATTTTGC\n+TATGGGCGGTGTTACGGCTATCCAATACACCAGCATTGTGTCCACTGCCCTGCCTGGGTT\n+TAAGCCTAGCAGACCTCAGGACTGGAGTTTGAGGGAGCTACGAATAAGAATCGGATAGAG\n+AAGGTAAGAATAGTTAATTGGAAGCCGGGTTCACCATTGTCAACGTCCCGCTGTTTGGGA\n+GCTTCGGTCCTTCAACGGTCAGTGAAAGTAAGTCCCAAACAGTTCCCACAGCCGCCAACA\n+AGCCAACTTCCAACCCTACAGTTTCCTTTGTGGAAAATCTAAGTCATTCCAGGCTCCAAC\n+AGCCTATCTAAAGCTCGCGGTGGAAGATACTGTCCCAGAGCTAAGGTTCTTGGTTAGTAC\n+CCACATCGAACAAGCGATTTATGCCATACGAACCTCGAATTGTGCCGAGTAGGCCAGCAA\n+AGATGTATACTCACTAGGTTCGACGATCACACAAGGGGTGACCTTCAGAAGTTACATGCG\n+ATGCCTTTCCCAGTGAATTCAGCGATTACCTTCTCCCCGAGCCCTGCGGATCCCTTCCAC\n+AACTCTTAGAGCCGTATAGAGCGGTCGTAAAAGCTCAGCCGTCCGTCGCAGACATTACTT\n+CGAAACTTTCTCACTTCAAAGCACTCAATAGAGTAACGTCACCATTTACGAAGGCGCTCG\n+CTTCCGCTCCATCCCGCAAATCTTACAGCGGACCTCATTGTGCGTAGCAGATCCTCTCTC\n+ACAAATCCAAAAGCAGTTAAAGATGCCCCGATAAGGTACTGGTTCACGGCAAAGGATGAC\n+CACCACCTGGTGATCTCACCACGTGTTGAATATTTCGGTTCAACCCCTTATAGGAAGGGA\n+ATACAACGCGTTGGTGCATGCAACACCCCGTGGTTCTGTCAATTAGGTGTCTTGTGTTCG\n+TAGATAGCGGCATACCTGCGTGTCTAAATCTGACGCG'..b'ACGGAGTTCTAAAGCTTAGTGAAGGCTCAAAGATGACTGAGGGAGAAACCGTCGG\n+CAGAGTATTCGCAAACCTCTCTGCCATATGTACGTGTGACCCCGGATCCGAACGCAACAT\n+AAAGGAGCCGAGGAGAGCACAGGCCTTAATGCCTAATTCGTTACGATAAGGGAGCAGTCT\n+CTAATATAACCCATCCTCGCCTATTGGTCGGATACGTCGGAGTTTAGCTGAGTGAAAAAA\n+GCTAATTAAATCGGACATAATGCGCTTACGAGCTATTTCGCAACCAATAGGAACTAGATG\n+CCCCTACACACTGAACTCATCAATTGCTGCATCATTGAGCGCGAAGATATGCCCGTTTGT\n+ATTCCGAAGAGCATTAGAAGGAGCCGCAGGTGCAAAATCATGGACGTTGTTAGTTCTGAA\n+ATCATAGTTGCTCTACTTTCATACTAATGAGTTACTATCACCGTTCGGGTATTTAAGTAG\n+CGCTTCCAGTCCCAACGGCGTAGTCATTGCCCGTCGTCGACAAACCTTTCTTGGTCCCCA\n+GCATTTAGTCTCGGACGCTTGCAAACTCGTTGCATATGTGGAAAAGCGTGGCAGAGGTCT\n+CGTACACAAGCCTCGCTTTCCTACAACGCGAACGTATGGGGAGGCTCCCTCTTTACGGCA\n+ACCAGACATGAAGGAACCTGACGCACTCCATTGATCCGAGTCTCCTAGACTGCCCGTTGC\n+CGAAGACGGGTCTTCGGGTCACCGCCTCCTCCTTGACGGAGTACCGGACCACTTGAAATT\n+TCGTGACATTACCCGAACTACAGTGGAAAGCTGCCCACTCCGGAAAAATGCCCTGGCCGA\n+TTCAATCGAAGAGCTTACGCACGTGATAGTGGGCGCTATTGAAGACCGAAGCTCTCGTCT\n+AATAGCCTGGTTTGACAATTAACCTTAGGAAAGCGGTGTGGAGCCTCCTGCTCCAAATCG\n+CGCTCTGATGTATGTTTGTACAGAAAGGCGAGAGAATTCGTAATGAATCGCATCCCGTCT\n+CCCTGATAAACTCTGTTCCAGATCGCTTCTCCGCAGTGGATCACACCGGAAACCCGTTCT\n+ATCACCTTGATCCTTCGACCGGGGGCATGCGAGTACGTTCGTCTAGTCCGGTAACGGGAG\n+TGTAAACCATTGTGAGAAGCGCCCCGCATCGGGGGGACCCACGACTTGCCTATGTCTTCA\n+TTATGACGCTGTTGAGCGGACACCTTTGAGTTATCTGCTCTATCACTAACTTCCGAGAGA\n+CTCCAATCCTCGTCCTCCCAACCAGCCGTGGTGCCTGTTGTAAATACAATGTGTTACGTT\n+TACTGCTTAGGGATGGTCCCCGTCCAAGGGCAGTTGCACCGGACAAACAGCTAGCTGCAC\n+ACATGGATGGAACTAGTCAACGCCATGAATAAGGGGTCGCAAATTGCGTCGACCGTGGTA\n+AGCAGATGACACACCAGTTTTACCGTAGGAGTTAATTCCTAGTTTCAGTGCCCCCACTTG\n+AGGTATGAAGTATGGACCACAAACTCAGGATACTCTGTATGACGAATTAACTAGAATTTC\n+GTTCACGTATCTTATCTGCCTGGTGACCATCATCGAAGCATAAGAATGGGGATGCATCTT\n+TTCGCTGTGCACTTGGCATGGTGGGTATCTCCGCTCACGCCAGAGGGGCTTTAGCTCACA\n+CTCAACGTTGGACTGTAGGCGCCCAACCTCGAGTCCGAAGAGGGGTATTCTCAATGCAGG\n+GGTCCAATTCTCTGCTAGTCAGCCTGTGCAGAAGACATTCCCTACGTGGCTGGGCAATTA\n+TAATCACGCGCATAATACGTGAAGCGATTTATGTCGGGAAGATTAGAATCTTGCCCGATT\n+AACAAGCCTTAGAAGTTTATGCCATAGGAGCTAGGGGCAATTTACTGTATCCCAGAATAA\n+CGACTCCCCAAGGACCGTGTCAGAAGATCCTTGTACTAAGGACACCGGCCAATAAAAGAC\n+GTTATTAACACCGTCGTAGCCTTTTCTGAAGCTTTTCAGACCTTTAAGGGCGTGTCATTG\n+AGCACTACGAAGGGGACCAAGGGGCTCCGACTCCTTATATGGTCAATCTCCTCGATAAAG\n+TTTCAATAACAACGCGCCTTAGGCCAGCAAGCGTCTTCATTCTGATGCCCAGAGGTTCGG\n+GTTGTATTCGAAATTGCCCGACTAGAAATTGTTTGAGAGACAACCGCGATTAGGTGCCCT\n+TTAGACCGTGTTGGAGCCTTAAAAACACCCGAGGCCGGGTTAGTAGTCCGGTTGTGAGTA\n+GTTAAGGGGCAAAATGAAGCGTAAGATTTTACGACCTACGCAACTGTTGGACCTCGATGC\n+ATTACAAATACTACGTAAGACATGTCTGGGCTGGAACTGTTAAAACCTGCAGCCTATAAG\n+AGTCCACCTGGGTGTCGTGATGGAGGAATCGGCGATCGGAGTTCTTGGTTCTATTCGGCC\n+TACCACCATGAATTGCTTAAGCTGAATCGCTGTATTCGTGGACGATAGATATAGTTCCCA\n+CGGTGATGAGATAGCCGACAGGAAACCCTGCGTCTAAACAGGCGTATGCTTCCGTGCGTC\n+GAGTAGGTGGGTGATAGTGTCAGGCATTTGGTTAAATTCGTCTCCTGGGCCGTCTCCACT\n+TCGGAATATTGCTATGAACTCTGCTGTCATAACGGTATCCAGGATGCAGCATTTCGCAAT\n+CGCCCTCGGTTTGTGGTTTGCACCCCCCGCCTAGATACGGATAAAGGAGGATGATTGTTG\n+CTTACGACCTCTGCCTATTGTAAGCTTAGAGACAAAAATCATCGCGACTGCAGAGAATCC\n+GCTATTATATTCGTGTGCTGTACCTTTGATCCCATAGCTGATGGAATACGACAGGAGTAG\n+CCCCCGATATTCTCTTTATTCCTTTGTAGTATTTACCATGACGTGGTTGCTCGATGTATG\n+TAGGCACTTCTATTTGACTATGCTATGCAGTATGACATTGGACAGCGTGAGTCGATGTCT\n+TATCCCGCAGCCCTGGGCCGGTTGTACGAATCGGGAATTTCCGGAACAGCGATGACTAGG\n+CCGGCTAACGAGACAAGTCCCTTGGAGCGATTTTCACCAGCGCTTAGAGCGGAGTCCCCG\n+CTCGCTAGTCACGAAGGCCTATTTACTGACCGCCCTTGCCGTATGTAGAGTAGCTCACCC\n+TTAGCTCCTCAGCCGTGGGTTCAAAGATCCACGCATTAAATTTCGAAGGAGTAGTCAGGT\n+GGAGCTGTACACATCACTTGTATTCAGATTGTCAACTAGGAAATCCAGTGTAGGAAAGCT\n+GCTTCTGATCCATGGGGCTGTATGCGGATTAGATAATAGGGTCATAGTCGTCTATAGGAA\n+TAGTATCAGTACTACAGATAGGCGGCTCGTGTTGGTACTATTTGCCAGCCGTTTGAGTGT\n+TTATCAATCTCACCGTTGTCCGAGCGCGTTGTCATCGAGACTGGCTTGCAAGCCAGGGAT\n+CCATCGTCTGGGCGGTCTCGGGCGGGCGAGTGTCTAGAGACTACAGCGATCTTGATCTTC\n+GCGTGTCGGTTTGCACGCCATGGTACATACTGGGCAACGTAGGAGGACCGCACCGAAGAC\n+TAACGTCAATAATATAACACCTCAAAAGGTACCATCGCAAATAGTGAGTATAGATGCACC\n+CTCACCAGCATCTCCAGTGGCGAATTATGCTCCTTTAAGTACTGTCCTGTCATCTTATTA\n+TACGGGAATATCGCATTCCCAACTATTTTTGACGCCGACGCCAGGGGCCATATCAATTAG\n+CTTTTAAAGTCTGCTACCCAAGTTCATACATGTGGTGAGGAATGTGGAATACATTAGGCT\n+AATATGATTCTGAATTCGTGGCCAACGGCATAAAT\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/velvetg_test1/lastgraph.