| Previous changeset 7:1eafcc450052 (2017-06-13) Next changeset 9:eb35257d2e29 (2019-03-20) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty |
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modified:
macros.xml sortmerna.xml |
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added:
test-data/forward_reads.fastq test-data/reverse_reads.fastq test-data/test1_aligned.fastq test-data/test1_bam.bam test-data/test1_blast.tabular test-data/test1_other.fastq test-data/test2_aligned.fasta test-data/test2_log.txt test-data/test3_aligned_forward.fastq test-data/test3_aligned_reverse.fastq test-data/test3_bam.bam test-data/test3_unaligned_forward.fastq test-data/test3_unaligned_reverse.fastq test-data/test4_bam.bam test-data/test4_biom.txt test-data/test4_de_novo.fasta test-data/test4_input.fasta |
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removed:
test-data/sortmerna_wrapper_accept1.fastq test-data/sortmerna_wrapper_accept2.fasta test-data/sortmerna_wrapper_other1.fastq test-data/sortmerna_wrapper_other2.fasta test-data/sortmerna_wrapper_sam1.sam test-data/sortmerna_wrapper_sam2.sam |
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| diff -r 1eafcc450052 -r 65c38d020fea macros.xml --- a/macros.xml Tue Jun 13 10:41:34 2017 -0400 +++ b/macros.xml Sun Sep 24 14:28:47 2017 -0400 |
| b |
| @@ -1,4 +1,35 @@ <?xml version="1.0" ?> <macros> <token name="@VERSION@">2.1b</token> + <xml name="db_prep"> + <param name="seed_length" type="integer" min="0" max="100" value="18" label="Seed length for database indexing" help="(-L)"/> + <param name="max_pos" type="integer" min="0" max="100000" value="10000" label="Maximum number of positions to store for each k-mer for database indexing" help="With 0, all positions are stored (--max_pos)"/> + </xml> + <xml name="output_alignments"> + <param name="print_all_reads" type="boolean" checked="false" truevalue="--print_all_reads" falsevalue="" label="Output null alignment strings for non-aligned reads"/> + <conditional name="blast"> + <param name="blast_output" type="select" label="Output BLAST report?"> + <option value="True">Yes</option> + <option value="False" selected="True">No</option> + </param> + <when value="True"> + <param name="blast_format" type="select" label="BLAST-like format?"> + <option value="0">pairwise (--blast '0')</option> + <option value="1">tabular BLAST -m 8 format (--blast '1')</option> + <option value="1 cigar">tabular + column for CIGAR (--blast '1 cigar')</option> + <option value="1 cigar qcov">tabular + columns for CIGAR and query coverage (--blast '1 cigar qcov')</option> + <option value="1 cigar qcov qstrand">tabular + columns for CIGAR, query coverage and strand (--blast '1 cigar qcov qstrand')</option> + </param> + </when> + <when value="False"/> + </conditional> + </xml> + <token name="@ALIGNMENTS@"> + $report.print_all_reads + --sam + --SQ + #if $report.blast.blast_output == 'True' + --blast '$report.blast.blast_format' + #end if + </token> </macros> \ No newline at end of file |
| b |
| diff -r 1eafcc450052 -r 65c38d020fea sortmerna.xml --- a/sortmerna.xml Tue Jun 13 10:41:34 2017 -0400 +++ b/sortmerna.xml Sun Sep 24 14:28:47 2017 -0400 |
| b |
| b'@@ -1,10 +1,11 @@\n-<tool id="bg_sortmerna" name="Filter with SortMeRNA" version="@VERSION@.4">\n- <description>Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data</description>\n+<tool id="bg_sortmerna" name="Filter with SortMeRNA" version="@VERSION@.5">\n+ <description>of ribosomal RNAs in metatranscriptomic data</description>\n <macros>\n <import>macros.xml</import>\n </macros>\n <requirements>\n <requirement type="package" version="@VERSION@">sortmerna</requirement>\n+ <requirement type="package" version="1.5">samtools</requirement>\n </requirements>\n <stdio>\n <regex match="This program builds a Burst trie on an input rRNA database"\n@@ -46,7 +47,7 @@\n #end for\n #end if\n \n- #if str( $databases_type.databases_selector ) != \'cached\':\n+ #if str( $databases_type.databases_selector ) != \'cached\'\n indexdb_rna \n --ref $ref \n -L $databases_type.seed_length \n@@ -54,85 +55,109 @@\n &&\n #end if\n \n- sortmerna \n- \t--ref $ref \n- \t--reads $input_reads \n- \t--aligned aligned\n-\t\n- \t#if str( $sequencing_type.sequencing_type_selector ) == \'paired\'\n- \t$sequencing_type.paired_type\n- \t#end if\n+ #if str( $sequencing_type.sequencing_type_selector ) == \'paired\'\n+ merge-paired-reads.sh\n+ \'$sequencing_type.forward_reads\'\n+ \'$sequencing_type.reverse_reads\'\n+ merged-reads.fastq\n+ &&\n+ #end if\n \n- \t$strand_search\n- \t$aligned_fastx.aligned_fastx_selector\n- \t#if $aligned_fastx.aligned_fastx_selector == \'--fastx\'\n- \t#if $aligned_fastx.other\n- \t\t--other other_file\n- \t#end if\n- \t#end if\n- \t$aligned_sam.aligned_sam_selector\n- \t#if $aligned_sam.aligned_sam_selector == \'--sam\'\n- \t$aligned_sam.sq\n- \t#end if\n- \t#if $aligned_blast.aligned_blast_selector == \'--blast\'\n- \t--blast "$aligned_blast.aligned_blast_format"\n- \t#end if\n-\n- \t$log\n-\n+ sortmerna \n+ --ref $ref\n+ --aligned aligned\n+ #if str( $sequencing_type.sequencing_type_selector ) == \'paired\'\n+ --reads merged-reads.fastq\n+ $sequencing_type.paired_type\n+ #else\n+ --reads \'$sequencing_type.reads\'\n+ #end if\n+ $strand_search\n+ $log\n+ $aligned_fastx.aligned_fastx_selector\n+ #if $aligned_fastx.aligned_fastx_selector == \'--fastx\'\n+ #if $aligned_fastx.other\n+ --other unaligned\n+ #end if\n+ #end if\n #if $report.report_type == \'best\'\n+ @ALIGNMENTS@\n+ #if $report.otu.otu_map == \'True\'\n+ --otu_map\n+ --id \'$report.otu.id\'\n+ --coverage \'$report.otu.coverage\'\n+ $report.otu.de_novo_otu\n+ #end if\n #if $report.report_best.report_best_type == \'1\'\n --best 1\n- --min_lis $report.report_best.report_best_min_lis\n+ --min_lis \'$report.report_best.report_best_min_lis\'\n #else\n- --best $report.report_best.report_best_value\n- --min_lis $report.report_best.report_best_min_lis\n+ --best \'$report.report_best.report_best_value\'\n+ --min_lis \'$report.report_best.report_best_min_lis\'\n #end if\n- #else\n+ #elif $report.report_type == \'num_alignments\'\n+ @ALIGNMENTS@\n #if $report.report_num_alignments.report_num_alignments_type == \'other_value\'\n- --num_alignments $report.report_num_alignments.report_num_alignments_value\n+ --num_alignments \'$report.report_num_alignments.report_num_alignments_value\'\n #else\n- --num_alignments $report.report_num_alignments.report_num_alignments_type\n+ --num_alignments \'$report.report_num_alignments.report_num_alignments_type\'\n #end if\n #end if\n+'..b'\n+ <param name="strand_search" value="" />\n+ <conditional name="databases_type">\n+ <param name="databases_selector" value="history" />\n+ <param name="database_name" value="ref_small.fasta" />\n+ <param name="seed_length" value="18" />\n+ <param name="max_pos" value="100000"/>\n+ </conditional>\n+ <conditional name="aligned_fastx">\n+ <param name="aligned_fastx_selector" value="--fastx" />\n+ <param name="other" value="True" />\n+ </conditional>\n+ <param name="log" value="False" />\n+ <conditional name="report">\n+ <param name="report_type" value="best" />\n+ <param name="report_num_alignments_type" value="1"/>\n+ <param name="print_all_reads" value="False" />\n+ <conditional name="blast">\n+ <param name="blast_output" value="False"/>\n+ </conditional>\n+ <conditional name="otu">\n+ <param name="otu_map" value="False"/>\n+ </conditional>\n+ </conditional>\n+ <param name="e_value" value="1"/>\n+ <param name="match" value="2"/>\n+ <param name="mismatch" value="-3" />\n+ <param name="gap_open" value="5"/>\n+ <param name="gap_ext" value="2"/>\n+ <param name="ambiguous_letter" value="-3"/>\n+ <output name="aligned_forward" file="test3_aligned_forward.fastq" />\n+ <output name="aligned_reverse" file="test3_aligned_reverse.fastq" />\n+ <output name="unaligned_forward" file="test3_unaligned_forward.fastq" />\n+ <output name="unaligned_reverse" file="test3_unaligned_reverse.fastq" />\n+ <output name="output_bam" file="test3_bam.bam" compare="sim_size" delta="200" />\n+ </test>\n+ <test>\n+ <conditional name="sequencing_type">\n+ <param name="sequencing_type_selector" value="not_paired" />\n+ <param name="reads" value="test4_input.fasta" />\n+ </conditional>\n+ <param name="strand_search" value="" />\n+ <conditional name="databases_type">\n+ <param name="databases_selector" value="history" />\n+ <param name="database_name" value="ref_small.fasta" />\n+ <param name="seed_length" value="18" />\n+ <param name="max_pos" value="100000"/>\n+ </conditional>\n+ <conditional name="aligned_fastx">\n+ <param name="aligned_fastx_selector" value="" />\n+ </conditional>\n+ <param name="log" value="False" />\n+ <conditional name="report">\n+ <param name="report_type" value="best" />\n+ <param name="report_num_alignments_type" value="1"/>\n+ <param name="print_all_reads" value="False" />\n+ <conditional name="blast">\n+ <param name="blast_output" value="False"/>\n+ </conditional>\n+ <conditional name="otu">\n+ <param name="otu_map" value="True"/>\n+ <param name="id" value="0.97"/>\n+ <param name="coverage" value="0.97" />\n+ <param name="de_novo_otu" value="True"/>\n+ </conditional>\n+ </conditional>\n+ <param name="e_value" value="1"/>\n+ <param name="match" value="2"/>\n+ <param name="mismatch" value="-3" />\n+ <param name="gap_open" value="5"/>\n+ <param name="gap_ext" value="2"/>\n+ <param name="ambiguous_letter" value="-3"/>\n+ <output name="output_bam" file="test4_bam.bam" compare="sim_size" delta="200" />\n+ <output name="output_biom" file="test4_biom.txt"/>\n+ <output name="output_de_novo" file="test4_de_novo.fasta"/>\n </test>\n </tests>\n <help>\n' |
