| Next changeset 1:8880fb74ef56 (2018-09-19) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit 8c25a8b21de04f75cdf12a33d8d9cfe2d15ed13a |
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added:
filtlong.xml test-data/output.fastq test-data/output_reference.fastq test-data/test.fastq test-data/test_reference.fasta test-data/test_reference_1.fastq.gz test-data/test_reference_2.fastq.gz |
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| diff -r 000000000000 -r a64b45c8b174 filtlong.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/filtlong.xml Mon Sep 17 16:16:07 2018 -0400 |
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| @@ -0,0 +1,110 @@ +<tool id="filtlong" name="filtlong" version="0.2.0"> + <description>Filtering long reads by quality</description> + <requirements> + <requirement type="package" version="0.2.0">filtlong</requirement> + </requirements> + <version_command>filtlong --version</version_command> + <command detect_errors="exit_code"><![CDATA[ +filtlong + #if $output_thresholds.target_bases: + --target_bases '$output_thresholds.target_bases' + #end if + #if $output_thresholds.keep_percent: + --keep_percent '$output_thresholds.keep_percent' + #end if + #if $output_thresholds.min_length: + --min_length '$output_thresholds.min_length' + #end if + #if $output_thresholds.min_mean_q: + --min_mean_q '$output_thresholds.min_mean_q' + #end if + #if $output_thresholds.min_window_q: + --min_window_q '$output_thresholds.min_window_q' + #end if + #if $external_references.assembly: + --assembly '$external_references.assembly' + #end if + #if $external_references.illumina_1: + --illumina_1 '$external_references.illumina_1' + #end if + #if $external_references.illumina_2: + --illumina_2 '$external_references.illumina_2' + #end if + --length_weight '$score_weights.length_weight' + --mean_q_weight '$score_weights.mean_q_weight' + --window_q_weight '$score_weights.window_q_weight' + $read_manipulation.trim + #if $read_manipulation.split: + --split '$read_manipulation.split' + #end if + #if $other.window_size: + --window_size '$other.window_size' + #end if + '$input_file' > output.fastq + ]]></command> + <inputs> + <param name="input_file" type="data" format="fastq" label="Input FASTQ" help="FASTQ of input reads"/> + <section name="output_thresholds" title="Output thresholds"> + <param argument="--target_bases" type="integer" min="0" optional="True" label="Total bases" help="Keep only the best reads up to this many total bases"/> + <param argument="--keep_percent" type="float" min="0" max="100" optional="True" label="Keep percentage" help="Keep only this percentage of the best reads (measured by bases)"/> + <param argument="--min_length" type="integer" min="0" optional="True" label="Min. length" help="Minimum length threshold"/> + <param argument="--min_mean_q" type="float" min="0" optional="True" label="Min. mean quality" help="Minimum mean quality threshold"/> + <param argument="--min_window_q" type="float" min="0" optional="True" label="Min. window quality" help="Minimum window quality threshold"/> + </section> + <section name="external_references" title="External references"> + <param argument="--assembly" type="data" format="fasta" optional="True" label="Reference assembly" help="Reference assembly in FASTA format"/> + <param argument="--illumina_1" type="data" format="fastq,fastq.gz" optional="True" label="Reference Illumina read" help="Reference Illumina reads in FASTQ format"/> + <param argument="--illumina_2" type="data" format="fastq,fastq.gz" optional="True" label="Reference Illumina read" help="Reference Illumina reads in FASTQ format"/> + </section> + <section name="score_weights" title="Score weights"> + <param argument="--length_weight" type="float" min="0" value="1" optional="True" label="Weight length score" help="Weight given to the length score (default: 1)"/> + <param argument="--mean_q_weight" type="float" min="0" value="1" optional="True" label="Weight mean quality" help="Weight given to the mean quality score (default: 1)"/> + <param argument="--window_q_weight" type="float" min="0" value="1" optional="True" label="Weight window quality" help="Weight given to the window quality score (default: 1)"/> + </section> + <section name="read_manipulation" title="Read manipulation"> + <param argument="--trim" type="boolean" checked="false" truevalue="--trim" falsevalue="" label="Trim non-k-mer-matching" help="Trim non-k-mer-matching bases from start/end of reads"/> + <param argument="--split" type="integer" min="0" optional="True" label="Split at