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/velvetg_test1/lastgraph.txt Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,135868 @@\n+1\t142858\t21\n+NODE\t1\t99975\t1866817\t1865182\t0\t0\n+TGCCAAGAGTCACCTGATGTTTGCGGTTATGCCCTACGGCGAAGATAATGAGATCGGTAGCCCCTACTTCCTTACTTCACCAACCCCTCTAACATTATGTGACTATTGATATGTTCTGGCCTAGTTAACCCGACTCTTCAAATATCTCAGAGTCCGCTGGATGGGATGGACTACCCAACCGGCATCTTGGTGCGGTCGAGTTGGCAAGGGACTTATTATTCATCATGTGCTACCGGCCCAGAATTTTTTGTTAAGAACTCTCGGTAAAGAATAATAAATTGTCTTACGCCTACCCGCTATTTTATGAAGTCGTACCGTGCTCGGACGCTATTTCTGTAGTACACCCGCACGAAAAGCCGAACTACGTAACGGTGTTCAGTAGTGGGTCCAATACAACGCCCTGTCGCCATTCTCGAATACTGGTTGGTAGGCCAGTCCCGTGTGAGTGTCTATTATCAATAGGCGAGTCGGACAGCTCTGGTTTGTGCTGAGTCTGTTAAAGCAAACATTGGATCATTCCGGGAGTGGGCGACAGACCCAGGAATCGGCGGCTGGTCAACACCATAGAGGTGGTCCTTTTGTGACCGTTGTTCCCGCAAATAACTCCTAAAGCACCCTTAAGCGTCGAATTCATTTAAGGGTATGCGCGAGCGTAGAGCGGTCCGGACGGCGATCCGCGAGGCTTCCCTCACAGAAACATCCATATGCGTTGTTCCGTACACATGTAATGGGAAATATCTTTACACCATGCATATCTCCACCCCTACATCGGGGTAGGGGGAACACAGATGTCATGCTCAGTGGAACTTGCCTTACAATACCTGTAAAACGATCAAAGCGGGACGTCATCAGGTCGTGCTGATGACTGTGCCTATCATTATAATTGATAAATACGCCAAGGCCCTTCTAGATCCGTGTTAAGAGTGCTCGAACGTAGGGACGCCGGTCTATCTGATAGGACCAATACGCTGTTGCAGTGCAAATCGAAAATAGTTATCTCTTCGTGGCGCACTGGACTAAGTACACCCCTAATGAGTAAACCGGAGTACCTAGGTGACAATCACGTCGGGCTAAGTAGCAGAATGCCTGTTCGATTAGATCCAATTGATATGCGCGTGTAAGCGACGAATGACAGGTCACGAATTTGGCAGGGATTATGTCCGGAACGGAATAAAACCAGGCGGTTACCAAGACAGGCCGTTGAGTTGGGTTGGCCCTATATCCGTATCCAGAGATACGTTACAACCGTACGACATCTGGACGAGGAACCCTTTGGGAAAATCAACAGGCATGTTCCGGCCGACAGCCTATTTTACGGCTGATCCAGTAACACCTTGCCAATGCCCTGAATAGGGGTCCAGTACTCCCAGCTCCCGAGGTCCCAGAATGGTATGACCGAAATCTAGTCACCCGATGCCTCGAAGCCAAGAGATTTGCCTTGACTGCGTTTCTGGCAGACCATAACCGCTTCGCTAGGTGTAGGCTATCTCAACGCTGTTACGCGACAGGTAGGCGGCCAGACGCACTCCCTTCTCCGACACTTTTACGATTGAACGAGCCTTCTCCTCGGACTGGCTCGCGGCCAGAGGGAACTTTGCCCGCGCGAGCTTAAGGACAGCCAAAGCCCAGTGAGGGAATCGACTACGTGCCACGGAATCGCCTCCCTTCGTTATAATAGCTGCCGTGCCAGTTGGCTATGCTGTAACCATTGTGGACCTGATACGCCAGATCGCCGTCGCTATTAAAGCTCGATTCGCAACCTACTTCCCGATGGCTCCGGCGGAGACTGAATTATCGTCCTCCGAAAGTATATCTGCAGGAATCCAAATTTAACGCATTGACCCTGTGTGGGGTCAAACGGCGGAGGGTCAGCGCATATATTCCGATGGTTTCTACGACAAGAAGAAGAAGGAACTCTGGCTGTATAGTGTTTTTTTATGTCAAGCCGCGTGGGGGTCGTTTATTGTCACCGGGTTTGGTTATAGCTTCTTTTCTGCCTGGTGGGAAATCTGCCAGTTACTCAATCGTGTTTAGCCAGAATCCGGAGCTGCGGGCTGGTGGACGCGCAGGGATAAAATTATGAGAGTTTGATTGCATGCCGCAGTAATTCTCCCGAGAGTTCGGGGGCTACACTCTATTGTCGAGCGGCACAGTTAGGATGCGCTCTCTCTGGCGTTCCACCCCCAAGTGACCACCCCGCGCTGCAGTATGTTACGCCGCATTAGTGAGACTATACTGAATGCCGTTTAGCAAACGAGGGTCTGTCCGGCGGTCCTTACTGCGCTGTCGATCGCAATTTTGAATGACTGTAACTGGAGCAGCACCCATAGGGGACGCCGCGACGTTATTTAATGCGACAGAGATGTATTCTTCCGTTAGTTCGCGTCCACCATAGGAGTTTCACCCAAACAGGGTAGTTTCCCCTTGAGCGGTGACCTTCGCGGTTAGCGCACCGTAACACTCGCACTAGGTCTCACCACATCCAGCAGCGTGAACTGAAATCACTTTAATGGGTATACGGCGAACCGCAGACCACGGTCCAGGGTGACAAGAAGCTATCTATTGCCAAGGTCTTCCCAGTTTGAGCGAGCTCGCCAGCCATTTCCCGCATCTAACCGAAAGGTCGTGCGCACCGGTATAAGACTCAACCGAATTGACAAAAGTCCGTTATTGTAGTGCAAGACTGCTAAGAGAACCCTACTGTTCAGCTTGGGTTCCATCCAATGCATTCCTCGCTCGGACGGAGGCTTTACCGGGCTCTTGGCCGAAATCAATTGTCTCCCTTAGACTGCCCTCACATATCACACGCACCCAAGGTCACCCAACAACACTCATGGAATGCCGCACGCTGAAATTTTGCTATGGGCGGTGTTACGGCTATCCAATACACCAGCATTGTGTCCACTGCCCTGCCTGGGTTTAAGCCTAGCAGACCTCAGGACTGGAGTTTGAGGGAGCTACGAATAAGAATCGGATAGAGAAGGTAAGAATAGTTAATTGGAAGCCGGGTTCACCATTGTCAACGTCCCGCTGTTTGGGAGCTTCGGTCCTTCAACGGTCAGTGAAAGTAAGTCCCAAACAGTTCCCACAGCCGCCAACAAGCCAACTTCCAACCCTACAGTTTCCTTTGTGGAAAATCTAAGTCATTCCAGGCTCCAACAGCCTATCTAAAGCTCGCGGTGGAAGATACTGTCCCAGAGCTAAGGTTCTTGGTTAGTACCCACATCGAACAAGCGATTTATGCCATACGAACCTCGAATTGTGCCGAGTAGGCCAGCAAAGATGTATACTCACTAGGTTCGACGATCACACAAGGGGTGACCTTCAGAAGTTACATGCGATGCCTTTCCCAGTGAATTCAGCGATTACCTTCTCCCCGAGCCCTGCGGATCCCTTCCACAACTCTTAGAGCCGTATAGAGCGGTCGTAAAAGCTCAGCCGTCCGTCGCAGACATTACTTCGAAACTTTCTCACTTCAAAGCACTCAATAGAGTAACGTCACCATTTACGAAGGCGCTCGCTTCCGCTCCATCCCGCAAATCTTACAGCGGACCTCATTGTGCGTAGCAGATCCTCTCTCACAAATCCAAAAGCAGTTAAAGATGCCCCGATAAGGTACTGGTTCACGGCAAAGGATGACCACCACCTGGTGATCTCACCACGTGTTGAATATTTCGGTTCAACCCCTTATAGGAAGGGAATACAACGCGTTGGTGCATGCAACACCCCGTGGTTCTGTCAATTAGGTGTCTTGTGTTCGTAGATAGCGGCATACCTGCGTGTCTAAATCTGACGCGTACTAGCAGTATGGCTTAGAGACACTGTGCATTGCTACTGCCCGTAAGCGGCGCGGAAGGCCGAGTTCACCGGAGAGCTTTCTTACTCTCAAGGAAGCTCTATCCAAGCGATACAGCCCGGCTCTTAACGCCT'..b'0\n+142331\t44713\t0\n+142334\t67506\t0\n+142336\t78303\t0\n+142338\t28426\t0\n+142339\t6496\t0\n+142342\t10462\t0\n+142343\t88559\t0\n+142345\t4161\t0\n+142347\t18\t0\n+142350\t51805\t0\n+142352\t90636\t0\n+142353\t3139\t0\n+142356\t13824\t0\n+142358\t46930\t0\n+142360\t90323\t13\n+142361\t74196\t0\n+142364\t29220\t0\n+142366\t71407\t10\n+142368\t6618\t0\n+142370\t46082\t0\n+142372\t60224\t0\n+142373\t36472\t0\n+142375\t50418\t0\n+142377\t91424\t0\n+142379\t61413\t0\n+142382\t52442\t0\n+142383\t36069\t0\n+142386\t62798\t0\n+142390\t55545\t0\n+142391\t70624\t0\n+142393\t48113\t0\n+142395\t88654\t0\n+142398\t16404\t0\n+142400\t15471\t0\n+142401\t55202\t0\n+142404\t31591\t0\n+142406\t33634\t0\n+142407\t28550\t0\n+142409\t15980\t0\n+142412\t77524\t0\n+142413\t80052\t0\n+142415\t4525\t0\n+142417\t95868\t0\n+142419\t32127\t0\n+142423\t74938\t9\n+142428\t12235\t0\n+142430\t53431\t0\n+142432\t18600\t0\n+142434\t7405\t0\n+142435\t22846\t0\n+142437\t16490\t0\n+142440\t3556\t0\n+142441\t30749\t0\n+142443\t75953\t0\n+142445\t79907\t0\n+142448\t48800\t0\n+142449\t70118\t0\n+142454\t25915\t0\n+142456\t44747\t0\n+142458\t86163\t0\n+142460\t57489\t0\n+142461\t80012\t1\n+142464\t65294\t0\n+142465\t91515\t9\n+142467\t4555\t0\n+142470\t19927\t0\n+142472\t61999\t0\n+142474\t91786\t0\n+142475\t11556\t0