| Next changeset 1:da90c37031bb (2016-06-21) |
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Commit message:
Uploaded first version of tagdust |
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added:
architecture.xml macros.xml paired.xml single.xml test-data/paired_READ1.fq test-data/paired_READ2.fq test-data/paired_un_READ1.fq test-data/paired_un_READ2.fq test-data/read1.fastq test-data/read1.fq test-data/read1_extracted.fastq test-data/read1_un.fq test-data/read2_extracted.fastq test-data/with_b_.fq test-data/with_b_BC_AAC.fq test-data/with_b_BC_GTA.fq test-data/with_b_un.fq tool-data/all_fasta.loc.sample tool-data/tagdust_architecture.loc.sample tool_data_table_conf.xml.sample tool_dependencies.xml |
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| diff -r 000000000000 -r 40c86e14b674 architecture.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/architecture.xml Mon May 09 04:08:01 2016 -0400 |
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| @@ -0,0 +1,42 @@ +<tool id="tagdust_architecture" name="Tagdust Architecture viewer" version="0.2"> + <description>Displays a tagdust Architecture file</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"></expand> + <expand macro="stdio"></expand> + <expand macro="version_command"></expand> + <command > + cp $architecture.fields.path architecture.txt ; + </command> + <inputs> + <expand macro="architecture"></expand> + </inputs> + <outputs> + <data format="txt" name="architecturefile" label="The tagdust architecture." from_work_dir="architecture.txt"/> + </outputs> + <tests> + <test> + <param name="architecture" value="test_F:NNNNNNNN_S:TATAGGG_R:N" /> + <output name="architecturefile" file="../tool-data/F:NNNNNNNN_S:TATAGGG_R:N.txt"/> + </test> + <test> + <param name="architecture" value="test_B:GTA_AAC_R:N" /> + <output name="architecturefile" file="../tool-data/B:GTA,AAC_R:N.txt"/> + </test> + <test> + <param name="architecture" value="test_R:N" /> + <output name="architecturefile" file="../tool-data/R:N.txt"/> + </test> + </tests> + <help> +<![CDATA[ +This tools simply prints out the selected architecture without running tagdust. + +Note both the single end and paired end tagdust tools will report the architecture to standard out. + +]]> +@tagdust-documentation@ + </help> + <expand macro="citations"></expand> +</tool> |
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| diff -r 000000000000 -r 40c86e14b674 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon May 09 04:08:01 2016 -0400 |
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| @@ -0,0 +1,179 @@ +<?xml version="1.0"?> +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="2.31">tagdust</requirement> + </requirements> + </xml> + <xml name="version_command"> + <version_command>tagdust --version | head -n 1 | awk '{ print $2 }'</version_command> + </xml> + <xml name="stdio"> + <stdio> + <exit_code range="1:" level="fatal" description="Error" /> + </stdio> + </xml> + <token name="@cat-archiecture@"> + echo using architecture ; + cat $architecture.fields.path ; + echo ; + </token> + <token name="@tagdust-call-minus-files@"> + mkdir output ; + tagdust -t\${GALAXY_SLOTS:-4} -o output/data + -arch $architecture.fields.path + #if $reference_source.reference_source_selector=='history': + -ref $reference_source.ref_file + #end if + #if $reference_source.reference_source_selector=='cached': + -ref $reference_source.ref_path.fields.path + #end if + </token> + <token name="@ls_and_barcode@"> + echo files in output folder ; + ls -al output ; + #if $include.barcode_files=="yes" + #if $architecture.fields.barcode=="yes" + cd output ; + ls *_BC_* > $barcode_files + #else + echo Selected architecture not expected to generate any barcode files > $barcode_files ; + echo To avoid this output set Choose to find the barcode files to No >> $barcode_files ; + #end if + #else + #if $architecture.fields.barcode=="yes" + echo ; + echo Tagdust not included in output at users request! ; + echo To get then set Choose to find the barcode files to Yes and run the tool again ; + #end if + #end if + </token> + <xml name="architecture"> + <param name="architecture" type="select" label="Using architecture"> + <options from_data_table="tagdust_architecture"/> + <validator type="no_options" message="No architecture found"/> + <!--filter name="barcode" value="yes" column="3"/--> + </param> + </xml> + <xml name="reference_source"> + <conditional name="reference_source"> + <param name="reference_source_selector" type="select" label="Choose the source for the reference fasta (If any)"> + <option value="none" selected="true">Do not include a reference fasta</option> + <option value="cached">Locally cached</option> + <option value="history">History</option> + </param> + <when value="none"/> + <when value="cached"> + <param name="ref_path" type="select" label="Using reference fasta"> + <options from_data_table="all_fasta"/> + <validator type="no_options" message="A built-in reference fasta is not available for the build associated with the selected input file"/> + </param> + </when> + <when value="history"> + <param name="ref_file" type="data" format="fasta" label="Using reference file" /> + </when> + </conditional> + </xml> + <xml name="include_barcode_file"> + <conditional name="include"> + <param name="barcode_files" type="select" label="Choose to find the barcode files (If any)"> + <option value="yes" selected="true">Yes. Look for possible barcode separated files.</option> + <option value="no" >No. Ignores all barcode files even if these are generated.</option> + </param> + <when value="yes"/> + <when value="no"/> + </conditional> + </xml> + <xml name="output_barcode"> + <data format="txt" name="barcode_files" label="Tagdust barcoded reads."> + <discover_datasets pattern="data_BC_(?P<designation>.+)\.fq" ext="fastq" directory="output" visible="true" /> + <filter>(include['barcode_files']=='yes')</filter> + </data> + </xml> + <token name="@tool-documentation@"> +<![CDATA[ + +Note: Output from Architecture with could have a Barcode HMM building block choose to find the barcode files. +....If no barcode files are found this will simply be empty. +....You may have refresh the history for all barcode files to show. + +Please contact the admin to add an architecture / HMM building blocks. +(There is Data Manager that they can use) + +]]> + </token> + <token name="@tagdust-documentation@"> +<![CDATA[ +==== + +Taken from The TagDust2 Manual http://tagdust.sourceforge.net (part of Version 2_31 download) + +Raw sequences produced by next generation sequencing (NGS) machines can contain adapter, linker, +barcode and fingerprint sequences. TagDust2 is a program to extract and correctly label the sequences +to be mapped in downstream pipelines. +TagDust allows users to specify the expected architecture of a read and converts it into a hidden +Markov model. The latter can assign sequences to a particular barcode (or index) even in the presence +of sequencing errors. Sequences not matching the architecture (primer dimers, contaminants etc.) are +automatically discarded + +TagDust requires an input file containing sequences and a user defined HMM architecture used to ex- +tract the reads. The architecture is composed of a selection of pre-defined building blocks representing +indices, barcodes, spacers and other sequences one might encounter in the raw output of a sequenced +sample. + +HMM Building Blocks + +TagDust comes with a set of pre-defined HMM building blocks. Each includes a silent state at the +beginning and end used to link blocks together. Each block is specified by a unique letter following +by a colon and some information about the sequence. + +Read +Segment modeling the read. +Code: R:N + +Optional +Segment modeling an optional single or short stretch of nucleotides. +Code: O:N + +G addition +Segment modeling the occasional addition of guanines to the reads. +(89.3% chance of a single G , 19.5% chance of 2 Gs..). +Code: G:G + +Barcode or Index +Segment modeling a set of barcode sequences. For each sequence a separate HMM is created. The +barcode sequences must be given as a comma separated list. A null model of the same length as the +barcode is automatically added and initialized to the background nucleotide frequencies. +Code: B:GTA,AAC + +Fingerprint or Unique Molecular Identifier - UMI +Segment modeling a fingerprint (or unique molecular identifiers). Insertions and deletions are by +default not allowed within a fingerprint segment. +Code: F:NNN + +Spacer +Segment modeling a pre-defined sequence. +Code: S:GTA + +Partial +This segment is used to model sequences that may only be partially present at the 5‘ or 3‘ end of +the read. The transition probabilities (orange and blue) are set automatically based on the length +distribution of exactly matching adapters. +Code: P:CCTTAA +]]> + </token> + <xml name="citations"> + <citations> + <citation type="bibtex"> + @misc{ + TagDust, + author = {Timo Lassmann}, + title = {TagDust on sourceforge}, + url = {http://tagdust.sourceforge.net/} + } + </citation> + <citation type="doi">10.1093/bioinformatics/btp527</citation> + <citation type="doi">10.1186/s12859-015-0454-y</citation> + </citations> + </xml> +</macros> |
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| diff -r 000000000000 -r 40c86e14b674 paired.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/paired.xml Mon May 09 04:08:01 2016 -0400 |
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| @@ -0,0 +1,95 @@ +<tool id="tagdust_paired_runner_2_31" name="Tagdust paired end runner" version="0.2"> + <description>Runs tagdust in paired end mode</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"></expand> + <expand macro="stdio"></expand> + <expand macro="version_command"></expand> + <command > + @cat-archiecture@ + cp $read1_file read1.fastq ; + cp $read2_file read2.fastq ; + @tagdust-call-minus-files@ + read1.fastq read2.fastq ; + @ls_and_barcode@ + </command> + <inputs> + <param name="read1_file" type="data" format="fastq,fastqsanger" label="Read 1 Fastq file to process" /> + <param name="read2_file" type="data" format="fastq,fastqsanger" label="Read 2 Fastq file to process" /> + <expand macro="reference_source"/> + <expand macro="architecture"/> + <expand macro="include_barcode_file"/> + <expand macro="architecture"></expand> + </inputs> + <outputs> + <data format="txt" name="logfile" label="Tagdust log on ${on_string}." from_work_dir="output/data_logfile.txt"/> + <data format_source="read1_file" name="extracted1" label="Tagdust extracted Read1 from ${on_string}." from_work_dir="output/data_READ1.fq"/> + <data format_source="read1_file" name="unextracted1" label="Tagdust un-extracted Read1 from ${on_string}." from_work_dir="output/data_un_READ1.fq"/> + <data format_source="read2_file" name="extracted2" label="Tagdust extracted Read2 from ${on_string}." from_work_dir="output/data_READ2.fq"/> + <data format_source="read2_file" name="unextracted2" label="Tagdust un-extracted Read2 from ${on_string}." from_work_dir="output/data_un_READ2.fq"/> + <expand macro="output_barcode"/> + </outputs> + <tests> + <!