| Next changeset 1:6de3e77073ad (2018-05-02) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 |
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added:
README.rst disco.xml test-data/ecoli_1K_1.fq test-data/ecoli_1K_2.fq test-data/ecoli_1K_interleaved.fq test-data/test1_contigs.fasta test-data/test1_graph_1.gfa test-data/test1_graph_1.gfa2 test-data/test1_graph_2.gfa test-data/test1_graph_2.gfa2 test-data/test1_graph_3.gfa test-data/test1_graph_3.gfa2 test-data/test1_scaffolds.fasta test-data/test2_contigs.fasta test-data/test2_scaffolds.fasta test-data/test3_contigs.fasta test-data/test3_scaffolds.fasta |
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| diff -r 000000000000 -r 6d447ebb2bf4 README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Fri Nov 03 15:44:23 2017 -0400 |
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| @@ -0,0 +1,28 @@ +DISCO memory usage +================== + + +By default, this tool is configured to limit the memory consumption to 4G. +You might need to lower this limit if the machine(s) executing the jobs have less memory available. +If you have a lot of reads to assemble and a machine with enough memory, you can increase it. + +In both cases, you can set the DISCO_MAX_MEMORY environmental variable in the destination section of the job_conf.xml file: + +``` +<?xml version="1.0"?> +<!-- A sample job config that explicitly configures job running the way it is configured by default (if there is no explicit config). --> +<job_conf> + <plugins> + <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/> + </plugins> + <handlers> + <handler id="main"/> + </handlers> + <destinations> + <destination id="local" runner="local"> + <env id="DISCO_MAX_MEMORY">4</env> + </destination> + </destinations> +</job_conf> +``` + |
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| diff -r 000000000000 -r 6d447ebb2bf4 disco.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/disco.xml Fri Nov 03 15:44:23 2017 -0400 |
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| b'@@ -0,0 +1,400 @@\n+<tool id="disco" name="DISCO" version="@WRAPPER_VERSION@.0">\n+ <description>to assemble metagenomics data using an overlap-layout-consensus (OLC) approach</description>\n+ <macros>\n+ <token name="@WRAPPER_VERSION@">1.2</token>\n+ <xml name="assembly_params">\n+ <param argument="minSequenceLengthTobePrinted" type="integer" value="1000" min="0" label="Minimum length of contigs or scaffolds to be printed"/>\n+ <param argument="MinOverlap4SimplifyGraph" type="integer" value="30" min="0" label="Minimum overlap length (bp) required to keep an edge between two reads during graph simplification" help="This minimum overlap length must be equal to 30 or larger than the MinOverlap4BuildGraph above. This allows you to try different minimum overlap lengths for assembly without redoing assembly graph construction. Edges with shorter overlap length than this parameter will be ignored during graph simplification. Increase this to reduce N50 and mis-assemblies"/>\n+ <param argument="minOverlapDifference4ClipBranches" type="integer" value="25" min="0" label="Minimum overlap length difference (bp) to clip branches" help="If a read has multiple edges, Disco clips the branches with overlap lengths less than the largest overlap of this read by this difference or more. Increase this to reduce N50 and mis-assemblies"/>\n+ <param argument="minUniquePEsupport" type="integer" value="3" min="0" label="Minumum number of paired-end reads that provide unique support to merge two edges" help="Increase this to reduce N50 and mis-assemblies"/>\n+ <param argument="minNonUniquePEsupport" type="integer" value="0" min="0" label="Minumum number of paired-end reads that provide non-unique support to merge two edgess"/>\n+ <param argument="minReadsCountInEdgeToBeNotDeadEnd" type="integer" value="10" min="0" label="Minimum number of reads in an edge to be not dead-end edge"/>\n+ <param argument="minEdgeLengthToBeNotDeadEnd" type="integer" value="1000" min="0" label="Minimum edge length (bp) to be not dead-end edge"/>\n+ <param argument="minFoldToBeShortBranch" type="integer" value="5" min="0" label="Minimum fold difference between two branches\' lengths to consider a branch to be short"/>\n+ <param argument="minReadsCountToHave0Flow" type="integer" value="15" min="0" label="Minimum number of reads for an edge to be kept even if it has 0 flow"/>\n+ <param argument="minEdgeLengthToHave0Flow" type="integer" value="1500" min="0" label="Minimum edge length for an edge to be kept even if it has 0 flow"/>\n+ <param argument="minReadsCountInEdgeToBe1MinFlow" type="integer" value="20" min="0" label="Minimum number of reads in an edge to be assigned with 1 minimum flow"/>\n+ <param argument="minEdgeLengthToBe1MinFlow" type="integer" value="2000" min="0" label="Minimum edge length to be assigned with 1 minimum flow"/>\n+ </xml>\n+ </macros>\n+ <requirements>\n+ <requirement type="package" version="@WRAPPER_VERSION@">disco</requirement>\n+ </requirements>\n+ <version_command>runDisco.sh --version</version_command>\n+ <command detect_errors="exit_code"><![CDATA[\n+runDisco.sh\n+ -n \\${GALAXY_SLOTS:-4}\n+ -m \\${DISCO_MAX_MEMORY:-4}\n+ -d .