\n+142478\t15654\t0\n+142479\t37757\t0\n+142481\t96816\t0\n+142484\t20185\t0\n+142486\t20670\t0\n+142487\t13252\t12\n+142489\t40206\t0\n+142492\t45161\t0\n+142493\t25142\t0\n+142495\t65805\t0\n+142498\t240\t0\n+142499\t88564\t0\n+142501\t99455\t0\n+142503\t19191\t0\n+142505\t79523\t0\n+142508\t32185\t0\n+142510\t68031\t0\n+142511\t69603\t0\n+142514\t43461\t0\n+142515\t36655\t0\n+142517\t57265\t0\n+142519\t31173\t0\n+142521\t69142\t0\n+142524\t95811\t0\n+142525\t46481\t0\n+142528\t98309\t0\n+142529\t39804\t0\n+142532\t63511\t3\n+142534\t16646\t0\n+142536\t80552\t0\n+142538\t78457\t0\n+142539\t84730\t0\n+142542\t87282\t2\n+142546\t41822\t0\n+142547\t65817\t0\n+142550\t87538\t0\n+142552\t52464\t0\n+142553\t61659\t0\n+142555\t36749\t0\n+142558\t68131\t0\n+142560\t82957\t0\n+142561\t71155\t0\n+142564\t87147\t0\n+142565\t19134\t0\n+142568\t28579\t0\n+142570\t93554\t0\n+142571\t236\t7\n+142574\t24232\t0\n+142576\t99544\t0\n+142577\t90449\t0\n+142579\t14821\t0\n+142582\t48434\t0\n+142583\t56727\t0\n+142585\t99332\t0\n+142587\t78619\t0\n+142590\t57482\t0\n+142591\t69119\t0\n+142593\t23293\t0\n+142595\t15502\t0\n+142597\t50475\t0\n+142599\t52639\t14\n+142601\t49725\t0\n+142604\t89870\t0\n+142606\t49395\t0\n+142608\t2360\t0\n+142610\t5284\t0\n+142611\t86544\t0\n+142614\t98102\t0\n+142615\t12959\t0\n+142618\t862\t0\n+142619\t54483\t0\n+142622\t90333\t0\n+142623\t80569\t0\n+142628\t10475\t0\n+142630\t60654\t0\n+142631\t12265\t0\n+142633\t17629\t0\n+142635\t68291\t0\n+142639\t3759\t0\n+142642\t10384\t0\n+142644\t33085\t0\n+142646\t78601\t0\n+142647\t82669\t0\n+142649\t41391\t0\n+142652\t58256\t0\n+142654\t90042\t14\n+142656\t72121\t0\n+142657\t98882\t0\n+142659\t3705\t0\n+142661\t16297\t0\n+142664\t77350\t0\n+142665\t74551\t0\n+142667\t86407\t0\n+142671\t86422\t0\n+142674\t70756\t1\n+142675\t55276\t0\n+142678\t21988\t0\n+142679\t94887\t0\n+142682\t81215\t0\n+142684\t34481\t0\n+142685\t81574\t0\n+142688\t3712\t7\n+142690\t71369\t1\n+142692\t18548\t0\n+142694\t594\t0\n+142695\t60183\t0\n+142699\t89385\t0\n+142702\t21538\t0\n+142703\t42740\t0\n+142705\t43203\t0\n+142708\t82532\t0\n+142710\t29057\t0\n+142711\t84329\t0\n+142713\t62077\t0\n+142716\t18464\t10\n+142717\t49614\t0\n+142720\t51671\t0\n+142722\t64835\t0\n+142723\t24564\t0\n+142725\t76005\t0\n+142728\t30287\t0\n+142730\t12796\t0\n+142731\t22432\t0\n+142733\t14307\t0\n+142735\t80538\t0\n+142737\t57459\t0\n+142740\t99388\t0\n+142741\t20298\t0\n+142744\t58697\t0\n+142746\t11244\t0\n+142747\t1304\t0\n+142749\t68060\t0\n+142751\t87290\t0\n+142753\t62386\t0\n+142755\t71552\t0\n+142758\t85401\t0\n+142760\t28216\t8\n+142762\t69184\t0\n+142763\t24808\t0\n+142766\t97383\t0\n+142768\t56657\t0\n+142770\t43389\t0\n+142771\t32839\t0\n+142773\t23210\t0\n+142776\t53417\t0\n+142777\t62316\t0\n+142780\t14965\t0\n+142781\t85221\t6\n+142784\t92936\t0\n+142785\t45796\t0\n+142788\t26269\t10\n+142790\t64666\t0\n+142791\t31679\t0\n+142793\t65909\t0\n+142796\t93378\t0\n+142797\t66084\t0\n+142799\t10856\t0\n+142801\t68906\t0\n+142803\t3240\t0\n+142806\t71812\t0\n+142807\t66262\t0\n+142810\t51530\t0\n+142811\t19893\t0\n+142813\t31303\t2\n+142815\t49171\t0\n+142817\t58919\t0\n+142819\t14356\t0\n+142822\t39259\t0\n+142824\t29407\t0\n+142830\t68025\t0\n+142832\t52307\t0\n+142833\t26382\t0\n+142836\t58604\t0\n+142838\t7161\t0\n+142840\t64827\t0\n+142841\t72446\t0\n+142844\t41819\t0\n+142846\t81766\t1\n+142848\t93117\t0\n+142854\t39619\t13\n+142856\t97686\t0\n+142857\t26549\t0\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/velvetg_test1/stats.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/velvetg_test1/stats.csv Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,2 @@
+ID lgth out in long_cov short1_cov short1_Ocov short2_cov short2_Ocov long_nb short1_nb short2_nb
+1 99975 0 0 0.000000 18.672838 18.656484 0.000000 0.000000 0 67972 0

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/velvetg_test1/unusedreads.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/velvetg_test1/unusedreads.fa Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,13992 @@\n+>SEQUENCE_4_length_35\n+CGAGATGTATACCTCTAACACTGTGTTCCAAGTAC\n+>SEQUENCE_20_length_35\n+AGGAATTAACTCCTACGGTGAAACTGGTGTGTCAT\n+>SEQUENCE_38_length_35\n+TTGCGCTCAGCTGTCTGCCGTTGACTTCCTTCAAC\n+>SEQUENCE_55_length_35\n+GCTTGCAACTGGTTGATAGTTCAGACGAATGGTCG\n+>SEQUENCE_62_length_35\n+ATATCGCCCCAGACCTGAGAGTGGCATGCCCGACC\n+>SEQUENCE_67_length_35\n+GTGCACCGCTTGCCCCTTTAGTGTAACAGATAGCA\n+>SEQUENCE_84_length_35\n+GAGTCTGCACGCTGGTCCCTTGACGGGCCTAGGGC\n+>SEQUENCE_124_length_35\n+CGATATGGATACGTCTTATCGGATTCGGCCGGTGG\n+>SEQUENCE_162_length_35\n+CCAACTCAGCCGCACGAAGCATGTCTGGTTAATAG\n+>SEQUENCE_179_length_35\n+ACCCCGTCCTGATGGTACGGGTCATTAAATCCAGG\n+>SEQUENCE_180_length_35\n+TGTCGACGTACACTTCGGCGGGGCAAGAAGCGTGT\n+>SEQUENCE_208_length_35\n+GAAAAGTTGACATGCCGTGTTTATAGACCAGAAGA\n+>SEQUENCE_242_length_35\n+ATTTGGAGTGAGTCGCGACGGATCTACCTTCCAAG\n+>SEQUENCE_302_length_35\n+ATTCTCATTCGTAATAGCCGTTGGCTGACTGTAGA\n+>SEQUENCE_315_length_35\n+CCAAGGTACTATCGTACTCTGCATGATTGCAAGCC\n+>SEQUENCE_320_length_35\n+CATCTTACAAGTTGAATAGCGGCTAAGAGTTAATA\n+>SEQUENCE_334_length_35\n+TTCGTAGATAGCGGCAAACCTGCGTGTCTAAATCT\n+>SEQUENCE_339_length_35\n+GCTGCTGGGCATGCTAGAGCCGACCAGTCGAATTG\n+>SEQUENCE_341_length_35\n+AGAGAGAGCGCATCCTAACTTTGCCGCTCGACAAT\n+>SEQUENCE_343_length_35\n+