| Next changeset 1:29151e779524 (2021-03-09) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96" |
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added:
purge_dups.xml test-data/calcuts_out.tsv test-data/cutoffs.tsv test-data/dups.bed test-data/ngsc_out.cov test-data/out.cov test-data/out.wig test-data/purge_dups_out.bed test-data/purged_out.fa test-data/split_out.fasta test-data/test.bam test-data/test.cov test-data/test.fasta test-data/test.paf test-data/test.stat |
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| diff -r 000000000000 -r 8ec117da1796 purge_dups.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/purge_dups.xml Fri Feb 05 17:52:51 2021 +0000 |
| [ |
| b'@@ -0,0 +1,330 @@\n+<tool id="purge_dups" name="Purge haplotigs" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">\n+ <description>and overlaps in an assembly based on read depth</description>\n+ <macros>\n+ <token name="@TOOL_VERSION@">1.2.5</token>\n+ <token name="@VERSION_SUFFIX@">0</token>\n+ </macros>\n+ <requirements>\n+ <requirement type="package" version="@TOOL_VERSION@">purge_dups</requirement>\n+ </requirements>\n+ <command detect_errors="exit_code"><![CDATA[\n+ #if $function_select.functions == "purge_dups":\n+ purge_dups\n+ #if $function_select.coverage:\n+ -c \'$function_select.coverage\'\n+ #end if\n+ #if $function_select.cutoffs:\n+ -T \'$function_select.cutoffs\'\n+ #end if\n+ #if $function_select.min_bad:\n+ -f $function_select.min_bad\n+ #end if\n+ #if $function_select.min_align:\n+ -a $function_select.min_align\n+ #end if\n+ #if $function_select.min_match:\n+ -b $function_select.min_match\n+ #end if\n+ #if $function_select.min_chain:\n+ -m $function_select.min_chain\n+ #end if\n+ #if $function_select.max_gap:\n+ -M $function_select.max_gap\n+ #end if\n+ #if $function_select.double_chain.chaining_rounds == "two":\n+ -2\n+ #if $function_select.double_chain.max_gap_2:\n+ -G $function_select.double_chain.max_gap_2\n+ #end if\n+ #end if\n+ #if $function_select.min_chain_score:\n+ -l $function_select.min_chain_score\n+ #end if\n+ #if $function_select.max_extend:\n+ -E $function_select.max_extend\n+ #end if\n+ \'$function_select.input\' > dups.bed 2> purge_dups.log\n+ #else if $function_select.functions == "split_fa":\n+ split_fa\n+ #if $function_select.split:\n+ -n $function_select.split\n+ #end if\n+ \'$function_select.input\' > split.fasta\n+ #else if $function_select.functions == "pbcstat":\n+ pbcstat\n+ #if $function_select.max_cov:\n+ -M $function_select.max_cov\n+ #end if\n+ #if $function_select.min_map_ratio:\n+ -f $function_select.min_map_ratio\n+ #end if\n+ #if $function_select.min_map_qual:\n+ -q $function_select.min_map_qual\n+ #end if\n+ #if $function_select.flank:\n+ -l $function_select.flank\n+ #end if\n+ $function_select.primary_alignments\n+ \'$function_select.input\'\n+ #else if $function_select.functions == "ngscstat":\n+ ngscstat\n+ #if $function_select.min_align_qual:\n+ -q $function_select.min_align_qual\n+ #end if\n+ ## #if $function_select.max_depth:\n+ ## -M $function_select.max_depth\n+ ## #end if\n+ #if $function_select.max_insert:\n+ -L $function_select.max_insert\n+ #end if\n+ \'$function_select.input\'\n+ #else if $function_select.functions == "calcuts":\n+ calcuts\n+ #if $function_select.min_depth:\n+ -f $function_select.min_depth\n+ #end if\n+ #if $function_select.low_depth:\n+ -l $function_select.low_depth\n+ #end if\n+ #if $function_select.transition:\n+ -m $function_select.transition\n+ #end if\n+ #if $function_select.upper_depth:\n+ -u $function_select.upper_depth\n+ #end if\n+ $function_select.ploidy\n+ \'$function_select.input\' > cutoffs.tsv 2>calcuts.log\n+ #else if $function_select.functions == "get_seqs":\n+ '..b' <param name="min_bad" value="0.01"/>\n+ <param name="min_align" value="10"/>\n+ <param name="min_match" value="100"/>\n+ <param name="min_chain" value="1"/>\n+ <param name="max_gap" value="1000"/>\n+ <conditional name="double_chain">\n+ <param name="chaining_rounds" value="two"/>\n+ <param name="max_gap_2" value="1001"/>\n+ </conditional>\n+ <param name="min_chain_score" value="1"/>\n+ <param name="max_extend" value="100"/>\n+ </conditional>\n+ <output name="purge_dups_bed" value="purge_dups_out.bed"/>\n+ </test>\n+ <!-- Split fa -->\n+ <test expect_num_outputs="1">\n+ <conditional name="function_select">\n+ <param name="functions" value="split_fa"/>\n+ <param name="input" value="test.fasta"/>\n+ <param name="split" value="-n"/>\n+ </conditional>\n+ <output name="split_fasta" value="split_out.fasta"/>\n+ </test>\n+ <!-- pbcstat -->\n+ <test expect_num_outputs="3">\n+ <conditional name="function_select">\n+ <param name="functions" value="pbcstat"/>\n+ <param name="input" value="test.paf"/>\n+ <param name="max_cov" value="1000"/>\n+ <param name="min_map_ratio" value="0.01"/>\n+ <param name="min_map_qual" value="1"/>\n+ <param name="flank" value="1"/>\n+ <param name="primary_alignments" value="-p"/>\n+ </conditional>\n+ <output name="pbcstat_cov" value="out.cov"/>\n+ <output name="pbcstat_wig" value="out.wig"/>\n+ </test>\n+ <!-- ngscstat -->\n+ <test expect_num_outputs="2">\n+ <conditional name="function_select">\n+ <param name="functions" value="ngscstat"/>\n+ <param name="input" value="test.bam"/>\n+ <param name="min_align_qual" value="10"/>\n+ <param name="max_insert" value="100"/>\n+ </conditional>\n+ <output name="ngscstat_cov" value="ngsc_out.cov"/>\n+ </test>\n+ <!