| b |
| diff -r 1eafcc450052 -r 65c38d020fea test-data/forward_reads.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/forward_reads.fastq Sun Sep 24 14:28:47 2017 -0400 |
| b |
| b'@@ -0,0 +1,4000 @@\n+@ERR1877483.1 M03099:23:000000000-APTLR:1:1101:19252:1849/1\n+CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCCATTCCCCGTGTGTGCTGCTTGCCTTCGGTTTGTATATCACTTTCTTTTTTGACGACTCTCTTTTTTTTATTACCTTTCTTTTTTTACTTTACCTACATTTTCTGCTCCGTCTTTCTTCTTTCCTTCTTCCTCTCTCATCCGTATGTTGCAACCTTTTTTCTTTTTTCCTTTTCTTTTATCTCTCTTTTTTGTTTCTTCACGTTTTCTTTTACCTCCCCTTTCTCTTCCTGTTAACTTCCTCCTAT\n++\n+@CCCCGGGCGGGGGGGGGGGGGGGGGGF9FGGFGFEFG<F+6@+C6CC,;6C,,69,9,9C,:+8,C,C,,,,,,,,,:6C<,,,8=,:,,,,5,99CC,,,<5,+++,+++++,5,,9,,+8>,,:,,,55,88,558=+,3,8=,8,,,,,,,,8,,,3,73++,8+,8@,8,7,7,,,3,,,,,3,,7,,6,2**,,,,7,2,,,4,7<,,40,,,,63,23++,+35+,++1+4+++1+++/*+20++++*+*22****+03*+*228*/**+20+++305*++***1*.)0*,)**\n+@ERR1877483.2 M03099:23:000000000-APTLR:1:1101:15851:1971/1\n+CCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGTGTTTTGGTTAATAACCGCAGCAATTTACGTTACCCGCAGAAGATGCACCGGCTACCTCCGTGCCAGCAGCCGCGTTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGTGCGTAACGCGCTCGCAGTCGTTCTGTCAAGTCGGTTGTTAAATCCCCGGGCTCAACCTGGGAACTGCATTCTAA\n++\n+6ABCCGGGFEGGGGGFGGGGGGFGFDGGGGFGGGGGGGGGGGDEGGGF8F9E@CC<8F,@F+@:F@@,CC,,,,,9CDCEDE7C+CFCFC,,,C,9CFFE,,,4++>++>+,,+:,CF,B8+BD<,@,,38+:++6,,::,,3+@B,3:,*3***,,,,7,,7<F**B7,3:><*@***,,*,4<<:8**4**4,7=8****;*;+++**;C**<<**/*;@+3<+++0*2*/**2*****)*.*02***2+<+*023***)1*9*:+700<C5***)/*++2;:5**))09*))2:6**/\n+@ERR1877483.3 M03099:23:000000000-APTLR:1:1101:23102:1978/1\n+CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGCAAGCCTGATCCAGCCATGCCGCGTGTGTGATGAAGGCCCTAGGGTTGTAAAGCTCTTTCCCCGGATAAGATAATGACGTTATCCGTAGAAGAAGCCCCTGCTAACTTCGTGCCAGCATCCGCGGTAATACGACTGGCGCTAGCGTTGTTCGGTATTACTGGTCGTAAAGCTCACGTAGGCTGATCGATCAGTCATGGGTGCAATCCCATGTCTCACCCCTGGCTCTGCCTTTCATACTTTCCCTCTGGATTATGTCAGAG\n++\n+CCCCCGGGGDGGGGGFGGGGGGGGGFGGGGGGGGGGGGGGGGG>CFGG8FEFFFEF8E,CFBGEGG,,E,C<,9,,CEE=C8=@,CC@FF9,9CCFFFE,,54+7++4,C,E,,9,,9+++,:5<++,++,,,,,33A:+8=,,,,75C+B+:=<,+,,@@+@+@@**@,,*****,,*1>*5>:14*=B>6**26F9BF:,,5*1*+*2?+4<3*<*2*++**5;*110*<<+<+3+*3**+*3<:+++*+3377*/*11****37+9*3+:++3+2330+++-7A+)***/.)2*)**/\n+@ERR1877483.4 M03099:23:000000000-APTLR:1:1101:22637:2119/1\n+CCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGGGAAACCCTGATGCAGCCATGCCGCGTGTGTGAAGAAGGCCTTCGGGTTGTAAAGCACTTTCAGTTGTGAGGAAAAGTTAGTAGTTAATACCTGCTAGCCGTGACGTTAACAACAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCGAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGCTAGATGTGAAAGCCCTGGGCTCAACCTGGGATGGTCATTTAGA\n++\n+88BCCGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGEFCFGGGGGGGGFFFGGGGGGGFFFFFGGGGGGGGGGGGGGFGGGGGGGFFGGGGGGGGGGGGGGGGGGGGGGGGG@FFFFGGGGGGGGFFGGGGGGGGFGGEGGFGGGGGGGGGGGGGGGGGGEGGGGGGGGFGCFGGGGGGGGGGGGGGGGGGGGGGGGGGGGDEGG>FGGGGGGGGC>CEEGEEGGGGGGGGF?ECGGGGCFDFGGFG>FCFGDFGGG(.::>4>F9:<7729F:\n+@ERR1877483.5 M03099:23:000000000-APTLR:1:1101:18265:2244/1\n+CCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGTGTTGTGGTTAATAACCGCAGCAATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTCTGTCAAGTCGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCGAA\n++\n+68ACCGGGFGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGBFFFFFFFEFFGGFFEFGGEGFGGFFGGGGGGGGGGGGGGGGGEGGFGGGGFDFGGGGGFGDEGFGGGGGGGGGCGGGGGGGGGFFGGGGGGGGGGGGGGFFGGGGGGGGEGGDFGGGFGFE8EFGEEGGGGGGGGGGEEGGGGFEE8EGFGGGGGGF?@FGCG*:CGCFFFGGG5EGGBGGEGEEE@CEDGGFGGGGCG6CFGGGFFG=CEGGEEGGGG:>FGFFF?F?BC>AF@>\n+@ERR1877483.6 M03099:23:000000000-APTLR:1:1101:12491:2265/1\n+CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGCAAGCCTGATCCAGCCATACCGCGTGGGTGAAGAAGGCCTTCGGGTTGTAAAGCCCTTTTGTTGGGAAAGAAATCCAGCCGGCTAATACCTGGTTGGGATGACGGTACCCAAAGAATAAGCACCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGGTGCAAGCGTTACTCGGAATTACTGGGCGTAAAGCGTGCGTAGGTGGTTGTTTAAGTCTGTTGTGAAAGCCCTGGGCTCAACCTGGGAACTGCAGTGGAA\n++\n+88BCCGGGEGGGGGGGGFFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGEGGFFGEEFFFFGGGGDCCFGGGGGGFGGGGGFFGGGGGEGE,FFEGGGGGGGCE@FFGGGGEFFFBCGGGGGGGEGEDEBDGGGGGGGGGGGGGFGGGGGFFGGFF>:CGDGGGGGFECB@CCGGGGGGFEEECBCCGGGGGCEEFGGGGGGGGGCC?CFG/:?@GGGGGGGDEE5CFG5CEC@CFGGGGCGG'..b'19:20365:24795/1\n+CCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGAT\n++\n+CCCCCGGGGGGGGGGGGGGGGGGCEGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGC<FFGGFGGGDGGGGGFGGDGGGDDGFGFFDAFGGGGGGGGGGGGGGGGGGFEFF7CFGGGGGGFGFCFFDGGGGGGGFGFGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGG?CFGGGGGGGGGGECEFFFGGG*:EEG@C?EGGGGGG>GGGGGG*8FGF99C7AC:FDFFD7CFGGGGCE5CEGGFGGGGFGGGFF4*)<>77DF\n+@ERR1877483.32953 M03099:22:000000000-APTMA:1:2119:9975:24853/1\n+CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCCATGCCGCGTGTGTGAAGAAGGTCTTCGGATTGTAAAGCACTTTAAGTTGGGAGGAAGGGCAGTAAGTTAATACCTTGCTGTTTTGACGTTACCAACAGAATAAGCACCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTCAGCAAGTTGGAGGTGAAATCCCCGGGCTCAACCTGGGAACTGCCTCCAAA\n++\n+CCCCCGG7C@CFGGGGGFGDGGCEFGGGG9FFGGGD9FFGGGGGGGGGCEFGGGGGDGGGGGGGGGGGGGGCFGFFGCEFFGGDGGFFEFFFAFGGEDGGC<BE@,>BF+?FFCFGFEF<@<EF9FGGGF,B,AAFGGGGGGGG3DF@FFFBF8DGFDFFFFFFCDGGGGFGGFFGGGCD7*@:@FC:><FC7FFF7CFGGGGECFG<F71=F>FFGBF<CFCEGFC@8BC>8C+CEEGGGGGGDGFFGGGGGFF*29:@FFF8CFG60<C:C7:?:5EG6CCCGG==FCCFG=:C6=>7*\n+@ERR1877483.32954 M03099:22:000000000-APTMA:1:2119:11950:24861/1\n+CCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCAATGCCGCGTGTGTGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGGTTGTGGTTAATAACCGCAGCAATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTCTGTCAAGTCGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCGAA\n++\n+CCCCCDGGGGGGGGGGGFGGGGEGGGGGG<CFGGGGGGGGGGGGGGGGFGDFDGG,FG9FAFGGFGG,CFGFFGCFGFGFE9CGEGGGGFEFGFGGGFGGGF94C+C:FCGGF7+3BF7+BFGGGGGG<FF+++@+,<FFGGG>C*FGG8:::FGGGGGGG7EGGGEGGGGGGGGGGGGGFGGGGFEGGGGGGGGFGGGGGGEGGGGGGDEG?CGGGGGEGGGGGGGGGGGGGGGGGGCEGDGGGGGGG>EGF+7<AGGCGDGEGGGGGFCCFGGGGG*@CEGGGG=FFGFFFFFGG??FC\n+@ERR1877483.32955 M03099:22:000000000-APTMA:1:2119:9959:24862/1\n+CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCCATGCCGCGTGTGTGAAGAAGGTCTTCGGATTGTAAAGCACTTTAAGTTGGGAGGAAGGGCAGTAAGTTAATACCTTGCTGTTTTGACGTTACCAACAGAATAAGCACCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTCAGCAAGTTGGAGGTGAAATCCCCGGGCTCAACCTGGGAACTGCCTCCAAA\n++\n+ACCCCGCE;FEG,CFEFGCGGGFGGFAFGF9EF<FFCEFFECFCFFGGGCFGFF@CEDGF@C@ECFGGGGGFDEEFGG<CEGGFGGGFFFFGFECEDFGGGGFFFGG<FCCCFGGGGGGGGGCFFGFGFGCFFGGGGGGGGDFFFGGEFCGGCFDGGCFGGGG,FFGDGCGFFFEFGG>FFFGGFGGGGCFECCDFGGGGEGCFEFGGGGG:<CGDFGE<;FGC9A:<5CEGD>CF5CE5C*:8ECGCEF<CGGG;CC:98F6=EFGEG7@6@=GGG<EFFF8*9=D7<FGFFFB6F274:\n+@ERR1877483.32956 M03099:22:000000000-APTMA:1:2119:14880:24914/1\n+ACGGGCGGTAAGTAGAGCCGATTCGTTGACAAGGTTGGCAAGGTCAGCACCGGTAAACCCGGGAGTACCCCTTGCTATCACTTTGAGATCTACCTCCCGGGATAGAGGTATCTTCCCCGAGTGAACAGCACGTATCTTCTCCCTTCCCTTAACATCAGGAACATCAGCAATGACCTGCCGGTCGAATCTACCAGGCCTTAAAAGAGCCGGATACAGAACATCAGGCCTGTTTGTGGCAGCTATGATTATCAAACCCTCAGTGGTTTCAAAACCGTCCATCTCAACAAGAAGCTTGTTGAGA\n++\n+CC8B@:FEFGCFF<FGGFGEFFEGGFF@@FFCFDFFGGGGGC,66,CFCFCFGGGGG@@F:B@=>6C,,6DFF8<<CFCFGGCGCEFGFFDFG<F54+8CE:><=FGGGGGFCF,CF<FFGFCFCFCFF@,@>3?FCFF<D9BFG8D8FFGG9DGFGGGG7BDACF,,@<BGCFCGDFCFG@CFCFCGG,DCG,<FC:FCGGG91FFCEGG@*?915?B:@FGCE78<*5?B+2*88*:5CC9E:CD7+A7+3995>84+<*;F7*A?<EC@C*A;83?+2:9C<+:676+)0*.:>6?**\n+@ERR1877483.32957 M03099:22:000000000-APTMA:1:2119:17520:25205/1\n+CCTCCGGGAGGCAGCAGTGGGGAATCTTAGACAATGGGGGCAACCCTGATCTAGCCATGCCGCGTGAGTGATGAAGGCCCTAGGGTTGTAAAGCTCTTTCAGCTGGGAAGATAATGACGGTACCAGCAGAAGAAGCCCCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGGGCTCGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGTAGGCGGACCGTAAAGTTGGGGGTGAAATCCCGGGGCTCAACCCCGGAACTGCCTTCAAAACTATCGGTCTGGATTTCGAGAGAG\n++\n+BCC-8@7:+6@CFDFGGDFGGG77EEFGGF<FFFFF-CFFECFCGGGD,@FFF9EEFFEC6CEGECE@GGGEE<CAFFE?FGGFCFFGGFEFGGG?BBFFFGGDGFD<FF8F?FFGAEGGGGGGFFC<A<EEE8EEFGGE7@G:=FGEFGGGGGDFGGGGFEGGDF*CF=CGG@:FGGGE7*=CGFDGGC9CC7*=:CFFC68CECECCCFGCEGGCFGGECGGGEG:*:/<F9+<5EGECC9<CC+AEEGDGC3:9EFC>95C=88<EEE7C6<++9<@CFCEGGGGG:+9CF?C*2>C<\n' |
| b |
| diff -r 1eafcc450052 -r 65c38d020fea test-data/reverse_reads.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reverse_reads.fastq Sun Sep 24 14:28:47 2017 -0400 |
| b |