CACACTTGGTATTCACTGCACCGGAAGAGTTATCA\n+>SEQUENCE_454_length_35\n+CGGTTACCTCCTCGCAGGTATCTTGTGACACTGTG\n+>SEQUENCE_484_length_35\n+GGGAATCGCGTGGAGATGGAAGAACCGCGGCACGT\n+>SEQUENCE_505_length_35\n+TTACCCGTATTAGGGCAAGTCCAGCCATAATCGTG\n+>SEQUENCE_514_length_35\n+GGCACTTCTATTTGATTATGCTATGCAGTATGACA\n+>SEQUENCE_551_length_35\n+TAAATCCTTGTTAAGATTGCTCGAACGTAGGGACG\n+>SEQUENCE_558_length_35\n+AAACCGGTGTTGAACCTCCCAGAGTTACACAGGGG\n+>SEQUENCE_559_length_35\n+GGATGCTTGAAGACGTAACGTGATTGAGGTGGAGA\n+>SEQUENCE_561_length_35\n+CATGGTAAGGCGTGGCATCGTTCCCATTTTGTCAC\n+>SEQUENCE_573_length_35\n+GTGCGTTCTTTTTGAAGGTCAACGCACGCAATTGA\n+>SEQUENCE_621_length_35\n+CGTCCTACTTTGTTCGCAGTATGCTAGTTCTATGA\n+>SEQUENCE_658_length_35\n+TTCGTGGGGCACCGTAAAAAGCGGACACAAGCAGT\n+>SEQUENCE_664_length_35\n+GACAGGAACTTGGTAACGCCAACGCGTGCTACCTA\n+>SEQUENCE_674_length_35\n+CAACGCCCCTTAACCTGTATTTGACTACGGAGGGA\n+>SEQUENCE_731_length_35\n+AAAAAGTGAGCGCTTTGAACGCGACTATTGATTCC\n+>SEQUENCE_733_length_35\n+CTACGCGCCTTCCCAGACCCACCAGAAACGCTAGG\n+>SEQUENCE_737_length_35\n+CGAACGCAACATAAAGTAGCCGAGGAGAGCACAGG\n+>SEQUENCE_746_length_35\n+CCTGTGCGGGATTAATTCATATTAGAGAGTAGCCA\n+>SEQUENCE_765_length_35\n+CCGGAAAATGGGAATCCACGCATAGACTCCCGGTA\n+>SEQUENCE_786_length_35\n+AATATGGACCAGTATTCTCCCGACGGCTAGGACAC\n+>SEQUENCE_822_length_35\n+TCAGCTTGCTACTTTGACTACGGCGTAGGTACACT\n+>SEQUENCE_832_length_35\n+CAAAACAGCCGTGTAGACGGGGGCTGGTAACCCGT\n+>SEQUENCE_852_length_35\n+CATCTGCAATTGTCACGAACTCGGGGGAGTTTACA\n+>SEQUENCE_857_length_35\n+GATGTGACTACATTGTCACCCACGATGAGCCAGAT\n+>SEQUENCE_885_length_35\n+ACACTCAGCCCCATACGGCACCATCGCAGATGGTT\n+>SEQUENCE_912_length_35\n+CGCGAAACCCTTGTTATCATAATCGTTTAACGCAC\n+>SEQUENCE_923_length_35\n+TAGTACCCTCCACAGGCCACGATCCGCCTTTTACC\n+>SEQUENCE_940_length_35\n+GAAGCCGGGTTCACCATTTTCAACGTCCCGCTGTT\n+>SEQUENCE_955_length_35\n+ACCTAATCCCTTAGACCACGTGACTCCGGTCTATG\n+>SEQUENCE_997_length_35\n+GCCAGTATTAGATGCGTAGGTAGCCCACCGCCGCT\n+>SEQUENCE_998_length_35\n+TGGACGGCGTGGCCTAGTATTCGTGTGTCCTATCA\n+>SEQUENCE_1000_length_35\n+TACAGTTCAAACTTATGCTTTCAGCATATATTGGA\n+>SEQUENCE_1005_length_35\n+TTGCCGTTCAAACATAATGGCTCGTTTTTTACCTC\n+>SEQUENCE_1016_length_35\n+GCCGATGACCCTTATGTATCCAAGCCTCATAGCCA\n+>SEQUENCE_1026_length_35\n+CAGATGGCGGTTACACGAACCCAACCTCACGACAC\n+>SEQUENCE_1035_length_35\n+CTGCGCGCCGGGCCACAGGCAAACGCGAAGCCCTG\n+>SEQUENCE_1043_length_35\n+GGGCTGTGTAGCCATGTAGTGCCCTATACCGTTCA\n+>SEQUENCE_1074_length_35\n+TTCCCCGGTTGGGCGGCTATTCGCCCCAATTAGAG\n+>SEQUENCE_1086_length_35\n+TGTATTGCTGACCTCGACCACCCAGCATTTGGGAC\n+>SEQUENCE_1133_length_35\n+GTATAGGTTGGGGTCGGGACTACAGGTGATCGGGC\n+>SEQUENCE_1135_length_35\n+GTTAGGTATTTAACCAACATGCTTCCCCTCGCAAA\n+>SEQUENCE_1203_length_35\n+GGTCAATGTCAGTAAGGCGCTATCCTACGGGACGC\n+>SEQUENCE_1220_length_35\n+TACCTAGTGTCACTGCAGAATGGGAATTGCGCCTG\n+>SEQUENCE_1222_length_35\n+CACGCCGGAATAGGGCCGCCTTGATACGCGCGGTT\n+>SEQUENCE_1223_length_35\n+TCGATCCGGCCTGGTAGCACGTGGCAGCGCTGCAG\n+>SEQ'..b'AAATTAGCAAATTGACCCATCGTAAACAGGAAA\n+>SEQUENCE_141763_length_35\n+GTTCCCAATCTCCCCGACCACACCCTTAAGGTGCA\n+>SEQUENCE_141765_length_35\n+ACTCTTTCATAAACTAAACCCAGAGCTTCCGGCTG\n+>SEQUENCE_141775_length_35\n+AGTGGTATCCTGTCGGCGTGGCATAAGGTCATTTC\n+>SEQUENCE_141788_length_35\n+AACAGAGCCTGGCGCGTGGACGGGACATATTTCAG\n+>SEQUENCE_141811_length_35\n+ATCTAATCAAGTGAGACGTCTCAGCTGGATTAGAT\n+>SEQUENCE_141812_length_35\n+TAGAAACTACACTTTATTTCATTATCTACAAAATA\n+>SEQUENCE_141840_length_35\n+AACCTAGTTACCCCATACCCTGCTTCGCGGAGAAT\n+>SEQUENCE_141842_length_35\n+CACGACCTGATGACGTCGCGCCTTGATCGTTTTAC\n+>SEQUENCE_141847_length_35\n+TTCACTGGGAAAGGCATCGCGTGTAACTTCTTAAG\n+>SEQUENCE_141868_length_35\n+TCTCATGGTATCGGAATTGATAGGACATACGCATA\n+>SEQUENCE_141914_length_35\n+TTTATCGAGGAGATTAACCATATAAGGAGTCGGAG\n+>SEQUENCE_141923_length_35\n+GGGACCGGCTGCCAGGTCTCAGATGGACGAACAAC\n+>SEQUENCE_141955_length_35\n+CCTGGGGCATGAGACGAACCCGATATACAATCCTA\n+>SEQUENCE_141977_length_35\n+TAAACAATAGCTATAGAGATGAATCGCGATCAACA\n+>SEQUENCE_142043_length_35\n+TGTCAGGGATTGGAGGCGCTAAAATTGGGTTGCGT\n+>SEQUENCE_142052_length_35\n+AAACATACATCAGAGCTCGATTTGGAGCAGGAGGC\n+>SEQUENCE_142064_length_35\n+GAGTACCTAGAAGTTCGAGTTGGGTCAGGACGTAG\n+>SEQUENCE_142080_length_35\n+GATCCGCCTTTTACCGCAATTACTTCATGTCCGCT\n+>SEQUENCE_142084_length_35\n+CGTAGGGTAATACTTAAGCCACGGTGACAGGCTAC\n+>SEQUENCE_142086_length_35\n+TAATGCAACCCAAATCTTTGACATTTGCTAGTATG\n+>SEQUENCE_142110_length_35\n+CCTGTTCTGGCATAATTCTACTGCCCCTGCGGGTC\n+>SEQUENCE_142124_length_35\n+AGGCGTAAGGCCACCTGGAAGGGAATGTACGATAC\n+>SEQUENCE_142136_length_35\n+ATGTGACTTACTTACCAATGTAATAAGACGACGGC\n+>SEQUENCE_142139_length_35\n+TTTCGCTCCAGGCTACTCGTAATTGCTGGCACATC\n+>SEQUENCE_142140_length_35\n+TAGGCGCCTTTCATCGTGTGAGACCCAGTGGCGTA\n+>SEQUENCE_142166_length_35\n+TGTAATGTGTTAACCTCGTGCTGTACAACCAGCTC\n+>SEQUENCE_142167_length_35\n+CACACTGAAGTGTTTCCTTCCAAACCCAGATTCAA\n+>SEQUENCE_142194_length_35\n+ACACGTTTTCAGGAGCCGCAATTATCCCGAAGGAG\n+>SEQUENCE_142197_length_35\n+CTGAATTGACGCGTCCTAAGATTTCGACAACGTAG\n+>SEQUENCE_142200_length_35\n+TGCCTCTATAGTAGAAGCGAAATAAGATCTGGTTC\n+>SEQUENCE_142207_length_35\n+TTTCTGATCTACGAAATCCCGGGTCCCTTCTGAGA\n+>SEQUENCE_142222_length_35\n+ATCTAGAACTCGTAGAAATTATAAAATAGACATGG\n+>SEQUENCE_142232_length_35\n+TGTCAGTTACCTTGGTAATGCTATGGTACCTATGC\n+>SEQUENCE_142233_length_35\n+GTATGAATGCCACAGGGTATCGGATTCAGCCGATT\n+>SEQUENCE_142252_length_35\n+ACAGTTGACTGGTGCGTGCGTGAGCCTACTGCCAT\n+>SEQUENCE_142274_length_35\n+TACATCTATGTACCATCTTAGACTGTCGGCGGAAC\n+>SEQUENCE_142313_length_35\n+TATACAGTACGCATCCATGATACCTGTGATCTTCA\n+>SEQUENCE_142333_length_35\n+CGTGTCGGTTGCTTCATAGAAACGCTGAATACCAT\n+>SEQUENCE_142388_length_35\n+GTGATCCTCCCATCACCTCCTCAGTAGGTGCCAAT\n+>SEQUENCE_142421_length_35\n+GAAGTATGGACCACAAACACAGGATACTCTGTATG\n+>SEQUENCE_142425_length_35\n+ACCTGAGGAAGGTGATTCGATCCCAACATTCCGAA\n+>SEQUENCE_142452_length_35\n+TGTTTGTGCCTGGTATTGTAGGTGCGTGTACTGAT\n+>SEQUENCE_142535_length_35\n+TGGATTTAACCGTACAAGTGCTTAGGGGGATCGCG\n+>SEQUENCE_142544_length_35\n+GACTGCGCACTATTCGTTGCGAACTCCTTGAGCTA\n+>SEQUENCE_142549_length_35\n+AGAGTTGTCAGTAGCCATTTCTTGCCGACGAGACA\n+>SEQUENCE_142598_length_35\n+AGAAATTACATTTTTGCCCGCACTGTTAGCAGTCG\n+>SEQUENCE_142609_length_35\n+ACCTGTACGTTCAGCGTGAGCGGATCAGTCTTGAT\n+>SEQUENCE_142626_length_35\n+TTTGAATGCCAGCTTCCCACCGGGTTGGGTTAGTG\n+>SEQUENCE_142638_length_35\n+AAGGGAATACAACGCGTAGGTGCATGCAACACCCC\n+>SEQUENCE_142669_length_35\n+TGTGACCAACTGGGCCGATCCGTGGCAGGTAAGCA\n+>SEQUENCE_142697_length_35\n+ATATCTGGAACAGCCATAAGTCGGGACATATCCAA\n+>SEQUENCE_142704_length_35\n+CCCCTATGTTAGTACGCCGCCCCTTACTTAAAGCC\n+>SEQUENCE_142745_length_35\n+CCTATAATCGGAGCTCTTCGTCGAGAAATATACGA\n+>SEQUENCE_142750_length_35\n+TGGGGTTCCTCACCCGATCGTAGGTAAAATGTCAC\n+>SEQUENCE_142761_length_35\n+GAGAATATATGTGCTTCTTACCGGCCCCTATGACG\n+>SEQUENCE_142782_length_35\n+ACAGCCTGTTATTTTTGTAGGACACGAGTCCTGCG\n+>SEQUENCE_142795_length_35\n+TCAGTTGGATCCTTCTACATCCTGACCCAACTCGC\n+>SEQUENCE_142826_length_35\n+ATCATCCATGTAGGAGAACAAGTTAGTGGTTTTTG\n+>SEQUENCE_142827_length_35\n+CAGTGCATGGGAGGTAACTGGGCGCAGAGGGCCAG\n+>SEQUENCE_142849_length_35\n+GAACACACTTAGCCTAGGGTGCACGGGTTCAATGA\n+>SEQUENCE_142852_length_35\n+GGATCCAATCCGCGTTGTCACTACACGACGTGAGG\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/velveth_test1/Log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/velveth_test1/Log Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,2 @@
+Fri May 28 13:27:22 2010
+ ./velveth /Users/jj/src/wf/galaxy/galaxy-central/test-data/velveth_test1 21 -shortPaired /Users/jj/src/wf/galaxy/galaxy-central/test-data/velvet_test_reads.fa

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/velveth_test1/Roadmaps
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/velveth_test1/Roadmaps Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,491267 @@\n+142858\t21\t1\n+ROADMAP 1\n+ROADMAP 2\n+ROADMAP 3\n+ROADMAP 4\n+ROADMAP 5\n+ROADMAP 6\n+ROADMAP 7\n+ROADMAP 8\n+ROADMAP 9\n+ROADMAP 10\n+ROADMAP 11\n+ROADMAP 12\n+ROADMAP 13\n+ROADMAP 14\n+ROADMAP 15\n+ROADMAP 16\n+ROADMAP 17\n+ROADMAP 18\n+ROADMAP 19\n+ROADMAP 20\n+ROADMAP 21\n+ROADMAP 22\n+ROADMAP 23\n+ROADMAP 24\n+ROADMAP 25\n+ROADMAP 26\n+ROADMAP 27\n+ROADMAP 28\n+ROADMAP 29\n+ROADMAP 30\n+ROADMAP 31\n+ROADMAP 32\n+ROADMAP 33\n+ROADMAP 34\n+ROADMAP 35\n+ROADMAP 36\n+ROADMAP 37\n+ROADMAP 38\n+ROADMAP 39\n+ROADMAP 40\n+ROADMAP 41\n+ROADMAP 42\n+ROADMAP 43\n+ROADMAP 44\n+ROADMAP 45\n+ROADMAP 46\n+ROADMAP 47\n+ROADMAP 48\n+ROADMAP 49\n+ROADMAP 50\n+ROADMAP 51\n+ROADMAP 52\n+ROADMAP 53\n+ROADMAP 54\n+ROADMAP 55\n+ROADMAP 56\n+ROADMAP 57\n+ROADMAP 58\n+ROADMAP 59\n+ROADMAP 60\n+-52\t1\t14\t0\n+ROADMAP 61\n+ROADMAP 62\n+ROADMAP 63\n+ROADMAP 64\n+ROADMAP 65\n+ROADMAP 66\n+ROADMAP 67\n+ROADMAP 68\n+ROADMAP 69\n+ROADMAP 70\n+ROADMAP 71\n+ROADMAP 72\n+22\t4\t0\t11\n+ROADMAP 73\n+ROADMAP 74\n+ROADMAP 75\n+ROADMAP 76\n+ROADMAP 77\n+ROADMAP 78\n+7\t9\t0\t1\n+ROADMAP 79\n+ROADMAP 80\n+ROADMAP 81\n+ROADMAP 82\n+ROADMAP 83\n+ROADMAP 84\n+ROADMAP 85\n+ROADMAP 86\n+ROADMAP 87\n+ROADMAP 88\n+ROADMAP 89\n+ROADMAP 90\n+ROADMAP 91\n+ROADMAP 92\n+ROADMAP 93\n+ROADMAP 94\n+ROADMAP 95\n+ROADMAP 96\n+ROADMAP 97\n+ROADMAP 98\n+ROADMAP 99\n+ROADMAP 100\n+ROADMAP 101\n+ROADMAP 102\n+ROADMAP 103\n+75\t1\t0\t14\n+ROADMAP 104\n+76\t0\t1\t15\n+ROADMAP 105\n+ROADMAP 106\n+ROADMAP 107\n+ROADMAP 108\n+ROADMAP 109\n+ROADMAP 110\n+ROADMAP 111\n+ROADMAP 112\n+ROADMAP 113\n+ROADMAP 114\n+ROADMAP 115\n+ROADMAP 116\n+ROADMAP 117\n+ROADMAP 118\n+ROADMAP 119\n+ROADMAP 120\n+ROADMAP 121\n+ROADMAP 122\n+ROADMAP 123\n+ROADMAP 124\n+ROADMAP 125\n+ROADMAP 126\n+ROADMAP 127\n+ROADMAP 128\n+ROADMAP 129\n+ROADMAP 130\n+ROADMAP 131\n+ROADMAP 132\n+ROADMAP 133\n+ROADMAP 134\n+ROADMAP 135\n+ROADMAP 136\n+ROADMAP 137\n+127\t8\t0\t7\n+ROADMAP 138\n+128\t0\t4\t15\n+ROADMAP 139\n+ROADMAP 140\n+ROADMAP 141\n+ROADMAP 142\n+ROADMAP 143\n+ROADMAP 144\n+ROADMAP 145\n+ROADMAP 146\n+ROADMAP 147\n+ROADMAP 148\n+ROADMAP 149\n+ROADMAP 150\n+ROADMAP 151\n+ROADMAP 152\n+ROADMAP 153\n+ROADMAP 154\n+ROADMAP 155\n+ROADMAP 156\n+ROADMAP 157\n+ROADMAP 158\n+ROADMAP 159\n+ROADMAP 160\n+ROADMAP 161\n+ROADMAP 162\n+ROADMAP 163\n+ROADMAP 164\n+ROADMAP 165\n+ROADMAP 166\n+ROADMAP 167\n+ROADMAP 168\n+ROADMAP 169\n+ROADMAP 170\n+ROADMAP 171\n+ROADMAP 172\n+ROADMAP 173\n+ROADMAP 174\n+ROADMAP 175\n+-161\t6\t10\t1\n+ROADMAP 176\n+ROADMAP 177\n+ROADMAP 178\n+ROADMAP 179\n+ROADMAP 180\n+ROADMAP 181\n+ROADMAP 182\n+ROADMAP 183\n+ROADMAP 184\n+ROADMAP 185\n+ROADMAP 186\n+ROADMAP 187\n+ROADMAP 188\n+ROADMAP 189\n+ROADMAP 190\n+ROADMAP 191\n+ROADMAP 192\n+ROADMAP 193\n+ROADMAP 194\n+ROADMAP 195\n+ROADMAP 196\n+ROADMAP 197\n+ROADMAP 198\n+ROADMAP 199\n+ROADMAP 200\n+ROADMAP 201\n+ROADMAP 202\n+ROADMAP 203\n+ROADMAP 204\n+ROADMAP 205\n+ROADMAP 206\n+ROADMAP 207\n+ROADMAP 208\n+ROADMAP 209\n+ROADMAP 210\n+ROADMAP 