-- Calcuts -->\n+ <test expect_num_outputs="2">\n+ <conditional name="function_select">\n+ <param name="functions" value="calcuts"/>\n+ <param name="input" value="test.stat"/>\n+ <param name="min_depth" value="0.01"/>\n+ <param name="low_depth" value="1"/>\n+ <param name="transition" value="1"/>\n+ <param name="upper_depth" value="100"/>\n+ <param name="ploidy" value="-d 0"/>\n+ </conditional>\n+ <output name="calcuts_tab" value="calcuts_out.tsv"/>\n+ </test>\n+ <!-- Get seqs -->\n+ <test expect_num_outputs="2">\n+ <conditional name="function_select">\n+ <param name="functions" value="get_seqs"/>\n+ <param name="fasta_input" value="split_out.fasta"/>\n+ <param name="bed_input" value="dups.bed"/>\n+ <param name="coverage" value="-c"/>\n+ <param name="length" value="10"/>\n+ <param name="haplotigs" value="-a"/>\n+ <param name="min_ratio" value=".01"/>\n+ <param name="end_trim" value="-e"/>\n+ <param name="split" value="-s"/>\n+ <param name="min_gap" value="100000"/>\n+ </conditional>\n+ <output name="get_seqs_purged" value="purged_out.fa"/>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+ .. class:: infomark\n+ \n+ **What it does**\n+\n+ The purge_dups tools are designed to remove haplotigs and contig overlaps in a de novo assembly based on read depth.\n+\n+ ]]></help>\n+ <citations>\n+ <citation type="doi">10.1093/bioinformatics/btaa025</citation>\n+ </citations>\n+</tool>\n' |
| b |
| diff -r 000000000000 -r 8ec117da1796 test-data/calcuts_out.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/calcuts_out.tsv Fri Feb 05 17:52:51 2021 +0000 |
| b |
| @@ -0,0 +1,1 @@ +1 0 0 1 1 100 |
| b |
| diff -r 000000000000 -r 8ec117da1796 test-data/cutoffs.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cutoffs.tsv Fri Feb 05 17:52:51 2021 +0000 |
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| @@ -0,0 +1,1 @@ +5 3 3 5 7 15 |
| b |
| diff -r 000000000000 -r 8ec117da1796 test-data/dups.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dups.bed Fri Feb 05 17:52:51 2021 +0000 |
| b |
| @@ -0,0 +1,1 @@ +gi|157734152 29655295 29712160 HAPLOTIG gi|528476637 |
| b |
| diff -r 000000000000 -r 8ec117da1796 test-data/ngsc_out.cov --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ngsc_out.cov Fri Feb 05 17:52:51 2021 +0000 |
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| b'@@ -0,0 +1,336 @@\n+>>chrM\t0\n+1\t0\t0\n+>GTATTCTTACTCCATAAACACATAGGCTTGGTCCTAGCCTTTTTATTAGT\t0\n+1\t0\t0\n+>CTAAATCACGTCTCTACGATTAAAAGGAGCAGGTATCAAGCACACTAGAA\t0\n+1\t0\t0\n+>ATAAAAATTAAGCTATGAACGAAAGTTCGACTAAGTCATATTAAATAAGG\t0\n+1\t0\t0\n+>ATAAATCTCCGGCGTAAAGCGTGTCAAAGACTAATACCAAAATAAAGTTA\t0\n+1\t0\t0\n+>AAGTGACTTTAATACCTCTGACTACACGATAGCTAAGACCCAAACTGGGA\t0\n+1\t0\t0\n+>AAGCTATTCGCCAGAGTACTACTAGCAACAGCCTAAAACTCAAAGGACTT\t0\n+1\t0\t0\n+>CCGATAAACCCCACCATCCCTTGCTAATTCAGCCTATATACCGCCATCTT\t0\n+1\t0\t0\n+>AACGTTAGGTCAAGGTGTAGCCCATGGGATGGAGAGAAATGGGCTACATT\t0\n+1\t0\t0\n+>TGGAGACTAAAGGAGGATTTAGCAGTAAATTAAGAATAGAGAGCTTAATT\t0\n+1\t0\t0\n+>CACAAATCATAACATAACATAAAACCGTGACCCAAACATATGAAAGGAGA\t0\n+1\t0\t0\n+>TGTAGCTTAAACAAAGCATCCAGCTTACACCTAGAAGATTTCACTCAAAA\t0\n+1\t0\t0\n+>TTAGTCACTTAACTAAAACATTCACCAAACCATTAAAGTATAGGAGATAG\t0\n+1\t0\t0\n+>ATGCATTAAAAGTACTAAACAGCAAAGCTTACCCCTTTTACCTTTTGCAT\t0\n+1\t0\t0\n+>CGAAACCAGACGAGCTACCTATGAACAGTTACAAATGAACCAACTCATCT\t0\n+1\t0\t0\n+>AGCCTGGTGATAGCTGGTTGTCCAGAAACAGAATTTCAGTTCAAATTTAA\t0\n+1\t0\t0\n+>AAAGGTACAGCTTTTTAGATACAGGTTACAACCTTCATTAGAGAGTAAGA\t0\n+1\t0\t0\n+>TTCAAGCTCAACGACACATCTATCTTAATCCCAACAATCAACCCAAACTA\t0\n+1\t0\t0\n+>TTAATATGAGTAACAAGAATTATTTCTCCTTGCATAAGCTTATATCAGAA\t0\n+1\t0\t0\n+>TCATCTATTTAAACCATTGTTAACCCAACACAGGCATGCATCTATAAGGA\t0\n+1\t0\t0\n+>ACCAAAAACATCACCTCTAGCATTTCCAGTATTAGAGGCACTGCCTGCCC\t0\n+1\t0\t0\n+>taatcacttgttccctaaatagggacttgtatgaatggccacacgagggt\t0\n+1\t0\t0\n+>cgggaatgactaaataagacgagaagaccctatggagcttTAATTAACTG\t0\n+1\t0\t0\n+>TTGATTGAATCAGCAATTTCGGTTGGGGTGACCTCGGAGAACAAAACAAC\t0\n+1\t0\t0\n+>TTGATCCAAACCATTGATCAACGGAACAAGTTACCCTAGGGATAACAGCG\t0\n+1\t0\t0\n+>TTGGATCAAGACATCCTAATGGTGCAACCGCTATTAAGGGTTCGTTTGTT\t0\n+1\t0\t0\n+>CGGTTTCTATCTATTCTATACTTTTCCCAGTACGAAAGGACAAGAAAAGT\t0\n+1\t0\t0\n+>AATCTAACTAATTTATAACTTCTACCGCCCTAGAACAGGGCTCgttaggg\t0\n+1\t0\t0\n+>caactcctctccctaacaacaTGTTCATAATTAACGTCCTCCTCCTAATT\t0\n+1\t0\t0\n+>CTTAGGCTATATGCAACTTCGCAAAGGACCCAACATCGTAGGCCCCTATG\t0\n+1\t0\t0\n+>CTACAACCACTAACATCATCGACATCCATATTCATCATCGCACCAATCCT\t0\n+1\t0\t0\n+>CACTAATCAACATAAACCTAGGAATTCTATTCATACTAGCCATGTCCAGC\t0\n+1\t0\t0\n+>CGCCCTAATTGGAGCTCTACGAGCAGTAGCACAAACCATCTCATACGAAG\t0\n+1\t0\t0\n+>ACATTATCAACACTTATTATTACCCAAGAATACCTCTGATTAATCTTCCC\t0\n+1\t0\t0\n+>ACCGAGCTCCATTTGACCTAACAGAAGGAGAATCAGAACTCGTCTCTGGA\t0\n+1\t0\t0\n+>ATACGCAAACATCATCATGATAAACATCTTCACAACAACCCTATTTCTAG\t0\n+1\t0\t0\n+>ATTAAAGCTCTCCTTCTAACATGTTCCTTCCTATGAATCCGAGCATCCTA\t0\n+1\t0\t0\n+>TACCACTCACACTAGCCCTCTGCATATGACACGTCTCACTTCCAATCATA\t0\n+1\t0\t0\n+>ACTTTGATAGAGTAAAACATAGAGGCTCAAACCCTCTTATTTctagaact\t0\n+1\t0\t0\n+>ttacaccatgtcctaCAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCAT\t0\n+1\t0\t0\n+>CTTCACAACTATTCTAATAACAGTTCTTCTAGGAACTATAATCGTTATAA\t0\n+1\t0\t0\n+>GCCATTATCCCTATCCTAATAAAAAAGTACAATCCCCGAACCATAGAAGC\t0\n+1\t0\t0\n+>TAGCGATCATCATTAACCTCATACACTCAGGCCAATGAACAATCACAAAA\t0\n+1\t0\t0\n+>ACTTGGACTCACACCATTCCACTTCTGAGTACCCGAAGTCACACAGGGCA\t0\n+1\t0\t0\n+>ATATCAATCCTATATCAAATCTCACCCTCAATTAACCTAAATATCTTATT\t0\n+1\t0\t0\n+>AAACCCAACTACGAAAAATCATAGCATACTCGTCAATCGCGCATATAGGA\t0\n+1\t0\t0\n+>ATTAATTTACATTATAATAACACTCACAATATTCATACTATTTATCCACA\t0\n+1\t0\t0\n+>CTAACCACTACACTAATCTTAATTACCTTACTATCCATAGGAGGCCTCCC\t0\n+1\t0\t0\n+>AAAATAGCAGCATCATCCTCCCCACACTAATAGCCATTATAGCACTACTC\t0\n+1\t0\t0\n+>CCCATCCACAAACAACATAAAAATAAAATGACAATTCGAAACCAAACGAA\t0\n+1\t0\t0\n+>ACCCCCATACTATCAATTTTGGACTAGGAATTTAGGTTAACATCCCAGAC\t0\n+1\t0\t0\n+>TAAGGACTGCGAGACTCTATCTCACATCAATTGAACGCAAATCAAACTCT\t0\n+1\t0\t0\n+>TTTAGTTAACAGCTAAATACCCTAATCAACTGGCTTCAATCTACTTCTCC\t0\n+1\t0\t0\n+>TCCTTTGAATTTGCAATTCAATGTGAAAATTCACCACGGGACTTGATAAG\t0\n+1\t0\t0\n+>CCATCTTACCTATGTTCATCAACCGCTGACTATTTTCAACTAACCACAAA\t0\n+1\t0\t0\n+>AACTGCCCTAAGCCTCCTAATCCGTGCTGAATTAGGCCAACCTGGGACCC\t0\n+1\t0\t0\n+>GTAATAATTTTCTTTATGGTCATACCCATTATAATCGGAGGATTCGGAAA\t0\n+1\t0\t0\n+>TAAACAACATAAGCTTCTGATTACTTCCCCCATCATTCCTACTTCTTCTC\t0\n+1\t0\t0\n+>TCCTCTAGCTGGAAATCTGGCGCATGCAGGAGCCTCTGTTGACTTAACCA\t0\n+1\t0\t0\n+>TTTATTACCACAATCATTAACATAAAACCACCAGCCCTATCCCAATATCA\t0\n+1\t0\t0\n+>TAGCCCTCCCGGTCCTAGCAGCAGGCATTACCATGCTTCTCACAGACCGT\t0\n+1\t0\t0\n+>TTATCAACACCTATTCTGATTCTTCGGACACCCCGAAGTCTATATTCTTA\t0\n+1\t0\t0\n+>AAAAAGGAACCTTTTGGCTACATGGGTATAGTGTGAGCTATAATATCCAT\t0\n+1\t0\t0\n+>TAGACGTTGACACACGAGCATACTTCACATCAGCTACCATAATCATCGCT\t0\n+1\t0\t0\n+>AAATATCAAATGATCTCCAGCTATACTCTGAGCTCTAGGCTTCATCTTCT\t0\n+1\t'..b'0\n+1\t0\t0\n+>GACTATCAAAAAAGAATATAATCTGAATCAACACTACAACCTATAGTCTA\t0\n+1\t0\t0\n+>CCTAAACTTCTCACTAATATTCTTCTCCGATCCCCTATCAGCCCCACTTC\t0\n+1\t0\t0\n+>CATCTATCTAAGGAACCACTAATCCGAAAAAAACTCTACATCACCATGCT\t0\n+1\t0\t0\n+>TCTCCTTCTACATCCTATTTGAAGCCACATTAGTTCCAACACTAATTATC\t0\n+1\t0\t0\n+>CCTATTCTACACACTAATAGGTTCCCTCCCACTCTTAGTTGCACTAATCT\t0\n+1\t0\t0\n+>AACCAAGCACTACCCGACTCTTGATCCAATATTTTCCTATGACTAGCATG\t0\n+1\t0\t0\n+>TCCCAAAAGCCCATGTAGAAGCCCCAATTGCCGGATCCATAGTGCTAGCA\t0\n+1\t0\t0\n+>ACTAAACCCCCAAACTAGCTTTATAGCCTACCCCTTCCTCATACTATCCC\t0\n+1\t0\t0\n+>AAATCACTTATTGCATACTCCTCTGTCAGCCACATAGCCCTAGTAATCGT\t0\n+1\t0\t0\n+>TAATCGCTCACGGCCTTACATCATCAATACTATTCTGCCTGGCAAACTCA\t0\n+1\t0\t0\n+>AACACTTCTTCCCCTTATAGCAGCCTGATGACTATTAGCCAGCCTAACCA\t0\n+1\t0\t0\n+>ATATCATCATTCTCATGATCAAATATTACCATTATCCTAATAGGAGCCAA\t0\n+1\t0\t0\n+>GAGGGAAATACACACACCATATCAACAGCATTAAACCTTCATTTACACGA\t0\n+1\t0\t0\n+>TAACCCTAAAATTATCCTAGGCTTTACGTACTGTAAATATAGTTTAACAA\t0\n+1\t0\t0\n+>CGAGAAAGTATGCAAGAACTGCTAATTCATGCCCCCATGTCCAACAAACA\t0\n+1\t0\t0\n+>CCAAAAAATTGGTGCAACTCCAAATAAAAGTAATCAACATGTTCTCCTCC\t0\n+1\t0\t0\n+>CTTCAATACCTACAAAAACAGCACGTTCCCGCATCATGTAAAAAACACTA\t0\n+1\t0\t0\n+>TCTGGACAAGAAACAATTATCTCAAACTGACACTGAATAACCATACAAAC\t0\n+1\t0\t0\n+>TACCAGTAGCCCTATTCGTAACATGATCTATTATGGAATTCTCCCTATGA\t0\n+1\t0\t0\n+>ATTCCTCATCACTATAATAATTCTAGTCACAGCTAACAACCTTTTCCAAC\t0\n+1\t0\t0\n+>TGATGATACGGCCGAACAGATGCCAACACCGCGGCCCTTCAAGCAATCCT\t0\n+1\t0\t0\n+>TATTCAACACCAACACATGAGACCTCCAACAAATCTTCATACTCGACCCC\t0\n+1\t0\t0\n+>ATCCGCTCAATTTGGACTCCACCCATGACTTCCTTCAGCCATAGAGGGCC\t0\n+1\t0\t0\n+>GTCTTCCTGCTAATCCGCTTCCATCCACTAATAGAAAACAACAAAACAAT\t0\n+1\t0\t0\n+>TCTGCGCACTCACTCAAAACGATATCAAAAAAATCATTGCTTTCTCCACC\t0\n+1\t0\t0\n+>CCTAGCATTCCTCCACATTTGCACTCACGCATTCTTCAAAGCTATACTAT\t0\n+1\t0\t0\n+>CGAAAAATAGGCGGACTATTTAATGCAATACCCTTCACCACCACATCTCT\t0\n+1\t0\t0\n+>ACTCCAAAGACCTCATCATCGAAACCGCCAACACATCGTACACCAACGCC\t0\n+1\t0\t0\n+>TACCCGAATCATCTTCTTTGCACTCCTAGGGCAACCCCGCTTCCTCCCTC\t0\n+1\t0\t0\n+>CTCTTAATTGGCAGCATTTTTGCCGGATTCTTCATCTCCAACAATATCTA\t0\n+1\t0\t0\n+>CCCTCGCAGTAACCATCCTAGGATTTACACTAGCCCTAGAACTAAGCTTG\t0\n+1\t0\t0\n+>CAACCTCCTAGGATACTACCCAACAATTATACACCGACTCCCACCGCTCG\t0\n+1\t0\t0\n+>TGACTAGAAAACATCCTGCCAAAATCTATCTCCCAGTTCCAAATAAAAAC\t0\n+1\t0\t0\n+>CATTCCTCATCACCCTTACCCTAAGCATACTACTTTTTAATCTCCACGAG\t0\n+1\t0\t0\n+>ATCACAACCCAAGCCCCATAACTATACAATGCAGCAGCCCCTATAATTTC\t0\n+1\t0\t0\n+>CACCACTAAACTTAAACACTACCCCCACTTCCTCACTCTTCAGAACATAT\t0\n+1\t0\t0\n+>AGTCGTATTAGACACCCATACCTCAGGATACTGCTCAGTAGCCATAGCCG\t0\n+1\t0\t0\n+>ATCAACCCCAAAAAGGACCCTCCAAAATTCATAATAATACCACAACCTAC\t0\n+1\t0\t0\n+>AAGAAAACCCCACAAAACTAACAACAAAAATAACACTCAAAATAAACACA\t0\n+1\t0\t0\n+>GAAAAATCATCGTTGTATTTCAACTATAAGAACACCAATGACAAACATCC\t0\n+1\t0\t0\n+>CCAGCCCCCTCAAACATTTCATCATGATGAAACTTCGGCTCCCTCCTAGG\t0\n+1\t0\t0\n+>ACACATCAGACACGACAACTGCCTTCTCATCCGTCACTCACATCTGCCGA\t0\n+1\t0\t0\n+>AATATTTTTTATCTGCCTCTTCATTCACGTAGGACGCGGCCTCTACTACG\t0\n+1\t0\t0\n+>ACAGTTATAGCTACAGCATTCATGGGCTATGTCCTACCATGAGGCCAAAT\t0\n+1\t0\t0\n+>ACATCGGTACTACCCTCGTCGAGTGAATCTGAGGTGGATTCTCAGTAGAC\t0\n+1\t0\t0\n+>CATCACAGCCCTGGTAGTCGTACATTTACTATTTCTTCACGAAACAGGAT\t0\n+1\t0\t0\n+>CCATATTATACAATTAAAGACATCCTAGGACTCCTCCTCCTGATCTTGCT\t0\n+1\t0\t0\n+>ACTACACCCCAGCTAACCCTCTCAGCACTCCCCCTCATATTAAACCAGAA\t0\n+1\t0\t0\n+>AGGCGGCGTATTAGCCCTAATCCTCTCCATCCTGATCCTAGCACTCATCC\t0\n+1\t0\t0\n+>CAATGCGTATTCTGACTCTTAGTGGCAGACTTACTGACACTAACATGAAT\t0\n+1\t0\t0\n+>CAATCCTCTACTTCTCCCTAATTCTCATTTTTATACCACTCGCAAGCACC\t0\n+1\t0\t0\n+>ACCCTGGTCTTGTAAACCAGAAAAGGGGGAAAACGTTTCCTCCCAAGGAC\t0\n+1\t0\t0\n+>TACTTAAACTATTCCTTGATTTCTTCCCCTAAACGACAACAATTTACCCT\t0\n+1\t0\t0\n+>CTGACATGCAATATCTTATGAATGGCCTATGTACGTCGTGCATTAAATTG\t0\n+1\t0\t0\n+>GTACATTATATTATTGATCGTGCATACCCCATCCAAGTCAAATCATTTCC\t0\n+1\t0\t0\n+>GCGGGAAATCAGCAACCCTCCCAACTACGTGTCCCAATCCTCGCTCCGGG\t0\n+1\t0\t0\n+>TCTTTCTTCAGGGCCATTCCCACCCAACCTCGCCCATTCTTTCCCCTTAA\t0\n+1\t0\t0\n+>CTGTGATTTCATGCATTTGGTATCTTTTTATATTTGGGGATGCTATGACT\t0\n+1\t0\t0\n+>CTTAAATTGAACGTTATTCCTCCGCATCAGCAACCATAAGGTGTTATTCA\t0\n+1\t0\t0\n+>ctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacct\t0\n+1\t0\t0\n+>gcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgc\t0\n+1\t0\t0\n+>ctgtgcacctACCCGCGCAGTAAGCAAGTAATATAGCTTTCTTAATCAAA\t0\n+1\t0\t0\n+>GCCAAACCCCAAAAACAAGACTAAACAATGCACAATACTTCATGAAGCTT\t0\n+1\t0\t0\n+>GAACTTTCCCCCCGCCATTAATACCAACATGCTACTTTAATCAATAAAAT\t0\n+1\t0\t0\n+>TTCTTCCCCC\t0\n+1\t0\t0\n' |