\n+ -o disco\n+ #if $input.library_type == "single"\n+ -inS \'$input.inS\'\n+ #else\n+ #if $input.paired_input.type == "separated"\n+ -in1 \'$input.paired_input.in1\'\n+ -in2 \'$input.paired_input.in2\'\n+ #else\n+ -inP \'$input.paired_input.inP\'\n+ #end if\n+ #end if\n+ $obg\n+ $osg\n+ -p \'$first_assembly_iteration_params\'\n+ -p2 \'$second_assembly_iteration_params\'\n+ -p3 \'$third_assembly_iteration_params\'\n+ ]]></command>\n+ <configfiles>\n+ <configfile name="first_assembly_iteration_params">\n+<![CDATA[\n+MinOverlap4BuildGraph = $MinOverlap4BuildGraph\n+PrintContigs = true\n+PrintScaffolds = tr'..b'\n+ <param name="PrintGFA2" value="false"/>\n+ <section name="first_assembly_iter_param">\n+ <param name="minSequenceLengthTobePrinted" value="1000"/>\n+ <param name="MinOverlap4SimplifyGraph" value="30"/>\n+ <param name="minOverlapDifference4ClipBranches" value="25"/>\n+ <param name="minUniquePEsupport" value="3"/>\n+ <param name="minNonUniquePEsupport" value="0"/>\n+ <param name="minReadsCountInEdgeToBeNotDeadEnd" value="10"/>\n+ <param name="minEdgeLengthToBeNotDeadEnd" value="1000"/>\n+ <param name="minFoldToBeShortBranch" value="5"/>\n+ <param name="minReadsCountToHave0Flow" value="15"/>\n+ <param name="minEdgeLengthToHave0Flow" value="1500"/>\n+ <param name="minReadsCountInEdgeToBe1MinFlow" value="20"/>\n+ <param name="minEdgeLengthToBe1MinFlow" value="2000"/>\n+ </section>\n+ <section name="second_assembly_iter_param">\n+ <param name="minSequenceLengthTobePrinted" value="1000"/>\n+ <param name="MinOverlap4SimplifyGraph" value="30"/>\n+ <param name="minOverlapDifference4ClipBranches" value="25"/>\n+ <param name="minUniquePEsupport" value="3"/>\n+ <param name="minNonUniquePEsupport" value="0"/>\n+ <param name="minReadsCountInEdgeToBeNotDeadEnd" value="10"/>\n+ <param name="minEdgeLengthToBeNotDeadEnd" value="1000"/>\n+ <param name="minFoldToBeShortBranch" value="5"/>\n+ <param name="minReadsCountToHave0Flow" value="15"/>\n+ <param name="minEdgeLengthToHave0Flow" value="1500"/>\n+ <param name="minReadsCountInEdgeToBe1MinFlow" value="20"/>\n+ <param name="minEdgeLengthToBe1MinFlow" value="2000"/>\n+ </section>\n+ <section name="third_assembly_iter_param">\n+ <param name="minSequenceLengthTobePrinted" value="1000"/>\n+ <param name="MinOverlap4SimplifyGraph" value="30"/>\n+ <param name="minOverlapDifference4ClipBranches" value="25"/>\n+ <param name="minUniquePEsupport" value="3"/>\n+ <param name="minNonUniquePEsupport" value="0"/>\n+ <param name="minReadsCountInEdgeToBeNotDeadEnd" value="10"/>\n+ <param name="minEdgeLengthToBeNotDeadEnd" value="1000"/>\n+ <param name="minFoldToBeShortBranch" value="5"/>\n+ <param name="minReadsCountToHave0Flow" value="15"/>\n+ <param name="minEdgeLengthToHave0Flow" value="1500"/>\n+ <param name="minReadsCountInEdgeToBe1MinFlow" value="20"/>\n+ <param name="minEdgeLengthToBe1MinFlow" value="2000"/>\n+ </section>\n+ <output name="contigs" value="test3_contigs.fasta" compare="sim_size" delta="5"/>\n+ <output name="scaffolds" value="test3_scaffolds.fasta" compare="sim_size" delta="5"/>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+DISCO is a multi threaded and multiprocess distributed memory overlap-layout-consensus (OLC) metagenome assembler. Disco was developed as a scalable assembler to assemble large metagenomes from billions of Illumina sequencing reads of complex microbial communities. Disco was parallelized for computer clusters in a hybrid architecture that integrated shared-memory multi-threading, point-to-point message passing, and remote direct memory access. The assembly and scaffolding were performed using an iterative overlap graph approach.\n+\n+The detailed user manual of the assembler and how to use it to acheive best results is provided here: http://disco.omicsbio.org/user-manual. This is a quick start guide generally for developers and testers. Users with limited experience with genome assembly are advised to use the user manual.\n+ ]]></help>\n+ <citations>\n+ </citations>\n+</tool>\n' |
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| diff -r 000000000000 -r 6d447ebb2bf4 test-data/ecoli_1K_1.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ecoli_1K_1.fq Fri Nov 03 15:44:23 2017 -0400 |
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| b'@@ -0,0 +1,8216 @@\n+@EAS20_8_6_1_9_1972/1 trim=6\n+ACCACCATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCG\n++\n+HHHHHHGHHHHFHHGGHHFHHHHHFHHFHFHHHHHFHHHHHFHHHHHHHHFHHFHFDHHGG@BGGHCDHE:;3)7.A973A:AA5>AD9G=D<D\n+@EAS20_8_6_1_163_1521/1\n+GCAGAAAACGTTCTGCATTTGCCACTGATGTACCGCCGAACTTCAACACTCGCATGGTTGTTACCTCGTTACCTTTGGTCGAAAAAAAAAGCCCGCACTG\n++\n+HGHHIHHHDHHHHHIHHIHHHHHHHHHBHHHHHFHCFHHHHHHHGHHHHHEHHFHHHGHHIHHHGHGHHHIHFHHHHHGH?5<<;BD>6>?BGEHHGHFG\n+@EAS20_8_6_1_178_1948/1\n+ATTCGAGGTAATGCCCCACTGCCAGCAGTTTTTCGACCGGATCGATAACAGTAACGTTGTGACCGCGCGCTTCTAATACGCCGGCCATAATGGCGATCGA\n++\n+GHHHHHHHHHGGHHHHHHGHHHHHHHEHHHHHHHHHHHHHFHHHEHHHHHHHFHFHIHHIHHHIHHHGHIIGGHBGGGHHFFGBHIFFGCIGGEFDG@AG\n+@EAS20_8_6_1_318_1522/1 trim=5\n+AAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCAC\n++\n+HHHHHHHHHHIHHHHHHHHHHHHHHHHHGEHHHHHEHHHHHHIHHHHGHHEHHGHBHDDEHHEGH?HEGGGIHDIGFFFEHE;EE;=AFE;AB/B\n+@EAS20_8_6_1_348_1372/1\n+AAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAAC\n++\n+HHHHHHHHHHHHHHHHHHHEHHGHHIHHHDHHHHHHHHHHFHHHGHHFHHH@HHHFHHHEHH<HH?