211\n+ROADMAP 212\n+ROADMAP 213\n+ROADMAP 214\n+ROADMAP 215\n+ROADMAP 216\n+ROADMAP 217\n+ROADMAP 218\n+ROADMAP 219\n+-135\t0\t5\t-1\n+ROADMAP 220\n+ROADMAP 221\n+ROADMAP 222\n+ROADMAP 223\n+ROADMAP 224\n+ROADMAP 225\n+ROADMAP 226\n+ROADMAP 227\n+ROADMAP 228\n+ROADMAP 229\n+ROADMAP 230\n+ROADMAP 231\n+ROADMAP 232\n+ROADMAP 233\n+ROADMAP 234\n+ROADMAP 235\n+ROADMAP 236\n+ROADMAP 237\n+ROADMAP 238\n+ROADMAP 239\n+ROADMAP 240\n+ROADMAP 241\n+ROADMAP 242\n+ROADMAP 243\n+ROADMAP 244\n+ROADMAP 245\n+ROADMAP 246\n+ROADMAP 247\n+ROADMAP 248\n+ROADMAP 249\n+ROADMAP 250\n+ROADMAP 251\n+ROADMAP 252\n+ROADMAP 253\n+ROADMAP 254\n+ROADMAP 255\n+ROADMAP 256\n+ROADMAP 257\n+ROADMAP 258\n+ROADMAP 259\n+ROADMAP 260\n+ROADMAP 261\n+ROADMAP 262\n+ROADMAP 263\n+ROADMAP 264\n+ROADMAP 265\n+ROADMAP 266\n+ROADMAP 267\n+ROADMAP 268\n+ROADMAP 269\n+ROADMAP 270\n+ROADMAP 271\n+ROADMAP 272\n+ROADMAP 273\n+ROADMAP 274\n+ROADMAP 275\n+ROADMAP 276\n+ROADMAP 277\n+ROADMAP 278\n+ROADMAP 279\n+ROADMAP 280\n+-57\t0\t5\t-1\n+ROADMAP 281\n+ROADMAP 282\n+ROADMAP 283\n+ROADMAP 284\n+ROADMAP 285\n+ROADMAP 286\n+ROADMAP 287\n+ROADMAP 288\n+ROADMAP 289\n+ROADMAP 290\n+ROADMAP 291\n+ROADMAP 292\n+ROADMAP 293\n+ROADMAP 294\n+ROADMAP 295\n+ROADMAP 296\n+ROADMAP 297\n+ROADMAP 298\n+ROADMAP 299\n+-118\t14\t2\t1\n+ROADMAP 300\n+ROADMAP 301\n+ROADMAP 302\n+ROADMAP 303\n+ROADM'..b'ROADMAP 142776\n+142\t0\t12\t15\n+-2826\t0\t8\t-1\n+-5514\t0\t9\t6\n+ROADMAP 142777\n+74\t0\t4\t15\n+10112\t0\t0\t4\n+ROADMAP 142778\n+-4182\t10\t6\t1\n+ROADMAP 142779\n+-476\t0\t14\t-1\n+ROADMAP 142780\n+14172\t0\t6\t9\n+-6630\t0\t14\t2\n+ROADMAP 142781\n+100328\t0\t11\t15\n+-1688\t2\t7\t-1\n+5057\t2\t0\t1\n+ROADMAP 142782\n+ROADMAP 142783\n+-5612\t0\t5\t3\n+9060\t0\t2\t4\n+26896\t0\t0\t1\n+-3204\t0\t14\t4\n+ROADMAP 142784\n+-3601\t0\t11\t-1\n+-6196\t0\t11\t8\n+ROADMAP 142785\n+163\t0\t2\t15\n+751\t0\t0\t1\n+-8481\t0\t0\t-1\n+ROADMAP 142786\n+164\t0\t6\t15\n+-5963\t0\t5\t-1\n+ROADMAP 142787\n+8427\t0\t12\t15\n+-32409\t0\t4\t-1\n+2566\t0\t0\t7\n+ROADMAP 142788\n+8428\t10\t3\t8\n+ROADMAP 142789\n+-4212\t0\t2\t-1\n+-4196\t0\t12\t0\n+ROADMAP 142790\n+4022\t0\t9\t15\n+-11734\t0\t1\t-1\n+-14352\t0\t5\t-1\n+-13787\t0\t4\t3\n+ROADMAP 142791\n+-6280\t0\t4\t-1\n+10086\t0\t0\t2\n+-13436\t0\t10\t2\n+ROADMAP 142792\n+6966\t9\t1\t7\n+ROADMAP 142793\n+-4840\t0\t2\t-1\n+4223\t0\t0\t6\n+578\t0\t0\t6\n+ROADMAP 142794\n+-85911\t0\t4\t-1\n+-3149\t0\t8\t-1\n+4224\t0\t0\t1\n+ROADMAP 142795\n+-82943\t0\t5\t-1\n+ROADMAP 142796\n+3604\t0\t5\t8\n+8333\t0\t0\t4\n+20374\t0\t0\t3\n+6801\t0\t0\t5\n+ROADMAP 142797\n+-12421\t0\t3\t-1\n+-13745\t0\t0\t-1\n+-7273\t0\t0\t-1\n+ROADMAP 142798\n+495\t0\t7\t15\n+10087\t0\t0\t3\n+-10029\t0\t14\t10\n+ROADMAP 142799\n+-8777\t0\t1\t-1\n+-8109\t0\t14\t1\n+ROADMAP 142800\n+10105\t0\t0\t7\n+11826\t0\t0\t8\n+ROADMAP 142801\n+2179\t0\t13\t15\n+7437\t0\t0\t4\n+8038\t0\t0\t3\n+6188\t0\t0\t6\n+ROADMAP 142802\n+1792\t0\t8\t15\n+-3764\t0\t6\t-1\n+2180\t0\t0\t1\n+ROADMAP 142803\n+10300\t0\t2\t9\n+-28296\t0\t2\t-1\n+-22094\t0\t3\t-1\n+-1365\t0\t14\t13\n+ROADMAP 142804\n+7880\t0\t14\t15\n+-28297\t0\t0\t-1\n+15304\t0\t0\t2\n+-9665\t0\t14\t13\n+ROADMAP 142805\n+22066\t0\t3\t13\n+32394\t0\t0\t2\n+-9157\t0\t1\t-1\n+1292\t0\t0\t1\n+ROADMAP 142806\n+-18288\t0\t3\t-1\n+15547\t0\t0\t2\n+ROADMAP 142807\n+1705\t0\t8\t15\n+-6400\t0\t13\t12\n+ROADMAP 142808\n+15643\t0\t0\t6\n+1706\t0\t0\t9\n+ROADMAP 142809\n+57402\t0\t7\t15\n+-2369\t2\t10\t5\n+ROADMAP 142810\n+4833\t0\t4\t9\n+ROADMAP 142811\n+5619\t0\t3\t11\n+-623\t0\t6\t-1\n+ROADMAP 142812\n+-466\t0\t8\t7\n+-231\t0\t14\t0\n+ROADMAP 142813\n+-1799\t2\t9\t-1\n+-3863\t2\t2\t-1\n+ROADMAP 142814\n+3696\t0\t11\t15\n+40852\t0\t0\t1\n+-20051\t0\t1\t-1\n+16353\t0\t0\t1\n+-8264\t0\t14\t7\n+ROADMAP 142815\n+-363\t0\t3\t-1\n+4137\t0\t0\t10\n+7356\t0\t0\t1\n+ROADMAP 142816\n+-698\t12\t10\t7\n+ROADMAP 142817\n+9995\t0\t7\t15\n+19596\t0\t0\t6\n+-5623\t0\t14\t13\n+ROADMAP 142818\n+19595\t0\t2\t4\n+12010\t0\t0\t2\n+9996\t0\t0\t11\n+ROADMAP 142819\n+19504\t0\t0\t1\n+8218\t0\t0\t14\n+ROADMAP 142820\n+-2590\t0\t7\t-1\n+19503\t0\t0\t6\n+14230\t0\t0\t1\n+ROADMAP 142821\n+1261\t1\t6\t15\n+16806\t1\t0\t5\n+ROADMAP 142822\n+1262\t0\t0\t15\n+ROADMAP 142823\n+6553\t0\t7\t15\n+13300\t0\t0\t7\n+ROADMAP 142824\n+5509\t0\t13\t14\n+-7552\t0\t8\t-1\n+13299\t0\t0\t5\n+ROADMAP 142825\n+-2109\t0\t9\t-1\n+5440\t0\t0\t5\n+ROADMAP 142826\n+ROADMAP 142827\n+114984\t0\t2\t4\n+ROADMAP 142828\n+-4300\t0\t2\t-1\n+3511\t0\t0\t3\n+-3117\t0\t6\t-1\n+645\t0\t0\t2\n+ROADMAP 142829\n+-16946\t2\t0\t-1\n+9461\t2\t0\t12\n+ROADMAP 142830\n+10582\t0\t5\t15\n+-20748\t0\t7\t4\n+15749\t0\t0\t2\n+ROADMAP 142831\n+-29136\t0\t3\t-1\n+26709\t0\t0\t2\n+-14917\t0\t1\t-1\n+14749\t0\t0\t2\n+-4048\t0\t14\t9\n+ROADMAP 142832\n+-9489\t0\t6\t-1\n+-16393\t0\t2\t-1\n+-29707\t0\t0\t-1\n+14750\t0\t0\t4\n+ROADMAP 142833\n+-2207\t0\t5\t4\n+-8024\t0\t0\t-1\n+-32410\t0\t8\t-1\n+34912\t0\t0\t1\n+-44854\t0\t1\t-1\n+9138\t0\t0\t1\n+ROADMAP 142834\n+-8842\t0\t2\t-1\n+1293\t0\t0\t12\n+ROADMAP 142835\n+3037\t0\t2\t15\n+-8672\t0\t5\t3\n+ROADMAP 142836\n+-5795\t0\t4\t-1\n+-930\t0\t14\t4\n+ROADMAP 142837\n+9804\t0\t2\t15\n+-12151\t0\t6\t4\n+ROADMAP 142838\n+-9543\t0\t12\t-1\n+17301\t0\t0\t2\n+ROADMAP 142839\n+-24034\t0\t0\t-1\n+-37633\t0\t2\t1\n+ROADMAP 142840\n+-26046\t0\t1\t-1\n+-7046\t0\t14\t1\n+ROADMAP 