| Next changeset 1:bb51c75a0157 (2022-07-27) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngmlr commit bae3393450ab5f0564a2fd2b06db6a3566504663" |
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added:
ngmlr.xml test-data/ngmlr-in1.fa test-data/ngmlr-in2.fa test-data/ngmlr-in3.fa.gz test-data/ngmlr-out1.sam test-data/ngmlr-out2.sam test-data/ngmlr-out3.sam test-data/ngmlr-out4.sam test-data/ngmlr-ref1.fa test-data/ngmlr-ref2.fa test-data/ngmlr-ref3.fa.gz |
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| diff -r 000000000000 -r 95e4757d8da7 ngmlr.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ngmlr.xml Thu Oct 29 15:43:54 2020 +0000 |
| [ |
| b'@@ -0,0 +1,178 @@\n+<?xml version="1.0"?>\n+<tool id="ngmlr" name="CoNvex" version="@VERSION@">\n+ <macros>\n+ <token name="@VERSION@">0.2.7</token>\n+ <xml name="rg_validator">\n+ <validator type="expression" message="This field can only accept printable characters, with the exception of single and double quotes">value.isprintable() and \'"\' not in value and "\'" not in value</validator>\n+ </xml>\n+ </macros>\n+ <requirements>\n+ <requirement type="package" version="@VERSION@">ngmlr</requirement>\n+ </requirements>\n+ <description>Gap-cost alignMents for Long Reads</description>\n+ <command detect_errors="exit_code"><![CDATA[\n+ ngmlr -t \\${GALAXY_SLOTS:-1} --no-progress --skip-write --output \'$alignments\'\n+ $bam_fix $no_smallinv $no_lowqualitysplit\n+ --reference \'$reference\'\n+ --query \'$query\'\n+ --presets $presets\n+ --min-identity $min_identity\n+ --min-residues $min_residues\n+ --match $match\n+ --mismatch $mismatch\n+ --gap-open $gap_open\n+ --gap-extend-max $gap_extend_max\n+ --gap-extend-min $gap_extend_min\n+ --gap-decay $gap_decay\n+ --kmer-length $kmer_length\n+ --kmer-skip $kmer_skip\n+ --bin-size $bin_size\n+ --max-segments $max_segments\n+ --subread-length $subread_length\n+ --subread-corridor $subread_corridor\n+\n+ #if str($sam_header.header_data) == \'yes\':\n+ #if $sam_header.rg_id:\n+ --rg-id \'$sam_header.rg_id\'\n+ #end if\n+ #if $sam_header.rg_sm:\n+ --rg-sm \'$sam_header.rg_sm\'\n+ #end if\n+ #if $sam_header.rg_lb:\n+ --rg-lb \'$sam_header.rg_lb\'\n+ #end if\n+ #if $sam_header.rg_pl:\n+ --rg-pl \'$sam_header.rg_pl\'\n+ #end if\n+ #if $sam_header.rg_ds:\n+ --rg-ds \'$sam_header.rg_ds\'\n+ #end if\n+ #if $sam_header.rg_dt:\n+ --rg-dt \'$sam_header.rg_dt\'\n+ #end if\n+ #if $sam_header.rg_pu:\n+ --rg-pu \'$sam_header.rg_pu\'\n+ #end if\n+ #if $sam_header.rg_pi:\n+ --rg-pi \'$sam_header.rg_pi\'\n+ #end if\n+ #if $sam_header.rg_pg:\n+ --rg-pg \'$sam_header.rg_pg\'\n+ #end if\n+ #if $sam_header.rg_cn:\n+ --rg-cn \'$sam_header.rg_cn\'\n+ #end if\n+ #if $sam_header.rg_fo:\n+ --rg-fo \'$sam_header.rg_fo\'\n+ #end if\n+ #if $sam_header.rg_ks:\n+ --rg-ks \'$sam_header.rg_ks\'\n+ #end if\n+ #end if\n+ ]]>\n+ </command>\n+ <inputs>\n+ <param argument="--reference" type="data" format="fasta,fastq,fasta.gz,fastq.gz" label="Reference genome" />\n+ <param argument="--query" type="data" format="fasta,fastq,fasta.gz,fastq.gz" label="Reads to align" />\n+ <param argument="--bam-fix" type="boolean" truevalue="--bam-fix" falsevalue="" checked="true" label="Report reads with > 64k CIGAR operations as unmapped" help="Required to be compatible with the BAM format" />\n+ <conditional name="sam_header">\n+ <param name="header_data" type="select" label="SAM Read Group" help="If a field is left blank it will be omitted from the output SAM">\n+ <option value="no">Do not set</option>\n+ <option value="yes">Set values</option>\n+ </param>\n+ <when value="yes">\n+ <param argument="--rg-id" type="text" label="Value for the read group ID field in the SAM/BAM header">\n+ <expand macro="rg_validator" />\n+ </param>\n+ <param '..b'nv" type="boolean" truevalue="--no-smallinv" falsevalue="" label="Don\'t detect small inversions" />\n+ <param argument="--no-lowqualitysplit" type="boolean" truevalue="--no-lowqualitysplit" falsevalue="" label="Split alignments with poor quality" />\n+ <param argument="--match" type="float" value="2" label="Match score" />\n+ <param argument="--mismatch" type="float" value="-5" label="Mismatch score" />\n+ <param argument="--gap-open" type="float" value="-5" label="Gap open score" />\n+ <param argument="--gap-extend-max" type="float" value="-5" label="Gap open extend max" />\n+ <param argument="--gap-extend-min" type="float" value="-1" label="Gap open extend min" />\n+ <param argument="--gap-decay" type="float" value="0.15" label="Gap extend decay" />\n+ <param argument="--kmer-length" type="integer" min="10" max="15" value="13" label="K-mer length in bases" />\n+ <param argument="--kmer-skip" type="integer" value="2" label="Number of k-mers to skip when building the lookup table from the reference" />\n+ <param argument="--bin-size" type="integer" value="4" label="Sets the size of the grid used during candidate search" />\n+ <param argument="--max-segments" type="integer" value="1" label="Max number of segments allowed for a read per kb" />\n+ <param argument="--subread-length" type="integer" value="256" label="Length of fragments reads are split into" />\n+ <param argument="--subread-corridor" type="integer" value="40" label="Length of corridor sub-reads are aligned with" />\n+ </inputs>\n+ <outputs>\n+ <data format="sam" name="alignments" label="${tool.name} on ${on_string} (Alignments)"/>\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="reference" value="ngmlr-ref1.fa" />\n+ <param name="query" value="ngmlr-in1.fa" />\n+ <output name="alignments" file="ngmlr-out1.sam" lines_diff="2" />\n+ </test>\n+ <test>\n+ <param name="reference" value="ngmlr-ref2.fa" />\n+ <param name="query" value="ngmlr-in2.fa" />\n+ <output name="alignments" file="ngmlr-out2.sam" lines_diff="2" />\n+ </test>\n+ <test>\n+ <param name="reference" value="ngmlr-ref3.fa.gz" />\n+ <param name="query" value="ngmlr-in3.fa.gz" />\n+ <param name="min_residues" value="0.01" />\n+ <output name="alignments" file="ngmlr-out3.sam" lines_diff="2" />\n+ </test>\n+ <test>\n+ <param name="reference" value="ngmlr-ref3.fa.gz" />\n+ <param name="query" value="ngmlr-in3.fa.gz" />\n+ <output name="alignments" file="ngmlr-out4.sam" lines_diff="2" />\n+ </test>\n+ </tests>\n+ <help>\n+ <![CDATA[\n+CoNvex Gap-cost alignMents for Long Reads (ngmlr) is a long-read mapper designed to sensitively align PacBilo or Oxford Nanopore to (large) reference genomes. It was designed to quickly and correctly align the reads, including those spanning (complex) structural variations. Ngmlr uses an SV aware k-mer search to find approximate mapping locations for a read and then a banded Smith-Waterman alignment algorithm to compute the final alignment. Ngmlr uses a convex gap cost model that penalizes gap extensions for longer gaps less than for shorter ones to compute precise alignments. The gap model allows ngmlr to account for both the sequencing error and real genomic variations at the same time and makes it especially effective at more precisely identifying the position of breakpoints stemming from structural variations. The k-mer search helps to detect and split reads that cannot be aligned linearly, enabling ngmlr to reliably align reads to a wide range of different structural variations including nested SVs (e.g. inversions flanked by deletions).\n+ ]]>\n+ </help>\n+ <citations>\n+ <citation type="doi">10.1038/s41592-018-0001-7</citation>\n+ </citations>\n+</tool>\n\\ No newline at end of file\n' |
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| diff -r 000000000000 -r 95e4757d8da7 test-data/ngmlr-in1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ngmlr-in1.fa Thu Oct 29 15:43:54 2020 +0000 |