nr. of bases" help="split reads at this many (or more) consecutive non-k-mer-matching bases"/> + </section> + <section name="other" title="Other"> + <param argument="--window_size" type="integer" min="0" value="250" optional="True" label="Sliding window size" help="size of sliding window used when measuring window quality (default: 250)"/> + </section> + </inputs> + <outputs> + <data name="outfile" format="fastq" from_work_dir="output.fastq" label="${tool.name} on ${on_string}: Filtered FASTQ"/> + </outputs> + <tests> + <test> + <param name="input_file" ftype="fastq" value="test.fastq"/> + <param name="min_length" value="1000"/> + <param name="keep_percent" value="50"/> + <param name="target_bases" value="500000000"/> + <output name="outfile" ftype="fastq" file="output.fastq"/> + </test> + <test> + <param name="input_file" ftype="fastq" value="test_reference.fasta"/> + <param name="illumina_1" ftype="fastq.gz" value="test_reference_1.fastq.gz"/> + <param name="illumina_2" ftype="fastq.gz" value="test_reference_2.fastq.gz"/> + <param name="min_length" value="1000"/> + <param name="keep_percent" value="90"/> + <param name="target_bases" value="500000000"/> + <param name="trim" value="True"/> + <param name="split" value="500"/> + <output name="outfile" ftype="fastq" file="output_reference.fastq"/> + </test> + </tests> + <help><![CDATA[ +Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter. + ]]></help> + <citations> + <citation type="bibtex"> + @misc{rrwick2017, + author = {Wick, Ryan}, + year = {2017}, + title = {Filtlong}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/rrwick/Filtlong}, + } + </citation> + </citations> +</tool> |
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| diff -r 000000000000 -r a64b45c8b174 test-data/output.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output.fastq Mon Sep 17 16:16:07 2018 -0400 |
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@@\n+@test_sort_2\n+AGCGGGACTCTTCCCGATCGGCCTGGAAAAACCACGGATTCCAATAGTACGTTCTGTTAGCTGGGTGTCTTTATGCATGCCAAGGTTCGAACCTCCGGCCATGTTGGATGTAGAAAAGGTAGCCAGCGAGAAGGAAGAAGGCCAAGGCTTCATATTACCCCGAATTCTCAAGGTGGATAAGGGGAACTAACGGTTGCGAGCATGAAGCTGGCTTCAATGGCCAGGCGACAGATTTACTCCACTTTCCGCTGCTTGTTCTGGATTGGGATGTTAACCCTTTGATCCCACAGAGGTCAGCGGAGAAAACAACGTCTAAATATAGTCGGACAGACTGTAGCGACCGGGTTAGCACTCCCTAATTTTATCCAAGTAGGCGGACACACCCTTACCACAGGGGCTCCAATGTTCGCTCATTTCCGTGGGTGTAGCAACGTCCTATTCTTCTGCTGACGCGAAGTAACGAGTATTCTCTTGGATTTTAACTGAGCTGTCACTCCGCGTGAAGGATAACCGGCTTGAGTAAAGGAGACGGTCAGTCGCAGAGGGCAACGCGCTATATACATTCGGTTTATTGAGTTCACCCTGGATAGTGACGCGGCCCTGATTGTAGGTCGGGGCAAACTCTGAAATTGCTACTCGTATACAGGGTTGTGCGCTCGTAAGGACTCCCCCCTGGCGTCGAAGCCAGTTCGACAAAATGGCCCCGGAAGACGTTATCTAGATGAGTCTGGGTGGCTTTCAAGAATTCGCCTATCTTGGGACCTGGCCCTAACGATCAGACAGGCGCACTGCTGATGAGGGCATGTACCGACCATACGGTTTTTCTTCAGGCAAATGCCCGTTCCGGTGTCCGTGGTCAAGACTCAAAATCTCCCCTAAGGCTGTCACGAATTAGAGTCTCGTGTGAGAGATTAATGTTAGCCCTCAGTGGGTCCCAATAAGAACCCACTAAGTAAGCCTCGCCGGTACGCAGACCTAGAGACTTGTTGGTGGGCAGCTTCTGCGCTGTTGGCATTCCGGCATAAGGAGAAACGTTATCGGCTGTCGGTGTCATCTGCCAGTGCTGGCGAGTCGAGCTTGTAGCACTCATTGAAGGTGGTGTGAGCTGCACGCCTCCACTAATTTAATCCCCGTCGCAAAGTTGGTCAGACCAGGCGCCTTCAGTGCACTGTGACAGCTGGAATTCCGACTCCGGAAAAGTGCAATGGGTGTCCAGTGGACGACTTCTTGTGACGCGCTCCCGCGCCGCGTCCACAGGGGGACTCGGCGAAAAGTACAAAAGTAGGGGGAGTGCCCTGAGGAGAGTGGAGCGTGCCGTCACCGGGTGACGGGTACAAGAACCTACTACTAGTGACGATGCTCTTAGATGGAGTGTAGCACGATCTTCACGGATAAAATAATGAAACTAACTGGGGCCGTTGGGCTCCCGAAGTATATGAACTGCGGCCATGTATGTTATGAATCCCCTCGGGTTCCAGGCTGCTCAAAAGTCTGCGTAGGAGTCTCATCGGGACCTATACTAGCTGGCGATGCGGAATACAGCGGCCTAGCTTTTATGCGATGTGCGGGGATAATTCTAATAGTTGCGGCTGGTCCATAACCGTGGACGTCGTATATTGGCAGACCTGCACAGTTGGTCCGATTAGACATACAGCACCCTTCTACATCCTGTTGTTCTGGAGAAGCCCACTCTAGTAGGACGATTTACCTATGGACATGCGGTGTCCTAATTCATCCTACCGGAATTCTCATGCACTTCTGCCTTTCCCCCGAACATTCTAGTGGTGGGCTCGAGCTGCTGATAATCCACTCCATTGGGTGATACGAGAGGCGAGTTTGCCTTAGTTTGCGCAGGTCATGAAACCAAGCAACCGCATGCTTAGCTGGCTAATTGTTCGACTCGGCCACCCGCAAACTGTCGAAACGCGTAGAAAGTACAATTCCGTAAGCGAGTTCGGAATCCAGACCCGCGGCAATGCCCTCTCTTCCTACGCAGCGACCCCCTGTTTACACAGACAAGGCCCCGATGGCCAATCGGGAGTCTCGACGAGTGCCATAGAGGCGCCCTACCGGCGTCAGTGGGGGTGATTAATCACTTCACTGGTTCACGGTGGGCTACGCGCTCACCTAGCTTCCCCGTAGTGTCTTGACGAGTGTGGGCCCAGAAGATGGAAGTTAAGGCTGGAGGAATAGATAACCATCGTACCTCCACTGGACGAGATAGCACTAAATCCTGGAAACGAGACGGATCCGAGAGTTCAGATAATGATCGAGATGGGACAACAGGCGAATCTCGCAAACGTGCTTCAAATTATAACGTCGCATACCGATTATGGGCTTTATCGCGAAACCTGACAGCGCTCCCTCAAATCCCTAGTTCGGAAAATCGTGTCGCCCCTACAGTCCATCACTCAACTTCACTTGAGCAATAAGTTTAGGGCGCGTCACTCTATCTACTTTACTGCTGAATGGACCCTTGTGTGGATCGTAAACCTACAAGTCCCTGGCACTGCCTGTTCTTGCGATGATAAGATTAAGTGTTTGCCCGTTTGCCAACTATCCCTCAAATCTCGTTGATGAACCTGCCCCTTCTGTTCCATTACGAATCGACCGCTCTAACTTTTGAATCTGTGGCATGGACCCCATCAAGAGGGACCAGCGTTCAGCGAGACTTCTACAAACTTACGTTACATTATGCCGTTCGCGGTGAGCGTGCGGTCAAGCATTCCAAAAGTACTCCGCGAGCCGTACAATCGACCTCTAGTATACTCCTGGTGCGGAGCAAACGATTTGAGCAGACCTCATATAGAATGTGCAATCGCTCTTTGTCGCAAAGCCACAACCAGTCACGCCGTTCGTCGACTACCACCCACTTCGTGGATGTGCGCCAAGTCTGTCTCCAGCTCTCAAGACTCATTTCAACTTGCCAATAACCTCAGTGCCTTGTCACTTCGAGTTCTTGAGGAATAGTCAGGGTCCTTAAACTTCATCGACTCGGCACAGTCTGTAGCCTCATGACTGCCCATTCCGGCCCGATGTGGAAGCGGTCCGGCTACTCAAATGCTCCCGGAGACCGAAGATTTCGGGACCTTTCGTTGTCAGACGCCAGTCATTGTTGCCTCTAACTGCATTGGAATCTGGCCCAAATAGAGATTGACCTCGGGAATCCGTCGCTGGTCAGGGCGTCGTACTCTGAACGGGACATCACTCCCGACCACCGGGGGGCGTCGTAGGTGCAGCAGACTGACAAATCCGTCCCAGTCGACTTATGTTCGCATGTCGTTATTAACTGCCTTGTACCTACGGTATGTATTGAACCACTGAGATCAGGGCAGGTTGAGCAAATTCATATCTCAAGGTGTGTCGAGAAAAAACCATTGAAGCTCTAGACCGGGAGTGCTGGTCAGAGTGCTCTGCTCACAAGGAAGCAATTCGGTGTTGGGTACCAATCAGAAATCACACCGTGGCTCTGAGCTTAATCCCTTGGGTTGGGCAACCGGGAGGACCAAGAGTACCGGCGACGGCCTCTGATTCTTGATGGTATAGGAGACATGCCTATACACGTTCGAGTGTAGTGACAGCATAGGATGCCTCAACGCTTTTACTCACGAGTGTGTGGTCCAATCTTGATGTCTAGACATGAGTTTTTCTAACGAGTGAACGGTATCCTATCCGCCCTCTGGATCAGCGGTTTCGGGGGTCCCTATGATGCTGTTCATATGCTCTGTCCATTGATTTGAGCCTACGGTATGAAGCACTCGCGGCGAAAAGGTTGCTGTAACCCGCGGGTGGTTACGATCTAATCTTCTGGTACGAAGGCGTGCCGTTACTCCAAAACTGGTACCTTGGTGTTTTTGCTGATCTCCAGAATTTTTGCTGTACTATTCCAAATTAGGAGTCATGAGTCCGGATTGTCATTCCGACAAGCAGTATTCCCAACAGAGAACACTTGCATACGCGTCAATGAT'..b'//1//00/00//00/01111/10/01/0//0/////11100/10/11/0001100//1//1/011101100/0/01110///00/0/0/1///10//10/010//0000///01/00/1/1/01///11/100/11110/111011///0101/1/000/11/00/0/1011/10/100/10111/001//101//1/1111011/11/1//1011100//0000/011100//110001/0/010/01101010000//11/1//0//1/110/1/0/1/0/0100/1//1//11/01//010//1/01//01//10110//01011//0/0///0///1001/11//01/011/01001/110//00/0/0/01/010/0//01101/010/00/00001/10////0//01111//0//000/0//110//00110//1//1000010100/0/1//0//101/1010100101/10/01000100/01000101/01///11/01//00010///00101/1010/0/000/00////1/001110/00/0010/10011/1//010/0011/011/00/011/0111/0/00//000///0100/1100101001/1//111/1/1/0///1/11/0/1/0/00//1110/0101///01/1/1////////101000/1/00/0//00/100//100/0/000///101/0//1/101/00011011000//1//1/11/10100//0/0/01000110101/00/1110/1010/111110000/1/0/1/00//1100/11/00/10/1000/00/01/00/01001111/1////1/0/1//0101/1/0011010110//1/0/0/110/1//00/11000/1/1/1//0010/011/0///10/0/0/011//10/10///0100000000//01100/00/00/0111//01//00/0110110/110/100010/1/1/1001/10///0//00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| diff -r 000000000000 -r a64b45c8b174 test-data/output_reference.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_reference.fastq Mon Sep 17 16:16:07 2018 -0400 |
| b |
| b'@@ -0,0 +1,2 @@\n+>reference\n+TGTATACACAACGGCGTCCCCGGTCTAGTAATAGAACCAACCTGTTCTACTTTAGAATACTGTGTCAATTTCTAACACCAGTTTGAAGTAACGAGAGCTTCCATTACGCATCTGCCGTCCGCCTACCGAACCACATTGAATATCGGCACCGAGTCGCCTATACTTGATTCCGAGTCATTACGGGGGCATGTCGTCAAAAAGGCCGGTCGCTCCTAACACCCGAGAGCTTACTATTTCGGATACAAACTTGGAACATACTGCAGGTGCTTCTTTCTGAGAATCCGTTTGTCATTTACCGCGTACGTGGCTAGTTATCAAGACAGGTCAAACCATGAGATGCATTCCGGATGCGTTACCGGTCCGACAACTATCGCGTCACAATCGCTGTTGGTGCTCTACACAAACTGTCATCGATATTCTGCAACGACAAGTCGACGTAGCCGGTCATGTCGAGAACTACGCTTAGTTACGAGAGCTGGATTGCACTACATAAGCGAGGACGCCTAGGTACAGGTGTACGGCACCCGATTGACCAAATCATGCCTAGGAGGCCATAGTTCCGGCGCTCGAATTCCAATTTATTTGTCCTAAGAGCCTGTCTTGTTTAGTGGATACTGTCGACCCAGCAGTTTATGACTAGCTACTGAGGGAATGGGCTAGCATCGTGAATTTACCGCAATCAGATAGAGTCACATCAGTGGTCCGTAGTGTCATACCATTGAACCAGGGTCATACTTGTGGAGGGAAGCAATCTAGGGGCTTAGACCGCAGTAGCCATTGTACTCCGGCGAGTAAGGTACGCTAATAAGGCCTGTATCTTTGAGGCTTGAAGGTAGGAGGACAAAACAACGCCAAACCTGGTGGTAATGCAATTTCCACCATGGCGGCGGTCGACGAGCGCTATATTGTACCGGCCGACGTCGGAGGTTTAGTATCAGTAAAAGATCGGGGCACCCACTGGTCCATGCGACTTCGCTGTCTCTGGGACTGTTGTTACCACCAGCGTACACGGGCCGGGCCGCGGGATGAATTTTTCCGCTCAGTCTCTCGCGAACCGCTTGCTTGTCAATTATCACCCTTAATGATTGCCCTGCATGGTAATGACACAACACAAACAATTACACGGACCACAAGAAGAAAATGGTAGGTACGGTGTTCAAGCGATATCCGATACAACACCGCTTGACCAAGAGCAGCCAATGAAGCTATTCCAATATTGAACTTTAGAAAGATCAGAGCAACCCTATGACGGGATGCGCCGCCCTGCGTTACACTCGTAGAATAAGAAGAAGGTTTTACTTGTGACTTGTGTGGGTAAATATCGTGTCTACTCAAGAGCACCGTGAGCGAAAAAAACGGATTCCGCCAGCTTTGACGACCGCGGTCCAACGATTTTTCCCAGTGCACCATTACAAACAACCTTATGTAACGATCGAATTTACGGCGCAGGAGTTTATATGACGGTGAGACGCGGTTTACGGTTTTCACCGTGGACAAGGGGATCTAGAGCAATGATTTTCTTGCGGTGGGTTCCGCAGCAACTCTGTCAGTACACTGTGTGTTTCTGACTCCGTGCCAGTATCATTTCAGGCCCGGACTGAGACTGACTTGACAGCATGAGTGTTAGAGCTAGACATGTAGCACAACTGAAGCGTACCCATTCTACCATATTTAGTCAATATAGAACCACGGTGAATCTGAGTCCCCGCTACACATTAGTCATGTCGGTCTACTGGCTGCGCTGACGGTCTAAGTCTATTGAAACGCTTTAAGAGTAGGCGTCGCGGGAGGCGGTGTCAGTCACGTACTCCTAGTGATAGCGCTTGAGGGGCGCGACCCAATACGCCTCATCTAGATAGTCCTCGGGAGCGATGCTCTCAGCTAAGCTCGGGGACGCTAGCTTTTATTAGCAATAAATCGTCGTGACGTCGTCGTGGAAGGCAGACATGCGCCACCGCACTTTAGATAGCCGGAAGTGCGTACCGACTATCCCAATGTTTCATTTTTAATACAGGTCTGTCATAGGCCAGTCGTGATAACTGCTGATTCGCCTCGTAGTAACACCTGCAGTAAGAATGGGTTGCAAAGGAAAAGAAATCTAGACTACGCTCGATACGGTAATCCAACACGTCTTGCCATCACCTAAGCGGGCCGCCATTGAATTCCATCCCCCGATCTCGCGAGCCGTCAGGTCGTTGATACCAGAACGCTATTTACTACCGGAAGTGCAGACAACGTTCCACGCGCTTAGGGAAGCTCCTTAACCGCCTTTCCCCCGAGGGTATCGGATTACCGTTCTTTCAGAATAGCCATTTAGCGAAGAACCCTGTTATGGTCTGGATCTATCTGGGCTGCCAATTTTTCGCACATAACACACGTACTTGTCGCTGGGCTCGGCGTTCGGCTATTTATTGTTACTTACGGCAAGAATTTTGGTTTCTGACAAGACTAGTTCCTTTGCGTAGTACAGCAACTACGAGGGTTCTACGGCTTGTGATGATACAATCGCGATCGACGCTCGGTACGGAATATCCTAACTGCATCTCCGTCAATTCTAGAGCCTGCGATATTAACTACAGTGCTTCCTGTATACACTACGCGCTATAGTTGGTATGAAATTAGACCTTCATGCGACACTCTGCCCGGAAGAGGCGGGGACCTGGACATGATCTGAATCGACATCCAATGCTGTCATGAACTGCTAGAAAAAAGTATAGTCAACACAAAAATAACAGCCCGTTTTTTGACCTATGGGTGATTGCTGACCCTAGGCTAGGAGTGGTCCCTCCTCAGCCTAATATATGCTTTAAAACTAAACGCACGCCTATTTCATCGCCATTTAGTGATACAGGTAGATAGGTCTGCCGAGAACCATCGAAGCAGGGACCTGGATGTGTGGCGCTTCACGGACAAAGGGGGTGAGCGTTCAGTAGCTGCATTGTACTTAAATGTACGGAGGTACAACCGTTTTTCCTCCATTATCTGTGTGGGCGAGGATCTAGCGTGGGGACCGCCATAGAACTAGAGAATGTCACTCGAGGTACCCTTGCCCGCATTACCCCACGTCGTAGGTCCTTGTTCACACCGGCGTTTCGTCACGGTTCCTTACGCAATCGGTGTTGCTCGCGGCCGCTGCGCTTCATATAGGTGGGCACTCGTACTAATGTGCCTCTAGTTCGTATGTTTTTCGCGTAATATCCGTGGTCCGCCCCAGGATGATAGCTGCTCAGGTCCCTTCTAGAGGGCTGTCCCTCTTGTACTAATCGGTGTCTTCTAGCCAATATCGTCTATTACTGCCGCCGACAAGCGACCGTTCTTGTTTGACGGACCGGTAGTTAGTAACCCCCAGGAACCGGCTCCTGAGTACGGCTGCTAACAGAAGCGCACCACATGATATGTACATATCTTTGCTATACCGAAAGTGGCCAAACACACATCGGAGTTACGGGATCGTGTACTAGCCCATGCGGTGTCAGGATAAAATCCGAGTACTACAAAAGCCAGGGTAGAAAAGGGGGGTGGCACTAAGCTTCAGTGAGAGTTCTGAGCTTGAGCCAGGGTTTTGTGAGAGTAAGATTCCATACAACCACGCCATCTAGCTGTGCCGGTACTAAGTAGGTCCTTTGCCCACCACACTCGCCGGAAATCCTTAGTGGTCTGGCACTTGTGAAGGATGCATGCTGGAGACTTTACCTCGCGAGCGTGTCCGCGGGCGTCTTTTTGTATAGGATCGCTAGAAGGCGCACACTCAATACATGCTAGACTTTGAGATACGCCGACGGAGAACTCTCTAGTCTTAGACGATAGGTATAGTGTGCTAACTGTGCCACGGGTCTTATTTTGGTTATCAATATATGACCCTCGCATGAATGCGTTGCTTTTTGCAACTCCCCTGAGCTCTTCAAGTGCGCGTTATCGTCACGTAAGGTGAGAAACTCACAAGGCAAAGGGGTATAGAGCCGTAGAGAAG'..b'ATATACAGTCATCCTGAGAGCAGTCCTTGCTATTAGATCATTTTTCGACTTCCCTTATCTAGAGGCAACATATGACAGCTTCATATATAAAAGATTGATGGACCCGCAACCATAGGCTCGTAGCTTGTGATTTTGTCTAATATAGGCTAGTCGAATTTAAGGTTTAGGTCCAGCCCGAGTTACCTTATGAAAATGTCCCAGAGATCCTTCGCACCGATCTGACTTTTGGCGCTAGTGTCAGTGCGCAAAATGGACGGCGTCGAGCGTACAAGCCGTCGCATGCCGTCAGGAAGTGGCAGGTCGACAATCTGGATTAATTGAGGGAACTAGAGCACATCTCAGGGCCAGCCGCTAAATTACTGTACGTCCCCATCCGTCAGACGGCGTGATCAGTGTTTTCAGGATGTTCCAGGATTCATAGTAACTGGATAAATTGCGTGCGCCTGGTTCCTGTTCCCCTTGATAGTTCTCCCTACGGTCCTATCCCATATCCGTCTTGTGGTGTCCGCGAGCGTCATTTGAATCGTGCAGGGCACAGGCAAACATTCACTCATGTATCCAATACTATTGATGGCCACGCTAGCCGTTTATTCGACTAGTCATCCTGACGCACAGGGGAGCTACGAAGCCTCGGGCACACATGCAAATAGAAATACCCACTTAGGCTACGTACAGAAGGAGTAAGTGAATGAAGAATCTCATGATAGTGCTTTGCTCAGGCGGACCTCTAGACCCATAAGGTGACTAGCGTGGAGTCAAACGACCAGTCGTGAGCCACTGTCCACGTGACCATCCTTGGAGTTACTATTGTAATACTGGGTATTGAGTTATTCGTCCGACCTGTAGCGGAAGAGTAGTGTTATCACCCCCGATCTCCTCCATAGTCGTTCGAAGGAGGACTAACTGGTTTAAGGCCCCCATATGACGTTCATTTGGTTTGCGTCTGGCGAGGGGTGGATCCCCAAAGAATGGGGAACAGTAGTCATCACACTTTGAAAAGCTACACTTCTGCGTGCGCGTGAATGTTCGATGTTTCTGGAATCTTAACCTATTTCTGAGAAGGTCATGAATCCTGCAACTCCATAGCCGTCTCTACAATCGGCCCTCTTTGTTACGACCCGTCAGCGAGAGCCCGCGAGCCTTGCTAGTAACAAACCGCCCCGGTCCGCGCCGTTTCTATCATCAGATGGCCGTATGATCCGGCAGATCCTCCAAACCACAGTCGTATCCTATCACGCCTCCCTTAGCTGGGTCCCGTGATCTGTCGATGCGGCCACTTATTTAATCAAATCCAATTGATGACGAGAGAAAGGCACCATTAAAGATTACAAACTGCTGAACCCTGGGGCGTAATTCCTTTCTTAACCATTTGTGCGCTGTCGAAGTTTACGAGGCCGCGGAGCCTGCTGCCGACATATGACCCCCGTGATCTTTGCTATATTCGGCTGCCGCCCGCTAACCGTATTAGTCGCCACTTTAGGCGACAAGTATTCCTGTACAGGCTGGTTCTTTCTGCTATCATCACACCGTGGGAATCGAGAGCCGGAATCGCTGCTGCTTCCAAAGGAGTGATGTTTATTTGACAACAGGGGTCCATAGGGTGTAGTAGAATTGTCCCGTTGGGCTTTAATTCGGGCTAGAGCCTTAGTCTAGGTTGAGTACATTTGATACACAACTTATGGCTCTAACGTCATCATCTTCCGCGCGCCTTCCGTTTCGGGCACTGGGTTAATTATTGAGGTCGAGGACAAAGACGAGTGGAGGTCAACCTTATCAGTATGATCTCAATTTATATATGCACAGCGCCAAACACCGACTCAAGGTACGCCACTGGCCACTCGGCACGCGGGCTCAAACTCAAACCAAGGTGACGTGGTACCCAGACTCCTAGATTGCAAGACTATCCCCAATGCTTTTGGCGGTCTCATCTACTCGAAAATTGTCTGTGCGGGGGCGTGGCATTTCTCCCACCTGCGGCCCTAAGGAGGAAGCATAGTACATCACTGGAAGCGACAAATGGACATGTGAATCTTTTGCCAGTATCTGAAGCGCTCCCCGCAGCCTTACCAACTTACAACTAAAGGCACCTCGAATCGCCTGGCGACGGCTCATTCGCGCTTCGATAAGGTCCTATAATCTAGGTGGTACCCGTACTCACAGTACGATATCGTTGGCCGGTAGTGAATAATCTACTATTCTAAACACGACTCTGGACTGTTTTGTAAATGGACACCGCCATACTTATTTGACTTCCTTTCACATTGTAGATGGGAGCCCGCTTGCGGACGGCTTTTATCGTTTGCACAACACAGGAAGGATCCATACTTATGGTGATTTTTTCTAACTACGCTGCATATGGAAAAGAGTCCAGGTGCTTGCAGAAGCTGCAAAAAAGGACGCCACGTCGCCCGTAACGAAGGGCAGGGCGGGTCTTTGATATACGCTCGCCATCTTGAAATAGGCTTCCCACGGACTGAACGGCGCCGCGCTCGGCAAGCATTTCGTGCCCGTCAAGGAAGCGCGTATCTATGGGTCAGTATTAGCATGTGACAGTTGACTTTGAGAGCCACAGCGTCTCACCCCTCGGGTCCCATAGTTATTTATCGACTATGGCCCGTGCAAGCAGTTTCCTTAGAGAATCGTTCAATTCATCCTTGAATATCTTCGTGACTATTATCACTAGTAAACAGTGCTCGCTCCGTTCTCCACCGCCTAGCACCGACGGTATTACCTCGGTACACCCCTACTCCGAAATGCACAATTACCATACTTCCATGCTCAGGTGCCATCGTATGAAGCCTACGCGTCTCGTAACGGGACAAGCCCTGAAATTACGGGGACAACACGAGCACATTTGTGTAGCTATGCCAGATGGGAATTAGGCTCATTCGGAAATTTGTTGCGAGAATCTTTCCGTCCTGATGATTGAAGGGAATGGCAACGGGGAGATTCTTTTCTCGCCGCAGGAAAGAATGACCGGTAACTTGAGGTCCCGCAAAAATTGAGCGGAGATCTGCAAGAATAGAATTAATTACATCCTGTCGACCTCGTTAGAAGGAGTAATACATACCGGAGGATCAAAGGGGCAGTAACTTAAAGCATGAGTTAGTGAACAACGTTGCCGGTCTTCAAAAGTTCAACTAGGTGCTGGGATCTGGTGTAGGAGCTGGCTAAAGGATCCTCGGCTAGGTGCCGGGCTCTCAAGCCCGGCGACAGTCTTTGATCACCCAGCTTCCGGCGGAATGTTAGGCTATCACCTAGGGGATTTACGACGCGTGTAGGGAGATATCCTGACGTCATGATGCACTCTAGCTTGTCCAGCGGCCAGCAACTCGAGGCATTCACTTCGTATCTGGAGCTCTCGAGTGTATACGCGGGGGTCACAGCGCGTACCCAACTGGTCTCACAAACCGTAGGACGGTCCTCGAGTCTTGCCACTGCGCCATGCTGTGGGACTCCGGGAGGCGACCCGGGCGGTAGATCGGTAGTCAGGGAGGCTATTATTTAGGAAGAATGCTTGAAATAGCTATCGCTAACGAGGCCGAAGCTGGAGCTGTAATCAACACTGACGAATAAATCCAGGCGCCTGGTCCATCCTGCGAGACAAACGTCTATAAAACGCGACGCCCATCTAGCCTGTGCGCAACAGAGCCACACTGTAGGAAATTAGTATACCACACTCAAGGGCTGGCCCTCGGGATGAAGTGCGGATCTGATGAGATAAGACACTGCCACGAACCGCCACGGGAAAAGGAATCAGCAGGCGCCTAGGTTCTGGAGTCTGGCGGGCACGCGTAAGTTCTACCGGGTACCACGGATTAGATACCCAGATTGGTTGTGTAAACTCATGTGGTGGTTTTCGGACCAAAGGTTCCGGGGCTGGAATTGCGGGGCCATCACACGGCCCCTGCCGTGTGACTGACACTGGCGATGATTTGGTGTACAGGGCCATCCGCGGCCTGGTACGGTACTATCGGAGGGCAGTCGGCCACCGAAAA\n' |
| b |
| diff -r 000000000000 -r a64b45c8b174 test-data/test.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.fastq Mon Sep 17 16:16:07 2018 -0400 |
| b |
| b'@@ -0,0 +1,12 @@\n+@test_sort_1\n+AGCGGGACTCTTCCCGAGGGGCCTGGAAATACCACGGATTCCAATAGTACGTTCTGTTAGCTGGGTGTCTTTATGCATGCCAAGGTTCGAACCTCCGGCCATGTTGGATGTTGAAAAGGTAGCCAGCGAGATGGAAGAAGGCCAAGGCTTCATATTACCCCGAATTCTCAAGGTGGATAAGGGGAACTAACGGCTGCGAGCATGCAGCTGGCATCAATGGCCAGGCGACAGATTTACTCTACTTTCCGCTGCTTGTTCTGGATTGGGATGTTAACCCTTTGATCCCACAGAGGTCAGCGGAGAAAACAACGTCTAAATATAGTCGGACAGACTGTAGCGACCCGGTTAGCACTCCCTAATTTTATCTAACTAGGCGGACACACTCTTACCACAGGGGCTCCAAGGTTCTCTCATTTCCGTGGGTGTAGCAACGTCCTATTCTTATGCGGACGCGAAGTAACGAGTATTCTCTTGGATTTTAACTGAGCTATCACTCCGCGTGAAGGATAACCGGCTTGACTAAAGGAGACGGTCAGTCGCAGAGGGCAACGCGCTATATACATTCGGTTTATTGAGTTCACCCTGGATAGTGACGCGGCCCTGGTTGTAGGTCGGGGCAAACTCTGAAATTGCTACTCGTATACAGGGTTGTGCGCTCGTAAGGACTCCCCCCTGGCGTCGAAGCTAGTTCGACAAAATGGCCCCGGAAGACGTTATCTAGATGAGTCTGGGTGGCTTTCAAGAATTCGCCTATCTTGGTACCTGGCCCTAACGATCAGACAGGCGCACTGCTGATGAGGGCATGTACCGACCATACGGTTTTTCTTCAGGCAAATGCCCGTTCCGGTGTCCGTGGTCAAGACTCAAAATCTCCCCTAAGGCTGTCACGAATTAGAGTTTCGTGTGAGAGATTAGTGTTAGCCCTCAGTGGGTCCTAATAAGAACCCACTAAGTTAGCCTCGCCGGTACGCAGACCTAGAGACTTGTTGGTGGGCAGCTTCTGCGCTGTTGGCATTCCTGCATAAAGAGAAACGTTATCGGCTGCCGGTGTCATCTGCCAGTGCTGCCGAGTCGAGCTTGTAGCACTCATTGAAGGTGCTGTGAGCTGCACGCCTCCACTAATTTAATCCCCGTCGCAAAGTTGGTCAGACCAGGAGCCTTCAGTGCACTGTGACAACTGGAATTCCGACTCCGGAAAAGTGCAATGGGTGTCCAGTGGACGACTTCTTGTGATTCGCGCCCGCGCCGCGTCCACAGGGGGACTCGGCGAAAAGTACAAAAGTAGGGGGAGCGCCCTGAGGAGAGTGGATCGTGCCGTCACCGGGTGACGGGTACAAGAACCTACTACTAGTGACGATGCTCTTAGATGGAGTGTAGCACGATCTTCACGGATAAAATAATGAAACAAACTGGGGCCGTTGGGCCCCCGAAGTATATGAACTGCGGCCATGTATGTTATGAATCCCCTCGGGTTCGAGGCTGCTCAAAAGTCTGCGTAGGACTCTCATCGGGACCTATACTAGATGGCGATGCGGAATACAGCGGCCTAGCTTTTATGCGATGTGCGGGGATAATTCTAATAGTTGCGGCTGGTCCATAACCGTGGACGTCGTATATTGGCAGACCTGCACAGTTGGTCCGATTAGACATACAGCACCCTTCTACATCCTGTTGTTCTGGAGAAGCCCACTCTAGTAGGACGGTTTACCTATGGACATGCGGTGTCCTAAATCATCCTACCGGAATTCTCATGCACTTCTGCCGTTCCCCCGAACATTCTAGTGGTGGGCTCGGGCTGCTGATAATCCACTCCATTGGGTGATACAAGAGGCGAGTTTGCCTTAGTTTGGGCAGGTCATGAAACCAAGCAACCGCATGCTTAGCTGGCTAATTGTTCGACTCGGCCACCAGCAAACTGTCGAAACGCGTAGAAAGTACAATTCCGTAAGCGAGTTCGGAATCCAGACCCGCGGCAATGCCCTCTCTTCCTACGCAGCGACCCCCTGTTTACACAGACAAGGCCCCGATGGCCAATCGGGAGTCTCGACGAGTGCCATAGAGGCGCCCTACCGGCGTCAGTGGGGGTGATTAATCACTTCACTGGTTCGCGGTGGGCTACGCGCTCACCTAGCTTCCCCGTAGTGTATTGACGAGTGTGGGCCCAGGATATGGAAGTTAAGGCTGGAGGAATAGATAACCGTCGTACCTCCCCTGGACGAGATAGCACTAAATCCTGGAAATGAGACGGATCCGAGAGTTCTGATAATGTTCGAGATGGGACAACAGGCGAATCTCGCAAACGTGCTTCAAAATATAACGTAGCATCCCGCTTATGGGCTTTATCGCGAAACCTGACAGCGCTCCCTCAAACCCCTAGTTCGGAAAATCGTGTCGCTCCTACAGTCCATCACTCAACTTCAGTTGAGCAATAAGTTTAGGGCGCGTCACTCTATCTACTTTACTGCTGAATGGACCCTTGTGTGGATCGTAAACCTTCAAGTCCCTGGGACTGCCTGTTCTTGCGATGATAAGATTAAGTGTTTGCCCGTTTGCCAACCATCCCTCAAATCTCGTTGATGAACCTGCCCCTTCTGTTCCATTACCAATCGACGGCTCTAACTTTTCAATCTGTGGCATGGACCCCATAAAGAGGGACCAGCGTTCAGGGAGACTTCTACAAACTTACGTTACATTATACCGTTCGCGGTGAGCGTGCGGTCAAGCATTCCAAAAGTACTCCGCGAGCCGTACGATCGACCTCTAGTATACTCCTGGTGCGGAGCAAACGATTTGAGCAGGCCTCATATAGAATGTGCAATCGCTCATTGTCGCAAAGCCACAACCAGTCACGCCGTTCGTCGACTACCACCCACTTCGTGGATGTGCGCCAAGTCTGTCTCCAGCTCTCAAGACTCATTGCAACTTGCCAATAACCTCAGTGCCTTGTCACTTCGAGTTCTTGAGGAATAGTCAGGGTCCTTAAACTTCATCGACTCGGCACAGTCTCTAGCCTCATTACTTCCCATTCCGGCCCGATGTGGAAGCGGTCCGGCTACTCAAATGCTCCCGGAGACCGAAGATTTCGGGACCTTTCGTTGTCAGACGCCAGTCATTGTTGCCTCTAACTGCATTGGAATCTGGCCCAAATAGAGATTGACCTCGGGAATCCGTCGCTGGGCAGGGCGTCGTACTCTGAACGGGACATCACTCCCGACCACCGGGGGGCGTCGTAGGTGCAGCAGACTGACAAATCCGTCCCAGTCGACTTATGTTCGCATGTCGTTATTAACTGCCTTGTACCTACGGTATGTACTGAACCACCGAGATCAGGGCAGGTTGAGCAAATTCATATCTCAAGGTGTGTCGAGAAAAAACGATTTAAGCTCTAGACCGGGAGTGCTGGTCAGAGTGTTCTGCTCACAAGGAAGCAATTCGGTGTTGGGTACCAATCAGAAATCACACCGTGGCTCTGAGCTTAATCCCTTGGGTTGGGCAACCGGGAGGACCAAGAGTACCGGCGACGGCCTCTGATTCTTGACGGTATAGGAGACATGCCTATACACGTTCGAGAGTAGTGACAGCATAGGATGCCTCAACGCTTTTACTCACGAGTGTGTGGTCCAATCTTGATGTCTAGACATGAGTTTTTCTAACGAGTGAACGGTATCCTATCCGCCCTCTGGATCAGCGGTTTCGGGGGTCCCTATGATGCTGTTCATATGCTCTGTCCATTGATTTGAGCCTACGGTATGAAGCACTCGCGGTGAAAAGGTTGCTGTAACCCGCGGGTGGTTACGATCTAATCTTCTGGTACGAAGGCGTGCCGTTACGCCAAAACTGGTACCTTGGTGTTTTTGCTGATCTCCAGAATTTTTGCTGTACTATTCCAATTTAGGAGTCATGAGTCCGGAATGTCATTCCGACAAGCAGTATTCCCAACAGAGAACACTTGCATACTCGTTAATGA'..b'//1//00/00//00/01111/10/01/0//0/////11100/10/11/0001100//1//1/011101100/0/01110///00/0/0/1///10//10/010//0000///01/00/1/1/01///11/100/11110/111011///0101/1/000/11/00/0/1011/10/100/10111/001//101//1/1111011/11/1//1011100//0000/011100//110001/0/010/01101010000//11/1//0//1/110/1/0/1/0/0100/1//1//11/01//010//1/01//01//10110//01011//0/0///0///1001/11//01/011/01001/110//00/0/0/01/010/0//01101/010/00/00001/10////0//01111//0//000/0//110//00110//1//1000010100/0/1//0//101/1010100101/10/01000100/01000101/01///11/01//00010///00101/1010/0/000/00////1/001110/00/0010/10011/1//010/0011/011/00/011/0111/0/00//000///0100/1100101001/1//111/1/1/0///1/11/0/1/0/00//1110/0101///01/1/1////////101000/1/00/0//00/100//100/0/000///101/0//1/101/00011011000//1//1/11/10100//0/0/01000110101/00/1110/1010/111110000/1/0/1/00//1100/11/00/10/1000/00/01/00/01001111/1////1/0/1//0101/1/0011010110//1/0/0/110/1//00/11000/1/1/1//0010/011/0///10/0/0/011//10/10///0100000000//01100/00/00/0111//01//00/0110110/110/100010/1/1/1001/10///0//00//11/1111/110/1/011/101000//000/1//001///01/00011/1////1101/1/1///1//00/110///0/0/1011/01/0//1////011//001/11100/11/01//101///000//0001///101110/1//00001101/001110/010//1000100/0/////11/0/////11/01011/1/000/11/00000///10/0/11111///0///01001////0010010/00//0000/01/01/1001/110111/1/////1010/11011/1//11/011//0100/1000111/0010///1010//1/010/110/010/1010/0//0/11000001/1101/100/1//111/00//11////101/11001/1////110///1001///0////0/1011/1/10000100//101//111//1///000110/00011/0001001111/100011/0010/1////000/1/00//101000001100101001/0/0000010/10/0011001///110110000/010//1000/00000100//011////1111/1000/11//111/////0/110011/0/0/101//1//1/111/0001//101/11000///11100110///100/1/01//1000000//1101///1/0//00/10000/111001/0001/1//11//0/0/110///11111//11011//1//1/00001/1110/100///1/0/1100010//011/010/11/01111/01//01/01/1010000011/11111/000///1/00011/011101/0/101/0101///101000/01/01010///1/1//0111//1/1//000/001111////01111/0/0//10/101/11010/0//0/100/11/1010//10110/001///10/01000/11001//11110111//011/00/010///1/0/0/////1100/0001/111/000/10101000/110110000000/00///110/10011/0//1//1/000/11100/01011///00/0/001100///1//1101/110/10001/111///1//000/101011001/11101/1/11001/1001//1//0110010101///010//100011010//010/1/11/1/10//1///0011001/////1/1010001/01110/01101///000//0/1//1010/011//1//000100//010011111///0100101010//001//0//1/0/1//0//1//10/1/11//0//0/10/1011111///100/11/101/1//00//1/10/111/110000/000//01///100/0//1000/101011/100/1/0/10110/11010//1/1011/0/00000/1/01/01/01////0/111/1010101010//1101//0//000000111100///00110/11111//000/01/00/11011/01/010110001011/1110////10111/0/1//00//0/01/00110//00/00/000/////100/1//0/0010//0/0011101/110/010//0100/00///11001/1/011//000/1/110//1//111010///011//11//111/11//111101/11/000101/1/0/0/100///0/0110/1/01010//0011101001010/01/10/0/0000110000/00///11/01110100/1/1/1//1/110//00/1///100//00111/11101/0/010//10/0//1///00/010/0//10//0/00/0//0011/0/01110/11100/1////10//01010011000101/1100000//01/1011100111/010110/010111001/1/100/10111/0000////1/00/111/10010101/00/001/10//01/1/10//001/0111/10/1/101/1011/10/10/10/111/1/0/1/10/101/01/1010/001/01101///11/0/00////1/0001/1///1101000101001/11111/10100/0/01////10//1/0/10/000//01/101000000/1////0001101///01/01//011/1/1//0/1/101//011//11010//110/1110///11//0000//1110/101//11000/0111001/11//00/001/11011//10//0/01110/00/////0100/1/1/00/1////0/1//00/0011/0/10100/1/000100/0/001//00/0/111////111/10////01110000///00111///01101///0///110/0/0//1//010/1/1/11/010/////01//1110///11/01100//0//11/01///0/10/1/1/1100////1/1110101////00000/////01/10/1/010001110/10101/101000000/00111/01//11////01111001//0///001/0///111111011/1/1/11111001/00/1/10000//0/0///1101/11111/1/1000/0/1111/110/0110000010///110100/0///011/0/1//10011100//////11///10/0//0///1100101/10011001101000//1111/1/01/1/0//11/10001//1//1/100111/10//0/0000//0/01/1/011/000/1/1/1100/01//1/100/01001///111101/1/110/01//1001/1111/1//0/011/1/1001/1//0/1//11//01/10/11/101//0/11/000//00/110/11/1110110//010100/1101/1///110010/11/11//11/0//1/01/01//0//1001/01001\n' |