-- Large dataset in github but not toolshed --> + <test> + <param name="read1_file" value="C75_S29_R1_001_extracted.fastq" ftype="fastq" /> + <param name="read2_file" value="C75_S29_R2_001_extracted.fastq" ftype="fastq" /> + <param name="architecture" value="R:N" /> + <param name="reference_source|reference_source_selector" value="history"/> + <param name="reference_source|ref_file" value="ercc_and_TPA_mouse_rRNA.fa" ftype="fasta"/> + <output name="logfile" > + <assert_contents> + <has_text text="Determining threshold for read0." /> + </assert_contents> + </output> + <output name="extracted1" file="C75_S29__READ1.fq" compare="sim_size" delta="10000"/> + <output name="unextracted1" file="C75_S29__un_READ1.fq" compare="sim_size" delta="10000"/> + <output name="extracted2" file="C75_S29__READ2.fq" compare="sim_size" delta="10000"/> + <output name="unextracted2" file="C75_S29__un_READ2.fq" compare="sim_size" delta="10000"/> + </test> + <test> + <param name="read1_file" value="read1_extracted.fastq" ftype="fastqsanger" /> + <param name="read2_file" value="read2_extracted.fastq" ftype="fastqsanger" /> + <param name="architecture" value="test_R:N" /> + <param name="reference_source|reference_source_selector" value="history"/> + <param name="reference_source|ref_file" value="ercc_and_TPA_mouse_rRNA.fa" ftype="fasta"/> + <output name="logfile" > + <assert_contents> + <has_text text="Determining threshold for read0." /> + </assert_contents> + </output> + <output name="extracted1" file="paired_READ1.fq" ftype="fastqsanger" compare="sim_size" delta="1000"/> + <output name="unextracted1" file="paired_un_READ1.fq" ftype="fastqsanger" compare="sim_size" delta="1000"/> + <output name="extracted2" file="paired_READ2.fq" ftype="fastqsanger" compare="sim_size" delta="1000"/> + <output name="unextracted2" file="paired_un_READ2.fq" ftype="fastqsanger" compare="sim_size" delta="1000"/> + </test> + <test> + <param name="read1_file" value="read1_extracted.fastq" ftype="fastq" /> + <param name="read2_file" value="read2_extracted.fastq" ftype="fastq" /> + <param name="architecture" value="test_R:N" /> + <param name="reference_source|reference_source_selector" value="cached"/> + <param name="ref_path" value="test_ercc_and_TPA_mouse_RNA"/> + <output name="logfile" > + <assert_contents> + <has_text text="Determining threshold for read0." /> + </assert_contents> + </output> + <output name="extracted1" file="paired_READ1.fq" compare="sim_size" delta="1000"/> + <output name="unextracted1" file="paired_un_READ1.fq" compare="sim_size" delta="1000"/> + <output name="extracted2" file="paired_READ2.fq" compare="sim_size" delta="1000"/> + <output name="unextracted2" file="paired_un_READ2.fq" compare="sim_size" delta="1000"/> + </test> + </tests> + <help> +<![CDATA[ +This tool runs Tagdust2 in paired end mode. + +]]> +@tool-documentation@ + +@tagdust-documentation@ + + </help> + <expand macro="citations"></expand> +</tool> |
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| diff -r 000000000000 -r 40c86e14b674 single.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/single.xml Mon May 09 04:08:01 2016 -0400 |
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| @@ -0,0 +1,87 @@ +<tool id="tagdust_single_runner_2_31" name="Tagdust single end runner" version="0.2"> + <description>Runs tagdust in single end mode</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="stdio"/> + <expand macro="version_command"/> + <command > + @cat-archiecture@ + cp $fastq_file input.fastq ; + @tagdust-call-minus-files@ + input.fastq ; + @ls_and_barcode@ + </command> + <inputs> + <param name="fastq_file" type="data" format="fastq,fastqsanger" label="Fastq file to process" /> + <expand macro="reference_source"/> + <expand macro="architecture"/> + <expand macro="include_barcode_file"/> + </inputs> + <outputs> + <data format="txt" name="logfile" label="Tagdust log on ${on_string} ." from_work_dir="output/data_logfile.txt"/> + <data format_source="fastq_file" name="extracted" label="Tagdust extracted reads from ${on_string}." from_work_dir="output/data.fq"/> + <data format_source="fastq_file" name="unextracted" label="Tagdust un-extracted reads from ${on_string}." from_work_dir="output/data_un.fq"/> + <expand macro="output_barcode"/> + </outputs> + <tests> + <!-- Large dataset in github but not toolshed --> + <!--test> + <param name="fastq_file" value="C75_S29_R1_001.fastq" ftype="fastq" /> + <param name="architecture" value="F:NNNNNNNN_S:TATAGGG_R:N" /> + <param name="include|barcode_files" value="no" /> + <output name="logfile" > + <assert_contents> + <has_text text="Determining threshold for read0." /> + </assert_contents> + </output> + <output name="extracted" file="C75_S29_R1_001.fq" compare="sim_size" delta="10000"/> + <output name="unextracted" file="C75_S29_R1_001_un.fq" compare="sim_size" delta="10000"/> + </test--> + <test> + <param name="fastq_file" value="read1.fastq" ftype="fastqsanger" /> + <param name="architecture" value="test_F:NNNNNNNN_S:TATAGGG_R:N" /> + <param name="barcode_files" value="no" /> + <output name="logfile" > + <assert_contents> + <has_text text="Determining threshold for read0." /> + </assert_contents> + </output> + <output name="extracted" file="read1.fq" ftype="fastqsanger" compare="sim_size" delta="1000"/> + <output name="unextracted" file="read1_un.fq" ftype="fastqsanger" compare="sim_size" delta="1000"/> + </test> + <test> + <param name="run_type_selector" value="single"/> + <param name="fastq_file" value="read1.fastq" ftype="fastq" /> + <param name="architecture" value="test_B:GTA_AAC_R:N" /> + <param name="include|barcode_files" value="yes" /> + <output name="logfile" > + <assert_contents> + <has_text text="Determining threshold for read0." /> + </assert_contents> + </output> + <output name="extracted" file="with_b_.fq"/> + <output name="unextracted" file="with_b_un.fq"/> + <output name="barcode_files"> + <assert_contents> + <has_line line="data_BC_AAC.fq" /> + <has_line line="data_BC_GTA.fq" /> + </assert_contents> + <discovered_dataset designation="AAC" ftype="fastq" file="with_b_BC_AAC.fq"/> + <discovered_dataset designation="GTA" ftype="fastq" file="with_b_BC_GTA.fq"/> + </output> + </test> + </tests> + <help> +<![CDATA[ +This tool runs Tagdust2 in single mode. + +]]> +@tool-documentation@ + +@tagdust-documentation@ + + </help> + <expand macro="citations"></expand> +</tool> |
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| diff -r 000000000000 -r 40c86e14b674 test-data/paired_READ1.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/paired_READ1.fq Mon May 09 04:08:01 2016 -0400 |
| b |
| b'@@ -0,0 +1,216 @@\n+@NB500968:8:H5CFGAFXX:1:11101:1121:1139___1:N:0:TCGTGAGC+TACTCCTT;FP:27828;RQ:34.83;RQ:-1.00\n+GGAGCGTCAGATGTGTATAAGAGACAGGTATTCCCTATAGTCTACATC\n++\n+EEEEEEEEEEEEEEEAAEEEEAEEEAEEE/EEE/EE<AAEEEEEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:7529:1175___1:N:0:TCCTGAGC+TACTCCTT;FP:17358;RQ:34.81;RQ:-1.00\n+AGCGTCAGATGTGTATAAGAGACAGCAACCCTAAAAATATCCA\n++\n+EEEE/EEEEEEA/EA<EEEE/AEEEE//E//6A/AE/A/AAE/\n+@NB500968:8:H5CFGAFXX:1:11101:5052:1198___1:N:0:TCCTGAGC+TACTCCTT;FP:38799;RQ:34.63;RQ:-1.00\n+GGTTTTTAGTGGCATTCATTGTGTGGATTCCTCTGTTGCTGCCCCTGGGCTAACAAGGGT\n++\n+EEEEEEE6EEEEAEEEEEEEEEEEAEEEEEEEEEEEEEAAE/AEEEEEAAAEEEE/EAEE\n+@NB500968:8:H5CFGAFXX:1:11101:15805:1205___1:N:0:TCCTGAGC+TACTCCTT;FP:44542;RQ:34.63;RQ:-1.00\n+GAGGGCCAGGCAGCTCAAAGCCTGAAGGAGGTACTTCAAGGAGGGTCCAGAGAAGCTGGG\n++\n+EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEE<EAAEEEEEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:11834:1217___1:N:0:TCCTGAGC+TACTCCTT;FP:56795;RQ:34.81;RQ:-1.00\n+AGCGTCAGATGTGTATAAGAGACAGGATTCCCCTATATAGCGACCC\n++\n+EEEEEEEEEEEEEEEEAEEEEEEEEEEAEEEEEEEEEA<EAEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:20105:1230___1:N:0:TCCTGAGC+TACTCCTT;FP:2265;RQ:34.63;RQ:-1.00\n+GTTGTTTCATGTTGCAATTTTTAGGTTACTTTTGAGTTGCTTAGGAATTGTTTTATTTAA\n++\n+EEEEEEEEEE/E/AEEEEE<E</EEAEEEEEEAAEAEEEAAE//EA//</E6EAAEA/6/\n+@NB500968:8:H5CFGAFXX:1:11101:14524:1264___1:N:0:TCCTGAGC+TACTCCTT;FP:7937;RQ:2.65;RQ:-1.00\n+CCCAACTTAATATTATAAAATTATCATAAAAACAACTACGAGCCCACGATACAACTGATA\n++\n+//EEEE<///A/AAA/A////E/<///E/6/E/E/E6///E//6E<//6/AA//E//A//\n+@NB500968:8:H5CFGAFXX:1:11101:14981:1265___1:N:0:TCCTGAGC+TACTCCTT;FP:26333;RQ:34.63;RQ:-1.00\n+GTCTGGTTAATTCCGATAACGAACGAGACTCTGGCATGCTAACTAGTTACGCGACCCCCG\n++\n+EEEEEEEEEEEEEAEEEEEEEEEAAEEEEEEEA<EEEEEEEEE6/E66A<A/<AA<A//6\n+@NB500968:8:H5CFGAFXX:1:11101:5538:1286___1:N:0:TCCTGAGC+TACTCCTT;FP:5079;RQ:34.62;RQ:-1.00\n+AGTGAACTAACTAGAAAACTTCTAACTAAAAGAATTACAGCTAGAAACCCCGAAACCAAA\n++\n+AAEEEEEEEEAE/AEEEEEEEAEEEEE/AE6/EEA<E/EA6EAAEEE6//6<<EEA/<<A\n+@NB500968:8:H5CFGAFXX:1:11101:12411:1441___1:N:0:TCCTGAGC+TACTCCTT;FP:46039;RQ:34.83;RQ:-1.00\n+GGGAGCGTCAGATGTGTATAAGAGACAGTCTCCCTATATTTTGGC\n++\n+//AEEE/EAEAEE/AEAE<EEEEAE/EAE<E/E</EEEE/6E/EE\n+@NB500968:8:H5CFGAFXX:1:11101:5889:1458___1:N:0:TCCTGAGC+TACTCCTT;FP:52002;RQ:34.83;RQ:-1.00\n+GAGCGTCAGATGTGTATAAGAGACAGCGTATCCCTATACCCCTTCGCTG\n++\n+EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:9851:1471___1:N:0:TCCTGAGC+TACTCCTT;FP:43356;RQ:3.17;RQ:-1.00\n+CCCCTGTCTCTTATACCNNN\n++\n+EEEEEA/AA/EEEEE//###\n+@NB500968:8:H5CFGAFXX:1:11101:5425:1488___1:N:0:TCCTGAGC+TACTCCTT;FP:13390;RQ:34.83;RQ:-1.00\n+GGAGCGTCAGATGTGTATAAGAGACAGACTCCCCTATATGGACACA\n++\n+EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:8024:1581___1:N:0:TCCTGAGC+TACTCCTT;FP:38311;RQ:34.63;RQ:-1.00\n+GTGACCCGCCGCTTCAGGGACCCGCTTCTCTCATCTTCCCCAAAGTTCTGGACAGATGAT\n++\n+EEEEEEEAEEEEEAEAEEEEEEEEEEAEEEEAEEEAEAEEEEEEEEAEEEEEEEEEE/A<\n+@NB500968:8:H5CFGAFXX:1:11101:23474:1673___1:N:0:TCCTGAGC+TACTCCTT;FP:2968;RQ:34.81;RQ:-1.00\n+AGCGTCAGATGTGTATAAGAGACAGAGGCGCCCTATAGAATATAT\n++\n+EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEE/EEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:21720:1786___1:N:0:TCCTGAGC+TACTCCTT;FP:16257;RQ:35.14;RQ:-1.00\n+GGGAGCGTCAGATGTGTATAAGAGAC\n++\n+EEEEEEEEEEEEEEEEEEEEEEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:9012:1809___1:N:0:TCCTGAGC+TACTCCTT;FP:4167;RQ:34.83;RQ:-1.00\n+GGGAGCGTCAGATGTGTATAAGAGACAGGTACCCCCTATATCATAGGC\n++\n+EEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:20110:1819___1:N:0:TCCTGAGC+TAATCCTT;FP:64559;RQ:34.63;RQ:-1.00\n+GGATTCTTGAAGTATAACAGGAGAATCAAATAATTAAAGAGGGGGCTGGAGAGATAGCT\n++\n+EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:24842:1887___1:N:0:TCCTGAGC+TACTCCTT;FP:13772;RQ:35.14;RQ:-1.00\n+GGGAGCGTCAGATGTGTATAAGAG\n++\n+EEEEEEEEEEEEEEEEEEEEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:16709:1904___1:N:0:TCCTGAGC+TACTCCTT;FP:5671;RQ:34.73;RQ:-1.00\n+GTTCCATGCGTCAATGTTTCTTCTGGATACAGCAGGCCTGTTCCCGGGAGTCAATGC\n++\n+EEEEEAEEEEEEEEEEAEEEEEEEEEEEAEE6<EEEEEAAA<EAEEEEEEEEEEE<E\n+@NB50'..b'TCCAGTC\n++\n+EEEEEEEEEEEEEEEEEEEEEA/E/AEEEEEAEEEEAE/<AAEEE<EAEEE<EEAEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:10463:2345___1:N:0:GCCTGAGC+TACTCCTT;FP:24337;RQ:34.81;RQ:-1.00\n+TCCAGCGTCAGATGTGTATAAGAGACAGAGTTCCCCTATAGAGAGACG\n++\n+EEEEEEEEEEE6EEEEA/A//E/EEEEEEEEEEEEEEAA/AAEEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:24405:2351___1:N:0:TCCTGAGC+TACTCCTT;FP:5580;RQ:35.18;RQ:-1.00\n+TCTGTCTCTTATACCNNNNN\n++\n+EEEEEEAEEEEEEEE#####\n+@NB500968:8:H5CFGAFXX:1:11101:6508:2370___1:N:0:TCCTGAGC+TACTCCTT;FP:64422;RQ:34.83;RQ:-1.00\n+GGAGCGTCAGATGTGTATAAGAGACAGCCCAGCCCTATACCGTCTAGCTG\n++\n+EEEEEEEEEEEEEAEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:21730:2488___1:N:0:TCGTGAGC+TACTCCTT;FP:57284;RQ:35.18;RQ:-1.00\n+AGCGTCAGATGTGTATCNNN\n++\n+EEEEEEEEEEEEEAEAE###\n+@NB500968:8:H5CFGAFXX:1:11101:20021:2516___1:N:0:TCCTGGGC+TACTCCTT;FP:28351;RQ:34.83;RQ:-1.00\n+GGAGCGTCAGATGAGTATAAGAGACAGTCATCCCCTATAGTCGTTCA\n++\n+EAEEAAEEAAE///E/EAAE/EAEE//EEE/EEEEEE/EE/EA6EEE\n+@NB500968:8:H5CFGAFXX:1:11101:4827:2579___1:N:0:TCCTGAGC+TACTCCTT;FP:8626;RQ:34.83;RQ:-1.00\n+GACAGCGTCAGATGTGTATAAGAGACAGGGAATCCCTATAGACTTTGC\n++\n+EEEEEEEEE/E<AAAEEEEEEEE/E/EEEEEEEEEEEAEEAEAAEEE/\n+@NB500968:8:H5CFGAFXX:1:11101:11758:2662___1:N:0:TCCTGAGC+TACTCCTT;FP:32308;RQ:34.83;RQ:-1.00\n+GACAGCGTCAGATGTGTATAAGAGACAGAGATGCCCTATAGACCGAAC\n++\n+EEEEEE/EAE/EEE/EEEAEE6E6EEEEEAAEA/E/AEEEA/E6EA/E\n+@NB500968:8:H5CFGAFXX:1:11101:23131:2747___1:N:0:TCCTGAGC+TACTCCTT;FP:61606;RQ:34.61;RQ:-1.00\n+CAGACGTTCGAATGGGTCGTCGCCGCCACGGGGGGCGTGCGATCGGCCCGAGGTTATCTA\n++\n+EEEEEEAEAEEEE/EEEAEEEEA/EEEEAEA/EA<EAAAEEAE<AE/A<<EEEA<<EEA<\n+@NB500968:8:H5CFGAFXX:1:11101:20373:2751___1:N:0:TCCTGATC+TACTCCTT;FP:283;RQ:34.93;RQ:-1.00\n+GGAGCGTCAGATGTGTATAAGAGACAGCCCTATACAGTGATC\n++\n+EEEEEEEEE<EEEEAEAEEEEEEEEEEEEEE/EEEEEE<EAA\n+@NB500968:8:H5CFGAFXX:1:11101:21204:2795___1:N:0:TCCTGAGC+TACTCCTT;FP:16279;RQ:34.81;RQ:-1.00\n+AGCGTCAGATGTGTATAAGAGACAGCTCCACCCTATAGGCCCTAACTG\n++\n+EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:17699:2880___1:N:0:TCCTGAGC+TACTCCTT;FP:52710;RQ:34.62;RQ:-1.00\n+CTTTGGAATCTTCACAAGCAGAACCAGTCAAAACCCCGGCAAGCACAAAGAGACTCTCCA\n++\n+EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE<EEEEEEEEEEE6AEAEAEEEEA\n+@NB500968:8:H5CFGAFXX:1:11101:2261:2941___1:N:0:TCCTGAGC+TACTCCTT;FP:2596;RQ:34.63;RQ:-1.00\n+GGCAGCATCAGATGTGTATAAGAGACAGAAGGAGCAGAGAGCGGCCAGCAACCGATGAGA\n++\n+EEEEEEEEEEEEEEAEEEAEEEEE///////EA//E/E/A/////E<EE//</E<<////\n+@NB500968:8:H5CFGAFXX:1:11101:25690:2959___1:N:0:TCCTGCGC+TACTCCTT;FP:27004;RQ:34.81;RQ:-1.00\n+AGCGTCAGATGTGTATAAGAGACAGGCCTCCCCTATAGCTTCGGA\n++\n+AE6EEEEEEEEEAAEEEEEEEEEEEEEEAEE/E/EAEEEEAEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:8090:2972___1:N:0:TCCTGAGC+TACTCCTT;FP:12902;RQ:34.81;RQ:-1.00\n+CAACGTCAGATGTGTATAAGAGACAGGGACCCCCTATAATTTATGCC\n++\n+EEEEEEEEEEEEEEEEEAAEEEEEEEEEAEE<EEEEEAE<EEEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:16936:3211___1:N:0:TCCTGAGC+TACTCCTT;FP:7401;RQ:34.83;RQ:-1.00\n+GAGCGTCAGATGTGTATAAGAGACAGTGCGTCCCTATAAAAGTGAACTG\n++\n+EEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEA/EEEAEAEEE\n+@NB500968:8:H5CFGAFXX:1:11101:6132:3257___1:N:0:TCCTGAGC+TACTCCTT;FP:7557;RQ:34.62;RQ:-1.00\n+CGTCAGATGTGTATAAGAGACAGCATTCCCCTATACACGCCTCCTGTCTCTTATAC\n++\n+EEEEAEEEEEEEEEEEEEEAEAEEAEEEEAEEEEEEEEEEEEEEEEAE/EEEEEEA\n+@NB500968:8:H5CFGAFXX:1:11101:3840:3285___1:N:0:TCCTGAGC+TACTCCTT;FP:16156;RQ:34.93;RQ:-1.00\n+GGGAGCGTCAGATGTGTATAAGAGACAGGTATACCCTATAG\n++\n+EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:2858:3312___1:N:0:TCCTGAGC+TACTCCTT;FP:14452;RQ:35.12;RQ:-1.00\n+AACGTCAGATGTGTATAAGAG\n++\n+EE/AE/E/EAAEEEEEEEAEE\n+@NB500968:8:H5CFGAFXX:1:11101:3641:3398___1:N:0:TCCTGAGC+TACTCCTT;FP:36051;RQ:35.14;RQ:-1.00\n+GCAGCGTCAGATGTGTATAAGAG\n++\n+EEEEEEEEEEEEEEEEEEEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:20540:3401___1:N:0:TCCTGAGC+TACTCCTT;FP:48603;RQ:34.81;RQ:-1.00\n+AGCGTCAGATGTGTATAAGAGACAGATCAACCCTATATGCCCTAACTG\n++\n+E/E///E/E</A/EEA<E/E/EEE/E</E///A/E6<E/A/<E/EEE/\n+@NB500968:8:H5CFGAFXX:1:11101:4772:3477___1:N:0:TCCTGAGC+AACTCCTT;FP:61788;RQ:3.33;RQ:-1.00\n+TAACTGTCTCTTATACACCN\n++\n+EEEEEEEAEEEAEEE<EEE#\n' |