@D>DHDEBEEGDFDCHECGB:?43CCCFG?90<6\n+@EAS20_8_6_1_389_646/1 trim=2\n+ACAGAGTACACAACATCCATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAAC\n++\n+HBHGGHHIGHHHGDHHGHHDHHHGDHFGGHHHHHHHHHHHHIHHGFGHHHHHGHGGHGGDHHEFHDDHGGGHHH=HDDB9FHGGEIEHICEB?DBBAE\n+@EAS20_8_6_1_513_951/1\n+TTTTGACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCGCAATTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAAAACATGTCCTGCATGG\n++\n+HHHHHDHHHHHHIHGHGIEEDFHBDDHGGGBC?C?IHD>GFHGHG?DDGEB?;?,DCF=D??F=BDBGE=DDGDG.>76?>EB>54+?;=5;BEBDAGGA\n+@EAS20_8_6_1_530_1080/1 trim=1\n+AAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAG\n++\n+EHHHHHHGHHFEHHHHHGHHHHHHGHH=BHHHEHHHHHHHEHFEEHHFDHHHHHHFGHHHHFHFHHEHFHFEHEEHB>EG=F?E=>FHE@CH5HB:81@\n+@EAS20_8_6_1_546_406/1\n+AAATAAAACATGTCCTGCATGGCATTAGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGCTGATTTGCCGTGGCGAGAAAATGTCGATCGCCAT\n++\n+HHHHHHGGGHHHHHHHHHHHHHIHHHHHHHHHHHHIFHHHHHHHHHHHIFHHHHHHHHHHHHHGHHHHFHHHHFHHHHEHHDH@8GFHHGHEFBHHGG5G\n+@EAS20_8_6_1_553_1132/1 correct\n+CGTTGATGCTATCCGGGCACTGCCCCAACAAACTAATGCCATGCAGGACATGTTTTATTTGGGCAAATTCCTGATCGACGAAAGTTTTCAATTGCGCCAG\n++\n+HHHHHIHHHHHHGHHHHHHHHHDHHHHHHHHHHHIGHH@HHHHHGHHFHDHHHHHHHHGGGHH=HDHHHFHHHGHHHFHH55445#A@@:55555EGGDE\n+@EAS20_8_6_1_594_142/1 trim=11\n+GGTTGTTACCTCGTTACCTTTGGTCGAAAAAAAAAGCCCGCACTGTCAGGTGCGGGCTTTTTTCTGTGTTTCCTGTACGCGTCAGCCCG\n++\n+HIHHHHHHHHHHHHHHHHHHHHHIHHFHDHHGEBEEEHHGHIIHHFHHEG@FAFHD;DEFHHH@E.:82=??:=:F5?E6;4<:@B?AE\n+@EAS20_8_6_1_641_1277/1 trim=50\n+GGGCTTTTTTCTGTGTTTCCTGTACGCGTCAGCCCGCACCGTTACCTGTG\n++\n+HHE=GHHHHHECGHHHG@FDHEFF7@@CAA?FA>FA?9;;>@;5=1AA+D\n+@EAS20_8_6_1_660_979/1 trim=5\n+AGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAAT\n++\n+HHEGHHHHHHHHHHHHHHHHGFFHHHFEEAHEHHGHHEHDFGHIHHHGGD<9F:FHFHHBC4EEEDEBGHHGE@BCBEDGGFFGACFG=4C39:B\n+@EAS20_8_6_1_763_241/1 trim=42\n+TTGTTACCTCGTTACCTTTGGTCGAAAAAAAAAGCCCGCACTGTCAGGTGCGGGCTTT\n++\n+GHHHIG@HHHHHHGHGIHHHHHHHEDDFEHCBGGHHHHH@HFFGGAGE;B+>3223;D\n+@EAS20_8_6_1_789_699/1\n+GCGAGTCCCGTCAAAAGTTCGGCAAAAATACGTTCGGCATCGCTGATATTGGGTAAAGCATCCTGGCCGCTAATGGTTTTTTCAATCATCGCCACCAGGT\n++\n+HGHHHHHHHHGHF@GHHGHHFHF@FD??F>CDHHFHHHHHBEFHHAHCHHHEHH@HHHDFHH;HGHGFHHF>1DDFF?FFEHFEHF0AE.2061585=@/\n+@EAS20_8_6_1_802_355/1 correct\n+AGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGAT\n++\n+HIHHHHHHIGHDHHHHH#HHFDFBB?DDA>EFGDFHHFHFHHHHHHHEGFHHHFGHBH=;FF@;FEGHHHHHFHCHHEHDFHEHHFHDH=?HEFEHEHAH\n+@EAS20_8_6_1_807_1707/1 trim=15\n+TCGGCATCGCTGATATTGGGTAAAGCATCCTGGCCGCTAATGGTTTTTTCAATCATCGCCACCAGGTGGTTGGTGATTTTGGCGG\n++\n+FHCEHGFHHHHGEEHHHHGHHFFHFHGHHHGHGFHH=HFCHHHHHEHEHHDFHHFFHHHHAHHBHA4>C6?@=8>5FBBFE?EEB\n+@EAS20_8_6_1_918_1054/1 correct trim=10\n+AACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCA\n++\n+HHGHHHHHHHHHHHHHHHHHHHHEHHFHHHHGHHHEHHHFIHGHFHHHFHGGFHC>D1D<AFD:CGGGGAB=FCECE23B/#8>=DD:EC\n+@EAS20_8'..b'<@>@8BG9G9\n+@EAS20_8_6_100_346_1515/1\n+TAATACGCCGGCCATAATGGCGATCGACATTTTCTCGCCACGGCAAATCAGCGCAGCGTTGATGCTATCCGGGCACTGCCCCAACAAACTAATGCCATGC\n++\n+FGDHEHHHHHHGHHHHHHHHBG?GEHHDDGHHHDH@GEEH?CHHFF?FDFEEFHEEFHGHHFFHEIHHGBGGEGDIGFEDEHBEHGEAFHGFH@HGGA?H\n+@EAS20_8_6_100_434_840/1 trim=47\n+ACCTGCCATCAGCACCATGTGATCAGCCGGAATGCGGCTTGCCGCAATACGGC\n++\n+HGHHHGHHHHHHGGHHHGHHHEGFHHHFHHDGHHEHGGHE:5=>9-<<.-BGB\n+@EAS20_8_6_100_451_465/1 correct\n+CGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGTTACTGTTATCGATCCGGTCGAAAAACTGCTGGCAGTGGGGCATTACCTCGAATCTACC\n++\n+FHHEHHHGHHHHHGFDHHBHBBDDDHEHHHGHIHHDHHEHHHHHEFHHHHHHI@HE=@FBFFCC#HHDHHEHHHH@HGADFF,=FB@F?F?FB4F?F@BB\n+@EAS20_8_6_100_452_1846/1 correct\n+CGCCAGCGGGAACCCCGGCTGGGCGGCGGCGAGTCCCGTCAAAAGTTCGGCAAAAATACGTTCGGCATCGCTGATATTGGGTAAAGCATCCTGGCCGCTA\n++\n+HFHHEHHHGHEEFEHHHHHHHGFHHHHHDHFGHFHGHHGH@B5>BAEHEHFF#?;-54457HHFAFACEFFCFAFGGGECGEEG#@@@AAFGGCDBHEE=\n+@EAS20_8_6_100_723_1564/1\n+TCTAATACGCCGGCCATAATGGCGATCGACATTTTCTCGCCACGGCAAATCAGCGCAGCGTTGATGCTATCCGGGCACTGCCCCAACAAACTAATGCCAT\n++\n+HHHHHHGHGHHHHHHHHDHHHGGHGFFHD=DFHHHFHHGGHHFHHHHHHHHDHGGHHHCHEHHGHGFHHHHGEG3H@HEDHHGHHFGEGGGGFFFGEGAG\n+@EAS20_8_6_100_776_1749/1 trim=5\n+GGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTTGACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCGCAAT\n++\n+H,/E8;GH88;?8AA=CFHFCF/F7FE0EA@1.=;ACFF>C=HFFFD=D=HFBFH1FFFG>@CD;GGFGBGAGGF8HHHHHHEHIHEH8H??,<A\n+@EAS20_8_6_100_779_871/1 trim=20\n+GTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAA\n++\n+GHHGGHGHHHHHHHCHHHFHHHFHHHHDFHHEHGHHEDHF?GG@::FGCDCB6E@F6:F<BFAC?EDF-:FEHFB:226A\n+@EAS20_8_6_100_816_1759/1 correct trim=47\n+AAAAAGCCCGCACTGTCAGGTGCGGGCTTTTTTCTGTGTTTCCTGTACGCGTC\n++\n+#GGHHHBHCGHHHHB@>DA@0#?8>/:/<=FFF/@,3/444(555<5/?3A,A\n+@EAS20_8_6_100_993_1119/1\n+GTCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACCATTACCACC\n++\n+?@FDBEFGF8BFGFGHHHHEHHHHEHBFHHHHGGHHH@HGFHHHDH5HB?GHDGDFDHEHIFHFHFFHFE?HDFCFGEHEGBE=HHGGGGGHFHHGGIEG\n+@EAS20_8_6_100_1153_966/1\n+AGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTTGACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCGC\n++\n+HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHDHHCHHHHGBFHHDHDHHHHFCHBHEGEHEHGGEHH@GEG8FFBEHFF:FBFDA+DFC;C3\n+@EAS20_8_6_100_1183_226/1 correct trim=26\n+TTGGGCAAATTCCTGATCGACGAAAGTTTTCAATTGCGCCAGCGGGAACCCCGGCTGGGCGGCGGCGAGTCCCG\n++\n+CFCCF?DCCDHEGHFHHHHFFFHD@HGEHHHGHHHGHHFHHHHGEEH:H>HHHDCFF#EADA366=A0A+8<AA\n+@EAS20_8_6_100_1263_900/1 correct trim=1\n+AGTGTTGAAGTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCCAGGCAGGGGCAGGTGGCCAC\n++\n+HGHHHHHHIHHHIHFBD?BCHHHHHDGHHHHEHHFCHFHHBHEHHHFHHDHHFEHHHGH=HEFFFHH@CFHBHEHHBGHGBCDBGFDH<EAF#9F#?@A\n+@EAS20_8_6_100_1277_357/1 trim=5\n+ACGTTCGGCATCGCTGATATTGGGTAAAGCATCCTGGCCGCTAATGGTTTTTTCAATCATCGCCACCAGGTGGTTGGTGATTTTGGCGGGGGCAG\n++\n+DEHHHHIEHHHHHHHHGIGHHHHHHHGHHHHEFEHHHHHHHHFEHHHHHHHHH@CGHGCHFHHE@FB<=F=FFFFFFDG;BFDFFGFEG@9B24C\n+@EAS20_8_6_100_1337_252/1 correct trim=16\n+GCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTTGACGGGACTCGCCGCCGCCCAGCCGG\n++\n+GBHHHHHHGGHHBHEG@BEHHDHAHGBHGHDGDDEH#EBEDBFDHHC2EDF9?@EEHHE?CCH=EHEGAGGGEE4AGA6E1G?F\n+@EAS20_8_6_100_1432_436/1 trim=3\n+GTAGATTCGAGGTAATGCCCCACTGCCAGCAGTTTTTCGACCGGATCGATAACAGTAACGTTGTGACCGCGCGCTTCTAATACGCCGGCCATAATGG\n++\n+HHHHHIHHGGHDGHHHHHEGHHHGHHDHHHEHHGHHHHGHHFHGDGHHDHECHDEGGFGGFGFFBGGEGEG?GBGHEHB9EGEDGDAEDEDE?DFBF\n+@EAS20_8_6_100_1457_1209/1 correct trim=7\n+TTGGGCAAATTCCTGATCGACGAAAGTTTTCAATTGCGCCAGCGGGAACCCCGGCTGGGCGGCGGCGAGTCCCGTCAAAAGTTCGGCAAAAAT\n++\n+HGHFFDBCBD#BBFFEDDFCHGHHEHCHHHEHHHHHHEAHHHGHBDGHEHEEGHGEE@GGGGFG?5C;A5:0;A4988-/>8@5>;<-37<?B\n+@EAS20_8_6_100_1609_245/1\n+GGTGGCCACCTGCCCCTGCCTGGCATTGCTTTCCAGAATATCGGCAACACGCAGAAAACGTTCTGCATTTGCCACTGATGTACCGCCGAACTTCAACACT\n++\n+BCBBDFHHHHHHEHHHHGHHHHHHDHHHHHHHGHHHGIHHHHHEHIDHGGIHHHFGHFHHGHHBGFFHHHHFHHFHHGHHIHHEHGFF=HGFHHBFFGBH\n+@EAS20_8_6_100_1637_1332/1\n+TGGTGCTAATGCGTTTCATGGATGTTGTGTACTCTGTAATTTTTATCTGTCTGTGCGCTATGCCTATATTGGTTAAAGTATTTAGTGACCTAAGTCAATA\n++\n+FHFHHFGGHGHFHGHHGHHHFEHHHGFFDFHFHHHGEDCGHHHHHG9HDGHFHGHHHEHEFGF=GAHEHHFEGFFGEHFHHHHFHHEBE?HHFHEGFDHH\n' |
| b |
| diff -r 000000000000 -r 6d447ebb2bf4 test-data/ecoli_1K_2.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ecoli_1K_2.fq Fri Nov 03 15:44:23 2017 -0400 |
| b |
| b'@@ -0,0 +1,8216 @@\n+@EAS20_8_6_1_9_1972/2 correct\n+GGTGGCCACCTGCCCCTGCCTGGCATTGCTTTCCAGAATATCGGCAACACGCAGAAAACGTTCTGCATTTGCCACTGATGTACCGCCGAACTTCAACACT\n++\n+HFHHHGHHHHHHHHHHHHGHHHHHHGHHHHHHHHHHHFHHGHHGHEHHHHHHEH;G?F<F?GDFF/EEFBD:DCHHH7A@?EEH@HH96:4F@#76=C@@\n+@EAS20_8_6_1_163_1521/2\n+GGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGTAACG\n++\n+HHGGFHHGHHHHHHHGFHHHHHHHCGHFHFHFHHHHHHGHHGHHDHHIEGEDFEHHCHHHHGCCGF>GFEFEGGFGGEIG1ACBCF?CD1?CADCD.DFB\n+@EAS20_8_6_1_178_1948/2\n+ATTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAAAACATGTCCTGCATGGCATTAGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGCTG\n++\n+HGHIHHHIHGGHHHHGHHFHHFDHHHHHGHHBHHHHHHGGGHHHHHHHHHFHHHHGHHFHFEDHGDHH>HGEFCHHCHHH=GGHBEGFFHEGGD@HHEEH\n+@EAS20_8_6_1_318_1522/2\n+AGAATATCGGCAACACGCAGAAAACGTTCTGCATTTGCCACTGATGTACCGCCGAACTTCAACACTCGCATGGTTGTTACCTCGTTACCTTTGGTCGAAA\n++\n+IGHFHHHDEHGHHEHHHEGHDHHHGHHHHHHEHHHHHDHHHHHGHHHHEGFAEHDGHFHHFDHFGHHHIGHIEGHHGGHFGFAHGHGFEHDHEEEB7<3<\n+@EAS20_8_6_1_348_1372/2\n+GGGCGGCGGCGAGTCCCGTCAAAAGTTCGGCAAAAATACGTTCGGCATCGCTGATATTGGGTAAAGCATCCTGGCCGCTAATGGTTTTTTCAATCATCGC\n++\n+HHHHHH@HGHHEHGHGHHHHDHHHHFHEHDDHHDHHHEEHHDHHHBFHCEGEHGGGDHHE@EFDAHHGHEDFGG:FDB<>=BDG?D=3BB>G?GGEGGD;\n+@EAS20_8_6_1_389_646/2 trim=17\n+TGCCACTGATGTACCGCCGAACTTCAACACTCGCATGGTTGTTACCTCGTTACCTTTGGTCGAAAAAAAAAGCCCGCACTGTC\n++\n+HGGGDHHHAHGHHHHGHIHHEHHHGHFHHHHHFHHEG=GHEEFEHEHHEEEDGHGHFHDFFFADDHHF:>0&D0A4?,?AE=?\n+@EAS20_8_6_1_513_951/2 correct\n+ATAACAGTAACGTTGTGACCGCGCGCTTCTAATACGCCGGCCATAATGGCGATCGACATTTTCTCGCCACGGCAAATCAGCGCAGCGTTGATGCTATCCG\n++\n+GHFHGHDHGHHHHHHFHHHEFHHHHHGHFHBHEHHHFDHHGGHHBEHHGHHHFFFBHHHHHGEGDHFIHHHHEEC?GEGDFE;<E+@5@>?E;=?#A)?=\n+@EAS20_8_6_1_530_1080/2\n+GAAAACGTTCTGCATTTGCCACTGATGTACCGCCGAACTTCAACACTCGCATGGTTGTTACCTCGTTACCTTTGGTCGAAAAAAAAAGCCCGCACTGTCA\n++\n+D?D?DG;FAFFGDGFDF?F:>=DD>GGGGGDAD:D+DD>DDFAFFDGFG4FFFFC<FF>BGCG/CFF59AFBD6DG@BA1.53;-:9:FG::F-:><>96\n+@EAS20_8_6_1_546_406/2\n+CGGGTGGACTCAGCAATATCGACGGTAGATTCGAGGTAATGCCCCACTGCCAGCAGTTTTTCGACCGGATCGATAACAGTAACGTTGTGACCGCGCGCTT\n++\n+HHHHEHHHHHHHIHHFHHHHHHHHHGHHHIHHHHHFGHHGHHHHHBHHGBHHEHGHCGGGGHAGHEGGGGHEDECGGFE8GGE=EGGC>FGE@DDECGDD\n+@EAS20_8_6_1_553_1132/2 trim=6\n+GGCGATGATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTTGACGGGACTCGCC\n++\n+HHHHHHHHHHHHFHHHHHHHHHHHHHHHHHHHEGHHHHHABGEEHHDHAGHDHGGHFFFGH@HDGGHGHEEFIIBFFFIEGD@EFG<E@EC<6B\n+@EAS20_8_6_1_594_142/2\n+AACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACC\n++\n+GGHHHHHHHHHFGHHHHHGHHHDGDHHHHHHHFH?EHHHHGDGEHHHHDHHHIHHGIHHEFFHHHHFGFHGEHCGGGEGA;HFH@DEFEBEEAHE??=?C\n+@EAS20_8_6_1_641_1277/2\n+GGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTA\n++\n+FFE?FEBFG?EHFHDHDFHDEHGAEEFGFHHH?GH;HAGGFF7AEHCCBH?0FG=2FAB4EHGB>BC0<?EE=9C=E;F;:;AAAA+,=,6E@2AC3?<>\n+@EAS20_8_6_1_660_979/2\n+CCATGCAGGACATGTTTTATTTGGGCAAATTCCTGATCGACGAAAGTTTTCAATTGCGCCAGCGGGAACCCCGGCTGGGCGGCGGCGAGTCCCGTCAAAA\n++\n+HDHHEFHH@FHHHEHHGGGGEEEHFFHHFGHHHHHGGHHDBFBF;FFFGFDFGGHHHHG<FHCHHA9=B?=G@@?EHED9F8DHEDD3EBC&GD3)-000\n+@EAS20_8_6_1_763_241/2\n+TATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGT\n++\n+HHFDFGHHHHHEHHCHHFGHBEEAGHBCGEGHHEHDHEHH=HHHHHHHHGHHDBFGHHDGBIHHHHCHEHBE>HHGHBHHFHEGEHGHBDEHEH=F:E??\n+@EAS20_8_6_1_789_699/2 correct trim=20\n+TGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCC\n++\n+H=BHHFAECGAHHHF<AF@FFEEEEHHHHFCHHHHHGHH=FEHHHEHH4E1DAA=FEG?AHDEH#*F;1/AA7(D<?)FF\n+@EAS20_8_6_1_802_355/2 correct\n+CTGTACGCGTCAGCCCGCACCGTTACCTGTGGTAATGGTGATGGTGGTGGTAATGGTGGTGCTAATGCGTTTCATGGATGTTGTGTACTCTGTAATTTTT\n++\n+HHHHHHHHHHHGGGGHHHHIHGGIHHHHGHHEAEBFFBCF=GGD?D@2C;?