| b |
| diff -r 000000000000 -r 8ec117da1796 test-data/out.cov --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.cov Fri Feb 05 17:52:51 2021 +0000 |
| b |
| @@ -0,0 +1,14 @@ +>gi|528476637:29857558-29915771 58214 +1 29093 0 +29094 29356 2 +29357 33376 0 +33377 41951 1 +41952 58214 0 +>gi|157734152:29655295-29712160 56866 +1 29214 0 +29215 29477 1 +29478 33498 0 +33499 42073 1 +42074 48471 0 +48472 56865 1 +56866 56866 0 |
| b |
| diff -r 000000000000 -r 8ec117da1796 test-data/out.wig --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.wig Fri Feb 05 17:52:51 2021 +0000 |
| b |
| @@ -0,0 +1,116 @@ +track type="wiggle_0" name="PB" +fixedStep chrom=gi|528476637:29857558-29915771 start=1 step=1024 span=1024 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +1 +1 +1 +1 +1 +1 +1 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +variableStep chrom=gi|528476637:29857558-29915771 span=1894 +56321 0 +fixedStep chrom=gi|157734152:29655295-29712160 start=1 step=1024 span=1024 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +1 +1 +1 +1 +1 +1 +1 +1 +0 +0 +0 +0 +0 +0 +0 +1 +1 +1 +1 +1 +1 +variableStep chrom=gi|157734152:29655295-29712160 span=1570 +55297 0 |
| b |
| diff -r 000000000000 -r 8ec117da1796 test-data/purge_dups_out.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/purge_dups_out.bed Fri Feb 05 17:52:51 2021 +0000 |
| b |
| @@ -0,0 +1,11 @@ +gi|568815454 1200216 1203631 JUNK +gi|568815567 1196244 1200852 JUNK +gi|568815551 1197321 1201446 JUNK +gi|568815561 1196951 1200436 JUNK +gi|568815569 1240288 1243708 JUNK +gi|568815529 1421891 1425306 JUNK +gi|568815564 1286641 1289973 JUNK +gi|568815592 29942469 29945883 JUNK +gi|342187237 5004 8419 JUNK +gi|528476637 29857558 29915771 JUNK +gi|157734152 29655295 29712160 JUNK |
| b |
| diff -r 000000000000 -r 8ec117da1796 test-data/purged_out.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/purged_out.fa Fri Feb 05 17:52:51 2021 +0000 |
| b |
| @@ -0,0 +1,2 @@ +>Sequence:1-608_1 +gttcgatgcc taaaatacct tcttttgtcc ctacacagac cacagttttc ctaatggctttacaccgact agaaattctt gtgcaagcac taattgaaag cggttggcct agagtgttaccggtttgtat agctgagcgc gtctcttgcc ctgatcaaag gttcattttc tctactttggaagacgttgt ggaagaatac aacaagtacg agtctctccc ccctggtttg ctgattactggatacagttg taataccctt cgcaacaccg cgtaactatc tatatgaatt attttccctttattatatgt agtaggttcg tctttaatct tcctttagca agtcttttac tgttttcgacctcaatgttc atgttcttag gttgttttgg ataatatgcg gtcagtttaa tcttcgttgtttcttcttaa aatatttatt catggtttaa tttttggttt gtacttgttc aggggccagttcattattta ctctgtttgt atacagcagt tcttttattt ttagtatgat tttaatttaaaacaattcta atggtcaaaa a |