| b |
| diff -r 000000000000 -r 40c86e14b674 test-data/paired_READ2.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/paired_READ2.fq Mon May 09 04:08:01 2016 -0400 |
| b |
| b'@@ -0,0 +1,216 @@\n+@NB500968:8:H5CFGAFXX:1:11101:1121:1139___1:N:0:TCGTGAGC+TACTCCTT;FP:27828;RQ:34.83;RQ:-1.00\n+GATGTAGACTATAGGGAATACCNNNNNNNNNNNNN\n++\n+A6AAAEEEEEEEEEEEAEE/E<#############\n+@NB500968:8:H5CFGAFXX:1:11101:7529:1175___1:N:0:TCCTGAGC+TACTCCTT;FP:17358;RQ:34.81;RQ:-1.00\n+GATGTGTAAAAGAGACAGAGGATAATTATAGGGATCCTGTCTCTAAAACACATCTGACGCTCCCTATACATAATA\n++\n+/AAAAE<A/E//EEE/EE//EEEEAEEEEEEEEEE/A/<EEE<<///<AE</AE//AAA//E/////EEE<6/A/\n+@NB500968:8:H5CFGAFXX:1:11101:5052:1198___1:N:0:TCCTGAGC+TACTCCTT;FP:38799;RQ:34.63;RQ:-1.00\n+GGATTGAGGCTAGAAACAGCTGCTTTTCTCACTTTCCCAGCAGCAAGACATCAATCTGTTGAGACCTCTCATTTT\n++\n+AA6AAEEAEEEEEEEEAAEEEEE///AEEA/<E/E<A//EEEEAE/EE//AE///E</EAEEA<EEEAEE/E/E/\n+@NB500968:8:H5CFGAFXX:1:11101:15805:1205___1:N:0:TCCTGAGC+TACTCCTT;FP:44542;RQ:34.63;RQ:-1.00\n+GCGTCAGATGTGGGTAGTCAGAAAAGCAGATGGATGGGGGCCTTGCCCAACCAGATCCAGGCCGAGTTCACCT\n++\n+AAAAAEEAEEEEEEEEEEEEEEA//EEEEEEEEEEEEEEEEEEAEE/E//EEEEAEAE/EEEEE<EEEEEEEA\n+@NB500968:8:H5CFGAFXX:1:11101:11834:1217___1:N:0:TCCTGAGC+TACTCCTT;FP:56795;RQ:34.81;RQ:-1.00\n+GGGTCGCTATATAGGGGAATCCNNNNNNNNNNNNN\n++\n+AAAAAEEEEEEEEEEEEEAEEE#############\n+@NB500968:8:H5CFGAFXX:1:11101:20105:1230___1:N:0:TCCTGAGC+TACTCCTT;FP:2265;RQ:34.63;RQ:-1.00\n+GTACACGTATTACTTCTGTTTGGTGAATTAAATAAAACAATTCCTAAGCAACTCAAAAGTAACCTAAAAATTGCA\n++\n+AA/A//EEE/EAEEEEEEE/EEEAEE6EEE<EEA<6E//E/EEAEE//EE/EEE<EAEE6</EEEEE/A/EEE/A\n+@NB500968:8:H5CFGAFXX:1:11101:14524:1264___1:N:0:TCCTGAGC+TACTCCTT;FP:7937;RQ:2.65;RQ:-1.00\n+GTATAAGAGACAGTTGGGACTTATAGGGTAAGTCN\n++\n+AAAAAEEEAEEEEAEEE/EEEEEAE<EE/EEEEE#\n+@NB500968:8:H5CFGAFXX:1:11101:14981:1265___1:N:0:TCCTGAGC+TACTCCTT;FP:26333;RQ:34.63;RQ:-1.00\n+GGACTTAATCAACGCAAGCTTATGACCCGCACTTACTGGGAATTCCTCGTTCATGGGGAATAATTGCAATCCCCG\n++\n+AA6AAEE/EE//EEE6EEEEEEEE/AAEEAEEEE/EEEEEAEEEE/EEEEEEEEEEEE/AEE<EEEEEEEEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:5538:1286___1:N:0:TCCTGAGC+TACTCCTT;FP:5079;RQ:34.62;RQ:-1.00\n+ATCACCAAGCTCGTTAGGCTTTTCACCTCTACCTAAAAATCTTCTCACTATTTTGCCACATAGACGAGTTGATT\n++\n+AAA/AEE/EEEEEEEAEEEEEEEE/EEEEE/EEEA</EEEEEEEEAAAEAEEEEE<EAE6EEEEEEEEEEEEAE\n+@NB500968:8:H5CFGAFXX:1:11101:12411:1441___1:N:0:TCCTGAGC+TACTCCTT;FP:46039;RQ:34.83;RQ:-1.00\n+GACAAAATATAGGGGGACTGTCTGTTATAGACGTCGGACGCGCGCCCCTATAAGGAATAGGGGTCTCTGAGAGA\n++\n+A/////E////////A///E/E///EEE///A//A/A//<///////E/////AEA//////////////////\n+@NB500968:8:H5CFGAFXX:1:11101:5889:1458___1:N:0:TCCTGAGC+TACTCCTT;FP:52002;RQ:34.83;RQ:-1.00\n+CAGCGAAGGGGTATAGGGATACGNNNNNNNNNNNN\n++\n+A/AAA//EEEEA/A/EEE////E############\n+@NB500968:8:H5CFGAFXX:1:11101:9851:1471___1:N:0:TCCTGAGC+TACTCCTT;FP:43356;RQ:3.17;RQ:-1.00\n+GTATAAGAGACAGGGGCCCGTTAAAGGGCCCNNNN\n++\n+/A6<//EA//E/E/A/EEE/E/E/E/6EEE/####\n+@NB500968:8:H5CFGAFXX:1:11101:5425:1488___1:N:0:TCCTGAGC+TACTCCTT;FP:13390;RQ:34.83;RQ:-1.00\n+GTATAAGAGACAGTGTGTCCATATAGGGGAGTCNN\n++\n+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEE##\n+@NB500968:8:H5CFGAFXX:1:11101:8024:1581___1:N:0:TCCTGAGC+TACTCCTT;FP:38311;RQ:34.63;RQ:-1.00\n+GAACTATGACTGTGAGCAGGCATTGTGGTTCTGCCCAAGCTACATCCAGATCACCCAGGCCTCTGGGTCTTTTGG\n++\n+AAAA6EAEE/E/EEEEEEEAEEEEEEEAEEEEAEEEEEAE6EEE6EEEAA/EEEEEE/A/E/AEAEE<EEEEA/<\n+@NB500968:8:H5CFGAFXX:1:11101:23474:1673___1:N:0:TCCTGAGC+TACTCCTT;FP:2968;RQ:34.81;RQ:-1.00\n+GATGTGTATAAGAGACAGATATAGACTATAGGGCGCCT\n++\n+A/AA////A//EA/6<EE6/EEE6////A//EE/E6//\n+@NB500968:8:H5CFGAFXX:1:11101:21720:1786___1:N:0:TCCTGAGC+TACTCCTT;FP:16257;RQ:35.14;RQ:-1.00\n+GTCTCTTATACACATCTGACGCTCCCCCCTATAGTTCAAAT\n++\n+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:9012:1809___1:N:0:TCCTGAGC+TACTCCTT;FP:4167;RQ:34.83;RQ:-1.00\n+GTGTATAAGAGACAGGCCTATGATATAGGGGGTAC\n++\n+AAAAAEEEEEEEEEEEEEAEE/EEEAE/AAEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:20110:1819___1:N:0:TCCTGAGC+TAATCCTT;FP:64559;RQ:34.63;RQ:-1.00\n+GAAGAGGGTATCAGATCCCTTGGATCTGGAGTCGCAGATGGCTGCGAGCCACCATGTGGGTTTTGAGAATTGAAG\n++\n+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEAEEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:24842:1887___1:N:0:TCCTGAGC+TACTCCTT;FP:13772;RQ:35.14;RQ:-1.00\n+CTCATAAACACATCAGGCGGACCCCGCAAAATAAAGGATCTATCTCTGATAAAGAACTGACGCTGCCGACGAAA\n'..b'EEEEEEEEEEEEEEEEEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:10463:2345___1:N:0:GCCTGAGC+TACTCCTT;FP:24337;RQ:34.81;RQ:-1.00\n+GTGTATAAGAGACAGCGTCTCTGTATAGGGGAAGT\n++\n+AAAA6E66E/E/A/A/E//EE//A///EEEE///E\n+@NB500968:8:H5CFGAFXX:1:11101:24405:2351___1:N:0:TCCTGAGC+TACTCCTT;FP:5580;RQ:35.18;RQ:-1.00\n+GTATAAGAGACAGACCCTATATATAGGGTCNNNNN\n++\n+AAAAAEEEEEEEEEEEEEEEAEAEEEEEEE#####\n+@NB500968:8:H5CFGAFXX:1:11101:6508:2370___1:N:0:TCCTGAGC+TACTCCTT;FP:64422;RQ:34.83;RQ:-1.00\n+CAGCTAGACGGTATAGGGCTGGGCNNNNNNNNNNN\n++\n+A/AAA/E/EEE//A/EEEAAEEEA###########\n+@NB500968:8:H5CFGAFXX:1:11101:21730:2488___1:N:0:TCGTGAGC+TACTCCTT;FP:57284;RQ:35.18;RQ:-1.00\n+ATACACATCTGACGCTCCCTATATGTAAAGANNNN\n++\n+AA/A///E</E/EEAE////////AEA//E/####\n+@NB500968:8:H5CFGAFXX:1:11101:20021:2516___1:N:0:TCCTGGGC+TACTCCTT;FP:28351;RQ:34.83;RQ:-1.00\n+CTAAAAGAGACAGTGCACGACTTAAGGGGATGAGTGTCTCGTATACACGTCTGACGCTCCCGCTATAAAACCACG\n++\n+//////E/E/E/E////EE/EE///E/EA//////E/E/////E/A///A//E/<<////A/E<///////E//E\n+@NB500968:8:H5CFGAFXX:1:11101:4827:2579___1:N:0:TCCTGAGC+TACTCCTT;FP:8626;RQ:34.83;RQ:-1.00\n+ATGTGTATAAGAGACAGTCGAAGTCTATAGGGATTCC\n++\n+AAAAAE/EA/E/E///E/A/A/EE//EE/E/E/E/AE\n+@NB500968:8:H5CFGAFXX:1:11101:11758:2662___1:N:0:TCCTGAGC+TACTCCTT;FP:32308;RQ:34.83;RQ:-1.00\n+GTGTATAAGAGACAGGTTCGGTCTATAGGGCATCT\n++\n+AAAAAEEEEEEEEEEEEEEEEEEEEEAEAEEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:23131:2747___1:N:0:TCCTGAGC+TACTCCTT;FP:61606;RQ:34.61;RQ:-1.00\n+GAATAAGAGACAGATGAGCAGTATAGGGAGCATATTATTGTCTCAAAGATTAAGCCATGCATGTCTAAGTACTAA\n++\n+A/AAAEEEEAEEAE<EEEEE/E6E///EE/EEE/6//6E/EEAAEEE/EAE<E//6AAAEEE/EE6AEE6EE//A\n+@NB500968:8:H5CFGAFXX:1:11101:20373:2751___1:N:0:TCCTGATC+TACTCCTT;FP:283;RQ:34.93;RQ:-1.00\n+GATGTGTATAAGAGACAGGATCACTTTATAGGCCN\n++\n+AAAAAEE6AAEE/E<EEEEAE/E6</A/EAEA/E#\n+@NB500968:8:H5CFGAFXX:1:11101:21204:2795___1:N:0:TCCTGAGC+TACTCCTT;FP:16279;RQ:34.81;RQ:-1.00\n+CAGTTAGGGCCTATAGGGTGGAGCNNNNNNNNNNN\n++\n+AAA<AEEEEEEEEEEEEEEEEEEE###########\n+@NB500968:8:H5CFGAFXX:1:11101:17699:2880___1:N:0:TCCTGAGC+TACTCCTT;FP:52710;RQ:34.62;RQ:-1.00\n+CATCTGACGCAGCCGACGAAAAAACATGTGTAGATCTCTGACTTCTCAGTATCATTAAATAAAAAAAATTGATGG\n++\n+AAAAAEEEEE/EEEEEEE6EEA//<<EEEE//E//EEEAE///E/6///E/EA/EA//////66A//<6A///AA\n+@NB500968:8:H5CFGAFXX:1:11101:2261:2941___1:N:0:TCCTGAGC+TACTCCTT;FP:2596;RQ:34.63;RQ:-1.00\n+CTCTTATACACATCTGATGCTGCCCCCTATATGCTCCTT\n++\n+A/AAAEAEE/E/AEEEEEEEEEEEEEE/E/A<EEEEE//\n+@NB500968:8:H5CFGAFXX:1:11101:25690:2959___1:N:0:TCCTGCGC+TACTCCTT;FP:27004;RQ:34.81;RQ:-1.00\n+GTGTATAAGAGACAGTCCGAAGCTATAGGGGCGGC\n++\n+A/AA/EEEEEE/6EEE//E//6EEEAAE/EE/EEE\n+@NB500968:8:H5CFGAFXX:1:11101:8090:2972___1:N:0:TCCTGAGC+TACTCCTT;FP:12902;RQ:34.81;RQ:-1.00\n+GGCATAAATTATAGGGGGTCCCNNNNNNNNNNNNN\n++\n+AAAAAEEEEEEEE6EAEEEEAE#############\n+@NB500968:8:H5CFGAFXX:1:11101:16936:3211___1:N:0:TCCTGAGC+TACTCCTT;FP:7401;RQ:34.83;RQ:-1.00\n+CAGTTCACTTTTATAGGGACGCACNNNNNNNNNNN\n++\n+AAAAAEEEEEEEEEEEEEEEEEEE###########\n+@NB500968:8:H5CFGAFXX:1:11101:6132:3257___1:N:0:TCCTGAGC+TACTCCTT;FP:7557;RQ:34.62;RQ:-1.00\n+GTATAAGAGACAGGAGGCGTGTATAGGGGAATGCN\n++\n+AAAAAEEEEEEEEEEEEEEEEEEEAEEEE6EEEE#\n+@NB500968:8:H5CFGAFXX:1:11101:3840:3285___1:N:0:TCCTGAGC+TACTCCTT;FP:16156;RQ:34.93;RQ:-1.00\n+CAATAGGGTATACCTGTCACTAATACACATCAGACGCTCCCCCCTATATAGTAAAT\n++\n+A/AAAE//EE/EEAE//E/EE/EEEEEEEEE/EEEAEEEE<A<A/</AE<EEAE<6\n+@NB500968:8:H5CFGAFXX:1:11101:2858:3312___1:N:0:TCCTGAGC+TACTCCTT;FP:14452;RQ:35.12;RQ:-1.00\n+CTCTTATACACATCTGACGTTCCCTATATGAGTCAT\n++\n+/AAAAEEAEEEEEEEEEEEEEEEEEAEEEEEEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:3641:3398___1:N:0:TCCTGAGC+TACTCCTT;FP:36051;RQ:35.14;RQ:-1.00\n+CTCTTATACACATCTGACGCTGCCCCTATAATGATATC\n++\n+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:20540:3401___1:N:0:TCCTGAGC+TACTCCTT;FP:48603;RQ:34.81;RQ:-1.00\n+CAGTTAGGGCAAAAAGGGTTGATNNNNNNNNNNNN\n++\n+AAAA//EEAE6/E//AAA//EEE############\n+@NB500968:8:H5CFGAFXX:1:11101:4772:3477___1:N:0:TCCTGAGC+AACTCCTT;FP:61788;RQ:3.33;RQ:-1.00\n+GTTTATAATAGACACATAACAATAAAAGAGTAACAATCACAAAAAAAAATAAGACTCTCACGACGAAACACCTTA\n++\n+A//A/E//E/A/E/A/E//A<E/////E/E//AE////E/AE</////EEA/E/A/E//AE/E///<<///A<A/\n' |
| b |
| diff -r 000000000000 -r 40c86e14b674 test-data/paired_un_READ1.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/paired_un_READ1.fq Mon May 09 04:08:01 2016 -0400 |
| b |