| b'@@ -0,0 +1,4000 @@\n+@ERR1877483.1 M03099:23:000000000-APTLR:1:1101:19252:1849/2\n+CACTACCCGGTTTTCTTATCCTCTTTTCTCCCCCCCCTTTCCCCCCTCCTTCTCCGTTTTTTTCCCTTTCCTCCCCTTCCCCTCTTTTTTTCCTTCCTCTTTCTTCCCCTTTCCCCTCTTCCCCCCTTTTTCCCCCCTCCTCTTCCTTTCTCCTCCTCTCCCCTTTTCTTTTTCCTTTCCTTTTTTCTCCCCCTTCTTTCCCCTCCTCCTTTCTCTCCCCCCTTCCTTCCCTTTTCTCCCCGTTCTTCCCTTCCCCCCCTTCCCCCCTCTTTTTTCCCCCCCTTCTCTCCCCCTTTTTCC\n++\n+--86,C,@+8+@,6,6,,;6C,,;C<-<;,;66+8+@+6<,,;,+8+,,,6,96,+9,66,+86:,,,,,,6,,,8,9,,:9,4,:,,::+,:,9949,,,,,,,5,,,,47,,84,4,,,,,,+++,,,6,7,33+++6,,2+,3,,,3++,,*,,,,*,,*43,/,3+,,,,*22+5,,,,22*,+13,*)*,2,2<+223),**(.*2.4+++*/*//4*(00)..).)0)).*))0*(0)((.)1())))(((((-,,0*2/),/,-)-0((.,((--((()).,.,****0+0()\n+@ERR1877483.2 M03099:23:000000000-APTLR:1:1101:15851:1971/2\n+CACTACAAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCTCCTGAGCGTCAGTCTTTGTCCAGTGGGCCGCCTTCGCCACCGGTTTTCCTCCAGATCTCTACGCATTTCACCGCTACACCTGGTATTCTCCCCCCCTCTACACTACTCAATCCTGCCAGTTTCGAATGCAGTTCCCAGGTTTAGCCCGTGGATTTCACATCCTACTTGCCATACCGCCTGCGTGCGCTTTACTCCCCGTAATTCCGATTTACGCTTGCCCCCTCCGTATTACCTCCGCTGCTGTCCCCTTCTTAGC\n++\n+-8AACFDEFGGF,CCE,CCCFC9CFC-EFEF66,@F@CCDE@C,C@E<,,,+8@66C,F<F<FAE<,,,,,,9++@=?=,BB,?,6+>+?C,5E@E8,,:499A,?<44@CFA,CB+6>@>,AEE8,,,9@=A,C?80=BEEG+=,,,,6==@,+6,7=8>,@D=D;+++859,+7;BC?,,4@:,,+8,:**4*66?F+5B,=>:**10=**9++*0,*7B*2A5/(680,88)>+)/2*-.)((6)92(-5)).(2(4(-00777<7(:08F)64).((46(34).4:2****30*).\n+@ERR1877483.3 M03099:23:000000000-APTLR:1:1101:23102:1978/2\n+CACTACCGGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTCAGCGTCAGTATTGGACCAGTTCGCCGCCTTCGCCACTGGTTTTCCTCCGAATATCTACGCATTTCACCTCTACACTCGTTATTCCACTCACCTCTTCCATACTCCAGTTCGCCAGTTTCATTCGCAGTTCCACGGTTCATCCCTCGGCTTTCACTCCTTACTTATCGCTCCGCCTACCTTCGCTTTACGCCCAGTACTTCCTCTCACCGCTCTCCCCCCTCCTTTTTCGCCGCCTGCTTTCCCCTCTTTATC\n++\n+9BCCCG<BEG>F7<CC,6ECED9CFC-CECEC@CCCFC:DE@FECFCAC,6+8@,:C,,9,,,:EC,C,9,+B+=:C@A<FE,8=,::54=9E=,4+++8+4A@,C+++8?AF,@<4>9,A,,,:+4++46,A,C,@+@DCDEFGA,6,@==,,*,333+>+3@,34,,+,,+++5;9;,,3*55*,+474,****1>F9+=,;>D+A9:4//B)))/1*9<*8F*79=.(,15)7)((**(2:7<?461))8*)((,(((.0:37)(1(.).7)2(((((,,((,))-).****20*-6\n+@ERR1877483.4 M03099:23:000000000-APTLR:1:1101:22637:2119/2\n+GACTACTAGGGTATCTAATCCTGTTCGCTACCCACACTTTCGCACATGAGCGTCAGTCTTTGGCCAGGGAGTCGCCTTCGCCACTGATGTTCCTCCAGATATCTACGCATTTCACCGCTACACCTGGAATTCCACTCCCCTCTCCAAGACTCTAGTCTGCCAGTTCTACATGACCATCCCAGGTTGAGCCCAGGGCTTTCACACCTAGCTTAACAAACCGCCTGCGTGCGCTTTACGCCCAGTAATTCCGATCAACGATCGTCCCCTCCGTCTTACCGCGGCTGCTGGCACGGGGTTAGC\n++\n+CCCCCEGGGGGGGGGGGGGGGDGFFGGGGGGGGGGGGGCFGGGGGDGFFFGGGGGGEFGGGGGGGGGGGFFFFGGGGGGGGGDGGGFGGGGGGGGGGGGGGGGGGFCEGDFGGFFGGDEGEEFGGF<EFFGGGGGGFGGE8EGFGGD8FGGG83BDADFGGGFFB;9E,?FFFFGGGFGD?EFD==EGFD7CFGG:@8FCCAC*:603ADEAABAF;CFGDGC7AD=(66>@DFEEFF@>*/86))9<6(6;)268((,/((/:97*(2-4(80)).46;6>7>0:??:025C*7?5*.6\n+@ERR1877483.5 M03099:23:000000000-APTLR:1:1101:18265:2244/2\n+GACTACAAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTGAGCGTCAGTCTTTGTCCAGGGGGCCGCCTTCGCCACCGGTATTCCTCCAGATCTCTACGCATTTCACCGCTACACCTGGAATTCTACCCCCCTCTACAAGACTCAAGCCTGCCAGTTTCGAATGCAGTTCCCAGGTTGAGCCCGGGGATTTCACATCCGACTTGACAGACCGCCTGCGTGCGCTTTACGCCCAGTAATTCCGATTAACGATTGCACCCCCCGTATTACCGCGGCTGCTGGCACGGAGTTAGC\n++\n+CCCCCDFGGGGGGGGGGGGGGGFFFGGGGGGGGGFEGGGGGEFGGGFGGGGGGGGECFGGGGGGGGGGGGGCGGFGFGGGGGGGGGGFDFGGGGGGGGGGGGGGFFFECEGFGGGGGGGEGGGGGGGGGGDFGGDCFG>EEGFFGGF?EGDCCGFGFGGGGGGFFGFGGGGFFFD<@FGGGGGFGGGGFEGGGGGDCC@FGFGF@GG7597@EAFFF@:78:56>C??BDB9D:AFB(7:/./8)).)64<:::2>62(332:9CD)4C>814FFFF6114029?4:?BFFGG59*2*.:\n+@ERR1877483.6 M03099:23:000000000-APTLR:1:1101:12491:2265/2\n+GACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGTGCCTCAGTGTCAGTGTTGGTCCAGGTAGCTGCCTTCGCCATGGATGTTCCTCCCGATCTCTACGCATTTCACTGCTACACCGGGAATTCCGCTACCCTCTACCACACTCTAGTTGTCCAGTTTCCACTGCAGTTCCCAGGTTGAGCCCAGGGCTTTCACAACAGACTTAAACAACCACCCACGCACGCCTTACGCCCAGTAAATCCGAGTACCGCTTGCACCCCTGCAACTTCCGCGGCCGCTGGCCCGAAGGAACC\n++\n+CCCCCEFFGGGGGGGGGGGGGGFCEEEFGGGFGGGGECECFEFDGGGG8FGGGGGGFGE@EFG9E<FFGGGGGGGGGGGGGGED@EACFGFFGGC=CFC7=F;,9EFG@CFGF,@CBFG;DDGGGGGE=EGA;FG+CD8BCD8FCGFFAEDFCFFGGGGGGGGDBB9DGCAFFFD9+CFFF,=FFD,=*@@F6:8+48B?;4=*8,*1;7@AA>8<0:84CG5<@82/(2((85*85(,4*,017).7).2,0=)6(1((((0AD*),*(())'..b'0-APTMA:1:2119:20365:24795/2\n+GACTACAAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTGAGCGTCAGTCTTCGTCCAGGGGGCCGCCTTCGCCACCGGTATTCCTCCAGATCTCTACGCATTTCACCGCTACACCTGGAATTCTACCCCCCTCTACGAGACTCAAGCTTGCCAGTATCAGATGCAGTTCCCAGGTTGAGCCCGGGGATTTCACATCTGACTTAACAAACCGCCTGCGTGCGCTTTACGCCCAGTCATTCCGATTAACGCTTGCACCCTCCGTATTACCGCGGCTGCTGGCACGGAGTTAG\n++\n+CCCCCGFDFGGGFGGGFGGCGGGGGGGGGGFEGFFGGGGGGEGGGGGGGDDFGCGGGGGGGGFGEGGG@7CGGGGGGGFGFFGGGGDGDGGGGDFGGGFGGGFG;F@FCEFDGGGGGGGGGFGFGGGGGGGFF=FAD=+>E6F5ED88CCFGGFAF6CFGGGFG,;A@@BFGGEFGGCGFCFGFF,8DFFEE<EG):8FGF?ACAGG3;EEEEEE618C85FD;?FB0<39>F06<:<9>C??*4:<<A0(341<B?F:(((+18)4:9(4(4.4:C,2,190(44?(3(5(((4=:)6\n+@ERR1877483.32953 M03099:22:000000000-APTMA:1:2119:9975:24853/2\n+GACTACAGGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGTGCATGAGCGTCAGTGTCATCCCAGGGGGCTGCCTTCGCCACTGGTGTTCCTTCCTATATCTACGCATTTCACCGCTACACAGGAAATTCCACCACCCTCTACCATACTCTAGCCCAGTAGTTTTGGAGGCAGTTCCCAGGTTGCGCCCGGGGATTTCTCCTCCAACTTCCTGACCCACCTACGCGCGCTTTACGCCCCGTAATTCCGATTACCGCTGTCACCCTTCGTATCACCGCGGCTGCTGCTACGACGTTAGC\n++\n+CCCCCG8FFGGGDGGFGGGGFGAFGFGFFG@FGGGGGGDFFD;@FFFCFGGGFGC:FEEFDACF@FB@:87FF@FD9,CDFGEGGG8FFGG?9,CFFGDFGGEGFGD@F74?C<EFFGEEFDGF@ECEA<AEGGGGGF+@DDF5=AEGGF9DDDFGG8DFGG?F,@9>76,8>8:C+7D93,1,@,3@C7:**;C>D>BB+:,*A68235<*.4*+(02*:<8@E87(:.6,(349(4(:*(-),44<2((-34)-19>(-4097.,8F:<0(()-2-21(-,40::))-62:9(2/2(.\n+@ERR1877483.32954 M03099:22:000000000-APTMA:1:2119:11950:24861/2\n+GGCTACTAGGGGTACTAATTCTCGTTTGTCCCCACGGTTTCGCACCTTCACGGTAGTCTTTATTCCGGCGACTCCCCTCGCCACCTGTAGTCCTCCAGGACTCTACGCAATTCACCGCCTCACCTGGAAATCTACCCCCCCCTTCCAGCATTCTACCTGCCCAGTTCCAATTCAGTTTCCCGGTTTAACCCCGGGGCTTCCACATCGACTTTACAGACCGCCCTCCTAGGCCTTACGCCCATTACATCCGATTAACGCCTTCACCCTCCGTATTCCCGCCTGCTCTGGCACCGTCTTAGG\n++\n+B-<,66;,;CF7,,6C,C,,;C68FF,,;;FGGCC@+:CF@,,,8FD@,,;6B6,,66;@F,,,C,,@+8+6+,,B,A,47C,4A,CCC?F,E,,9,9,+4,,,,4++++8C,C9C++614?EF,4B,4,93,4,E1=+8++4*532,,,++,++,32,,@,*,6<;9,@,,,,+7+*>D,*:*4*,++?C*8EG)):F**)+()3*(,(;).7//;(=))2)(()()))(,.),4-(4C*,)0))641(((-().(,(4()+9=F((1(,,,4)40((((((())))).)(,,,*2)-)\n+@ERR1877483.32955 M03099:22:000000000-APTMA:1:2119:9959:24862/2\n+GACTACAGGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGTGCATGAGCGTCAGTGTCATCCCAGGGGGCTGCCTTCGCCACTGGTGTTCCTTCCTATATCTACGCATTTCACCGCTACACAGGAAATTCCACCACCCTCTACCATACTCTAGCCCAGTAGTTTTGGAGGCAGTTCCCAGGTTGAGCCCGGGGATTTCACCTCCAACTTGCTGAACCACCTACGCGCGCCTTACGACCAGTAATTCCGATTAACGCTTGCACCCTTCGTATTACCGCGGCAGCTGCTACTCTGTTAGC\n++\n+CCCCCFFGCFGGGFFE9<FFGGGEDEFFFGEFGCFGGG@FGGGGGFFFEECGEE:FFGGADFFF,CFGCF7FFG:AA?FG,BBFF?CF=EEG,F9F:CFECAACFGF@FGG9FAFF@EGCGFG@@C8E<FEGEFG8AFC=D?DFGGGGGGFFFFFFGC==F;D63E2@EDFD>C5F8EE>A64CFGFFGF@5*547CFE25:;=A;C@055*98>F3;F4C<6(5>69;:0(/()((,,2*.6:6)-)-5?13(6:03:02439772:C:?12.)6749909(-80(()--))).:<)-5\n+@ERR1877483.32956 M03099:22:000000000-APTMA:1:2119:14880:24914/2\n+GCGACGGGTACGAGAGAGATCAGTGGGAATAGAAATGAAAGGAGGCGGAAGTAAGAACACAAACGAGTCGGTGTAATCTAAATGGAGAGGAGGACTAAGGTGCTGAATACGGCTGGAGCTAGGGGGGTGGCACATGGTCGATACTGACTGATCAACTGTGATGTCGCTCTTAGTAGTGGTGGAACAGGACTGGATATGGCTATTAGGACTGGGTATCATAAACATGCTACTATGGGTAACTTACTACGACAACACTTGGAGGCTAACATCACTATGTAACTATCGAAAGTGAGATTACGAT\n++\n+--8,86+86+,8,68+:B8,;6CC--,,,,;6,,;,,,,,,,,,,8+8+6+,<<,,,,:,,9,:,6+8,68+86,,,,4,,,:,:,,,8,,+88+,9B<,9A,9@;A==9+++88+,,,,,,84++***4+*,++7*21****)++++++*331)*+++++39:+*(/**23+3*+*(2C***+0*2***+*1*+**039>)0)/0:248*(..)).)3*00*-.)).)*,).).(4)(,0--2)))(-(((((()-).).(*0)),4:7)).-))2))))--)-((-,))))))30),(-\n+@ERR1877483.32957 M03099:22:000000000-APTMA:1:2119:17520:25205/2\n+GACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTCAGCGTCAGTATCGAGCCAGTGAGCCGCCTTCGCCACTGGTGTTCCTCCGAATATCTACGAATCTCACCTCTACACTCGGACTTCCACTCACCTCTCTCGAACTCCCGACCGATAGTTTTGACGGCAGTTCCGGGGTTGAGCCCCGGGATTTCACCCCCAACTTTACGGTCCGCCTACGTGCGCTTTACGCCCGGTCCTTCCGATCACCGCTATCCCCCTCCGTACTACCGTGTCTGCTGGCCCGTACGTCGC\n++\n+--8ABFGE<@7<<FCFGGGF,CCCFA<FGG8DCECC+CCCEGGGDFF@FFFCFCC7EFGDC,,BFCF@D<,F8@4@FCGCEF7BEG,CEEGGGGEGF+,@@FGFGG?:,@+C;FFEC@DEGCG,B<:C6@C@FFFFFFC8FEDDGGG,@FGG,+:CGGGC7F*@=E*>B,+*@>5@;CGG>5C@CE74C<C*7=E3<5?FFC>8:731;8C3563)61:)7;7(.58:?342(:A<8?>G*-3)(6<4211(4-(419B0(.<?F7,39(38((.)2((((.)).60((((--((*0((4\n' |
| b |
| diff -r 1eafcc450052 -r 65c38d020fea test-data/sortmerna_wrapper_accept1.fastq --- a/test-data/sortmerna_wrapper_accept1.fastq Tue Jun 13 10:41:34 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,4 +0,0 @@ -@read1 -GCCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAGAGTGGAATACCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACC -+read1 -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII |
| b |
| diff -r 1eafcc450052 -r 65c38d020fea test-data/sortmerna_wrapper_accept2.fasta --- a/test-data/sortmerna_wrapper_accept2.fasta Tue Jun 13 10:41:34 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ ->read1 -GCCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAGAGTGGAATACCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACC |
| b |
