| Previous changeset 1:8880fb74ef56 (2018-09-19) Next changeset 3:41b2ad601cf0 (2022-02-24) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit fe7fac8c3287f5de0fe92d20fc39f71045240889" |
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modified:
filtlong.xml test-data/output_reference.fastq |
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added:
macros.xml test-data/test.fastq.gz test-data/test_reference.fasta.gz |
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removed:
test-data/test.fastq test-data/test_reference.fasta |
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| diff -r 8880fb74ef56 -r a72af9de6bf5 filtlong.xml --- a/filtlong.xml Wed Sep 19 08:21:21 2018 -0400 +++ b/filtlong.xml Wed Mar 31 08:19:02 2021 +0000 |
| [ |
| @@ -1,8 +1,9 @@ -<tool id="filtlong" name="filtlong" version="0.2.0"> +<tool id="filtlong" name="filtlong" version="@WRAPPER_VERSION@+galaxy1" profile="@PROFILE@"> <description>Filtering long reads by quality</description> - <requirements> - <requirement type="package" version="0.2.0">filtlong</requirement> - </requirements> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> <version_command>filtlong --version</version_command> <command detect_errors="exit_code"><![CDATA[ filtlong @@ -43,7 +44,7 @@ '$input_file' > output.fastq ]]></command> <inputs> - <param name="input_file" type="data" format="fastqsanger" label="Input FASTQ" help="FASTQ of input reads"/> + <param name="input_file" type="data" format="fastqsanger,fastqsanger.gz" 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)"/> @@ -52,7 +53,7 @@ <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="--assembly" type="data" format="fasta,fasta.gz" optional="True" label="Reference assembly" help="Reference assembly in FASTA format"/> <param argument="--illumina_1" type="data" format="fastqsanger,fastqsanger.gz" optional="True" label="Reference Illumina read" help="Reference Illumina reads in FASTQ format"/> <param argument="--illumina_2" type="data" format="fastqsanger,fastqsanger.gz" optional="True" label="Reference Illumina read" help="Reference Illumina reads in FASTQ format"/> </section> @@ -74,14 +75,15 @@ </outputs> <tests> <test> - <param name="input_file" ftype="fastqsanger" value="test.fastq"/> + <param name="input_file" ftype="fastqsanger" value="test.fastq.gz"/> <param name="min_length" value="1000"/> <param name="keep_percent" value="50"/> <param name="target_bases" value="500000000"/> <output name="outfile" ftype="fastqsanger" file="output.fastq"/> </test> <test> - <param name="input_file" ftype="fastqsanger" value="test_reference.fasta"/> + <param name="input_file" ftype="fastqsanger" value="test.fastq.gz"/> + <param name="assembly" ftype="fasta.gz" value="test_reference.fasta.gz"/> <param name="illumina_1" ftype="fastqsanger.gz" value="test_reference_1.fastq.gz"/> <param name="illumina_2" ftype="fastqsanger.gz" value="test_reference_2.fastq.gz"/> <param name="min_length" value="1000"/> |