| @@ -0,0 +1,112 @@ +@NB500968:8:H5CFGAFXX:1:11101:15939:1071___1:N:0:TCCTGAGC+TACTCCTT;FP:23586;RQ:34.63;RQ:-1.00 +GGCACGTCAGATGAGTATAAGAGACAGCAAATAGGTATAGGGGGCACGTCAGATGAGTAA ++ +EAEEEEEEA///A/EAEEE/EAEEEEEEEEEEAEEE//E/AA/E6AE/EE/<E////A// +@NB500968:8:H5CFGAFXX:1:11101:11473:1333___1:N:0:TCCTGAGC+TACTCCTT;FP:48246;RQ:35.03;RQ:-1.00 +GACAGCGTCAGATGTGTATAAGAGACAGGGTATC ++ +EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE +@NB500968:8:H5CFGAFXX:1:11101:2141:1369___1:N:0:TCCTGAGC+TACTCCTT;FP:0;RQ:1.56;RQ:-1.00 +NNNNNNNNNNNNNNNNNNNN ++ +#################### +@NB500968:8:H5CFGAFXX:1:11101:19474:1422___1:N:0:TCCTGAGC+TACTCCTT;FP:5233;RQ:35.03;RQ:-1.00 +GGAGCGTCAGATGTGTATAAGAGACAGGTACCC ++ +EEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEE +@NB500968:8:H5CFGAFXX:1:11101:8662:1469___1:N:0:TCCTGAGC+TACTCCTT;FP:62135;RQ:35.03;RQ:-1.00 +GGAGCGTCAGATGTGTATAAGAGACAGGTTATC ++ +EEEEEEEEEEEEEAEAE<AEAEEEEEEEEEE<E +@NB500968:8:H5CFGAFXX:1:11101:21998:1542___1:N:0:TCCTGAGC+TACTCCTT;FP:15180;RQ:35.09;RQ:-1.00 +GGCGTCAGATGTGTATAAGAGACAGGG ++ +EEEEEEEAEEEEEEEEEEEEEEEEEEE +@NB500968:8:H5CFGAFXX:1:11101:2814:1550___1:N:0:TCCTGAGC+TACTCCTT;FP:0;RQ:1.56;RQ:-1.00 +NNNNNNNNNNNNNNNNNNNN ++ +#################### +@NB500968:8:H5CFGAFXX:1:11101:8843:1628___1:N:0:TCCTGAGC+TACTCCTT;FP:44455;RQ:34.63;RQ:-1.00 +GGCGTTCAGCCACCCGAGATTGAGCAATAACAGGTCTGTGATGCCCTTAGATGTCCGGGG ++ +EEEEEEEEEAEAEEEEEEEEEEE6/AEEEEAAEE6EA<EEEEE<EEEEEEEEE/AAAAEA +@NB500968:8:H5CFGAFXX:1:11101:1482:1752___1:N:0:TCCTGAGC+TACTCCTT;FP:20529;RQ:35.03;RQ:-1.00 +GGGAGCGTCAGATGTGTATAAGAGACAGTTTTACCC ++ +E/EEEEEEEEEE</EEEEEEEEEEEEEEEEE<EAEA +@NB500968:8:H5CFGAFXX:1:11101:12567:1818___1:N:0:TCCTGAGC+TACTCCTT;FP:61471;RQ:34.63;RQ:-1.00 +GAGCCGCCTGGATACCGCAGCTAGGAATAATGGAATAGGACCGCGGTTCTATTTTGTTGG ++ +EEEEE/EA/EEEAEEEEEA/EEAEEEEE/EEEA/EEAEAEE/A<E/EEEAA<<A6AA<// +@NB500968:8:H5CFGAFXX:1:11101:26750:1960___1:N:0:TCCTGAGC+TACTCCTT;FP:578;RQ:35.03;RQ:-1.00 +GGGAGCGTCAGATGTGTATAAGAGACAGCTGACCC ++ +EEEAEEEAEEAEAEAEE/EEEEAEAAEEEEE/EEE +@NB500968:8:H5CFGAFXX:1:11101:21600:1964___1:N:0:TCCTGAGC+TACTCCTT;FP:38123;RQ:18.05;RQ:-1.00 +GAACGAGACTCTGGCATGCTAACTAGTTACGCGACCCCCGAGCGGTCGGCGTCCCCCAA ++ +EEEEEEAEE/AAAEEEEEEEEEEEEEE<EEEAEEEEAAAEAAEEEE<EA<A<EA<<E<E +@NB500968:8:H5CFGAFXX:1:11101:11625:2006___1:N:0:TCCTGAGC+TACTCCTT;FP:4030;RQ:35.03;RQ:-1.00 +GACAGCGTCAGATGTGTATAAGAGACAGCAACCACC ++ +AEA66E/<AEAEE/E/EEAEEEEAEEEEEAEEEEEE +@NB500968:8:H5CFGAFXX:1:11101:10474:2017___1:N:0:TCCTGAGC+TACTCCTT;FP:16506;RQ:35.03;RQ:-1.00 +GGAGCGTCAGATGTGTATAAGAGACAGTCGTCC ++ +EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE +@NB500968:8:H5CFGAFXX:1:11101:23302:2031___1:N:0:TCCTGAGC+TACTCCTT;FP:9055;RQ:34.81;RQ:-1.00 +AGCGTCAGATGTGTATAAGAGACAGATCGTCCCTATAGCTCCAATC ++ +EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEAEEEEEEAEE +@NB500968:8:H5CFGAFXX:1:11101:19822:2253___1:N:0:TCCTGAGC+TACTCCTT;FP:41486;RQ:34.63;RQ:-1.00 +GACGTGCAAATCGGTCGTCCGACCTGGGTATAGGGGCGAAAGACTAATCGAACCATCTAG ++ +EEEEEEEEEEEEEAEEEEEEEEEEEEAEEEEEAEAEE/EEEEEEEEE<<EEEEAEEEA// +@NB500968:8:H5CFGAFXX:1:11101:5499:2506___1:N:0:TCCTGAGC+TACTCCTT;FP:0;RQ:1.56;RQ:-1.00 +NNNNNNNNNNNNNNNNNNNN ++ +#################### +@NB500968:8:H5CFGAFXX:1:11101:25015:2619___1:N:0:TCCTGAGC+TACTCCTT;FP:0;RQ:1.56;RQ:-1.00 +NNNNNNNNNNNNNNNNNNNN ++ +#################### +@NB500968:8:H5CFGAFXX:1:11101:25905:2738___1:N:0:TCCTGAGC+TACTCCTT;FP:0;RQ:1.56;RQ:-1.00 +NNNNNNNNNNNNNNNNNNNN ++ +#################### +@NB500968:8:H5CFGAFXX:1:11101:10694:2817___1:N:0:TCCTGAGC+TACTCCTT;FP:10036;RQ:34.83;RQ:-1.00 +GGAGCGTCAGATGTGTATAAGAGACAGCCCTTCCCTATACGCTTGGCC ++ +EEEEEEEEEEEEE<EEEEAEEEEEEEEEE/A<E<EEEA/EEEAEEEE/ +@NB500968:8:H5CFGAFXX:1:11101:8407:2853___1:N:0:TCCTGAGC+TACTCCTT;FP:21171;RQ:34.62;RQ:-1.00 +AGAGGGACAAGTGGCGTTCAGCCACCCGAGATTGAGCAATAACAGGTCTGTGATGCCCTT ++ +/EEEEEEAEEEEEAEEEEEEEEEAEAEEAAEEEE/EEEAAAEA//EEEAEAAA/EAEAE6 +@NB500968:8:H5CFGAFXX:1:11101:11672:2944___1:N:0:TCCTGAGC+AACTCCTT;FP:32501;RQ:34.63;RQ:-1.00 +GGGTGAAATACTGTGAGGAACCCAGAAGTGAGTGGAAAGATAACTGGCTTTTTTTTTTTT ++ +AEEEEEEEEEEEAAAEEEEEAA<E/EEEEEEEAAEAEEEE<EEE<</EE6AA/6/<66// +@NB500968:8:H5CFGAFXX:1:11101:15968:2945___1:N:0:TCCTGAGC+TACTCCTT;FP:8706;RQ:34.63;RQ:-1.00 +GCAAATCGGTCGTCCGACCTGGGTATAGGGGCGAAAGGCTAATCGAACCATCTAGTAG ++ +EEEEEEEAEEEEEEEEEEEEEEEEAEEEEEEAEEEEE<EEEEAAEAEEAE<AEAEEEE +@NB500968:8:H5CFGAFXX:1:11101:22125:3141___1:N:0:TCCTGAGC+TACTCCTT;FP:65197;RQ:35.07;RQ:-1.00 +AGCGTCAGATGTGTATAAGAGACAGCTC ++ +EEEEEEEEEEEEEEEEEEEEEEEAEEEE +@NB500968:8:H5CFGAFXX:1:11101:6707:3162___1:N:0:TCCTGAGC+TACTCCTT;FP:0;RQ:1.56;RQ:-1.00 +NNNNNNNNNNNNNNNNNNNN ++ +#################### +@NB500968:8:H5CFGAFXX:1:11101:24232:3202___1:N:0:TCCTGAGC+TACTCCTT;FP:19483;RQ:34.63;RQ:-1.00 +GTTGGTTTTCGGAACTGAGGCCATGATTAAGATGGACGGCCGGGGGCATTCGTATTGCG ++ +EEEEEEEEEEAEEEEEEE/E<EEEEEA</EEE/A/EE<E666<EEAEEEE/6/A66/66 +@NB500968:8:H5CFGAFXX:1:11101:6680:3212___1:N:0:TCCTGAGC+TACTCCTT;FP:62506;RQ:34.81;RQ:-1.00 +TCCAGCGTCAGATGTGTATAAGAGACAGCTCCTCCCTATAAG ++ +EEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEE +@NB500968:8:H5CFGAFXX:1:11101:19438:3463___1:N:0:TCCTGAGC+TACTCCTT;FP:0;RQ:1.56;RQ:-1.00 +NNNNNNNNNNNNNNNNNNNN ++ +#################### |
| b |
| diff -r 000000000000 -r 40c86e14b674 test-data/paired_un_READ2.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/paired_un_READ2.fq Mon May 09 04:08:01 2016 -0400 |
| b |
| @@ -0,0 +1,112 @@ +@NB500968:8:H5CFGAFXX:1:11101:15939:1071___1:N:0:TCCTGAGC+TACTCCTT;FP:23586;RQ:34.63;RQ:-1.00 +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN ++ +################################### +@NB500968:8:H5CFGAFXX:1:11101:11473:1333___1:N:0:TCCTGAGC+TACTCCTT;FP:48246;RQ:35.03;RQ:-1.00 +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN ++ +################################### +@NB500968:8:H5CFGAFXX:1:11101:2141:1369___1:N:0:TCCTGAGC+TACTCCTT;FP:0;RQ:1.56;RQ:-1.00 +GATGTGTATAAGAAACAGACCACATATATAGGGGGGAGCGTCAGATGTGTATAAGAGACAGCCCCCCCCAATAGA ++ +AAAAAEEEEEEEAEEEEE/E/EAEEEEEAEEEA/EEEEEEEAA//AEEEE/</AA/////////AAEE////AA/ +@NB500968:8:H5CFGAFXX:1:11101:19474:1422___1:N:0:TCCTGAGC+TACTCCTT;FP:5233;RQ:35.03;RQ:-1.00 +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN ++ +################################### +@NB500968:8:H5CFGAFXX:1:11101:8662:1469___1:N:0:TCCTGAGC+TACTCCTT;FP:62135;RQ:35.03;RQ:-1.00 +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN ++ +################################### +@NB500968:8:H5CFGAFXX:1:11101:21998:1542___1:N:0:TCCTGAGC+TACTCCTT;FP:15180;RQ:35.09;RQ:-1.00 +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN ++ +################################### +@NB500968:8:H5CFGAFXX:1:11101:2814:1550___1:N:0:TCCTGAGC+TACTCCTT;FP:0;RQ:1.56;RQ:-1.00 +CCGTCAGATGAGTATAAGAGACAGGTAAGACATAAAGAGCGTAGTTGTCTCTAATACACATCTGACGCTGCCGA ++ +/AAA6AEEE//E/EAAEE6/EEEEEEEE//EE/E/EE/AE/<A//</AE/E////AE<A/<A/6/E<EEAAEEE +@NB500968:8:H5CFGAFXX:1:11101:8843:1628___1:N:0:TCCTGAGC+TACTCCTT;FP:44455;RQ:34.63;RQ:-1.00 +GGGCAGGGACTTAATCAACGCAAGCTTATGACCCGCACTTACTGGGAATTCCTCGTTCATGGGGAATAATTGCAA ++ +AAAAAEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEAEEEEEEEEEE<EEEEEEEEEEEE<AA/E6EEAA6 +@NB500968:8:H5CFGAFXX:1:11101:1482:1752___1:N:0:TCCTGAGC+TACTCCTT;FP:20529;RQ:35.03;RQ:-1.00 +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN ++ +################################### +@NB500968:8:H5CFGAFXX:1:11101:12567:1818___1:N:0:TCCTGAGC+TACTCCTT;FP:61471;RQ:34.63;RQ:-1.00 +GGTCATGGGAATAACGCCGCCGCATCGCCAGTCGGCATCGTTTATGGTCGGAACTACGACGGTATCTGATCGT ++ +AA/AAEEAEEE//AEAEEEEEEEEEEAEEEEEEEE/EAEE<EE<EA/<E<EEEEE6EEEE/EEEEEE/EEAEE +@NB500968:8:H5CFGAFXX:1:11101:26750:1960___1:N:0:TCCTGAGC+TACTCCTT;FP:578;RQ:35.03;RQ:-1.00 +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN ++ +################################### +@NB500968:8:H5CFGAFXX:1:11101:21600:1964___1:N:0:TCCTGAGC+TACTCCTT;FP:38123;RQ:18.05;RQ:-1.00 +GCAATCCCCGATCCCCATCACGAATGGGGTTCAACGGGTTACCCGCGCCTGCCGGCGTAGGGTAGGCACACG ++ +AAAAAEEEEEEAEEEEE/E/EEE6/EEEEEEEE/EEEEEEAEEEEEEAEEEAEEEEEEEEEAEE<EAEAEEE +@NB500968:8:H5CFGAFXX:1:11101:11625:2006___1:N:0:TCCTGAGC+TACTCCTT;FP:4030;RQ:35.03;RQ:-1.00 +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN ++ +################################### +@NB500968:8:H5CFGAFXX:1:11101:10474:2017___1:N:0:TCCTGAGC+TACTCCTT;FP:16506;RQ:35.03;RQ:-1.00 +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN ++ +################################### +@NB500968:8:H5CFGAFXX:1:11101:23302:2031___1:N:0:TCCTGAGC+TACTCCTT;FP:9055;RQ:34.81;RQ:-1.00 +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN ++ +################################### +@NB500968:8:H5CFGAFXX:1:11101:19822:2253___1:N:0:TCCTGAGC+TACTCCTT;FP:41486;RQ:34.63;RQ:-1.00 +GGCTTCTTACCCATTTAAAGTTTGAGAATAGGTTGAGATCGTTTCGGCCCCAAGACCTCTAATCATTCGCTTTA ++ +AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEAEEEEEEEE< +@NB500968:8:H5CFGAFXX:1:11101:5499:2506___1:N:0:TCCTGAGC+TACTCCTT;FP:0;RQ:1.56;RQ:-1.00 +GATTTGCCTTATAGGGAGCGTCAGATTTGTATAAGAGACAGCTCCACCCTATACTCGCCGC ++ +A//A<<AA<////A/E/E6<///A//////////////6///<////////////////// +@NB500968:8:H5CFGAFXX:1:11101:25015:2619___1:N:0:TCCTGAGC+TACTCCTT;FP:0;RQ:1.56;RQ:-1.00 +GCGTCAGATGTGAGCGTCAGATGTGTATAAGAGACAGGATCCCCCTATAGCAAGAAG ++ +AAAA/AAA<//A/E6A6EEE//A/6//</A6E/AE6/EE<EAEEEA</AEE///AAE +@NB500968:8:H5CFGAFXX:1:11101:25905:2738___1:N:0:TCCTGAGC+TACTCCTT;FP:0;RQ:1.56;RQ:-1.00 +GTCAGATGTGTATAAGAGACAGTGTGTGAGTATAGGGAAACC ++ +/AAAAEE/AEAA////AEAA/AAEE/EEEAE/E//AE/E/EA +@NB500968:8:H5CFGAFXX:1:11101:10694:2817___1:N:0:TCCTGAGC+TACTCCTT;FP:10036;RQ:34.83;RQ:-1.00 +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN ++ +################################### +@NB500968:8:H5CFGAFXX:1:11101:8407:2853___1:N:0:TCCTGAGC+TACTCCTT;FP:21171;RQ:34.62;RQ:-1.00 +CACTTACTGGGAATTCCTCGTTCATGGGGAATAATTGCAATCCCCGATCCCCATCACGGATGGGGTTCAACGGGT ++ +AAA6AEEEEEEE/EE/EEEEEEEEEEEEEEA6EEEEEEEE<EEEE</EEEAEEEEAEEEEEEEEAEEEE/EAEEA +@NB500968:8:H5CFGAFXX:1:11101:11672:2944___1:N:0:TCCTGAGC+AACTCCTT;FP:32501;RQ:34.63;RQ:-1.00 +AAAACCCTAACTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +A/AA<//6/6//////66666666/6///AEE//EE/</AE</E/<EEEAEEEEEA////<EEE/E<E<A///<6 +@NB500968:8:H5CFGAFXX:1:11101:15968:2945___1:N:0:TCCTGAGC+TACTCCTT;FP:8706;RQ:34.63;RQ:-1.00 +GATGTGGCGTCGGCATCGGGCGCCTTAACCCGGCGTTCGGTTCATCCCGCAGCGCCAGTTCTGCTTACCAAAAGT ++ +AAAA/EEEEEEEEEAEEEEEEE/EEEEAEEEEEEEEEEEEEAEEE<<EEA<AEE//AAA<EAA/EEEEEEEEEE< +@NB500968:8:H5CFGAFXX:1:11101:22125:3141___1:N:0:TCCTGAGC+TACTCCTT;FP:65197;RQ:35.07;RQ:-1.00 +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN ++ +################################### +@NB500968:8:H5CFGAFXX:1:11101:6707:3162___1:N:0:TCCTGAGC+TACTCCTT;FP:0;RQ:1.56;RQ:-1.00 +GCGTAAGAAAAATATAAAACACACTTAAACTCAATAAGTCCATAAATACTATTAAACACAAAAAAAGCATCCAAA ++ +///A/A/E</</EA<///A//<//E/EE//6EA/<//A/</6E//6//<///<//A6<<A/AA//////////</ +@NB500968:8:H5CFGAFXX:1:11101:24232:3202___1:N:0:TCCTGAGC+TACTCCTT;FP:19483;RQ:34.63;RQ:-1.00 +TGATTAATGAAAACATTCTTGGCAAATGCTTTCGCTCTGGTCCGTCTTGCGCCGGTCCAAGAATTTCACCTCTAG ++ +AA/AAE/AA/E6/E/EEA<AAEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEA6AAEE/E/EEEEA<EAEE +@NB500968:8:H5CFGAFXX:1:11101:6680:3212___1:N:0:TCCTGAGC+TACTCCTT;FP:62506;RQ:34.81;RQ:-1.00 +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN ++ +################################### +@NB500968:8:H5CFGAFXX:1:11101:19438:3463___1:N:0:TCCTGAGC+TACTCCTT;FP:0;RQ:1.56;RQ:-1.00 +GCGTCGAGATGTGTATAAGAGACAGCCGAGCTCTATAGGGCAAGT ++ +AAAAAEEEEEEEEEEE<AEEEEEEEEEEEEEEEEEEEEEAEEEEE |
| b |
| diff -r 000000000000 -r 40c86e14b674 test-data/read1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/read1.fastq Mon May 09 04:08:01 2016 -0400 |
| b |
| b'@@ -0,0 +1,400 @@\n+@NB500968:8:H5CFGAFXX:1:11101:15939:1071 1:N:0:TCCTGAGC+TACTCCTT\n+CCTAAGAGTATAGGGGGCACGTCAGATGAGTATAAGAGACAGCAAATAGGTATAGGGGGCACGTCAGATGAGTAA\n++\n+AAAAA6/AEEEEEEEEAEEEEEEA///A/EAEEE/EAEEEEEEEEEEAEEE//E/AA/E6AE/EE/<E////A//\n+@NB500968:8:H5CFGAFXX:1:11101:1121:1139 1:N:0:TCGTGAGC+TACTCCTT\n+CGTAGTCATATAGGGGGAGCGTCAGATGTGTATAAGAGACAGGTATTCCCTATAGTCTACATC\n++\n+AAAAAEEEEAEE<EEEEEEEEEEEEEEEEEAAEEEEAEEEAEEE/EEE/EE<AAEEEEEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:7529:1175 1:N:0:TCCTGAGC+TACTCCTT\n+CAATTATGTATAGGGAGCGTCAGATGTGTATAAGAGACAGCAACCCTAAAAATATCCA\n++\n+AAAAAEA/EEEEEEEEEEE/EEEEEEA/EA<EEEE/AEEEE//E//6A/AE/A/AAE/\n+@NB500968:8:H5CFGAFXX:1:11101:5052:1198 1:N:0:TCCTGAGC+TACTCCTT\n+GCCTGATTTATAGGGGGTTTTTAGTGGCATTCATTGTGTGGATTCCTCTGTTGCTGCCCCTGGGCTAACAAGGGT\n++\n+AAAAAEEEEEEEE<AEEEEEEE6EEEEAEEEEEEEEEEEAEEEEEEEEEEEEEAAE/AEEEEEAAAEEEE/EAEE\n+@NB500968:8:H5CFGAFXX:1:11101:15805:1205 1:N:0:TCCTGAGC+TACTCCTT\n+GGTCTTTGTATAGGGGAGGGCCAGGCAGCTCAAAGCCTGAAGGAGGTACTTCAAGGAGGGTCCAGAGAAGCTGGG\n++\n+AAAAAEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEE<EAAEEEEEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:11834:1217 1:N:0:TCCTGAGC+TACTCCTT\n+TCTCTCGTTATAGGGAGCGTCAGATGTGTATAAGAGACAGGATTCCCCTATATAGCGACCC\n++\n+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEAEEEEEEEEEA<EAEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:20105:1230 1:N:0:TCCTGAGC+TACTCCTT\n+AAGATCGCTATAGGGGTTGTTTCATGTTGCAATTTTTAGGTTACTTTTGAGTTGCTTAGGAATTGTTTTATTTAA\n++\n+6AAAA//EEEAEAEEEEEEEEEEEE/E/AEEEEE<E</EEAEEEEEEAAEAEEEAAE//EA//</E6EAAEA/6/\n+@NB500968:8:H5CFGAFXX:1:11101:14524:1264 1:N:0:TCCTGAGC+TACTCCTT\n+ACTTAAACTATAAGTCCCAACTTAATATTATAAAATTATCATAAAAACAACTACGAGCCCACGATACAACTGATA\n++\n+AAAAA//EEE<EEEA//EEEE<///A/AAA/A////E/<///E/6/E/E/E6///E//6E<//6/AA//E//A//\n+@NB500968:8:H5CFGAFXX:1:11101:14981:1265 1:N:0:TCCTGAGC+TACTCCTT\n+CGCGTCTCTATAGGGGTCTGGTTAATTCCGATAACGAACGAGACTCTGGCATGCTAACTAGTTACGCGACCCCCG\n++\n+AAAAAEEEEEEE<EAEEEEEEEEEEEEEAEEEEEEEEEAAEEEEEEEA<EEEEEEEEE6/E66A<A/<AA<A//6\n+@NB500968:8:H5CFGAFXX:1:11101:5538:1286 1:N:0:TCCTGAGC+TACTCCTT\n+ACATTCCTTATAGGGAGTGAACTAACTAGAAAACTTCTAACTAAAAGAATTACAGCTAGAAACCCCGAAACCAAA\n++\n+6AAAAEEEEE<E</<AAEEEEEEEEAE/AEEEEEEEAEEEEE/AE6/EEA<E/EA6EAAEEE6//6<<EEA/<<A\n+@NB500968:8:H5CFGAFXX:1:11101:11473:1333 