<6?BFBFF>BCCE?BBDGDBD>2HF?8?C?:19?0&5-#=:/;6DHGD>\n+@EAS20_8_6_1_807_1707/2 trim=1\n+GAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCCAGG\n++\n+FCFF2FBBFBEHGHH?D=AAFDGGCCHHHHBHEEHDEFAFFGGGDGGABIGECHEBBBHFHHHDDFEGGEEFD=1=BDDDCCGEEDDJCBBDDE;BEAG\n+@EAS20_8_6_1_918_1054/2 correct\n+GCCAGCGGGAACCCCGGCTGGGCGGCGGCGAGTCCCGT'..b'6_100_346_1515/2\n+TGCCGAACTTTTGACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCGCAATTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAAAACATGTC\n++\n+AADA@BBFBDHCGGBHHHGHH=HEHFHHH@HFHHFFDHFE;HHEHGF<CGHHH@FGGG1F<B9BDHHHH=H?HE6GFADFEBHBDFD/BGF1F??HGHGF\n+@EAS20_8_6_100_434_840/2\n+AGTGCCCGGATAGCATCAACGCTGCGCTGATTTGCCGTGGCGAGAAAATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGTTAC\n++\n+HHHGHHFHGGHHEFHHH>FHHHHHFHFHHEHHHFFHHHHDHHGHHBAHHHFHHEHFHHGBIHHEFIFGEDGGC;FE80>ABC4CAEGG;A182;916>98\n+@EAS20_8_6_100_451_465/2 correct trim=22\n+GTTGCGTCCAAGCACCACCAGTTCGCCTTTTTCATTACCGGCGGTGAAACCTGCCATCAGCACCATGTGATCAGCCGG\n++\n+HIHHDHHHHGHIGHHHHGHHHFHHIHIHHHHHIHHHHHGIH@HH>A;AD95#+43=?C:35:6865/9;13=<:?B?C\n+@EAS20_8_6_100_452_1846/2 correct\n+CTGCGTGTTGCCGATATTCTGGAAAGCAATGCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGA\n++\n+HHHHHGHHHHGHHHFHHHHGHGHDHHFHBEHHHFHFGHHGHHHDHE#HEDF?CF?DFD:E252+7CBF?14:*:AA;:C9;9;+ABAD8#64<::;3+<7\n+@EAS20_8_6_100_723_1564/2 correct trim=2\n+TGCCGAACGTATTTTTGCCGAACTTTTGACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCGCAATTGAAAACTTTCGTCGATCAGGAATTTG\n++\n+HHHEHEHEH?HHEEHEEGHHBEFEEHHHFHHHHHHFHEHFEHHFHGHHGHED/EHDHEH@A88D@C(E6BEEHD@5?CE:AG;D@C;;2@>#8.95?C\n+@EAS20_8_6_100_776_1749/2\n+TCTCGCCACGGCAAATCAGCGCAGCGTTGATGCTATCCGGGCACTGCCCCAACAAACTAATGCCATGCAGGACATGTTTTATTTGGGCAAATTCCTGATC\n++\n+F3G30CEG?GDD4D=H<8BFEF8HDGHHH1HHFFEHDHB1;5>;<8EDC8??@ADEHH@HEEEHFHHHHHHEHHHG:@FFFGA6AEHH@=EHH;HFC/FF\n+@EAS20_8_6_100_779_871/2\n+AAAGTTTTCAATTGCGCCAGCGGGAACCCCGGCTGGGCGGCGGCGAGTCCCGTCAAAAGTTCGGCAAAAATACGTTCGGCATCGCTGATATTGGGTAAAG\n++\n+FGEFCEHFFFBHHFHHHHEEHHHBCFAFEHGHGHH7B@:EDFHDE5CAABBHCB7@8?A8?FB3BBADBDG>;;CF=FGGD52B0?A2A?;;=;BA5DAE\n+@EAS20_8_6_100_816_1759/2\n+AAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAAC\n++\n+63;=>>3>>?DECADBBDCG?@7?5DCEEEGGGECGGGCGGGDCGGFCG6FGBCGGGGG>DGCGGBEGG>4E7?GFGG<GGGGEG;,GBADD8ADG>2EF\n+@EAS20_8_6_100_993_1119/2 trim=60\n+TGGTTGTTACCTCGTTACCTTTGGTCGAAAAAAAAAGCCC\n++\n+B>BBB=F:FGFHFBHHHHHHHDHDGHEH=HHHHGE>8DC=\n+@EAS20_8_6_100_1153_966/2\n+TCGCCACGGCAAATCAGCGCAGCGTTGATGCTATCCGGGCACTGCCCCAACAAACTAATGCCATGCAGGACATGTTTTATTTGGGCAAATTCCTGATCGA\n++\n+HHGHHHHHHGHHHHHGHHHHHHHHHHGHHHHHHHHHGHGHHHHH;HFDEHFDHDHHHHHGDHHHHDGHFGBGHHCGGHFH>ECGGHGECFFDFFD?DDDB\n+@EAS20_8_6_100_1183_226/2 correct trim=40\n+AATGCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCAC\n++\n+DDBBD@EEEGDHHEHBCBB0=GCGC4?.6=D8CF89:DFBGG5==*83<#?/:;+E@ABB\n+@EAS20_8_6_100_1263_900/2\n+AAGTTCGGCAAAAATACGTTCGGCATCGCTGATATTGGGTAAAGCATCCTGGCCGCTAATGGTTTTTTCAATCATCGCCACCAGGTGGTTGGTGATTTTG\n++\n+HHHEHHHEGIHHHGHGGHHHHHHHHHHHHHH=HFHHHHHFHHHGEHHFHHHGEBHHHBCHHDEGHGGF@G@HGEE=F;C9H39H=FEHFHHEFH?=AEFE\n+@EAS20_8_6_100_1277_357/2 trim=5\n+GCGAGTGTTGAAGTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCCAGGCAGGGGCAGG\n++\n+FFFHFHHHHHHHHGHHDHHBBHHHHHHEEEH<GHGH@FHHHHGGHGHHHFGHHGGHGGHHHFBEFFEHHHECGIIFHEGEEDFEEH//EBD4=EF\n+@EAS20_8_6_100_1337_252/2 correct\n+CATAATGGCGATCGACATTTTCTCGCCACGGCAAATCAGCGCAGCGTTGATGCTATCCGGGCACTGCCCCAACAAACTAATGCCATGCAGGACATGTTTT\n++\n+HHHHBHEECG=FEEFH.HHH=GEGE@HEF<BFHHBHHAHHBBBB>DGHH8HDF/=F=FF==;/FFCGGHDGBHG-B<@BFE=:FE5=E98E=E-H=@C#C\n+@EAS20_8_6_100_1432_436/2\n+CAATTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAAAACATGTCCTGCATGGCATTAGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGC\n++\n+HHHHHFHHGHHHHHGGHHHHGHHHHHHHHGHHHGHHHGGGEEEHHHHHHFHEDGGGHHFHHHDGHBFGFF>BHH8FBF0F@>DFGHHBBEH>FBD@DHEG\n+@EAS20_8_6_100_1457_1209/2 correct trim=11\n+GCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTGAAAAAACCATTAGCGGCCAGG\n++\n+HHHHBGHHHFH?HHHHCCFDB=?D=HHEEAEFEHGEB=HHC68C5??B==B=F<;C7=ECH=HE:?CE>@?<EB1.-87<<#3C9@>??\n+@EAS20_8_6_100_1609_245/2 correct trim=16\n+TCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGGCTTTTTT\n++\n+HHEHHHGHHGHHHHDIHHHHHHHHHFHAFHFHHEIFDHFH8HHHFHHHGHHHEEB<8FFFCG>FE==9D9#0:?45/<#;B8=D\n+@EAS20_8_6_100_1637_1332/2\n+ATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTT\n++\n+HHGEHGHHHHGHIGHAHEHEHEIHGGHHHHHHHGGHHHHFHEGDGCCCHHHGHHDHHIHFEEHHHHHGHIHHHFHHIEIHHHHFAEEEHHIEHDHFFHFH\n' |
| b |
| diff -r 000000000000 -r 6d447ebb2bf4 test-data/ecoli_1K_interleaved.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ecoli_1K_interleaved.fq Fri Nov 03 15:44:23 2017 -0400 |
| b |