| diff -r 1eafcc450052 -r 65c38d020fea test-data/sortmerna_wrapper_sam1.sam --- a/test-data/sortmerna_wrapper_sam1.sam Tue Jun 13 10:41:34 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,3 +0,0 @@ -@HD VN:1.0 SO:unsorted -@PG ID:sortmerna VN:1.0 CL:sortmerna --ref /tmp/tmpY80cK0/files/000/dataset_2.dat,dataset_2 --reads /tmp/tmpY80cK0/files/000/dataset_1.dat --aligned aligned --fastx --other other_file.dat dat -a 1 -read1 0 EncFa169 645 255 2S87M * 0 0 GCCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAGAGTGGAATACCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:169 NM:i:1 |
| b |
| diff -r 1eafcc450052 -r 65c38d020fea test-data/sortmerna_wrapper_sam2.sam --- a/test-data/sortmerna_wrapper_sam2.sam Tue Jun 13 10:41:34 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,3 +0,0 @@ -@HD VN:1.0 SO:unsorted -@PG ID:sortmerna VN:1.0 CL:sortmerna --ref /tmp/tmpY80cK0/files/000/dataset_7.dat,dataset_7 --reads /tmp/tmpY80cK0/files/000/dataset_6.dat --aligned aligned --fastx --other other_file.dat dat -a 1 -read1 0 EncFa169 645 255 2S87M * 0 0 GCCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAGAGTGGAATACCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACC * AS:i:169 NM:i:1 |
| b |
| diff -r 1eafcc450052 -r 65c38d020fea test-data/test1_aligned.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test1_aligned.fastq Sun Sep 24 14:28:47 2017 -0400 |
| b |
| @@ -0,0 +1,4 @@ +@read1 +GCCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAGAGTGGAATACCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACC ++read1 +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII |
| b |
| diff -r 1eafcc450052 -r 65c38d020fea test-data/test1_bam.bam |
| b |
| Binary file test-data/test1_bam.bam has changed |
| b |
| diff -r 1eafcc450052 -r 65c38d020fea test-data/test1_blast.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test1_blast.tabular Sun Sep 24 14:28:47 2017 -0400 |
| b |
| @@ -0,0 +1,1 @@ +read1 EncFa169 98.9 87 1 0 3 89 645 731 1.54e-40 149 2S87M 97.8 |
| b |
| diff -r 1eafcc450052 -r 65c38d020fea test-data/test2_aligned.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test2_aligned.fasta Sun Sep 24 14:28:47 2017 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>read1 +GCCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAGAGTGGAATACCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACC |
| b |
| diff -r 1eafcc450052 -r 65c38d020fea test-data/test2_log.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test2_log.txt Sun Sep 24 14:28:47 2017 -0400 |
| b |
| @@ -0,0 +1,34 @@ + Sat Sep 23 09:30:45 2017 + + Command: sortmerna --ref /private/var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmpuYZa_K/files/000/dataset_2.dat,dataset_2 --aligned aligned --reads /private/var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmpuYZa_K/files/000/dataset_1.dat --log --fastx -e 1.0 --match 2 --mismatch -3 --gap_open 5 --gap_ext 2 -N -3 -a 1 + Process pid = 14406 + Parameters summary: + Index: dataset_2 + Seed length = 18 + Pass 1 = 18, Pass 2 = 9, Pass 3 = 3 + Gumbel lambda = 0.605605 + Gumbel K = 0.332977 + Minimal SW score based on E-value = 17 + Number of seeds = 2 + Edges = 4 (as integer) + SW match = 2 + SW mismatch = -3 + SW gap open penalty = 5 + SW gap extend penalty = 2 + SW ambiguous nucleotide = -3 + SQ tags are not output + Number of threads = 1 (OpenMP is not supported with your current C++ compiler). + Reads file = /private/var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmpuYZa_K/files/000/dataset_1.dat + + Results: + Total reads = 1 + Total reads passing E-value threshold = 1 (100.00%) + Total reads failing E-value threshold = 0 (0.00%) + Minimum read length = 89 + Maximum read length = 89 + Mean read length = 89 + By database: + /private/var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmpuYZa_K/files/000/dataset_2.dat 100.00% + + Sat Sep 23 09:30:45 2017 + |
| b |
| diff -r 1eafcc450052 -r 65c38d020fea test-data/test3_aligned_forward.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test3_aligned_forward.fastq Sun Sep 24 14:28:47 2017 -0400 |
| b |
| b'@@ -0,0 +1,3812 @@\n+@ERR1877483.1 M03099:23:000000000-APTLR:1:1101:19252:1849/1\n+CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCCATTCCCCGTGTGTGCTGCTTGCCTTCGGTTTGTATATCACTTTCTTTTTTGACGACTCTCTTTTTTTTATTACCTTTCTTTTTTTACTTTACCTACATTTTCTGCTCCGTCTTTCTTCTTTCCTTCTTCCTCTCTCATCCGTATGTTGCAACCTTTTTTCTTTTTTCCTTTTCTTTTATCTCTCTTTTTTGTTTCTTCACGTTTTCTTTTACCTCCCCTTTCTCTTCCTGTTAACTTCCTCCTAT\n++\n+@CCCCGGGCGGGGGGGGGGGGGGGGGGF9FGGFGFEFG<F+6@+C6CC,;6C,,69,9,9C,:+8,C,C,,,,,,,,,:6C<,,,8=,:,,,,5,99CC,,,<5,+++,+++++,5,,9,,+8>,,:,,,55,88,558=+,3,8=,8,,,,,,,,8,,,3,73++,8+,8@,8,7,7,,,3,,,,,3,,7,,6,2**,,,,7,2,,,4,7<,,40,,,,63,23++,+35+,++1+4+++1+++/*+20++++*+*22****+03*+*228*/**+20+++305*++***1*.)0*,)**\n+@ERR1877483.2 M03099:23:000000000-APTLR:1:1101:15851:1971/1\n+CCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGTGTTTTGGTTAATAACCGCAGCAATTTACGTTACCCGCAGAAGATGCACCGGCTACCTCCGTGCCAGCAGCCGCGTTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGTGCGTAACGCGCTCGCAGTCGTTCTGTCAAGTCGGTTGTTAAATCCCCGGGCTCAACCTGGGAACTGCATTCTAA\n++\n+6ABCCGGGFEGGGGGFGGGGGGFGFDGGGGFGGGGGGGGGGGDEGGGF8F9E@CC<8F,@F+@:F@@,CC,,,,,9CDCEDE7C+CFCFC,,,C,9CFFE,,,4++>++>+,,+:,CF,B8+BD<,@,,38+:++6,,::,,3+@B,3:,*3***,,,,7,,7<F**B7,3:><*@***,,*,4<<:8**4**4,7=8****;*;+++**;C**<<**/*;@+3<+++0*2*/**2*****)*.*02***2+<+*023***)1*9*:+700<C5***)/*++2;:5**))09*))2:6**/\n+@ERR1877483.3 M03099:23:000000000-APTLR:1:1101:23102:1978/1\n+CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGCAAGCCTGATCCAGCCATGCCGCGTGTGTGATGAAGGCCCTAGGGTTGTAAAGCTCTTTCCCCGGATAAGATAATGACGTTATCCGTAGAAGAAGCCCCTGCTAACTTCGTGCCAGCATCCGCGGTAATACGACTGGCGCTAGCGTTGTTCGGTATTACTGGTCGTAAAGCTCACGTAGGCTGATCGATCAGTCATGGGTGCAATCCCATGTCTCACCCCTGGCTCTGCCTTTCATACTTTCCCTCTGGATTATGTCAGAG\n++\n+CCCCCGGGGDGGGGGFGGGGGGGGGFGGGGGGGGGGGGGGGGG>CFGG8FEFFFEF8E,CFBGEGG,,E,C<,9,,CEE=C8=@,CC@FF9,9CCFFFE,,54+7++4,C,E,,9,,9+++,:5<++,++,,,,,33A:+8=,,,,75C+B+:=<,+,,@@+@+@@**@,,*****,,*1>*5>:14*=B>6**26F9BF:,,5*1*+*2?+4<3*<*2*++**5;*110*<<+<+3+*3**+*3<:+++*+3377*/*11****37+9*3+:++3+2330+++-7A+)***/.)2*)**/\n+@ERR1877483.4 M03099:23:000000000-APTLR:1:1101:22637:2119/1\n+CCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGGGAAACCCTGATGCAGCCATGCCGCGTGTGTGAAGAAGGCCTTCGGGTTGTAAAGCACTTTCAGTTGTGAGGAAAAGTTAGTAGTTAATACCTGCTAGCCGTGACGTTAACAACAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCGAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGCTAGATGTGAAAGCCCTGGGCTCAACCTGGGATGGTCATTTAGA\n++\n+88BCCGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGEFCFGGGGGGGGFFFGGGGGGGFFFFFGGGGGGGGGGGGGGFGGGGGGGFFGGGGGGGGGGGGGGGGGGGGGGGGG@FFFFGGGGGGGGFFGGGGGGGGFGGEGGFGGGGGGGGGGGGGGGGGGEGGGGGGGGFGCFGGGGGGGGGGGGGGGGGGGGGGGGGGGGDEGG>FGGGGGGGGC>CEEGEEGGGGGGGGF?ECGGGGCFDFGGFG>FCFGDFGGG(.::>4>F9:<7729F:\n+@ERR1877483.5 M03099:23:000000000-APTLR:1:1101:18265:2244/1\n+CCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGTGTTGTGGTTAATAACCGCAGCAATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTCTGTCAAGTCGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCGAA\n++\n+68ACCGGGFGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGBFFFFFFFEFFGGFFEFGGEGFGGFFGGGGGGGGGGGGGGGGGEGGFGGGGFDFGGGGGFGDEGFGGGGGGGGGCGGGGGGGGGFFGGGGGGGGGGGGGGFFGGGGGGGGEGGDFGGGFGFE8EFGEEGGGGGGGGGGEEGGGGFEE8EGFGGGGGGF?@FGCG*:CGCFFFGGG5EGGBGGEGEEE@CEDGGFGGGGCG6CFGGGFFG=CEGGEEGGGG:>FGFFF?F?BC>AF@>\n+@ERR1877483.6 M03099:23:000000000-APTLR:1:1101:12491:2265/1\n+CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGCAAGCCTGATCCAGCCATACCGCGTGGGTGAAGAAGGCCTTCGGGTTGTAAAGCCCTTTTGTTGGGAAAGAAATCCAGCCGGCTAATACCTGGTTGGGATGACGGTACCCAAAGAATAAGCACCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGGTGCAAGCGTTACTCGGAATTACTGGGCGTAAAGCGTGCGTAGGTGGTTGTTTAAGTCTGTTGTGAAAGCCCTGGGCTCAACCTGGGAACTGCAGTGGAA\n++\n+88BCCGGGEGGGGGGGGFFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGEGGFFGEEFFFFGGGGDCCFGGGGGGFGGGGGFFGGGGGEGE,FFEGGGGGGGCE@FFGGGGEFFFBCGGGGGGGEGEDEBDGGGGGGGGGGGGGFGGGGGFFGGFF>:CGDGGGGGFECB@CCGGGGGGFEEECBCCGGGGGCEEFGGGGGGGGGCC?CFG/:?@GGGGGGGDEE5CFG5CEC@CFGGGGCGG'..b'19:14312:24605/1\n+CCTACGGGAGGCAGCAGTGGGGAATTTTGGACAATGGGCGCAAGCCTGATCCAGCCATGCCGCGTGTCTGAAGAAGGCCTTCGGGTTGTAAAGGACTTTTGTTCGGGAGGAAATCCCGCTGGTTAATACCTGGCGGGGATGACAGTACCGGAAGAATAAGCACCGGCTAACTACGTGCCAGCAGCCGCGGGAATACGTAGGGTGCAGGCGTTTACCGGATTTCTTGGGCGAAAGGCGTGCGCAGGCGGTTTGGCAGTCCGATGGTGAAGGCCCCGGCCCCAACCTGGGAACGGCATTGGAG\n++\n+CCCCCGGG@GGEBCFGGFFGGGEFGGGGGGFGDFGGGGGGGGGGGGGGE<9EFFGGFFGGGGGGGGEFGGGCDFGGGGGGGGGDGGGGGGGGGGGGGGGGGGGGGCEFGGGGFGDGFEDEGGGGGGGGGGGGGGGGGCFCFGEFDFGGGFGCFC@DFGCGFCGGGGGGGDCGCFCFGGGCCFFFGFGEGC*:E6@@C:CFCC::8::*/*;**/++;*?*/+++2AF8;:*:C8*/://*2*/:**:CEGE*/6C5*+*1**/*2+<90+8EG5EG*)**;*;:6E=/>+*.