1:N:0:TCCTGAGC+TACTCCTT\n+GTTACTCGTATAGGGGACAGCGTCAGATGTGTATAAGAGACAGGGTATC\n++\n+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:2141:1369 1:N:0:TCCTGAGC+TACTCCTT\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n++\n+###################################\n+@NB500968:8:H5CFGAFXX:1:11101:24482:1380 1:N:0:TCCTGAGC+TACTCCTT\n+GTGTATAAGAGACAGGCCTAATATATAGGGGGCGCCAGTCCTCCGATTGACTGAGTCGCCCGGGTACCCGTGTAT\n++\n+AAAAAEE/E/E/<EEEE/EAEE<EEEEEEEEEEEEEAEEA/E/EAEEEEEEEEEEEEEEE<E/EE<<6EEAEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:2671:1393 1:N:0:TCCTGAGC+TACTCCTT\n+GGTCCCCTATAAGGGGATTCTGTCTCTTATACCNN\n++\n+///AA6E/6AA///EAE//E6E6E6E/6AAE/E##\n+@NB500968:8:H5CFGAFXX:1:11101:19474:1422 1:N:0:TCCTGAGC+TACTCCTT\n+ACCACTACTATAGGGGGAGCGTCAGATGTGTATAAGAGACAGGTACCC\n++\n+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:12411:1441 1:N:0:TCCTGAGC+TACTCCTT\n+GTATTCCTTATAGGGGGGAGCGTCAGATGTGTATAAGAGACAGTCTCCCTATATTTTGGC\n++\n+AAAAA//AEEEEEEE//AEEE/EAEAEE/AEAE<EEEEAE/EAE<E/E</EEEE/6E/EE\n+@NB500968:8:H5CFGAFXX:1:11101:5889:1458 1:N:0:TCCTGAGC+TACTCCTT\n+TAGTAGAGTATAGGGGAGCGTCAGATGTGTATAAGAGACAGCGTATCCCTATACCCCTTCGCTG\n++\n+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:8662:1469 1:N:0:TCCTGAGC+TACTCCTT\n+TTAGGTCTTATAGGGGGAGCGTCAGATGTGTATAAGAGACAGGTTATC\n++\n+AAAAAEEEEEEEEEEEEEEEEEEEEEEEAEAE<AEAEEEEEEEEEE<E\n+@NB500968:8:H5CFGAFXX:1:11101:9851:1471 1:N:0:TCCTGAGC+TACTCCTT\n+GGGCCCTATAACGGGCCCCTGTCTCTTATACCNNN\n++\n+AAAA6EEEEEEEAEEEEEEEA/AA/EEEEE//###\n+@NB500968:8:H5CFGAFXX:1:11101:7850:1487 1:N:0:TCCTGAGC+TACTCCTT\n+ATTCCAATATAGGGGACCCACATCTTCCTCTGCTTCTAGATGAAGGATGTATTCTTCTTCCTCTTCTTCCTCTG\n++\n+AAAAAEEE/EEE/EEEEEEAAEEE/EEEEEAEEEEEEEEEEEEEEAEAE6EEA<EEEAEE<6E/<EE<<E6E/<\n+@NB500968:8:H5CFGAFXX:1:11101:5425:1488 1:N:0:TCCTGAGC+TACTCCTT\n+ATCAC'..b'GCTTTTTTTTTTTT\n++\n+AAAAAEAEEEEEE<AAEEEEEEEEEEEAAAEEEEEAA<E/EEEEEEEAAEAEEEE<EEE<</EE6AA/6/<66//\n+@NB500968:8:H5CFGAFXX:1:11101:15968:2945 1:N:0:TCCTGAGC+TACTCCTT\n+AGAGAAAGTATAGGGGCAAATCGGTCGTCCGACCTGGGTATAGGGGCGAAAGGCTAATCGAACCATCTAGTAG\n++\n+AAAAAEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEAEEEEEEAEEEEE<EEEEAAEAEEAE<AEAEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:25690:2959 1:N:0:TCCTGCGC+TACTCCTT\n+CGGCCTTATATAGGGAGCGTCAGATGTGTATAAGAGACAGGCCTCCCCTATAGCTTCGGA\n++\n+AAAA6EEE//6EEA/AE6EEEEEEEEEAAEEEEEEEEEEEEEEAEE/E/EAEEEEAEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:8090:2972 1:N:0:TCCTGAGC+TACTCCTT\n+ATAGCGCGTATAGGGCAACGTCAGATGTGTATAAGAGACAGGGACCCCCTATAATTTATGCC\n++\n+AAAAAEEEEEAEEEEEEEEEEEEEEEEEEEEEAAEEEEEEEEEAEE<EEEEEAE<EEEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:23310:3069 1:N:0:TCCTGAGC+TACTCCTT\n+CAGGCCAATCGTATAGGGGTTGATACTCAAGTCTACTTGTTCCCTTTTATTTAATCCTGAACCCCATCCCATGGA\n++\n+AAA/AEEEEEEEAE//EEE////EAA//EE/EEEEEE//EEE/E/E/EEEEEEE<A<E/AEE//AE/<AAEEEE/\n+@NB500968:8:H5CFGAFXX:1:11101:9254:3110 1:N:0:TCCTGAGC+TACTCCTT\n+TGTTATAAGGCGTCAGATGTGTATAAGAGACAGGGATCCCCTATAAAGAGCCTAAC\n++\n+AAAAAEEEEEEEEEEEEEEEEEEEAEEEE<EAEEE/EEEEEEEEE/EEEEEEEAA/\n+@NB500968:8:H5CFGAFXX:1:11101:22125:3141 1:N:0:TCCTGAGC+TACTCCTT\n+TTTGGGTCTATAGGGAGCGTCAGATGTGTATAAGAGACAGCTC\n++\n+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:6707:3162 1:N:0:TCCTGAGC+TACTCCTT\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n++\n+###################################\n+@NB500968:8:H5CFGAFXX:1:11101:4099:3187 1:N:0:TCCTGAGC+TACTCCTT\n+GTATAAGAGACAGCCAGCCTCTATAGGGGTGCTTGCAGGGGAGGGAAAAGGGGGAAAGCGGGCAACCAGTTTCC\n++\n+AAAAAAEAE6E6EEEEEAEEA<EEEEEEEEEEEEEEEEEEEEEEEEEEAEE/EEAEEEEEEEEEEEEEAE/E//\n+@NB500968:8:H5CFGAFXX:1:11101:24232:3202 1:N:0:TCCTGAGC+TACTCCTT\n+CATAACGTTATAGGGGTTGGTTTTCGGAACTGAGGCCATGATTAAGATGGACGGCCGGGGGCATTCGTATTGCG\n++\n+AAAAAEEEEEAE///EEEEEEEEEEAEEEEEEE/E<EEEEEA</EEE/A/EE<E666<EEAEEEE/6/A66/66\n+@NB500968:8:H5CFGAFXX:1:11101:16936:3211 1:N:0:TCCTGAGC+TACTCCTT\n+ACTATGGCTATAGGGGAGCGTCAGATGTGTATAAGAGACAGTGCGTCCCTATAAAAGTGAACTG\n++\n+AAAAAEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEA/EEEAEAEEE\n+@NB500968:8:H5CFGAFXX:1:11101:6680:3212 1:N:0:TCCTGAGC+TACTCCTT\n+TTCAAGGGTATAGGGTCCAGCGTCAGATGTGTATAAGAGACAGCTCCTCCCTATAAG\n++\n+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:15733:3232 1:N:0:TCCTGAGC+TACTCCTT\n+TCCCCTATATTTGGGGACTGTCTCTTATACACCNN\n++\n+AAAAAEEE/EEEEEEEEEEEEEEEEEEEEEEEE##\n+@NB500968:8:H5CFGAFXX:1:11101:3009:3242 1:N:0:TCCTGAGC+TACTCCTT\n+GGTTAAGGCTAGCCTATTCTACATAGAGTGTTCTAGGCCTTCCAGGGCCACATAGACTCTTGTTTCAAAAAAAT\n++\n+A//AAEEEEEEEEEEEAEE/EEEEAAEE/AAEEEAEEEEAEEEEAEEEEEEEEEEEEEEA6EEEE<EEE/A/EA\n+@NB500968:8:H5CFGAFXX:1:11101:6132:3257 1:N:0:TCCTGAGC+TACTCCTT\n+ACTCGACCTATAGGGCGTCAGATGTGTATAAGAGACAGCATTCCCCTATACACGCCTCCTGTCTCTTATAC\n++\n+AAAAA/EEE6E/EEEEEEEAEEEEEEEEEEEEEEAEAEEAEEEEAEEEEEEEEEEEEEEEEAE/EEEEEEA\n+@NB500968:8:H5CFGAFXX:1:11101:3840:3285 1:N:0:TCCTGAGC+TACTCCTT\n+ATTTACTATATAGGGGGGAGCGTCAGATGTGTATAAGAGACAGGTATACCCTATAG\n++\n+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:2858:3312 1:N:0:TCCTGAGC+TACTCCTT\n+ATGACTCATATAGGGAACGTCAGATGTGTATAAGAG\n++\n+AAAAAE/EE/A/<AEEE/AE/E/EAAEEEEEEEAEE\n+@NB500968:8:H5CFGAFXX:1:11101:3641:3398 1:N:0:TCCTGAGC+TACTCCTT\n+GATATCATTATAGGGGCAGCGTCAGATGTGTATAAGAG\n++\n+AAAAAEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:20540:3401 1:N:0:TCCTGAGC+TACTCCTT\n+GTTCTCGTTATAGGGAGCGTCAGATGTGTATAAGAGACAGATCAACCCTATATGCCCTAACTG\n++\n+AAA6AE/AAEEEEEEE/E///E/E</A/EEA<E/E/EEE/E</E///A/E6<E/A/<E/EEE/\n+@NB500968:8:H5CFGAFXX:1:11101:18503:3442 1:N:0:TCCTGAGC+TACTCCGT\n+TAATCCCTATAAGGGATTACTGACTCTTATACATGTATCTAATACACATCTCCGAGCCCACGAGACTCCTGAGCA\n++\n+AAAAAE/AAEEEEEEAAE/E//////EEAA///A/E/<///AEEEE/E/EE<<///E<EEE/E/AE6/EEEE//6\n+@NB500968:8:H5CFGAFXX:1:11101:19438:3463 1:N:0:TCCTGAGC+TACTCCTT\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n++\n+###################################\n+@NB500968:8:H5CFGAFXX:1:11101:4772:3477 1:N:0:TCCTGAGC+AACTCCTT\n+TTACCCTATACTGGGTAACTGTCTCTTATACACCN\n++\n+AAAAAEEEEAEEEEAEEEEEEEAEEEAEEE<EEE#\n' |
| b |
| diff -r 000000000000 -r 40c86e14b674 test-data/read1.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/read1.fq Mon May 09 04:08:01 2016 -0400 |
| b |
| b'@@ -0,0 +1,328 @@\n+@NB500968:8:H5CFGAFXX:1:11101:15939:1071 1:N:0:TCCTGAGC+TACTCCTT;FP:23586;RQ:34.63\n+GGCACGTCAGATGAGTATAAGAGACAGCAAATAGGTATAGGGGGCACGTCAGATGAGTAA\n++\n+EAEEEEEEA///A/EAEEE/EAEEEEEEEEEEAEEE//E/AA/E6AE/EE/<E////A//\n+@NB500968:8:H5CFGAFXX:1:11101:1121:1139 1:N:0:TCGTGAGC+TACTCCTT;FP:27828;RQ:34.83\n+GGAGCGTCAGATGTGTATAAGAGACAGGTATTCCCTATAGTCTACATC\n++\n+EEEEEEEEEEEEEEEAAEEEEAEEEAEEE/EEE/EE<AAEEEEEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:7529:1175 1:N:0:TCCTGAGC+TACTCCTT;FP:17358;RQ:34.81\n+AGCGTCAGATGTGTATAAGAGACAGCAACCCTAAAAATATCCA\n++\n+EEEE/EEEEEEA/EA<EEEE/AEEEE//E//6A/AE/A/AAE/\n+@NB500968:8:H5CFGAFXX:1:11101:5052:1198 1:N:0:TCCTGAGC+TACTCCTT;FP:38799;RQ:34.63\n+GGTTTTTAGTGGCATTCATTGTGTGGATTCCTCTGTTGCTGCCCCTGGGCTAACAAGGGT\n++\n+EEEEEEE6EEEEAEEEEEEEEEEEAEEEEEEEEEEEEEAAE/AEEEEEAAAEEEE/EAEE\n+@NB500968:8:H5CFGAFXX:1:11101:15805:1205 1:N:0:TCCTGAGC+TACTCCTT;FP:44542;RQ:34.63\n+GAGGGCCAGGCAGCTCAAAGCCTGAAGGAGGTACTTCAAGGAGGGTCCAGAGAAGCTGGG\n++\n+EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEE<EAAEEEEEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:11834:1217 1:N:0:TCCTGAGC+TACTCCTT;FP:56795;RQ:34.81\n+AGCGTCAGATGTGTATAAGAGACAGGATTCCCCTATATAGCGACCC\n++\n+EEEEEEEEEEEEEEEEAEEEEEEEEEEAEEEEEEEEEA<EAEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:20105:1230 1:N:0:TCCTGAGC+TACTCCTT;FP:2265;RQ:34.63\n+GTTGTTTCATGTTGCAATTTTTAGGTTACTTTTGAGTTGCTTAGGAATTGTTTTATTTAA\n++\n+EEEEEEEEEE/E/AEEEEE<E</EEAEEEEEEAAEAEEEAAE//EA//</E6EAAEA/6/\n+@NB500968:8:H5CFGAFXX:1:11101:14524:1264 1:N:0:TCCTGAGC+TACTCCTT;FP:7937;RQ:2.65\n+CCCAACTTAATATTATAAAATTATCATAAAAACAACTACGAGCCCACGATACAACTGATA\n++\n+//EEEE<///A/AAA/A////E/<///E/6/E/E/E6///E//6E<//6/AA//E//A//\n+@NB500968:8:H5CFGAFXX:1:11101:14981:1265 1:N:0:TCCTGAGC+TACTCCTT;FP:26333;RQ:34.63\n+GTCTGGTTAATTCCGATAACGAACGAGACTCTGGCATGCTAACTAGTTACGCGACCCCCG\n++\n+EEEEEEEEEEEEEAEEEEEEEEEAAEEEEEEEA<EEEEEEEEE6/E66A<A/<AA<A//6\n+@NB500968:8:H5CFGAFXX:1:11101:5538:1286 1:N:0:TCCTGAGC+TACTCCTT;FP:5079;RQ:34.62\n+AGTGAACTAACTAGAAAACTTCTAACTAAAAGAATTACAGCTAGAAACCCCGAAACCAAA\n++\n+AAEEEEEEEEAE/AEEEEEEEAEEEEE/AE6/EEA<E/EA6EAAEEE6//6<<EEA/<<A\n+@NB500968:8:H5CFGAFXX:1:11101:11473:1333 1:N:0:TCCTGAGC+TACTCCTT;FP:48246;RQ:35.03\n+GACAGCGTCAGATGTGTATAAGAGACAGGGTATC\n++\n+EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:2141:1369 1:N:0:TCCTGAGC+TACTCCTT;FP:0;RQ:1.56\n+NNNNNNNNNNNNNNNNNNNN\n++\n+####################\n+@NB500968:8:H5CFGAFXX:1:11101:19474:1422 1:N:0:TCCTGAGC+TACTCCTT;FP:5233;RQ:35.03\n+GGAGCGTCAGATGTGTATAAGAGACAGGTACCC\n++\n+EEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:12411:1441 1:N:0:TCCTGAGC+TACTCCTT;FP:46039;RQ:34.83\n+GGGAGCGTCAGATGTGTATAAGAGACAGTCTCCCTATATTTTGGC\n++\n+//AEEE/EAEAEE/AEAE<EEEEAE/EAE<E/E</EEEE/6E/EE\n+@NB500968:8:H5CFGAFXX:1:11101:5889:1458 1:N:0:TCCTGAGC+TACTCCTT;FP:52002;RQ:34.83\n+GAGCGTCAGATGTGTATAAGAGACAGCGTATCCCTATACCCCTTCGCTG\n++\n+EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:8662:1469 1:N:0:TCCTGAGC+TACTCCTT;FP:62135;RQ:35.03\n+GGAGCGTCAGATGTGTATAAGAGACAGGTTATC\n++\n+EEEEEEEEEEEEEAEAE<AEAEEEEEEEEEE<E\n+@NB500968:8:H5CFGAFXX:1:11101:9851:1471 1:N:0:TCCTGAGC+TACTCCTT;FP:43356;RQ:3.17\n+CCCCTGTCTCTTATACCNNN\n++\n+EEEEEA/AA/EEEEE//###\n+@NB500968:8:H5CFGAFXX:1:11101:5425:1488 1:N:0:TCCTGAGC+TACTCCTT;FP:13390;RQ:34.83\n+GGAGCGTCAGATGTGTATAAGAGACAGACTCCCCTATATGGACACA\n++\n+EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:21998:1542 1:N:0:TCCTGAGC+TACTCCTT;FP:15180;RQ:35.09\n+GGCGTCAGATGTGTATAAGAGACAGGG\n++\n+EEEEEEEAEEEEEEEEEEEEEEEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:2814:1550 1:N:0:TCCTGAGC+TACTCCTT;FP:0;RQ:1.56\n+NNNNNNNNNNNNNNNNNNNN\n++\n+####################\n+@NB500968:8:H5CFGAFXX:1:11101:8024:1581 1:N:0:TCCTGAGC+TACTCCTT;FP:38311;RQ:34.63\n+GTGACCCGCCGCTTCAGGGACCCGCTTCTCTCATCTTCCCCAAAGTTCTGGACAGATGAT\n++\n+EEEEEEEAEEEEEAEAEEEEEEEEEEAEEEEAEEEAEAEEEEEEEEAEEEEEEEEEE/A<\n+@NB500968:8:H5CFGAFXX:1:11101:8843:1628 1:N:0:TCCTGAGC+TACTCCTT;FP:44455;RQ:34.63\n+GGCGTTCAGCCACCCGAGATTGAGCAATAACAGGTCTGTGATGCCCTTAGATGTCCGGGG\n++\n+EEEEEEEEEAEAEEEEEEEEEEE6/AEEEEAAEE6EA<EEEEE<EEEEEEEEE/AAAAEA'..b'TGGGTCGTCGCCGCCACGGGGGGCGTGCGATCGGCCCGAGGTTATCTA\n++\n+EEEEEEAEAEEEE/EEEAEEEEA/EEEEAEA/EA<EAAAEEAE<AE/A<<EEEA<<EEA<\n+@NB500968:8:H5CFGAFXX:1:11101:20373:2751 1:N:0:TCCTGATC+TACTCCTT;FP:283;RQ:34.93\n+GGAGCGTCAGATGTGTATAAGAGACAGCCCTATACAGTGATC\n++\n+EEEEEEEEE<EEEEAEAEEEEEEEEEEEEEE/EEEEEE<EAA\n+@NB500968:8:H5CFGAFXX:1:11101:21204:2795 1:N:0:TCCTGAGC+TACTCCTT;FP:16279;RQ:34.81\n+AGCGTCAGATGTGTATAAGAGACAGCTCCACCCTATAGGCCCTAACTG\n++\n+EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:10694:2817 1:N:0:TCCTGAGC+TACTCCTT;FP:10036;RQ:34.83\n+GGAGCGTCAGATGTGTATAAGAGACAGCCCTTCCCTATACGCTTGGCC\n++\n+EEEEEEEEEEEEE<EEEEAEEEEEEEEEE/A<E<EEEA/EEEAEEEE/\n+@NB500968:8:H5CFGAFXX:1:11101:8407:2853 1:N:0:TCCTGAGC+TACTCCTT;FP:21171;RQ:34.62\n+AGAGGGACAAGTGGCGTTCAGCCACCCGAGATTGAGCAATAACAGGTCTGTGATGCCCTT\n++\n+/EEEEEEAEEEEEAEEEEEEEEEAEAEEAAEEEE/EEEAAAEA//EEEAEAAA/EAEAE6\n+@NB500968:8:H5CFGAFXX:1:11101:17699:2880 1:N:0:TCCTGAGC+TACTCCTT;FP:52710;RQ:34.62\n+CTTTGGAATCTTCACAAGCAGAACCAGTCAAAACCCCGGCAAGCACAAAGAGACTCTCCA\n++\n+EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE<EEEEEEEEEEE6AEAEAEEEEA\n+@NB500968:8:H5CFGAFXX:1:11101:2261:2941 1:N:0:TCCTGAGC+TACTCCTT;FP:2596;RQ:34.63\n+GGCAGCATCAGATGTGTATAAGAGACAGAAGGAGCAGAGAGCGGCCAGCAACCGATGAGA\n++\n+EEEEEEEEEEEEEEAEEEAEEEEE///////EA//E/E/A/////E<EE//</E<<////\n+@NB500968:8:H5CFGAFXX:1:11101:11672:2944 1:N:0:TCCTGAGC+AACTCCTT;FP:32501;RQ:34.63\n+GGGTGAAATACTGTGAGGAACCCAGAAGTGAGTGGAAAGATAACTGGCTTTTTTTTTTTT\n++\n+AEEEEEEEEEEEAAAEEEEEAA<E/EEEEEEEAAEAEEEE<EEE<</EE6AA/6/<66//\n+@NB500968:8:H5CFGAFXX:1:11101:15968:2945 1:N:0:TCCTGAGC+TACTCCTT;FP:8706;RQ:34.63\n+GCAAATCGGTCGTCCGACCTGGGTATAGGGGCGAAAGGCTAATCGAACCATCTAGTAG\n++\n+EEEEEEEAEEEEEEEEEEEEEEEEAEEEEEEAEEEEE<EEEEAAEAEEAE<AEAEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:25690:2959 1:N:0:TCCTGCGC+TACTCCTT;FP:27004;RQ:34.81\n+AGCGTCAGATGTGTATAAGAGACAGGCCTCCCCTATAGCTTCGGA\n++\n+AE6EEEEEEEEEAAEEEEEEEEEEEEEEAEE/E/EAEEEEAEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:8090:2972 