| b'@@ -0,0 +1,16432 @@\n+@EAS20_8_6_1_9_1972/1 trim=6\n+ACCACCATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCG\n++\n+HHHHHHGHHHHFHHGGHHFHHHHHFHHFHFHHHHHFHHHHHFHHHHHHHHFHHFHFDHHGG@BGGHCDHE:;3)7.A973A:AA5>AD9G=D<D\n+@EAS20_8_6_1_9_1972/2 correct\n+GGTGGCCACCTGCCCCTGCCTGGCATTGCTTTCCAGAATATCGGCAACACGCAGAAAACGTTCTGCATTTGCCACTGATGTACCGCCGAACTTCAACACT\n++\n+HFHHHGHHHHHHHHHHHHGHHHHHHGHHHHHHHHHHHFHHGHHGHEHHHHHHEH;G?F<F?GDFF/EEFBD:DCHHH7A@?EEH@HH96:4F@#76=C@@\n+@EAS20_8_6_1_163_1521/1\n+GCAGAAAACGTTCTGCATTTGCCACTGATGTACCGCCGAACTTCAACACTCGCATGGTTGTTACCTCGTTACCTTTGGTCGAAAAAAAAAGCCCGCACTG\n++\n+HGHHIHHHDHHHHHIHHIHHHHHHHHHBHHHHHFHCFHHHHHHHGHHHHHEHHFHHHGHHIHHHGHGHHHIHFHHHHHGH?5<<;BD>6>?BGEHHGHFG\n+@EAS20_8_6_1_163_1521/2\n+GGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGTAACG\n++\n+HHGGFHHGHHHHHHHGFHHHHHHHCGHFHFHFHHHHHHGHHGHHDHHIEGEDFEHHCHHHHGCCGF>GFEFEGGFGGEIG1ACBCF?CD1?CADCD.DFB\n+@EAS20_8_6_1_178_1948/1\n+ATTCGAGGTAATGCCCCACTGCCAGCAGTTTTTCGACCGGATCGATAACAGTAACGTTGTGACCGCGCGCTTCTAATACGCCGGCCATAATGGCGATCGA\n++\n+GHHHHHHHHHGGHHHHHHGHHHHHHHEHHHHHHHHHHHHHFHHHEHHHHHHHFHFHIHHIHHHIHHHGHIIGGHBGGGHHFFGBHIFFGCIGGEFDG@AG\n+@EAS20_8_6_1_178_1948/2\n+ATTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAAAACATGTCCTGCATGGCATTAGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGCTG\n++\n+HGHIHHHIHGGHHHHGHHFHHFDHHHHHGHHBHHHHHHGGGHHHHHHHHHFHHHHGHHFHFEDHGDHH>HGEFCHHCHHH=GGHBEGFFHEGGD@HHEEH\n+@EAS20_8_6_1_318_1522/1 trim=5\n+AAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCAC\n++\n+HHHHHHHHHHIHHHHHHHHHHHHHHHHHGEHHHHHEHHHHHHIHHHHGHHEHHGHBHDDEHHEGH?HEGGGIHDIGFFFEHE;EE;=AFE;AB/B\n+@EAS20_8_6_1_318_1522/2\n+AGAATATCGGCAACACGCAGAAAACGTTCTGCATTTGCCACTGATGTACCGCCGAACTTCAACACTCGCATGGTTGTTACCTCGTTACCTTTGGTCGAAA\n++\n+IGHFHHHDEHGHHEHHHEGHDHHHGHHHHHHEHHHHHDHHHHHGHHHHEGFAEHDGHFHHFDHFGHHHIGHIEGHHGGHFGFAHGHGFEHDHEEEB7<3<\n+@EAS20_8_6_1_348_1372/1\n+AAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAAC\n++\n+HHHHHHHHHHHHHHHHHHHEHHGHHIHHHDHHHHHHHHHHFHHHGHHFHHH@HHHFHHHEHH<HH?@D>DHDEBEEGDFDCHECGB:?43CCCFG?90<6\n+@EAS20_8_6_1_348_1372/2\n+GGGCGGCGGCGAGTCCCGTCAAAAGTTCGGCAAAAATACGTTCGGCATCGCTGATATTGGGTAAAGCATCCTGGCCGCTAATGGTTTTTTCAATCATCGC\n++\n+HHHHHH@HGHHEHGHGHHHHDHHHHFHEHDDHHDHHHEEHHDHHHBFHCEGEHGGGDHHE@EFDAHHGHEDFGG:FDB<>=BDG?D=3BB>G?GGEGGD;\n+@EAS20_8_6_1_389_646/1 trim=2\n+ACAGAGTACACAACATCCATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAAC\n++\n+HBHGGHHIGHHHGDHHGHHDHHHGDHFGGHHHHHHHHHHHHIHHGFGHHHHHGHGGHGGDHHEFHDDHGGGHHH=HDDB9FHGGEIEHICEB?DBBAE\n+@EAS20_8_6_1_389_646/2 trim=17\n+TGCCACTGATGTACCGCCGAACTTCAACACTCGCATGGTTGTTACCTCGTTACCTTTGGTCGAAAAAAAAAGCCCGCACTGTC\n++\n+HGGGDHHHAHGHHHHGHIHHEHHHGHFHHHHHFHHEG=GHEEFEHEHHEEEDGHGHFHDFFFADDHHF:>0&D0A4?,?AE=?\n+@EAS20_8_6_1_513_951/1\n+TTTTGACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCGCAATTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAAAACATGTCCTGCATGG\n++\n+HHHHHDHHHHHHIHGHGIEEDFHBDDHGGGBC?C?IHD>GFHGHG?DDGEB?;?,DCF=D??F=BDBGE=DDGDG.>76?>EB>54+?;=5;BEBDAGGA\n+@EAS20_8_6_1_513_951/2 correct\n+ATAACAGTAACGTTGTGACCGCGCGCTTCTAATACGCCGGCCATAATGGCGATCGACATTTTCTCGCCACGGCAAATCAGCGCAGCGTTGATGCTATCCG\n++\n+GHFHGHDHGHHHHHHFHHHEFHHHHHGHFHBHEHHHFDHHGGHHBEHHGHHHFFFBHHHHHGEGDHFIHHHHEEC?GEGDFE;<E+@5@>?E;=?#A)?=\n+@EAS20_8_6_1_530_1080/1 trim=1\n+AAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAG\n++\n+EHHHHHHGHHFEHHHHHGHHHHHHGHH=BHHHEHHHHHHHEHFEEHHFDHHHHHHFGHHHHFHFHHEHFHFEHEEHB>EG=F?E=>FHE@CH5HB:81@\n+@EAS20_8_6_1_530_1080/2\n+GAAAACGTTCTGCATTTGCCACTGATGTACCGCCGAACTTCAACACTCGCATGGTTGTTACCTCGTTACCTTTGGTCGAAAAAAAAAGCCCGCACTGTCA\n++\n+D?D?DG;FAFFGDGFDF?F:>=DD>GGGGGDAD:D+DD>DDFAFFDGFG4FFFFC<FF>BGCG/CFF59AFBD6DG@BA1.53;-:9:FG::F-:><>96\n+@EAS20_8_6_1_546_406/1\n+AAATAAAACATGTCCTGCATGGCATTAGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGCTGATTTGCCGTGGCGAGAAAATGTCGATCGCCAT\n++\n+HHHHHHGGGHHHHHHHHHHHHHIHHHHHHHHHHHHIFHHHHHHHHHHHIFHHHHHHHHHHHHHGHHHHFHHHHFHHHHEHHDH@8GFHHGHEFBHHGG5G\n+@EAS20_8_6_1_546_406/2\n+CGGGTGGACTCAGCAATATCGACGGTAGA'..b'CGCCGCCGCCCAGCCGGGGTTCCCGCTGGCGC\n++\n+HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHDHHCHHHHGBFHHDHDHHHHFCHBHEGEHEHGGEHH@GEG8FFBEHFF:FBFDA+DFC;C3\n+@EAS20_8_6_100_1153_966/2\n+TCGCCACGGCAAATCAGCGCAGCGTTGATGCTATCCGGGCACTGCCCCAACAAACTAATGCCATGCAGGACATGTTTTATTTGGGCAAATTCCTGATCGA\n++\n+HHGHHHHHHGHHHHHGHHHHHHHHHHGHHHHHHHHHGHGHHHHH;HFDEHFDHDHHHHHGDHHHHDGHFGBGHHCGGHFH>ECGGHGECFFDFFD?DDDB\n+@EAS20_8_6_100_1183_226/1 correct trim=26\n+TTGGGCAAATTCCTGATCGACGAAAGTTTTCAATTGCGCCAGCGGGAACCCCGGCTGGGCGGCGGCGAGTCCCG\n++\n+CFCCF?DCCDHEGHFHHHHFFFHD@HGEHHHGHHHGHHFHHHHGEEH:H>HHHDCFF#EADA366=A0A+8<AA\n+@EAS20_8_6_100_1183_226/2 correct trim=40\n+AATGCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCAC\n++\n+DDBBD@EEEGDHHEHBCBB0=GCGC4?.6=D8CF89:DFBGG5==*83<#?/:;+E@ABB\n+@EAS20_8_6_100_1263_900/1 correct trim=1\n+AGTGTTGAAGTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCCAGGCAGGGGCAGGTGGCCAC\n++\n+HGHHHHHHIHHHIHFBD?BCHHHHHDGHHHHEHHFCHFHHBHEHHHFHHDHHFEHHHGH=HEFFFHH@CFHBHEHHBGHGBCDBGFDH<EAF#9F#?@A\n+@EAS20_8_6_100_1263_900/2\n+AAGTTCGGCAAAAATACGTTCGGCATCGCTGATATTGGGTAAAGCATCCTGGCCGCTAATGGTTTTTTCAATCATCGCCACCAGGTGGTTGGTGATTTTG\n++\n+HHHEHHHEGIHHHGHGGHHHHHHHHHHHHHH=HFHHHHHFHHHGEHHFHHHGEBHHHBCHHDEGHGGF@G@HGEE=F;C9H39H=FEHFHHEFH?=AEFE\n+@EAS20_8_6_100_1277_357/1 trim=5\n+ACGTTCGGCATCGCTGATATTGGGTAAAGCATCCTGGCCGCTAATGGTTTTTTCAATCATCGCCACCAGGTGGTTGGTGATTTTGGCGGGGGCAG\n++\n+DEHHHHIEHHHHHHHHGIGHHHHHHHGHHHHEFEHHHHHHHHFEHHHHHHHHH@CGHGCHFHHE@FB<=F=FFFFFFDG;BFDFFGFEG@9B24C\n+@EAS20_8_6_100_1277_357/2 trim=5\n+GCGAGTGTTGAAGTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCCAGGCAGGGGCAGG\n++\n+FFFHFHHHHHHHHGHHDHHBBHHHHHHEEEH<GHGH@FHHHHGGHGHHHFGHHGGHGGHHHFBEFFEHHHECGIIFHEGEEDFEEH//EBD4=EF\n+@EAS20_8_6_100_1337_252/1 correct trim=16\n+GCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTTGACGGGACTCGCCGCCGCCCAGCCGG\n++\n+GBHHHHHHGGHHBHEG@BEHHDHAHGBHGHDGDDEH#EBEDBFDHHC2EDF9?