142841\n+-229\t0\t7\t-1\n+2204\t0\t0\t7\n+ROADMAP 142842\n+13202\t0\t7\t10\n+2203\t0\t0\t12\n+ROADMAP 142843\n+10862\t0\t2\t14\n+-22113\t0\t0\t-1\n+-14512\t0\t5\t3\n+ROADMAP 142844\n+18149\t0\t6\t10\n+-110932\t0\t10\t-1\n+ROADMAP 142845\n+-6100\t0\t1\t-1\n+-10001\t0\t0\t-1\n+6665\t0\t0\t3\n+-945\t0\t14\t5\n+ROADMAP 142846\n+12606\t1\t3\t9\n+3563\t1\t0\t8\n+ROADMAP 142847\n+-1108\t0\t7\t-1\n+10487\t0\t0\t7\n+ROADMAP 142848\n+324\t0\t5\t15\n+-3870\t0\t4\t-1\n+ROADMAP 142849\n+ROADMAP 142850\n+-1693\t0\t11\t-1\n+-5352\t0\t13\t10\n+ROADMAP 142851\n+18304\t0\t3\t7\n+3305\t0\t0\t11\n+ROADMAP 142852\n+ROADMAP 142853\n+-6214\t0\t8\t-1\n+21795\t0\t0\t5\n+ROADMAP 142854\n+-1168\t13\t10\t8\n+ROADMAP 142855\n+8553\t0\t7\t14\n+10541\t0\t0\t2\n+933\t0\t0\t6\n+ROADMAP 142856\n+934\t0\t2\t15\n+954\t0\t0\t2\n+ROADMAP 142857\n+-10835\t0\t0\t-1\n+-16083\t0\t1\t-1\n+-6046\t0\t14\t2\n+ROADMAP 142858\n+-4180\t0\t1\t-1\n+-6338\t0\t1\t-1\n+4558\t0\t0\t11\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/velveth_test1/Sequences
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/velveth_test1/Sequences Sat Feb 21 16:33:42 2015 +0100

b'@@ -0,0 +1,285716 @@\n+>SEQUENCE_0_length_35\t1\t1\n+GGATATAGGGCCAACCCAACTCAACGGCCTGTCTT\n+>SEQUENCE_1_length_35\t2\t1\n+CGACGAATGACAGGTCACGAATTTGGCGGGGATTA\n+>SEQUENCE_2_length_35\t3\t1\n+CCAAATAGGTCCTTACATCATGAGACGGGCCAAAT\n+>SEQUENCE_3_length_35\t4\t1\n+CGAGATGTATACCTCTAACACTGTGTTCCAAGTAC\n+>SEQUENCE_4_length_35\t5\t1\n+AAGCTCCCGCAATGGATCTTGTGACGGGCTGCTCG\n+>SEQUENCE_5_length_35\t6\t1\n+GCCGGTACAAACAGGAGGCAGGCAGTTCTAGTTCC\n+>SEQUENCE_6_length_35\t7\t1\n+TGCAGGTCAGGGTTCGTCATGCCTAGTGCAACGCC\n+>SEQUENCE_7_length_35\t8\t1\n+GTTCGCTACCAGCTTGTGGACCAGGAGGGTAACCC\n+>SEQUENCE_8_length_35\t9\t1\n+CTTAATACCATGAGTCGAAGAAAATTAACTTGGGG\n+>SEQUENCE_9_length_35\t10\t1\n+CATGGAGTAAGTCCTAGTAGCCTTGTGCATGGCGT\n+>SEQUENCE_10_length_35\t11\t1\n+TGTCCCTGTCACTGGAGTGATCTTTTATTCTCACC\n+>SEQUENCE_11_length_35\t12\t1\n+CTCATGCGTAATTTTAGCCGCCACGGCTATGCGTG\n+>SEQUENCE_12_length_35\t13\t1\n+CTTAGTCCTACAGGTTTTGCTATCCATTAAGCTGC\n+>SEQUENCE_13_length_35\t14\t1\n+ATATCTCGGTGCAGGGATGTTCAACATCATCACAC\n+>SEQUENCE_14_length_35\t15\t1\n+CGTCCATCGCCGATGAAATCCTGCTCAGGAGTGGA\n+>SEQUENCE_15_length_35\t16\t1\n+ACGCGTAGTCCTCTTGCGGCTTCCGCGCCCCGGGA\n+>SEQUENCE_16_length_35\t17\t1\n+CTTGAGCGGTGACCTTCGCGGTTAGCGCACCGTAA\n+>SEQUENCE_17_length_35\t18\t1\n+AGTGGTTTCAGTTCACGCTGCTGGATGTGGTGAGA\n+>SEQUENCE_18_length_35\t19\t1\n+ACTAGTCAACGCCATGAATAAGGGGTCGCAAATTG\n+>SEQUENCE_19_length_35\t20\t1\n+AGGAATTAACTCCTACGGTGAAACTGGTGTGTCAT\n+>SEQUENCE_20_length_35\t21\t1\n+CGCTGAATAAGCAAAATGCGTCGGCTGGGTCGACA\n+>SEQUENCE_21_length_35\t22\t1\n+GGAGACACGCCTGGCACGAGCGGAGGGATAGCTGT\n+>SEQUENCE_22_length_35\t23\t1\n+GAACGTGAGCTTCAATGGTGCCAAAATCGATAAAG\n+>SEQUENCE_23_length_35\t24\t1\n+CAGCACGTGGTTACTAGTCGTAAAGCCCCAAATAG\n+>SEQUENCE_24_length_35\t25\t1\n+TTTCCCTCCGTAGACAAATAGAGGTTAAGGGGCGT\n+>SEQUENCE_25_length_35\t26\t1\n+TTCTCTTCGTGTGAGGCCCTACGCTGTAAGATCCT\n+>SEQUENCE_26_length_35\t27\t1\n+CGGATTGGTCTAGCGTTGGAACTTGTCCGTCATGC\n+>SEQUENCE_27_length_35\t28\t1\n+CGCCTCAGAGCTGTGCTGATGGGTGTCCCCAGTCT\n+>SEQUENCE_28_length_35\t29\t1\n+CCAAGGGGCTCCTGTCGATCCTTGAGTCATTCATC\n+>SEQUENCE_29_length_35\t30\t1\n+AGCTCATTTTGCCGCGCCTGTAAGTCGCATCACAA\n+>SEQUENCE_30_length_35\t31\t1\n+CAGTTGACGAGTTACCGCTTACCCAGACGATTACG\n+>SEQUENCE_31_length_35\t32\t1\n+CCGAAGCGGAGGACAAGAAATTATCCCTATCAATT\n+>SEQUENCE_32_length_35\t33\t1\n+AACGCATTGACCTTGTGTGGGGTCAAACGGCGGAG\n+>SEQUENCE_33_length_35\t34\t1\n+CAGAGTTCCTTCTTCTTCTTGTCGTAGAAACCATC\n+>SEQUENCE_34_length_35\t35\t1\n+GTGGCTTCCCGGTATTGTAACGGGGGGAACCACGG\n+>SEQUENCE_35_length_35\t36\t1\n+CAGCAAGGGGCATACAGCACATCATGTCGCAACTC\n+>SEQUENCE_36_length_35\t37\t1\n+CAACTCGAACGTCTTAGTACTCCACAGATAGAATG\n+>SEQUENCE_37_length_35\t38\t1\n+TTGCGCTCAGCTGTCTGCCGTTGACTTCCTTCAAC\n+>SEQUENCE_38_length_35\t39\t1\n+ACCGTTGCAACTCCACATACCACCCCAGTACCCCA\n+>SEQUENCE_39_length_35\t40\t1\n+CCGGGATAAACCAGAAAAAAAGGCTCGTGACTGTC\n+>SEQUENCE_40_length_35\t41\t1\n+TCAGTTTATCAGCCTCGAGGCCACGATCGAGCCAG\n+>SEQUENCE_41_length_35\t42\t1\n+GCCCACATATTACGACGATGCGGCCCCGCTCTCTA\n+>SEQUENCE_42_length_35\t43\t1\n+GGACTATTCTAAATAAGCGGGTACAACTTACGTAG\n+>SEQUENCE_43_length_35\t44\t1\n+TTCCGCGCCGTCGAGTACAAAACGTCGCAATTTAA\n+>SEQUENCE_44_length_35\t45\t1\n+TATACATGTAGAGACTACGATAAAATTGAAGGGGA\n+>SEQUENCE_45_length_35\t46\t1\n+CCGGTCTATGATCCCTAATGAAAACGTTGATTCCC\n+>SEQUENCE_46_length_35\t47\t1\n+TGGTTTCTCACCGCAATCGGACCTTGCGGGTATGA\n+>SEQUENCE_47_length_35\t48\t1\n+CGTTGCGAGAGCAATCTATCAAGAGGATAAGCGCA\n+>SEQUENCE_48_length_35\t49\t1\n+AGGTAAGGATAGGGGCAAACGCGCGAAGGACACCC\n+>SEQUENCE_49_length_35\t50\t1\n+GACATATAGTCACTTGCTGTCGAATCGTAGTGGCT\n+>SEQUENCE_50_length_35\t51\t1\n+ACCATATAAGGAGTCGGAGCCCCTTGGTCCCCTTC\n+>SEQUENCE_51_length_35\t52\t1\n+GACGTTATTAACACCGTCGTAGCCTTTTCTGAAGC\n+>SEQUENCE_52_length_35\t53\t1\n+GGCTGAGGCCCGCCCCGAAACTTAATAGCCAGAAC\n+>SEQUENCE_53_length_35\t54\t1\n+TTCATACCGAGTCATACGTCGTCTTAGAGCGCATC\n+>SEQUENCE_54_length_35\t55\t1\n+GCTTGCAACTGGTTGATAGTTCAGACGAATGGTCG\n+>SEQUENCE_55_length_35\t56\t1\n+GGAATCAATAGTCGCGTTCAGAGCGCTCACTTTTT\n+>SEQUENCE_56_length_35\t57\t1\n+CGGAACACTAATCACCTTCCTAGTCGGCGGTAACA\n+>SEQUENCE_57_length_35\t58\t1\n+AGTTGGCCACTAAAGCTTACCCTCGAATGACTTCC\n+>SEQUENCE_58_length_35\t59\t1\n+GGCAATTTACTGTATCCCAGAATAACGACTCCCCA\n+>SEQUENCE_59_length_35\t