1:N:0:TCCTGAGC+TACTCCTT;FP:12902;RQ:34.81\n+CAACGTCAGATGTGTATAAGAGACAGGGACCCCCTATAATTTATGCC\n++\n+EEEEEEEEEEEEEEEEEAAEEEEEEEEEAEE<EEEEEAE<EEEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:22125:3141 1:N:0:TCCTGAGC+TACTCCTT;FP:65197;RQ:35.07\n+AGCGTCAGATGTGTATAAGAGACAGCTC\n++\n+EEEEEEEEEEEEEEEEEEEEEEEAEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:6707:3162 1:N:0:TCCTGAGC+TACTCCTT;FP:0;RQ:1.56\n+NNNNNNNNNNNNNNNNNNNN\n++\n+####################\n+@NB500968:8:H5CFGAFXX:1:11101:24232:3202 1:N:0:TCCTGAGC+TACTCCTT;FP:19483;RQ:34.63\n+GTTGGTTTTCGGAACTGAGGCCATGATTAAGATGGACGGCCGGGGGCATTCGTATTGCG\n++\n+EEEEEEEEEEAEEEEEEE/E<EEEEEA</EEE/A/EE<E666<EEAEEEE/6/A66/66\n+@NB500968:8:H5CFGAFXX:1:11101:16936:3211 1:N:0:TCCTGAGC+TACTCCTT;FP:7401;RQ:34.83\n+GAGCGTCAGATGTGTATAAGAGACAGTGCGTCCCTATAAAAGTGAACTG\n++\n+EEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEA/EEEAEAEEE\n+@NB500968:8:H5CFGAFXX:1:11101:6680:3212 1:N:0:TCCTGAGC+TACTCCTT;FP:62506;RQ:34.81\n+TCCAGCGTCAGATGTGTATAAGAGACAGCTCCTCCCTATAAG\n++\n+EEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:6132:3257 1:N:0:TCCTGAGC+TACTCCTT;FP:7557;RQ:34.62\n+CGTCAGATGTGTATAAGAGACAGCATTCCCCTATACACGCCTCCTGTCTCTTATAC\n++\n+EEEEAEEEEEEEEEEEEEEAEAEEAEEEEAEEEEEEEEEEEEEEEEAE/EEEEEEA\n+@NB500968:8:H5CFGAFXX:1:11101:3840:3285 1:N:0:TCCTGAGC+TACTCCTT;FP:16156;RQ:34.93\n+GGGAGCGTCAGATGTGTATAAGAGACAGGTATACCCTATAG\n++\n+EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:2858:3312 1:N:0:TCCTGAGC+TACTCCTT;FP:14452;RQ:35.12\n+AACGTCAGATGTGTATAAGAG\n++\n+EE/AE/E/EAAEEEEEEEAEE\n+@NB500968:8:H5CFGAFXX:1:11101:3641:3398 1:N:0:TCCTGAGC+TACTCCTT;FP:36051;RQ:35.14\n+GCAGCGTCAGATGTGTATAAGAG\n++\n+EEEEEEEEEEEEEEEEEEEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:20540:3401 1:N:0:TCCTGAGC+TACTCCTT;FP:48603;RQ:34.81\n+AGCGTCAGATGTGTATAAGAGACAGATCAACCCTATATGCCCTAACTG\n++\n+E/E///E/E</A/EEA<E/E/EEE/E</E///A/E6<E/A/<E/EEE/\n+@NB500968:8:H5CFGAFXX:1:11101:19438:3463 1:N:0:TCCTGAGC+TACTCCTT;FP:0;RQ:1.56\n+NNNNNNNNNNNNNNNNNNNN\n++\n+####################\n+@NB500968:8:H5CFGAFXX:1:11101:4772:3477 1:N:0:TCCTGAGC+AACTCCTT;FP:61788;RQ:3.33\n+TAACTGTCTCTTATACACCN\n++\n+EEEEEEEAEEEAEEE<EEE#\n' |
| b |
| diff -r 000000000000 -r 40c86e14b674 test-data/read1_extracted.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/read1_extracted.fastq Mon May 09 04:08:01 2016 -0400 |
| b |
| b'@@ -0,0 +1,328 @@\n+@NB500968:8:H5CFGAFXX:1:11101:15939:1071___1:N:0:TCCTGAGC+TACTCCTT;FP:23586;RQ:34.63\n+GGCACGTCAGATGAGTATAAGAGACAGCAAATAGGTATAGGGGGCACGTCAGATGAGTAA\n++\n+EAEEEEEEA///A/EAEEE/EAEEEEEEEEEEAEEE//E/AA/E6AE/EE/<E////A//\n+@NB500968:8:H5CFGAFXX:1:11101:1121:1139___1:N:0:TCGTGAGC+TACTCCTT;FP:27828;RQ:34.83\n+GGAGCGTCAGATGTGTATAAGAGACAGGTATTCCCTATAGTCTACATC\n++\n+EEEEEEEEEEEEEEEAAEEEEAEEEAEEE/EEE/EE<AAEEEEEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:7529:1175___1:N:0:TCCTGAGC+TACTCCTT;FP:17358;RQ:34.81\n+AGCGTCAGATGTGTATAAGAGACAGCAACCCTAAAAATATCCA\n++\n+EEEE/EEEEEEA/EA<EEEE/AEEEE//E//6A/AE/A/AAE/\n+@NB500968:8:H5CFGAFXX:1:11101:5052:1198___1:N:0:TCCTGAGC+TACTCCTT;FP:38799;RQ:34.63\n+GGTTTTTAGTGGCATTCATTGTGTGGATTCCTCTGTTGCTGCCCCTGGGCTAACAAGGGT\n++\n+EEEEEEE6EEEEAEEEEEEEEEEEAEEEEEEEEEEEEEAAE/AEEEEEAAAEEEE/EAEE\n+@NB500968:8:H5CFGAFXX:1:11101:15805:1205___1:N:0:TCCTGAGC+TACTCCTT;FP:44542;RQ:34.63\n+GAGGGCCAGGCAGCTCAAAGCCTGAAGGAGGTACTTCAAGGAGGGTCCAGAGAAGCTGGG\n++\n+EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEE<EAAEEEEEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:11834:1217___1:N:0:TCCTGAGC+TACTCCTT;FP:56795;RQ:34.81\n+AGCGTCAGATGTGTATAAGAGACAGGATTCCCCTATATAGCGACCC\n++\n+EEEEEEEEEEEEEEEEAEEEEEEEEEEAEEEEEEEEEA<EAEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:20105:1230___1:N:0:TCCTGAGC+TACTCCTT;FP:2265;RQ:34.63\n+GTTGTTTCATGTTGCAATTTTTAGGTTACTTTTGAGTTGCTTAGGAATTGTTTTATTTAA\n++\n+EEEEEEEEEE/E/AEEEEE<E</EEAEEEEEEAAEAEEEAAE//EA//</E6EAAEA/6/\n+@NB500968:8:H5CFGAFXX:1:11101:14524:1264___1:N:0:TCCTGAGC+TACTCCTT;FP:7937;RQ:2.65\n+CCCAACTTAATATTATAAAATTATCATAAAAACAACTACGAGCCCACGATACAACTGATA\n++\n+//EEEE<///A/AAA/A////E/<///E/6/E/E/E6///E//6E<//6/AA//E//A//\n+@NB500968:8:H5CFGAFXX:1:11101:14981:1265___1:N:0:TCCTGAGC+TACTCCTT;FP:26333;RQ:34.63\n+GTCTGGTTAATTCCGATAACGAACGAGACTCTGGCATGCTAACTAGTTACGCGACCCCCG\n++\n+EEEEEEEEEEEEEAEEEEEEEEEAAEEEEEEEA<EEEEEEEEE6/E66A<A/<AA<A//6\n+@NB500968:8:H5CFGAFXX:1:11101:5538:1286___1:N:0:TCCTGAGC+TACTCCTT;FP:5079;RQ:34.62\n+AGTGAACTAACTAGAAAACTTCTAACTAAAAGAATTACAGCTAGAAACCCCGAAACCAAA\n++\n+AAEEEEEEEEAE/AEEEEEEEAEEEEE/AE6/EEA<E/EA6EAAEEE6//6<<EEA/<<A\n+@NB500968:8:H5CFGAFXX:1:11101:11473:1333___1:N:0:TCCTGAGC+TACTCCTT;FP:48246;RQ:35.03\n+GACAGCGTCAGATGTGTATAAGAGACAGGGTATC\n++\n+EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:2141:1369___1:N:0:TCCTGAGC+TACTCCTT;FP:0;RQ:1.56\n+NNNNNNNNNNNNNNNNNNNN\n++\n+####################\n+@NB500968:8:H5CFGAFXX:1:11101:19474:1422___1:N:0:TCCTGAGC+TACTCCTT;FP:5233;RQ:35.03\n+GGAGCGTCAGATGTGTATAAGAGACAGGTACCC\n++\n+EEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:12411:1441___1:N:0:TCCTGAGC+TACTCCTT;FP:46039;RQ:34.83\n+GGGAGCGTCAGATGTGTATAAGAGACAGTCTCCCTATATTTTGGC\n++\n+//AEEE/EAEAEE/AEAE<EEEEAE/EAE<E/E</EEEE/6E/EE\n+@NB500968:8:H5CFGAFXX:1:11101:5889:1458___1:N:0:TCCTGAGC+TACTCCTT;FP:52002;RQ:34.83\n+GAGCGTCAGATGTGTATAAGAGACAGCGTATCCCTATACCCCTTCGCTG\n++\n+EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:8662:1469___1:N:0:TCCTGAGC+TACTCCTT;FP:62135;RQ:35.03\n+GGAGCGTCAGATGTGTATAAGAGACAGGTTATC\n++\n+EEEEEEEEEEEEEAEAE<AEAEEEEEEEEEE<E\n+@NB500968:8:H5CFGAFXX:1:11101:9851:1471___1:N:0:TCCTGAGC+TACTCCTT;FP:43356;RQ:3.17\n+CCCCTGTCTCTTATACCNNN\n++\n+EEEEEA/AA/EEEEE//###\n+@NB500968:8:H5CFGAFXX:1:11101:5425:1488___1:N:0:TCCTGAGC+TACTCCTT;FP:13390;RQ:34.83\n+GGAGCGTCAGATGTGTATAAGAGACAGACTCCCCTATATGGACACA\n++\n+EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:21998:1542___1:N:0:TCCTGAGC+TACTCCTT;FP:15180;RQ:35.09\n+GGCGTCAGATGTGTATAAGAGACAGGG\n++\n+EEEEEEEAEEEEEEEEEEEEEEEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:2814:1550___1:N:0:TCCTGAGC+TACTCCTT;FP:0;RQ:1.56\n+NNNNNNNNNNNNNNNNNNNN\n++\n+####################\n+@NB500968:8:H5CFGAFXX:1:11101:8024:1581___1:N:0:TCCTGAGC+TACTCCTT;FP:38311;RQ:34.63\n+GTGACCCGCCGCTTCAGGGACCCGCTTCTCTCATCTTCCCCAAAGTTCTGGACAGATGAT\n++\n+EEEEEEEAEEEEEAEAEEEEEEEEEEAEEEEAEEEAEAEEEEEEEEAEEEEEEEEEE/A<\n+@NB500968:8:H5CFGAFXX:1:11101:8843:1628___1:N:0:TCCTGAGC+TACTCCTT;FP:44455;RQ:34.63\n+GGCGTTCAGCCACCCGAGATTGAGCAATAACAGGTCTGTGATGCCCTTAGATGTCCGGGG\n++\n+EEEEEEEEEAEAEEEE'..b'TCTA\n++\n+EEEEEEAEAEEEE/EEEAEEEEA/EEEEAEA/EA<EAAAEEAE<AE/A<<EEEA<<EEA<\n+@NB500968:8:H5CFGAFXX:1:11101:20373:2751___1:N:0:TCCTGATC+TACTCCTT;FP:283;RQ:34.93\n+GGAGCGTCAGATGTGTATAAGAGACAGCCCTATACAGTGATC\n++\n+EEEEEEEEE<EEEEAEAEEEEEEEEEEEEEE/EEEEEE<EAA\n+@NB500968:8:H5CFGAFXX:1:11101:21204:2795___1:N:0:TCCTGAGC+TACTCCTT;FP:16279;RQ:34.81\n+AGCGTCAGATGTGTATAAGAGACAGCTCCACCCTATAGGCCCTAACTG\n++\n+EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:10694:2817___1:N:0:TCCTGAGC+TACTCCTT;FP:10036;RQ:34.83\n+GGAGCGTCAGATGTGTATAAGAGACAGCCCTTCCCTATACGCTTGGCC\n++\n+EEEEEEEEEEEEE<EEEEAEEEEEEEEEE/A<E<EEEA/EEEAEEEE/\n+@NB500968:8:H5CFGAFXX:1:11101:8407:2853___1:N:0:TCCTGAGC+TACTCCTT;FP:21171;RQ:34.62\n+AGAGGGACAAGTGGCGTTCAGCCACCCGAGATTGAGCAATAACAGGTCTGTGATGCCCTT\n++\n+/EEEEEEAEEEEEAEEEEEEEEEAEAEEAAEEEE/EEEAAAEA//EEEAEAAA/EAEAE6\n+@NB500968:8:H5CFGAFXX:1:11101:17699:2880___1:N:0:TCCTGAGC+TACTCCTT;FP:52710;RQ:34.62\n+CTTTGGAATCTTCACAAGCAGAACCAGTCAAAACCCCGGCAAGCACAAAGAGACTCTCCA\n++\n+EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE<EEEEEEEEEEE6AEAEAEEEEA\n+@NB500968:8:H5CFGAFXX:1:11101:2261:2941___1:N:0:TCCTGAGC+TACTCCTT;FP:2596;RQ:34.63\n+GGCAGCATCAGATGTGTATAAGAGACAGAAGGAGCAGAGAGCGGCCAGCAACCGATGAGA\n++\n+EEEEEEEEEEEEEEAEEEAEEEEE///////EA//E/E/A/////E<EE//</E<<////\n+@NB500968:8:H5CFGAFXX:1:11101:11672:2944___1:N:0:TCCTGAGC+AACTCCTT;FP:32501;RQ:34.63\n+GGGTGAAATACTGTGAGGAACCCAGAAGTGAGTGGAAAGATAACTGGCTTTTTTTTTTTT\n++\n+AEEEEEEEEEEEAAAEEEEEAA<E/EEEEEEEAAEAEEEE<EEE<</EE6AA/6/<66//\n+@NB500968:8:H5CFGAFXX:1:11101:15968:2945___1:N:0:TCCTGAGC+TACTCCTT;FP:8706;RQ:34.63\n+GCAAATCGGTCGTCCGACCTGGGTATAGGGGCGAAAGGCTAATCGAACCATCTAGTAG\n++\n+EEEEEEEAEEEEEEEEEEEEEEEEAEEEEEEAEEEEE<EEEEAAEAEEAE<AEAEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:25690:2959___1:N:0:TCCTGCGC+TACTCCTT;FP:27004;RQ:34.81\n+AGCGTCAGATGTGTATAAGAGACAGGCCTCCCCTATAGCTTCGGA\n++\n+AE6EEEEEEEEEAAEEEEEEEEEEEEEEAEE/E/EAEEEEAEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:8090:2972___1:N:0:TCCTGAGC+TACTCCTT;FP:12902;RQ:34.81\n+CAACGTCAGATGTGTATAAGAGACAGGGACCCCCTATAATTTATGCC\n++\n+EEEEEEEEEEEEEEEEEAAEEEEEEEEEAEE<EEEEEAE<EEEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:22125:3141___1:N:0:TCCTGAGC+TACTCCTT;FP:65197;RQ:35.07\n+AGCGTCAGATGTGTATAAGAGACAGCTC\n++\n+EEEEEEEEEEEEEEEEEEEEEEEAEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:6707:3162___1:N:0:TCCTGAGC+TACTCCTT;FP:0;RQ:1.56\n+NNNNNNNNNNNNNNNNNNNN\n++\n+####################\n+@NB500968:8:H5CFGAFXX:1:11101:24232:3202___1:N:0:TCCTGAGC+TACTCCTT;FP:19483;RQ:34.63\n+GTTGGTTTTCGGAACTGAGGCCATGATTAAGATGGACGGCCGGGGGCATTCGTATTGCG\n++\n+EEEEEEEEEEAEEEEEEE/E<EEEEEA</EEE/A/EE<E666<EEAEEEE/6/A66/66\n+@NB500968:8:H5CFGAFXX:1:11101:16936:3211___1:N:0:TCCTGAGC+TACTCCTT;FP:7401;RQ:34.83\n+GAGCGTCAGATGTGTATAAGAGACAGTGCGTCCCTATAAAAGTGAACTG\n++\n+EEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEA/EEEAEAEEE\n+@NB500968:8:H5CFGAFXX:1:11101:6680:3212___1:N:0:TCCTGAGC+TACTCCTT;FP:62506;RQ:34.81\n+TCCAGCGTCAGATGTGTATAAGAGACAGCTCCTCCCTATAAG\n++\n+EEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:6132:3257___1:N:0:TCCTGAGC+TACTCCTT;FP:7557;RQ:34.62\n+CGTCAGATGTGTATAAGAGACAGCATTCCCCTATACACGCCTCCTGTCTCTTATAC\n++\n+EEEEAEEEEEEEEEEEEEEAEAEEAEEEEAEEEEEEEEEEEEEEEEAE/EEEEEEA\n+@NB500968:8:H5CFGAFXX:1:11101:3840:3285___1:N:0:TCCTGAGC+TACTCCTT;FP:16156;RQ:34.93\n+GGGAGCGTCAGATGTGTATAAGAGACAGGTATACCCTATAG\n++\n+EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:2858:3312___1:N:0:TCCTGAGC+TACTCCTT;FP:14452;RQ:35.12\n+AACGTCAGATGTGTATAAGAG\n++\n+EE/AE/E/EAAEEEEEEEAEE\n+@NB500968:8:H5CFGAFXX:1:11101:3641:3398___1:N:0:TCCTGAGC+TACTCCTT;FP:36051;RQ:35.14\n+GCAGCGTCAGATGTGTATAAGAG\n++\n+EEEEEEEEEEEEEEEEEEEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:20540:3401___1:N:0:TCCTGAGC+TACTCCTT;FP:48603;RQ:34.81\n+AGCGTCAGATGTGTATAAGAGACAGATCAACCCTATATGCCCTAACTG\n++\n+E/E///E/E</A/EEA<E/E/EEE/E</E///A/E6<E/A/<E/EEE/\n+@NB500968:8:H5CFGAFXX:1:11101:19438:3463___1:N:0:TCCTGAGC+TACTCCTT;FP:0;RQ:1.56\n+NNNNNNNNNNNNNNNNNNNN\n++\n+####################\n+@NB500968:8:H5CFGAFXX:1:11101:4772:3477___1:N:0:TCCTGAGC+AACTCCTT;FP:61788;RQ:3.33\n+TAACTGTCTCTTATACACCN\n++\n+EEEEEEEAEEEAEEE<EEE#\n' |
| b |
| diff -r 000000000000 -r 40c86e14b674 test-data/read1_un.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/read1_un.fq Mon May 09 04:08:01 2016 -0400 |
| b |