@EEHHE?CCH=EHEGAGGGEE4AGA6E1G?F\n+@EAS20_8_6_100_1337_252/2 correct\n+CATAATGGCGATCGACATTTTCTCGCCACGGCAAATCAGCGCAGCGTTGATGCTATCCGGGCACTGCCCCAACAAACTAATGCCATGCAGGACATGTTTT\n++\n+HHHHBHEECG=FEEFH.HHH=GEGE@HEF<BFHHBHHAHHBBBB>DGHH8HDF/=F=FF==;/FFCGGHDGBHG-B<@BFE=:FE5=E98E=E-H=@C#C\n+@EAS20_8_6_100_1432_436/1 trim=3\n+GTAGATTCGAGGTAATGCCCCACTGCCAGCAGTTTTTCGACCGGATCGATAACAGTAACGTTGTGACCGCGCGCTTCTAATACGCCGGCCATAATGG\n++\n+HHHHHIHHGGHDGHHHHHEGHHHGHHDHHHEHHGHHHHGHHFHGDGHHDHECHDEGGFGGFGFFBGGEGEG?GBGHEHB9EGEDGDAEDEDE?DFBF\n+@EAS20_8_6_100_1432_436/2\n+CAATTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAAAACATGTCCTGCATGGCATTAGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGC\n++\n+HHHHHFHHGHHHHHGGHHHHGHHHHHHHHGHHHGHHHGGGEEEHHHHHHFHEDGGGHHFHHHDGHBFGFF>BHH8FBF0F@>DFGHHBBEH>FBD@DHEG\n+@EAS20_8_6_100_1457_1209/1 correct trim=7\n+TTGGGCAAATTCCTGATCGACGAAAGTTTTCAATTGCGCCAGCGGGAACCCCGGCTGGGCGGCGGCGAGTCCCGTCAAAAGTTCGGCAAAAAT\n++\n+HGHFFDBCBD#BBFFEDDFCHGHHEHCHHHEHHHHHHEAHHHGHBDGHEHEEGHGEE@GGGGFG?5C;A5:0;A4988-/>8@5>;<-37<?B\n+@EAS20_8_6_100_1457_1209/2 correct trim=11\n+GCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTGAAAAAACCATTAGCGGCCAGG\n++\n+HHHHBGHHHFH?HHHHCCFDB=?D=HHEEAEFEHGEB=HHC68C5??B==B=F<;C7=ECH=HE:?CE>@?<EB1.-87<<#3C9@>??\n+@EAS20_8_6_100_1609_245/1\n+GGTGGCCACCTGCCCCTGCCTGGCATTGCTTTCCAGAATATCGGCAACACGCAGAAAACGTTCTGCATTTGCCACTGATGTACCGCCGAACTTCAACACT\n++\n+BCBBDFHHHHHHEHHHHGHHHHHHDHHHHHHHGHHHGIHHHHHEHIDHGGIHHHFGHFHHGHHBGFFHHHHFHHFHHGHHIHHEHGFF=HGFHHBFFGBH\n+@EAS20_8_6_100_1609_245/2 correct trim=16\n+TCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGGCTTTTTT\n++\n+HHEHHHGHHGHHHHDIHHHHHHHHHFHAFHFHHEIFDHFH8HHHFHHHGHHHEEB<8FFFCG>FE==9D9#0:?45/<#;B8=D\n+@EAS20_8_6_100_1637_1332/1\n+TGGTGCTAATGCGTTTCATGGATGTTGTGTACTCTGTAATTTTTATCTGTCTGTGCGCTATGCCTATATTGGTTAAAGTATTTAGTGACCTAAGTCAATA\n++\n+FHFHHFGGHGHFHGHHGHHHFEHHHGFFDFHFHHHGEDCGHHHHHG9HDGHFHGHHHEHEFGF=GAHEHHFEGFFGEHFHHHHFHHEBE?HHFHEGFDHH\n+@EAS20_8_6_100_1637_1332/2\n+ATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTT\n++\n+HHGEHGHHHHGHIGHAHEHEHEIHGGHHHHHHHGGHHHHFHEGDGCCCHHHGHHDHHIHFEEHHHHHGHIHHHFHHIEIHHHHFAEEEHHIEHDHFFHFH\n' |
| b |
| diff -r 000000000000 -r 6d447ebb2bf4 test-data/test1_contigs.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test1_contigs.fasta Fri Nov 03 15:44:23 2017 -0400 |
| b |
| @@ -0,0 +1,11 @@ +>contig_0000000001 Coverage: 76.176 Length: 1000 +AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAAT +TAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCAT +TAGCACCACCATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGG +CTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCG +ATATTCTGGAAAGCAATGCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTGAAAAAACCAT +TAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTTGACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCG +CAATTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAAAACATGTCCTGCATGGCATTAGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGC +TGATTTGCCGTGGCGAGAAAATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGTTACTGTTATCGATCCGGTCGAAAAACTGCT +GGCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCTGAGTCCACCCGCCGTATTGCGGCAAGCCGCATTCCGGCTGATCACATGGTGCTGATGGCA +GGTTTCACCGCCGGTAATGAAAAAGGCGAACTGGTGGTGCTTGGACGCAACGGTTCCGACTACTCTGCTGCGGTGCTGGCTGCCTGTTTACGCGCCGATT |
| b |
| diff -r 000000000000 -r 6d447ebb2bf4 test-data/test1_graph_1.gfa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test1_graph_1.gfa Fri Nov 03 15:44:23 2017 -0400 |
| b |
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| b |
| diff -r 000000000000 -r 6d447ebb2bf4 test-data/test1_graph_1.gfa2 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test1_graph_1.gfa2 Fri Nov 03 15:44:23 2017 -0400 |
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| diff -r 000000000000 -r 6d447ebb2bf4 test-data/test1_graph_2.gfa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test1_graph_2.gfa Fri Nov 03 15:44:23 2017 -0400 |
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| diff -r 000000000000 -r 6d447ebb2bf4 test-data/test1_graph_2.gfa2 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test1_graph_2.gfa2 Fri Nov 03 15:44:23 2017 -0400 |
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| diff -r 000000000000 -r 6d447ebb2bf4 test-data/test1_graph_3.gfa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test1_graph_3.gfa Fri Nov 03 15:44:23 2017 -0400 |
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| diff -r 000000000000 -r 6d447ebb2bf4 test-data/test1_graph_3.gfa2 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test1_graph_3.gfa2 Fri Nov 03 15:44:23 2017 -0400 |
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| diff -r 000000000000 -r 6d447ebb2bf4 test-data/test1_scaffolds.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test1_scaffolds.fasta Fri Nov 03 15:44:23 2017 -0400 |
| b |