*0(:*<:60\n+@ERR1877483.32952 M03099:22:000000000-APTMA:1:2119:20365:24795/1\n+CCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGAT\n++\n+CCCCCGGGGGGGGGGGGGGGGGGCEGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGC<FFGGFGGGDGGGGGFGGDGGGDDGFGFFDAFGGGGGGGGGGGGGGGGGGFEFF7CFGGGGGGFGFCFFDGGGGGGGFGFGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGG?CFGGGGGGGGGGECEFFFGGG*:EEG@C?EGGGGGG>GGGGGG*8FGF99C7AC:FDFFD7CFGGGGCE5CEGGFGGGGFGGGFF4*)<>77DF\n+@ERR1877483.32953 M03099:22:000000000-APTMA:1:2119:9975:24853/1\n+CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCCATGCCGCGTGTGTGAAGAAGGTCTTCGGATTGTAAAGCACTTTAAGTTGGGAGGAAGGGCAGTAAGTTAATACCTTGCTGTTTTGACGTTACCAACAGAATAAGCACCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTCAGCAAGTTGGAGGTGAAATCCCCGGGCTCAACCTGGGAACTGCCTCCAAA\n++\n+CCCCCGG7C@CFGGGGGFGDGGCEFGGGG9FFGGGD9FFGGGGGGGGGCEFGGGGGDGGGGGGGGGGGGGGCFGFFGCEFFGGDGGFFEFFFAFGGEDGGC<BE@,>BF+?FFCFGFEF<@<EF9FGGGF,B,AAFGGGGGGGG3DF@FFFBF8DGFDFFFFFFCDGGGGFGGFFGGGCD7*@:@FC:><FC7FFF7CFGGGGECFG<F71=F>FFGBF<CFCEGFC@8BC>8C+CEEGGGGGGDGFFGGGGGFF*29:@FFF8CFG60<C:C7:?:5EG6CCCGG==FCCFG=:C6=>7*\n+@ERR1877483.32954 M03099:22:000000000-APTMA:1:2119:11950:24861/1\n+CCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCAATGCCGCGTGTGTGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGGTTGTGGTTAATAACCGCAGCAATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTCTGTCAAGTCGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCGAA\n++\n+CCCCCDGGGGGGGGGGGFGGGGEGGGGGG<CFGGGGGGGGGGGGGGGGFGDFDGG,FG9FAFGGFGG,CFGFFGCFGFGFE9CGEGGGGFEFGFGGGFGGGF94C+C:FCGGF7+3BF7+BFGGGGGG<FF+++@+,<FFGGG>C*FGG8:::FGGGGGGG7EGGGEGGGGGGGGGGGGGFGGGGFEGGGGGGGGFGGGGGGEGGGGGGDEG?CGGGGGEGGGGGGGGGGGGGGGGGGCEGDGGGGGGG>EGF+7<AGGCGDGEGGGGGFCCFGGGGG*@CEGGGG=FFGFFFFFGG??FC\n+@ERR1877483.32955 M03099:22:000000000-APTMA:1:2119:9959:24862/1\n+CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCCATGCCGCGTGTGTGAAGAAGGTCTTCGGATTGTAAAGCACTTTAAGTTGGGAGGAAGGGCAGTAAGTTAATACCTTGCTGTTTTGACGTTACCAACAGAATAAGCACCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTCAGCAAGTTGGAGGTGAAATCCCCGGGCTCAACCTGGGAACTGCCTCCAAA\n++\n+ACCCCGCE;FEG,CFEFGCGGGFGGFAFGF9EF<FFCEFFECFCFFGGGCFGFF@CEDGF@C@ECFGGGGGFDEEFGG<CEGGFGGGFFFFGFECEDFGGGGFFFGG<FCCCFGGGGGGGGGCFFGFGFGCFFGGGGGGGGDFFFGGEFCGGCFDGGCFGGGG,FFGDGCGFFFEFGG>FFFGGFGGGGCFECCDFGGGGEGCFEFGGGGG:<CGDFGE<;FGC9A:<5CEGD>CF5CE5C*:8ECGCEF<CGGG;CC:98F6=EFGEG7@6@=GGG<EFFF8*9=D7<FGFFFB6F274:\n+@ERR1877483.32957 M03099:22:000000000-APTMA:1:2119:17520:25205/1\n+CCTCCGGGAGGCAGCAGTGGGGAATCTTAGACAATGGGGGCAACCCTGATCTAGCCATGCCGCGTGAGTGATGAAGGCCCTAGGGTTGTAAAGCTCTTTCAGCTGGGAAGATAATGACGGTACCAGCAGAAGAAGCCCCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGGGCTCGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGTAGGCGGACCGTAAAGTTGGGGGTGAAATCCCGGGGCTCAACCCCGGAACTGCCTTCAAAACTATCGGTCTGGATTTCGAGAGAG\n++\n+BCC-8@7:+6@CFDFGGDFGGG77EEFGGF<FFFFF-CFFECFCGGGD,@FFF9EEFFEC6CEGECE@GGGEE<CAFFE?FGGFCFFGGFEFGGG?BBFFFGGDGFD<FF8F?FFGAEGGGGGGFFC<A<EEE8EEFGGE7@G:=FGEFGGGGGDFGGGGFEGGDF*CF=CGG@:FGGGE7*=CGFDGGC9CC7*=:CFFC68CECECCCFGCEGGCFGGECGGGEG:*:/<F9+<5EGECC9<CC+AEEGDGC3:9EFC>95C=88<EEE7C6<++9<@CFCEGGGGG:+9CF?C*2>C<\n' |
| b |
| diff -r 1eafcc450052 -r 65c38d020fea test-data/test3_aligned_reverse.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test3_aligned_reverse.fastq Sun Sep 24 14:28:47 2017 -0400 |
| b |
| b'@@ -0,0 +1,3812 @@\n+@ERR1877483.1 M03099:23:000000000-APTLR:1:1101:19252:1849/2\n+CACTACCCGGTTTTCTTATCCTCTTTTCTCCCCCCCCTTTCCCCCCTCCTTCTCCGTTTTTTTCCCTTTCCTCCCCTTCCCCTCTTTTTTTCCTTCCTCTTTCTTCCCCTTTCCCCTCTTCCCCCCTTTTTCCCCCCTCCTCTTCCTTTCTCCTCCTCTCCCCTTTTCTTTTTCCTTTCCTTTTTTCTCCCCCTTCTTTCCCCTCCTCCTTTCTCTCCCCCCTTCCTTCCCTTTTCTCCCCGTTCTTCCCTTCCCCCCCTTCCCCCCTCTTTTTTCCCCCCCTTCTCTCCCCCTTTTTCC\n++\n+--86,C,@+8+@,6,6,,;6C,,;C<-<;,;66+8+@+6<,,;,+8+,,,6,96,+9,66,+86:,,,,,,6,,,8,9,,:9,4,:,,::+,:,9949,,,,,,,5,,,,47,,84,4,,,,,,+++,,,6,7,33+++6,,2+,3,,,3++,,*,,,,*,,*43,/,3+,,,,*22+5,,,,22*,+13,*)*,2,2<+223),**(.*2.4+++*/*//4*(00)..).)0)).*))0*(0)((.)1())))(((((-,,0*2/),/,-)-0((.,((--((()).,.,****0+0()\n+@ERR1877483.2 M03099:23:000000000-APTLR:1:1101:15851:1971/2\n+CACTACAAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCTCCTGAGCGTCAGTCTTTGTCCAGTGGGCCGCCTTCGCCACCGGTTTTCCTCCAGATCTCTACGCATTTCACCGCTACACCTGGTATTCTCCCCCCCTCTACACTACTCAATCCTGCCAGTTTCGAATGCAGTTCCCAGGTTTAGCCCGTGGATTTCACATCCTACTTGCCATACCGCCTGCGTGCGCTTTACTCCCCGTAATTCCGATTTACGCTTGCCCCCTCCGTATTACCTCCGCTGCTGTCCCCTTCTTAGC\n++\n+-8AACFDEFGGF,CCE,CCCFC9CFC-EFEF66,@F@CCDE@C,C@E<,,,+8@66C,F<F<FAE<,,,,,,9++@=?=,BB,?,6+>+?C,5E@E8,,:499A,?<44@CFA,CB+6>@>,AEE8,,,9@=A,C?80=BEEG+=,,,,6==@,+6,7=8>,@D=D;+++859,+7;BC?,,4@:,,+8,:**4*66?F+5B,=>:**10=**9++*0,*7B*2A5/(680,88)>+)/2*-.)((6)92(-5)).(2(4(-00777<7(:08F)64).((46(34).4:2****30*).\n+@ERR1877483.3 M03099:23:000000000-APTLR:1:1101:23102:1978/2\n+CACTACCGGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTCAGCGTCAGTATTGGACCAGTTCGCCGCCTTCGCCACTGGTTTTCCTCCGAATATCTACGCATTTCACCTCTACACTCGTTATTCCACTCACCTCTTCCATACTCCAGTTCGCCAGTTTCATTCGCAGTTCCACGGTTCATCCCTCGGCTTTCACTCCTTACTTATCGCTCCGCCTACCTTCGCTTTACGCCCAGTACTTCCTCTCACCGCTCTCCCCCCTCCTTTTTCGCCGCCTGCTTTCCCCTCTTTATC\n++\n+9BCCCG<BEG>F7<CC,6ECED9CFC-CECEC@CCCFC:DE@FECFCAC,6+8@,:C,,9,,,:EC,C,9,+B+=:C@A<FE,8=,::54=9E=,4+++8+4A@,C+++8?AF,@<4>9,A,,,:+4++46,A,C,@+@DCDEFGA,6,@==,,*,333+>+3@,34,,+,,+++5;9;,,3*55*,+474,****1>F9+=,;>D+A9:4//B)))/1*9<*8F*79=.(,15)7)((**(2:7<?461))8*)((,(((.0:37)(1(.).7)2(((((,,((,))-).****20*-6\n+@ERR1877483.4 M03099:23:000000000-APTLR:1:1101:22637:2119/2\n+GACTACTAGGGTATCTAATCCTGTTCGCTACCCACACTTTCGCACATGAGCGTCAGTCTTTGGCCAGGGAGTCGCCTTCGCCACTGATGTTCCTCCAGATATCTACGCATTTCACCGCTACACCTGGAATTCCACTCCCCTCTCCAAGACTCTAGTCTGCCAGTTCTACATGACCATCCCAGGTTGAGCCCAGGGCTTTCACACCTAGCTTAACAAACCGCCTGCGTGCGCTTTACGCCCAGTAATTCCGATCAACGATCGTCCCCTCCGTCTTACCGCGGCTGCTGGCACGGGGTTAGC\n++\n+CCCCCEGGGGGGGGGGGGGGGDGFFGGGGGGGGGGGGGCFGGGGGDGFFFGGGGGGEFGGGGGGGGGGGFFFFGGGGGGGGGDGGGFGGGGGGGGGGGGGGGGGGFCEGDFGGFFGGDEGEEFGGF<EFFGGGGGGFGGE8EGFGGD8FGGG83BDADFGGGFFB;9E,?FFFFGGGFGD?EFD==EGFD7CFGG:@8FCCAC*:603ADEAABAF;CFGDGC7AD=(66>@DFEEFF@>*/86))9<6(6;)268((,/((/:97*(2-4(80)).46;6>7>0:??:025C*7?5*.6\n+@ERR1877483.5 M03099:23:000000000-APTLR:1:1101:18265:2244/2\n+GACTACAAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTGAGCGTCAGTCTTTGTCCAGGGGGCCGCCTTCGCCACCGGTATTCCTCCAGATCTCTACGCATTTCACCGCTACACCTGGAATTCTACCCCCCTCTACAAGACTCAAGCCTGCCAGTTTCGAATGCAGTTCCCAGGTTGAGCCCGGGGATTTCACATCCGACTTGACAGACCGCCTGCGTGCGCTTTACGCCCAGTAATTCCGATTAACGATTGCACCCCCCGTATTACCGCGGCTGCTGGCACGGAGTTAGC\n++\n+CCCCCDFGGGGGGGGGGGGGGGFFFGGGGGGGGGFEGGGGGEFGGGFGGGGGGGGECFGGGGGGGGGGGGGCGGFGFGGGGGGGGGGFDFGGGGGGGGGGGGGGFFFECEGFGGGGGGGEGGGGGGGGGGDFGGDCFG>EEGFFGGF?EGDCCGFGFGGGGGGFFGFGGGGFFFD<@FGGGGGFGGGGFEGGGGGDCC@FGFGF@GG7597@EAFFF@:78:56>C??BDB9D:AFB(7:/./8)).)64<:::2>62(332:9CD)4C>814FFFF6114029?4:?BFFGG59*2*.:\n+@ERR1877483.6 M03099:23:000000000-APTLR:1:1101:12491:2265/2\n+GACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGTGCCTCAGTGTCAGTGTTGGTCCAGGTAGCTGCCTTCGCCATGGATGTTCCTCCCGATCTCTACGCATTTCACTGCTACACCGGGAATTCCGCTACCCTCTACCACACTCTAGTTGTCCAGTTTCCACTGCAGTTCCCAGGTTGAGCCCAGGGCTTTCACAACAGACTTAAACAACCACCCACGCACGCCTTACGCCCAGTAAATCCGAGTACCGCTTGCACCCCTGCAACTTCCGCGGCCGCTGGCCCGAAGGAACC\n++\n+CCCCCEFFGGGGGGGGGGGGGGFCEEEFGGGFGGGGECECFEFDGGGG8FGGGGGGFGE@EFG9E<FFGGGGGGGGGGGGGGED@EACFGFFGGC=CFC7=F;,9EFG@CFGF,@CBFG;DDGGGGGE=EGA;FG+CD8BCD8FCGFFAEDFCFFGGGGGGGGDBB9DGCAFFFD9+CFFF,=FFD,=*@@F6:8+48B?;4=*8,*1;7@AA>8<0:84CG5<@82/(2((85*85(,4*,017).7).2,0=)6(1((((0AD*),*(())'..b'000-APTMA:1:2119:14312:24605/2\n+GACTACCGGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGTGCATGAGCGTCAGTGTCATCCCAGGGGGCTGCCTTCGCCATCGGTATTCCTCCGCATCTCTACGCATTTCACTGCTACACGCGGAATTCTACCCCCCTCTGACGCACTCTAGTCTTGCAGTCTCCAATGCCGTTCCCAGGTTGAGCCCGGGGCTTTCCCATCAGACTTGCCAAACCGCCTGCGCACGCTTTACGCCCAGTAATTCCGATTAACGCTTGCACCCACCGATTCCTCCGGCCTCCTGGCACGGCGTTTCC\n++\n+C<BB8FG7FGGG7EEFCDGFFFFEEEFGGGGGGGEFGEFGGGGFGG9BFGACGCCCGGGGAGFGGEFFGGGGGGGCGGGECFGGGCEEAFFGGFGCGDEGECFGFGDGGGGAFGGDFEAEF9?:7CGGGDGEGGGFGGGECEGFCDED6>CF7>87;CFGFFAFFGE9D6;,,?4?D58E9B>C902*;?E*:EDD<>C:+7+6;A*7;;>/7(//61;/7C)(8)149D>4-4<A616CC6(*).5<28:3:14>(16:?FC05)(-*(((4)))0.(,((((4(.,((.,(((**())\n+@ERR1877483.32952 M03099:22:000000000-APTMA:1:2119:20365:24795/2\n+GACTACAAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTGAGCGTCAGTCTTCGTCCAGGGGGCCGCCTTCGCCACCGGTATTCCTCCAGATCTCTACGCATTTCACCGCTACACCTGGAATTCTACCCCCCTCTACGAGACTCAAGCTTGCCAGTATCAGATGCAGTTCCCAGGTTGAGCCCGGGGATTTCACATCTGACTTAACAAACCGCCTGCGTGCGCTTTACGCCCAGTCATTCCGATTAACGCTTGCACCCTCCGTATTACCGCGGCTGCTGGCACGGAGTTAG\n++\n+CCCCCGFDFGGGFGGGFGGCGGGGGGGGGGFEGFFGGGGGGEGGGGGGGDDFGCGGGGGGGGFGEGGG@7CGGGGGGGFGFFGGGGDGDGGGGDFGGGFGGGFG;F@FCEFDGGGGGGGGGFGFGGGGGGGFF=FAD=+>E6F5ED88CCFGGFAF6CFGGGFG,;A@@BFGGEFGGCGFCFGFF,8DFFEE<EG):8FGF?ACAGG3;EEEEEE618C85FD;?FB0<39>F06<:<9>C??*4:<<A0(341<B?F:(((+18)4:9(4(4.4:C,2,190(44?(3(5(((4=:)6\n+@ERR1877483.32953 M03099:22:000000000-APTMA:1:2119:9975:24853/2\n+GACTACAGGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGTGCATGAGCGTCAGTGTCATCCCAGGGGGCTGCCTTCGCCACTGGTGTTCCTTCCTATATCTACGCATTTCACCGCTACACAGGAAATTCCACCACCCTCTACCATACTCTAGCCCAGTAGTTTTGGAGGCAGTTCCCAGGTTGCGCCCGGGGATTTCTCCTCCAACTTCCTGACCCACCTACGCGCGCTTTACGCCCCGTAATTCCGATTACCGCTGTCACCCTTCGTATCACCGCGGCTGCTGCTACGACGTTAGC\n++\n+CCCCCG8FFGGGDGGFGGGGFGAFGFGFFG@FGGGGGGDFFD;@FFFCFGGGFGC:FEEFDACF@FB@:87FF@FD9,CDFGEGGG8FFGG?9,CFFGDFGGEGFGD@F74?C<EFFGEEFDGF@ECEA<AEGGGGGF+@DDF5=AEGGF9DDDFGG8DFGG?F,@9>76,8>8:C+7D93,1,@,3@C7:**;C>D>BB+:,*A68235<*.4*+(02*:<8@E87(:.6,(349(4(:*(-),44<2((-34)-19>(-4097.,8F:<0(()-2-21(-,40::))-62:9(2/2(.