| @@ -0,0 +1,72 @@ +@NB500968:8:H5CFGAFXX:1:11101:24482:1380 1:N:0:TCCTGAGC+TACTCCTT;RQ:0.00 +GTGTATAAGAGACAGGCCTAATATATAGGGGGCGCCAGTCCTCCGATTGACTGAGTCGCCCGGGTACCCGTGTAT ++ +AAAAAEE/E/E/<EEEE/EAEE<EEEEEEEEEEEEEAEEA/E/EAEEEEEEEEEEEEEEE<E/EE<<6EEAEEEE +@NB500968:8:H5CFGAFXX:1:11101:2671:1393 1:N:0:TCCTGAGC+TACTCCTT;RQ:0.15 +GGTCCCCTATAAGGGGATTCTGTCTCTTATACCNN ++ +///AA6E/6AA///EAE//E6E6E6E/6AAE/E## +@NB500968:8:H5CFGAFXX:1:11101:7850:1487 1:N:0:TCCTGAGC+TACTCCTT;RQ:0.68 +ATTCCAATATAGGGGACCCACATCTTCCTCTGCTTCTAGATGAAGGATGTATTCTTCTTCCTCTTCTTCCTCTG ++ +AAAAAEEE/EEE/EEEEEEAAEEE/EEEEEAEEEEEEEEEEEEEEAEAE6EEA<EEEAEE<6E/<EE<<E6E/< +@NB500968:8:H5CFGAFXX:1:11101:13010:1719 1:N:0:TCCTGAGC+TACTCCTT;RQ:0.00 +AAGACAGTGTGATTATATAGGGGACAGCGTCAGATGTGTATAAGAGACAGCTAAGCCCTATACGTTTTTTC ++ +/A/AAEAAEEEE/E/EAEAAEE</EEEEEEAEEEEAAEAAAEAEEEAEEEEE/EE/EEE6A/EEEAEEEEA +@NB500968:8:H5CFGAFXX:1:11101:15935:1725 1:N:0:GCCTGAGC+TACTCCTT;RQ:0.00 +GTGTATAAGAAACAGGCTTTATATAGGGGCACCGTCAGATGTGTATAAGAGACAGTTGTCCCCTATACCACGC ++ +/AAAAEEEEAEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE/E<<EEEEE/EE<EEEE/AEEEEEEEAEEE +@NB500968:8:H5CFGAFXX:1:11101:12108:1890 1:N:0:TCCTGAGC+TACTCCTT;RQ:0.02 +CAGTTAGGTGTTATAGGGATCCCAAGACAAGGTTTCTCTGTGTCTATCCCTGGCTGTCCTTGAACTTCGGCAT ++ +6AAAA66EAE6EEEEEAE/EAAEEE/EEEEAEEEEEE/EEEEE/EAEEE/E/EAEEE<<EE/EAEEE6/EEE< +@NB500968:8:H5CFGAFXX:1:11101:6961:1984 1:N:0:TCCTGAGC+TACTCCTT;RQ:17.82 +GGATGTCGCTATAGGGCGCCGCCGCCTCCTCCTCCTCTCTCGCGCTCTCTGTCCCGCCTGGTCCTGTCCCACCC ++ +AAAAAAEEEEEEEEEEEEEAEAAEEE</EEEE/EEEEEEAEEEAAEEEEEEEEEEEEEEAEEEAEEEEAE/EEE +@NB500968:8:H5CFGAFXX:1:11101:20646:1998 1:N:0:TCCTGAGC+TACTCCTT;RQ:0.00 +CCGCAAGTGCGTTCGAAGTGTCGATGATCAATGTGTCCTGCAATTCACATTAATTCTCGCAGCTAGCTGCGTT ++ +AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEAEEEEEEAEEEEEEEEEEEEEEEEAAEE +@NB500968:8:H5CFGAFXX:1:11101:19922:2125 1:N:0:TCCTGAGC+TACTCCTT;RQ:0.08 +GTATAAGAGACAGCGATACTTTATAGGGGGGCCGTGTGCAGACCCGCGTGTGGCGCAGGCAAGGACCCTGAAAAT ++ +AAAAAEE/EAEEEEEEEEEEEEEEEE/EEEEEEEEAEEEEEEEEEEEEAEEA<<EEEEEEEEEEEEEEEEEEEA< +@NB500968:8:H5CFGAFXX:1:11101:14935:2297 1:N:0:TCCTGAGC+TACTCCTT;RQ:0.05 +GATGTGCATAAAAGACAGATAGTACGTATAGGGGGGAGCGTCAGATGTTTATAAGAGACAGAATCGCCCTATAG ++ +AAAAAAAEEAEEEEEEEEEEEEEEEEEEEEEEEAEEEEEAE/A/EEAE/E/6/E///E/E/</E///A/AA/</ +@NB500968:8:H5CFGAFXX:1:11101:13250:2472 1:N:0:TCCTGAGC+TACTCCTT;RQ:0.00 +GTCTCCGCCCTTGCTGACTTTCCATCATTTTTAAGATCAGGTGGAACTGGAGCCTCTGCCTGTGGCTGATCTGAG ++ +AAAAAEAA/EAA<EEEEE/EEAAEEAE<EEA/E//EE/E/EEAAEEEEA6A/6EAA6/6<6/<//A/<AAE6AA/ +@NB500968:8:H5CFGAFXX:1:11101:8485:2792 1:N:0:TCCTGAGC+TACTCCTT;RQ:0.00 +CGTCAGATGTGGTCCCGCTCACCATGCCGCTGCTGTAGCCGCTCACCAACCTCCTGTGCCCCCCGCAACTCAT ++ +AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEE6EEEEEEEEEEEEEEEEEEEEEEEE +@NB500968:8:H5CFGAFXX:1:11101:23310:3069 1:N:0:TCCTGAGC+TACTCCTT;RQ:0.02 +CAGGCCAATCGTATAGGGGTTGATACTCAAGTCTACTTGTTCCCTTTTATTTAATCCTGAACCCCATCCCATGGA ++ +AAA/AEEEEEEEAE//EEE////EAA//EE/EEEEEE//EEE/E/E/EEEEEEE<A<E/AEE//AE/<AAEEEE/ +@NB500968:8:H5CFGAFXX:1:11101:9254:3110 1:N:0:TCCTGAGC+TACTCCTT;RQ:0.00 +TGTTATAAGGCGTCAGATGTGTATAAGAGACAGGGATCCCCTATAAAGAGCCTAAC ++ +AAAAAEEEEEEEEEEEEEEEEEEEAEEEE<EAEEE/EEEEEEEEE/EEEEEEEAA/ +@NB500968:8:H5CFGAFXX:1:11101:4099:3187 1:N:0:TCCTGAGC+TACTCCTT;RQ:0.00 +GTATAAGAGACAGCCAGCCTCTATAGGGGTGCTTGCAGGGGAGGGAAAAGGGGGAAAGCGGGCAACCAGTTTCC ++ +AAAAAAEAE6E6EEEEEAEEA<EEEEEEEEEEEEEEEEEEEEEEEEEEAEE/EEAEEEEEEEEEEEEEAE/E// +@NB500968:8:H5CFGAFXX:1:11101:15733:3232 1:N:0:TCCTGAGC+TACTCCTT;RQ:0.15 +TCCCCTATATTTGGGGACTGTCTCTTATACACCNN ++ +AAAAAEEE/EEEEEEEEEEEEEEEEEEEEEEEE## +@NB500968:8:H5CFGAFXX:1:11101:3009:3242 1:N:0:TCCTGAGC+TACTCCTT;RQ:0.00 +GGTTAAGGCTAGCCTATTCTACATAGAGTGTTCTAGGCCTTCCAGGGCCACATAGACTCTTGTTTCAAAAAAAT ++ +A//AAEEEEEEEEEEEAEE/EEEEAAEE/AAEEEAEEEEAEEEEAEEEEEEEEEEEEEEA6EEEE<EEE/A/EA +@NB500968:8:H5CFGAFXX:1:11101:18503:3442 1:N:0:TCCTGAGC+TACTCCGT;RQ:0.07 +TAATCCCTATAAGGGATTACTGACTCTTATACATGTATCTAATACACATCTCCGAGCCCACGAGACTCCTGAGCA ++ +AAAAAE/AAEEEEEEAAE/E//////EEAA///A/E/<///AEEEE/E/EE<<///E<EEE/E/AE6/EEEE//6 |
| b |
| diff -r 000000000000 -r 40c86e14b674 test-data/read2_extracted.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/read2_extracted.fastq Mon May 09 04:08:01 2016 -0400 |
| b |
| b'@@ -0,0 +1,328 @@\n+@NB500968:8:H5CFGAFXX:1:11101:15939:1071___1:N:0:TCCTGAGC+TACTCCTT;FP:23586;RQ:34.63\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n++\n+###################################\n+@NB500968:8:H5CFGAFXX:1:11101:1121:1139___1:N:0:TCGTGAGC+TACTCCTT;FP:27828;RQ:34.83\n+GATGTAGACTATAGGGAATACCNNNNNNNNNNNNN\n++\n+A6AAAEEEEEEEEEEEAEE/E<#############\n+@NB500968:8:H5CFGAFXX:1:11101:7529:1175___1:N:0:TCCTGAGC+TACTCCTT;FP:17358;RQ:34.81\n+GATGTGTAAAAGAGACAGAGGATAATTATAGGGATCCTGTCTCTAAAACACATCTGACGCTCCCTATACATAATA\n++\n+/AAAAE<A/E//EEE/EE//EEEEAEEEEEEEEEE/A/<EEE<<///<AE</AE//AAA//E/////EEE<6/A/\n+@NB500968:8:H5CFGAFXX:1:11101:5052:1198___1:N:0:TCCTGAGC+TACTCCTT;FP:38799;RQ:34.63\n+GGATTGAGGCTAGAAACAGCTGCTTTTCTCACTTTCCCAGCAGCAAGACATCAATCTGTTGAGACCTCTCATTTT\n++\n+AA6AAEEAEEEEEEEEAAEEEEE///AEEA/<E/E<A//EEEEAE/EE//AE///E</EAEEA<EEEAEE/E/E/\n+@NB500968:8:H5CFGAFXX:1:11101:15805:1205___1:N:0:TCCTGAGC+TACTCCTT;FP:44542;RQ:34.63\n+GCGTCAGATGTGGGTAGTCAGAAAAGCAGATGGATGGGGGCCTTGCCCAACCAGATCCAGGCCGAGTTCACCT\n++\n+AAAAAEEAEEEEEEEEEEEEEEA//EEEEEEEEEEEEEEEEEEAEE/E//EEEEAEAE/EEEEE<EEEEEEEA\n+@NB500968:8:H5CFGAFXX:1:11101:11834:1217___1:N:0:TCCTGAGC+TACTCCTT;FP:56795;RQ:34.81\n+GGGTCGCTATATAGGGGAATCCNNNNNNNNNNNNN\n++\n+AAAAAEEEEEEEEEEEEEAEEE#############\n+@NB500968:8:H5CFGAFXX:1:11101:20105:1230___1:N:0:TCCTGAGC+TACTCCTT;FP:2265;RQ:34.63\n+GTACACGTATTACTTCTGTTTGGTGAATTAAATAAAACAATTCCTAAGCAACTCAAAAGTAACCTAAAAATTGCA\n++\n+AA/A//EEE/EAEEEEEEE/EEEAEE6EEE<EEA<6E//E/EEAEE//EE/EEE<EAEE6</EEEEE/A/EEE/A\n+@NB500968:8:H5CFGAFXX:1:11101:14524:1264___1:N:0:TCCTGAGC+TACTCCTT;FP:7937;RQ:2.65\n+GTATAAGAGACAGTTGGGACTTATAGGGTAAGTCN\n++\n+AAAAAEEEAEEEEAEEE/EEEEEAE<EE/EEEEE#\n+@NB500968:8:H5CFGAFXX:1:11101:14981:1265___1:N:0:TCCTGAGC+TACTCCTT;FP:26333;RQ:34.63\n+GGACTTAATCAACGCAAGCTTATGACCCGCACTTACTGGGAATTCCTCGTTCATGGGGAATAATTGCAATCCCCG\n++\n+AA6AAEE/EE//EEE6EEEEEEEE/AAEEAEEEE/EEEEEAEEEE/EEEEEEEEEEEE/AEE<EEEEEEEEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:5538:1286___1:N:0:TCCTGAGC+TACTCCTT;FP:5079;RQ:34.62\n+ATCACCAAGCTCGTTAGGCTTTTCACCTCTACCTAAAAATCTTCTCACTATTTTGCCACATAGACGAGTTGATT\n++\n+AAA/AEE/EEEEEEEAEEEEEEEE/EEEEE/EEEA</EEEEEEEEAAAEAEEEEE<EAE6EEEEEEEEEEEEAE\n+@NB500968:8:H5CFGAFXX:1:11101:11473:1333___1:N:0:TCCTGAGC+TACTCCTT;FP:48246;RQ:35.03\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n++\n+###################################\n+@NB500968:8:H5CFGAFXX:1:11101:2141:1369___1:N:0:TCCTGAGC+TACTCCTT;FP:0;RQ:1.56\n+GATGTGTATAAGAAACAGACCACATATATAGGGGGGAGCGTCAGATGTGTATAAGAGACAGCCCCCCCCAATAGA\n++\n+AAAAAEEEEEEEAEEEEE/E/EAEEEEEAEEEA/EEEEEEEAA//AEEEE/</AA/////////AAEE////AA/\n+@NB500968:8:H5CFGAFXX:1:11101:19474:1422___1:N:0:TCCTGAGC+TACTCCTT;FP:5233;RQ:35.03\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n++\n+###################################\n+@NB500968:8:H5CFGAFXX:1:11101:12411:1441___1:N:0:TCCTGAGC+TACTCCTT;FP:46039;RQ:34.83\n+GACAAAATATAGGGGGACTGTCTGTTATAGACGTCGGACGCGCGCCCCTATAAGGAATAGGGGTCTCTGAGAGA\n++\n+A/////E////////A///E/E///EEE///A//A/A//<///////E/////AEA//////////////////\n+@NB500968:8:H5CFGAFXX:1:11101:5889:1458___1:N:0:TCCTGAGC+TACTCCTT;FP:52002;RQ:34.83\n+CAGCGAAGGGGTATAGGGATACGNNNNNNNNNNNN\n++\n+A/AAA//EEEEA/A/EEE////E############\n+@NB500968:8:H5CFGAFXX:1:11101:8662:1469___1:N:0:TCCTGAGC+TACTCCTT;FP:62135;RQ:35.03\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n++\n+###################################\n+@NB500968:8:H5CFGAFXX:1:11101:9851:1471___1:N:0:TCCTGAGC+TACTCCTT;FP:43356;RQ:3.17\n+GTATAAGAGACAGGGGCCCGTTAAAGGGCCCNNNN\n++\n+/A6<//EA//E/E/A/EEE/E/E/E/6EEE/####\n+@NB500968:8:H5CFGAFXX:1:11101:5425:1488___1:N:0:TCCTGAGC+TACTCCTT;FP:13390;RQ:34.83\n+GTATAAGAGACAGTGTGTCCATATAGGGGAGTCNN\n++\n+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEE##\n+@NB500968:8:H5CFGAFXX:1:11101:21998:1542___1:N:0:TCCTGAGC+TACTCCTT;FP:15180;RQ:35.09\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n++\n+###################################\n+@NB500968:8:H5CFGAFXX:1:11101:2814:1550___1:N:0:TCCTGAGC+TACTCCTT;FP:0;RQ:1.56\n+CCGTCAGATGAGTATAAGAGACAGGTAAGACATAAAGAGCGTAGTTGTCTCTAATACACATCTGACGCTGCCGA\n++\n+/AAA6AEEE//E/EAAEE6/EEEEEEEE//EE/E/EE/AE/<A//</AE/E////AE<A/<A/6/E<EEAAEEE\n+@NB500968:8:H5CFGAFXX:1:11101:8024:1'..b'2795___1:N:0:TCCTGAGC+TACTCCTT;FP:16279;RQ:34.81\n+CAGTTAGGGCCTATAGGGTGGAGCNNNNNNNNNNN\n++\n+AAA<AEEEEEEEEEEEEEEEEEEE###########\n+@NB500968:8:H5CFGAFXX:1:11101:10694:2817___1:N:0:TCCTGAGC+TACTCCTT;FP:10036;RQ:34.83\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n++\n+###################################\n+@NB500968:8:H5CFGAFXX:1:11101:8407:2853___1:N:0:TCCTGAGC+TACTCCTT;FP:21171;RQ:34.62\n+CACTTACTGGGAATTCCTCGTTCATGGGGAATAATTGCAATCCCCGATCCCCATCACGGATGGGGTTCAACGGGT\n++\n+AAA6AEEEEEEE/EE/EEEEEEEEEEEEEEA6EEEEEEEE<EEEE</EEEAEEEEAEEEEEEEEAEEEE/EAEEA\n+@NB500968:8:H5CFGAFXX:1:11101:17699:2880___1:N:0:TCCTGAGC+TACTCCTT;FP:52710;RQ:34.62\n+CATCTGACGCAGCCGACGAAAAAACATGTGTAGATCTCTGACTTCTCAGTATCATTAAATAAAAAAAATTGATGG\n++\n+AAAAAEEEEE/EEEEEEE6EEA//<<EEEE//E//EEEAE///E/6///E/EA/EA//////66A//<6A///AA\n+@NB500968:8:H5CFGAFXX:1:11101:2261:2941___1:N:0:TCCTGAGC+TACTCCTT;FP:2596;RQ:34.63\n+CTCTTATACACATCTGATGCTGCCCCCTATATGCTCCTT\n++\n+A/AAAEAEE/E/AEEEEEEEEEEEEEE/E/A<EEEEE//\n+@NB500968:8:H5CFGAFXX:1:11101:11672:2944___1:N:0:TCCTGAGC+AACTCCTT;FP:32501;RQ:34.63\n+AAAACCCTAACTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n++\n+A/AA<//6/6//////66666666/6///AEE//EE/</AE</E/<EEEAEEEEEA////<EEE/E<E<A///<6\n+@NB500968:8:H5CFGAFXX:1:11101:15968:2945___1:N:0:TCCTGAGC+TACTCCTT;FP:8706;RQ:34.63\n+GATGTGGCGTCGGCATCGGGCGCCTTAACCCGGCGTTCGGTTCATCCCGCAGCGCCAGTTCTGCTTACCAAAAGT\n++\n+AAAA/EEEEEEEEEAEEEEEEE/EEEEAEEEEEEEEEEEEEAEEE<<EEA<AEE//AAA<EAA/EEEEEEEEEE<\n+@NB500968:8:H5CFGAFXX:1:11101:25690:2959___1:N:0:TCCTGCGC+TACTCCTT;FP:27004;RQ:34.81\n+GTGTATAAGAGACAGTCCGAAGCTATAGGGGCGGC\n++\n+A/AA/EEEEEE/6EEE//E//6EEEAAE/EE/EEE\n+@NB500968:8:H5CFGAFXX:1:11101:8090:2972___1:N:0:TCCTGAGC+TACTCCTT;FP:12902;RQ:34.81\n+GGCATAAATTATAGGGGGTCCCNNNNNNNNNNNNN\n++\n+AAAAAEEEEEEEE6EAEEEEAE#############\n+@NB500968:8:H5CFGAFXX:1:11101:22125:3141___1:N:0:TCCTGAGC+TACTCCTT;FP:65197;RQ:35.07\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n++\n+###################################\n+@NB500968:8:H5CFGAFXX:1:11101:6707:3162___1:N:0:TCCTGAGC+TACTCCTT;FP:0;RQ:1.56\n+GCGTAAGAAAAATATAAAACACACTTAAACTCAATAAGTCCATAAATACTATTAAACACAAAAAAAGCATCCAAA\n++\n+///A/A/E</</EA<///A//<//E/EE//6EA/<//A/</6E//6//<///<//A6<<A/AA//////////</\n+@NB500968:8:H5CFGAFXX:1:11101:24232:3202___1:N:0:TCCTGAGC+TACTCCTT;FP:19483;RQ:34.63\n+TGATTAATGAAAACATTCTTGGCAAATGCTTTCGCTCTGGTCCGTCTTGCGCCGGTCCAAGAATTTCACCTCTAG\n++\n+AA/AAE/AA/E6/E/EEA<AAEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEA6AAEE/E/EEEEA<EAEE\n+@NB500968:8:H5CFGAFXX:1:11101:16936:3211___1:N:0:TCCTGAGC+TACTCCTT;FP:7401;RQ:34.83\n+CAGTTCACTTTTATAGGGACGCACNNNNNNNNNNN\n++\n+AAAAAEEEEEEEEEEEEEEEEEEE###########\n+@NB500968:8:H5CFGAFXX:1:11101:6680:3212___1:N:0:TCCTGAGC+TACTCCTT;FP:62506;RQ:34.81\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n++\n+###################################\n+@NB500968:8:H5CFGAFXX:1:11101:6132:3257___1:N:0:TCCTGAGC+TACTCCTT;FP:7557;RQ:34.62\n+GTATAAGAGACAGGAGGCGTGTATAGGGGAATGCN\n++\n+AAAAAEEEEEEEEEEEEEEEEEEEAEEEE6EEEE#\n+@NB500968:8:H5CFGAFXX:1:11101:3840:3285___1:N:0:TCCTGAGC+TACTCCTT;FP:16156;RQ:34.93\n+CAATAGGGTATACCTGTCACTAATACACATCAGACGCTCCCCCCTATATAGTAAAT\n++\n+A/AAAE//EE/EEAE//E/EE/EEEEEEEEE/EEEAEEEE<A<A/</AE<EEAE<6\n+@NB500968:8:H5CFGAFXX:1:11101:2858:3312___1:N:0:TCCTGAGC+TACTCCTT;FP:14452;RQ:35.12\n+CTCTTATACACATCTGACGTTCCCTATATGAGTCAT\n++\n+/AAAAEEAEEEEEEEEEEEEEEEEEAEEEEEEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:3641:3398___1:N:0:TCCTGAGC+TACTCCTT;FP:36051;RQ:35.14\n+CTCTTATACACATCTGACGCTGCCCCTATAATGATATC\n++\n+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:20540:3401___1:N:0:TCCTGAGC+TACTCCTT;FP:48603;RQ:34.81\n+CAGTTAGGGCAAAAAGGGTTGATNNNNNNNNNNNN\n++\n+AAAA//EEAE6/E//AAA//EEE############\n+@NB500968:8:H5CFGAFXX:1:11101:19438:3463___1:N:0:TCCTGAGC+TACTCCTT;FP:0;RQ:1.56\n+GCGTCGAGATGTGTATAAGAGACAGCCGAGCTCTATAGGGCAAGT\n++\n+AAAAAEEEEEEEEEEE<AEEEEEEEEEEEEEEEEEEEEEAEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:4772:3477___1:N:0:TCCTGAGC+AACTCCTT;FP:61788;RQ:3.33\n+GTTTATAATAGACACATAACAATAAAAGAGTAACAATCACAAAAAAAAATAAGACTCTCACGACGAAACACCTTA\n++\n+A//A/E//E/A/E/A/E//A<E/////E/E//AE////E/AE</////EEA/E/A/E//AE/E///<<///A<A/\n' |
| b |
| diff -r 000000000000 -r 40c86e14b674 test-data/with_b_BC_AAC.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/with_b_BC_AAC.fq Mon May 09 04:08:01 2016 -0400 |
| b |
| @@ -0,0 +1,24 @@ +@NB500968:8:H5CFGAFXX:1:11101:19474:1422 1:N:0:TCCTGAGC+TACTCCTT;RQ:1.20 +ACTACTATAGGGGGAGCGTCAGATGTGTATAAGAGACAGGTACCC ++ +AAEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEE +@NB500968:8:H5CFGAFXX:1:11101:24842:1887 1:N:0:TCCTGAGC+TACTCCTT;RQ:1.02 +CTATATATAGGGGGGAGCGTCAGATGTGTATAAGAG ++ +AAEEAEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEE +@NB500968:8:H5CFGAFXX:1:11101:16709:1904 1:N:0:TCCTGAGC+TACTCCTT;RQ:1.18 +GAGCTTATAGGGGTTCCATGCGTCAATGTTTCTTCTGGATACAGCAGGCCTGTTCCCGGGAGTCAATGC ++ +AAEEEEEEEEEAEEEEEAEEEEEEEEEEAEEEEEEEEEEEAEE6<EEEEEAAA<EAEEEEEEEEEEE<E +@NB500968:8:H5CFGAFXX:1:11101:5814:2162 1:N:0:TCCTGAGC+TACTCCTT;RQ:1.18 +GCTCTTATAGGGGCCCTTGGCTTCACCACACTTTCTACTGGAAATGTGCCTTTTCCTCCATTGCTGCTAC ++ +AAEEEA/EE/E/EEEEEEEEEEEEEEEAAEEEAEEEEEA/EEEEEE<EEEAEAAEEAEEE<AAEAEEAAE +@NB500968:8:H5CFGAFXX:1:11101:24405:2351 1:N:0:TCCTGAGC+TACTCCTT;RQ:1.21 +CTATATATAGGGTCTGTCTCTTATACCNNNNN ++ +AAEEEAEEEEEEEEEEEEAEEEEEEEE##### +@NB500968:8:H5CFGAFXX:1:11101:20373:2751 1:N:0:TCCTGATC+TACTCCTT;RQ:1.15 +CACGTTATAGGGGGAGCGTCAGATGTGTATAAGAGACAGCCCTATACAGTGATC ++ +AAEEEEEEEEEEEEEEEEEEE<EEEEAEAEEEEEEEEEEEEEE/EEEEEE<EAA |