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| b'@@ -0,0 +1,6 @@\n+>m140612_020550_42156_c100652082550000001823118110071460_s1_p0/49/0_11124>m140612_020550_42156_c100652082550000001823118110071460_s1_p0/66/1019_13505>m140612_020550_42156_c100652082550000001823118110071460_s1_p0/66/13545_26663>m140612_020550_42156_c100652082550000001823118110071460_s1_p0/66/26699_39808\n+AAAATATCAGTAAAATCAGATTGACCTCAAACCCTGTATCTTTCAAAAAAGACATAATTTTGTTTTTCAAGCATTGTTATTAGGTATAGTAAAAATGATTTTTTTTCTTTGTTTTTTTGTTTTGAGACAGAGTCTTTCTCACTCTGTTGCCCAGGCTGGAGTGCAGTGGCGTGATCTTGGCTCACTGCAACCTCCACCTCCCAGGTTCAAGCAATTCTCTTGCCTCAGCCTCCCCAGTAGCTGGGATTACAGGTTTGTGCCACCACACCCAGTTAATCTTCATATTTTTGTAGAGAAACGGTTTTGCTATGTTGGCCAGGCTGGTCTCAAACTCCTGACCTCAAGTGATCTGCCCACGTAGGCCTCCCAAAGTGCTGGGATTACAGGTGTGAGCCACCATGCCCAGTCTATAGGTTATATCTCCTTAATGTTACAAATTGATGAAGATTAAGTAAATAAACCTCAGCAATGACTAATACATATTTTTAAACATCTACTTTTGCTTCTCATAATCACTGAGCATCCATTTGAGCTTTATTCTTCTTTTCTTCCTTTTTTTGATAATGCTGGCAGACTTGATGAACCAATAGCATCTGACCTTCACAAACTAGGCAGAGTTTCAAAATAAGGTGACTCGTTACATTTGTTTGGATTACTTTTTGAATCCCCACATTTTCTCACGTTGGCACAATTTTGCTTCAAGTGCATCATGGAATAGATGAGACAACAGGAAGCGATAGGCTTTCCCTATTCAGTGAGTCAGGCAGTAACCAAGAGATTAATGTGAATGAATTCAGGGCTTGTGAAGGCATCATTTCTCATCAAATGGAACTGTACCCTGCTGGACGGAAGTCTGAATATGTGTGATCTAATGCAGAGGTTCCAACTGATGTGACCCACAATGTTGTCACCACCACCTCCCTCCTTGTCCTCGCTAATGACCTAAGGTGTGTCCACCATGGAAAAATCTTTCTGTTACCAGAAACGGATCCCCATCCAGACTCTAAGAGAGGGTTCTTGGACCTTGTGCAAGAAAGAATTCAGGGCAAGTCCATAGAGCAAAGTGAAAGCAAATTTATTAAGAAAGTAGAGGAATAAAGAATGGGGGCTGGGCGCGGTGGCTCATGCCTGTAATCCCAGCACTTGGGAGGACGAGGCAAGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACAGTGAAACCCTGTCTCTACCAAAAATACAAAAAAGTTAGCCGGGCGTGGTGGCGGGCACCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCATGAACCCGGGAGGTGGAGGTCGCAGTGAGCTGAGATCATGCCACTGCACTCTAGCCTCTAGCCTGGGTGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAAAAAGAATGGCTATTCCATAGCTAGAGCAGCCTTGAGAACTGCTGGTTGGCCACTTTTATGGTATTTTCTTGATTATGTGCTAAACAAGAGGTGGATTATTCATGAGTTTTCCAGGAAAGGGGTGAGCTATTCCCAGAACTGAGGGTTCCCCCCATTTTAGACCATATAGGATGATTCCCTACATTGCCATGGCATTTGTAAACTGTCATGGTGCTGGTGGAAGTGTCTTTTAGCATGCTAATATATTATAATTAACATCTAATGAGCATTGAGCACAACCAACAGTGACTTTCATCTCCATTTTCATTTTGGTGAGATTTAGCCAGCTTCTTTACAGCAAACCGCTTTGTCAGCAAGGTCTTTGGGACCTGTATTTTTGGCTGACCTCCTATTTTATCCTGTGACTAAAAATGCCCAGCCTCCTTGGAAGGCAACCCCATAGGTCTTAGCCTCATTTTACCTAGCCCCTATGCAAGATAGAGTTGCTCTGGTTCCAAAGCCTCTGAAATTTCATGTCTAATTGATGATCCCAAGATATTCAACCGTGTGTTCTGTGTCCTGGATGCTCCCCCTTCACCTTTGGCTGCCAATGCTGAGAGGCAGAAATAGGAGAGAATAGGCTCTGGGGGTCTGCTGGGCATTCATTCACGGAAACTGGAAGGATGGCTGGTCCTCTAAGGACACCAATTCTGGTCCACAGGCCAGACCTGCTAGCCCTTACCTCCTGTGATGGTTACTTTCAGGTGTTAACTGACTGGATAGCTGGTTAAGCACCATTTCCGGGTGTGTCTGTGAAAGTATGTTTGTGTGCGAATCCGGGGACTGACGGGGGAAGATCGGCTCTCATTGTGGGTGGGCATCATCCAATCAGCAGGGTGCCTAGATAGGACAAAAAGGCAGAGGAAAGGTGAATTTGTTTTTCCAAAAAGGATATTCTGGAACTGGGATGTCTCTTTTCTCCTGTCCTTGGACATCAGAACTCCAGGGTCTTAGGCCTTTGAACTTGGGAACTTGCGCCAGCAGACCCCTGGGCTCTCAGGCCTTCAGCCTCAGACTGAGAGTCACATCATGAACTTTCCTGGTTGTGAGGCCTTCAGCCTTGGACAGCTATGCTGCTGGCTCCCCTGGTTCTCCAGCTTGCAGAAAGCCTATCATGGGACTTCTCAGGCTCCGTAATTGCATAAGCCAATCAATTCCCTTAATAAATCCTCTCTCTCGTATACCTATCTATACCTCTCTACATATTAATATATCCTATTTGTTCTGTCTCTGGAGAACTCTTAACTAATATACTTCCATTACGTGGGAATTTCCCAGATGCTGAATTGAGGAAAATGACATTTTTTTTAACGTTACTGTTGGTTACCTCCCTATATAGTCAGTTCTTTTGCATCTGTTTGTTTGGATCAGCAGAAGGCAACAGTGAGACCCCACCCAATATCTTCTCTTCTCTCTAGAAAGTACTCTGAACATATAATGCTGTGAACATGGCAGGTCTTATCATGTTTTCAAGATGATGAGATATGTATTGCATATTAAATATTCATACCTGGATATTAAATACTCAGGTTTTTAAAAAATCTTATAACCATTCTAACTGACCATGATCCCAGATGGAACCCCTGCCCGCGTCATTGCTTTTGTCTCTGCCACCTGGCTGCCCCTCTAGACAGCTTCCTTTCCTTCCTGGGCTGCTCCCAGGCAACTCAAAAAACTCAACTTCCTCCCCCAAAACTCAAATTCTTACTTTTTACGTAGAGCAAATGAAGTCTGTCTCAGCTTTCTTGTGAAGGAAAAGCTGCTTCAGTCAGTTGTGTTTTTAAATAACACCCCTTCCCACTTTGTGTAACAGAATGTTTTAGAAGCTTATGCTTAAAAATTTTTTTTCAGCCACAAATTGAGGCAGACTCCTTTGATCAAGGTATTTTGTATTGGCTGAAAGTGTGCTTCTGTGGAGGGCTGGTGCAGGGAGCTGTAATTGAGAGAGTGGGAGGAGTAGCCAGGAAGGAAACTGTTGATGAGCATGACTGTATGGGGGGGTCAGCCCAGCTGGAAAAAGGCCAGGACTTATGGAGAAAGGGCATGTGAGGCAGAGAGACGAGGGGGGAGTTTATTGGCTTCTACTGAGTTACTGAATGTTCTTTCTTCTTAGATCTATAAGAAAAATTAAGTAATAAATCCTAAAAAGGCAAATGACAAAATTTACATTCTTTATTTTTCAAAAAGAACTTAGAAAACAAGGACAAGAAGGATATTTTTAAA'..b'118110071460_s1_p0/157668/1089_6689\n+AAAATATCAGTAAAATCAGATTGACCTCAAACCCTGTATCTTTCAAAAAAGACATAATTTTGTTTTTCAAGCATTGTTATTAGGTATAGTAAAAATGATTTTTTTTCTTTGTTTTTTTGTTTTGAGACAGAGTCTTTCTCACTCTGTTGCCCAGGCTGGAGTGCAGTGGCGTGATCTTGGCTCACTGCAACCTCCACCTCCCAGGTTCAAGCAATTCTCTTGCCTCAGCCTCCCCAGTAGCTGGGATTACAGGTTTGTGCCACCACACCCAGTTAATCTTCATATTTTTGTAGAGAAACGGTTTTGCTATGTTGGCCAGGCTGGTCTCAAACTCCTGACCTCAAGTGATCTGCCCACGTAGGCCTCCCAAAGTGCTGGGATTACAGGTGTGAGCCACCATGCCCAGTCTATAGGTTATATCTCCTTAATGTTACAAATTGATGAAGATTAAGTAAATAAACCTCAGCAATGACTAATACATATTTTTAAACATCTACTTTTGCTTCTCATAATCACTGAGCATCCATTTGAGCTTTATTCTTCTTTTCTTCCTTTTTTTGATAATGCTGGCAGACTTGATGAACCAATAGCATCTGACCTTCACAAACTAGGCAGAGTTTCAAAATAAGGTGACTCGTTACATTTGTTTGGATTACTTTTTGAATCCCCACATTTTCTCACGTTGGCACAATTTTGCTTCAAGTGCATCATGGAATAGATGAGACAACAGGAAGCGATAGGCTTTCCCTATTCAGTGAGTCAGGCAGTAACCAAGAGATTAATGTGAATGAATTCAGGGCTTGTGAAGGCATCATTTCTCATCAAATGGAACTGTACCCTGCTGGACGGAAGTCTGAATATGTGTGATCTAATGCAGAGGTTCCAACTGATGTGACCCACAATGTTGTCACCACCACCTCCCTCCTTGTCCTCGCTAATGACCTAAGGTGTGTCCACCATGGAAAAATCTTTCTGTTACCAGAAACGGATCCCCATCCAGACTCTAAGAGAGGGTTCTTGGACCTTGTGCAAGAAAGAATTCAGGGCAAGTCCATAGAGCAAAGTGAAAGCAAATTTATTAAGAAAGTAGAGGAATAAAGAATGGGGGCTGGGCGCGGTGGCTCATGCCTGTAATCCCAGCACTTGGGAGGACGAGGCAAGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACAGTGAAACCCTGTCTCTACCAAAAATACAAAAAAGTTAGCCGGGCGTGGTGGCGGGCACCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCATGAACCCGGGAGGTGGAGGTCGCAGTGAGCTGAGATCATGCCACTGCACTCTAGCCTCTAGCCTGGGTGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAAAAAGAATGGCTATTCCATAGCTAGAGCAGCCTTGAGAACTGCTGGTTGGCCACTTTTATGGTATTTTCTTGATTATGTGCTAAACAAGAGGTGGATTATTCATGAGTTTTCCAGGAAAGGGGTGAGCTATTCCCAGAACTGAGGGTTCCCCCCATTTTAGACCATATAGGATGATTCCCTACATTGCCATGGCATTTGTAAACTGTCATGGTGCTGGTGGAAGTGTCTTTTAGCATGCTAATATATTATAATTAACATCTAATGAGCATTGAGCACAACCAACAGTGACTTTCATCTCCATTTTCATTTTGGTGAGATTTAGCCAGCTTCTTTACAGCAAACCGCTTTGTCAGCAAGGTCTTTGGGACCTGTATTTTTGGCTGACCTCCTATTTTATCCTGTGACTAAAAATGCCCAGCCTCCTTGGAAGGCAACCCCATAGGTCTTAGCCTCATTTTACCTAGCCCCTATGCAAGATAGAGTTGCTCTGGTTCCAAAGCCTCTGAAATTTCATGTCTAATTGATGATCCCAAGATATTCAACCGTGTGTTCTGTGTCCTGGATGCTCCCCCTTCACCTTTGGCTGCCAATGCTGAGAGGCAGAAATAGGAGAGAATAGGCTCTGGGGGTCTGCTGGGCATTCATTCACGGAAACTGGAAGGATGGCTGGTCCTCTAAGGACACCAATTCTGGTCCACAGGCCAGACCTGCTAGCCCTTACCTCCTGTGATGGTTACTTTCAGGTGTTAACTGACTGGATAGCTGGTTAAGCACCATTTCCGGGTGTGTCTGTGAAAGTATGTTTGTGTGCGAATCCGGGGACTGACGGGGGAAGATCGGCTCTCATTGTGGGTGGGCATCATCCAATCAGCAGGGTGCCTAGATAGGACAAAAAGGCAGAGGAAAGGTGAATTTGTTTTTCCAAAAAGGATATTCTGGAACTGGGATGTCTCTTTTCTCCTGTCCTTGGACATCAGAACTCCAGGGTCTTAGGCCTTTGAACTTGGGAACTTGCGCCAGCAGACCCCTGGGCTCTCAGGCCTTCAGCCTCAGACTGAGAGTCACATCATGAACTTTCCTGGTTGTGAGGCCTTCAGCCTTGGACAGCTATGCTGCTGGCTCCCCTGGTTCTCCAGCTTGCAGAAAGCCTATCATGGGACTTCTCAGGCTCCGTAATTGCATAAGCCAATCAATTCCCTTAATAAATCCTCTCTCTCGTATACCTATCTATACCTCTCTACATATTAATATATCCTATTTGTTCTGTCTCTGGAGAACTCTTAACTAATATACTTCCATTACGTGGGAATTTCCCAGATGCTGAATTGAGGAAAATGACATTTTTTTTAACGTTACTGTTGGTTACCTCCCTATATAGTCAGTTCTTTTGCATCTGTTTGTTTGGATCAGCAGAAGGCAACAGTGAGACCCCACCCAATATCTTCTCTTCTCTCTAGAAAGTACTCTGAACATATAATGCTGTGAACATGGCAGGTCTTATCATGTTTTCAAGATGATGAGATATGTATTGCATATTAAATATTCATACCTGGATATTAAATACTCAGGTTTTTAAAAAATCTTATAACCATTCTAACTGACCATGATCCCAGATGGAACCCCTGCCCGCGTCATTGCTTTTGTCTCTGCCACCTGGCTGCCCCTCTAGACAGCTTCCTTTCCTTCCTGGGCTGCTCCCAGGCAACTCAAAAAACTCAACTTCCTCCCCCAAAACTCAAATTCTTACTTTTTACGTAGAGCAAATGAAGTCTGTCTCAGCTTTCTTGTGAAGGAAAAGCTGCTTCAGTCAGTTGTGTTTTTAAATAACACCCCTTCCCACTTTGTGTAACAGAATGTTTTAGAAGCTTATGCTTAAAAATTTTTTTTCAGCCACAAATTGAGGCAGACTCCTTTGATCAAGGTATTTTGTATTGGCTGAAAGTGTGCTTCTGTGGAGGGCTGGTGCAGGGAGCTGTAATTGAGAGAGTGGGAGGAGTAGCCAGGAAGGAAACTGTTGATGAGCATGACTGTATGGGGGGGTCAGCCCAGCTGGAAAAAGGCCAGGACTTATGGAGAAAGGGCATGTGAGGCAGAGAGACGAGGGGGGAGTTTATTGGCTTCTACTGAGTTACTGAATGTTCTTTCTTCTTAGATCTATAAGAAAAATTAAGTAATAAATCCTAAAAAGGCAAATGACAAAATTTACATTCTTTATTTTTCAAAAAGAACTTAGAAAACAAGGACAAGAAGGATATTTTTAAAATGTAATATAGACCATATTAAACCAATATTATGGTTGACAGTATTTAAGAGAAAAAGACAAATGACTAAAATTGATATTAAAACATTTATTGAGCATTTACTGTGTGTGAGGCATTGGATTTGTTGCCTAACATGAATTAGTTCATTTAAACCTCATAAAAGTCATACAAGGTATATATTCTAATACCCCTATTTAAATAATTAGGAAACTGAGGCAAAAGGAGTTTAAATAAGTTGCCTAATTATTAAGTCTCCT\n\\ No newline at end of file\n' |
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| diff -r 000000000000 -r 95e4757d8da7 test-data/ngmlr-in2.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ngmlr-in2.fa Thu Oct 29 15:43:54 2020 +0000 |
| b |
| b'@@ -0,0 +1,118 @@\n+>100bp\n+GGGGGTCTCCCCCATTGACTTTCAGATGGCCACTTTCTCCTGTGTCTATCACATGGTCTTCGCTCTGTGTACACGTGCCCCTGGTGTCTGTCTCCCTCT\n+>200bp\n+GGGGGTCTCCCCCATTGACTTTCAGATGGCCACTTTCTCCTGTGTCTATCACATGGTCTTCGCTCTGTGTACACGTGCCCCTGGTGTCTGTCTCCCTCT\n+GTGTCCTAATCTTCCCTTCTTATAAAGACACCACGCATATTGGATCAGGGCCTGGGTTAACTTAATTATCTTTTAAAGGCCCTATTTCCAAATATAATC\n+>300bp\n+GGGGGTCTCCCCCATTGACTTTCAGATGGCCACTTTCTCCTGTGTCTATCACATGGTCTTCGCTCTGTGTACACGTGCCCCTGGTGTCTGTCTCCCTCT\n+GTGTCCTAATCTTCCCTTCTTATAAAGACACCACGCATATTGGATCAGGGCCTGGGTTAACTTAATTATCTTTTAAAGGCCCTATTTCCAAATATAATC\n+ACATTCTGAGGTACTGGGAGTGCTTTGACATAAGAATTTTGGAGATACACAATTCATCCCACGACACCATTCATCATTTCTCTTCAGAGAATCAGGTTT\n+>400bp\n+GGGGGTCTCCCCCATTGACTTTCAGATGGCCACTTTCTCCTGTGTCTATCACATGGTCTTCGCTCTGTGTACACGTGCCCCTGGTGTCTGTCTCCCTCT\n+GTGTCCTAATCTTCCCTTCTTATAAAGACACCACGCATATTGGATCAGGGCCTGGGTTAACTTAATTATCTTTTAAAGGCCCTATTTCCAAATATAATC\n+ACATTCTGAGGTACTGGGAGTGCTTTGACATAAGAATTTTGGAGATACACAATTCATCCCACGACACCATTCATCATTTCTCTTCAGAGAATCAGGTTT\n+AATATTTCTATATCTTTCTCCTTACTTCTTGTTTTCTTAATGATTTTGCATAAGACAATTTATTAAAAATATGTTCATATTTTTGACATACAAATTTTC\n+>500bp\n+GGGGGTCTCCCCCATTGACTTTCAGATGGCCACTTTCTCCTGTGTCTATCACATGGTCTTCGCTCTGTGTACACGTGCCCCTGGTGTCTGTCTCCCTCT\n+GTGTCCTAATCTTCCCTTCTTATAAAGACACCACGCATATTGGATCAGGGCCTGGGTTAACTTAATTATCTTTTAAAGGCCCTATTTCCAAATATAATC\n+ACATTCTGAGGTACTGGGAGTGCTTTGACATAAGAATTTTGGAGATACACAATTCATCCCACGACACCATTCATCATTTCTCTTCAGAGAATCAGGTTT\n+AATATTTCTATATCTTTCTCCTTACTTCTTGTTTTCTTAATGATTTTGCATAAGACAATTTATTAAAAATATGTTCATATTTTTGACATACAAATTTTC\n+CTGGGTTTTTATAAATACACAAATTTTTTTTGGTCTCTTGATTCTTTTCAGCTCTGTTATTTTCCAATGATTTCGTATTGTGTGTGATAGAAGCAGAAT\n+>600bp\n+GGGGGTCTCCCCCATTGACTTTCAGATGGCCACTTTCTCCTGTGTCTATCACATGGTCTTCGCTCTGTGTACACGTGCCCCTGGTGTCTGTCTCCCTCT\n+GTGTCCTAATCTTCCCTTCTTATAAAGACACCACGCATATTGGATCAGGGCCTGGGTTAACTTAATTATCTTTTAAAGGCCCTATTTCCAAATATAATC\n+ACATTCTGAGGTACTGGGAGTGCTTTGACATAAGAATTTTGGAGATACACAATTCATCCCACGACACCATTCATCATTTCTCTTCAGAGAATCAGGTTT\n+AATATTTCTATATCTTTCTCCTTACTTCTTGTTTTCTTAATGATTTTGCATAAGACAATTTATTAAAAATATGTTCATATTTTTGACATACAAATTTTC\n+CTGGGTTTTTATAAATACACAAATTTTTTTTGGTCTCTTGATTCTTTTCAGCTCTGTTATTTTCCAATGATTTCGTATTGTGTGTGATAGAAGCAGAAT\n+AGTAAACAAAAGTTCATTCTGGAATTAGATTGCCTGGATTTTGTTATAGTCTCTTCCCACTTACTATCTGAGTAACTTTGAGCTCGTCCCTTCCATTGG\n+>800bp\n+GGGGGTCTCCCCCATTGACTTTCAGATGGCCACTTTCTCCTGTGTCTATCACATGGTCTTCGCTCTGTGTACACGTGCCCCTGGTGTCTGTCTCCCTCT\n+GTGTCCTAATCTTCCCTTCTTATAAAGACACCACGCATATTGGATCAGGGCCTGGGTTAACTTAATTATCTTTTAAAGGCCCTATTTCCAAATATAATC\n+ACATTCTGAGGTACTGGGAGTGCTTTGACATAAGAATTTTGGAGATACACAATTCATCCCACGACACCATTCATCATTTCTCTTCAGAGAATCAGGTTT\n+AATATTTCTATATCTTTCTCCTTACTTCTTGTTTTCTTAATGATTTTGCATAAGACAATTTATTAAAAATATGTTCATATTTTTGACATACAAATTTTC\n+CTGGGTTTTTATAAATACACAAATTTTTTTTGGTCTCTTGATTCTTTTCAGCTCTGTTATTTTCCAATGATTTCGTATTGTGTGTGATAGAAGCAGAAT\n+AGTAAACAAAAGTTCATTCTGGAATTAGATTGCCTGGATTTTGTTATAGTCTCTTCCCACTTACTATCTGAGTAACTTTGAGCTCGTCCCTTCCATTGG\n+TTTCTTCATCCCCTTATACAGGGAAAATAGAACCAACCTTGTAGAGTTGTTGTCAGAATTTAAGTAATATGGGCAAAGCACACAGAACAGTTTCTAAAC\n+CAACATTAAACAACAAATGATTAACACTTAGGAATGACACCTTTAGATAGCTCCATGATTAGTACATAAGAATCATATAAAAGAGTAGGTGTTACCTTT\n+>1000bp\n+GGGGGTCTCCCCCATTGACTTTCAGATGGCCACTTTCTCCTGTGTCTATCACATGGTCTTCGCTCTGTGTACACGTGCCCCTGGTGTCTGTCTCCCTCT\n+GTGTCCTAATCTTCCCTTCTTATAAAGACACCACGCATATTGGATCAGGGCCTGGGTTAACTTAATTATCTTTTAAAGGCCCTATTTCCAAATATAATC\n+ACATTCTGAGGTACTGGGAGTGCTTTGACATAAGAATTTTGGAGATACACAATTCATCCCACGACACCATTCATCATTTCTCTTCAGAGAATCAGGTTT\n+AATATTTCTATATCTTTCTCCTTACTTCTTGTTTTCTTAATGATTTTGCATAAGACAATTTATTAAAAATATGTTCATATTTTTGACATACAAATTTTC\n+CTGGGTTTTTATAAATACACAAATTTTTTTTGGTCTCTTGATTCTTTTCAGCTCTGTTATTTTCCAATGATTTCGTATTGTGTGTGATAGAAGCAGAAT\n+AGTAAACAAAAGTTCATTCTGGAATTAGATTGCCTGGATTTTGTTATAGTCTCTTCCCACTTACTATCTGAGTAACTTTGAGCTCGTCCCTTCCATTGG\n+TTTCTTCATCCCCTTATACAGGGAAAATAGAACCAACCTTGTAGAGTTGTTGTCAGAATTTAAGTAATATGGGCAAAGCACACAGAACAGTTTCTAAAC\n+CAACATTAAACAACAAATGATTAACACTTAGGAATGACACCTTTAGATAGCTCCATGATTAGTACATAAGAATCATATAAAAGAGTAGGTGTTACCTTT\n+AAAATATAAAATATGAAAAGTAAACAAGAGAAGAAGCATAGGTTTTGTGAACAAATCTGTGCTTCTGTAAGAAAGCAGCTAAATAGAAGAAAATACATC\n+AGGCTTTGCCAATCAAAATTGATACTAAACATTTAGCTGTGCAAACTTAGAAAAATAAGCTCTCCTCTCTCAGCTTC'..b'CTTAATTATCTTTTAAAGGCCCTATTTCCAAATATAATC\n+ACATTCTGAGGTACTGGGAGTGCTTTGACATAAGAATTTTGGAGATACACAATTCATCCCACGACACCATTCATCATTTCTCTTCAGAGAATCAGGTTT\n+AATATTTCTATATCTTTCTCCTTACTTCTTGTTTTCTTAATGATTTTGCATAAGACAATTTATTAAAAATATGTTCATATTTTTGACATACAAATTTTC\n+CTGGGTTTTTATAAATACACAAATTTTTTTTGGTCTCTTGATTCTTTTCAGCTCTGTTATTTTCCAATGATTTCGTATTGTGTGTGATAGAAGCAGAAT\n+AGTAAACAAAAGTTCATTCTGGAATTAGATTGCCTGGATTTTGTTATAGTCTCTTCCCACTTACTATCTGAGTAACTTTGAGCTCGTCCCTTCCATTGG\n+TTTCTTCATCCCCTTATACAGGGAAAATAGAACCAACCTTGTAGAGTTGTTGTCAGAATTTAAGTAATATGGGCAAAGCACACAGAACAGTTTCTAAAC\n+CAACATTAAACAACAAATGATTAACACTTAGGAATGACACCTTTAGATAGCTCCATGATTAGTACATAAGAATCATATAAAAGAGTAGGTGTTACCTTT\n+AAAATATAAAATATGAAAAGTAAACAAGAGAAGAAGCATAGGTTTTGTGAACAAATCTGTGCTTCTGTAAGAAAGCAGCTAAATAGAAGAAAATACATC\n+AGGCTTTGCCAATCAAAATTGATACTAAACATTTAGCTGTGCAAACTTAGAAAAATAAGCTCTCCTCTCTCAGCTTCACTTCTGACCTGTAAGACCAAA\n+AGAATAGTTTTCTGTATATCATGGACAATGCTTGTTACATCGATTAAGAAAAAAAGTGTCAGTTTTCTAGTTTCTACTTCTTCTAGGATGTCTGTAAAT\n+TCAAAATGGTTGTCCAGCTCTGTGAAGTTAAAATTTATTCACAAATTCCTATAAACAGATTTGTTTTTTTGCCATGTGTTTCTGCCCAAGACTTTTTAA\n+GTCCTCAGAATGAATCCTGACTTGTTATTGTGGCCACTTTCTATGTTGATGTGCGCAGCACACCATAGTCCATCAAAGTCGTTCCTCTGCAGTTAGTTA\n+ATTCACTGGGGCCACAGGCTACCCACACCAATGGCTACAAGGCTACAGAAATCTAATACATCATCTTCTTTTCACTGTAGCAGAACATCTCTTTTCCTT\n+TTAACTATAATTGCAAAACCTGCATAGAGGGACAAGATTAACAAAAATATGCTCTCCTATCCACTTTAAACAGCCTAAAAAAATGGCTCTCTGCAACAA\n+CATGGACTAATCTGAGAGAACAATTTAAATGTACAACCTTTGTCCTTTCCATTTGGGTGGATTTGGCAACAGATAACCCAATAATCTGATTTCCATGAA\n+GGGTCCAGAATAAAATTCATATTTTGTGCCAGAATAATATTTAGTTTTACACTCGCAAAACTAACAACTGTATTTGGCAATGCAATGGTAAACTAGTTA\n+GAAAAGCCCCCTGCTCTGAAGAACTTAAGAATTGAAATGACTGCGAGATCCAATTTAAGTCAAAATAAGAGTGTGTGTGTGTGGCTGTGTGTGTGTGTG\n+>2200bp\n+GGGGGTCTCCCCCATTGACTTTCAGATGGCCACTTTCTCCTGTGTCTATCACATGGTCTTCGCTCTGTGTACACGTGCCCCTGGTGTCTGTCTCCCTCT\n+GTGTCCTAATCTTCCCTTCTTATAAAGACACCACGCATATTGGATCAGGGCCTGGGTTAACTTAATTATCTTTTAAAGGCCCTATTTCCAAATATAATC\n+ACATTCTGAGGTACTGGGAGTGCTTTGACATAAGAATTTTGGAGATACACAATTCATCCCACGACACCATTCATCATTTCTCTTCAGAGAATCAGGTTT\n+AATATTTCTATATCTTTCTCCTTACTTCTTGTTTTCTTAATGATTTTGCATAAGACAATTTATTAAAAATATGTTCATATTTTTGACATACAAATTTTC\n+CTGGGTTTTTATAAATACACAAATTTTTTTTGGTCTCTTGATTCTTTTCAGCTCTGTTATTTTCCAATGATTTCGTATTGTGTGTGATAGAAGCAGAAT\n+AGTAAACAAAAGTTCATTCTGGAATTAGATTGCCTGGATTTTGTTATAGTCTCTTCCCACTTACTATCTGAGTAACTTTGAGCTCGTCCCTTCCATTGG\n+TTTCTTCATCCCCTTATACAGGGAAAATAGAACCAACCTTGTAGAGTTGTTGTCAGAATTTAAGTAATATGGGCAAAGCACACAGAACAGTTTCTAAAC\n+CAACATTAAACAACAAATGATTAACACTTAGGAATGACACCTTTAGATAGCTCCATGATTAGTACATAAGAATCATATAAAAGAGTAGGTGTTACCTTT\n+AAAATATAAAATATGAAAAGTAAACAAGAGAAGAAGCATAGGTTTTGTGAACAAATCTGTGCTTCTGTAAGAAAGCAGCTAAATAGAAGAAAATACATC\n+AGGCTTTGCCAATCAAAATTGATACTAAACATTTAGCTGTGCAAACTTAGAAAAATAAGCTCTCCTCTCTCAGCTTCACTTCTGACCTGTAAGACCAAA\n+AGAATAGTTTTCTGTATATCATGGACAATGCTTGTTACATCGATTAAGAAAAAAAGTGTCAGTTTTCTAGTTTCTACTTCTTCTAGGATGTCTGTAAAT\n+TCAAAATGGTTGTCCAGCTCTGTGAAGTTAAAATTTATTCACAAATTCCTATAAACAGATTTGTTTTTTTGCCATGTGTTTCTGCCCAAGACTTTTTAA\n+GTCCTCAGAATGAATCCTGACTTGTTATTGTGGCCACTTTCTATGTTGATGTGCGCAGCACACCATAGTCCATCAAAGTCGTTCCTCTGCAGTTAGTTA\n+ATTCACTGGGGCCACAGGCTACCCACACCAATGGCTACAAGGCTACAGAAATCTAATACATCATCTTCTTTTCACTGTAGCAGAACATCTCTTTTCCTT\n+TTAACTATAATTGCAAAACCTGCATAGAGGGACAAGATTAACAAAAATATGCTCTCCTATCCACTTTAAACAGCCTAAAAAAATGGCTCTCTGCAACAA\n+CATGGACTAATCTGAGAGAACAATTTAAATGTACAACCTTTGTCCTTTCCATTTGGGTGGATTTGGCAACAGATAACCCAATAATCTGATTTCCATGAA\n+GGGTCCAGAATAAAATTCATATTTTGTGCCAGAATAATATTTAGTTTTACACTCGCAAAACTAACAACTGTATTTGGCAATGCAATGGTAAACTAGTTA\n+GAAAAGCCCCCTGCTCTGAAGAACTTAAGAATTGAAATGACTGCGAGATCCAATTTAAGTCAAAATAAGAGTGTGTGTGTGTGGCTGTGTGTGTGTGTG\n+TGTGTATGAATAAAGGCAGGTAATATTCCATGTCAAATTCTGTATAGAATGTGAAAGAGAAAACAGATTGAGAATAGATGAACTTGGCAATCAGAAGAT\n+TTACAGTAGAATAGAGGAAAGATTATAGTAGTATAGTTTGTGAGTAGTGGGTATTACTATGTTTGAAATAAAAAAGCTATTTTTAGTAATTTAATAAAA\n+TATTTAGTTGATAGTACTTTTATTTTTGATCGATAAATATAAATGCATTGTTTATATTTTGTGAAAACACACATGGAAGATATTACCCAGGTGTGCTGA\n+ATGTTTCCCATTCCTCCCTACCTTACATCCCTGTTGACCTCCAGGAGGCTATCCAGGAAGCTGATCTCAGTAAACTGCATATGCATACAGAGTGTTCAT\n+philipp_@kronig(4639.ngmlr_test:0):/project/ngs/philipp/sv-paper/testcases/hs37d5$\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 95e4757d8da7 test-data/ngmlr-in3.fa.gz |
| b |
| Binary file test-data/ngmlr-in3.fa.gz has changed |
| b |
| diff -r 000000000000 -r 95e4757d8da7 test-data/ngmlr-out1.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ngmlr-out1.sam Thu Oct 29 15:43:54 2020 +0000 |
| b |
| b'@@ -0,0 +1,6 @@\n+@HD\tVN:1.0\tSO:unsorted\n+@SQ\tSN:6\tLN:139652\n+@PG\tID:ngmlr\tPN:nextgenmap-lr\tVN:0.2.7\tCL:ngmlr -t 1 --no-progress --skip-write --output /tmp/tmp_8wdkhyd/files/4/1/0/dataset_4109bb35-5e9e-46cd-b1cd-35cf360f9fcb.dat --bam-fix --reference /tmp/tmp_8wdkhyd/files/a/5/6/dataset_a566d2ad-2be8-4f54-9c13-a173eb2641e2.dat --query /tmp/tmp_8wdkhyd/files/e/0/e/dataset_e0ea1371-ce67-4ad5-9b01-95f81aa8e928.dat --presets pacbio --min-identity 0.65 --min-residues 0.25 --match 2.0 --mismatch -5.0 --gap-open -5.0 --gap-extend-max -5.0 --gap-extend-min -1.0 --gap-decay 0.15 --kmer-length 13 --kmer-skip 2 --bin-size 4 --max-segments 1 --subread-length 256 --subread-corridor 40\n+m140612_020550_42156_c100652082550000001823118110071460_s1_p0/49/0_11124>m140612_020550_42156_c100652082550000001823118110071460_s1_p0/66/1019_13505>m140612_020550_42156_c100652082550000001823118110071460_s1_p0/66/13545_26663>m140612_020550_42156_c1\t0\t6\t112357\t60\t3929M4S\t*\t0\t0\tAAAATATCAGTAAAATCAGATTGACCTCAAACCCTGTATCTTTCAAAAAAGACATAATTTTGTTTTTCAAGCATTGTTATTAGGTATAGTAAAAATGATTTTTTTTCTTTGTTTTTTTGTTTTGAGACAGAGTCTTTCTCACTCTGTTGCCCAGGCTGGAGTGCAGTGGCGTGATCTTGGCTCACTGCAACCTCCACCTCCCAGGTTCAAGCAATTCTCTTGCCTCAGCCTCCCCAGTAGCTGGGATTACAGGTTTGTGCCACCACACCCAGTTAATCTTCATATTTTTGTAGAGAAACGGTTTTGCTATGTTGGCCAGGCTGGTCTCAAACTCCTGACCTCAAGTGATCTGCCCACGTAGGCCTCCCAAAGTGCTGGGATTACAGGTGTGAGCCACCATGCCCAGTCTATAGGTTATATCTCCTTAATGTTACAAATTGATGAAGATTAAGTAAATAAACCTCAGCAATGACTAATACATATTTTTAAACATCTACTTTTGCTTCTCATAATCACTGAGCATCCATTTGAGCTTTATTCTTCTTTTCTTCCTTTTTTTGATAATGCTGGCAGACTTGATGAACCAATAGCATCTGACCTTCACAAACTAGGCAGAGTTTCAAAATAAGGTGACTCGTTACATTTGTTTGGATTACTTTTTGAATCCCCACATTTTCTCACGTTGGCACAATTTTGCTTCAAGTGCATCATGGAATAGATGAGACAACAGGAAGCGATAGGCTTTCCCTATTCAGTGAGTCAGGCAGTAACCAAGAGATTAATGTGAATGAATTCAGGGCTTGTGAAGGCATCATTTCTCATCAAATGGAACTGTACCCTGCTGGACGGAAGTCTGAATATGTGTGATCTAATGCAGAGGTTCCAACTGATGTGACCCACAATGTTGTCACCACCACCTCCCTCCTTGTCCTCGCTAATGACCTAAGGTGTGTCCACCATGGAAAAATCTTTCTGTTACCAGAAACGGATCCCCATCCAGACTCTAAGAGAGGGTTCTTGGACCTTGTGCAAGAAAGAATTCAGGGCAAGTCCATAGAGCAAAGTGAAAGCAAATTTATTAAGAAAGTAGAGGAATAAAGAATGGGGGCTGGGCGCGGTGGCTCATGCCTGTAATCCCAGCACTTGGGAGGACGAGGCAAGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACAGTGAAACCCTGTCTCTACCAAAAATACAAAAAAGTTAGCCGGGCGTGGTGGCGGGCACCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCATGAACCCGGGAGGTGGAGGTCGCAGTGAGCTGAGATCATGCCACTGCACTCTAGCCTCTAGCCTGGGTGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAAAAAGAATGGCTATTCCATAGCTAGAGCAGCCTTGAGAACTGCTGGTTGGCCACTTTTATGGTATTTTCTTGATTATGTGCTAAACAAGAGGTGGATTATTCATGAGTTTTCCAGGAAAGGGGTGAGCTATTCCCAGAACTGAGGGTTCCCCCCATTTTAGACCATATAGGATGATTCCCTACATTGCCATGGCATTTGTAAACTGTCATGGTGCTGGTGGAAGTGTCTTTTAGCATGCTAATATATTATAATTAACATCTAATGAGCATTGAGCACAACCAACAGTGACTTTCATCTCCATTTTCATTTTGGTGAGATTTAGCCAGCTTCTTTACAGCAAACCGCTTTGTCAGCAAGGTCTTTGGGACCTGTATTTTTGGCTGACCTCCTATTTTATCCTGTGACTAAAAATGCCCAGCCTCCTTGGAAGGCAACCCCATAGGTCTTAGCCTCATTTTACCTAGCCCCTATGCAAGATAGAGTTGCTCTGGTTCCAAAGCCTCTGAAATTTCATGTCTAATTGATGATCCCAAGATATTCAACCGTGTGTTCTGTGTCCTGGATGCTCCCCCTTCACCTTTGGCTGCCAATGCTGAGAGGCAGAAATAGGAGAGAATAGGCTCTGGGGGTCTGCTGGGCATTCATTCACGGAAACTGGAAGGATGGCTGGTCCTCTAAGGACACCAATTCTGGTCCACAGGCCAGACCTGCTAGCCCTTACCTCCTGTGATGGTTACTTTCAGGTGTTAACTGACTGGATAGCTGGTTAAGCACCATTTCCGGGTGTGTCTGTGAAAGTATGTTTGTGTGCGAATCCGGGGACTGACGGGGGAAGATCGGCTCTCATTGTGGGTGGGCATCATCCAATCAGCAGGGTGCCTAGATAGGACAAAAAGGCAGAGGAAAGGTGAATTTGTTTTTCCAAAAAGGATATTCTGGAACTGGGATGTCTCTTTTCTCCTGTCCTTGGACATCAGAACTCCAGGGTCTTAGGCCTTTGAACTTGGGAACTTGCGCCAGCAGACCCCTGGGCTCTCAGGCCTTCAGCCTCAGACTGAGAGTCACATCATGAACTTTCCTGGTTGTGAGGCCTTCAGCCTTGGACAGCTATGCTGCTGGCTCCCCTGGTTCTCCAGCTTGCAGAAAGCCTATCATGGGACTTCTCAGGCTCCGTAATTGCATAAGCCAATCAATTCCCTTAATAAATCCTCTCTCTCGTATACCTATCTATACCTCTCTACATATTAATATATCCTATTTGTTCTGTCTCTGGAGAACTCTTAACTAATATACTTCCATTACGTGGGAATTTCCCAGATGCTGAATTGAGGAAAATGACATTTTTTTTAACGTTACTGTTGGTTACCTCCCTATATAGTCAGTTCTTTTGCATCTGTTTGTTTGGATCAGCAGAAGGCAACAGTGAGACCCCACCCAATATCTTCTCTTCTCTCTAGAAAGTACTCTGAACATATAATGCTGTGAACATGGCAGGTCTTATCATGTTTTCAAGATGATGAGATATGTATTGCATATTAAATATTCATACCTGGATATTAAATACTCAGGTTTTTAAAAAATCTTATAACCATTCTAACTGACCATGATCCCAGATGGAACCCCTG'..b'TCTTTCAAAAAAGACATAATTTTGTTTTTCAAGCATTGTTATTAGGTATAGTAAAAATGATTTTTTTTCTTTGTTTTTTTGTTTTGAGACAGAGTCTTTCTCACTCTGTTGCCCAGGCTGGAGTGCAGTGGCGTGATCTTGGCTCACTGCAACCTCCACCTCCCAGGTTCAAGCAATTCTCTTGCCTCAGCCTCCCCAGTAGCTGGGATTACAGGTTTGTGCCACCACACCCAGTTAATCTTCATATTTTTGTAGAGAAACGGTTTTGCTATGTTGGCCAGGCTGGTCTCAAACTCCTGACCTCAAGTGATCTGCCCACGTAGGCCTCCCAAAGTGCTGGGATTACAGGTGTGAGCCACCATGCCCAGTCTATAGGTTATATCTCCTTAATGTTACAAATTGATGAAGATTAAGTAAATAAACCTCAGCAATGACTAATACATATTTTTAAACATCTACTTTTGCTTCTCATAATCACTGAGCATCCATTTGAGCTTTATTCTTCTTTTCTTCCTTTTTTTGATAATGCTGGCAGACTTGATGAACCAATAGCATCTGACCTTCACAAACTAGGCAGAGTTTCAAAATAAGGTGACTCGTTACATTTGTTTGGATTACTTTTTGAATCCCCACATTTTCTCACGTTGGCACAATTTTGCTTCAAGTGCATCATGGAATAGATGAGACAACAGGAAGCGATAGGCTTTCCCTATTCAGTGAGTCAGGCAGTAACCAAGAGATTAATGTGAATGAATTCAGGGCTTGTGAAGGCATCATTTCTCATCAAATGGAACTGTACCCTGCTGGACGGAAGTCTGAATATGTGTGATCTAATGCAGAGGTTCCAACTGATGTGACCCACAATGTTGTCACCACCACCTCCCTCCTTGTCCTCGCTAATGACCTAAGGTGTGTCCACCATGGAAAAATCTTTCTGTTACCAGAAACGGATCCCCATCCAGACTCTAAGAGAGGGTTCTTGGACCTTGTGCAAGAAAGAATTCAGGGCAAGTCCATAGAGCAAAGTGAAAGCAAATTTATTAAGAAAGTAGAGGAATAAAGAATGGGGGCTGGGCGCGGTGGCTCATGCCTGTAATCCCAGCACTTGGGAGGACGAGGCAAGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACAGTGAAACCCTGTCTCTACCAAAAATACAAAAAAGTTAGCCGGGCGTGGTGGCGGGCACCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCATGAACCCGGGAGGTGGAGGTCGCAGTGAGCTGAGATCATGCCACTGCACTCTAGCCTCTAGCCTGGGTGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAAAAAGAATGGCTATTCCATAGCTAGAGCAGCCTTGAGAACTGCTGGTTGGCCACTTTTATGGTATTTTCTTGATTATGTGCTAAACAAGAGGTGGATTATTCATGAGTTTTCCAGGAAAGGGGTGAGCTATTCCCAGAACTGAGGGTTCCCCCCATTTTAGACCATATAGGATGATTCCCTACATTGCCATGGCATTTGTAAACTGTCATGGTGCTGGTGGAAGTGTCTTTTAGCATGCTAATATATTATAATTAACATCTAATGAGCATTGAGCACAACCAACAGTGACTTTCATCTCCATTTTCATTTTGGTGAGATTTAGCCAGCTTCTTTACAGCAAACCGCTTTGTCAGCAAGGTCTTTGGGACCTGTATTTTTGGCTGACCTCCTATTTTATCCTGTGACTAAAAATGCCCAGCCTCCTTGGAAGGCAACCCCATAGGTCTTAGCCTCATTTTACCTAGCCCCTATGCAAGATAGAGTTGCTCTGGTTCCAAAGCCTCTGAAATTTCATGTCTAATTGATGATCCCAAGATATTCAACCGTGTGTTCTGTGTCCTGGATGCTCCCCCTTCACCTTTGGCTGCCAATGCTGAGAGGCAGAAATAGGAGAGAATAGGCTCTGGGGGTCTGCTGGGCATTCATTCACGGAAACTGGAAGGATGGCTGGTCCTCTAAGGACACCAATTCTGGTCCACAGGCCAGACCTGCTAGCCCTTACCTCCTGTGATGGTTACTTTCAGGTGTTAACTGACTGGATAGCTGGTTAAGCACCATTTCCGGGTGTGTCTGTGAAAGTATGTTTGTGTGCGAATCCGGGGACTGACGGGGGAAGATCGGCTCTCATTGTGGGTGGGCATCATCCAATCAGCAGGGTGCCTAGATAGGACAAAAAGGCAGAGGAAAGGTGAATTTGTTTTTCCAAAAAGGATATTCTGGAACTGGGATGTCTCTTTTCTCCTGTCCTTGGACATCAGAACTCCAGGGTCTTAGGCCTTTGAACTTGGGAACTTGCGCCAGCAGACCCCTGGGCTCTCAGGCCTTCAGCCTCAGACTGAGAGTCACATCATGAACTTTCCTGGTTGTGAGGCCTTCAGCCTTGGACAGCTATGCTGCTGGCTCCCCTGGTTCTCCAGCTTGCAGAAAGCCTATCATGGGACTTCTCAGGCTCCGTAATTGCATAAGCCAATCAATTCCCTTAATAAATCCTCTCTCTCGTATACCTATCTATACCTCTCTACATATTAATATATCCTATTTGTTCTGTCTCTGGAGAACTCTTAACTAATATACTTCCATTACGTGGGAATTTCCCAGATGCTGAATTGAGGAAAATGACATTTTTTTTAACGTTACTGTTGGTTACCTCCCTATATAGTCAGTTCTTTTGCATCTGTTTGTTTGGATCAGCAGAAGGCAACAGTGAGACCCCACCCAATATCTTCTCTTCTCTCTAGAAAGTACTCTGAACATATAATGCTGTGAACATGGCAGGTCTTATCATGTTTTCAAGATGATGAGATATGTATTGCATATTAAATATTCATACCTGGATATTAAATACTCAGGTTTTTAAAAAATCTTATAACCATTCTAACTGACCATGATCCCAGATGGAACCCCTGCCCGCGTCATTGCTTTTGTCTCTGCCACCTGGCTGCCCCTCTAGACAGCTTCCTTTCCTTCCTGGGCTGCTCCCAGGCAACTCAAAAAACTCAACTTCCTCCCCCAAAACTCAAATTCTTACTTTTTACGTAGAGCAAATGAAGTCTGTCTCAGCTTTCTTGTGAAGGAAAAGCTGCTTCAGTCAGTTGTGTTTTTAAATAACACCCCTTCCCACTTTGTGTAACAGAATGTTTTAGAAGCTTATGCTTAAAAATTTTTTTTCAGCCACAAATTGAGGCAGACTCCTTTGATCAAGGTATTTTGTATTGGCTGAAAGTGTGCTTCTGTGGAGGGCTGGTGCAGGGAGCTGTAATTGAGAGAGTGGGAGGAGTAGCCAGGAAGGAAACTGTTGATGAGCATGACTGTATGGGGGGGTCAGCCCAGCTGGAAAAAGGCCAGGACTTATGGAGAAAGGGCATGTGAGGCAGAGAGACGAGGGGGGAGTTTATTGGCTTCTACTGAGTTACTGAATGTTCTTTCTTCTTAGATCTATAAGAAAAATTAAGTAATAAATCCTAAAAAGGCAAATGACAAAATTTACATTCTTTATTTTTCAAAAAGAACTTAGAAAACAAGGACAAGAAGGATATTTTTAAAATGTAATATAGACCATATTAAACCAATATTATGGTTGACAGTATTTAAGAGAAAAAGACAAATGACTAAAATTGATATTAAAACATTTATTGAGCATTTACTGTGTGTGAGGCATTGGATTTGTTGCCTAACATGAATTAGTTCATTTAAACCTCATAAAAGTCATACAAGGTATATATTCTAATACCCCTATTTAAATAATTAGGAAACTGAGGCAAAAGGAGTTTAAATAAGTTGCCTAATTATTAAGTCTCCT\t*\tAS:i:7858\tNM:i:0\tXI:f:1\tXS:i:0\tXE:i:7858\tXR:i:3929\tMD:Z:3929\tSV:i:2\tQS:i:0\tQE:i:3929\tCV:f:99.898300\t\n' |
| b |
| diff -r 000000000000 -r 95e4757d8da7 test-data/ngmlr-out2.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ngmlr-out2.sam Thu Oct 29 15:43:54 2020 +0000 |
| b |
| b'@@ -0,0 +1,15 @@\n+@HD\tVN:1.0\tSO:unsorted\n+@SQ\tSN:chr21\tLN:19615\n+@PG\tID:ngmlr\tPN:nextgenmap-lr\tVN:0.2.7\tCL:ngmlr -t 1 --no-progress --skip-write --output /tmp/tmp_8wdkhyd/files/b/8/1/dataset_b819ac8e-dd9f-4a2c-afbc-2ea046adbd9a.dat --bam-fix --reference /tmp/tmp_8wdkhyd/files/1/0/c/dataset_10c1d605-41d9-418a-a38f-e137f80a6117.dat --query /tmp/tmp_8wdkhyd/files/7/8/b/dataset_78bfa92a-ac57-4081-95ad-11d77b252303.dat --presets pacbio --min-identity 0.65 --min-residues 0.25 --match 2.0 --mismatch -5.0 --gap-open -5.0 --gap-extend-max -5.0 --gap-extend-min -1.0 --gap-decay 0.15 --kmer-length 13 --kmer-skip 2 --bin-size 4 --max-segments 1 --subread-length 256 --subread-corridor 40\n+100bp\t0\tchr21\t8914\t60\t8M1I4M1I25M1D8M1I51M\t*\t0\t0\tGGGGGTCTCCCCCATTGACTTTCAGATGGCCACTTTCTCCTGTGTCTATCACATGGTCTTCGCTCTGTGTACACGTGCCCCTGGTGTCTGTCTCCCTCT\t*\tAS:i:172\tNM:i:4\tXI:f:0.96\tXS:i:0\tXE:i:172\tXR:i:99\tMD:Z:37^G59\tSV:i:0\tQS:i:0\tQE:i:99\tCV:f:100.000000\t\n+200bp\t0\tchr21\t8914\t60\t8M1I4M1I25M1D8M1I150M\t*\t0\t0\tGGGGGTCTCCCCCATTGACTTTCAGATGGCCACTTTCTCCTGTGTCTATCACATGGTCTTCGCTCTGTGTACACGTGCCCCTGGTGTCTGTCTCCCTCTGTGTCCTAATCTTCCCTTCTTATAAAGACACCACGCATATTGGATCAGGGCCTGGGTTAACTTAATTATCTTTTAAAGGCCCTATTTCCAAATATAATC\t*\tAS:i:370\tNM:i:4\tXI:f:0.9799\tXS:i:0\tXE:i:370\tXR:i:198\tMD:Z:37^G158\tSV:i:0\tQS:i:0\tQE:i:198\tCV:f:100.000000\t\n+300bp\t0\tchr21\t8914\t60\t8M1I4M1I25M1D8M1I249M\t*\t0\t0\tGGGGGTCTCCCCCATTGACTTTCAGATGGCCACTTTCTCCTGTGTCTATCACATGGTCTTCGCTCTGTGTACACGTGCCCCTGGTGTCTGTCTCCCTCTGTGTCCTAATCTTCCCTTCTTATAAAGACACCACGCATATTGGATCAGGGCCTGGGTTAACTTAATTATCTTTTAAAGGCCCTATTTCCAAATATAATCACATTCTGAGGTACTGGGAGTGCTTTGACATAAGAATTTTGGAGATACACAATTCATCCCACGACACCATTCATCATTTCTCTTCAGAGAATCAGGTTT\t*\tAS:i:568\tNM:i:4\tXI:f:0.9866\tXS:i:0\tXE:i:568\tXR:i:297\tMD:Z:37^G257\tSV:i:2\tQS:i:0\tQE:i:297\tCV:f:100.000000\t\n+400bp\t0\tchr21\t8914\t60\t8M1I4M1I25M1D8M1I253M1D58M1D10M1I5M1D16M1D3M2S\t*\t0\t0\tGGGGGTCTCCCCCATTGACTTTCAGATGGCCACTTTCTCCTGTGTCTATCACATGGTCTTCGCTCTGTGTACACGTGCCCCTGGTGTCTGTCTCCCTCTGTGTCCTAATCTTCCCTTCTTATAAAGACACCACGCATATTGGATCAGGGCCTGGGTTAACTTAATTATCTTTTAAAGGCCCTATTTCCAAATATAATCACATTCTGAGGTACTGGGAGTGCTTTGACATAAGAATTTTGGAGATACACAATTCATCCCACGACACCATTCATCATTTCTCTTCAGAGAATCAGGTTTAATATTTCTATATCTTTCTCCTTACTTCTTGTTTTCTTAATGATTTTGCATAAGACAATTTATTAAAAATATGTTCATATTTTTGACATACAAATTTTC\t*\tAS:i:735\tNM:i:9\tXI:f:0.9774\tXS:i:0\tXE:i:735\tXR:i:394\tMD:Z:37^G261^T58^T15^G16^G3\tSV:i:2\tQS:i:0\tQE:i:394\tCV:f:99.494949\t\n+500bp\t0\tchr21\t8914\t60\t8M1I4M1I25M1D8M1I253M1D58M1D10M1I5M1D26M1I13M1I39M1I39M\t*\t0\t0\tGGGGGTCTCCCCCATTGACTTTCAGATGGCCACTTTCTCCTGTGTCTATCACATGGTCTTCGCTCTGTGTACACGTGCCCCTGGTGTCTGTCTCCCTCTGTGTCCTAATCTTCCCTTCTTATAAAGACACCACGCATATTGGATCAGGGCCTGGGTTAACTTAATTATCTTTTAAAGGCCCTATTTCCAAATATAATCACATTCTGAGGTACTGGGAGTGCTTTGACATAAGAATTTTGGAGATACACAATTCATCCCACGACACCATTCATCATTTCTCTTCAGAGAATCAGGTTTAATATTTCTATATCTTTCTCCTTACTTCTTGTTTTCTTAATGATTTTGCATAAGACAATTTATTAAAAATATGTTCATATTTTTGACATACAAATTTTCCTGGGTTTTTATAAATACACAAATTTTTTTTGGTCTCTTGATTCTTTTCAGCTCTGTTATTTTCCAATGATTTCGTATTGTGTGTGATAGAAGCAGAAT\t*\tAS:i:907\tNM:i:13\tXI:f:0.9739\tXS:i:0\tXE:i:907\tXR:i:495\tMD:Z:37^G261^T58^T15^G16G22T77\tSV:i:2\tQS:i:0\tQE:i:495\tCV:f:100.000000\t\n+600bp\t0\tchr21\t8914\t60\t8M1I4M1I25M1D8M1I253M1D58M1D10M1I5M1D26M1I13M1I39M1I51M1D4M1D34M1I1M1I46M\t*\t0\t0\tGGGGGTCTCCCCCATTGACTTTCAGATGGCCACTTTCTCCTGTGTCTATCACATGGTCTTCGCTCTGTGTACACGTGCCCCTGGTGTCTGTCTCCCTCTGTGTCCTAATCTTCCCTTCTTATAAAGACACCACGCATATTGGATCAGGGCCTGGGTTAACTTAATTATCTTTTAAAGGCCCTATTTCCAAATATAATCACATTCTGAGGTACTGGGAGTGCTTTGACATAAGAATTTTGGAGATACACAATTCATCCCACGACACCATTCATCATTTCTCTTCAGAGAATCAGGTTTAATATTTCTATATCTTTCTCCTTACTTCTTGTTTTCTTAATGATTTTGCATAAGACAATTTATTAAAAATATGTTCATATTTTTGACATACAAATTTTCCTGGGTTTTTATAAATACACAAATTTTTTTTGGTCTCTTGATTCTTTTCAGCTCTGTTATTTTCCAATGATTTCGTATTGTGTGTGATAGAAGCAGAATAGTAAACAAAAGTTCATTCTGGAATTAGATTGCCTGGATTTTGTTATAGTCTCTTCCCACTTACTATCTGAGTAACTTTGAGCTCGTCCCTTCCATTGG\t*\tAS:i:1081\tNM:i:17\tXI:f:0.9717\tXS:i:0\tXE:i:1081\tXR:i:594\tMD:Z:37^G261^T58^T15^G16G22T89^C4^T81\tSV:i:2\tQS:i:0\tQE:i:594\tCV:f:100.000000\t\n+800bp\t0\tchr21\t8914\t60\t8M1I4M1I25M1D8M1I253M1D58M1D10M1I5M1D26M1I13M1I39M1I51M1D4M1D34M1I1M1I55M1I8M1I81M1I76M'..b'CTCCATGATTAGTACATAAGAATCATATAAAAGAGTAGGTGTTACCTTTAAAATATAAAATATGAAAAGTAAACAAGAGAAGAAGCATAGGTTTTGTGAACAAATCTGTGCTTCTGTAAGAAAGCAGCTAAATAGAAGAAAATACATCAGGCTTTGCCAATCAAAATTGATACTAAACATTTAGCTGTGCAAACTTAGAAAAATAAGCTCTCCTCTCTCAGCTTCACTTCTGACCTGTAAGACCAAAAGAATAGTTTTCTGTATATCATGGACAATGCTTGTTACATCGATTAAGAAAAAAAGTGTCAGTTTTCTAGTTTCTACTTCTTCTAGGATGTCTGTAAATTCAAAATGGTTGTCCAGCTCTGTGAAGTTAAAATTTATTCACAAATTCCTATAAACAGATTTGTTTTTTTGCCATGTGTTTCTGCCCAAGACTTTTTAAGTCCTCAGAATGAATCCTGACTTGTTATTGTGGCCACTTTCTATGTTGATGTGCGCAGCACACCATAGTCCATCAAAGTCGTTCCTCTGCAGTTAGTTAATTCACTGGGGCCACAGGCTACCCACACCAATGGCTACAAGGCTACAGAAATCTAATACATCATCTTCTTTTCACTGTAGCAGAACATCTCTTTTCCTTTTAACTATAATTGCAAAACCTGCATAGAGGGACAAGATTAACAAAAATATGCTCTCCTATCCACTTTAAACAGCCTAAAAAAATGGCTCTCTGCAACAACATGGACTAATCTGAGAGAACAATTTAAATGTACAACCTTTGTCCTTTCCATTTGGGTGGATTTGGCAACAGATAACCCAATAATCTGATTTCCATGAAGGGTCCAGAATAAAATTCATATTTTGTGCCAGAATAATATTTAGTTTTACACTCGCAAAACTAACAACTGTATTTGGCAATGCAATGGTAAACTAGTTAGAAAAGCCCCCTGCTCTGAAGAACTTAAGAATTGAAATGACTGCGAGATCCAATTTAAGTCAAAATAAGAGTGTGTGTGTGTGGCTGTGTGTGTGTGTG\t*\tAS:i:3221\tNM:i:53\tXI:f:0.9705\tXS:i:0\tXE:i:3221\tXR:i:1782\tMD:Z:37^G261^T58^T15^G16G22T89^C4^T255^C149^T422^C29^A13^G225^T29^A104^T15\tSV:i:2\tQS:i:0\tQE:i:1782\tCV:f:100.000000\t\n+2200bp\t0\tchr21\t8914\t52\t8M1I4M1I25M1D8M1I253M1D58M1D10M1I5M1D26M1I13M1I39M1I51M1D4M1D34M1I1M1I55M1I8M1I81M1I76M1D99M1I30M1I20M1D74M1I14M1I61M1I57M1I4M1I113M1I3M1I13M1I29M1I23M1I31M1D29M1D11M1I2M1D9M1I11M1I24M1I74M1I91M1I16M1D17M1I12M1D26M1I33M1I3M1I7M1I2M1I32M1I1M1I30M1I27M1I6M1I44M1I22M1I29M1D1M1D26M1D52M1I19M1D68M1I79M82S\t*\t0\t0\tGGGGGTCTCCCCCATTGACTTTCAGATGGCCACTTTCTCCTGTGTCTATCACATGGTCTTCGCTCTGTGTACACGTGCCCCTGGTGTCTGTCTCCCTCTGTGTCCTAATCTTCCCTTCTTATAAAGACACCACGCATATTGGATCAGGGCCTGGGTTAACTTAATTATCTTTTAAAGGCCCTATTTCCAAATATAATCACATTCTGAGGTACTGGGAGTGCTTTGACATAAGAATTTTGGAGATACACAATTCATCCCACGACACCATTCATCATTTCTCTTCAGAGAATCAGGTTTAATATTTCTATATCTTTCTCCTTACTTCTTGTTTTCTTAATGATTTTGCATAAGACAATTTATTAAAAATATGTTCATATTTTTGACATACAAATTTTCCTGGGTTTTTATAAATACACAAATTTTTTTTGGTCTCTTGATTCTTTTCAGCTCTGTTATTTTCCAATGATTTCGTATTGTGTGTGATAGAAGCAGAATAGTAAACAAAAGTTCATTCTGGAATTAGATTGCCTGGATTTTGTTATAGTCTCTTCCCACTTACTATCTGAGTAACTTTGAGCTCGTCCCTTCCATTGGTTTCTTCATCCCCTTATACAGGGAAAATAGAACCAACCTTGTAGAGTTGTTGTCAGAATTTAAGTAATATGGGCAAAGCACACAGAACAGTTTCTAAACCAACATTAAACAACAAATGATTAACACTTAGGAATGACACCTTTAGATAGCTCCATGATTAGTACATAAGAATCATATAAAAGAGTAGGTGTTACCTTTAAAATATAAAATATGAAAAGTAAACAAGAGAAGAAGCATAGGTTTTGTGAACAAATCTGTGCTTCTGTAAGAAAGCAGCTAAATAGAAGAAAATACATCAGGCTTTGCCAATCAAAATTGATACTAAACATTTAGCTGTGCAAACTTAGAAAAATAAGCTCTCCTCTCTCAGCTTCACTTCTGACCTGTAAGACCAAAAGAATAGTTTTCTGTATATCATGGACAATGCTTGTTACATCGATTAAGAAAAAAAGTGTCAGTTTTCTAGTTTCTACTTCTTCTAGGATGTCTGTAAATTCAAAATGGTTGTCCAGCTCTGTGAAGTTAAAATTTATTCACAAATTCCTATAAACAGATTTGTTTTTTTGCCATGTGTTTCTGCCCAAGACTTTTTAAGTCCTCAGAATGAATCCTGACTTGTTATTGTGGCCACTTTCTATGTTGATGTGCGCAGCACACCATAGTCCATCAAAGTCGTTCCTCTGCAGTTAGTTAATTCACTGGGGCCACAGGCTACCCACACCAATGGCTACAAGGCTACAGAAATCTAATACATCATCTTCTTTTCACTGTAGCAGAACATCTCTTTTCCTTTTAACTATAATTGCAAAACCTGCATAGAGGGACAAGATTAACAAAAATATGCTCTCCTATCCACTTTAAACAGCCTAAAAAAATGGCTCTCTGCAACAACATGGACTAATCTGAGAGAACAATTTAAATGTACAACCTTTGTCCTTTCCATTTGGGTGGATTTGGCAACAGATAACCCAATAATCTGATTTCCATGAAGGGTCCAGAATAAAATTCATATTTTGTGCCAGAATAATATTTAGTTTTACACTCGCAAAACTAACAACTGTATTTGGCAATGCAATGGTAAACTAGTTAGAAAAGCCCCCTGCTCTGAAGAACTTAAGAATTGAAATGACTGCGAGATCCAATTTAAGTCAAAATAAGAGTGTGTGTGTGTGGCTGTGTGTGTGTGTGTGTGTATGAATAAAGGCAGGTAATATTCCATGTCAAATTCTGTATAGAATGTGAAAGAGAAAACAGATTGAGAATAGATGAACTTGGCAATCAGAAGATTTACAGTAGAATAGAGGAAAGATTATAGTAGTATAGTTTGTGAGTAGTGGGTATTACTATGTTTGAAATAAAAAAGCTATTTTTAGTAATTTAATAAAATATTTAGTTGATAGTACTTTTATTTTTGATCGATAAATATAAATGCATTGTTTATATTTTGTGAAAACACACATGGAAGATATTACCCAGGTGTGCTGAATGTTTCCCATTCCTCCCTACCTTACATCCCTGTTGACCTCCAGGAGGCTATCCAGGAAGCTGATCTCAGTAAACTGCATATGCATACAGAGTGTTCATNNNNNNNNNNNNNNGNNNNNNNGNNNNTNNTNNNNNNNNNNCTNNGNNNNNNNNNNNNNNANNNNTNNTCANNNNNNNNNNN\t*\tAS:i:3928\tNM:i:66\tXI:f:0.9699\tXS:i:0\tXE:i:3928\tXR:i:2178\tMD:Z:37^G261^T58^T15^G16G22T89^C4^T255^C149^T422^C29^A13^G225^T29^A262^A1^A26^A71^T117A23T5\tSV:i:2\tQS:i:0\tQE:i:2178\tCV:f:96.371681\t\n' |
| b |
| diff -r 000000000000 -r 95e4757d8da7 test-data/ngmlr-out3.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ngmlr-out3.sam Thu Oct 29 15:43:54 2020 +0000 |
| b |
| b'@@ -0,0 +1,215 @@\n+@HD\tVN:1.0\tSO:unsorted\n+@SQ\tSN:1/16146929_16160414\tLN:13485\n+@SQ\tSN:11/92864813_92880913\tLN:16100\n+@SQ\tSN:13/73677590_73687657\tLN:10067\n+@SQ\tSN:19/35531611_35541678\tLN:10067\n+@SQ\tSN:20/52642072_52663009\tLN:20937\n+@SQ\tSN:2/19979093_19989093\tLN:10000\n+@SQ\tSN:22/37122124_37132266\tLN:10142\n+@SQ\tSN:2/58359291_58369291\tLN:10000\n+@SQ\tSN:2/83370031_83380361\tLN:10330\n+@SQ\tSN:2/83370229_83380584\tLN:10355\n+@SQ\tSN:9/14627539_14637646\tLN:10107\n+@PG\tID:ngmlr\tPN:nextgenmap-lr\tVN:0.2.7\tCL:ngmlr -t 1 --no-progress --skip-write --output /tmp/tmp_8wdkhyd/files/e/c/9/dataset_ec9a5fa6-55f5-487e-be63-57abe8127bed.dat --bam-fix --reference /tmp/tmp_8wdkhyd/files/4/9/d/dataset_49d2613f-f974-46ad-9155-2e8b53414907.dat --query /tmp/tmp_8wdkhyd/files/d/1/0/dataset_d1003571-e511-4cc5-97f2-38a5c3b1762d.dat --presets pacbio --min-identity 0.65 --min-residues 0.01 --match 2.0 --mismatch -5.0 --gap-open -5.0 --gap-extend-max -5.0 --gap-extend-min -1.0 --gap-decay 0.15 --kmer-length 13 --kmer-skip 2 --bin-size 4 --max-segments 1 --subread-length 256 --subread-corridor 40\n+m54026_160730_141255/23593063/13850_17814\t16\t2/83370031_83380361\t6021\t16\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\t*\t0\t0\tTCTTTTGTGACGCGAACTTTCTTTACTCCTGATTATATAGCATACGCACATTCAGACACGAGCAGCCACCTGCTCATTTTTCATTTCTTCCCCTCCTCTACATATCTACGTAAATGGTATATCACAGGATATTCTTTTAATTTGATTATCAGCAGGAAAGCATAACAGTTATCTAAAGATGATAAGAAAATCCTGCAGAAGTAGCTCCCATTATCAAGCGTGACCCTTGATTTGAGCATTTATACCATGCGCCCTAGGCAGCTTCCCTCAGCCAGAACCAGCTTATAGCTACGCCTTTACTTAATAGACATGTCTATTTATGCCCAGTCAGTGTCTCTAGCGAAAAGTTGGCCAATTAATTACAATGGTTGTTGCCGTTTTCTTGTGTTTTGATCATAAAAAGCGAGTCAACTTCATTGGAATCCCAGTTTTCTTTCCTTCTTTGGATAACTGCAATTACAAAACATCTGCTCCTAATTATGCTCTGATTAACTTTGCAACAATTCAAATCAACACAGCCCTGCTGTGTTTTGCTCCTCAAGGCGTCGCCTATGTAGATGCAAACCACTGAATGTACTTGCTATGCAAACTATTTAACAAATCATATCCACAACGCACATATATCCAAGTATCTACTACATTACGACCAAAATGTATGATGGTTTCCATAAGAAAACAATAAATCAAACAAAAAAAAAAAAAACAAACAACACCACGACTTCATACCACAAGCGAAAAAGTAAAAAAAAGAGAGAGATGAAATTTATGACCAGCATTCTTCCCCTTTTTTTTTTTTTTTTTTTTTTTTGTGTGAAGAATAATTATTTGCTATCATGTCGGCAAGATATTCTGCACTTTTT'..b'CAGCTCGTCCAGGAACTTTTCAGCAGAGGAGTGAATATAGTATACTATTGAATTTGTGCTTTAACGCAGAGCTTCCCAGGGCAAAAACTCTTAAACCCTAAAATGGCCTAGCGATAGTAGGAAGCAATAAAAAACTTCAATATCTGAGCTAAAAATAAACTGCCAGGCACAACCTTGCTTCTGGGTATGTATACCCAAGGGAAAATAAACCCGATGTGGTCAAAAGGAGGTTATCTGCACTCCCATGGTGCTTGCAACACTATTCACAATAATCAAGATACAGGCATAAATCACTAGTGTGTGGTCAATGGGTTAATAAGGATAAAGTAGTGGTCCGGAACCAAGATAGTAGTTGTGGTTAATGAAGAACACATTTTTTGCGTTAGCCACAAGTGTGTTTTTTATCATATATATTGGTGTTCTGTTTGTGTAATCGATGTATCTCCATATATATGGAGGCGACTTATGCACCCATATAGACACATAACATTTACAAAATCTACACACCCTTATAATAACATAGGACACAACAAACCAACACCCACAACGCCAGGGACTCTTATGGCAGCATAAAAAGGACATCCCGGAAACAGTTGCAAAACATCCCGGGAGTGGCACTGGAGGACATTCTGGCTAAGCAAGGGTGACCAATAAGCCCAGCCACGGGAACAACTACCTGTAAGGAATGCTCCTTTCTTGATAGGTAGGGAATCACTAAAAAGAAAGTAATAAACTTTTATGCAAGGGGACAGAGCATTAGAAACAGTAGTTTGTCGGGATGAGACCTGGGGGAAAAATGGGGCGATTGCTCGTCAAAAGGTGTTACAAAACGTTCAGGTATAAGGATGAATGAGTGTTCTGGGGATGTCTATGTACGGAAGCAGGGTGACTGTAGTTAGTGAATGTGTACTGTGTTGGATTCTTGAAATCCTGCGAAGAGAGTAGATCTTAAGTGATTCTAACAAAAATAAAATTGTGACATACGCGTGAGTTGATGTGTTAAATATGGATTAACTTTCATTGTTTGGGTATTCATTTTGCAATGTAATACATGTATCAAAAACATCACATTGTATAAAGGAGATATTTTTTGTTATATTATTGGCAAACATATCTCGAATAAAGCTGGGAGGGCAAATCTCACATCAACCCTTAATAATAACAGGGAAGCACATGTTCACCAAGAATTGGGTAAAGGCAATGTTTTAATAGATAAAACAGGTAAGCAAAAGAACCATGGGAGAAACGACCCTTTGTTCACACTAAGGGTATCGGTACATTTATGGCCAAGAATGACTTCAGGCAGAAAAAAGGTGGCTTCAGAAGAGGGGTGACATAATTTTCCCCAGTATGTTGGGAAGGGTTTGAGTGGATGAAAATAAGAATGCCGGCAAGGATTAGAGAAACATTTCGCAATGTCCCACCAGGTTACTGAAAGGGCAGTGGTTTTTAGAGGGCTGGATCCTGGAGGAGGGGTAGAATATGAGTGGTGTTGTGGACAATTTAGTAGGCTTAGAGGGGCAGCCACAAGAAAACAACACCACAATTTTAAAAGGGAAGGAGGGAAAACACAACTTGGGCGGAGAAAAGCGAAAAATTGAAGACTACAAATTAAGGTCCTGTGCTTGGCCCCGCCCAAAGGCCCAAATGTAATTCATGGTCGCTATTGTTTTAGGGCACTGGCTACTTCAATAGTTCCCCTTTGTGCTGTTTCCTATCTTCTGCCCCCCTGTTTTACTCATAGAAAAAAAGGTGATGGCAAAGCTGTCAGCTCTATAAACAGGAAGCTGCTGAACAAATTAATCTCAATATAAGGACCCGCCTTCGGCTGGTAGCTTTCATGCTGCCAACAGTGTTGTGTGGGTTCTGGCCCAATTCTGGTGCTGAGTCTAGACTTCAAAGGTTATTGACAGTCAGGCATTCCCCCCAAGATCATCAGGAGGTGTGAAAAAGAGAACCTTATAGAGACAGCAAGCTTGTTGTAGAAGAAATTAAAAATCTCTGATACTGGTACAAGCAGTATTACGATGACATGGAACTGGTTATTCATCTTGGCTCAAGGGGGACCGGG\t*\tAS:i:1044\tNM:i:400\tXI:f:0.779\tXS:i:0\tXE:i:1044\tXR:i:1771\tMD:Z:5^A7^A19^G45T7^A27^A24^T131T7T6A52G63A29A0A10A2T1T13A10T17T2T8^A12T23T14T10T9T15T4^T5^T6C10T8^A7A18^A8^T13T22^A45G9G12^AA14^T5T2^T15^A31^T1C2T20G24^A27^A0A5T1T3T21^A20^T3A8T2T24T18T6A13C13^A14^A32^C7^T24T3T4C29T1T1^G13^A25^G41^G18^TT9C18T13T0T6T15T9T18^G21^A8T22^G5^A4^A4A6T3T14^T2A8\tSV:i:0\tSA:Z:2/58359291_58369291,5838,+,1152S23M1I8M2I34M1I10M1I22M2I16M1I3M1I2M1I9M1I24M1D6M1I4M1I3M1D15M1I7M1I6M1I1M1D5M1I8M1I3M1I3M1I2M2I3M1D27M1D1M1I8M1I2M1D9M4I24M1I2M1D1M1D11M1D1M2I13M3I5M1I4M1D25M3I7M5I9M2I2M1I20M1I13M1D5M1I18M1I9M4I17M1I1M2I4M1I4M32I12M1I2M1I2M1D3M1I12M1I5M1I23M8I1M1I6M2I4M1I6M1I3M1I3M1D18M1I14M1I11M1D18M3I1M3I5M2I1M1I7M2I3M1I13M2I33M1D2M1I4M1I8M2I5M1I5M1I11M1I9M1I3M1D23M1I12M1I3M1D13M1D10M1I3M1I21M2I2M1I5M1I2M1D22M3I2M1I1M1I14M1I7M2I9M1I7M1I32M1I24M4I4M1D3M1I5M2I7M1I11M2I1M1I2M1I5M1I3M2I8M2I12M6I3M1I6M1I1M1I2M1I16M1I2M2I13M1I1M1I13M1I2M1I4M1D8M3I8M1I1M1I5M1I17M1D4M1I35M3I45M2I28M1I6M3I4M1I9M1I4M18I8M2I3M1D8M1I3M1I8M3I15M7I21M1I2M1I5M1I2M1I1M1I14M1I5M1I4M2I1M1I19M3I5M1I10M2I3M2I13M1I1M1I5M1I1M1I1M2I7M1I1M1I2M1I1M1I8M1I25M1I3M1I9M1I17M1I4M12I8M1I10M3I4M1I3M3I6M1I9M3I7M3I2M1D3M1I6M1D6M1I2M3I2M1I3M1I7M5I9M1D4M1I9M1I2M1D5M3I22M1I16M1I4M1I5M1I5M1D1M1I13M2I2M1I3M1I12M3I4M1I16M3I5M1I1M1I10M2I4M1I12M6450S,35,432;2/58359291_58369291,9398,+,5437S14M1I17M1I4M1I1M1I29M1I1M1I4M2I5M1I9M3I12M1D5M1I16M2I4M1I56M1I3M1I3M1I5M7I34M1I13M1I32M1D52M1I14M1I8M1I26M1D3M1D2M1I14M1I16M2I9M1I9M1I7M1I8M1D1M1D22M1D2M1D7M1I10M1D11M1I8M1I11M2D5M1I8M1I5M1I20M1D14M1D6M1I6M1I19M3561S,44,95;2/58359291_58369291,5108,+,296S15M1I5M4I7M1D1M1D3M1I5M1I3M1I5M1I14M1I6M1I9M1I6M1I18M2I26M1D27M1I10M1I12M1I10M1D18M2I3M2I8M2D24M2I12M1I9M2I2M1I6M1I7M1I13M1I3M1D3M1D8M1I1M1I10M1I2M1I9M1I5M1D15M1D14M1I11M1I3M1I2M4I10M1D12M3I1M2I7M1I3M1I8M1I12M2I5M2I11M1I3M2I1M2I27M1D13M1I5M5I1M1I4M6I6M3I23M1I4M1I1M1I2M4I6M1I8M1I12M1I21M1I11M1I10M1I3M8649S,35,129;\tQS:i:3557\tQE:i:5328\tCV:f:18.382811\t\n' |
| b |
| diff -r 000000000000 -r 95e4757d8da7 test-data/ngmlr-out4.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ngmlr-out4.sam Thu Oct 29 15:43:54 2020 +0000 |
| b |
| b'@@ -0,0 +1,215 @@\n+@HD\tVN:1.0\tSO:unsorted\n+@SQ\tSN:1/16146929_16160414\tLN:13485\n+@SQ\tSN:11/92864813_92880913\tLN:16100\n+@SQ\tSN:13/73677590_73687657\tLN:10067\n+@SQ\tSN:19/35531611_35541678\tLN:10067\n+@SQ\tSN:20/52642072_52663009\tLN:20937\n+@SQ\tSN:2/19979093_19989093\tLN:10000\n+@SQ\tSN:22/37122124_37132266\tLN:10142\n+@SQ\tSN:2/58359291_58369291\tLN:10000\n+@SQ\tSN:2/83370031_83380361\tLN:10330\n+@SQ\tSN:2/83370229_83380584\tLN:10355\n+@SQ\tSN:9/14627539_14637646\tLN:10107\n+@PG\tID:ngmlr\tPN:nextgenmap-lr\tVN:0.2.7\tCL:ngmlr -t 1 --no-progress --skip-write --output /tmp/tmp_8wdkhyd/files/c/2/a/dataset_c2ac7220-a6e2-48d2-9513-132f3dd94c21.dat --bam-fix --reference /tmp/tmp_8wdkhyd/files/4/f/9/dataset_4f9d04b1-e2c7-40d6-aae6-85459ee3f3ad.dat --query /tmp/tmp_8wdkhyd/files/8/3/4/dataset_8341245f-b510-45d9-9a26-1ccbb7f44f38.dat --presets pacbio --min-identity 0.65 --min-residues 0.25 --match 2.0 --mismatch -5.0 --gap-open -5.0 --gap-extend-max -5.0 --gap-extend-min -1.0 --gap-decay 0.15 --kmer-length 13 --kmer-skip 2 --bin-size 4 --max-segments 1 --subread-length 256 --subread-corridor 40\n+m54026_160730_141255/23593063/13850_17814\t16\t2/83370031_83380361\t6021\t16\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\t*\t0\t0\tTCTTTTGTGACGCGAACTTTCTTTACTCCTGATTATATAGCATACGCACATTCAGACACGAGCAGCCACCTGCTCATTTTTCATTTCTTCCCCTCCTCTACATATCTACGTAAATGGTATATCACAGGATATTCTTTTAATTTGATTATCAGCAGGAAAGCATAACAGTTATCTAAAGATGATAAGAAAATCCTGCAGAAGTAGCTCCCATTATCAAGCGTGACCCTTGATTTGAGCATTTATACCATGCGCCCTAGGCAGCTTCCCTCAGCCAGAACCAGCTTATAGCTACGCCTTTACTTAATAGACATGTCTATTTATGCCCAGTCAGTGTCTCTAGCGAAAAGTTGGCCAATTAATTACAATGGTTGTTGCCGTTTTCTTGTGTTTTGATCATAAAAAGCGAGTCAACTTCATTGGAATCCCAGTTTTCTTTCCTTCTTTGGATAACTGCAATTACAAAACATCTGCTCCTAATTATGCTCTGATTAACTTTGCAACAATTCAAATCAACACAGCCCTGCTGTGTTTTGCTCCTCAAGGCGTCGCCTATGTAGATGCAAACCACTGAATGTACTTGCTATGCAAACTATTTAACAAATCATATCCACAACGCACATATATCCAAGTATCTACTACATTACGACCAAAATGTATGATGGTTTCCATAAGAAAACAATAAATCAAACAAAAAAAAAAAAAACAAACAACACCACGACTTCATACCACAAGCGAAAAAGTAAAAAAAAGAGAGAGATGAAATTTATGACCAGCATTCTTCCCCTTTTTTTTTTTTTTTTTTTTTTTTGTGTGAAGAATAATTATTTGCTATCATGTCGGCAAGATATTCTGCACTTTTT'..b'CAGCTCGTCCAGGAACTTTTCAGCAGAGGAGTGAATATAGTATACTATTGAATTTGTGCTTTAACGCAGAGCTTCCCAGGGCAAAAACTCTTAAACCCTAAAATGGCCTAGCGATAGTAGGAAGCAATAAAAAACTTCAATATCTGAGCTAAAAATAAACTGCCAGGCACAACCTTGCTTCTGGGTATGTATACCCAAGGGAAAATAAACCCGATGTGGTCAAAAGGAGGTTATCTGCACTCCCATGGTGCTTGCAACACTATTCACAATAATCAAGATACAGGCATAAATCACTAGTGTGTGGTCAATGGGTTAATAAGGATAAAGTAGTGGTCCGGAACCAAGATAGTAGTTGTGGTTAATGAAGAACACATTTTTTGCGTTAGCCACAAGTGTGTTTTTTATCATATATATTGGTGTTCTGTTTGTGTAATCGATGTATCTCCATATATATGGAGGCGACTTATGCACCCATATAGACACATAACATTTACAAAATCTACACACCCTTATAATAACATAGGACACAACAAACCAACACCCACAACGCCAGGGACTCTTATGGCAGCATAAAAAGGACATCCCGGAAACAGTTGCAAAACATCCCGGGAGTGGCACTGGAGGACATTCTGGCTAAGCAAGGGTGACCAATAAGCCCAGCCACGGGAACAACTACCTGTAAGGAATGCTCCTTTCTTGATAGGTAGGGAATCACTAAAAAGAAAGTAATAAACTTTTATGCAAGGGGACAGAGCATTAGAAACAGTAGTTTGTCGGGATGAGACCTGGGGGAAAAATGGGGCGATTGCTCGTCAAAAGGTGTTACAAAACGTTCAGGTATAAGGATGAATGAGTGTTCTGGGGATGTCTATGTACGGAAGCAGGGTGACTGTAGTTAGTGAATGTGTACTGTGTTGGATTCTTGAAATCCTGCGAAGAGAGTAGATCTTAAGTGATTCTAACAAAAATAAAATTGTGACATACGCGTGAGTTGATGTGTTAAATATGGATTAACTTTCATTGTTTGGGTATTCATTTTGCAATGTAATACATGTATCAAAAACATCACATTGTATAAAGGAGATATTTTTTGTTATATTATTGGCAAACATATCTCGAATAAAGCTGGGAGGGCAAATCTCACATCAACCCTTAATAATAACAGGGAAGCACATGTTCACCAAGAATTGGGTAAAGGCAATGTTTTAATAGATAAAACAGGTAAGCAAAAGAACCATGGGAGAAACGACCCTTTGTTCACACTAAGGGTATCGGTACATTTATGGCCAAGAATGACTTCAGGCAGAAAAAAGGTGGCTTCAGAAGAGGGGTGACATAATTTTCCCCAGTATGTTGGGAAGGGTTTGAGTGGATGAAAATAAGAATGCCGGCAAGGATTAGAGAAACATTTCGCAATGTCCCACCAGGTTACTGAAAGGGCAGTGGTTTTTAGAGGGCTGGATCCTGGAGGAGGGGTAGAATATGAGTGGTGTTGTGGACAATTTAGTAGGCTTAGAGGGGCAGCCACAAGAAAACAACACCACAATTTTAAAAGGGAAGGAGGGAAAACACAACTTGGGCGGAGAAAAGCGAAAAATTGAAGACTACAAATTAAGGTCCTGTGCTTGGCCCCGCCCAAAGGCCCAAATGTAATTCATGGTCGCTATTGTTTTAGGGCACTGGCTACTTCAATAGTTCCCCTTTGTGCTGTTTCCTATCTTCTGCCCCCCTGTTTTACTCATAGAAAAAAAGGTGATGGCAAAGCTGTCAGCTCTATAAACAGGAAGCTGCTGAACAAATTAATCTCAATATAAGGACCCGCCTTCGGCTGGTAGCTTTCATGCTGCCAACAGTGTTGTGTGGGTTCTGGCCCAATTCTGGTGCTGAGTCTAGACTTCAAAGGTTATTGACAGTCAGGCATTCCCCCCAAGATCATCAGGAGGTGTGAAAAAGAGAACCTTATAGAGACAGCAAGCTTGTTGTAGAAGAAATTAAAAATCTCTGATACTGGTACAAGCAGTATTACGATGACATGGAACTGGTTATTCATCTTGGCTCAAGGGGGACCGGG\t*\tAS:i:1044\tNM:i:400\tXI:f:0.779\tXS:i:0\tXE:i:1044\tXR:i:1771\tMD:Z:5^A7^A19^G45T7^A27^A24^T131T7T6A52G63A29A0A10A2T1T13A10T17T2T8^A12T23T14T10T9T15T4^T5^T6C10T8^A7A18^A8^T13T22^A45G9G12^AA14^T5T2^T15^A31^T1C2T20G24^A27^A0A5T1T3T21^A20^T3A8T2T24T18T6A13C13^A14^A32^C7^T24T3T4C29T1T1^G13^A25^G41^G18^TT9C18T13T0T6T15T9T18^G21^A8T22^G5^A4^A4A6T3T14^T2A8\tSV:i:0\tSA:Z:2/58359291_58369291,5838,+,1152S23M1I8M2I34M1I10M1I22M2I16M1I3M1I2M1I9M1I24M1D6M1I4M1I3M1D15M1I7M1I6M1I1M1D5M1I8M1I3M1I3M1I2M2I3M1D27M1D1M1I8M1I2M1D9M4I24M1I2M1D1M1D11M1D1M2I13M3I5M1I4M1D25M3I7M5I9M2I2M1I20M1I13M1D5M1I18M1I9M4I17M1I1M2I4M1I4M32I12M1I2M1I2M1D3M1I12M1I5M1I23M8I1M1I6M2I4M1I6M1I3M1I3M1D18M1I14M1I11M1D18M3I1M3I5M2I1M1I7M2I3M1I13M2I33M1D2M1I4M1I8M2I5M1I5M1I11M1I9M1I3M1D23M1I12M1I3M1D13M1D10M1I3M1I21M2I2M1I5M1I2M1D22M3I2M1I1M1I14M1I7M2I9M1I7M1I32M1I24M4I4M1D3M1I5M2I7M1I11M2I1M1I2M1I5M1I3M2I8M2I12M6I3M1I6M1I1M1I2M1I16M1I2M2I13M1I1M1I13M1I2M1I4M1D8M3I8M1I1M1I5M1I17M1D4M1I35M3I45M2I28M1I6M3I4M1I9M1I4M18I8M2I3M1D8M1I3M1I8M3I15M7I21M1I2M1I5M1I2M1I1M1I14M1I5M1I4M2I1M1I19M3I5M1I10M2I3M2I13M1I1M1I5M1I1M1I1M2I7M1I1M1I2M1I1M1I8M1I25M1I3M1I9M1I17M1I4M12I8M1I10M3I4M1I3M3I6M1I9M3I7M3I2M1D3M1I6M1D6M1I2M3I2M1I3M1I7M5I9M1D4M1I9M1I2M1D5M3I22M1I16M1I4M1I5M1I5M1D1M1I13M2I2M1I3M1I12M3I4M1I16M3I5M1I1M1I10M2I4M1I12M6450S,35,432;2/58359291_58369291,9398,+,5437S14M1I17M1I4M1I1M1I29M1I1M1I4M2I5M1I9M3I12M1D5M1I16M2I4M1I56M1I3M1I3M1I5M7I34M1I13M1I32M1D52M1I14M1I8M1I26M1D3M1D2M1I14M1I16M2I9M1I9M1I7M1I8M1D1M1D22M1D2M1D7M1I10M1D11M1I8M1I11M2D5M1I8M1I5M1I20M1D14M1D6M1I6M1I19M3561S,44,95;2/58359291_58369291,5108,+,296S15M1I5M4I7M1D1M1D3M1I5M1I3M1I5M1I14M1I6M1I9M1I6M1I18M2I26M1D27M1I10M1I12M1I10M1D18M2I3M2I8M2D24M2I12M1I9M2I2M1I6M1I7M1I13M1I3M1D3M1D8M1I1M1I10M1I2M1I9M1I5M1D15M1D14M1I11M1I3M1I2M4I10M1D12M3I1M2I7M1I3M1I8M1I12M2I5M2I11M1I3M2I1M2I27M1D13M1I5M5I1M1I4M6I6M3I23M1I4M1I1M1I2M4I6M1I8M1I12M1I21M1I11M1I10M1I3M8649S,35,129;\tQS:i:3557\tQE:i:5328\tCV:f:18.382811\t\n' |