\n+@ERR1877483.32954 M03099:22:000000000-APTMA:1:2119:11950:24861/2\n+GGCTACTAGGGGTACTAATTCTCGTTTGTCCCCACGGTTTCGCACCTTCACGGTAGTCTTTATTCCGGCGACTCCCCTCGCCACCTGTAGTCCTCCAGGACTCTACGCAATTCACCGCCTCACCTGGAAATCTACCCCCCCCTTCCAGCATTCTACCTGCCCAGTTCCAATTCAGTTTCCCGGTTTAACCCCGGGGCTTCCACATCGACTTTACAGACCGCCCTCCTAGGCCTTACGCCCATTACATCCGATTAACGCCTTCACCCTCCGTATTCCCGCCTGCTCTGGCACCGTCTTAGG\n++\n+B-<,66;,;CF7,,6C,C,,;C68FF,,;;FGGCC@+:CF@,,,8FD@,,;6B6,,66;@F,,,C,,@+8+6+,,B,A,47C,4A,CCC?F,E,,9,9,+4,,,,4++++8C,C9C++614?EF,4B,4,93,4,E1=+8++4*532,,,++,++,32,,@,*,6<;9,@,,,,+7+*>D,*:*4*,++?C*8EG)):F**)+()3*(,(;).7//;(=))2)(()()))(,.),4-(4C*,)0))641(((-().(,(4()+9=F((1(,,,4)40((((((())))).)(,,,*2)-)\n+@ERR1877483.32955 M03099:22:000000000-APTMA:1:2119:9959:24862/2\n+GACTACAGGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGTGCATGAGCGTCAGTGTCATCCCAGGGGGCTGCCTTCGCCACTGGTGTTCCTTCCTATATCTACGCATTTCACCGCTACACAGGAAATTCCACCACCCTCTACCATACTCTAGCCCAGTAGTTTTGGAGGCAGTTCCCAGGTTGAGCCCGGGGATTTCACCTCCAACTTGCTGAACCACCTACGCGCGCCTTACGACCAGTAATTCCGATTAACGCTTGCACCCTTCGTATTACCGCGGCAGCTGCTACTCTGTTAGC\n++\n+CCCCCFFGCFGGGFFE9<FFGGGEDEFFFGEFGCFGGG@FGGGGGFFFEECGEE:FFGGADFFF,CFGCF7FFG:AA?FG,BBFF?CF=EEG,F9F:CFECAACFGF@FGG9FAFF@EGCGFG@@C8E<FEGEFG8AFC=D?DFGGGGGGFFFFFFGC==F;D63E2@EDFD>C5F8EE>A64CFGFFGF@5*547CFE25:;=A;C@055*98>F3;F4C<6(5>69;:0(/()((,,2*.6:6)-)-5?13(6:03:02439772:C:?12.)6749909(-80(()--))).:<)-5\n+@ERR1877483.32957 M03099:22:000000000-APTMA:1:2119:17520:25205/2\n+GACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTCAGCGTCAGTATCGAGCCAGTGAGCCGCCTTCGCCACTGGTGTTCCTCCGAATATCTACGAATCTCACCTCTACACTCGGACTTCCACTCACCTCTCTCGAACTCCCGACCGATAGTTTTGACGGCAGTTCCGGGGTTGAGCCCCGGGATTTCACCCCCAACTTTACGGTCCGCCTACGTGCGCTTTACGCCCGGTCCTTCCGATCACCGCTATCCCCCTCCGTACTACCGTGTCTGCTGGCCCGTACGTCGC\n++\n+--8ABFGE<@7<<FCFGGGF,CCCFA<FGG8DCECC+CCCEGGGDFF@FFFCFCC7EFGDC,,BFCF@D<,F8@4@FCGCEF7BEG,CEEGGGGEGF+,@@FGFGG?:,@+C;FFEC@DEGCG,B<:C6@C@FFFFFFC8FEDDGGG,@FGG,+:CGGGC7F*@=E*>B,+*@>5@;CGG>5C@CE74C<C*7=E3<5?FFC>8:731;8C3563)61:)7;7(.58:?342(:A<8?>G*-3)(6<4211(4-(419B0(.<?F7,39(38((.)2((((.)).60((((--((*0((4\n' |
| b |
| diff -r 1eafcc450052 -r 65c38d020fea test-data/test3_bam.bam |
| b |
| Binary file test-data/test3_bam.bam has changed |
| b |
| diff -r 1eafcc450052 -r 65c38d020fea test-data/test3_unaligned_forward.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test3_unaligned_forward.fastq Sun Sep 24 14:28:47 2017 -0400 |
| b |
| b'@@ -0,0 +1,188 @@\n+@ERR1877483.32476 M03099:22:000000000-APTMA:1:2119:6395:7637/1\n+AGCCCACGAGACCGTGCCCACGAGACCGAGCCCACGAGACCGAGCCCACGAGACCGAGCCCACGAGACCAATCCCACGCGACCAAGCCAACGAGAGCCTGCCAGCGACCCCCCACCGACTACTTCCTGACGACGGTTCCTTTCCCTCTACTAAATCTCATCCCCTGCTCACTGCGTCCAAGCGTCACCGGAAATACACATACCTACATCTCTAGTCGTCCTTACTTGTCTTTACTCGTGTCCATACTGTTCTTTTAGTCAACTGTAACATGCCATTTTTCTATGTTGTTCTATCCTTTGTT\n++\n+ACCCCGGECG@@6@,;FEF<FE:FE7<@+@CFGGGG:@:+D:@FG:CEC++8@B7F7+@@7<BF+C=++,:,,B,B=++@++@+,,++,,33++++:,3,3,B,:83++8@@***8***5*,,,,,,8,8*::<*8**,<,,,,,,+,,,,22,,,,8?FC,*4+<@,,,777</;**2+0***2*20***/*0++3++2++02+0++030+++2</2C**+++++0+303<+++<C****2<<+*++03++2+*+0+*29>?+<++++++0++3++*++0++02+3**0+*0*(3*+/2*\n+@ERR1877483.32486 M03099:22:000000000-APTMA:1:2119:14420:7911/1\n+ACGAGCCCACGAGACGAGCCCACGAGACGAGCCCACGAGACGAGCCCACGCGACGAGCCCACGTGACGATCCCACGAGACAAGCCCCCCCGACGCGCCCACGAGACGAGCCCCCGCTACGAACCCACGAGACGAGCCCACGAGACGAGCCCACGAGACGAGCCCACGAGACGAGCCCACAAAACACGCCCTCAGCCCGTACTCCGTCGACTTGCTCAAACAAACAAACCAAACATCGCAATTCACTTGCTCAATGCCTCCACATAAAACTTACTCCGACACCACTGTCGAATCACTTCTAT\n++\n+CC<@@:FFGEGGD+@FFC@6DEGFGC@@7+@FFFA@@@CF7,67@CFCF:+@+C>+4CFF,8=+9,A+B:EC?,<+4++@,,B,DD+@+6@+6@++5CC+3*5**5****1:+1****1**,4<FC71<*<*+**4CE5:8:2::/:*:CEE5**/*:**/**AC***2/:AE**:*;5***;****:8****++****/1*<8//*2**2*3+0++2AF885:**22*****2++*****0++3+++++++++*++0***0++3+03<+3+3++221**12**9+2+/1*)1*(+*+*20\n+@ERR1877483.32493 M03099:22:000000000-APTMA:1:2119:16611:8029/1\n+AGCCCACGAGACCGAGCCCACGAGACGAGCCCACGAGACGAGCCCACGAGACGAGCCCACGAGACGGACCCACGCCGCGAGTCCACTAGTCGACCTCACGTGCCGAGCCCCCCCCCGCGCCCCCCGACATACCCCCCCCTACCGACCCCACCCACCCCGTCTCACTACCTAGCCGCCGCCTCCCCCCGCCATCGTCACAACCCACCCAACAGAGAGCTCCAAGTCCACCCGCTCTCAGCATACACACTCCGTCCATCACCACATCCTCCCTCCCACCTCTTGCACTGCCCTTCACCCTCAC\n++\n+CCCCCDFGGGGE@CCEGGFFGGEDCF;CE7@FFCG@+6CFG7FDFFGGC:+@,F@FFD8F=++@C::=7FE<+++++844>4:?<<,,,,<>3+++3,BB,,+:++8FF<+@********4<F:F1**4*0,002::E5*/*0**:**2****1**/:*1*;;+3+++03++2**/*/********2*/:**+222**+0*288**/******+**2<+3+++++33<*/***:13+0++39C03+*****/***+332*058++*+0*;*8*C**22*++0+323+0C*<)*1)+/1)66\n+@ERR1877483.32499 M03099:22:000000000-APTMA:1:2119:19507:8186/1\n+AGCCCACGAGACCGAGCCCACGAGACCGAGCCCACGAGACCGAGCCCACGAGACCGAGCCCACGAGACCGAGCCCACGAGACCGAGCCCACGAGACCGAGCCCACTAGACCCAGCCCACGAGACCGCGCCCACGAGACCCAACCCACTAGACCGTTCCCACCATCCCGAGCCCACCATACCTAGCCCACTACACACCGCCCACGCCACCCCACCCACCACACCGCACCCCCATGATCTATCACACCTGAACCAGCACACGAGACCCACACCACGACTGACGGTCACACTCCACCGCATCCA\n++\n+CCCCCGGGGGGGGGEGGGGGGEGE@FGGGGGGGGGGCFDGFEGGGGGGGEG+C@F:7FFGGGGF:>CGGE@EGGGGGD7+:FGB+@CFCDFGE:3CC+@FFECEF,@@DEC,8>CFEDC5**1*=*4=<4<CFC:*<CC*8*877<:,2,3A6*1*0,A+**/+01:**:*:F*;*;3+2;++6C*2***+3+;+***1:*8C5***/;8**/*1:******/*/*/*1****00++++3++30<**+*+3;A55******)*/**/;*/*2/**:*)+3***/*2?6***/*0(*)*008\n+@ERR1877483.32513 M03099:22:000000000-APTMA:1:2119:13480:8544/1\n+AGCCCACGAGACCGAGCCCACGAGACCGAGCCCACGAGACCGAGCCCACGAGACCGAGCCCACGAGACCGAGCCCACGAGACCGAGCCCACGAGACCGTGCCCACCAGACCGAGCCCACGAAACCGAGCCCACCAGCCCGATCCCACGAGACCGCGACCACGAGACCGAGCCCAAGATACCGTGCCCACGAGCCCGACTCCCACGTCCCCAACCATCTTCACCTGATAAAACCACATTCGACTCAACGTGTCTACACCTCCACAGCTACCGAACCTATCCTCCCCCACGATCTACCTCCCG\n++\n+CCCCCGGGGGGGGGGGGGGGGGGGGGGGGDEGGGDE>@:FGCC7CFGGGG@:CGFC+@FCF8FFCCCFF@C+@CFFG7>@FF7@>=FC=FGGCF+:+C+3C<FCC+,8,@DC7*:>8D7<7*=1F77*=*8C7*****=***1<87+*2*1*/****/**/*1*2:8*:*::****22<C?****2;+1***1*//2/*/2**0**/***2*1/*+++000+3++*++++++2***++0+2;*/+0*//*+2++*0:**2/7*+**32<*8*****+00+++*****2)*/)*/)+*+.*-\n+@ERR1877483.32525 M03099:22:000000000-APTMA:1:2119:11271:8937/1\n+AGCCCACGAGACCGAGCCCACGAGACCGAGCCCACGAGACCGAGCCCACGAGACCGAGCCCACGAGACCGAGCCCACGAGACCGAGCCCACGAGACCGTGCCCACGAGACCGAGCCCACGAAACCGAGCCCACTAGACCGTGCCGACGAGATCGAGCCCACGTGAATGAGTCCAAGAGACCGAGCTCACAAGACAGATGCAACCGGGACCCGCCCACGATAGCTATCCCACGTGCGTCATCTCAATAATCCCTCGCAAGTGCACTCACCCCAATAACACGTGACACTACCATTGCGACAGT\n++\n+CCCCCGGGGGGGGGGGGGFDEGGGGGCGCEGGGGGGGGGGGFEGGGGGGGFGGGGGCBGGGGGCF:@FGEGGGGGGFGC:B@7+8@FCD<F=FFC:>5+3+>>BF*3:@FG**:F>FFG:C***,4*:BF*<@:,<<E:<*8F7*/**1/?*0****2/2;**/;*+00<++2+<+**2AC*22**+<+++2**+20++<2++0**2**1******1**2**3+03++++088*/*/2**'..b'9:19368:19712/1\n+AGCCCACGAGACCGAGCCCACGAGACCGAGCCCACGAGACCGAGCCCACGAGACCGAGCCCACGAGACCGAGCCCACGAGACCTAGCCCACGAGACCGAGCCCACGAGACCGAGCCCACTAGACCGAGCCCACGAGACAGAGCCCACGACAACGAGCCCACGAGACCGAGCCCACCAGACTCGTTGCAATAACGTGTGCCCACTTCCACTTCACAAAAAACCACGTCTATACTACTCTACTCTGACTTCATAGCTCACCTTACGGCTCACGACTACTGAAGCTTTCAGGCCTCAGCGATAA\n++\n+CCCCCGGGGGGGGGGEGGDGGGGEEGGDCGFGFFGGFFGBFE7FCGGGGGGEGGDCCC:FFEE@:>CCFC8+@FGGGEEDF:F,=F8=DFGCFFGG3@::7FBFD+**@CEC7B@FGGG,,3?,8<7*<::FCFE@<*2,,,,8*4<F>***1*1**/2***/::*2**:*2/2;*2/;*+<*;***+33++3:**32+<;AE>C+++<++++++0/;*1**/***/2*+20++<++0+++2+++++++3<+++*+++*+3*0**:**2+2*2**<+*<++++02+00***)2/(3)*)--\n+@ERR1877483.32864 M03099:22:000000000-APTMA:1:2119:18423:20592/1\n+ACGAGCCCACGAGACCGAGCCCACGAGACCGAGCCCACGAGACCGCCCCCACGACACCTATCCCCCGCGCCCAGCCCCCCGAACCCCAGCCCACCACCCCTACCCCCCTAGACCCACCCCACAAGACCCAGCCCACGCGACCAAACCAACCACCCCCCCCACACACACCCCACACCACCCAACCCAACCAACCGAACCCAACCCACACGACCCAAACCACGCCACCCAGACCCCACCACACACCCCCCACCCCCCCCAACACTCCCCCCCCACGACCAGCCCAACACCTCCACACCCGACC\n++\n+CCCC@CGGGGFGECFCC@FGFG8C:6++@CCE+@6C-@+C+8CDF7+@:F++@B++@C,C,,C,++++++8@+,,BF+8+++3+@FE++D<F,3+3++@++:,@3D*5**,,88,,**8*8*1,,38,,8,,8********<****=88******1**1::C8C85:*2*2***/*;/**1*2*2**/***2;***2?C5**/*:8*****2/*/*8;*;***********2*****;;/**:******/****)2*****1+*2*2/****2***/9****1//*:****)2)(*)*)1-\n+@ERR1877483.32898 M03099:22:000000000-APTMA:1:2119:24030:22105/1\n+ACGGGCGTCGGAAGCATCAGGGCCCGACAGTGCCAGTCCTGCCATGGGATGGGCGGCAACGAACCGCGCCCTGCCGGGATGGTTCTCAATGCTGCGGCAAACGGCGTCTTTTACCGAACCGGCATCTATCACCACGGTCTGATCTCCGGTGCGGTCAAGAATACCGGGAAGAATAGCGATGGTGGTATCGACCGGGACGGTGATCAGGACCAGCGAGGCATCACTGAGTGAGTTCTCCAGTGAGGTGCTCCTGTCAACCCGTCCCCTTGAAAGCGCCTGCTGCAAATGGCCGGCATTTGTT\n++\n+CCCBCGGGGGGGGGGGGGFGGGGGGGGGFEGFGGGGGGGGGGG@FEGGFGGDFGDFGGGGGGGGG@FCEGGCEFGFEF>:FGFEFGGGFGGGFFGGGGGGGGCFGGGGGGGG<FEGCGGGG:FGGGDGFGFFGGG@CCFCF9,FFFG7FGCCFGGGFGGGGGC:FE:CEEEG8CDGGDGGGCFGGGGGGEGGEEGGEGGGC>EEFGGGGGGF/@CE8CEGFGC9<<FGFGGGGGGGGG?FGGCCDFCDCFGGGGG9C?F*:>GEGGG>*<8<EGEGEGFG?FCCF7C?=CC5DB>E*+/:*\n+@ERR1877483.32926 M03099:22:000000000-APTMA:1:2119:7498:23338/1\n+ACGGGCGGTGGCGATCTCGTGGACGATGACGTTGATCCTCGTCTCCCCGGATACGGGGATGAAGCTGCAGCCGGTGCCGTCTCTGACCAGCTGGGCCTCCAGCTGCCTGCCCGCAAAGCCGGCGATGAAGCCGCGGGCCCGGTTCTCGGCGCCGAGGGCGGTCAGGACCTTCGATACGTCGATCCCCTTCCCTCCGGCGTAGCTCTCCTCCCGGATTATCCTGTTGGGGACGTCCTCCCTCATCACGTCGATGAGGAGGGTCCGATCGAGGGCTGGGTTGATGGTTATGGTGTAAATCATC\n++\n+CCCCCFFGGGGGG+FFFFGGGGGGGGGGGGGGGGFFGGGFDEFEFGFGFFGGGGGGEGGGGGGGGEGGFGGGGGGGGGG?FGGGGGGGGGGE8FC=FGGG@CGGCCFAFGGGGGC7:FFFEEGGCFGAFFGGD*3:F:C<:7<FGGGCFGCGGD<?8>EGG>CGG8<CFFFGF8CFG5EF5CGGGGGGGGGGGGGGEGGGG*@?@?CCFFFGE>EG>CCCFFC?@+*:8:CEE:EEFGGFG=7@9920;E>89<DGG?D*ACFGEEECG;C*86:;ECEG++<CFC+<C+3/>74+*2*2A\n+@ERR1877483.32949 M03099:22:000000000-APTMA:1:2119:22063:24539/1\n+ACGGGCGGTGTGTACACATCTCCGAGCCCACGAGACAGCCCACGAGACATCCTACGAGACCGCCCGCAAGAAAGCCCCCGAGACATCCCACCCTCCGGCCCTCCAAGAGAACGACCACGCGGCCCACGTGCCCCGACACCTAAGCGGGTCCTAGAAGGCGCAAGCACGACTCCCTCCGTGCTAGGGTCAGCCCTCATACGACGGAAACCCGCGATCTTCTTAATCAACGTTCGCTAGAACACCCTAGGCTGACTCCGACGAACAGACTGCAGGACCGACGCTCGACCCCGCAACCACCACG\n++\n+CCCCCD@CFG@BE,CF<,CCFGGDE:@FCA@@@@:@<F,,@@6+++++C,,,,9:,6,7@6:CCC+4+@>F,,,:,+4@++4++4,:,B,A+8=+++3++@+=+:,,:<,,,63+++++++3*******,**3*4**4**,,,,,******8><,,8*<<5**2**0*****+/02**1;;*+0**22*;+*2***+2<0;**//**0*;*1**::*<+,+3333<+**1*;***2*++3**:*8?00*+**0+*+*/)**)2/0;*+3;++**//2)****/*)2**/22)1.,*9*)/-\n+@ERR1877483.32956 M03099:22:000000000-APTMA:1:2119:14880:24914/1\n+ACGGGCGGTAAGTAGAGCCGATTCGTTGACAAGGTTGGCAAGGTCAGCACCGGTAAACCCGGGAGTACCCCTTGCTATCACTTTGAGATCTACCTCCCGGGATAGAGGTATCTTCCCCGAGTGAACAGCACGTATCTTCTCCCTTCCCTTAACATCAGGAACATCAGCAATGACCTGCCGGTCGAATCTACCAGGCCTTAAAAGAGCCGGATACAGAACATCAGGCCTGTTTGTGGCAGCTATGATTATCAAACCCTCAGTGGTTTCAAAACCGTCCATCTCAACAAGAAGCTTGTTGAGA\n++\n+CC8B@:FEFGCFF<FGGFGEFFEGGFF@@FFCFDFFGGGGGC,66,CFCFCFGGGGG@@F:B@=>6C,,6DFF8<<CFCFGGCGCEFGFFDFG<F54+8CE:><=FGGGGGFCF,CF<FFGFCFCFCFF@,@>3?FCFF<D9BFG8D8FFGG9DGFGGGG7BDACF,,@<BGCFCGDFCFG@CFCFCGG,DCG,<FC:FCGGG91FFCEGG@*?915?B:@FGCE78<*5?B+2*88*:5CC9E:CD7+A7+3995>84+<*;F7*A?<EC@C*A;83?+2:9C<+:676+)0*.:>6?**\n' |
| b |
| diff -r 1eafcc450052 -r 65c38d020fea test-data/test3_unaligned_reverse.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test3_unaligned_reverse.fastq Sun Sep 24 14:28:47 2017 -0400 |
| b |
| b'@@ -0,0 +1,188 @@\n+@ERR1877483.32476 M03099:22:000000000-APTMA:1:2119:6395:7637/2\n+CCCTCCTCTCATATTATTTGATCCCTGCTCTCTACTTGCTCGTTCATGCGCACCTCTTCAGTACAATTGTTTTGCCTCCGTAGTCTTTGGTCCTACGCATAACTACGCATTTCACTGTTCAATGCTAATTGCCATTCCTCTCTCTCTTAATCATTCGAGCGTTCCACCACTCCAAGTCCATCTCGTGTCCTGTGTCTTTCAACTCTTTCTTACCTCTGTGTCTGATCCTGTGTTCCGTCCGTTCATTCTCATTTATCATAGCTCCCTGTTATGTATCCATTCTTCGCGTTCTGTATGGG\n++\n+-6,,6@FE,,,,,<9,,,<,,=,6-C<E,;@,,,,,,,6C,,@,C6;E;+,++7;,,,;,,6,6,,,,,6,,;@<,,59:@,889,,,,,:?BF9=,@F7,99E,,,+4,,:,9E,9,4,,,,99A,,,,,9:9,,,+94;=,+99,,3,+?,3+,,,,+++31:,16@+,,@,*6+*,,,,,,,+,66,3,6,,+269++*,*+@+;3*,*;)*5*)52+,+**+0***0)*5**))0**0)3)**/2**2*/*/***1*7,+**))0*****/9+**11*0**-(,((/6..)4+((\n+@ERR1877483.32486 M03099:22:000000000-APTMA:1:2119:14420:7911/2\n+CCGGTCTGTGTGTGCCCTATCGCCTCTATCGTCCCGCCATTTCCTTCCAGTCTTTGTCTTCTATACCCATCTTACGCTTCTGACGCTCCCCACTGTTGCCATGCTGTCTCTCGCTCTTCAATTCTTAGCATTCAACATGCCACGCTGCTCATGCCGCGCTTTCTTCCCTACTCCACTTGTTAGATTGATTATCTCTGTGTGTGCGCATGATTGCTATCGTCTTGTCATGTAGCTCTATGACTATCCACAATGTGGCACTCTCTTCTGCTGTGTGCAGTTCTCTCGAAACTGTTGACATATT\n++\n+8A,6,@,;,<C,C,,,,;,BC,,,-;6<,,,,;8@:7F68;,C,<EE@CCE,,,<C<FF9,C,C,,<,,C,C@,E,=@,8E,5C,,8,8:,,+9,C,,,,,,,,,9:,,9C=@,,,9,,,,:,<,,,,9?A8A9,,,+,,,,23++++,4+3,+*+++6+36+,,3*,,,6,2,*,+3,7,,,,@8@++,,,2,7+++85+04****0)*,*313+*)*0/8*1/***/4***:**/**,,*11*(*((-.****(0*(./)231:.)1/)(/())+)))/1741)(((.))/).++))))\n+@ERR1877483.32493 M03099:22:000000000-APTMA:1:2119:16611:8029/2\n+ACTACTCTATCCTCTCCCCCCCCCCTACATTCGCTGTTTCTTACCTCCTTCTTCCTTCTTAATTCCCTCCCCCCCATTTCTTTCTTCATCATTTATCGAATCTCATCTCTGCCCCGCTATTCCGTCTGCCCCCGCCTCACCCTGTCACCTCGTTTTGCTCCTCATCCTCTCCACTTCCTCTGTTCCATATCCTATTCTCTCCACCTACTCGAATGTCTCCCGTCGCATACTTTCCTCCTCATCCACTCCTATCGTCCCTTCCGCTTCCGTCTTGTCCCTTCTGACTCGACTATATCTTT\n++\n+,,8;,,,,6,;C;CCC<,,776+8@+,,6,,CE,8,,6<,9C,,,,,9,6C<,C,6B,,,,,9,<6,,6,6,7+++95B,@55,,,,<C?5,95:,,++,>+@>,,9,559,,4++++++9,,,8,,+,66A++1+=+,,13+32,,,+5:+3++@,,,7*,,,0,,,,,1,B?81,,,,,,,5,++,,65@C1+47448,0+0*(05,6(((//)2:+8)(,2,,..676)))/9)83()0.9).5((.))5-,((())2)..((/)-.(((-*).))6(4).)).(.((()+0))).\n+@ERR1877483.32499 M03099:22:000000000-APTMA:1:2119:19507:8186/2\n+CTGGCATTTCATCTCCTTCAGCTCCACTTGTTGTTTACCGGGTTTTCTTTGTACTTCTACTCACCACTCCTAGTTAGCTCTGTACTGTGGGCTACTCCGGGACCCGATGCAGCCTGCTCTGCGTCACTCGATTGCTGGTCAGCTCAGCCCATACTCTTGCTTTGACCTTGGATCGTGTTCGCCACACTGTCCTTTAGGTCCTGATCATGTGTATGATCTCGCCACCTTGCTCGACTTCGTCGCCACCATTCACCCTCGTGATTCTTACGACGCGTGAGTACGCATTATGTTATGGTAG\n++\n+6,8,,6,,,,,,,,;,,,,,,,,;6,=<,;;66C,6,;C,++6,,:@E6,,;,,,,<C,6C,,,,6,,6;6,,,<,,,,,,::,,,,<,B,,:,,,,:,++++6,@@+,89,9,,,,,,9,,+8+++,9=@<9+,,+,,,9@538,,,4++,+366,,,6,+3,,0,6,7,6,*+6),,3+6+++,0=,,,+,,+2+,++*,*17+*3*7****+**,+2,30)*)-)+0/*/)/)(**0((/-((/-/)9)1)((/1(((*+3+))3(((((-()-()).((((().).))5)++))\n+@ERR1877483.32513 M03099:22:000000000-APTMA:1:2119:13480:8544/2\n+ACTCACACCGTCTATAATTCTCTCCGCCCCCCCTGCCTTTGTCCCTCAGCTTCTGTCAGTTCTCTGCATCTGGCCTTATCTCCTGGCGTTATCCCCTAGACTTCTGGTGTTTACGCCTACCTCTGCAATTTCATCTTACCCATCACTCTGTCAGTTTCACTGTTTCCGTCACCTTTCCAATTTTGACTCCTGGGTTTTTCGCCGTTACTAATGTTCTCGCCATTCACGCTCTCCCGCCCACCTCATCAGACATCTGCTGTCTCCTTCACAGTTACAGTGTATGTCTGTAGTTACATCGTA\n++\n+-8,,66C,,7,,,,,,,,,<,,6-;CE,++8@++,6,,,,;,C,,@,6,,,CF,,,,6,9,,,,,,6,,,,6,A,5A,,,,,,,,,6+8+4B,,5,,,94,,94,,,,9,=,,5+6+,6,,,,,9,,,,93AE,4=+,,49,5,,67,7++4=;3,,,,C,+,:@*3+,6+1,+,+1,,63,,7@+2+3,,+6>7+33+01:0*4*))3,****+2*6*/5*)*+*1))-((*((-/(4*/(*((1).)))()/))).).)4+*;))*)))))))*))).).)--))))))..4+<)(-(\n+@ERR1877483.32525 M03099:22:000000000-APTMA:1:2119:11271:8937/2\n+ACCTGCTGTTTCATCTATCCCTTCTTTTTAGTTTCCCGTCAGTTCCTTTGCTTTTCTTTCTCTTATCCACATCTGATTCTTCATCCTCTTACTGTATTATATCTCTCCGTGTCCTCGCTAGATTTCACCTACTACCGACTTAACTTGTGCTCACGACTGACAATATCTCGTACAATGACTGATTTCGTTGTGTGTCTCTCACTGCTGGCTAACTATATAGCTTACATGCTCTTACTACACGATGATCGCTCACTGCGTGAGTGCCATCGGTACAGCAGAATATGTGTCCTCGTCTTTAGTA\n++\n+8-,,,6,,=6F,,=CF,C,,,=C8--<,,;,6<,;;6,C6@,C,E,;,,6F9;,;,@,,6;<,E,6;,,C,,6C,,5AEC,,;?C,,,,,,9C,@5,69A,,9,,@,,+,,:,,9@,+6,+,,6,,,,,59,:=9,+,68,,,3,,@;,9+3,+*++++,9,+,,9;,,,+++++7+0,,,6,7,,86+,++033==+5+6*,*+@+))5,))5*+*5,2?<+*)+**5+3*9*1**3)3*))**31))0))****'..b'CCTTAACTTCATCCCATTTTCCCACTCTCCTTATCAGTTCATCGTTTCCTGCGTGCACTTTCATCCACGTCTTATGCAACCCCCTCCATTGACCATTCACAAGCACCCTCCATCCCCCTGCTGTCCCATCCGCTTCTCCGTCGATATGACGTGTGCTACAC\n++\n+8A6,8@,C,C6EC,C,C,;,;C86-,;,;+,,@::+@+,C,,6,<,,<@6C6,6,;,<E,<;C@C66,:<,C,5<=BFBBCE,+=F,@E<,,:,5,CA?4,,,,,,,4,B,,,94,,4@F,4CF5,,,942A9,4,0,94,,4,9E,,,=+,+*,,939,C+,,,1@E,@,3@;,?9@,3,,6,6,++,,36++++2,++*,*3,+))0,)***1**,5+8*)1*)**4*3*).*2*/,,))*))))(-(**0((((0/3),/28))2((//(,)2)((((((((.)-((-(,)0+),(\n+@ERR1877483.32845 M03099:22:000000000-APTMA:1:2119:19368:19712/2\n+TTAGCCACACGCTACAGAGCAGAGACAGAGTTCATTCACGTGACTGGAGTGCGCACAGGCGTAAGGACTCGTAGAAGAGCGATTATTGTGATCCTCTCTGCCTAGCCCGACGGGGGCCTCCACGCTTCACCGTGCCTTTATGCAAAGGACGTCGCTGACACCGTCAGCGCCGCGCGTGTGGGCACCCCAACCTCTACACGCCCGACTGCCGTGTTCTTGATGTAACATGTCTGTCGATTGCGCCTTATGACCTGTCACAACTGCACACACATACCTCAGCCTTCACGGGTTTGTACACG\n++\n+,,,,,,6,=,++,,+,,,66,6-C,,,;,,,,6,,6,6,,,,,,,,,,,,,66@@+@;,6C6+,6,99CC<,,,8,,BB,+44,,,,,,5,5,5,6,,9,,,,,4,,,44@+C7:>+++,33,>++8+,,,8,@D6,,,,,5E,,3@87+53<+4:9*3,3*34/1*,4**4)=D1*3:1*//**5**43**+*2*3**-/()1)-((*((-()()+0*,0-)*)))*()6<>).((*33)*-((-)))))()()))-).1)/6)(*((,(.).*.)(()((-)).(-(((((*+)-)(\n+@ERR1877483.32864 M03099:22:000000000-APTMA:1:2119:18423:20592/2\n+CGGGCGGTGTGTGCTGATACTATGCTTGGCCGCCAATTCCTTTAAGTTT\n++\n+8,,,@F@+6,,;,CECEGCFGGCC-C,C@EFCF+++C<<EECC,6@,CC\n+@ERR1877483.32898 M03099:22:000000000-APTMA:1:2119:24030:22105/2\n+ACGGCCGATTTGTGCATGGCACGGCAATATATTCCCCCCCTCATATATGGGCCGCGAGCACTACCCATTCCGTCTTCATCGGGTCGGGGGGCACATCCCACACTCAACGTCCCACACGCTTTTGCGCTGCCCACTCGATCACGTGATCGACTCGCTCCTTAGTGGGCATTTTAGCACTTGTCTCCCCATGGCGGCTAGGCTGTAGGTGAGCCGAGTGCGGACTCATCTTTCACCGACTTGCGCAGCGAGTACTCGTAGCAGACCCGGCGCTGACCACCAGCCACTGCAGTGTACGACCGT\n++\n+--,,,6+686,66;<F,,,;,;8++66,,,;6B,,,,+6++8C9,,55,,,6,66@+++8:CE,6,,9,9C=,B,,<,,59?+A48+4++*1162,,,6,2*1,,,,5***1=,4=7*8**42,8******1+**0***;*2*0***+1*1*2/75**+2+0*+**-:2++2<C7+*)++09:++2*9***21**)1*2**(*)*+2.-(+(,(()()*)/*),)*)))*..).(((((,+(()(((((,()))-,4(()),*.).-(),((((()*((,((((5)))(.())--**((,\n+@ERR1877483.32926 M03099:22:000000000-APTMA:1:2119:7498:23338/2\n+GCCCAGTCCCCCCCTACTGCCAGCTGCGCCGTTAAGTCAGGCGGGCCAGCTCCGAATCTAGAGGATAACGACTACAACAGAAATAAGCAGAATGATTAAAGCCCCACATCACGGCGGCTAACCTGCATGCACACTACTCTCGTCTAAACCCATGGCCGACACGTTCCAATGACCTCACCAGCTGCCCACCATTAATAACTGCCTCGATCTCATGTGCTAGCCTCGAGCTCCTCACACACTTCAGCGTAACGCCGCCTCACCCACCCACCACATACCTTCAACATCCTGTGCTTCTTCTA\n++\n+-A<@,,,,,,6++7+:,,;,66,--,6++,++68,,,,6,,C++++8,,,9,6,+,4,<,,,,4,,5:C=F4B+4,,4,44<<9,B,,,,9,A,5,,,,8,4A+++++,,,,3+3+++4+:,,:5@<B9:,3,,,4*3,@<*0*,1,,,*/***1D,*4:4)*60(*++++4+)+*(/*+=*3++*1;7**01+++1,**.+3*<<((.24)-)1.)020,7).),(())(((),,((**))2-)(((((,((((4(((((1)))(,1(.(..))2)).)))..)())..)).-++)))\n+@ERR1877483.32949 M03099:22:000000000-APTMA:1:2119:22063:24539/2\n+CGCTACTGGCGTACCTAATCCCGTTCCCTACCCTCCCCTGCGTACCTACCCGCGATTAAGTGTGCTGCAGGCTTCATTCACCATAGGTCTTGCCCTCAATCCCAACGAATTTCACTGCTACAGCCATAGTTTAACCTGGCTCTCCATACCCCATGTCTACCATTCATTGCAGCCTTTGTCTATCTGCACTCTTGAATTGCAACATTAATTCACCTCATCCCCACCTTACTCTTTGTTCTCTACGTCAGTACCCACATCTGTCACCACTCGCTATGTACCACGCTCTCTCACCACTTCAGG\n++\n+6,8,7+,,=,+87+,,<,,;C<,;-,,,6;,6C,,86B,,C+B6@,;,,;CF++@7CF,,6,<,,,,::,CFC,<,A4,<,,,9,6,<B,,,:,,4E,9,,,9,,B:,+,+4,,5CC,,,,,,,49E?<,,,4CEDD,9@,,3,,,,3,0+++*,@D,633*7,7*,,6,,63*,+*,7,,8,,,3++,8=+,7++2,+5*,)*,+*0*7*5:**1),<+<9)1<:56@?/*1**/01,5**2>5((/*0****((0.**/,+1*)(2,(.,((/3))//6(1((()/./)(.,<2))))\n+@ERR1877483.32956 M03099:22:000000000-APTMA:1:2119:14880:24914/2\n+GCGACGGGTACGAGAGAGATCAGTGGGAATAGAAATGAAAGGAGGCGGAAGTAAGAACACAAACGAGTCGGTGTAATCTAAATGGAGAGGAGGACTAAGGTGCTGAATACGGCTGGAGCTAGGGGGGTGGCACATGGTCGATACTGACTGATCAACTGTGATGTCGCTCTTAGTAGTGGTGGAACAGGACTGGATATGGCTATTAGGACTGGGTATCATAAACATGCTACTATGGGTAACTTACTACGACAACACTTGGAGGCTAACATCACTATGTAACTATCGAAAGTGAGATTACGAT\n++\n+--8,86+86+,8,68+:B8,;6CC--,,,,;6,,;,,,,,,,,,,8+8+6+,<<,,,,:,,9,:,6+8,68+86,,,,4,,,:,:,,,8,,+88+,9B<,9A,9@;A==9+++88+,,,,,,84++***4+*,++7*21****)++++++*331)*+++++39:+*(/**23+3*+*(2C***+0*2***+*1*+**039>)0)/0:248*(..)).)3*00*-.)).)*,).).(4)(,0--2)))(-(((((()-).).(*0)),4:7)).-))2))))--)-((-,))))))30),(-\n' |