| b |
| diff -r 000000000000 -r 40c86e14b674 test-data/with_b_BC_GTA.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/with_b_BC_GTA.fq Mon May 09 04:08:01 2016 -0400 |
| b |
| @@ -0,0 +1,16 @@ +@NB500968:8:H5CFGAFXX:1:11101:11473:1333 1:N:0:TCCTGAGC+TACTCCTT;RQ:1.18 +ACTCGTATAGGGGACAGCGTCAGATGTGTATAAGAGACAGGGTATC ++ +AAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE +@NB500968:8:H5CFGAFXX:1:11101:12411:1441 1:N:0:TCCTGAGC+TACTCCTT;RQ:11.24 +TTCCTTATAGGGGGGAGCGTCAGATGTGTATAAGAGACAGTCTCCCTATATTTTGGC ++ +AA//AEEEEEEE//AEEE/EAEAEE/AEAE<EEEEAE/EAE<E/E</EEEE/6E/EE +@NB500968:8:H5CFGAFXX:1:11101:19922:2125 1:N:0:TCCTGAGC+TACTCCTT;RQ:11.21 +TAAGAGACAGCGATACTTTATAGGGGGGCCGTGTGCAGACCCGCGTGTGGCGCAGGCAAGGACCCTGAAAAT ++ +AAEE/EAEEEEEEEEEEEEEEEE/EEEEEEEEAEEEEEEEEEEEEAEEA<<EEEEEEEEEEEEEEEEEEEA< +@NB500968:8:H5CFGAFXX:1:11101:4099:3187 1:N:0:TCCTGAGC+TACTCCTT;RQ:11.21 +TAAGAGACAGCCAGCCTCTATAGGGGTGCTTGCAGGGGAGGGAAAAGGGGGAAAGCGGGCAACCAGTTTCC ++ +AAAEAE6E6EEEEEAEEA<EEEEEEEEEEEEEEEEEEEEEEEEEEAEE/EEAEEEEEEEEEEEEEAE/E// |
| b |
| diff -r 000000000000 -r 40c86e14b674 test-data/with_b_un.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/with_b_un.fq Mon May 09 04:08:01 2016 -0400 |
| b |
| b'@@ -0,0 +1,360 @@\n+@NB500968:8:H5CFGAFXX:1:11101:15939:1071 1:N:0:TCCTGAGC+TACTCCTT;RQ:0.00\n+CCTAAGAGTATAGGGGGCACGTCAGATGAGTATAAGAGACAGCAAATAGGTATAGGGGGCACGTCAGATGAGTAA\n++\n+AAAAA6/AEEEEEEEEAEEEEEEA///A/EAEEE/EAEEEEEEEEEEAEEE//E/AA/E6AE/EE/<E////A//\n+@NB500968:8:H5CFGAFXX:1:11101:1121:1139 1:N:0:TCGTGAGC+TACTCCTT;RQ:0.00\n+CGTAGTCATATAGGGGGAGCGTCAGATGTGTATAAGAGACAGGTATTCCCTATAGTCTACATC\n++\n+AAAAAEEEEAEE<EEEEEEEEEEEEEEEEEAAEEEEAEEEAEEE/EEE/EE<AAEEEEEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:7529:1175 1:N:0:TCCTGAGC+TACTCCTT;RQ:0.02\n+CAATTATGTATAGGGAGCGTCAGATGTGTATAAGAGACAGCAACCCTAAAAATATCCA\n++\n+AAAAAEA/EEEEEEEEEEE/EEEEEEA/EA<EEEE/AEEEE//E//6A/AE/A/AAE/\n+@NB500968:8:H5CFGAFXX:1:11101:5052:1198 1:N:0:TCCTGAGC+TACTCCTT;RQ:0.02\n+GCCTGATTTATAGGGGGTTTTTAGTGGCATTCATTGTGTGGATTCCTCTGTTGCTGCCCCTGGGCTAACAAGGGT\n++\n+AAAAAEEEEEEEE<AEEEEEEE6EEEEAEEEEEEEEEEEAEEEEEEEEEEEEEAAE/AEEEEEAAAEEEE/EAEE\n+@NB500968:8:H5CFGAFXX:1:11101:15805:1205 1:N:0:TCCTGAGC+TACTCCTT;RQ:0.02\n+GGTCTTTGTATAGGGGAGGGCCAGGCAGCTCAAAGCCTGAAGGAGGTACTTCAAGGAGGGTCCAGAGAAGCTGGG\n++\n+AAAAAEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEE<EAAEEEEEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:11834:1217 1:N:0:TCCTGAGC+TACTCCTT;RQ:0.00\n+TCTCTCGTTATAGGGAGCGTCAGATGTGTATAAGAGACAGGATTCCCCTATATAGCGACCC\n++\n+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEAEEEEEEEEEA<EAEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:20105:1230 1:N:0:TCCTGAGC+TACTCCTT;RQ:0.75\n+AAGATCGCTATAGGGGTTGTTTCATGTTGCAATTTTTAGGTTACTTTTGAGTTGCTTAGGAATTGTTTTATTTAA\n++\n+6AAAA//EEEAEAEEEEEEEEEEEE/E/AEEEEE<E</EEAEEEEEEAAEAEEEAAE//EA//</E6EAAEA/6/\n+@NB500968:8:H5CFGAFXX:1:11101:14524:1264 1:N:0:TCCTGAGC+TACTCCTT;RQ:0.02\n+ACTTAAACTATAAGTCCCAACTTAATATTATAAAATTATCATAAAAACAACTACGAGCCCACGATACAACTGATA\n++\n+AAAAA//EEE<EEEA//EEEE<///A/AAA/A////E/<///E/6/E/E/E6///E//6E<//6/AA//E//A//\n+@NB500968:8:H5CFGAFXX:1:11101:14981:1265 1:N:0:TCCTGAGC+TACTCCTT;RQ:0.02\n+CGCGTCTCTATAGGGGTCTGGTTAATTCCGATAACGAACGAGACTCTGGCATGCTAACTAGTTACGCGACCCCCG\n++\n+AAAAAEEEEEEE<EAEEEEEEEEEEEEEAEEEEEEEEEAAEEEEEEEA<EEEEEEEEE6/E66A<A/<AA<A//6\n+@NB500968:8:H5CFGAFXX:1:11101:5538:1286 1:N:0:TCCTGAGC+TACTCCTT;RQ:0.02\n+ACATTCCTTATAGGGAGTGAACTAACTAGAAAACTTCTAACTAAAAGAATTACAGCTAGAAACCCCGAAACCAAA\n++\n+6AAAAEEEEE<E</<AAEEEEEEEEAE/AEEEEEEEAEEEEE/AE6/EEA<E/EA6EAAEEE6//6<<EEA/<<A\n+@NB500968:8:H5CFGAFXX:1:11101:2141:1369 1:N:0:TCCTGAGC+TACTCCTT;RQ:0.83\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n++\n+################################\n+@NB500968:8:H5CFGAFXX:1:11101:24482:1380 1:N:0:TCCTGAGC+TACTCCTT;RQ:0.80\n+GTGTATAAGAGACAGGCCTAATATATAGGGGGCGCCAGTCCTCCGATTGACTGAGTCGCCCGGGTACCCGTGTAT\n++\n+AAAAAEE/E/E/<EEEE/EAEE<EEEEEEEEEEEEEAEEA/E/EAEEEEEEEEEEEEEEE<E/EE<<6EEAEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:2671:1393 1:N:0:TCCTGAGC+TACTCCTT;RQ:0.02\n+GGTCCCCTATAAGGGGATTCTGTCTCTTATACCNN\n++\n+///AA6E/6AA///EAE//E6E6E6E/6AAE/E##\n+@NB500968:8:H5CFGAFXX:1:11101:5889:1458 1:N:0:TCCTGAGC+TACTCCTT;RQ:0.01\n+TAGTAGAGTATAGGGGAGCGTCAGATGTGTATAAGAGACAGCGTATCCCTATACCCCTTCGCTG\n++\n+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:8662:1469 1:N:0:TCCTGAGC+TACTCCTT;RQ:0.85\n+TTAGGTCTTATAGGGGGAGCGTCAGATGTGTATAAGAGACAGGTTATC\n++\n+AAAAAEEEEEEEEEEEEEEEEEEEEEEEAEAE<AEAEEEEEEEEEE<E\n+@NB500968:8:H5CFGAFXX:1:11101:9851:1471 1:N:0:TCCTGAGC+TACTCCTT;RQ:0.01\n+GGGCCCTATAACGGGCCCCTGTCTCTTATACCNNN\n++\n+AAAA6EEEEEEEAEEEEEEEA/AA/EEEEE//###\n+@NB500968:8:H5CFGAFXX:1:11101:7850:1487 1:N:0:TCCTGAGC+TACTCCTT;RQ:0.02\n+ATTCCAATATAGGGGACCCACATCTTCCTCTGCTTCTAGATGAAGGATGTATTCTTCTTCCTCTTCTTCCTCTG\n++\n+AAAAAEEE/EEE/EEEEEEAAEEE/EEEEEAEEEEEEEEEEEEEEAEAE6EEA<EEEAEE<6E/<EE<<E6E/<\n+@NB500968:8:H5CFGAFXX:1:11101:5425:1488 1:N:0:TCCTGAGC+TACTCCTT;RQ:1.00\n+ATCACATGTATAGGGGGAGCGTCAGATGTGTATAAGAGACAGACTCCCCTATATGGACACA\n++\n+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:21998:1542 1:N:0:TCCTGAGC+TACTCCTT;RQ:0.01\n+ATGTCATATATAGGGGGCGTCAGATGTGTATAAGAGACAGGG\n++\n+AAAAA6EEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:2814:1550 1:N:0:TCCTGAGC+TACTCCTT;RQ:0.83\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n'..b'T;RQ:0.02\n+CTTGTTCCTATAGGGGGGTGAAATACTGTGAGGAACCCAGAAGTGAGTGGAAAGATAACTGGCTTTTTTTTTTTT\n++\n+AAAAAEAEEEEEE<AAEEEEEEEEEEEAAAEEEEEAA<E/EEEEEEEAAEAEEEE<EEE<</EE6AA/6/<66//\n+@NB500968:8:H5CFGAFXX:1:11101:15968:2945 1:N:0:TCCTGAGC+TACTCCTT;RQ:0.02\n+AGAGAAAGTATAGGGGCAAATCGGTCGTCCGACCTGGGTATAGGGGCGAAAGGCTAATCGAACCATCTAGTAG\n++\n+AAAAAEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEAEEEEEEAEEEEE<EEEEAAEAEEAE<AEAEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:25690:2959 1:N:0:TCCTGCGC+TACTCCTT;RQ:0.00\n+CGGCCTTATATAGGGAGCGTCAGATGTGTATAAGAGACAGGCCTCCCCTATAGCTTCGGA\n++\n+AAAA6EEE//6EEA/AE6EEEEEEEEEAAEEEEEEEEEEEEEEAEE/E/EAEEEEAEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:8090:2972 1:N:0:TCCTGAGC+TACTCCTT;RQ:0.80\n+ATAGCGCGTATAGGGCAACGTCAGATGTGTATAAGAGACAGGGACCCCCTATAATTTATGCC\n++\n+AAAAAEEEEEAEEEEEEEEEEEEEEEEEEEEEAAEEEEEEEEEAEE<EEEEEAE<EEEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:23310:3069 1:N:0:TCCTGAGC+TACTCCTT;RQ:0.02\n+CAGGCCAATCGTATAGGGGTTGATACTCAAGTCTACTTGTTCCCTTTTATTTAATCCTGAACCCCATCCCATGGA\n++\n+AAA/AEEEEEEEAE//EEE////EAA//EE/EEEEEE//EEE/E/E/EEEEEEE<A<E/AEE//AE/<AAEEEE/\n+@NB500968:8:H5CFGAFXX:1:11101:9254:3110 1:N:0:TCCTGAGC+TACTCCTT;RQ:0.00\n+TGTTATAAGGCGTCAGATGTGTATAAGAGACAGGGATCCCCTATAAAGAGCCTAAC\n++\n+AAAAAEEEEEEEEEEEEEEEEEEEAEEEE<EAEEE/EEEEEEEEE/EEEEEEEAA/\n+@NB500968:8:H5CFGAFXX:1:11101:22125:3141 1:N:0:TCCTGAGC+TACTCCTT;RQ:0.02\n+TTTGGGTCTATAGGGAGCGTCAGATGTGTATAAGAGACAGCTC\n++\n+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:6707:3162 1:N:0:TCCTGAGC+TACTCCTT;RQ:0.83\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n++\n+################################\n+@NB500968:8:H5CFGAFXX:1:11101:24232:3202 1:N:0:TCCTGAGC+TACTCCTT;RQ:0.02\n+CATAACGTTATAGGGGTTGGTTTTCGGAACTGAGGCCATGATTAAGATGGACGGCCGGGGGCATTCGTATTGCG\n++\n+AAAAAEEEEEAE///EEEEEEEEEEAEEEEEEE/E<EEEEEA</EEE/A/EE<E666<EEAEEEE/6/A66/66\n+@NB500968:8:H5CFGAFXX:1:11101:16936:3211 1:N:0:TCCTGAGC+TACTCCTT;RQ:0.02\n+ACTATGGCTATAGGGGAGCGTCAGATGTGTATAAGAGACAGTGCGTCCCTATAAAAGTGAACTG\n++\n+AAAAAEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEA/EEEAEAEEE\n+@NB500968:8:H5CFGAFXX:1:11101:6680:3212 1:N:0:TCCTGAGC+TACTCCTT;RQ:0.02\n+TTCAAGGGTATAGGGTCCAGCGTCAGATGTGTATAAGAGACAGCTCCTCCCTATAAG\n++\n+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:15733:3232 1:N:0:TCCTGAGC+TACTCCTT;RQ:0.02\n+TCCCCTATATTTGGGGACTGTCTCTTATACACCNN\n++\n+AAAAAEEE/EEEEEEEEEEEEEEEEEEEEEEEE##\n+@NB500968:8:H5CFGAFXX:1:11101:3009:3242 1:N:0:TCCTGAGC+TACTCCTT;RQ:0.02\n+GGTTAAGGCTAGCCTATTCTACATAGAGTGTTCTAGGCCTTCCAGGGCCACATAGACTCTTGTTTCAAAAAAAT\n++\n+A//AAEEEEEEEEEEEAEE/EEEEAAEE/AAEEEAEEEEAEEEEAEEEEEEEEEEEEEEA6EEEE<EEE/A/EA\n+@NB500968:8:H5CFGAFXX:1:11101:6132:3257 1:N:0:TCCTGAGC+TACTCCTT;RQ:0.03\n+ACTCGACCTATAGGGCGTCAGATGTGTATAAGAGACAGCATTCCCCTATACACGCCTCCTGTCTCTTATAC\n++\n+AAAAA/EEE6E/EEEEEEEAEEEEEEEEEEEEEEAEAEEAEEEEAEEEEEEEEEEEEEEEEAE/EEEEEEA\n+@NB500968:8:H5CFGAFXX:1:11101:3840:3285 1:N:0:TCCTGAGC+TACTCCTT;RQ:0.02\n+ATTTACTATATAGGGGGGAGCGTCAGATGTGTATAAGAGACAGGTATACCCTATAG\n++\n+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:2858:3312 1:N:0:TCCTGAGC+TACTCCTT;RQ:0.02\n+ATGACTCATATAGGGAACGTCAGATGTGTATAAGAG\n++\n+AAAAAE/EE/A/<AEEE/AE/E/EAAEEEEEEEAEE\n+@NB500968:8:H5CFGAFXX:1:11101:3641:3398 1:N:0:TCCTGAGC+TACTCCTT;RQ:0.15\n+GATATCATTATAGGGGCAGCGTCAGATGTGTATAAGAG\n++\n+AAAAAEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEE\n+@NB500968:8:H5CFGAFXX:1:11101:20540:3401 1:N:0:TCCTGAGC+TACTCCTT;RQ:0.86\n+GTTCTCGTTATAGGGAGCGTCAGATGTGTATAAGAGACAGATCAACCCTATATGCCCTAACTG\n++\n+AAA6AE/AAEEEEEEE/E///E/E</A/EEA<E/E/EEE/E</E///A/E6<E/A/<E/EEE/\n+@NB500968:8:H5CFGAFXX:1:11101:18503:3442 1:N:0:TCCTGAGC+TACTCCGT;RQ:0.01\n+TAATCCCTATAAGGGATTACTGACTCTTATACATGTATCTAATACACATCTCCGAGCCCACGAGACTCCTGAGCA\n++\n+AAAAAE/AAEEEEEEAAE/E//////EEAA///A/E/<///AEEEE/E/EE<<///E<EEE/E/AE6/EEEE//6\n+@NB500968:8:H5CFGAFXX:1:11101:19438:3463 1:N:0:TCCTGAGC+TACTCCTT;RQ:0.83\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n++\n+################################\n+@NB500968:8:H5CFGAFXX:1:11101:4772:3477 1:N:0:TCCTGAGC+AACTCCTT;RQ:0.86\n+TTACCCTATACTGGGTAACTGTCTCTTATACACCN\n++\n+AAAAAEEEEAEEEEAEEEEEEEAEEEAEEE<EEE#\n' |
| b |
| diff -r 000000000000 -r 40c86e14b674 tool-data/all_fasta.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/all_fasta.loc.sample Mon May 09 04:08:01 2016 -0400 |
| b |
| @@ -0,0 +1,17 @@ +#This file lists the locations and dbkeys of all the fasta files + +#This file has the format (white space characters are TAB characters): +# +#<unique_build_id> <dbkey> <display_name> <file_path> +# +#So, all_fasta.loc could look something like this: +# +#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa +# +#Your all_fasta.loc file should contain an entry for each individual +#fasta file. So there will be multiple fasta files for each build, +#such as with hg19 above. +# + |
| b |
| diff -r 000000000000 -r 40c86e14b674 tool-data/tagdust_architecture.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/tagdust_architecture.loc.sample Mon May 09 04:08:01 2016 -0400 |
| b |
| @@ -0,0 +1,15 @@ +#This is a location file for tagdust reference fasta files + +#See tagdust reference manual for architecture recommendatons + +#If the architecure file include a barcode HMM (B:) set the nacode field to yes +#Otherwise leave is as no + +#Planemo does not handle commas in value field well so avoid these if including the file in testing. + +#file has this format (white space characters are TAB characters): +# +#value dbkey name barcode path +# + + |
| b |
| diff -r 000000000000 -r 40c86e14b674 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Mon May 09 04:08:01 2016 -0400 |
| b |
| @@ -0,0 +1,11 @@ +<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> +<tables> + <table name="all_fasta" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/all_fasta.loc" /> + </table> + <table name="tagdust_architecture"> + <columns>value, dbkey, name, barcode, path</columns> + <file path="tool-data/tagdust_architecture.loc" /> + </table> + </tables> |
| b |
| diff -r 000000000000 -r 40c86e14b674 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon May 09 04:08:01 2016 -0400 |
| b |
| @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="tagdust" version="2.31"> + <repository changeset_revision="1b0267fab15a" name="package_tagdust_2_31" owner="brenninc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |