| Previous changeset 1:e100f3f4d80e (2018-09-27) |
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Commit message:
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit 05f8373310ce1728426b89f33b643406e0cba54b" |
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modified:
macros.xml wtdbg.xml |
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added:
test-data/test1.fastq test-data/test1_head.fa test-data/test1_tail.fastq |
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removed:
test-data/consensus_result1.fa test-data/consensus_result2.fa test-data/consensus_result3.fa test-data/dbg.ctg.lay test-data/ecoli-reads.fa test-data/ecoli-ref.fa test-data/result1.alignments test-data/result1.ctg.lay |
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| diff -r e100f3f4d80e -r 2668027a533b macros.xml --- a/macros.xml Thu Sep 27 17:52:13 2018 -0400 +++ b/macros.xml Sat Jan 29 12:49:28 2022 +0000 |
| b |
| @@ -1,22 +1,39 @@ -<macros> - <xml name="requirements"> - <requirements> - <requirement type="package" version="2.0">wtdbg</requirement> - <yield/> - </requirements> - </xml> - <xml name="citations"> - <citations> - <citation type="bibtex"> -@misc{githubwtdbg-2, - author = {Ruan, Jue}, - year = {2018}, - title = {wtdbg-2}, - publisher = {GitHub}, - journal = {GitHub repository}, - url = {https://github.com/ruanjue/wtdbg2}, -}</citation> - <yield /> - </citations> - </xml> -</macros> +<macros> + <token name="@TOOL_VERSION@">2.5</token> + <token name="@VERSION_SUFFIX@">0</token> + <xml name="citations"> + <citations> + <citation type="doi">doi:10.1038/s41592-019-0669-3</citation> + </citations> + </xml> + <token name="@ASM_OPTIONS@"> + -X $asm.X + -L $asm.L + -k $asm.k + -p $asm.p + -K $asm.K + -s $asm.s + -e $asm.e + $asm.realign + $asm.contained_reads + </token> + <token name="@CNS_OPTIONS@"> + -j $cns.j + -M $cns.M + -X $cns.X + -I $cns.I + -D $cns.D + -b $cns.b + -H $cns.H + -B $cns.B + -W $cns.W + -w $cns.w + -A $cns.A + -S $cns.S + -R $cns.R + -c $cns.c + -C $cns.C + -F $cns.F + -N $cns.N + </token> +</macros> |
| b |
| diff -r e100f3f4d80e -r 2668027a533b test-data/consensus_result1.fa --- a/test-data/consensus_result1.fa Thu Sep 27 17:52:13 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,231 +0,0 @@\n->ctg1 len=15016\n-GCGGTGGTGCAGAGTGGCGGCGTAATGCGACGCGCAGACGGGCTCAATTCCGCCAATGCCAAACGGCTTACTTCCAGATAATCATCCGTTTCCGGCATCC\n-AGCGCGGCGATTTTGTCGTTTTCGCTGCGCGGAAAGCATTAACACCGGCACCGCGCTCCACTGGCGCAGGTCGCGGATAAACTCAATCCCATCACCATCG\n-GGCAGGCTTCGGAGATCGAGAATAACCAAATCTGGCTTACGGGTTGCCGCTGCTTCCAGCAAGCCGCGTTGCAGCGTTTCGGCTCAAAGACGCGCATCCT\n-GTCGCCCTCCAGCGCCGTGCGCAGAAAGCGACGAATAGCCTGTTCATCTTCTTCAACAATCAGAACGTTTGTCACATATCCTCGCTGAAATTCTTCAGTT\n-CAGGGGCAGTTTGCTGGGGAAGCGGTAACACGAAAACAGGCACCACCTTCCGGTCGGTTGAACGTGGGTAATAGTGCCCCGTGTACATCCACTTATCGCC\n-CGACAAACTGCCAGTCCAAGCCCTACCCCCGGTACTGCCGACTCTTTATTCCCGCGAGCAAACTTATCAAATATCGTCTGCTCCTGGCCTGGCGGAAGAC\n-CGGGGCCGTTATCCCAGACATCCAGTTGTAGATTTTCGCCCTCAACGTGGGCATCGATACCAATTTCGGCCTGCGCACCCGCATATTTCACCGCGTTCTC\n-CAGCAGATTAATCAGCACCCGTTCAAAGAGGGCCCGTCAACGTGGATTAAGGTCATGGTTCTGGCAGAGAAAGATTGATGGGCGACGATAAACCCGGTTC\n-CAGCATTTGCAGCGCGCTGCCGACTACTTCTTCCAGCGTTAACCACTCTTTCTTCAAATTAAAGCCGCCGGACTGGAATTCGCGCCATACTCCAGTAGAT\n-TATTCAATTCAGTCGGTAGTGTTCAGCACATGCTGACGGATCCGCTGGCCTGGCGGGCGGGGTGATCCTTCGCTTGCCAGACCGAGCGTTAAGATTTCTG\n-CCTGACCAAACAGCACCGTAAGCGGCGCGTAACCGCGAAAAGCGCTGCCAGCAGGCGTTGCGGATCTGTTCAATGCCCGCTTGCCATCCGCGCCTGTTCT\n-TCGCTGGCGGTGGTTACGCGCCGCCGCTCAAGGGCATTGGCGACCAACAGCGTAACGTCTTCCAGCAGGCGCTGCTGTTCCGGGATCATCAACTGGCGCA\n-GATTCCCGGCTCCACCACCACCAGCCCAGGGTAGTTTTCGCCGCTTTTTATGGCAAAATCTGGTACGGTACACCGGGTAACGTGTCGGTGCCCGCGCCCG\n-CAGGCAGGCCTTTATCAAACTCCACTCGCGGCGATGGCATCGTCCCACGGCGTCATTCCTGCGGATGTTAACGGCTGCAATTTACCGTTGTCATCGGGCA\n-ACAACACCCGACTGCGGGCATGAAACGGAGGCAATAAATTGTCTGCTGGTGGCAGCGATATCCTGCGGACTGCACCACCGCCAGAGCTTTCGACATTTCA\n-TATAAGTGCCGTGTGCGCGTTCGCGGTAACGGGCTACCCGCGCCTGATAACGCACGCCAGCAGTAAGGTTCCTGATCACCAGCCCGACGGTTAACATCAC\n-CGCGAAGGTCAGCAGATATTGCACATCAGAGACGGCGAGCGTGCTGCGTGGGGCGATAAAAAAGAGATCGAACTCACTACATTAATGACGGTGGCAACCA\n-CTGAAGGCCAGCGTCCATAAATAGCGCCACCACCACCACGCCAAGCAGATACAGCAGCATCACCAGGTTGGCGCATCAACGCCATCAGCCACTGCATGGC\n-AATTACAAGAGATAACGGCGCATAACGCGGCGGCAACCACGCATCCCTGAATTTGTACACGCCACTTGTCTTTAAAAGAGCGGTTATCCGGCGCGTTGTT\n-AATCGTGCGGGCGGGTGGTCATCGGGCGCGACCAGCACCTGATCGAGATCGGGGCGATGCGCGCCAGTCGGTCAGCAAACGTCTCCCGACGCCACCAGCG\n-GCGCGAGGCCGCGACTGAGAATAATCTTACGAGATTATGTTCACGGGCATAACGCACTACCGCTTTCTCTCTTCCGCTGGATCAACAGAAAGTGTTGCCG\n-TCTCCAGCCCAGTTCCTGCGCCAGACGGGCGCGCTGAGAATTGCCCGACGTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATAACACCGCGCC\n-AGACGCCACCCAGCCGTGACGCCAGCCGCAGCTGCGCGGACCAGTTTTTCGCCGCCGGTGTTATGGCCGATGCATAAAGGATCGCGTCGCGTGTGCCACT\n-TTCTCTTCTGCCAGACGCCCCCGCCAGGCGCGCATTTGCTCATCAACGCGATCGGCAGTACGGCGTAGTGCCAGTTCATGCAGGGCGACCAGATTACCTT\n-TGCGGAAAAAATGTTCAATGGCGCGCTCCGCCTGCCCGGCAATATAGACTTTGCCTTCTCTCAGCCGCTGGCGCAGATCGTCCGGGGCAAGTCCACCAGC\n-ACCACGTCGTCGGCGGCATCGAAAAGGATCGGGCACGGTTTCCCGTACCTGAATTCCGGTGACGCCGCTGACCACATCATTCAGACTTTCCAGATGCTGA\n-ACGTTGACGGTAGTGAAAACATCAATGCCAGCTTCCAGCAGTTCTTCGATATCCTGCCAGCGTTTGGGATGACGGGAACCTGGCGCATTACTGTGCGCCA\n-GTTCGTCCATTAAGATCAGCGCCGGGCGGCGGGCGAGGGCGGCATCGAGATCAAACTCGCTGATATGCCGCCCACGGTACGCCTGGCGTTTTAACGGCAG\n-AACAGCCAGCCCTTCCAGCATGGCGGCGGTATCTTTCGCCCGTGGGTTTCTACCACGCCAACCACAATATCCAGCCCTTGCGCCCGCAGTCGCTGGGCTT\n-CTGCCAGCATCGCCCAGGTCTTCCCGACGCCTGCACAGGCACCGAAGAAAACTTTCAGCTTCCCCGATGCGGCGCGGCAGTTTGTTCCAGCAGACGATCG\n-GGGTCGGGACGTAAGGGTTCGTTATTCATCAAGTTTATCCAGCGCCAGATTGAGTTCATCACTGACAACCGGCTGGCCGATATATTTCACCAGCGGTTGT\n-TGGCTGTATTTTGCGATCAGTTGCGTGAGCTGTCTAACGCTGAGATTACGCGCTTTCGCCACGCGTGGATTTGCCAGGCCGCCGCTTGCGGGTGATATTA\n-TTGTCCAGCCCGCTTGCCGATGCCGTCACCAGTTCAACCGGAACGCTCGCGCTGGCATCCGGGTTAGCGGCCCGTAATGCAGCAACGCGTGCGGCTATTA\n-GTTTATCCAGCTCAGGGTTACTGACCGCCAGATTGCTCCCGCCAGAAGCCTGTGGATTATAGGGCATTTCTGCCGTTGCCGACGGGCGACCATGAAAATA\n-GCCGTTGCCGGTAAAATTCTGCCCGATTAATGCCGAACCGCGCACCGTATCACCTTCACGAATCAACGAACCATTACCCGCCAGGAAACCACCATTGCCC\n-CAGTACGGTGGTCAGCAGCGGGTAAACGCCGCCAGTAATCAATAACAGAAAGATAAATGTTGATAATGCCGACGTAATCCACTCATGGTAAACTCACACC\n-AGACCGCAAACGGTCAGCGGTAAATCAATGACTTTGATACCGATAAACGGCACCAGCAGCCCACCCAGACCGTAAATCCATAAGTTACGGCGCAACATGG\n-CAGAAGCGGTAAGCGGTTTATAACTCACGCCTTTAACGCCAGGGGAATCAAAAAGACGATAATCAAGGCGTTGAAAATCACCGCACTGAGGATTGCGGAG\n-TCGGGCGAATGCAGGCACATGATGTTCAGCGCATTTAACTGCGGATACGTTGCCGCGAATGCCGCCGGAATAATGGCGAAGTATTTC'..b'TCCGCACCAATTGCGGCCACCAGGCCGGAAACAAACCCAAGCA\n-TGGCGAACTCACACCTGGCGTGGTACGCAGCAGTTTTTCCCGCACCGAGTGTGCGCCACACCACCAGCTCCTGATGACGCTGACGCATTCCCACCTGCAC\n-CTGTGCCAGCAACAGCAACATACCGCAGGCGGTGACCAGTACCACCATCACTTCCAGCGCCCGACTTACCTGCTCCAGCACCTGACCGACCTGTTTTAAA\n-AATCGCGCCAATATCTAACAGGCTAATGGTCGGGAACTGGCGGTTGAGTTGTGTCAACATGCCGTTGCCATTCTCCCAGCGGAAACTGGTAAGCCAGCTC\n-TGCGGTTGCCGTCTAATGCCCCCTTCAGGGAAAATAAAATAGAAATTAGGCCGCAGACTTTCCCAGTCCACTTTGCGCAGGCTGGTCACTTTAGCGCGGA\n-ACTCCTGGGTATCGCCCATAAAAGTCACGGTATCACCGAGGGCAACGTTTAAGCGTTTCGCCAGCCCCTCTTCCATCGACACTTCATCGGCTTTTGGCGG\n-CCAGTTACCGGCGACAATCGGATTATGATCGGGCCGCGTATTTTGCCAGGTAAGATTGAGTTCGCGGTTAAGCGCCTCATCTTCATTACCTTCTGTCGGT\n-TTATCGTTAATCGCCGTCAGCCGCGCCCGCACCACCGGATAAAACGATTCCGGGACTATCTGATGTTCCGCGAGGAACGCTTTAGCGGTGCTACCTGTTC\n-TGTGGCGATGTTAATTAAAAAGTAGTTCGCTTCTTGAGGTAGCTGCTGCTGCCAGCGGTCGAGCAGATCGCCACGCAACACCAGCAGCAGTGCCAGCAGC\n-ATAAAGGAGAGCGAAAATGCCGAAAGCTGACTTAACGTTGACCACGGCTGACGTAACAGGCGGCTAACCGCCAGGCGCAGAGGCAGCGATTTCAGCGTCA\n-TGCGGCGAAGTACATTCAGCAGCATCCAGCCCAGCACACCGCACAGCAAAGCCAGTACTACCGCGCCCGCCAGCACCGCCCAAAGCAGCATGCTGCCACC\n-CATTAATCCGGCGAGCAGCAGCACAACCACCACACTGACAATCGGCAGATAAAACTTCAGCGGCCAGACGTTCGCTACCACATCATTACGTAATACGCGT\n-AAAGCTGGCAAGGCCAGCAAATAAGCGATATGGTCGTAGCCCCACCAGCAGCGAGATGACCGCCATGGTGCCAAGCGCCCACGTTAATGGCCAGAGGCTG\n-GCTGGCGGTAGTGCAGCAGGCGAAACGGGCTTGAGCAGCACCATCAACACGTTTTCGAACAACAGGCCTATGGGTCTCACCGGTAACGGCTGAAAGCGTC\n-AGCACCATCAACCACTGACCGACGATTAGCTTACGCAGTTGCGCCTGCCCTGCCCCCAGCGTTTTGAGGATCGCCACCAGATCGTAGCGACTGCGACAGT\n-ACGATTCATCGCTACCGCCACCGCTGCCACTGCCAGCAGCAAGGTCAGAAGCGCCGAAAGCAGCAGGAACTGTTGCGAGCGTTCCATCGATCGCCCCAGC\n-GCGCCTTCGTCCTGTTCCAGACCGTACCAGCGTTGTTCGGGTTTAAGCCGAGGTAACAACTATTTCTCATAGCCGTCGAGCTGGTTCTCGTTGCCGCCGG\n-AATTTATAACGCCAGGTGACCTGACTTCGGCTGTAATGGCTCCGGTTTTATCGACATCCGCCAGGATTCATCATCAGACGCGGAGCCATCTGAAGGGGTT\n-AAAACCGGAATCCGTTCCTGAATCACTTCTCCGGCAATCCGCAAGGTGGCATCGCCCACGTCAATGGTGTGTCGCCCGTTTTCAGGTTAAGCAGTGCCAT\n-CAGGCGTGGGGCCAGCAATACGCTGCCCGCCTGCGGTTTCAGGCCAGGGGGATTAGTTTGCAGATCGCCATACATCGGGTAGATATCATCCACCGCTTTG\n-ACGTTCGCCAGCTGCGGTGTGTCGCCTGCAAGGTCATTGTGGCGAAAGTCAGCTGCTTGCCGACTTTCAGGCCGCGCTTTTGCGCTTCCTCCAGCCACGC\n-TTGCGGCACTTCGCGTGAACTGCGCAACGCCCGATCGCCCGCCATAAACTTTCACGGTTTTGCTGGCTGGCCCTTCTCCATGCGATCGCTGATTGCCCAG\n-CGCCAGCATCGCAGGCCACCGCCAGGCTTAGCGCCAGCCAGACAATTAATATGACGGCGAACGCCATTCGCGCCAGAACCAACGTGCAATCATGCTTCCT\n-CCTGCAACTGCCTGTTCACCAGCCGTAAGCAGCGGTCGCAGCGTGCTGCCAGTTGCAGGTCGGGTCACCATAATCAACGTGGTGCCATGTTCACGGTTGA\n-GGAAAACAGCAGGTCGGCAATTTTATCGCCCGTCTGGCGGTCAAGGTTGCCGGTGGGTTCGTCGGCAAACAGCACACATCAGGTCGACCATTAAAGGCTC\n-GTGCCAGCGCCACTCGTTGCTGTTCACCGCCGGAAAGCTGTGCCGGAAGATGATCCAGACGTTTGCCCCTGCCCTAACTGTTCGAGCAACGCTTTCGCCC\n-CGTTAGCGACTTTCCGCGCTACTCACCGCGCAGCAGCATTGGAAGCTCGACGTTTTCCAGCGCGTTGGCGGTAGGAATTAACATAAATGACTGAAAACAA\n-AGCCGACGTGCTTCGCGCGCAATCTTGCCCGCGCTTCGTCCATATTATGTGAAGCGGTTGTCCCACCAGACTCACTTCGCCACTGCTGCTGTCATCAAGC\n-CCGGCGAGGATCGCCAGCAGCAGGTTGACTTACCCGATCCCGACTCGCCCACCAGTGCGATGGTCTCGCCGTTTGATAACCAGCTCAACTCCGGTGAGGA\n-TGGAGAGTTCATGCTCCCCTGACCGACGGACCTTAAGATGATGAACCAGCAATGTTTTCCCGCTGGCATTTGCCCTTCCTGTTCCTGGTCACCATTAACC\n-TTCCGTGCCGCCGCAGCGGCCGTTATTGATTCTGGGTGATAGCCTGAGCGCCGGGTATCGAATGTCTGCCAGCGCGGCTGGCCTGCCTTGTTGAATGATA\n-AGTGGCAGAGTAAAGAGCATCGGTAGTTAATGCCAGCATCAGCGGCGACACCTCGCAACAAGGACTGGCGCGCCTTCCGGCTCTGCTGAAACAGCATCAG\n-CCACGTTGGGTGCTGGTTGAACTAATGGGCAATGACGGTTTGCGTGGTTTCAGCCACAGCAAACCGAGCAAACGCTGCGCCCGGATTTTGCAGGATGTCA\n-AAGCCGTAACGCTGAACCATTGTTAATGCAAATACGTCTGCCTGCAAACTATGGTCGCCGTTATAATGGAAGCCTTTAGCGCCATTTACCCCAAACTCGC\n-CAAAGAGTTTGATGTTCCGCTGCTGCCCATTTTTATGGAAGAGGTCTACCTCAAGCCACAATGGATGCAGGATGACGGTATTCATCCCAACCGCGACGCC\n-CAGCCGTTTATTGCCGACTGGATGGCAGAAGCAGTTGCAGCCTTTAGTAAATCATGACTCATAAAGCAACGGAGATCCTGACAGGTAAAGTTATGCAAAA\n-ATCGGTCTTAATTACCGGATGTTCCAGTGGAATTGGCCTGGAAAGCGCGCTCGAATTAAAACGCCAGGGTTTCATGTGTGCTGGCAGGTTGCCGGAAACC\n-GGATGATGTTGAGCGCGCGCAGACAGCATGGGATTTACCGGCGTGATCGATCTGGATTCACCAGAAAGTGTTGATCGCGCAGCCGACAGGAGGTGATCGC\n-CCTGACCGATAGTGTCTGTATCGGGATCTTTAACAATGCCGGATTCGGCATGTATGGCTACTTTCCACCATCAGCCGTGCGCAGATGGAACAGCAGTTTC\n-CGCCAACTTTTCGGCGCACACCAGCGTCACCATGCGCCTGTTACCCGCGATGTTACCGCACGGTGAAGGGCGTATTG\n' |
| b |