| b |
| diff -r 000000000000 -r 8ec117da1796 test-data/split_out.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/split_out.fasta Fri Feb 05 17:52:51 2021 +0000 |
| b |
| @@ -0,0 +1,2 @@ +>Sequence:1-608 +gttcgatgcc taaaatacct tcttttgtcc ctacacagac cacagttttc ctaatggctttacaccgact agaaattctt gtgcaagcac taattgaaag cggttggcct agagtgttaccggtttgtat agctgagcgc gtctcttgcc ctgatcaaag gttcattttc tctactttggaagacgttgt ggaagaatac aacaagtacg agtctctccc ccctggtttg ctgattactggatacagttg taataccctt cgcaacaccg cgtaactatc tatatgaatt attttccctttattatatgt agtaggttcg tctttaatct tcctttagca agtcttttac tgttttcgacctcaatgttc atgttcttag gttgttttgg ataatatgcg gtcagtttaa tcttcgttgtttcttcttaa aatatttatt catggtttaa tttttggttt gtacttgttc aggggccagttcattattta ctctgtttgt atacagcagt tcttttattt ttagtatgat tttaatttaaaacaattcta atggtcaaaa a |
| b |
| diff -r 000000000000 -r 8ec117da1796 test-data/test.bam |
| b |
| Binary file test-data/test.bam has changed |
| b |
| diff -r 000000000000 -r 8ec117da1796 test-data/test.cov --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.cov Fri Feb 05 17:52:51 2021 +0000 |
| b |
| @@ -0,0 +1,13 @@ +>gi|528476637:29857558-29915771 58214 +1 29092 0 +29093 29357 2 +29358 33375 0 +33376 41952 1 +41953 58214 0 +>gi|157734152:29655295-29712160 56866 +1 29213 0 +29214 29478 1 +29479 33497 0 +33498 42074 1 +42075 48470 0 +48471 56866 1 |
| b |
| diff -r 000000000000 -r 8ec117da1796 test-data/test.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.fasta Fri Feb 05 17:52:51 2021 +0000 |
| b |
| @@ -0,0 +1,11 @@ +>Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +gttcgatgcc taaaatacct tcttttgtcc ctacacagac cacagttttc ctaatggctt +tacaccgact agaaattctt gtgcaagcac taattgaaag cggttggcct agagtgttac +cggtttgtat agctgagcgc gtctcttgcc ctgatcaaag gttcattttc tctactttgg +aagacgttgt ggaagaatac aacaagtacg agtctctccc ccctggtttg ctgattactg +gatacagttg taataccctt cgcaacaccg cgtaactatc tatatgaatt attttccctt +tattatatgt agtaggttcg tctttaatct tcctttagca agtcttttac tgttttcgac +ctcaatgttc atgttcttag gttgttttgg ataatatgcg gtcagtttaa tcttcgttgt +ttcttcttaa aatatttatt catggtttaa tttttggttt gtacttgttc aggggccagt +tcattattta ctctgtttgt atacagcagt tcttttattt ttagtatgat tttaatttaa +aacaattcta atggtcaaaa a \ No newline at end of file |
| b |
| diff -r 000000000000 -r 8ec117da1796 test-data/test.paf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.paf Fri Feb 05 17:52:51 2021 +0000 |
| b |
| b'@@ -0,0 +1,245 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|
| b |
| diff -r 000000000000 -r 8ec117da1796 test-data/test.stat --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.stat Fri Feb 05 17:52:51 2021 +0000 |
| b |
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