60\t1\n+AGCTTCAGAAAAGGCTACGACGGTGTTAATAACGT\n+>SEQUENCE_60_length_35\t61\t1\n+AGAGTAA'..b'AT\n+>SEQUENCE_142804_length_35\t142805\t1\n+TCCGGGGTCAAATAGACAGCGGAGCCCTCAACCCT\n+>SEQUENCE_142805_length_35\t142806\t1\n+ACACCCTGCCCTTGGGCTTAGACGCGTGCCCGTGG\n+>SEQUENCE_142806_length_35\t142807\t1\n+AATGACCAGGAACAGGCAGGTTTTTATCTACCTGC\n+>SEQUENCE_142807_length_35\t142808\t1\n+CCAGGCGAGCGTCTGCTGGAAGATAACCCTTGATC\n+>SEQUENCE_142808_length_35\t142809\t1\n+CGGCCACCGGAGCATAAGGTCAATAGATCGGTCAA\n+>SEQUENCE_142809_length_35\t142810\t1\n+TGAACCGTGATATCAGATGACCACCCCTAAGTCGC\n+>SEQUENCE_142810_length_35\t142811\t1\n+CCTAGTGCTATCCTGTATCTAAGTTCATCACAGTC\n+>SEQUENCE_142811_length_35\t142812\t1\n+TGTGCGCTGCACCTGAGAATTAGAGACAGAGGTGA\n+>SEQUENCE_142812_length_35\t142813\t1\n+ATCACCGGTCACCTCGACTGTCCATTAACGGTCTC\n+>SEQUENCE_142813_length_35\t142814\t1\n+TCGTCTCAATATGTAAAACATGGTAGTGTGTGAGC\n+>SEQUENCE_142814_length_35\t142815\t1\n+GCAGTCTACCCCTGGGGTATGAGCTGCCGCCTCTG\n+>SEQUENCE_142815_length_35\t142816\t1\n+AAGATCAGTGCCTTCTCTGTATCAACTGCTCCCTG\n+>SEQUENCE_142816_length_35\t142817\t1\n+TCTCGGAGGGCGTAGTAAATGGTAGAATTTACGAA\n+>SEQUENCE_142817_length_35\t142818\t1\n+GTATGTAAGTAAACTCCACGTGGCTGCTCTGAGGT\n+>SEQUENCE_142818_length_35\t142819\t1\n+CGAACAGTGTACTGGTGCATGTGCCGGAGAGAAAC\n+>SEQUENCE_142819_length_35\t142820\t1\n+CGGCGTGCCGCGTAGCTCGCACCCCCGAGCGTTAA\n+>SEQUENCE_142820_length_35\t142821\t1\n+GGTGCCCGCCGATACTAATTACGGTCGCTTGACCG\n+>SEQUENCE_142821_length_35\t142822\t1\n+GATTAAAACCATGATACCCTGTCCTTCAGACGTGG\n+>SEQUENCE_142822_length_35\t142823\t1\n+AAAATGAACGGGCAGAATGCGAGAGCAACATCAAG\n+>SEQUENCE_142823_length_35\t142824\t1\n+CAAGACGCGACTGACACTTAATTGATCCGACTTGT\n+>SEQUENCE_142824_length_35\t142825\t1\n+GGTCCGTTCTTCGAAGCAGAGCGAAGCGCGCTCAC\n+>SEQUENCE_142825_length_35\t142826\t1\n+ATCATCCATGTAGGAGAACAAGTTAGTGGTTTTTG\n+>SEQUENCE_142826_length_35\t142827\t1\n+CAGTGCATGGGAGGTAACTGGGCGCAGAGGGCCAG\n+>SEQUENCE_142827_length_35\t142828\t1\n+AGCCTAAGATCACGTATCCCATACAGCCCACCGGG\n+>SEQUENCE_142828_length_35\t142829\t1\n+ATAGCGTGGTGTCCTTATTATATCTCGCAGGCTGT\n+>SEQUENCE_142829_length_35\t142830\t1\n+CCGGGGTATTTGAAATGAGTCGCCAACCGTGGGAG\n+>SEQUENCE_142830_length_35\t142831\t1\n+AGCAAGACCTGCAGCTACTGCCTTGGAGGTGGGTG\n+>SEQUENCE_142831_length_35\t142832\t1\n+TCCAGTTCCTTCAAAAGGTTATCCACGTTCGTGCA\n+>SEQUENCE_142832_length_35\t142833\t1\n+TTTCCGAATGACGCCAACGCGGGAATGACGTGCCA\n+>SEQUENCE_142833_length_35\t142834\t1\n+TAATTAGTTGCAAAGTTGAAGGCCAGTCTTGTTGG\n+>SEQUENCE_142834_length_35\t142835\t1\n+TGTCTACCTTCAGTTCGTTGGAAGGACAACGATCC\n+>SEQUENCE_142835_length_35\t142836\t1\n+CAGGACTACTCGCGGAACCGACAGGATGGGGTAAG\n+>SEQUENCE_142836_length_35\t142837\t1\n+GCGCAATGGGAAAAAATACCATGGGTGCCGGTTCA\n+>SEQUENCE_142837_length_35\t142838\t1\n+GAGTCAGGATAGCGTCAATCCATCCGGATTTGGCA\n+>SEQUENCE_142838_length_35\t142839\t1\n+TATCAAGCCATTGAAGTCTACTAACACCTCAGGTT\n+>SEQUENCE_142839_length_35\t142840\t1\n+GGGCTGAGAGCCGGGCCTCTTTGTCCTTAAACGAA\n+>SEQUENCE_142840_length_35\t142841\t1\n+ACGTATCAGAGAAAGTCCAAGCTTGATCGTAAAGG\n+>SEQUENCE_142841_length_35\t142842\t1\n+CCATTCAACCCTTACCGCTAGACGACGGTCGCGGA\n+>SEQUENCE_142842_length_35\t142843\t1\n+CGAAGCTTCTCTCAATCACATACGTGCAAGCGACG\n+>SEQUENCE_142843_length_35\t142844\t1\n+TATACGCTGGTGGGATGATAAGCTCAGGGCCTTAG\n+>SEQUENCE_142844_length_35\t142845\t1\n+TAAGATATTATAGAGGGACAGACTATGTTGTTGTC\n+>SEQUENCE_142845_length_35\t142846\t1\n+ATATCATCAAAGACTCTTTGTGAAGTGGGGCTGTA\n+>SEQUENCE_142846_length_35\t142847\t1\n+TGTAAGCCATTATGATTACACGATTCCTCTAACTA\n+>SEQUENCE_142847_length_35\t142848\t1\n+CGCTGAGGCTGAATACGCGGTTAAGCAGACCCTAC\n+>SEQUENCE_142848_length_35\t142849\t1\n+GAACACACTTAGCCTAGGGTGCACGGGTTCAATGA\n+>SEQUENCE_142849_length_35\t142850\t1\n+ATAGAGGAGCCCGATCTTTTGAAATATGCCTCATA\n+>SEQUENCE_142850_length_35\t142851\t1\n+GGTCGCGAACTACGGATAATGATTAACCCATTGGA\n+>SEQUENCE_142851_length_35\t142852\t1\n+GGATCCAATCCGCGTTGTCACTACACGACGTGAGG\n+>SEQUENCE_142852_length_35\t142853\t1\n+CTCTATTCGTCGTATGCCCGCTTTCAAAGCGTATT\n+>SEQUENCE_142853_length_35\t142854\t1\n+AACCACTAGCTCGCCCTCCAGCTTCTTACGTTATC\n+>SEQUENCE_142854_length_35\t142855\t1\n+GCCCCTCTGGCGTGAGCGGAGATACCCACCATGCC\n+>SEQUENCE_142855_length_35\t142856\t1\n+GTATCTTATCTGCCTGGTGACCATCATCGAAGCAT\n+>SEQUENCE_142856_length_35\t142857\t1\n+GAGACAGACCACAATACTGTGATGTAAAGCGCGCG\n+>SEQUENCE_142857_length_35\t142858\t1\n+TATCTTTTATCGTTTCACAGGGGGCCAGGGGCGCG\n'

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/velveth_test1/output.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/velveth_test1/output.html Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,6 @@
+<html><head><title>Velvet Galaxy Composite Dataset </title></head><p/>
+<div>Generated:<p/> Uses: Paired-End Reads </div>
+<div>Velveth dataset:<p/><ul>
+<li><a href="Sequences" type="text/plain">Sequences (Sequences)</a></li>
+<li><a href="Roadmaps" type="text/plain">Roadmaps (Roadmaps)</a></li>
+</ul></div></html>

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/wc_gnu_out_1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/wc_gnu_out_1.tabular Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,2 @@
+#lines words characters
+65 390 4202

diff -r 3378d12591ea -r a712b378e090 rnaseq/cutadapt/test-data/wc_gnu_out_2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/wc_gnu_out_2.tabular Sat Feb 21 16:33:42 2015 +0100

@@ -0,0 +1,1 @@
+65 390 4202