| b |
| diff -r 000000000000 -r 95e4757d8da7 test-data/ngmlr-ref1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ngmlr-ref1.fa Thu Oct 29 15:43:54 2020 +0000 |
| b |
| b'@@ -0,0 +1,2 @@\n+>6 6:112,565,266-112,706,826 hs37d5\n+GTCTCTTATGAATGGAATTTCAGGGTGTCTATTGGCATTAATGGTGGCAGACAACAATTTCAAAGGAACAATATAAAATGAGGCAATTATTCATGTACTACAATTAAACCGCAGCCCATCTCCAGATATTCAGACCATTTAATCTCCAAATAGCAGGCATTTAACACCTCATCTGTGACCTGGGGGTTGACAGAACCACCTAGGACTCAGGACAGATAGCAGGAAAAGAGGTAACACTTAGGTAACACCTTCAGCTTGTCAAATTGTATCACTGTTCATCAAAGGGAAACACACACATGTAGCCATGAAGTTTGAAAGGCATCCTGGACTACCTCTGCTGTGGAAGAAGAGGCTTGCCAGGGTTTTCAGAACCCGAATTTGTGCTGTGGCTCTGTGTTGTGATTCTAGAGGGTTCTATAGTCCTAGCATCCCAGGGCCTGAGGCTTACTAGACATTTCTCTTCCCTTTGGCTGGTGTCTATGTTATGTGTTTCTTTGGACTGACATTTGGCTTTCTAGAGCTGCTTGGTTCAGCATGCCATGTTGCATTTCACTTTGTACATAGACAACAGTGTTCCATGTAATAGTTGTGTGTGTGAGGGAAGTTTTAGTGAAGGTACTTTTGATTCCTAGAGTCCTTGATTTCCTTTGAAGCAATCATGCCACTCCAAAATGGCATAATTTCAAAATAAATATTAATATGCAAAGTCTTCATCATGCTCAGGGGCCCTTTTAGCTGTAGAGTACAGCCTGGATGACTGGTCTACTCTGCAAAGACTTGTGCTAATGCAGCTGTTAATGTTACGGGATTTCTCTAACTCATCAGTTCTCATGAAGTAAAAAATGTGTATACTTCACTCCATTTAGGTAAACACGGATCTCTAGCCTCCACCAAAACACAACATAAAAACTAAGAAAGTCCTGGGAGTGAAAAGAAGGTCATTTTGCATATTACTCAAATTATATTCACCCGTCTCTCCTCCCGCTTTTAACAGAATTTGTTTATGTATTTTTTTCTTTATGGAGAGGATTTGGGCTGAATATGGAAATTTTCCCATTACCATTCAGCTTCAGAATGTTGTTTCCCCCAAGTTTCTCATGATAAAAAGACTCAGATTCAGAGCCGAACTGCTGGCAGCTGAATTTCATTAAGACTTTGATGGGAAACTTAAGTTGGAATTACAAACATCTGTGGTTAAACTTCCCTTTAGTAAACCATTTCCCAGAATTTAACTTTACCACACCAAGAGCCAAAAAGAAAAACAGTTGAAAAAAGAATGCTGCTCTTTTGCAAATATGAGTAGGTATTTAAATATTCTTCTGTATGGTCACTATACATCAATAGACTAGGTTTACTTATTTTAGAAAAAAATGATTGTTTGGAAATGCTAAGGTTTGGACTCAAAGCATATACTAGCAATCTGGTTTTAATGGCTTTTAACCAATCAAAGTTCTCAAAATTATGTCTGGCCATCATTATATTTATGTGGTTACTATAAGCCAGAAAAAACTCTAAAGTAGGGGAGTGTTTTTGGCATTTTAATTCAAGAAACTGTGACAAGTCAGATTTAGTATTTAATTATGAGAGGAAAAAAGGTATTATCCTTGTCATATCAAAGCTGCTTTTTTTTTTTTTTTTTTGAGATAGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAATGGCACAATCTCCGCTCACTGCAACCTCCGCCTCCCGAGTTCAAGGAATTCTCTGCTTCAGCCTCCCAAGTAGCTGGGATTACAGGCACCTGCCACCATGTCCAGCTAATTTTTTTGTATTTTTAGTAGAGGCGGGGTCTCACCATCTTGGCCAGGCTGGTCTTGAACTCCTGACTTTGTGATCCACCCATCTTGGCCTCCCAAAGTGTTGGGATTACAGGCGTGAGCCACCGTGCCCAGCTGCTGTTGGCTTTTTTCTTTAGCTTTTCTAGGGATTTAGCATTCATTTCTCTTAACTGCTCAGATCCTCCTATTGCTGGGGAAAGGCTGTTTAAAGAACCATAAAAGACACAATGATTATAAAAACTAAATGACAGCCTTCTTCTCCAATGTTGGATAATCAGCAAATTTTAAGCAAAAGTTAAAAGTACTCGAATTTATGGAATAAGTAAAGAGTTTGATAACAAAATACTTTTAACAAGATAGTGTAGAGCTTTACCTGAAGATAGACAGAGGCAGAGAGTGGAAAAATGAGGGAAAGGAAGGAGGGACAGACTGAGAGAAATGAGGGCTAACTTTGTGTTGGGCAGCTTACATATATTATTTCATTTAAATTTCACAAGAATTTTGCAAGGCAGGTGTATTTCTATTTATTTTACAATCAAAGGAACTGAGTATCTAAAAGATGGTCCAATTTGCCCAAAGTCAAACAGCTAGAAAGTTGTGGAGCTGGATTCACAGCGCATCTGTCTGGTTGTAAGCCCATATTCTGCCTGTAACGAAAGGTGAACTTCAAAATATTGTAAAGCAGAGGCTGCAAATAAATGATCTTTAGGCTGAATCTGGCCCTCAGATGTACTCAGCCTACAGGGCATTAAAAAAAATTTGAGTCAGCAATTTCACTTATGAATCCAAATTCTGTCTTCTTTTGAAAAAGACACAACAAAACAAAACAAAACCAGAAGACCTGGCAATGCTGAGAGGTGGCTGCCACTCTGGAAGAGGGATTCTTCCATTTCCTGTTATCGAGGCCCACCACTCACAGGATGCGTTTCTTTACCGAGCTAGATTCACTCAATTCTTTTTTACCTGGCCCCTATAAGACTCCAAGTCTTAAAACTTTCTCTGTACCATATGATCCAGCAATTCCACTTCTAGGTATACACTCCCAAAAAACTGAAAGCAAGAACTCAAACAGAGGCTTGTACAGCAATATTCATAGCAGCATTACTCACAGTAGCCAAAAGGTAGAAACGACCCAAATGTCCATCAACAAAATGAATGGACAAAACATAGTGTACATATAAACAGAGTATTATTCAGTTTTAAAAAGGAATGCAATTCTGACACATGCTACAACATGGGTGAGCCTCAAAGACATTATGCCAAATGAAATAAGCTAGGCACAAAAGGATAAGTACTGCATGATTATGTATATGGAGTATTTAGAGTAGTTAAATTCATAGAGACAAAGTAGAATTGTTGTTGCCAGGGGCTGGAGGAAGGAGTTAATCGGAAGTTATCATTTAATGGGTTTCAGTTTGGGAAAATGAAAAAGTTCTGGAGATTGATGGTGATGGTTTTATAACAATGTGAATATAGTCAATGCCACTGAACTGTGCCCTTAAAAATAGTTCAAATGGCCAGGTGCAGTGGCTCATGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCAGGCAGATCACAAGGTCAGGAGATTGAGACCATCCTGGCTAACACGGTGAAACCCGTCTCTACTAAAAATACAAAAAATTAGCCAGGCATGGTGGCACACGCTTGTAGTCCCAGCTACTCGGGAGGCTGATGCAGGAGAATTGCTTGAACCCGGGAGGCAGAGGTTGCAGCGAGCCAAGATAGCACCACTGTACTCCAGCCTGGGTGACAGAGGGAGACTCTGTCTCAAAAAAAAAAAAAAAAAAAGTTCAAATGGCAAAGTTTCTGTTATTTTTATTTTATCATGTTAAAAGAAAAGACTTCCTCTGGTTAAATCAGAGAACCCTGGAACACTAGGGAATGGAATTCTTTACTTTTTAGCAATGTTATAATAAATTCCATAACATAGACCAGGTATTCCATAGGTAATACTGTTATGAATTTCCTACTTATTAATCTAAATCAACAGCTTTTAAGATAGACTGTAGCATCACGTGGAGGACACACCCTAGAATATCATTATAAAGAGAAAATAGGATAAGGAGACTCTATAGTTGAAAAAAAAAGTGCTCTATCAGGAAGACTCCCTGGTA'..b'GACTCAGAAGGCATTTTGTTCTTTAGAAGGCTTTCTTTCTTTCTCCACTGGCTTTATTGAGGTGTAGTTGAGAAATTAAAAAAAGTATACTCAGAGTGTACAATGTGATGCTTTGATATACCTATACATTGTATAATGATTTCCACAAACTAATCAACACATTCATCACCATGCATACTCCTTTTTTGGGGGTGTATTTGTGGTTAGGACACTTAAGATCTACTCCTTCAGCAAATTTCAAGTAAATAACACAATATTAATCAGTCACCATGGCTAACCATTAGATTTGCAGAACTTATCTATTATACCTGAAAGTTCGTGCCTTTTGACCAACATTTCCCCACATTCCCCCTACAACAACATGGATGAACCTGGAGGACGTTCTGCTAAGTGAAATAAGCCAGACACAGAAAGACTAATACTGTACAATTTCATTTATATGTGGACCCTAAAAAGTCAAGCTCGTAGAGAGTAAAACGGTTGCTGGTGGGGCTTCTGAAGAGGGGGATTCTTCTCTGGTGTGGCAGATCTTGCCTGTTAGCAGAATGGGAATTTAATGTGTAATTCTAGTTTACCATCACATAGGGCATATTGCAAGCTTTATTTTGTTTAATTTTACTTATGTATTTTATTTTATTTCTATACATTCTGTGCCCAGGCTGGAGTGCAGTGGCACAATCACAGCTCACTGCAGCCTCCACACACTGGGCTCAAGTGATCCTCCTGCCTTAGCTTCTCAAGTAACTGGGACGGCAGGCGTGAGCCACTGTGTCCAGCCCTGTTTAATTTTCTAGCAGGAATTAAGCACCACATAGAGATGATTTTTTTGATTATTTAGGAACAAGGCAGAGTCTTTGGTGAATGAAGGGGAAGCACTCTGCAAGATATTAACAGGCCAGTATAGTGTACTTTCCTAAGAACGGAAATTACAAGTGTTTCATTAAGAAATATAAATTGTTGACATAATTTTAATCCACAGCATTATTTAAATTGCCTAGTTCAAGATTATTTTGAGAAAACAATTAACTGTGGCAATTCTAATTAAATTCCCTTGATGTGTATATTGGAAAAATATATAAAGCACAGATTGTAAAATAAAGAACAGCATTGGAAAGTTTCAAAATATATATTTTTAAGAAAAGCTAAAATAAGAGTCAAAATGAATTTGTTTGGATTCAGATTTTGAGTATATTTTGGTTCAGAATTTTCTGCTTGAAGTAAATAGAGACAGTTTAAAACTGATTAACATAATCGAGCCACCAAAATACTTTAAATTCTGTCACTAAACTGGAATTTAATCTGTGTTTCCTGAAGTAAGATAAAGCAATCCAACTTTTGATAATTAGACTGGTACTTCTTGGAGGAGTAAATAAGCCAAGGATAAGTAATTCCCACCTCTGCTCTAAGAGTCTTAGCATGTGGAATACTGAGGGGAGAAGACCAGGCCCTGGTGGACAAGAGAGAGTGGGAGATGGGAACTCTACTGAGTCTTGGTCACCAGGAACAATGCTGCCTTTAATCTACTACCTGAGTTGGCTGTATAATTTCTGGTACCCAATGCAAAATGAAAATTTTGGGCCCCTTAATGAAAAACAGGAAAAAAAGTGCTTTTAAGGTTCTAAAGTATAAAGCTTTGTTTCTGTATTCCATGGGCCCTCTCTCTCATCTTCTCATGGTGGTTTTTGTTATTTAATGTCCTAAATGAAATAAATTATTAGCATAAATTTTTACCATTCATCTTTATAATGTACAATGCCCGTTTTAAATGCAAATACAAAAGTATTTAACTTGGATGCAGAATCACTGAACTCACATAATTTGAATTTTATACATGCATATGTATTTTGTTCTTCCCAGCATAGTGGAAAACCTGCTGAAAATAACCCAAATGTTTTTATTTTACTTCTTGATATGTGTACAATATGGGTTACCCTGTCTTTCTCTTTCTTTTCCTTTCCTTCTGTATCATCACTTTCGGTGTAAGTCCTTGAATAATACAGGAAAGTGATACAAGTAAGAAAGAATATGATAGTTTCTTAGTCATGAATGTTCTAGAACATCATTGCCTCCTTTCTGAGATCTGGGTTGAAGGGAAAATGTGGCTATCAATGTCCCATTTACTCAGTCGTGGATATAACACATTCATCCTGCACTTTGAGTGTTGCTGGACTCCCATGCATTGCTGGTCCACTGGAACTTTACACTCATGGGACTCTTGAATGCTATATGCAAATAGGGCAGCAAGGCATGCCCTAAATGCAGACTGTGTGCAGCTCCTCTGCTCGTGCTTCATTGTGTTTTCAGACTTCACTTACAAAAAAGTTCAAAGATAGTATCATTAAGAATCCAAAGACGGTGACAGCTAGAGCATGAAACCAAGTGCAGGGCTCTTCTGCACATGGCTTCCTGTACAATTGCACTGGTTATAAAGCCATGGAACCAGCCTTGCCTGCAACAGTCAATTTGTTCAGATAGCACCTCGAGATTTACACTATTTGTCTTTAGAGTAGCAGGCCTTCCAGGGCATGAGGCTCAGTCAAAAGGAGGCCCACGAGGAAACATTCACAATGCATTTAGCACTAGCTCCTTCACCTCAGTGGTGAATTCCTACACTACACGATGATCTGCCCTTGTGCCCAGGCCACAGTCCAAACTGTGAGATCAGTTGTCAAAATGTCTGGAAGTGGGTGGGACATGTTAAAGATTCCCAGGGGATTCCAAAGTGTAGATTATGTTAAGAACCACTACTTCACTGCTACTTCTTCTTGTTACTGAAAGTATGACCCCTAGACCAGTAACATCAGCATCAATCACCTGGCAGCTTGCCAGGAACACAGAACCTCAGGCCCCACACCTACCATGTCAGGTCAGAATCTGCATTTTCATCTGCAATTACACTTTGAGAAGCATGGCTGCAGCTGGATGGGCCCTTTGTAACACCTAGAAGTTGACTCCTTAGGCTCTTCTATAAACACTGGTTATTAGCCCTGGTTGTACATTTAAATGATCTGTTTTATTCTAGCACCTAAGTATATACATTCATTACATTTATTTTTATGTTTAATAATTGTTTATCAGAATTGTGCAATTGGATTATTTTAACCAATTGAGTTTTATTAACAACAAATGTCATTAAGATTTATTTTAATGCTTGGAAACATATAATCATAAAATTAAAATATGTTTTAATGTTTTAACCTACATATGAAATTTGGCTACAGAGAAATATAATGTGTGACCAAAAAAACCTATAAATATATTAAAGCATAAATTAGATTTCAGTAGTAAAAAGTATGTGAAGAAGTAGATTGGAAATATGAAATAAAGGAGAAAATGCGCATAAAAATTTTGACTGTTCAAGATGGACATGTTCATGTATTTTTTAAGTGGCTGATGATAGATGTAAAATCCTGATGGTTTTTTCATTCCATTGGATACACTTAAAAGAGTAATATAACAGTTTTATTTTAAGATATTAAAAGGTCAATACTTGAAATAGGCCAACAACTAAATTACTTCTAACTGTTTACATTTATGATGATGAAAACACTAGACAACAATGTCTTTATTTTGGTTTCAATATTTATAATATACCAGGGATTATGTTATTTGCAACAATTTAAATTTCTGATGAAACATATTAAATGCCAGTATGTGAGAGGTACATAATTTTTCAAAATTCTACAGATGTAAAATAATTTGAAGACCACTGAGATACATGGGAGGACCTAAGAATCTCATGGGCATCTTTGAATTTCTCAGCCTGCAGCCTCCCTGTGGTCCACTTACCAGCACACATTCATTTTCTAGTATCCTACGCATCACTTTGAGAGGAACATGAAGGACAATTCTTTTGCTGAGTCTTCTGTGTTGCCTAAACTTTTCCTTCTCACTGGTGAGGCTACTTAAACCTGGGCATGGCCTGAGTTGTTGAACAATCACAGACTTACTTGTTATTGTATTCCCCCGA\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 95e4757d8da7 test-data/ngmlr-ref2.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ngmlr-ref2.fa Thu Oct 29 15:43:54 2020 +0000 |
| b |
| b'@@ -0,0 +1,2 @@\n+>chr21 21:21,444,718-21,464,625 hs37d5\n+ATACTGACATCCATGTAGATACATTTTTCCTGAAATGATGATTAGTGAAAAATTGAGTCTACATTATTTCACTTCAATAATTTAAAATTTTATTGAAGAGTTTATTATACAGCAATAATAAAAAAAGATAAGTATTTCCATTCTCATGATGATTTTGGCCACAATGAAAAGGGAGGTGCATTCCAGGACTATAATAATGGTTCAATACTGGGAAATTTATTAATACAGACTAATATACACAAATTAAGTTATAGGCCTTAGGAAAAAACTATATGTGTATATTTGCAATACTTTAAAGCCTTTCAGAGAAGTCAGCATCCATTCCTAATTACATATATTTTTCATGAGAATGTAGAAAGATATGGTTAATTCCTTCAAGCGATAAAATATATATACCTCAATTGGAAAGTCCACATCTTAATGGGTAAAAACATACAGGTAGTCCCACAAGAGTACTGAAAAAAAGTGCATGCCCACTCTCCTCACTGTTATTTAATATTGTTATTAGTTGATGCAGTTAGATACAATTGTCACACAAACTAGAGCAGCAGAAAAAAAAGTGTCTCTATTTGCAGATGACAATAATATATATCAATAATATATATAGATGCCTAAATGATAAAATATAAAATAATGCAAGTTGGCAGGTTATATTTTTAAAAAATCACTATTATATCTATATTCGCCTACTTATCTGTTTATTATCTATTTGCCATCCAACTTTCTGTTTATGCCAATTAGATAATGGAAAGACATCCTTTTTTCCTCATTTAGAACCACTCAACATCATCATGAAGTCATTTCTACATAATTGATTTATAAATTTGACGTTATCCCAAGATAAATCATAAGCGTTTTTATTTATGAAGCTAAATAAATGAATACTAAAATTATTATAAAAATAAATACACAGAATAGAGAAATATTTAAAAGTAAAGCTGTGAGGGAGGACTAGCCTTATTGAATATAAAAATAGTTCACTAAGGTTTTATCATTGAAATGATAACTATGTGTGGATACCCAAGAGAAGGGTATAGAAAGCTGAAAATAGACCCAGTTACATATATTAATCTAGTTAATAATGAAGGTGTTATCTCAAATTACTGAAGAAAATTGAACTTCTTAATACATGAATATTTATTTGAAATATGGTAAAATCAGATTTAATACTCAGAGCTTATATAGGAGAAAAACCCAAATTGTTCAGAGATCTAAATGTCAAGCATAGAATGTTGAGAGGCAAGAAAGAACCCCATGGTTTGAATTGGAATAAGGGATTTCAATGTGAACTTATGATGTCTAAAATATGTATATGCATGCATATATGCATATGTAATATATATTTCACTTATGTATAAATATGTGTTTTATAATAAATAATATATTTGTACACTTCTGCATTTACTTATCTCTATTTGTTAAAATGATCTAAATGCAAAATCATTCCAATAGCAATGAGTTCATATAACTATCTAACATCCAGATCTTGTTTTTTAATACCATTCTTCACTAAAAGAAGTCAGCTCTTTCACAGAATTGCTGATTCTAAGGGTAGGCCAGAGGAGGTAAAACATGAGTCTGGAAAATTTTATTTGCCATAAAGGAGGAATGTGATCAAACAGTAGAAAATTATGGAGATAAACAATGTTGAACATATATCACAAAGACACAGGAATCAGCTTAAAGGGGTTCCTCATAGCCAAGTCTAGGACCATTTGAGCACCTAAGTATTTAAACTCAGTGATAAATAATACACCCTTAAGTATAAGAATTCAGGGGTCCATAACTATAAGAAGAAATATGTGGGGACTTGTTACAGATCATAGATTAGTAAATAAAAAAAATGGCAATCATGCTGTGGACAAAATCAGCAAATATCATTCGCCAGGTGGTCCAAATTAACATCACTAATGCCAGGCAGATGGCATGAGTTTCCAGATGTTACTTTCTGTCAAGGACATGTTGGACTTAGGTAATAGGCAGCCTGAGGATGTGTAAGCTTCATTTATAAAGAAGGAAGTATAATACATATTTAAAAATCAATTTTAATAAAATTGGAAAATAAAAAGGGAAAAAGACTGAAAACTTCTATGTCAATTTAAGAAAAGTATGAAGAATTTTTCTAGATTGAAGTAGACTAAAGAGAAATGATATGCAAATGTAACAGGTGATCCCAGAATGGATTTTCCTTGGAGAGAGAAAAATGTGCTATAAATCATATTATGTGCTCAGTTGGCAAAAATGGGTATGGAAGGTACTGTATCAGAGTTAAATTTGTTGAAGTTGATAATGTCATTTTTTAAAGGAATTTTCTTGTTCCTAATATATTTAATGTAAAGATCGATGATATATGCATCTAACTCTCAAATAGTTCAGCAAAATTATATATATATAACTACATATGTGTGTACATATATATGTACACATATATCTAATACATAAGATGTATATATACATGCATACATACCTACACAGAGAGCGCAATGGGGCAAAATATCAATGAGAGGTGAATCTGACTGGTAAAGGATACTCTTTGTACTATTCTTGAAATGCTTTGTAAGTTCAAAATTATATCTGAAATAAAACAAAAAAATTTCAAACTGAAGATATTTTGATTATATTGAGACTGATGTTTTAAAGTCCCAAGAAGCAGGTCCTGAGATAAAAATGGGTAAGTCAATGATTTTTATAAAACCTGGTGGCAAGACAAACAGGTAAATCAATGGCAAATTTAAGATTAGGAAGTGGAACGAGCTCAACAAGGATATGATTTCATCCTTGAAGACAGTGTTCAGCTTGATCCCATAGGGAACTTAGAAATGAAGTCAAGCCCCAGTATTGTTCTGCTCCATCAATGGCAAGGGAGCTGAACTTCTGGCTTTCCTGGATGGCAGAAAAAGGAGGCTCCCATTAGGAGGAGTGCAATTCTCAGAAGAATTTGGGTGGCTGGCCTGTGGAAAACGGATGCAGTAGGAAGTGAGGATGAGGGCTTACAGAAAAGGTAGAAAGGAATCTCAGAAGAGCTAGATGAAACACTACCTCATGCTTTTATAGTTTAAAATTCCCCTGAATAGATTTTTAAAGTAACATGTAAATTTGGAAGAGATGAAAACTTTGAATTATTTAAATACAGAGATGATGGTTGTTCCATTCCAGACATCATTTTTGAAGGTTAGCTATCATGTGCCAGATGTCTTACAAAAAATAGGTGTGTGTGTGTGTGTGTGTGTGTGTGCTGTTTTTGTTATTATTTATCTTAAACTCTCTGGACATATAAAACCTGTTTTGCTTTAGTAATTAAAGGCAACTTTTTTTCTAAAACTTAGTGCTAAGTGCTCAATACCTAAGGAGAGAATTAGATCAAACAATGTGGTTTTAATATACTTTTTGTCTTCACTAATATAAGGAGATAACCTATTGGGGGTTTCATATTTTCTCCATAATGTTCATAAGGTGTGCTATCGGCATTTCAGCAATATAGCCTCCTTGTGGGCTATAGCATTTCAATCATTACAGGAAATTTCACTTCTCTGGACTCCATCTGCAAAAGATCAGTAGCGCTCTTCCTCCCCCACATTGAATTACATAAAAAACTGCTTTCATCTGTATATAACATGTGATTCTAAACATCCCTTAGGTTTAAGTGGCTATAGTATGTATTAGCATAATATTGAAGTTTAAGGAAAGTAAGAGTTTAAACATTCAATGTAGACATTGCTAAATGTTTTCTTCCAATTTGAAGGGTTACAGCATGTTACTTTTTTTCTTGAGTGTTATCAAACTCAAAAGATAATAGCTAATTTACAGAACATTATTTCTACTGGGAAAAAATAATCACATTTAATGTTATCAAAGATATGGATATAATCTAAATAATTTTAACTGTGCTTAGGTTATATTTAAACATTAAAGATAGCATTTCTTAAAAATTAGTATTTTTTA'..b'AGTGCGGTCAGTGTATTGAAGTAAATTTTAAAAATTCAAATTATTCACTAACAAACAGCACATTTTCTTTAACAATTAAGTAGCCAAGATTTCATAGCAATATAATAAAAAAAAAATGTTATTCGTTTTCCTTTTAATGCAAAATAATTCTGAACTAAAAAGAATGCATTCAAATCATGTTTATCTGAAACTTTTGCTTTTTAAATTACTTTTATTTACTCACTTAAATTTTATTAGCCTACTGACACACAATATTTCAATTTGTAGTAATAATGCTTTAAAAGCCCAAGGTTTTACTTTAATAATTTTAGTGTGTTAATTTTTAAGAACTCAAATTGTTAAGTATTATTCATAGAACAATTATTCCAATGTTCTCCTGAACTATAAAGCTACTGTACACGAGAGTGAATTGGTTATAGAAATGGAGACAGGGAGCAGATTTTTTTCAATGTAATTAAAATAAATTTGAACTGAATAAAGTTCAATGTATTTCAGATTTAATAGGCATTGTATTTACTAATAAAAAAATTGCATGCTTGAACTTACTTAACCTTGGAGAGTAGAGGTAGCTTTTCATTAATCTCCTTTTTTAAAGTTGGATGAGGTTATGTAACTGAAATAGACATTAAAATTGAAGAGACATTCTTCATGGATTACAGAACAGTATTTGGAAGGAAACCAAATCATTAAAATATCACCAATAAATAATTAAATTTGCTTATTACATTGAAAGGACAGAACTAGAATAAAATTTATTGAGGCTACTGTGAGCCAAAGGCTTTATATAAATTATTATGTTATATCTTCATAATACTCTTTTGTGGTAGATATTTTCTCATATATTAAAGTTGGAAAAACAGGTTTAGGGAAGTTAAGTCAATTTCAAAAATACCAAATGAGTAAGAAGTACAAATCAGGATCTTATCTAGTTCTGTCTGACTCCAGTGGCAGTGATGTGTGCATTACATATTTGCGTGTGTGTGTCAAAAGAAGAGCAAAGGAGACTTTAGAAGAGATGCTGATTAAAGAAGATCAGAGGCAGAGACGGGCGGATCATGAGGTCAAGAGATTGAGACCATCCCGGCCAACATGGTGAAACCCTGTCTCTGCTAAAAATAGAAAAGTTAGCCAGGCATGGTGGCGGGTGCCTGTAGCCCCAGCTACTCAGGCGGCTGAGGCAGGAGAATGATTTGAACCTGGGAGGGGGAGGTTGCAGTGAGCCGAGATCACGCCACTGCACTCCAACCTGGAGACAGAGCAACACTCTGTCTCAACAAAAAAAAAAAAAAAAAAAAAGAAGATCAGAAATATCTTTTTTACTTTCTCTTCCCATTTTTTTAGAATTTTATTGAAGTATAAATGAAATACCATAAACTGCAAATATTGATAAATTTTGATACGTGTATGTCTAGTGCAAATAATGAAGATAATGAAAATATTGCATATCTGTCAACCAAAAATATGTTATTTATACCCGTTTGTACTTTCTCCATCCTGCCTCTTTTTACTACTTCCTCCCACTCCTAACAACAGCTGATCTGCTTTCTGTCACTATAAGATTAGTTAGTATTTTGTATAAATGGACTGATTACAGGAGCCACCTTTTTTTCTGACTTTTTTCATTTAGGATAATTATTTTGAGATTAATCCATGTAGCTACAGGTATCAAAAATCTGTTCCTTTGTATTGTTGAGTAGTATTCCATTGTAAGGATATACTGTAATTTGTTTGTTTATACACTTAATGGACATTTGGATTTTACTAGTTCCTGGTTATTGCAAAGAGAGCTTCATCCTTTTCCAGAGTTCATATGAACCTACACTTTTTCTCCTATTCATGCAACTCATAGCACCTATCATATGCTATGTGAATGTTTATGTGTGTATATATAAAAACATATATATACACACATATAAACATATATACACATATATAAACATATATACATATATAAACATATATACACACATATATAAACATATATATACACATATATAAACATATATAAACATATATATATACACATATATAAACATATATATACACACATATATATATATTTGATTAAACTCTTTTTGGAGTAGTTGTACCATTTTACACTCGCATCAGCAGTATATGAGAGTTCTAGTTCAACCACATCCTTGTCAACACTTTGTATTTTTTCTTAATTTTCTTTTTGAAAAAAATCTAGCCTTCTAATAAATGTGCATTGACATACTATTACAGATTTGCTTTGTATTTCCCTAAAGACTAATGATTTCCAGCCTCTTTTAATAAATTTATTTGCCATTCGTATATCCTTTTTTATGAAGAGCCTCTTCATATCTTGAGCACAGTTTTAAAATTTGAGTTTTTTTCTTATTATTGTATTTTACAAGTGCATCATATATCTTAAATAAAATCCTTTACCGCATACAAGATTTACAAATATTTTTTCTAATATCTGGCTTAAATTTTTATTTTATTTCTAATGTCTTCCAAAAATTAGAAGTTCTTCAATTCGATAAAGCACATTTTATCAATTCATTTATTTTTTAAATAAATTATGATTTTGTTGTCTTATTTAGGAAAACTTTGCCTATTTCATGGTCACACAGATGTTCTCTTAAGGTTTCTTCTAGAAGATTCTGTTTTAGATTTTAACTTTAGGTCTATGGTGCATAGTAAGGATAAAGATACCATGCATATTTCCTTTTTTTAAAAAAAATGGACATTAATTATTGGTTTTGTTTGTTTGTGTTTTGAGACAGAGTCTCAGTTTGTTGCCCAGACTGGAGTACAGTGGCGTGAACACAGCTCACTGCAGCCTTGAACTTCTGGGCTCAAGTGATCCTCCCACGTCAGCCTCCCCAAGTAGCTGGGACTACAGGTATGGATCATCACGCTCATCTAATTTTTGTATTTTTTGTAGAGACTAGATTTTGCTATGTTGCCTAGGTTGGTCTCAAACTCTTGGGCTCAAGTGATCAGCCCACCTACGCCTCCCAAAGTGCTGGAATTACAGCCTGAGCCACCGTGTCGGCCATTAATTGTTTTACCACTGTGATAATCAGCCTTATGTGTAAAGCTGATTAAGCTATAGTTCCTAATTATTCAATCTAACATCTAAGTTTTGTTCAAAGACGTTTCTGTAGATATTATTAAGTGAGGAAGATGATTCTAGATAATCACGGTGGGCCTGAATCAGTCAGTTGAAAAGCCTTAAGAGAAGGCGGGAGTTTTCCCTGAGGAGGAAGCCATTCTGCCCATGGACTGCAACCTCAGCTCATGTCTAGAATACGTGAAGTGTTTCAGCTTGCCCTCCCTGACAGCCTTCCCTATGCCAATGCCTTGCGATAAATCTCTGTCCTCTCTCTCTCTCCTTCGCTCCCACCTTCTCTCTCCCACTTACTTACCCTACTGGTTCTGTTCTCTGGTGGAACACTGACTGATGCTACCACCGTTTCCTGAAAAAGATTATTTCTTTTCTCCGTAAATTGCCTTTACATTTTTGTCGAAGATCAATTGTATGAATATGTGTAAGTCCATTACTAGGCTTTCCTATTTTTTGAGACTGAGTCTTACTCTGTCACCCAGGCTAGAGTGCAGTGGCGCGACCTCGGCTCCCTGCAAGCTCCGCCTCCCAGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCACCACCACGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATAGTCTCGATCTCCTGACCTGGTGATCTGCCCGGCTCGGCCTCCCAAAGTGCTGGGATTACAGGTGTCGCCACTGAGCCCGGCCGTCCATTACTAGACTCTTATCTGTTCTATTAATTTGTTGGACTATCCACCACTACCTACCATGCTGTCTTGACTACTGCATTTTTATCATATATATTGGAATCAGATAGCATAAATTTTCATGGGAGAGAAGCTGAGATAA\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 95e4757d8da7 test-data/ngmlr-ref3.fa.gz |
| b |
| Binary file test-data/ngmlr-ref3.fa.gz has changed |