| Next changeset 1:1c6c961851de (2024-03-15) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphmap commit a1461f1e83079de821b269125c49eca2460e7693 |
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added:
graphmap_align.xml macros.xml test-data/E.coli_contigs.fasta test-data/Loman_E.coli_MAP006-1_2D_50x_first_500_reads.fasta test-data/result1_map.bam test-data/result1_owler.mhap test-data/result2_map.bam test-data/result2_owler.mhap test-data/result3_map.bam |
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| diff -r 000000000000 -r 190175f4e143 graphmap_align.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/graphmap_align.xml Thu Sep 27 15:26:47 2018 -0400 |
| [ |
| @@ -0,0 +1,63 @@ +<tool id="graphmap_align" name="Mapper" version="@VERSION@"> + <description>for long, error-prone reads, like Nanopore ONT and PacBio</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"> + <![CDATA[ + ln -s '$r' ref.${r.ext} && + ln -s '$d' reads.${d.ext} && + + graphmap align + -r ref.${r.ext} + -d reads.${d.ext} + #if $preset: + -x $preset + #end if + -t \${GALAXY_SLOTS:-4} | + samtools view -b -u | samtools sort -@ "\${GALAXY_SLOTS:-4}" -T tmp -O bam -o output.bam - + ]]></command> + <inputs> + <param argument="-r" type="data" format="fasta,fastq" label="reference sequence" /> + <param argument="-d" type="data" format="fasta,fastq" label="reads" /> + <param name="preset" type="select" optional="True" label="Pre-set parameters to increase sensitivity for different sequencing technologies. (-x)"> + <option value="illumina">illumina preset</option> + <option value="overlap">overlap preset</option> + <option value="sensitive">sensitive preset</option> + </param> +<!-- + <param type="data" name="reference" format="fasta,fastq" label="Sequences"/> + <param type="data" name="reads" format="fasta,fastq" label="Sequences"/> + <param type="data" name="overlaps" format="sam,tabular" label="Overlaps"/> + <param type="data" name="corrected_reads" format="fasta,fasta.gz,fastq,fastq.gz" label="Target sequences"/> --> + + </inputs> + <outputs> + <data name="output" format="bam" from_work_dir="output.bam" /> + </outputs> + <tests> + <test> + <param name="r" value="Loman_E.coli_MAP006-1_2D_50x_first_500_reads.fasta"/> + <param name="d" value="E.coli_contigs.fasta"/> + <output name="output" ftype="bam" file="result1_map.bam"/> + </test> + <test> + <param name="r" value="Loman_E.coli_MAP006-1_2D_50x_first_500_reads.fasta"/> + <param name="d" value="E.coli_contigs.fasta"/> + <param name="preset" value="illumina"/> + <output name="output" ftype="bam" file="result2_map.bam"/> + </test> + <test> + <param name="r" value="Loman_E.coli_MAP006-1_2D_50x_first_500_reads.fasta"/> + <param name="d" value="E.coli_contigs.fasta"/> + <param name="preset" value="sensitive"/> + <output name="output" ftype="bam" file="result3_map.bam"/> + </test></tests> + <help><![CDATA[ + GraphMap - A very accurate and sensitive long-read, high error-rate sequence mapper + GraphMap (c) by Ivan Sovic, Mile Sikic and Niranjan Nagarajan + GraphMap is licensed under The MIT License. + ]]></help> + <expand macro="citations" /> +</tool> \ No newline at end of file |
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| diff -r 000000000000 -r 190175f4e143 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Sep 27 15:26:47 2018 -0400 |
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| @@ -0,0 +1,26 @@ +<macros> + <token name="@VERSION@">0.5.2</token> + + <xml name="requirements"> + <requirements> + <requirement type="package" version="0.5.2">graphmap</requirement> + <requirement type="package" version="1.9">samtools</requirement> + <yield/> + </requirements> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1038/ncomms11307</citation> + <citation type="bibtex"> +@misc{githubgraphmap, + author = {LastTODO, FirstTODO}, + year = {TODO}, + title = {graphmap}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/isovic/graphmap}, +}</citation> + <yield /> + </citations> + </xml> +</macros> \ No newline at end of file |
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| diff -r 000000000000 -r 190175f4e143 test-data/E.coli_contigs.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/E.coli_contigs.fasta Thu Sep 27 15:26:47 2018 -0400 |
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| b'@@ -0,0 +1,376 @@\n+>contig_1\n+AAGAAACATAAACAGAACGTCAGTAATCCAGCAAACTGACGGTTACGAAATAGGCGCGGC\n+GACAATAATCTCGTTCTTTCACCACCTCCGGCGTCAGATTCGGATTCACAGCACATCGGG\n+ACCAACGCGTTGGTGCAAACGGATGCGTGGTCCAGTTGTTCCGGGAGTCAACATCTCTAC\n+AGGCTTGAGGACCGCAAATCTCATGGAGCCCCAGTATCGCAGTTTTGTTGCACTATCCCG\n+CGTGTTTCAGGCGAGTGTTCTACCTCGAGTAGCCCGTTACAGAAGTCAAATGCGGCTCTA\n+GCACGAGTCGTAAAGAGGTGGCACCCCGCTAGGAGGGGCTAAGCATTGGCTCAGGAAACT\n+GCTGTATTAAAGAATTCGGTTGTACGGTTCCGCAAGTGAGGTCGGCCTCTAGGTCAAAAG\n+CGTCCAGTAAAGCTAATATTGTCACCGATAAGGTTGATTAACTGCTCGAAGGAAATTTAA\n+AACCATTGAGGAGGATAAGAGCGATATCGCAGTGGACCCAATTAGTGGTTCATTCTATTG\n+CCAGCGACCCATGTATATTCGGAACGTGAGGGTGAAACGTGCCTCCATGTAGAGCTTCAG\n+AGCAGGCATTAGATGCTGGTACAGCCTTTTCGTCGTCATTAATCGGGGTAAGTTACTTAA\n+TGCGACAACAGGATGCGCTTTTCGGGGCAAAATTGAAGAGCGTAGTCATGCGGGCGAACG\n+CCAGTGCGTGCTCGCCAGTAGCGTCGCACTGCATTAAGAAGCCGTTTGCGCCAGCCGTTA\n+AAGAGCGTTTCTGGTTCTACGGTGATAATATGATTTCTGGTGATCCGTGTTGCACCGGAC\n+CCATAGTTCCAGCACTTTCTTCAGTTCTAGTGATAGCGCGCCTGATATGGCTTTCGGAGA\n+TACACCCCAACCCAACGCTTTCATGATAACCGCGATCGGGTGGGAGCCGTTAGACACCAC\n+CCGTTATCATAGGCCACTGGTCAGTTAATTAAATGCAGAGTGCCCCGGCAAACATTTCCT\n+CGCCCCGATAATCGCTCCTGGGAAGAATCATGCTTCCCTGGATGTACGAACGAGAATTGA\n+CCCGCGGCGCCCGCATGGGAGATCGTGCGATTCGTCTGCCAGTTGTGCTTCTTTCGCCGC\n+CTGGTTGTACAACATGCCGTGCGGTTTGACATGACGCATTACGCGCTATCCAGCGCACGG\n+GAAATTCCTTCAGGCGCCACCAATTTTAGATACAGCGTCTGGGCGTAAACGGGGTTTCTG\n+GCGGCATCCAGCTGACGCGCTGCGAAATAAAATTTTCCCCTGTCGGGAAAACTCGGGTGA\n+GCGCCAATCGCGACACCATTTTATTGCTTCCACGCACGCAGCCTGCATGATTTGCGCATC\n+GCCTGCATGAAATCCACAGGCAATATTGTGCAGAGGAAACCAGCGTTAATAGCTCTGCGT\n+TGCTGGCGCATCGCTTCGCCCAAGTTCGGCGTTCAGGTCAATTTTCATTGTGCAGCCGCC\n+ACGCTAATTGTTCAAAAGTAACTGTTGCTGATTTGCCGTGCTTTTTAGTGCCTCTTCCAG\n+TGAACACTGGACAAAATGAATCGGCTGACCGAGCGGCGAATTTGCGCCAGATGGTACATA\n+TCAGCCTCTCAATGATACAGGCAATACGCGGGTAACCACCGGTGGTCTTGCCGTCGTTCA\n+TCAACACAATACTGCTGCCCGTCCTCTTGGCACCTGCACCACGCCCGGTGACAAACCGTG\n+AGATAACAGTTCGCGATCGGTGGTGCGTTTTAAATGTCCCCTGTAAGCGATAGCCATGCG\n+GTTATTTGCGAGCCGGCTGCCAGGCGAACGCCAGAATGCATATCCTGCGAGGCGCGATTG\n+AACTCATGATATTCCGAGTGGCGGCAAGGCGCGAATTGCGGTTGCCCCACAGCAGCTGTT\n+TAACGCCCTGCGCTTCCATAGAATTGGTACGCTTCGATTTGCCAATCGGGAGTCGGTCAC\n+CATCCTTCAGTAAACGGCCTTCCCAGCCCGCCAATCCCCATTTGCAATCACTGCGCGGTG\n+CTGCATGAGCCCATTACCGGCGGAACATCAATACCACCCGCGACCGCCAGATAACTGCGC\n+ATGTAGCGTCTTCGTGGAGGCATCCGTCAGCGTTAAACGCTGGCCTGCTGTTTTCATCGG\n+CAATCGCCAGCCGGTCCAGACGCATTATCATCCAGCCGCGCTGTCGCAACCGGCACCCGT\n+CAGAGCCGAAACCACCCATCAGTTTCGAACCTAACAGTTAACTGACCGAGCGCTGATCTC\n+CATAGCGGGGGCATTGGCGTCATTACCACCAGTATAAGTGCAATGCGTAACGCGGGCATA\n+TCAGTGCGCCGCAGTGGCTGATATCCGACTGGCGAAACCGTGACGACCGCCATCCTGCAC\n+GCGCGTATACATGCCCGCACGAATAATCTTCAGCATACTCCCTCCTTCTGCGTACAAAGC\n+CGCGGAACCTGTCTCCAGGGACGGTGTAATACAAGATGGGTTCGTCACGCGCGCCGGATT\n+AATAAGGACGATGAGTGAGGTATGACCAATCAACTGCCAGCCACCCGGCGTTGCCATAGG\n+GATAAACACCAGTGCGGCCCGCCGATCCCGACAGAACCTGCCGCTGAAAGCCACCGCGGT\n+TCAGCGCCGTGGCGTGTGTAGTTGTTCCGGCAAACTCCCGAGATACGGGAAGCCCGGTTT\n+GAAAACCTAAAAACCAGACCACGTATTCCACGCATAGAGTTATGCAATTCAACAACCTGT\n+TCGCTCAACCCGCAATGCGCCGCGACCACCGCCAAATCCGGTCCGCCTGCCACCGTAAAC\n+CAAGGGGATTTCAATCAAAGCGAGACTCGTGGGTGCCAGCGCCTCGCTCCTCTCCACCAG\n+CGTTGCAAACGCTCTATGGCATCCAGCGCCAGCGACTCAGGATTACGCAAAATCACCGTG\n+ATATTTGTTCCACCTGCCGGGAAACCTGTTCAACCACATTCGGCAATATATCCACCAGAC\n+ACCCTGCGCCAGTCGCCAGGATCCCGGTTTCTGGCTAGCCAGTTCACCGGCGGTTCTCAG\n+TTCCAGCACTACCGCCGTTTCCACCTATCAGATAACAACGCGCTCGTTGCACTTTCACGT\n+GTGGGACTATTATTCGTTATGCAGGATTAGGAATATCAATACAAAGGTCACATCAAGATT\n+TCGTATTTTCACTTCAGCCACTCGCTCAATGCGCGAATACCACCACGTTCAGAGTGGCAG\n+ATGGTGACCTGCAGCATAAAATGCAATCCCTGCTCGCGGGCCTGAATGAATGGTCTTTCA\n+GAAAACTTCGCCAGGACCAACAGGCATCCACGCCAAACGCGGCGGCTATCGATAAAACTT\n+GCCCGCCGCCCGTGCACCAGGCGACGCGCTGGACCACCTCAGTCCGGTATCGCCACACCA\n+TAACGGCTTACGTCCCAGACGCTTTCAATCCAGGAAGCCAGCTGGGCAGTCCCGGCACAG\n+GCAATTGAGTTTCGCCCCACGGCACCAACGGCTCATTTCGCCCATGACCGTGATCCCCCA\n+ATGCGCCGCCAGCTGTGCCATGTTATTGCCCAGCTCAGGATGTGCGTCAAGCGGCAAATG\n+CCAGCCATATAAGGTTGATATCAGGTTTCGCCAGCAACGTTTTTAAACGGTTACGCTTCA\n+TTCCGCGAATGACCGGAGACTCTCTCCTTCCAGAAGTAGCCATGATGCACATGACCGCAT\n+CCGCGCCCAGACGCACTGCCTCATCGAGCAAAGCCTGGGTGCGTGGTGACACCGGTAACA\n+CAATTTTGCACCGTCTCTTTGCCTTCCCACTGCAAACCATTCGGCGTGGTAATCACTAAT\n+C'..b'TGACCGTGAGATGAACTG\n+GAAGCAATATCTTTGTGCCATTCTCGGCCTGAACATGCTGGGGCTGGCGGTGCTGTTTTT\n+ATGTTGCTCGGTTCACACTAGTCTGCCGCTGTAATCTGGACACCAGCAGTTGCCGAGGGC\n+TGTCGTGCGATGATCTGGCGCTGAATACCGCCGTCAGCTTTGTCACCAATACCAACTGGC\n+AATCTTGTAGCGTGAAACCACGTTGAGCTACTTTTCAGCCAGATGGCGGGCTTAACGGTG\n+CAAAACTTTCTTTCTGCCGCCAGCGGGATTGCGGTGATTTTTGCCCTCATCCGTGCGTTT\n+ACCCGCCAGAGCATAGCAGCACGCTGCGGGAATGCCTGCGTACATCCTGCTACGCATCAC\n+GTTATGGGTGCTAGTCCCTCGTGGCGTTGTTGATTGCACGTTTGTATTCAACAAGGTGCG\n+CTGCAAAACTTTCTGCCTTATCAGGCTGTGAATAGCCGTTGAAGGCGCGCAACAGCTGTT\n+ACCCATGGGGCCTGTAGCTTCTCAGGAAGCGATCAAGATGCTCGGTACTAACGGCGGTGG\n+CTTCTTTAATGCCAACTCGTCGCATCCGTTTGAAAACCCCAACCGCACTGACCAACTTCG\n+TGCAGATGCTGGCGATCTTCTTGATCCCAACGGCGCTGCCTTTGCCTTTGGTGAAGTGAT\n+GGGCGATCGCCGCCAGGGGCGCATGTTGCTGTGGGCGATGTCAGTGATTTGTCATCTGCG\n+TAGGCGTGGTGCGTGGTAAGAAGTTCAGGGTAATCCTCATCTGCTGGCACTGGGCACGGA\n+CAGCAGCATCAATATGGAAGGTAAAAGAGCCGTTTGCGTGCTGGTCAGTAGCCTGTTTCG\n+CGTCGTGACGGGCGGCTTCCTGTGGCGCGGTGATTGCGATGCATGATTCGTTTACCGCTC\n+TGCGTGGCATGGTGCCGATGTGGCTGATGCAAATTGGTGAAAGGGTGTTCGGCGGTGTCG\n+GTTCTGAGTCTTTACGCATGATGCTGTTTGTCCTGCTGGCGGTGTTTATTGCCGGGCTGA\n+TGATTGGTCGTACACCGGAATATCTGGGTACAAAATCGACGTACGCGAGATGAAACTGAC\n+TGCACTGGCAATTCTGGTTACCCCGACGCTGGTGCTGATGGGCGCGGCGTTGGCGATGAT\n+GACCGACGCCGGACGGTGAGCGCCATGCTCAACCCTGGCCCGCACTGGTTTTAGCGAAGT\n+GCTGTACGCCGGTGTCATACCCGCCGCTAACAACAACGGCAGCGCTTTGCCGGATCCCAG\n+CGCCAACTCTCCGTTCTGGAACTGTTTACTGGCGTTCTGCATGTTTGTCGGTTGCTTCGG\n+GTGATTATCCCGGTGATGGCAATTGCCGGTTCGCTGGTGAGAGCCAAGCCGCCAGCTCCG\n+GCACATGCTGCCAACGCACGGCCCGCTGTTTGTTGGCCTGTTAATCGGCACCGTGTTGCT\n+GGTTGGCGCACTGACCTTTATCCCTGCCCTGGCGCTTGGTCCCGTGGCGGAATACCTCTC\n+CTGATGATATTGAGTGAGCACTGAATATGAGTCGTAAACAACTGGCGCTATTCGAACCAA\n+CACTTGTCGTTCAGGCAGCTGAAAGAAGCGGTGAAAATTAAACCCGCAGGGCGCAATGGC\n+GCAATCCGGTAGATGTTTATCGTCTGTATCGGCAGTCTGCTGACCACCTGTATTAGCATC\n+GCGATGGCAAGCGGTGCGCAGTGCCCGGCAATGCGCTGTTTAGCGCGGCCGTTGGCTGTG\n+GGTCTGCGATACTGTTAGCTAAGTTTGCCACCGCCGAGTGAGCGTGGCAGAAGGCCGCAG\n+TAAAGCGCAGGCCAACAGTCTGAAAAAGGGGTGACTGCCTTTGCCCGCAAGCTGCGTGAG\n+ACACGAGATATGGCGCTGCGGCGGACAAAGTTCCTTGCCGACCAACTTCGTAAAGGCGAT\n+ATCGTACTGGTAGAAGCTGGCGATATTATCCCCTGCGATGGTGAAGTTATTGAAGGGGGT\n+GCATCGGTCGATGAAAGCGCCAGCCCACCGAAACGGCAACCGTGTGTATCCGTGAATCGC\n+GGCGGCGATTTGCCGCGTCACCACGGCGGCACGTAGCGTGATTCTGGACGCGAGCTGCCC\n+GGTCATTGTAGCGGTATAGACGGCGAGACATGTCTGCATCGCGATCGACTCGCCGATGGT\n+GGAAGTGCGCAGCTGAGGGGACTGAGAACGAATCGCCCTGACCATTCTGGTGGTACATCG\n+CCCGTGACTATCGTCTTTGCTGGCAGCGCCACAGCGCGTGACGGTTTTCACGCTGTGCTG\n+CGCGCGGTACTGCTGCAGTCAGCGTAACGGGTCACTGGTGGCGCTGCTGGTCTGTCTGAG\n+CAACCACAGCAGATGCGCGGCCTGTTGTCATGTCCGGCGTCGCCGGGATGAGCCGGATGA\n+CTAGGCGCGAATGTGATTGCCACCAGCGGACGGGCAGATTCGAGAGCGGCACGGCAGGTG\n+ACGTTGACGGTCCTGCTACTGGATAAAGACCCGGGCACCATCACACTCGGTATAACCGTC\n+AGGCGTCGGAGTTTATCGCGCGCGCAGGCGTGGGATGAAAACAGCGCTGGCTCGACGCTC\n+GGATGACTGGCTTCGCTGAGCGGCGATCCGAAACGCCGGAAGGCCGCAGTATTGTGTGAT\n+CCTCGCCAAGCAGCGTTTTAACCTGCGCGAGCGCGATGTGCAGTCGCTGAGGTTGCCACC\n+TTTGTACCGTTTGATCTGCGCAAAGCCGGTCGAGCGCCGTAATCGACAACCTGACAACGA\n+TGATCGCGTAAAGGTTCTGTCGATGCCATTCGTCGCCATGTTGAGTAGACGCTATTTCAG\n+GTTCAAAGTCGATCCGATGCGCGTCAGGGAGCCACGCCGCTGGTGGTGGAAGGTTCTCGT\n+GTGCTGGGCGTTATCGTGATGAAAGATATCGTCAAAGGCGGTATTAAAGAGCGCTTCGCC\n+CAGCTGCGCAAAATGGAATTAAACGGTGATGATTACCGGCGATAACCGTCCTGACTGCCG\n+CCGCGATTGCGGGCGCGGAAGACCGGTGCGTCGATGATTTTCTCGCCGAAGCGACACCGG\n+AGGCCAAGCTGGCATTGATCCGTCAGTATCAGCGGCGGAAGGTCGTTTGGTAGCGATGAC\n+CGGCGACGGCACCAACGATGCTCCGGCTGGCGCAGGCAGATGTCGCGTGGCGATGAACTC\n+CGGCACCCAGGCGGCGAAAGAGGCGGTAATATGGTCGATCTCGACTCTAACCCGACCAAG\n+TCCGATTTCGAGGTGGTGCACATTGGCAAACAGATGCTGATGACCCGTGAGCTCGCTGAC\n+CACCTTCAGCATTGCCAACGGATGGCGAAGTACTTCGCGATTATTCGTATCGCGGCAACG\n+GTTACGCAAATGCGCTGAACATCATGTGCCTGCATTCGCCCGACTCGGAAGCAATCCTCA\n+TGCGGTGATTTTCGAACTCTACCCTGATTATCGTCTTTTGATTCCCCCGGGCGTTATAAA\n+CCGCTTAGGTTAACGAGGTTCTGCCATGTTGCGCCGGGTAACTTGGATTTACGGTCTGGG\n+TGGGCTGCTGCTGTTTTATCGCACCAAAGTCATTAAGGTGGTTCGAATCGTTTGCGGTCT\n+GGTGTGAGTTTACCATGAGTGGATTACGTTCATTATCAACATTTATCTTCTGTTATTGAT\n+TACTGGCGGCGTTTACCCGCTTCACGGTCACTGGGGCAATGGTGGTTTCCCTGGCAGGCC\n+AATGGTTTCGTTGATTCGTGAATGTAAGCGGCGGTTCGGCATTAATCGGCAGAATTTGTC\n+ACCGGCAACGGCTTTCATGGTCGCCCGTCGGCAACGGCAGAAATGCCCCGACCAGGTCCA\n+GCAACAGAAG\n' 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| diff -r 000000000000 -r 190175f4e143 test-data/Loman_E.coli_MAP006-1_2D_50x_first_500_reads.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Loman_E.coli_MAP006-1_2D_50x_first_500_reads.fasta Thu Sep 27 15:26:47 2018 -0400 |
| b |
| b'@@ -0,0 +1,1000 @@\n+>a019fb87-85b7-495a-b6dc-789a2f8c4572_Basecall_2D_000_2d LomanLabz_PC_Ecoli_K12_MG1655_20150924_MAP006_1_5005_1_ch206_file49_strand_twodirections MAP006/MAP006-1_downloads/pass/LomanLabz_PC_Ecoli_K12_MG1655_20150924_MAP006_1_5005_1_ch206_file49_strand.fast5\n+TACGCATAAGCGCCAAAAGCACGCCGGGCGACCATAATGAGAAGATGCTCACCGCCAGCGTCAACAGTAAGTAGACGATGAGAGCGCCAGGGTAAACAGTTTGCACGGGCCGCGACGAAGGCAGTCGATAATGCCGCCATTGCTGGGATGCTCGCCCCCAGACGCGCATAGGCATAACCGGAAAACATCGCCACAATACCGCCAAAGCAAAGGCGACCCCAGGTCGAGGCTTCCATTAGCAATGCAGCCTGCCCCAGCAGCGCGAAGATCGCCGCCCCCACCATTGCCCCGGATTATCGATGGAAACGACGTTCCAGACCGCGGGTTTGTTACCGTTATTACCTTCCGTGTTTCATCATGTAATAGCAGCCCTTAGTAAACACGTTATAGCCGAAAAATTGCTTAGCGACCGATGCCACCATTTTTGACCGCGAACACTGTTGCCATCTTCGTCCAGCGGTGGTGAGAGAACGCGGCAATTCCCATCACTCCAGGGGACGACCACGCCAGAATACCGCCACCTACACCCGGTTTACGCCCGGTAAACCAACACGATACGCCCAGTCACCGGGAACATACCCAAGACTACAGCCCTTCCATCATCATTTCGTAAGAATGTACGGCACGTTGTCGGCCTGAAGAACGCGTTCCTGCGTCAACGATTCGCACACCACCTGCGCCGCGCTTGTCGCGCCAAGCGTTGCCAGTTCGCTACGTGGTCGAGGAGCCCTTGGAGCACTGACGGGTATACACGTCACAGGCTTCCCATTGCATCACAATAGAGATATCCGGCGGAGTAAGCAGCCAGGCTATGGCCCGGTTATGGAGACTTTATTTGTTTGTTCCGACTGGTTAACTTCGTCAGAGAGCGCTACCTGCTCGCCAGCAGTTTGCTTTGGATATGTAAATTCGCTGCCAGCGTTGTTCAACAGTTTTCAGCGTTAATCAGGCTATCTTAGGCAATAGCGCCAGGATAGATTCACCAGTGGCGGGAAATCGTTTGCCGCGGATGCAACTCTAAGGCGATAACTGAGTTACGGGGCAAGATCCGGTCGGGTCCCCACTAGGGATCTTTGTGTCGTACCGCCTGCGGGCCGCACATCTTCCAACGCAAGGGCTAACGTACAGAGACTTTCGAGATGGATTCCAGTGCAAAGCGTAATCACTGTCACCGCACTACGACGTTGCCATCGCGCAGTACACGATAGCCACTGCCGCCAGTTGACCTGGTACATTCGCCGAAGGGAATGTAATCGGGCATTTTGTCCGCCGTTAAGTGAGTGAGAAATTGGGTGTAAGCCTGATCTGTTACGGAATTGCCTGCTGTAATTTGTTTGCATCTAACAATATTTTCTTGTTAACTCCTTTTATAAGTCTCGGGAGGTAATTCCTCACCGGCTGGTGCCGATTTCAGGCATCCTGATTTAACTTAGCACCGGAGACTTAACTACAGGAAAACACAAAGAGATAAATGTCTAATCCTGATGCAAAAACTGCATCAGCAAATTTTTAATCTTTACGGACTTTTACCGCCTGGTTTATTAATTTCTTGACCTTCCCCTTGCTGAAGGTTTAACCTTTATCACAGCCAGTCAAAACCGTGTGTAAAGGGATGTTTATGTCAAACTATCGACCTGACCCTCTGGACGGCCTGTCTGCGGCGGTCACTGCGTTAAACGCGTGAAAGAAAGTCTTGAACAGCGTCGTCCGGGATGTTGAGCAGGCGGATGTGTCTATCACTGAAGCACGTTACCGGGACTGCCGAACAGGCTCGCTAAATTGAAACCATCAAACAAGCGGGTTATGACGCATCTGTAAGCCACCCAAAGGCTAAACCGCCACAGCCGTGACTGTTATGTT\n+>d74a5991-1f66-4b48-b387-07319ac37082_Basecall_2D_000_2d LomanLabz_PC_Ecoli_K12_MG1655_20150924_MAP006_1_5005_1_ch92_file5_strand_twodirections MAP006/MAP006-1_downloads/pass/LomanLabz_PC_Ecoli_K12_MG1655_20150924_MAP006_1_5005_1_ch92_file5_strand.fast5\n+AAGCTGATATTGCTAGCCATATCGTGGCTACCCATATGAATACTGCCAATCAGATGAAAATGGCGATTGCCGGGGGAGGGTGATATCGATGGCAGGCCAGGTGTAATGATTACCGCGCGACGCATCGGAGGCGACCCGTTTTTACCCGGTGTACAACAGATTACAGGCCACGACCTCCCTTTGTGAAATATCATGCCCTCGCGCGGTGAGGGATGGCGCAATCGGCGATTGGCGACTTGTTTAATGTGTTTGTATGATTCAGTATGTTCTTGCATCGCTATTCACAAGGAAGCAACAGTTAAAACCATGAAACAGGCAACAAGAAAACCGACGACACCACAGCAGATATTCTTCTCTATGAATATCTGGAAGCCTGATTTGAAAATCAATGAGTTAGCAGAGTTGCTGCATGTTCATCGGGTGAGTTTTAGTGCACTGATCAATAACAATCGTAAACTCACTACTCCATATGCATTTTGTCTCCATTTTGGAAACACAGTCGATTTTGGCTAATACCATCCAAGTCGTGGTTGGGAAGTTGAAAACAACATGCGCACCGAGGAAGAATTGGACGGATTGAAACATGTAGGGCTGATTTGGCGCCGTGAAGAGCGTGCAAAAAGGTCGCGTAAGGCCAAACACCTCCATCTCGTAGGCCGGATAAGGCGTTCACGGAGTGCGGCATGAGGCGTGGATCCGAGCTTACCGGTCTTAGGACCCTCCAAACTTGCTGAACTGCGTCTAGCGGATAAGGCGTTTACGCCGCATCCGGCATCCGAGCACCACATTGCCTGATGCGACGCTTACGCGTCTTATCAGGCCTACAAATCCTGTGCCTGAACCGTAGGCCGGATAAGGCGTTTACGGAGCATGAGCGGCATTCCATGCGTCGATGCCAAGTGCGCCACCCTAAAGCAGCGCATCCGCATGATGTACTTATTCCTTCGGGTTTAAACCGCAGCAAACCGGTTGGCGTTACTCACTACGGTAATCGACGCCGAGAGCGCCATTGCCGCTCCGGCGATAGCCCGGGTTAAGCAGTGTTCCAGTGAACGCCAAATACCGGCGGCGACCGGAACCCGCATGATACTGTTGTAGATAAACGCACCGAGCAGGTTCTGCTTCATGTTGTGCAGCCCTTCGCGCGGGAAAGCGAGCGCATCCGCAACGCCCATCAGGCTATGGCGCATCAGGGTAATCGCCGCGGTTCAATGGCAACAATACCTCATGCCACCCATCGCAATGCCGACATCCGCCTGAGCCAGCGCTCCGCGCGTCGTTAATGCCGTCGCCCACCATTGCCACCTGACGTCCTTCACTTTGCAGATGTTATCCAACCTTCATAGTTACTCGTCCGGCTACGCGGTCGCGATCACCTCATCAATCCCTGCTTTCTTTAGGAAGTGCATTGGCGGTGGTTCGCTTATAGAGACGTCAGCTCATCGGCGACTAATCTCAGTTGTATGCAGTTCCGCCACGCTATCACTACGAACACGGATCGCGTACTGCGCACCAGGGCTACTCGCTTTCCCGTCAACCGCAGCACAGGCGTTGCCCCTTGCGAATTGCCTGAGCAGCTGCCTTGGCCACTTCGATAGCTTTG'..b'GGATGATGCCGTTTGCTGTGGCATTACAGAAAACGGGCGAGCGTGCCGCTGGCGGTGAAAGGGCTCATCTGACATTGAGGTGTGGTTACGGGCCACATATGATGCTGGGGTGTTTGTTTGTCTTGTCGGCGGTTATTGGGCTATTTATCTCCTAATACCGCGACGGCGGTGTTACGATGGCTCCGATTGCGCTGGCTGCTGCCAAAACGATGGGGGTGTCGCCGGTGGTCCCATTCGCGATGGTCGTGGCGATGGCAAGCATCCGCCGCCTTTATGACACTCCATTCTTTCACCTGTTAACACACTGGTTTTAGGTCCGGGAAATGCACTTCAGTGATTTGTGAAGTTGGGGGTACCGTTCACCATTATCGTGATGGCGGTTTGTGTATGGGTGTTGACCCCGATGCTATGTTTCCGTTTTGACAAGAGCCTGATGTCGCATCCGGCGCTTATTGCCTGATGCAAGACGCAGACTCCGGCTGCTTACAGCGGTGAATCCTGGCTAATCTCATCGAGCGAAAGATGGAAATGGAACAAATATTTCCATGAAGCATCTAGTCCATCTCCTTGGCTGCGACGCCGCATTCAGCGCGTCGCTGCGAAGTCGGTTTTGCCACGACACAAGAATTCTTTGAGTCTCGTCGGCCGCGAGTTCTTCCAGACATTCAGATATATGCACACAGTGCATTATTCGCCTGTTTCACCAGCGAGATTTTCTTCATCGGGTATGCATGCACTCGTCAATTAACGGCGCAAATATCCCGCAGCTCTTCCGGAACCGTCATCGACCAGTTTTGCTGAGCGATTTTCTCAATAGCCTTGTACTCCTGAGCGATTTGCGAATTGAAGTATTTCACCGGAGTAGGGGGAGCAGTGCCCCCCTTACCCACGTGCCTGAGGCATCGTGGTACATCGCCAGTAAAGCGATACGTTCGGCGTTGACATTACCGCCAAATTTTCGATTTTGATAGCTTGCCAGCGCATGGGCGACCATCGCTACCTGCAAAAACTGTGTTCGCAACATTTTCGTCCCGCACGTTGCGCAGGAGTGGGATGGAGCATTCTTAATGCGTGCCAGGCGGGAGAGAGATGGGCAAAAAATGGCTCTGTTTCATACCTGACCTTACGTATGATGACATCATCAGGTCATTGTGGCGGGATAACGCTGCCGGATGCAATCTCCGGCAGTGAAGTGAGAATTACAGTCGATGATAACCAGAAAAAGGGAAACGCGAACTTGCTAAGACAGCTCATCATCGACACGCGGTAGCGTACAAATGCGGAAACTTAAGCGGCCACGGCCAGTTGAATGCGTCCCTTGCACCAACAGAACTTTTTCCCTGCAACAGGAAATTCGAACCATAGGATTTCTGATCGTCGTGAATGTTAAGCGTTTGGCGTCGATTTTCGGAAGCACTAGAACCCCGAATGTTTCCGCCCGCAGGAAACGCCCGGAATATCGTTGTAATCAGTTCCCCACGCGCGGTTACACGCTGCTCATAACAGATAAAGAATGCCAGGGGTAATAAATTCACTGATGCTCTGGACTATCAGGCCCCGGTCTGAATGGCGTGTTGCGCAGGAACGTTAGCACACAGGCGCATTGAAGCGCAGCCCATTTCCCAGGACCTTCGATGTAGCCTTTGGCGTGTTTTTCGGCCCGTTCAACTCGCAATCGCCACCCCTGACGGAAGCCTGCAACGCGGTACGTTTCGACAGTCCGTTAAAGCATATTCACCAGCATTATCAGGTGCCAGCGGCGACGTGAGTGATGCTCAGCGTCGTAGGAATTTTGTCATAAATTTCATCGGCGACGATGGAGATTATGCTGACGTGCAATCTCCACAATCTCCATTAAAGCTCTTTGGAATATACCGCGCCGGTTGGGTTATTTGGGTTGATAATAACGGATCCCACGCGTACGAGGCGTAATTTAGCGCCGAATATCATCGGAGTCCGGGAACCAGTCAGAGGATTCATCGCAAAGATAATGCACCGCTTTACCGCTGGAAAGCGAAACCGCCGCGGTCCAGAGTGGGTAATCTGGTGCAGGAACCAACATTTCGTCCCCGCTGTTCATAGCAATGCCTTGCATTGCCTGAAAGCAATAAGCTCGAATACACCATTGCCGATGTAAATATCTTCGCAAGTGTAACATCAAGCATGCCACGAGCCTGGTAGTGCTGCATGATGGCTTCACTAGGAGGATAAAGACCTTTGGAATCGGAAAATACCCTTGAGCGAGCTTAACCCATGCGTATCACGTCAACGAGGATTTCATCTGGCGCGTCAAATGGGGCATCGCTGGGTTGCCGATGTTCAGTTTCAGTACCTTGTTACCTTCTTCTTCCAGGCGTTTGCTTCTTTCAGCACCGGACCACGGATGTCATAACAGACATTCTAAATTTGCTGGATTTTCAATGGGGGACATGAATCTTGACCTTTTGCTGTTATCGCGCCACTCCCTGCCGTGGAAGTCAGCTTAGAACAATGTGATAACTCCCCCCAGGACGGTGTTTGAAGACAGGTCTGCAGAATAAGATTTTGCCAGAGGGGAAGGCTCGATTGTGCTGTTAATAACTTAATAATGACAAAATAATGAGGTGTATGCTTTACATGCAATGTTATAGTGAATTGTTCTGATTCTCTTAATTGTAAAGTGTCTGGTTTTATCTTAAAGATAATTGTGAAAATGCCTCATTTAAGAATTCACTAATGAAACGCGATGATTTCCTCATTACGGAGTTTAACTGCGTGGTGATGATTTCGAGGTGTCGCAATGGGGGCAAGTGTGAAACTATTGTTAAGCGGAATTAATGAATGAGGATGATGCTAATTAATTATTATTTAATATTCAAAAGTATTTCTTTTGATGTTGCTTATTAATAAAGAAGATTACTTTGCCTAACATAACATAACTTTGCATCAGATAATTCGCAATGACCCTTATAAATAAAGGTTTTGGGGGTAAAAATGCTCGGATAAATGACGGATTGCTGCTCTTGATGCCTAACTCGATGCTGTTGGTACGTTCCGCGTATGACCAGCGATGATGCTGCACGAGAGTGGAACAAGCATACGGATTTACATTTATACAAACACGCGCATGTCATAAATAGAAAAGAGTGAGTAACTTAATAGATATGCGTCAACCCTGAAGATATATTCTGTGATCTACTTCAGGCATTATAACTGAGAACAATGTGGCTTGGCCTTTTAGTGCAACTCATTGCATTTTTACTTTCGTCCCGGGTTCCGGATGAAACTGCCAGGGAGGCACATTACAAATGAAATTGCTTGTTTGTGTGCACAGCATTAACCAGCTCATGAGCCGCCAGTAATGATAATATGATAAGTGCAAATCGTCCGATAATTAACCTCATGACCTCGGAGGTCAACTTGCTGAGAACATTTGTTGCTGTTGCCGTACGGACATTTTCTGCTGCCGCATGATGCCGCTGTGTCGTACTCAGTCCGCCGTAAGTCAGCAATGCAGCGTCTGGAACAACTTCCGTTGGGAAAGAACTGTTCGCCTCTATTCTGACGGTCGCAACAAACTGTTAAACCTCTGAACATCTCAATTCAATTCTTGGTTACGCCAGGAAAATCCTGCGTTTTAATGGCGGCTTGAGGGCCATCTCATCATTAAGTATTTCAGTAATCTTCAGGGCGTATGGTGTCAACTATCGGTGTGCTTCAGTATCGGAATCTGCCGATACGTGATTAGCTTTTCCTGTTAAATCGCGTGAGTTTCATTTATCCGAAATTAGCCCCTGGGAGATGTCCGCGTTAAAACGGGCATGCCTATGGCAGAAATGCTGGGAATTCTACGAGGAAGTGGATTTGATGGTGTAACCCCATCGTCCTTCAGCGTTTAAGTACGCATTGAACCTGCGTACCTCGCCAACACACTGGTACTGCGCAGCGCAAATACATATTGCAAAAGGCGAGCCGTACGCTTGTATTGCTGGTAGATATGTACACGTTCTGTTTATGTA\n' |
| b |
| diff -r 000000000000 -r 190175f4e143 test-data/result1_map.bam |
| b |
| Binary file test-data/result1_map.bam has changed |
| b |
| diff -r 000000000000 -r 190175f4e143 test-data/result1_owler.mhap --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/result1_owler.mhap Thu Sep 27 15:26:47 2018 -0400 |
| b |
| @@ -0,0 +1,7 @@ +1 157 0.742839 3672 1 9 16450 22450 0 37 16202 16211 +1 274 0.53044 1234 1 11806 22431 22450 0 20 10204 10347 +1 88 0.385767 1033 1 7562 21300 22450 0 116 13873 13893 +1 195 0.487916 953 0 11533 20585 22450 0 98 9532 9604 +1 379 0.605011 837 0 12349 18896 22450 0 67 6652 6798 +1 272 0.362138 656 0 10341 18896 22450 0 297 9092 9187 +1 165 0.317569 333 0 9157 17275 22450 0 970 6975 7029 |
| b |
| diff -r 000000000000 -r 190175f4e143 test-data/result2_map.bam |
| b |
| Binary file test-data/result2_map.bam has changed |
| b |
| diff -r 000000000000 -r 190175f4e143 test-data/result2_owler.mhap --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/result2_owler.mhap Thu Sep 27 15:26:47 2018 -0400 |
| b |
| @@ -0,0 +1,7 @@ +1 157 0.742839 3672 1 9 16450 22450 0 37 16202 16211 +1 274 0.53044 1234 1 11806 22431 22450 0 20 10204 10347 +1 88 0.385767 1033 1 7562 21300 22450 0 116 13873 13893 +1 195 0.487916 953 0 11533 20585 22450 0 98 9532 9604 +1 379 0.605011 837 0 12349 18896 22450 0 67 6652 6798 +1 272 0.362138 656 0 10341 18896 22450 0 297 9092 9187 +1 165 0.317569 333 0 9157 17275 22450 0 970 6975 7029 |
| b |
| diff -r 000000000000 -r 190175f4e143 test-data/result3_map.bam |
| b |
| Binary file test-data/result3_map.bam has changed |