| b |
| diff -r 1eafcc450052 -r 65c38d020fea test-data/test4_bam.bam |
| b |
| Binary file test-data/test4_bam.bam has changed |
| b |
| diff -r 1eafcc450052 -r 65c38d020fea test-data/test4_biom.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test4_biom.txt Sun Sep 24 14:28:47 2017 -0400 |
| b |
| @@ -0,0 +1,1 @@ +EncFa169 1p_error_4 |
| b |
| diff -r 1eafcc450052 -r 65c38d020fea test-data/test4_de_novo.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test4_de_novo.fasta Sun Sep 24 14:28:47 2017 -0400 |
| b |
| @@ -0,0 +1,40 @@ +>1p_error_2 reference=AY466476 amplicon=432..713 errors=76%G +GUGCCAGCAGCCGCGGUAAUACGAAGGGGGCUAGCGUUGUUCGGAGUUACUGGCGUAAAGGCGCGUAGCGGCCUGGAAGUUAGCGUGAAGCCCUGGCUCA +>1p_error_3 reference=JN430627 amplicon=421..712 errors=1%C +CUGCCAGCAGCCGCGGUAACACGUAAGGGGCGAGCGUUGUUCGGAAUUAUUGGGCGUAAAGGGCACGUAGGCGGCACGGUAAGCCUGGUGUGAAAGACCG +>1p_error_5 reference=FJ890890 amplicon=455..746 description="Bacteria;Cyanobacteria;Chloroplast +GUGCCAGCAGCCGCGGUAAGACAGAGGAUGCAAGCGUUAUCCGGAAUGAUUGGGCGUAAAGCGUCUGUAGGUUGUUUAAAAAGUAUUUUGUUAAAGAUUA +>1p_error_6 reference=JN449148 amplicon=487..779 errors=39%C +GUGCCAGCAGCCGCGGUAAUACGUAAGGGGCGAGCGUUCCUCGGAAUUACUGGGCGUAAAGGGCGUGUAGGUGGUCUUGCAAGUCGAUUGGUAAAAGACC +>1p_error_7 reference=EF019112 amplicon=467..758 errors=8%U,40%A +GUGCCAGUAGCCGCGGUAAGACGUAGGGGGCGAGCGUUAAUCGGAAUUAUUGGGCGUAAAGCGUGCGUAGGCGGAUUCGUAAGUCGGGGUUGAAAUAUCC +>1p_error_8 reference=EF020331 amplicon=491..782 errors=53+G +GUGCCAGCAGCCGCGGUAAUACGUAGGCAGCAAGCGUUGUUCGGAAUUACUGGGGCGUAAAGAGUGUGUAGGCGGUUUUCUAAGUUUGGUGUGAAAUCUCC +>1p_error_9 reference=FJ879628 amplicon=498..789 errors=18+C +GUGCCAGCAGCCGCGGUACAUACGUAGGGGGCAAGCGUUAUCCGGAUUUACUGGGUGUAAAGGGAGCGUAGGUGGCAGGGCAAGUCAGAUGUGAAAACCCG +>1p_error_10 reference=EU134170 amplicon=467..758 description="Bacteria;Chloroflexi;Anaerolineae;Anaerolineales;Anaerolineaceae;uncultured +GUGCCAGCAGCCGCGGUAAAACGUAGGAGGCGAGCGUUAUCCGGAUUUACUGGGCGUAAAGCGUGCGCAGGCGGUCCGACAGGUCGGGCGUGAAAUCUCC +>1p_error_11 reference=EU490280 amplicon=472..764 errors=63+U +GUGCCAGCAGCCGCGGUAAAACGUAGGGGGCUAGCGUUACCCGGAUUCACUGGGCGUAAAGCGUGGUGUAGGCGGUCCGGCAAGUCGGAUGUGAAAUCCCA +>1p_error_12 reference=FJ202663 amplicon=453..744 description="Bacteria;Proteobacteria;Alphaproteobacteria;Rhodospirillales;Rhodospirillaceae;Thalassospira +GUGCCAGCAGCCGCGGUAAUACGAAGGGAGCAAGCGUUGUUCGGAAUUACUGGGCGUAAAGGGCGUGUAGGCGGAUUAUCAAGUUAGGGGUGAAAUCCCG +>1p_error_13 reference=DQ522159 amplicon=503..793 errors=7+C +GUGCCAGCCAGCCGCGGUAAUACAUAGGUUGCAAGCGUUAUCCGGAUUUAUUGGGCGUAAAGCAAGCGCAGGUUGGUUAUCAAGUCUAGUGUGAAAGGCAA +>1p_error_14 reference=EU773708 amplicon=499..791 errors=58%U +GUGCCAGCAGCCGCGGUAAUACAGAGGUCUCAAGCGUUGUUCGGAAUCACUGGGCGUUAAGGGUACGUAGGCGGCCGCAUAAGUCGUGCGUGAAAGGCAG +>1p_error_15 reference=HM448227 amplicon=517..808 errors=59%U +GUGCCAGCAGCCGCGGUAAUACGUAGGUCCCGAGCGUUGCGCGAAUUCACUGGGCGUAUAGCGUCCGCAGCCGGACGGGUAAGCGGUGCGUCAAAGCCCA +>1p_error_16 reference=GQ139098 amplicon=511..802 errors=1%A +AUGCCAGCAGCCGCGGUAACACGUAGGGGGCAAGCGUUGUUCGGAAUUAUUAGGCGUAAAGGGCAGGCAGGCGGACCUGCAAGUUUUCUGUUAAAGACGU +>1p_error_17 reference=AB100473 amplicon=660..951 errors=57%C +GUGCCAGCAGCCGCGGUAAUACGUAGGGAGCAAGCGUUGUCCGGAUUUACUGGGUGCAAAGGGCGUGUAGGCGGGAAGGCAGGUCAGAUGUGAAAUCUAU +>1p_error_18 reference=FJ802352 amplicon=495..786 errors=16%A +GUGCCAGCAGCCGCGAUAAUACGAAGGGGGCUAGCGUUGCUCGGAAUCACUGGGCGUAAAGCGCGCGUAGGCGGCUUUCUAAGUCAGGGGUGAAAUCCCG +>1p_error_19 reference=GQ138466 amplicon=520..812 description="Bacteria;Firmicutes;Clostridia;Clostridiales;uncultured +GUGCCAGCAGCCGCGGUAAUACGUAGGGGGCGAGCGUUGUCCGGAAUGACUGGGCGUAAAGGGUGUGUAGGCGGUUUAGCAAGUUAGAUGUGAAAUACCC +>1p_error_20 reference=EU857742 amplicon=514..805 errors=18%G +GUGCCAGCAGCCGCGGUGAUACGUAAGGGGCGAGCGUUGUUCGGAAUUAUUGGGCGUAAAGGGUACGUAGGCGGAUUAACAGGCAUUAAGAUAAAGCCAA +>1p_error_21 reference=HQ588409 amplicon=540..831 errors=90%G +GUGCCAGCAGCCGCGGUAAUACAUAGGGGGCAAGCGUUGUCCGGAAUUAUUGGGCGUAAAGAGUAUGUAGGCGGUUUAUUAAGUCGGUAGGUGAAAGGCU +>1p_error_22 reference=EU488153 amplicon=481..771 errors=96%C +GUGCCAGCAGCCGCGGUAACACAUAGAGGACGAGCGUUAUCCGGAUUUACUGGGCGUAAAGAGCGUUGAGGCGGUUCCGUAAGUUGGGCGUUAAACCUCC |
| b |
| diff -r 1eafcc450052 -r 65c38d020fea test-data/test4_input.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test4_input.fasta Sun Sep 24 14:28:47 2017 -0400 |
| b |
| @@ -0,0 +1,44 @@ +>1p_error_1 reference=AY697866 amplicon=489..787 errors=14-,19%C +GUGCCAGCAGCCGGGUACUACGGAGGAUGCAAGCGUUAUCCGGAUUUAUUUGGGUUUAAAGGGUCCGUAGGCGGUAUUUUAAGUCAGAGGUGAAAGCCU +>1p_error_2 reference=AY466476 amplicon=432..713 errors=76%G +GUGCCAGCAGCCGCGGUAAUACGAAGGGGGCUAGCGUUGUUCGGAGUUACUGGCGUAAAGGCGCGUAGCGGCCUGGAAGUUAGCGUGAAGCCCUGGCUCA +>1p_error_3 reference=JN430627 amplicon=421..712 errors=1%C +CUGCCAGCAGCCGCGGUAACACGUAAGGGGCGAGCGUUGUUCGGAAUUAUUGGGCGUAAAGGGCACGUAGGCGGCACGGUAAGCCUGGUGUGAAAGACCG +>1p_error_4 reference=GU812306 amplicon=598..880 errors=95%G +GUGCCAGCAGCCGCGGUAAUACGUAGGUGGCAAGCGUUAUCCGGAUUUAUUGGGCGUAAAGCGAGCGCAGGCGGUUUUUUAAGUCUGAUGUGAAGGCCCU +>1p_error_5 reference=FJ890890 amplicon=455..746 description="Bacteria;Cyanobacteria;Chloroplast +GUGCCAGCAGCCGCGGUAAGACAGAGGAUGCAAGCGUUAUCCGGAAUGAUUGGGCGUAAAGCGUCUGUAGGUUGUUUAAAAAGUAUUUUGUUAAAGAUUA +>1p_error_6 reference=JN449148 amplicon=487..779 errors=39%C +GUGCCAGCAGCCGCGGUAAUACGUAAGGGGCGAGCGUUCCUCGGAAUUACUGGGCGUAAAGGGCGUGUAGGUGGUCUUGCAAGUCGAUUGGUAAAAGACC +>1p_error_7 reference=EF019112 amplicon=467..758 errors=8%U,40%A +GUGCCAGUAGCCGCGGUAAGACGUAGGGGGCGAGCGUUAAUCGGAAUUAUUGGGCGUAAAGCGUGCGUAGGCGGAUUCGUAAGUCGGGGUUGAAAUAUCC +>1p_error_8 reference=EF020331 amplicon=491..782 errors=53+G +GUGCCAGCAGCCGCGGUAAUACGUAGGCAGCAAGCGUUGUUCGGAAUUACUGGGGCGUAAAGAGUGUGUAGGCGGUUUUCUAAGUUUGGUGUGAAAUCUCC +>1p_error_9 reference=FJ879628 amplicon=498..789 errors=18+C +GUGCCAGCAGCCGCGGUACAUACGUAGGGGGCAAGCGUUAUCCGGAUUUACUGGGUGUAAAGGGAGCGUAGGUGGCAGGGCAAGUCAGAUGUGAAAACCCG +>1p_error_10 reference=EU134170 amplicon=467..758 description="Bacteria;Chloroflexi;Anaerolineae;Anaerolineales;Anaerolineaceae;uncultured +GUGCCAGCAGCCGCGGUAAAACGUAGGAGGCGAGCGUUAUCCGGAUUUACUGGGCGUAAAGCGUGCGCAGGCGGUCCGACAGGUCGGGCGUGAAAUCUCC +>1p_error_11 reference=EU490280 amplicon=472..764 errors=63+U +GUGCCAGCAGCCGCGGUAAAACGUAGGGGGCUAGCGUUACCCGGAUUCACUGGGCGUAAAGCGUGGUGUAGGCGGUCCGGCAAGUCGGAUGUGAAAUCCCA +>1p_error_12 reference=FJ202663 amplicon=453..744 description="Bacteria;Proteobacteria;Alphaproteobacteria;Rhodospirillales;Rhodospirillaceae;Thalassospira +GUGCCAGCAGCCGCGGUAAUACGAAGGGAGCAAGCGUUGUUCGGAAUUACUGGGCGUAAAGGGCGUGUAGGCGGAUUAUCAAGUUAGGGGUGAAAUCCCG +>1p_error_13 reference=DQ522159 amplicon=503..793 errors=7+C +GUGCCAGCCAGCCGCGGUAAUACAUAGGUUGCAAGCGUUAUCCGGAUUUAUUGGGCGUAAAGCAAGCGCAGGUUGGUUAUCAAGUCUAGUGUGAAAGGCAA +>1p_error_14 reference=EU773708 amplicon=499..791 errors=58%U +GUGCCAGCAGCCGCGGUAAUACAGAGGUCUCAAGCGUUGUUCGGAAUCACUGGGCGUUAAGGGUACGUAGGCGGCCGCAUAAGUCGUGCGUGAAAGGCAG +>1p_error_15 reference=HM448227 amplicon=517..808 errors=59%U +GUGCCAGCAGCCGCGGUAAUACGUAGGUCCCGAGCGUUGCGCGAAUUCACUGGGCGUAUAGCGUCCGCAGCCGGACGGGUAAGCGGUGCGUCAAAGCCCA +>1p_error_16 reference=GQ139098 amplicon=511..802 errors=1%A +AUGCCAGCAGCCGCGGUAACACGUAGGGGGCAAGCGUUGUUCGGAAUUAUUAGGCGUAAAGGGCAGGCAGGCGGACCUGCAAGUUUUCUGUUAAAGACGU +>1p_error_17 reference=AB100473 amplicon=660..951 errors=57%C +GUGCCAGCAGCCGCGGUAAUACGUAGGGAGCAAGCGUUGUCCGGAUUUACUGGGUGCAAAGGGCGUGUAGGCGGGAAGGCAGGUCAGAUGUGAAAUCUAU +>1p_error_18 reference=FJ802352 amplicon=495..786 errors=16%A +GUGCCAGCAGCCGCGAUAAUACGAAGGGGGCUAGCGUUGCUCGGAAUCACUGGGCGUAAAGCGCGCGUAGGCGGCUUUCUAAGUCAGGGGUGAAAUCCCG +>1p_error_19 reference=GQ138466 amplicon=520..812 description="Bacteria;Firmicutes;Clostridia;Clostridiales;uncultured +GUGCCAGCAGCCGCGGUAAUACGUAGGGGGCGAGCGUUGUCCGGAAUGACUGGGCGUAAAGGGUGUGUAGGCGGUUUAGCAAGUUAGAUGUGAAAUACCC +>1p_error_20 reference=EU857742 amplicon=514..805 errors=18%G +GUGCCAGCAGCCGCGGUGAUACGUAAGGGGCGAGCGUUGUUCGGAAUUAUUGGGCGUAAAGGGUACGUAGGCGGAUUAACAGGCAUUAAGAUAAAGCCAA +>1p_error_21 reference=HQ588409 amplicon=540..831 errors=90%G +GUGCCAGCAGCCGCGGUAAUACAUAGGGGGCAAGCGUUGUCCGGAAUUAUUGGGCGUAAAGAGUAUGUAGGCGGUUUAUUAAGUCGGUAGGUGAAAGGCU +>1p_error_22 reference=EU488153 amplicon=481..771 errors=96%C +GUGCCAGCAGCCGCGGUAACACAUAGAGGACGAGCGUUAUCCGGAUUUACUGGGCGUAAAGAGCGUUGAGGCGGUUCCGUAAGUUGGGCGUUAAACCUCC |