| b |
| diff -r 000000000000 -r a64b45c8b174 test-data/test_reference.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_reference.fasta Mon Sep 17 16:16:07 2018 -0400 |
| b |
| b'@@ -0,0 +1,1001 @@\n+>reference\n+TGTATACACAACGGCGTCCCCGGTCTAGTAATAGAACCAACCTGTTCTACTTTAGAATACTGTGTCAATTTCTAACACCAGTTTGAAGTAACGAGAGCTT\n+CCATTACGCATCTGCCGTCCGCCTACCGAACCACATTGAATATCGGCACCGAGTCGCCTATACTTGATTCCGAGTCATTACGGGGGCATGTCGTCAAAAA\n+GGCCGGTCGCTCCTAACACCCGAGAGCTTACTATTTCGGATACAAACTTGGAACATACTGCAGGTGCTTCTTTCTGAGAATCCGTTTGTCATTTACCGCG\n+TACGTGGCTAGTTATCAAGACAGGTCAAACCATGAGATGCATTCCGGATGCGTTACCGGTCCGACAACTATCGCGTCACAATCGCTGTTGGTGCTCTACA\n+CAAACTGTCATCGATATTCTGCAACGACAAGTCGACGTAGCCGGTCATGTCGAGAACTACGCTTAGTTACGAGAGCTGGATTGCACTACATAAGCGAGGA\n+CGCCTAGGTACAGGTGTACGGCACCCGATTGACCAAATCATGCCTAGGAGGCCATAGTTCCGGCGCTCGAATTCCAATTTATTTGTCCTAAGAGCCTGTC\n+TTGTTTAGTGGATACTGTCGACCCAGCAGTTTATGACTAGCTACTGAGGGAATGGGCTAGCATCGTGAATTTACCGCAATCAGATAGAGTCACATCAGTG\n+GTCCGTAGTGTCATACCATTGAACCAGGGTCATACTTGTGGAGGGAAGCAATCTAGGGGCTTAGACCGCAGTAGCCATTGTACTCCGGCGAGTAAGGTAC\n+GCTAATAAGGCCTGTATCTTTGAGGCTTGAAGGTAGGAGGACAAAACAACGCCAAACCTGGTGGTAATGCAATTTCCACCATGGCGGCGGTCGACGAGCG\n+CTATATTGTACCGGCCGACGTCGGAGGTTTAGTATCAGTAAAAGATCGGGGCACCCACTGGTCCATGCGACTTCGCTGTCTCTGGGACTGTTGTTACCAC\n+CAGCGTACACGGGCCGGGCCGCGGGATGAATTTTTCCGCTCAGTCTCTCGCGAACCGCTTGCTTGTCAATTATCACCCTTAATGATTGCCCTGCATGGTA\n+ATGACACAACACAAACAATTACACGGACCACAAGAAGAAAATGGTAGGTACGGTGTTCAAGCGATATCCGATACAACACCGCTTGACCAAGAGCAGCCAA\n+TGAAGCTATTCCAATATTGAACTTTAGAAAGATCAGAGCAACCCTATGACGGGATGCGCCGCCCTGCGTTACACTCGTAGAATAAGAAGAAGGTTTTACT\n+TGTGACTTGTGTGGGTAAATATCGTGTCTACTCAAGAGCACCGTGAGCGAAAAAAACGGATTCCGCCAGCTTTGACGACCGCGGTCCAACGATTTTTCCC\n+AGTGCACCATTACAAACAACCTTATGTAACGATCGAATTTACGGCGCAGGAGTTTATATGACGGTGAGACGCGGTTTACGGTTTTCACCGTGGACAAGGG\n+GATCTAGAGCAATGATTTTCTTGCGGTGGGTTCCGCAGCAACTCTGTCAGTACACTGTGTGTTTCTGACTCCGTGCCAGTATCATTTCAGGCCCGGACTG\n+AGACTGACTTGACAGCATGAGTGTTAGAGCTAGACATGTAGCACAACTGAAGCGTACCCATTCTACCATATTTAGTCAATATAGAACCACGGTGAATCTG\n+AGTCCCCGCTACACATTAGTCATGTCGGTCTACTGGCTGCGCTGACGGTCTAAGTCTATTGAAACGCTTTAAGAGTAGGCGTCGCGGGAGGCGGTGTCAG\n+TCACGTACTCCTAGTGATAGCGCTTGAGGGGCGCGACCCAATACGCCTCATCTAGATAGTCCTCGGGAGCGATGCTCTCAGCTAAGCTCGGGGACGCTAG\n+CTTTTATTAGCAATAAATCGTCGTGACGTCGTCGTGGAAGGCAGACATGCGCCACCGCACTTTAGATAGCCGGAAGTGCGTACCGACTATCCCAATGTTT\n+CATTTTTAATACAGGTCTGTCATAGGCCAGTCGTGATAACTGCTGATTCGCCTCGTAGTAACACCTGCAGTAAGAATGGGTTGCAAAGGAAAAGAAATCT\n+AGACTACGCTCGATACGGTAATCCAACACGTCTTGCCATCACCTAAGCGGGCCGCCATTGAATTCCATCCCCCGATCTCGCGAGCCGTCAGGTCGTTGAT\n+ACCAGAACGCTATTTACTACCGGAAGTGCAGACAACGTTCCACGCGCTTAGGGAAGCTCCTTAACCGCCTTTCCCCCGAGGGTATCGGATTACCGTTCTT\n+TCAGAATAGCCATTTAGCGAAGAACCCTGTTATGGTCTGGATCTATCTGGGCTGCCAATTTTTCGCACATAACACACGTACTTGTCGCTGGGCTCGGCGT\n+TCGGCTATTTATTGTTACTTACGGCAAGAATTTTGGTTTCTGACAAGACTAGTTCCTTTGCGTAGTACAGCAACTACGAGGGTTCTACGGCTTGTGATGA\n+TACAATCGCGATCGACGCTCGGTACGGAATATCCTAACTGCATCTCCGTCAATTCTAGAGCCTGCGATATTAACTACAGTGCTTCCTGTATACACTACGC\n+GCTATAGTTGGTATGAAATTAGACCTTCATGCGACACTCTGCCCGGAAGAGGCGGGGACCTGGACATGATCTGAATCGACATCCAATGCTGTCATGAACT\n+GCTAGAAAAAAGTATAGTCAACACAAAAATAACAGCCCGTTTTTTGACCTATGGGTGATTGCTGACCCTAGGCTAGGAGTGGTCCCTCCTCAGCCTAATA\n+TATGCTTTAAAACTAAACGCACGCCTATTTCATCGCCATTTAGTGATACAGGTAGATAGGTCTGCCGAGAACCATCGAAGCAGGGACCTGGATGTGTGGC\n+GCTTCACGGACAAAGGGGGTGAGCGTTCAGTAGCTGCATTGTACTTAAATGTACGGAGGTACAACCGTTTTTCCTCCATTATCTGTGTGGGCGAGGATCT\n+AGCGTGGGGACCGCCATAGAACTAGAGAATGTCACTCGAGGTACCCTTGCCCGCATTACCCCACGTCGTAGGTCCTTGTTCACACCGGCGTTTCGTCACG\n+GTTCCTTACGCAATCGGTGTTGCTCGCGGCCGCTGCGCTTCATATAGGTGGGCACTCGTACTAATGTGCCTCTAGTTCGTATGTTTTTCGCGTAATATCC\n+GTGGTCCGCCCCAGGATGATAGCTGCTCAGGTCCCTTCTAGAGGGCTGTCCCTCTTGTACTAATCGGTGTCTTCTAGCCAATATCGTCTATTACTGCCGC\n+CGACAAGCGACCGTTCTTGTTTGACGGACCGGTAGTTAGTAACCCCCAGGAACCGGCTCCTGAGTACGGCTGCTAACAGAAGCGCACCACATGATATGTA\n+CATATCTTTGCTATACCGAAAGTGGCCAAACACACATCGGAGTTACGGGATCGTGTACTAGCCCATGCGGTGTCAGGATAAAATCCGAGTACTACAAAAG\n+CCAGGGTAGAAAAGGGGGGTGGCACTAAGCTTCAGTGAGAGTTCTGAGCTTGAGCCAGGGTTTTGTGAGAGTAAGATTCCATACAACCACGCCATCTAGC\n+TGTGCCGGTACTAAGTAGGTCCTTTGCCCACCACACTCGCCGGAAATCCTTAGTGGTCTGGCACTTGTGAAGGATGCATGCTGGAGACTTTACCTCGCGA\n+GCGTGTCCGCGGGCGTCTTTTTGTATAGGATCGCTAGAAGGCGCACACTCAATACATGCTAGACTTTGAGATACGCCGACGGAGAACTCTCTAGTCTTAG\n+ACGATAGGTATAGTGTGCTAACTGTGCCACGGGTCTTATTTTGGTTATCAATATATGACCCTCGCATGAATGCGTTGCTTTTTGCAACTCC'..b'CTTCATATATAAAAGATTGA\n+TGGACCCGCAACCATAGGCTCGTAGCTTGTGATTTTGTCTAATATAGGCTAGTCGAATTTAAGGTTTAGGTCCAGCCCGAGTTACCTTATGAAAATGTCC\n+CAGAGATCCTTCGCACCGATCTGACTTTTGGCGCTAGTGTCAGTGCGCAAAATGGACGGCGTCGAGCGTACAAGCCGTCGCATGCCGTCAGGAAGTGGCA\n+GGTCGACAATCTGGATTAATTGAGGGAACTAGAGCACATCTCAGGGCCAGCCGCTAAATTACTGTACGTCCCCATCCGTCAGACGGCGTGATCAGTGTTT\n+TCAGGATGTTCCAGGATTCATAGTAACTGGATAAATTGCGTGCGCCTGGTTCCTGTTCCCCTTGATAGTTCTCCCTACGGTCCTATCCCATATCCGTCTT\n+GTGGTGTCCGCGAGCGTCATTTGAATCGTGCAGGGCACAGGCAAACATTCACTCATGTATCCAATACTATTGATGGCCACGCTAGCCGTTTATTCGACTA\n+GTCATCCTGACGCACAGGGGAGCTACGAAGCCTCGGGCACACATGCAAATAGAAATACCCACTTAGGCTACGTACAGAAGGAGTAAGTGAATGAAGAATC\n+TCATGATAGTGCTTTGCTCAGGCGGACCTCTAGACCCATAAGGTGACTAGCGTGGAGTCAAACGACCAGTCGTGAGCCACTGTCCACGTGACCATCCTTG\n+GAGTTACTATTGTAATACTGGGTATTGAGTTATTCGTCCGACCTGTAGCGGAAGAGTAGTGTTATCACCCCCGATCTCCTCCATAGTCGTTCGAAGGAGG\n+ACTAACTGGTTTAAGGCCCCCATATGACGTTCATTTGGTTTGCGTCTGGCGAGGGGTGGATCCCCAAAGAATGGGGAACAGTAGTCATCACACTTTGAAA\n+AGCTACACTTCTGCGTGCGCGTGAATGTTCGATGTTTCTGGAATCTTAACCTATTTCTGAGAAGGTCATGAATCCTGCAACTCCATAGCCGTCTCTACAA\n+TCGGCCCTCTTTGTTACGACCCGTCAGCGAGAGCCCGCGAGCCTTGCTAGTAACAAACCGCCCCGGTCCGCGCCGTTTCTATCATCAGATGGCCGTATGA\n+TCCGGCAGATCCTCCAAACCACAGTCGTATCCTATCACGCCTCCCTTAGCTGGGTCCCGTGATCTGTCGATGCGGCCACTTATTTAATCAAATCCAATTG\n+ATGACGAGAGAAAGGCACCATTAAAGATTACAAACTGCTGAACCCTGGGGCGTAATTCCTTTCTTAACCATTTGTGCGCTGTCGAAGTTTACGAGGCCGC\n+GGAGCCTGCTGCCGACATATGACCCCCGTGATCTTTGCTATATTCGGCTGCCGCCCGCTAACCGTATTAGTCGCCACTTTAGGCGACAAGTATTCCTGTA\n+CAGGCTGGTTCTTTCTGCTATCATCACACCGTGGGAATCGAGAGCCGGAATCGCTGCTGCTTCCAAAGGAGTGATGTTTATTTGACAACAGGGGTCCATA\n+GGGTGTAGTAGAATTGTCCCGTTGGGCTTTAATTCGGGCTAGAGCCTTAGTCTAGGTTGAGTACATTTGATACACAACTTATGGCTCTAACGTCATCATC\n+TTCCGCGCGCCTTCCGTTTCGGGCACTGGGTTAATTATTGAGGTCGAGGACAAAGACGAGTGGAGGTCAACCTTATCAGTATGATCTCAATTTATATATG\n+CACAGCGCCAAACACCGACTCAAGGTACGCCACTGGCCACTCGGCACGCGGGCTCAAACTCAAACCAAGGTGACGTGGTACCCAGACTCCTAGATTGCAA\n+GACTATCCCCAATGCTTTTGGCGGTCTCATCTACTCGAAAATTGTCTGTGCGGGGGCGTGGCATTTCTCCCACCTGCGGCCCTAAGGAGGAAGCATAGTA\n+CATCACTGGAAGCGACAAATGGACATGTGAATCTTTTGCCAGTATCTGAAGCGCTCCCCGCAGCCTTACCAACTTACAACTAAAGGCACCTCGAATCGCC\n+TGGCGACGGCTCATTCGCGCTTCGATAAGGTCCTATAATCTAGGTGGTACCCGTACTCACAGTACGATATCGTTGGCCGGTAGTGAATAATCTACTATTC\n+TAAACACGACTCTGGACTGTTTTGTAAATGGACACCGCCATACTTATTTGACTTCCTTTCACATTGTAGATGGGAGCCCGCTTGCGGACGGCTTTTATCG\n+TTTGCACAACACAGGAAGGATCCATACTTATGGTGATTTTTTCTAACTACGCTGCATATGGAAAAGAGTCCAGGTGCTTGCAGAAGCTGCAAAAAAGGAC\n+GCCACGTCGCCCGTAACGAAGGGCAGGGCGGGTCTTTGATATACGCTCGCCATCTTGAAATAGGCTTCCCACGGACTGAACGGCGCCGCGCTCGGCAAGC\n+ATTTCGTGCCCGTCAAGGAAGCGCGTATCTATGGGTCAGTATTAGCATGTGACAGTTGACTTTGAGAGCCACAGCGTCTCACCCCTCGGGTCCCATAGTT\n+ATTTATCGACTATGGCCCGTGCAAGCAGTTTCCTTAGAGAATCGTTCAATTCATCCTTGAATATCTTCGTGACTATTATCACTAGTAAACAGTGCTCGCT\n+CCGTTCTCCACCGCCTAGCACCGACGGTATTACCTCGGTACACCCCTACTCCGAAATGCACAATTACCATACTTCCATGCTCAGGTGCCATCGTATGAAG\n+CCTACGCGTCTCGTAACGGGACAAGCCCTGAAATTACGGGGACAACACGAGCACATTTGTGTAGCTATGCCAGATGGGAATTAGGCTCATTCGGAAATTT\n+GTTGCGAGAATCTTTCCGTCCTGATGATTGAAGGGAATGGCAACGGGGAGATTCTTTTCTCGCCGCAGGAAAGAATGACCGGTAACTTGAGGTCCCGCAA\n+AAATTGAGCGGAGATCTGCAAGAATAGAATTAATTACATCCTGTCGACCTCGTTAGAAGGAGTAATACATACCGGAGGATCAAAGGGGCAGTAACTTAAA\n+GCATGAGTTAGTGAACAACGTTGCCGGTCTTCAAAAGTTCAACTAGGTGCTGGGATCTGGTGTAGGAGCTGGCTAAAGGATCCTCGGCTAGGTGCCGGGC\n+TCTCAAGCCCGGCGACAGTCTTTGATCACCCAGCTTCCGGCGGAATGTTAGGCTATCACCTAGGGGATTTACGACGCGTGTAGGGAGATATCCTGACGTC\n+ATGATGCACTCTAGCTTGTCCAGCGGCCAGCAACTCGAGGCATTCACTTCGTATCTGGAGCTCTCGAGTGTATACGCGGGGGTCACAGCGCGTACCCAAC\n+TGGTCTCACAAACCGTAGGACGGTCCTCGAGTCTTGCCACTGCGCCATGCTGTGGGACTCCGGGAGGCGACCCGGGCGGTAGATCGGTAGTCAGGGAGGC\n+TATTATTTAGGAAGAATGCTTGAAATAGCTATCGCTAACGAGGCCGAAGCTGGAGCTGTAATCAACACTGACGAATAAATCCAGGCGCCTGGTCCATCCT\n+GCGAGACAAACGTCTATAAAACGCGACGCCCATCTAGCCTGTGCGCAACAGAGCCACACTGTAGGAAATTAGTATACCACACTCAAGGGCTGGCCCTCGG\n+GATGAAGTGCGGATCTGATGAGATAAGACACTGCCACGAACCGCCACGGGAAAAGGAATCAGCAGGCGCCTAGGTTCTGGAGTCTGGCGGGCACGCGTAA\n+GTTCTACCGGGTACCACGGATTAGATACCCAGATTGGTTGTGTAAACTCATGTGGTGGTTTTCGGACCAAAGGTTCCGGGGCTGGAATTGCGGGGCCATC\n+ACACGGCCCCTGCCGTGTGACTGACACTGGCGATGATTTGGTGTACAGGGCCATCCGCGGCCTGGTACGGTACTATCGGAGGGCAGTCGGCCACCGAAAA\n' |
| b |
| diff -r 000000000000 -r a64b45c8b174 test-data/test_reference_1.fastq.gz |
| b |
| Binary file test-data/test_reference_1.fastq.gz has changed |
| b |
| diff -r 000000000000 -r a64b45c8b174 test-data/test_reference_2.fastq.gz |
| b |
| Binary file test-data/test_reference_2.fastq.gz has changed |