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| diff -r 8880fb74ef56 -r a72af9de6bf5 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Mar 31 08:19:02 2021 +0000 |
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| @@ -0,0 +1,10 @@ +<macros> + <token name="@WRAPPER_VERSION@">0.2.0</token> + <token name="@PROFILE@">20.01</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@WRAPPER_VERSION@">filtlong</requirement> + </requirements> + </xml> +</macros> + |
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| diff -r 8880fb74ef56 -r a72af9de6bf5 test-data/output_reference.fastq --- a/test-data/output_reference.fastq Wed Sep 19 08:21:21 2018 -0400 +++ b/test-data/output_reference.fastq Wed Mar 31 08:19:02 2021 +0000 |
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| b'@@ -1,2 +1,12 @@\n->reference\n-TGTATACACAACGGCGTCCCCGGTCTAGTAATAGAACCAACCTGTTCTACTTTAGAATACTGTGTCAATTTCTAACACCAGTTTGAAGTAACGAGAGCTTCCATTACGCATCTGCCGTCCGCCTACCGAACCACATTGAATATCGGCACCGAGTCGCCTATACTTGATTCCGAGTCATTACGGGGGCATGTCGTCAAAAAGGCCGGTCGCTCCTAACACCCGAGAGCTTACTATTTCGGATACAAACTTGGAACATACTGCAGGTGCTTCTTTCTGAGAATCCGTTTGTCATTTACCGCGTACGTGGCTAGTTATCAAGACAGGTCAAACCATGAGATGCATTCCGGATGCGTTACCGGTCCGACAACTATCGCGTCACAATCGCTGTTGGTGCTCTACACAAACTGTCATCGATATTCTGCAACGACAAGTCGACGTAGCCGGTCATGTCGAGAACTACGCTTAGTTACGAGAGCTGGATTGCACTACATAAGCGAGGACGCCTAGGTACAGGTGTACGGCACCCGATTGACCAAATCATGCCTAGGAGGCCATAGTTCCGGCGCTCGAATTCCAATTTATTTGTCCTAAGAGCCTGTCTTGTTTAGTGGATACTGTCGACCCAGCAGTTTATGACTAGCTACTGAGGGAATGGGCTAGCATCGTGAATTTACCGCAATCAGATAGAGTCACATCAGTGGTCCGTAGTGTCATACCATTGAACCAGGGTCATACTTGTGGAGGGAAGCAATCTAGGGGCTTAGACCGCAGTAGCCATTGTACTCCGGCGAGTAAGGTACGCTAATAAGGCCTGTATCTTTGAGGCTTGAAGGTAGGAGGACAAAACAACGCCAAACCTGGTGGTAATGCAATTTCCACCATGGCGGCGGTCGACGAGCGCTATATTGTACCGGCCGACGTCGGAGGTTTAGTATCAGTAAAAGATCGGGGCACCCACTGGTCCATGCGACTTCGCTGTCTCTGGGACTGTTGTTACCACCAGCGTACACGGGCCGGGCCGCGGGATGAATTTTTCCGCTCAGTCTCTCGCGAACCGCTTGCTTGTCAATTATCACCCTTAATGATTGCCCTGCATGGTAATGACACAACACAAACAATTACACGGACCACAAGAAGAAAATGGTAGGTACGGTGTTCAAGCGATATCCGATACAACACCGCTTGACCAAGAGCAGCCAATGAAGCTATTCCAATATTGAACTTTAGAAAGATCAGAGCAACCCTATGACGGGATGCGCCGCCCTGCGTTACACTCGTAGAATAAGAAGAAGGTTTTACTTGTGACTTGTGTGGGTAAATATCGTGTCTACTCAAGAGCACCGTGAGCGAAAAAAACGGATTCCGCCAGCTTTGACGACCGCGGTCCAACGATTTTTCCCAGTGCACCATTACAAACAACCTTATGTAACGATCGAATTTACGGCGCAGGAGTTTATATGACGGTGAGACGCGGTTTACGGTTTTCACCGTGGACAAGGGGATCTAGAGCAATGATTTTCTTGCGGTGGGTTCCGCAGCAACTCTGTCAGTACACTGTGTGTTTCTGACTCCGTGCCAGTATCATTTCAGGCCCGGACTGAGACTGACTTGACAGCATGAGTGTTAGAGCTAGACATGTAGCACAACTGAAGCGTACCCATTCTACCATATTTAGTCAATATAGAACCACGGTGAATCTGAGTCCCCGCTACACATTAGTCATGTCGGTCTACTGGCTGCGCTGACGGTCTAAGTCTATTGAAACGCTTTAAGAGTAGGCGTCGCGGGAGGCGGTGTCAGTCACGTACTCCTAGTGATAGCGCTTGAGGGGCGCGACCCAATACGCCTCATCTAGATAGTCCTCGGGAGCGATGCTCTCAGCTAAGCTCGGGGACGCTAGCTTTTATTAGCAATAAATCGTCGTGACGTCGTCGTGGAAGGCAGACATGCGCCACCGCACTTTAGATAGCCGGAAGTGCGTACCGACTATCCCAATGTTTCATTTTTAATACAGGTCTGTCATAGGCCAGTCGTGATAACTGCTGATTCGCCTCGTAGTAACACCTGCAGTAAGAATGGGTTGCAAAGGAAAAGAAATCTAGACTACGCTCGATACGGTAATCCAACACGTCTTGCCATCACCTAAGCGGGCCGCCATTGAATTCCATCCCCCGATCTCGCGAGCCGTCAGGTCGTTGATACCAGAACGCTATTTACTACCGGAAGTGCAGACAACGTTCCACGCGCTTAGGGAAGCTCCTTAACCGCCTTTCCCCCGAGGGTATCGGATTACCGTTCTTTCAGAATAGCCATTTAGCGAAGAACCCTGTTATGGTCTGGATCTATCTGGGCTGCCAATTTTTCGCACATAACACACGTACTTGTCGCTGGGCTCGGCGTTCGGCTATTTATTGTTACTTACGGCAAGAATTTTGGTTTCTGACAAGACTAGTTCCTTTGCGTAGTACAGCAACTACGAGGGTTCTACGGCTTGTGATGATACAATCGCGATCGACGCTCGGTACGGAATATCCTAACTGCATCTCCGTCAATTCTAGAGCCTGCGATATTAACTACAGTGCTTCCTGTATACACTACGCGCTATAGTTGGTATGAAATTAGACCTTCATGCGACACTCTGCCCGGAAGAGGCGGGGACCTGGACATGATCTGAATCGACATCCAATGCTGTCATGAACTGCTAGAAAAAAGTATAGTCAACACAAAAATAACAGCCCGTTTTTTGACCTATGGGTGATTGCTGACCCTAGGCTAGGAGTGGTCCCTCCTCAGCCTAATATATGCTTTAAAACTAAACGCACGCCTATTTCATCGCCATTTAGTGATACAGGTAGATAGGTCTGCCGAGAACCATCGAAGCAGGGACCTGGATGTGTGGCGCTTCACGGACAAAGGGGGTGAGCGTTCAGTAGCTGCATTGTACTTAAATGTACGGAGGTACAACCGTTTTTCCTCCATTATCTGTGTGGGCGAGGATCTAGCGTGGGGACCGCCATAGAACTAGAGAATGTCACTCGAGGTACCCTTGCCCGCATTACCCCACGTCGTAGGTCCTTGTTCACACCGGCGTTTCGTCACGGTTCCTTACGCAATCGGTGTTGCTCGCGGCCGCTGCGCTTCATATAGGTGGGCACTCGTACTAATGTGCCTCTAGTTCGTATGTTTTTCGCGTAATATCCGTGGTCCGCCCCAGGATGATAGCTGCTCAGGTCCCTTCTAGAGGGCTGTCCCTCTTGTACTAATCGGTGTCTTCTAGCCAATATCGTCTATTACTGCCGCCGACAAGCGACCGTTCTTGTTTGACGGACCGGTAGTTAGTAACCCCCAGGAACCGGCTCCTGAGTACGGCTGCTAACAGAAGCGCACCACATGATATGTACATATCTTTGCTATACCGAAAGTGGCCAAACACACATCGGAGTTACGGGATCGTGTACTAGCCCATGCGGTGTCAGGATAAAATCCGAGTACTACAAAAGCCAGGGTAGAAAAGGGGGGTGGCACTAAGCTTCAGTGAGAGTTCTGAGCTTGAGCCAGGGTTTTGTGAGAGTAAGATTCCATACAACCACGCCATCTAGCTGTGCCGGTACTAAGTAGGTCCTTTGCCCACCACACTCGCCGGAAATCCTTAGTGGTCTGGCACTTGTGAAGGATGCATGCTGGAGACTTTACCTCGCGAGCGTGTCCGCGGGCGTCTTTTTGTATAGGATCGCTAGAAGGCGCACACTCAATACATGCTAGACTTTGAGATACGCCGACGGAGAACTCTCTAGTCTTAGACGATAGGTATAGTGTGCTAACTGTGCCACGGGTCTTATTTTGGTTATCAATATATGACCCTCGCATGAATGCGTTGCTTTTTGCAACTCCCCTGAGCTCTTCAAGTGCGCGTTATCGTCACGTAAGGTGAGAAACTCACAAGGCAAAGGGGTATAGAGCCGTAGAGAA'..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 8880fb74ef56 -r a72af9de6bf5 test-data/test.fastq --- a/test-data/test.fastq Wed Sep 19 08:21:21 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,12 +0,0 @@\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 8880fb74ef56 -r a72af9de6bf5 test-data/test.fastq.gz |
| b |
| Binary file test-data/test.fastq.gz has changed |
| b |
| diff -r 8880fb74ef56 -r a72af9de6bf5 test-data/test_reference.fasta --- a/test-data/test_reference.fasta Wed Sep 19 08:21:21 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,1001 +0,0 @@\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 8880fb74ef56 -r a72af9de6bf5 test-data/test_reference.fasta.gz |
| b |
| Binary file test-data/test_reference.fasta.gz has changed |