| @@ -0,0 +1,11 @@ +>scaff_0000000001 Coverage: 76.176 Length: 1000 +AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAAT +TAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCAT +TAGCACCACCATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGG +CTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCG +ATATTCTGGAAAGCAATGCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTGAAAAAACCAT +TAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTTGACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCG +CAATTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAAAACATGTCCTGCATGGCATTAGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGC +TGATTTGCCGTGGCGAGAAAATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGTTACTGTTATCGATCCGGTCGAAAAACTGCT +GGCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCTGAGTCCACCCGCCGTATTGCGGCAAGCCGCATTCCGGCTGATCACATGGTGCTGATGGCA +GGTTTCACCGCCGGTAATGAAAAAGGCGAACTGGTGGTGCTTGGACGCAACGGTTCCGACTACTCTGCTGCGGTGCTGGCTGCCTGTTTACGCGCCGATT |
| b |
| diff -r 000000000000 -r 6d447ebb2bf4 test-data/test2_contigs.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test2_contigs.fasta Fri Nov 03 15:44:23 2017 -0400 |
| b |
| @@ -0,0 +1,11 @@ +>contig_0000000001 Coverage: 96.648 Length: 1000 +AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAAT +TAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCAT +TAGCACCACCATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGG +CTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCG +ATATTCTGGAAAGCAATGCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTGAAAAAACCAT +TAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTTGACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCG +CAATTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAAAACATGTCCTGCATGGCATTAGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGC +TGATTTGCCGTGGCGAGAAAATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGTTACTGTTATCGATCCGGTCGAAAAACTGCT +GGCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCTGAGTCCACCCGCCGTATTGCGGCAAGCCGCATTCCGGCTGATCACATGGTGCTGATGGCA +GGTTTCACCGCCGGTAATGAAAAAGGCGAACTGGTGGTGCTTGGACGCAACGGTTCCGACTACTCTGCTGCGGTGCTGGCTGCCTGTTTACGCGCCGATT |
| b |
| diff -r 000000000000 -r 6d447ebb2bf4 test-data/test2_scaffolds.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test2_scaffolds.fasta Fri Nov 03 15:44:23 2017 -0400 |
| b |
| @@ -0,0 +1,11 @@ +>scaff_0000000001 Coverage: 96.648 Length: 1000 +AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAAT +TAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCAT +TAGCACCACCATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGG +CTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCG +ATATTCTGGAAAGCAATGCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTGAAAAAACCAT +TAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTTGACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCG +CAATTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAAAACATGTCCTGCATGGCATTAGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGC +TGATTTGCCGTGGCGAGAAAATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGTTACTGTTATCGATCCGGTCGAAAAACTGCT +GGCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCTGAGTCCACCCGCCGTATTGCGGCAAGCCGCATTCCGGCTGATCACATGGTGCTGATGGCA +GGTTTCACCGCCGGTAATGAAAAAGGCGAACTGGTGGTGCTTGGACGCAACGGTTCCGACTACTCTGCTGCGGTGCTGGCTGCCTGTTTACGCGCCGATT |
| b |
| diff -r 000000000000 -r 6d447ebb2bf4 test-data/test3_contigs.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test3_contigs.fasta Fri Nov 03 15:44:23 2017 -0400 |
| b |
| @@ -0,0 +1,11 @@ +>contig_0000000001 Coverage: 56.59 Length: 1000 +AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAAT +TAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCAT +TAGCACCACCATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGG +CTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCG +ATATTCTGGAAAGCAATGCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTGAAAAAACCAT +TAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTTGACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCG +CAATTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAAAACATGTCCTGCATGGCATTAGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGC +TGATTTGCCGTGGCGAGAAAATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGTTACTGTTATCGATCCGGTCGAAAAACTGCT +GGCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCTGAGTCCACCCGCCGTATTGCGGCAAGCCGCATTCCGGCTGATCACATGGTGCTGATGGCA +GGTTTCACCGCCGGTAATGAAAAAGGCGAACTGGTGGTGCTTGGACGCAACGGTTCCGACTACTCTGCTGCGGTGCTGGCTGCCTGTTTACGCGCCGATT |
| b |
| diff -r 000000000000 -r 6d447ebb2bf4 test-data/test3_scaffolds.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test3_scaffolds.fasta Fri Nov 03 15:44:23 2017 -0400 |
| b |
| @@ -0,0 +1,11 @@ +>scaff_0000000001 Coverage: 56.59 Length: 1000 +AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAAT +TAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCAT +TAGCACCACCATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGG +CTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCG +ATATTCTGGAAAGCAATGCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTGAAAAAACCAT +TAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTTGACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCG +CAATTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAAAACATGTCCTGCATGGCATTAGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGC +TGATTTGCCGTGGCGAGAAAATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGTTACTGTTATCGATCCGGTCGAAAAACTGCT +GGCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCTGAGTCCACCCGCCGTATTGCGGCAAGCCGCATTCCGGCTGATCACATGGTGCTGATGGCA +GGTTTCACCGCCGGTAATGAAAAAGGCGAACTGGTGGTGCTTGGACGCAACGGTTCCGACTACTCTGCTGCGGTGCTGGCTGCCTGTTTACGCGCCGATT |