| diff -r e100f3f4d80e -r 2668027a533b test-data/consensus_result2.fa --- a/test-data/consensus_result2.fa Thu Sep 27 17:52:13 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,231 +0,0 @@\n->ctg1 len=15021\n-GCGGTGGTGCAGAGTGGCGGCGTAATGCGACGCGCAGACGGGCTCAATTCCGCCAATGCCAAACGGCTTACTTCCAGATAATCATCCGTTTCCGGCATCC\n-AGCGCGGCGATTTTGTCGTTTTCGCTGCGCGGAAAGCATTAACACCGGCACCGCGCTCCACTGGCGCAGGTCGCGGATAAACTCAATCCCATCACCATCG\n-GGCAGGCTTCGGAGATCGAGAATAACCAAATCTGGCTTACGGGTTGCCGCTGCTTCCAGCAAGCCGCGTTGCAGCGTTTCGGCTCAAAGACGCGCATCCT\n-GTCGCCCTCCAGCGCCGTGCGCAGAAAGCGACGAATAGCCTGTTCATCTTCTTCAACAATCAGAACGTTTGTCACATATCCTCGCTGAAATTCTTCAGTT\n-CAGGGGCAGTTTGCTGGGGAAGCGGTAACACGAAAACAGGCACCACCTTCCGGTCGGTTGAACGTGGGTAATAGTGCCCCGTGTACATCCACTTATCGCC\n-CGACAAACTGCCAGTCCAAGCCCTACCCCCGGTACTGCCGACTCTTTATTCCCGCGAGCAAACTTATCAAATATCGTCTGCTCCTGGCCTGGCGGAAGAC\n-CGGGGCCGTTATCCCAGACATCCAGTTGTAGATTTTCGCCCTCAACGTGGGCATCGATACCAATTTCGGCCTGCGCACCCGCATATTTCACCGCGTTCTC\n-CAGCAGATTAATCAGCACCCGTTCAAAGAGGGCCCGTCAACGTGGATTAAGGTCATGGTTCTGGCAGAGAAAGATTGATGGGCGACGATAAACCCGGTTC\n-CAGCATTTGCAGCGCGCTGCCGACTACTTCTTCCAGCGTTAACCACTCTTTCTTCAAATTAAAGCCGCCGGACTGGAATTCGCGCCATACTCCAGTAGAT\n-TATTCAATTCAGTCGGTAGTGTTCAGCACATGCTGACGGATCCGCTGGCCTGGCGGGCGGGGTGATCCTTCGCTTGCCAGACCGAGCGTTAAGATTTCTG\n-CCTGACCAAACAGCACCGTAAGCGGCGCGTAACCGCGAAAAGCGCTGCCAGCAGGCGTTGCGGATCTGTTCAATGCCCGCTTGCCATCCGCGCCTGTTCT\n-TCGCTGGCGGTGGTTACGCGCCGCCGCTCAAGGGCATTGGCGACCAACAGCGTAACGTCTTCCAGCAGGCGCTGCTGTTCCGGGATCATCAACTGGCGCA\n-GATTCCCGGCTCCACCACCACCAGCCCAGGGTAGTTTTCGCCGCTTTTTATGGCAAAATCTGGTACGGTACACCGGGTAACGTGTCGGTGCCCGCGCCCG\n-CAGGCAGGCCTTTATCAAACTCCACTCGCGGCGATGGCATCGTCCCACGGCGTCATTCCTGCGGATGTTAACGGCTGCAATTTACCGTTGTCATCGGGCA\n-ACAACACCCGACTGCGGGCATGAAACGGAGGCAATAAATTGTCTGCTGGTGGCAGCGATATCCTGCGGACTGCACCACCGCCAGAGCTTTCGACATTTCA\n-TATAAGTGCCGTGTGCGCGTTCGCGGTAACGGGCTACCCGCGCCTGATAACGCACGCCAGCAGTAAGGTTCCTGATCACCAGCCCGACGGTTAACATCAC\n-CGCGAAGGTCAGCAGATATTGCACATCAGAGACGGCGAGCGTGCTGCGTGGGGCGATAAAAAAGAGATCGAACTCACTACATTAATGACGGTGGCAACCA\n-CTGAAGGCCAGCGTCCATAAATAGCGCCACCACCACCACGCCAAGCAGATACAGCAGCATCACCAGGTTGGCGCATCAACGCCATCAGCCACTGCATGGC\n-AATTACAAGAGATAACGGCGCATAACGCGGCGGCAACCACGCATCCCTGAATTTGTACACGCCACTTGTCTTTAAAAGAGCGGTTATCCGGCGCGTTGTT\n-AATCGTGCGGGCGGGTGGTCATCGGGCGCGACCAGCACCTGATCGAGATCGGGGCGATGCGCGCCAGTCGGTCAGCAAACGTCTCCCGACGCCACCAGCG\n-GCGCGAGGCCGCGACTGAGAATAATCTTACGAGATTATGTTCACGGGCATAACGCACTACCGCTTTCTCTCTTCCGCTGGATCAACAGAAAGTGTTGCCG\n-TCTCCAGCCCAGTTCCTGCGCCAGACGGGCGCGCTGAGAATTGCCCGACGTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATAACACCGCGCC\n-AGACGCCACCCAGCCGTGACGCCAGCCGCAGCTGCGCGGACCAGTTTTTCGCCGCCGGTGTTATGGCCGATGCATAAAGGATCGCGTCGCGTGTGCCACT\n-TTCTCTTCTGCCAGACGCCCCCGCCAGGCGCGCATTTGCTCATCAACGCGATCGGCAGTACGGCGTAGTGCCAGTTCATGCAGGGCGACCAGATTACCTT\n-TGCGGAAAAAATGTTCAATGGCGCGCTCCGCCTGCCCGGCAATATAGACTTTGCCTTCTCTCAGCCGCTGGCGCAGATCGTCCGGGGCAAGTCCACCAGC\n-ACCACGTCGTCGGCGGCATCGAAAAGGATCGGGCACGGTTTCCCGTACCTGAATTCCGGTGACGCCGCTGACCACATCATTCAGACTTTCCAGATGCTGA\n-ACGTTGACGGTAGTGAAAACATCAATGCCAGCTTCCAGCAGTTCTTCGATATCCTGCCAGCGTTTGGGATGACGGGAACCTGGCGCATTACTGTGCGCCA\n-GTTCGTCCATTAAGATCAGCGCCGGGCGGCGGGCGAGGGCGGCATCGAGATCAAACTCGCTGATATGCCGCCCACGGTACGCCTGGCGTTTTAACGGCAG\n-AACAGCCAGCCCTTCCAGCATGGCGGCGGTATCTTTCGCCCGTGGGTTTCTACCACGCCAACCACAATATCCAGCCCTTGCGCCCGCAGTCGCTGGGCTT\n-CTGCCAGCATCGCCCAGGTCTTCCCGACGCCTGCACAGGCACCGAAGAAAACTTTCAGCTTCCCCGATGCGGCGCGGCAGTTTGTTCCAGCAGACGATCG\n-GGGTCGGGACGTAAGGGTTCGTTATTCATCAAGTTTATCCAGCGCCAGATTGAGTTCATCACTGACAACCGGCTGGCCGATATATTTCACCAGCGGTTGT\n-TGGCTGTATTTTGCGATCAGTTGCGTGAGCTGTCTAACGCTGAGATTACGCGCTTTCGCCACGCGTGGATTTGCCAGGCCGCCGCTTGCGGGTGATATTA\n-TTGTCCAGCCCGCTTGCCGATGCCGTCACCAGTTCAACCGGAACGCTCGCGCTGGCATCCGGGTTAGCGGCCCGTAATGCAGCAACGCGTGCGGCTATTA\n-GTTTATCCAGCTCAGGGTTACTGACCGCCAGATTGCTCCCGCCAGAAGCCTGTGGATTATAGGGCATTTCTGCCGTTGCCGACGGGCGACCATGAAAATA\n-GCCGTTGCCGGTAAAATTCTGCCCGATTAATGCCGAACCGCGCACCGTATCACCTTCACGAATCAACGAACCATTGGCCTGCCAGGGAAACCACCATTGC\n-CCCAGTACGGTGGTCAGCAGCGGGTAAACGCCGCCAGTAATCAATAAATAGAAAGATAAATGTTGATAATGCCGGACGTAATCCACTCATGGTAAACCTC\n-ACACCAGACCGCAAACGGTCAGCAGTAAATCAATGACTTTGATACCGATAAACGGCACCAGCAGCCCACCCAGACCGTAAATCCATAAGTTACGGCGCAA\n-CATGGCAGAAGCGGTAAGCGGTTTATAACTCACGCCTTTAACGCCAGGGGAATCAAAAAGACGATAATCAAGGCGTTGAAAATCACCGCACTGAGGATTG\n-CGGAGTCGGGCGAATGCAGGCACATGATGTTCAGCGCATTTAACTGCGGATACGTTGCCGCGAATGCCGCCGGAATAATGGCGAAGT'..b'CGCACCAATTGCGGCCACCAGGCCAAAACAA\n-ACGAAGCATGGCGAACTCACACCTGGCGTGGTACGCAGCAGTTTTTCCCGCACCGAGTGTGCGCCACACCACCAGCTCCTGATGACGCTGACGCATTCCC\n-ACCTGCACCTGTGCCAGCAACAGCAACATACCGCAGGCGGTGACCAGTACCATTCATCACTTCCAGCGCCCGACGCATCTTTGCTCCAGCACCTGACCGA\n-CCTGTTTTAAAAATCGCGCCAATACCTAACAGGCTAATGGTCGGGAACTTGCGGTTGAGTTGCGTCAACATGCCGTTGCCATTCTCCAGCGGAAACTGGT\n-AAGCCAGTCCTGCGGTTGCCCGTTCAATGCCCTTCAGGGAAAATAAAATAGAAATTAGGGCCAGACCTTCTCCCAGTCCACTTTGCGCAGGCTGGTCACT\n-TTAGCGCGGAACTCCTGGGTATCGCCCATAAAAGTCACGGTATCACCGAGGGCAACGTTTGCTGCTTGCCAGCCCTCTTCCATCGACACTTCATCGGCTT\n-TTGGCGGCCAGTTACCGGCGACACCGGATTATGATCGGGCCAGCGTATTTTGCCAGGTAAGATTGAGTTCGCGGTTAAGCGCCTCATCTTCATTACCTTC\n-TGTCGGCTTATCGTTAATCGCCGTCAGCCGCGCCCGCACCACCGGATAAAACGATCTCCGGGACTATCTGATGTTCCGCGAGGAACGCTTTAGCGGTGCT\n-ACCTGTTCTGTGGCGATGTTAATTAAAAAGTAGTCTGGGCTTGAGGTAGCGCTGCTGCTGCCAGCGGTCGAGCAGATCGCCACGCAACACCAGCAGCAGT\n-GCCAGCAGCATGCTGAGAGCGAAAATGCCGAAAGCTGACTTAACGTTGACCACGGCTGACGTAACAGGCGGCTAACCGCCAGGCGCGCAGAGGCAGCGAT\n-TTCAGTCATGCGGCGAAGCAATATTCAGCAGCATCCAGCCCAGCACACCGCACAGCAGCCAGTACTACCGCGCCCAAGCCAGCACCACTGCCTAAAGCAG\n-CATGCTGCCACCCATTAATCCGGCGAGCAGCAGCACAACCACCACACTGACAATCGGCAGATAAAACTTCAGCGGCCAGACGTTCGCTACCACATCATTA\n-CGTAATACGCGTAAAGCTGGCAAGGCCAGCAAATAAGCGATATGGTCGTAGCCCCACCAGCAGCGAGATGACCGCCATGGTGCCAAGCGCCCACGTTAAT\n-GGCCAGAGGCTGGCTGGCGGTAGTGCAGCAGGCGAAACGGGCTTGAGCAGCACCATCAACACGTTTTCGAACAACAGGCCTATGGGTCTCACCGGTAACG\n-GCTGAAAGCGTCAGCACCATCAACCACTGACCGACGATTAGCTTACGCAGTTGCGCCTGCCCTGCCCCCAGCGTTTTGAGGATCGCCACCAGATCGTAGC\n-GACTGCGACAGTACGATTCATCGCTACCGCCACCGCTGCCACTGCCAGCAGCAAGGTCAGAAGCGCCGAAAGCAGCAGGAACTGTTGCGAGCGTTCCATC\n-GATCGCCCCAGCGCGCCTTCGTCCTGTTCCAGACCGTACCAGCGTTGTTCGGGTTTAAGCCGAGGTAACAACTATTTCTCATAGCCGTCGAGCTGGTTCT\n-CGTTGCCGCCGGAATTTATAACGCCAGGTGACCTGACTTCGGCTGTAATGGCTCCGGTTTTATCGACATCCGCCAGGATTCATCATCAGACGCGGAGCCA\n-TCTGAAGGGGTTAAAACCGGAATCCGTTCCTGAATCACTTCTCCGGCAATCCGCAAGGTGGCATCGCCCACGTCAATGGTGTGTCGCCCGTTTTCAGGTT\n-AAGCAGTGCCATCAGGCGTGGGGCCAGCAATACGCTGCCCGCCTGCGGTTTCAGGCCAGGGGGATTAGTTTGCAGATCGCCATACATCGGGTAGATATCA\n-TCCACCGCTTTGACGTTCGCCAGCTGCGGTGTGTCGCCTGCAAGGTCATTGTGGCGAAAGTCAGCTGCTTGCCGACTTTCAGGCCGCGCTTTTGCGCTTC\n-CTCCAGCCACGCTTGCGGCACTTCGCGTGAACTGCGCAACGCCCGATCGCCCGCCATAAACTTTCACGGTTTTGCTGGCTGGCCCTTCTCCATGCGATCG\n-CTGATTGCCCAGCGCCAGCATCGCAGGCCACCGCCAGGCTTAGCGCCAGCCAGACAATTAATATGACGGCGAACGCCATTCGCGCCAGAACCAACGTGCA\n-ATCATGCTTCCTCCTGCAACTGCCTGTTCACCAGCCGTAAGCAGCGGTCGCAGCGTGCTGCCAGTTGCAGGTCGGGTCACCATAATCAACGTGGTGCCAT\n-GTTCACGGTTGAGGAAAACAGCAGGTCGGCAATTTTATCGCCCGTCTGGCGGTCAAGGTTGCCGGTGGGTTCGTCGGCAAACAGCACACATCAGGTCGAC\n-CATTAAAGGCTCGTGCCAGCGCCACTCGTTGCTGTTCACCGCCGGAAAGCTGTGCCGGAAGATGATCCAGACGTTTGCCCCTGCCCTAACTGTTCGAGCA\n-ACGCTTTCGCCCCGTTAGCGACTTTCCGCGCTACTCACCGCGCAGCAGCATTGGAAGCTCGACGTTTTCCAGCGCGTTGGCGGTAGGAATTAACATAAAT\n-GACTGAAAACAAAGCCGACGTGCTTCGCGCGCAATCTTGCCCGCGCTTCGTCCATATTATGTGAAGCGGTTGTCCCACCAGACTCACTTCGCCACTGCTG\n-CTGTCATCAAGCCCGGCGAGGATCGCCAGCAGCAGGTTGACTTACCCGATCCCGACTCGCCCACCAGTGCGATGGTCTCGCCGTTTGATAACCAGCTCAA\n-CTCCGGTGAGGATGGAGAGTTCATGCTCCCCTGACCGACGGACCTTAAGATGATGAACCAGCAATGTTTTCCCGCTGGCATTTGCCCTTCCTGTTCCTGG\n-TCACCATTAACCTTCCGTGCCGCCGCAGCGGCCGTTATTGATTCTGGGTGATAGCCTGAGCGCCGGGTATCGAATGTCTGCCAGCGCGGCTGGCCTGCCT\n-TGTTGAATGATAAGTGGCAGAGTAAAGAGCATCGGTAGTTAATGCCAGCATCAGCGGCGACACCTCGCAACAAGGACTGGCGCGCCTTCCGGCTCTGCTG\n-AAACAGCATCAGCCACGTTGGGTGCTGGTTGAACTAATGGGCAATGACGGTTTGCGTGGTTTCAGCCACAGCAAACCGAGCAAACGCTGCGCCCGGATTT\n-TGCAGGATGTCAAAGCCGTAACGCTGAACCATTGTTAATGCAAATACGTCTGCCTGCAAACTATGGTCGCCGTTATAATGGAAGCCTTTAGCGCCATTTA\n-CCCCAAACTCGCCAAAGAGTTTGATGTTCCGCTGCTGCCCATTTTTATGGAAGAGGTCTACCTCAAGCCACAATGGATGCAGGATGACGGTATTCATCCC\n-AACCGCGACGCCCAGCCGTTTATTGCCGACTGGATGGCAGAAGCAGTTGCAGCCTTTAGTAAATCATGACTCATAAAGCAACGGAGATCCTGACAGGTAA\n-AGTTATGCAAAAATCGGTCTTAATTACCGGATGTTCCAGTGGAATTGGCCTGGAAAGCGCGCTCGAATTAAAACGCCAGGGTTTCATGTGTGCTGGCAGG\n-TTGCCGGAAACCGGATGATGTTGAGCGCGCGCAGACAGCATGGGATTTACCGGCGTGATCGATCTGGATTCACCAGAAAGTGTTGATCGCGCAGCCGACA\n-GGAGGTGATCGCCCTGACCGATAGTGTCTGTATCGGGATCTTTAACAATGCCGGATTCGGCATGTATGGCTACTTTCCACCATCAGCCGTGCGCAGATGG\n-AACAGCAGTTTCCGCCAACTTTTCGGCGCACACCAGCGTCACCATGCGCCTGTTACCCGCGATGTTACCGCACGGTGAAGGGCGTATTG\n' |
| b |
| diff -r e100f3f4d80e -r 2668027a533b test-data/consensus_result3.fa --- a/test-data/consensus_result3.fa Thu Sep 27 17:52:13 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,231 +0,0 @@\n->ctg1 len=15016\n-GCGGTGGTGCAGAGTGGCGGCGTAATGCGACGCGCAGACGGGCTCAATTCCGCCAATGCCAAACGGCTTACTTCCAGATAATCATCCGTTTCCGGCATCC\n-AGCGCGGCGATTTTGTCGTTTTCGCTGCGCGGAAAGCATTAACACCGGCACCGCGCTCCACTGGCGCAGGTCGCGGATAAACTCAATCCCATCACCATCG\n-GGCAGGCTTCGGAGATCGAGAATAACCAAATCTGGCTTACGGGTTGCCGCTGCTTCCAGCAAGCCGCGTTGCAGCGTTTCGGCTCAAAGACGCGCATCCT\n-GTCGCCCTCCAGCGCCGTGCGCAGAAAGCGACGAATAGCCTGTTCATCTTCTTCAACAATCAGAACGTTTGTCACATATCCTCGCTGAAATTCTTCAGTT\n-CAGGGGCAGTTTGCTGGGGAAGCGGTAACACGAAAACAGGCACCACCTTCCGGTCGGTTGAACGTGGGTAATAGTGCCCCGTGTACATCCACTTATCGCC\n-CGACAAACTGCCAGTCCAAGCCCTACCCCCGGTACTGCCGACTCTTTATTCCCGCGAGCAAACTTATCAAATATCGTCTGCTCCTGGCCTGGCGGAAGAC\n-CGGGGCCGTTATCCCAGACATCCAGTTGTAGATTTTCGCCCTCAACGTGGGCATCGATACCAATTTCGGCCTGCGCACCCGCATATTTCACCGCGTTCTC\n-CAGCAGATTAATCAGCACCCGTTCAAAGAGGGCCCGTCAACGTGGATTAAGGTCATGGTTCTGGCAGAGAAAGATTGATGGGCGACGATAAACCCGGTTC\n-CAGCATTTGCAGCGCGCTGCCGACTACTTCTTCCAGCGTTAACCACTCTTTCTTCAAATTAAAGCCGCCGGACTGGAATTCGCGCCATACTCCAGTAGAT\n-TATTCAATTCAGTCGGTAGTGTTCAGCACATGCTGACGGATCCGCTGGCCTGGCGGGCGGGGTGATCCTTCGCTTGCCAGACCGAGCGTTAAGATTTCTG\n-CCTGACCAAACAGCACCGTAAGCGGCGCGTAACCGCGAAAAGCGCTGCCAGCAGGCGTTGCGGATCTGTTCAATGCCCGCTTGCCATCCGCGCCTGTTCT\n-TCGCTGGCGGTGGTTACGCGCCGCCGCTCAAGGGCATTGGCGACCAACAGCGTAACGTCTTCCAGCAGGCGCTGCTGTTCCGGGATCATCAACTGGCGCA\n-GATTCCCGGCTCCACCACCACCAGCCCAGGGTAGTTTTCGCCGCTTTTTATGGCAAAATCTGGTACGGTACACCGGGTAACGTGTCGGTGCCCGCGCCCG\n-CAGGCAGGCCTTTATCAAACTCCACTCGCGGCGATGGCATCGTCCCACGGCGTCATTCCTGCGGATGTTAACGGCTGCAATTTACCGTTGTCATCGGGCA\n-ACAACACCCGACTGCGGGCATGAAACGGAGGCAATAAATTGTCTGCTGGTGGCAGCGATATCCTGCGGACTGCACCACCGCCAGAGCTTTCGACATTTCA\n-TATAAGTGCCGTGTGCGCGTTCGCGGTAACGGGCTACCCGCGCCTGATAACGCACGCCAGCAGTAAGGTTCCTGATCACCAGCCCGACGGTTAACATCAC\n-CGCGAAGGTCAGCAGATATTGCACATCAGAGACGGCGAGCGTGCTGCGTGGGGCGATAAAAAAGAGATCGAACTCACTACATTAATGACGGTGGCAACCA\n-CTGAAGGCCAGCGTCCATAAATAGCGCCACCACCACCACGCCAAGCAGATACAGCAGCATCACCAGGTTGGCGCATCAACGCCATCAGCCACTGCATGGC\n-AATTACAAGAGATAACGGCGCATAACGCGGCGGCAACCACGCATCCCTGAATTTGTACACGCCACTTGTCTTTAAAAGAGCGGTTATCCGGCGCGTTGTT\n-AATCGTGCGGGCGGGTGGTCATCGGGCGCGACCAGCACCTGATCGAGATCGGGGCGATGCGCGCCAGTCGGTCAGCAAACGTCTCCCGACGCCACCAGCG\n-GCGCGAGGCCGCGACTGAGAATAATCTTACGAGATTATGTTCACGGGCATAACGCACTACCGCTTTCTCTCTTCCGCTGGATCAACAGAAAGTGTTGCCG\n-TCTCCAGCCCAGTTCCTGCGCCAGACGGGCGCGCTGAGAATTGCCCGACGTTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATAACACCGCGCC\n-AGACGCCACCCAGCCGTGACGCCAGCCGCAGCTGCGCGGACCAGTTTTTCGCCGCCGGTGTTATGGCCGATGCATAAAGGATCGCGTCGCGTGTGCCACT\n-TTCTCTTCTGCCAGACGCCCCCGCCAGGCGCGCATTTGCTCATCAACGCGATCGGCAGTACGGCGTAGTGCCAGTTCATGCAGGGCGACCAGATTACCTT\n-TGCGGAAAAAATGTTCAATGGCGCGCTCCGCCTGCCCGGCAATATAGACTTTGCCTTCTCTCAGCCGCTGGCGCAGATCGTCCGGGGCAAGTCCACCAGC\n-ACCACGTCGTCGGCGGCATCGAAAAGGATCGGGCACGGTTTCCCGTACCTGAATTCCGGTGACGCCGCTGACCACATCATTCAGACTTTCCAGATGCTGA\n-ACGTTGACGGTAGTGAAAACATCAATGCCAGCTTCCAGCAGTTCTTCGATATCCTGCCAGCGTTTGGGATGACGGGAACCTGGCGCATTACTGTGCGCCA\n-GTTCGTCCATTAAGATCAGCGCCGGGCGGCGGGCGAGGGCGGCATCGAGATCAAACTCGCTGATATGCCGCCCACGGTACGCCTGGCGTTTTAACGGCAG\n-AACAGCCAGCCCTTCCAGCATGGCGGCGGTATCTTTCGCCCGTGGGTTTCTACCACGCCAACCACAATATCCAGCCCTTGCGCCCGCAGTCGCTGGGCTT\n-CTGCCAGCATCGCCCAGGTCTTCCCGACGCCTGCACAGGCACCGAAGAAAACTTTCAGCTTCCCCGATGCGGCGCGGCAGTTTGTTCCAGCAGACGATCG\n-GGGTCGGGACGTAAGGGTTCGTTATTCATCAAGTTTATCCAGCGCCAGATTGAGTTCATCACTGACAACCGGCTGGCCGATATATTTCACCAGCGGTTGT\n-TGGCTGTATTTTGCGATCAGTTGCGTGAGCTGTCTAACGCTGAGATTACGCGCTTTCGCCACGCGTGGATTTGCCAGGCCGCCGCTTGCGGGTGATATTA\n-TTGTCCAGCCCGCTTGCCGATGCCGTCACCAGTTCAACCGGAACGCTCGCGCTGGCATCCGGGTTAGCGGCCCGTAATGCAGCAACGCGTGCGGCTATTA\n-GTTTATCCAGCTCAGGGTTACTGACCGCCAGATTGCTCCCGCCAGAAGCCTGTGGATTATAGGGCATTTCTGCCGTTGCCGACGGGCGACCATGAAAATA\n-GCCGTTGCCGGTAAAATTCTGCCCGATTAATGCCGAACCGCGCACCGTATCACCTTCACGAATCAACGAACCATTACCCGCCAGGAAACCACCATTGCCC\n-CAGTACGGTGGTCAGCAGCGGGTAAACGCCGCCAGTAATCAATAACAGAAAGATAAATGTTGATAATGCCGACGTAATCCACTCATGGTAAACTCACACC\n-AGACCGCAAACGGTCAGCGGTAAATCAATGACTTTGATACCGATAAACGGCACCAGCAGCCCACCCAGACCGTAAATCCATAAGTTACGGCGCAACATGG\n-CAGAAGCGGTAAGCGGTTTATAACTCACGCCTTTAACGCCAGGGGAATCAAAAAGACGATAATCAAGGCGTTGAAAATCACCGCACTGAGGATTGCGGAG\n-TCGGGCGAATGCAGGCACATGATGTTCAGCGCATTTAACTGCGGATACGTTGCCGCGAATGCCGCCGGAATAATGGCGAAGTATTTC'..b'TCCGCACCAATTGCGGCCACCAGGCCGGAAACAAACCCAAGCA\n-TGGCGAACTCACACCTGGCGTGGTACGCAGCAGTTTTTCCCGCACCGAGTGTGCGCCACACCACCAGCTCCTGATGACGCTGACGCATTCCCACCTGCAC\n-CTGTGCCAGCAACAGCAACATACCGCAGGCGGTGACCAGTACCACCATCACTTCCAGCGCCCGACTTACCTGCTCCAGCACCTGACCGACCTGTTTTAAA\n-AATCGCGCCAATATCTAACAGGCTAATGGTCGGGAACTGGCGGTTGAGTTGTGTCAACATGCCGTTGCCATTCTCCCAGCGGAAACTGGTAAGCCAGCTC\n-TGCGGTTGCCGTCTAATGCCCCCTTCAGGGAAAATAAAATAGAAATTAGGCCGCAGACTTTCCCAGTCCACTTTGCGCAGGCTGGTCACTTTAGCGCGGA\n-ACTCCTGGGTATCGCCCATAAAAGTCACGGTATCACCGAGGGCAACGTTTAAGCGTTTCGCCAGCCCCTCTTCCATCGACACTTCATCGGCTTTTGGCGG\n-CCAGTTACCGGCGACAATCGGATTATGATCGGGCCGCGTATTTTGCCAGGTAAGATTGAGTTCGCGGTTAAGCGCCTCATCTTCATTACCTTCTGTCGGT\n-TTATCGTTAATCGCCGTCAGCCGCGCCCGCACCACCGGATAAAACGATTCCGGGACTATCTGATGTTCCGCGAGGAACGCTTTAGCGGTGCTACCTGTTC\n-TGTGGCGATGTTAATTAAAAAGTAGTTCGCTTCTTGAGGTAGCTGCTGCTGCCAGCGGTCGAGCAGATCGCCACGCAACACCAGCAGCAGTGCCAGCAGC\n-ATAAAGGAGAGCGAAAATGCCGAAAGCTGACTTAACGTTGACCACGGCTGACGTAACAGGCGGCTAACCGCCAGGCGCAGAGGCAGCGATTTCAGCGTCA\n-TGCGGCGAAGTACATTCAGCAGCATCCAGCCCAGCACACCGCACAGCAAAGCCAGTACTACCGCGCCCGCCAGCACCGCCCAAAGCAGCATGCTGCCACC\n-CATTAATCCGGCGAGCAGCAGCACAACCACCACACTGACAATCGGCAGATAAAACTTCAGCGGCCAGACGTTCGCTACCACATCATTACGTAATACGCGT\n-AAAGCTGGCAAGGCCAGCAAATAAGCGATATGGTCGTAGCCCCACCAGCAGCGAGATGACCGCCATGGTGCCAAGCGCCCACGTTAATGGCCAGAGGCTG\n-GCTGGCGGTAGTGCAGCAGGCGAAACGGGCTTGAGCAGCACCATCAACACGTTTTCGAACAACAGGCCTATGGGTCTCACCGGTAACGGCTGAAAGCGTC\n-AGCACCATCAACCACTGACCGACGATTAGCTTACGCAGTTGCGCCTGCCCTGCCCCCAGCGTTTTGAGGATCGCCACCAGATCGTAGCGACTGCGACAGT\n-ACGATTCATCGCTACCGCCACCGCTGCCACTGCCAGCAGCAAGGTCAGAAGCGCCGAAAGCAGCAGGAACTGTTGCGAGCGTTCCATCGATCGCCCCAGC\n-GCGCCTTCGTCCTGTTCCAGACCGTACCAGCGTTGTTCGGGTTTAAGCCGAGGTAACAACTATTTCTCATAGCCGTCGAGCTGGTTCTCGTTGCCGCCGG\n-AATTTATAACGCCAGGTGACCTGACTTCGGCTGTAATGGCTCCGGTTTTATCGACATCCGCCAGGATTCATCATCAGACGCGGAGCCATCTGAAGGGGTT\n-AAAACCGGAATCCGTTCCTGAATCACTTCTCCGGCAATCCGCAAGGTGGCATCGCCCACGTCAATGGTGTGTCGCCCGTTTTCAGGTTAAGCAGTGCCAT\n-CAGGCGTGGGGCCAGCAATACGCTGCCCGCCTGCGGTTTCAGGCCAGGGGGATTAGTTTGCAGATCGCCATACATCGGGTAGATATCATCCACCGCTTTG\n-ACGTTCGCCAGCTGCGGTGTGTCGCCTGCAAGGTCATTGTGGCGAAAGTCAGCTGCTTGCCGACTTTCAGGCCGCGCTTTTGCGCTTCCTCCAGCCACGC\n-TTGCGGCACTTCGCGTGAACTGCGCAACGCCCGATCGCCCGCCATAAACTTTCACGGTTTTGCTGGCTGGCCCTTCTCCATGCGATCGCTGATTGCCCAG\n-CGCCAGCATCGCAGGCCACCGCCAGGCTTAGCGCCAGCCAGACAATTAATATGACGGCGAACGCCATTCGCGCCAGAACCAACGTGCAATCATGCTTCCT\n-CCTGCAACTGCCTGTTCACCAGCCGTAAGCAGCGGTCGCAGCGTGCTGCCAGTTGCAGGTCGGGTCACCATAATCAACGTGGTGCCATGTTCACGGTTGA\n-GGAAAACAGCAGGTCGGCAATTTTATCGCCCGTCTGGCGGTCAAGGTTGCCGGTGGGTTCGTCGGCAAACAGCACACATCAGGTCGACCATTAAAGGCTC\n-GTGCCAGCGCCACTCGTTGCTGTTCACCGCCGGAAAGCTGTGCCGGAAGATGATCCAGACGTTTGCCCCTGCCCTAACTGTTCGAGCAACGCTTTCGCCC\n-CGTTAGCGACTTTCCGCGCTACTCACCGCGCAGCAGCATTGGAAGCTCGACGTTTTCCAGCGCGTTGGCGGTAGGAATTAACATAAATGACTGAAAACAA\n-AGCCGACGTGCTTCGCGCGCAATCTTGCCCGCGCTTCGTCCATATTATGTGAAGCGGTTGTCCCACCAGACTCACTTCGCCACTGCTGCTGTCATCAAGC\n-CCGGCGAGGATCGCCAGCAGCAGGTTGACTTACCCGATCCCGACTCGCCCACCAGTGCGATGGTCTCGCCGTTTGATAACCAGCTCAACTCCGGTGAGGA\n-TGGAGAGTTCATGCTCCCCTGACCGACGGACCTTAAGATGATGAACCAGCAATGTTTTCCCGCTGGCATTTGCCCTTCCTGTTCCTGGTCACCATTAACC\n-TTCCGTGCCGCCGCAGCGGCCGTTATTGATTCTGGGTGATAGCCTGAGCGCCGGGTATCGAATGTCTGCCAGCGCGGCTGGCCTGCCTTGTTGAATGATA\n-AGTGGCAGAGTAAAGAGCATCGGTAGTTAATGCCAGCATCAGCGGCGACACCTCGCAACAAGGACTGGCGCGCCTTCCGGCTCTGCTGAAACAGCATCAG\n-CCACGTTGGGTGCTGGTTGAACTAATGGGCAATGACGGTTTGCGTGGTTTCAGCCACAGCAAACCGAGCAAACGCTGCGCCCGGATTTTGCAGGATGTCA\n-AAGCCGTAACGCTGAACCATTGTTAATGCAAATACGTCTGCCTGCAAACTATGGTCGCCGTTATAATGGAAGCCTTTAGCGCCATTTACCCCAAACTCGC\n-CAAAGAGTTTGATGTTCCGCTGCTGCCCATTTTTATGGAAGAGGTCTACCTCAAGCCACAATGGATGCAGGATGACGGTATTCATCCCAACCGCGACGCC\n-CAGCCGTTTATTGCCGACTGGATGGCAGAAGCAGTTGCAGCCTTTAGTAAATCATGACTCATAAAGCAACGGAGATCCTGACAGGTAAAGTTATGCAAAA\n-ATCGGTCTTAATTACCGGATGTTCCAGTGGAATTGGCCTGGAAAGCGCGCTCGAATTAAAACGCCAGGGTTTCATGTGTGCTGGCAGGTTGCCGGAAACC\n-GGATGATGTTGAGCGCGCGCAGACAGCATGGGATTTACCGGCGTGATCGATCTGGATTCACCAGAAAGTGTTGATCGCGCAGCCGACAGGAGGTGATCGC\n-CCTGACCGATAGTGTCTGTATCGGGATCTTTAACAATGCCGGATTCGGCATGTATGGCTACTTTCCACCATCAGCCGTGCGCAGATGGAACAGCAGTTTC\n-CGCCAACTTTTCGGCGCACACCAGCGTCACCATGCGCCTGTTACCCGCGATGTTACCGCACGGTGAAGGGCGTATTG\n' |
| b |
| diff -r e100f3f4d80e -r 2668027a533b test-data/dbg.ctg.lay --- a/test-data/dbg.ctg.lay Thu Sep 27 17:52:13 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,359 +0,0 @@\n->ctg1 nodes=16 len=16896\n-E\t0\tN19\t+\tN15\t+\n-S\tS0000000025\t+\t0\t2048\tTTGGTAGCGCTACGTTTCAGTTACGTATTGCTACTTGCCTGTCGCTCTATCTTCGGCGTCTGCTTGGGTGTTTTAACCTGAGTGCCGGGCGTTTTCCATCAATTGCAATGACGTCTTTATCATTTGATGAATGGCAATCACGCATCCAGTTAATAAAGCACTCGTGAAATTTTGCAGGACTGATACAGGATACAACTCTGGCAATAATTATCGTGAACAGAATACCATTTTCAAAATCACCATATTGCTTCAGAAAATCGAGATGTGTTTCCCCGTCCTCTATATCTTCCCAACTTTCTGCACCAGAAATAACGGCAAAATAGTCAATAGTAGGATGCCTGACAATTTTGTCTCCTACCAGGCTTATCTGTAATCGGGAATAATAGAAATATGTTCCATCAATTTTTTAAGTTCATTTGTTCACCTTATTTATGTAAGGAGTATTTGATCATGTATAAGCTATGAAAAACAGCTTTAGGTAATAAGATATCTCAATTTTTAAACATAAAATGCGAATTATTTAGTACAAAATGGCGTTGCGTGATCTTTCCTGGGATACAACTCTGGCAATGGTATCGTGAACAGGGCCATTTTCAAAATCACCATATTGTACAAAATCGAGATGTGTTTCCCCGAAATCCTCTATATCTTCCAACCCTTCTGCAGAAATAGCAGCACAAATGATCCAACAGTAGAGATATCTGACCGTTTATGCACCGCACAGGCTTGTCTGTAATCAGATTAATAATGAAATATGTTCCATCAATTTTTTAAGTTCCATTTGTTCACCTTATTTATGTAAAGGGTATTTGATCATGTATAAGCTATGAAAAAACAGCTTTAGACAATAGTAATGTCTCAATTGTTGAACTTAAATTCGAATTATTTAGTACAAAAGTAGCGTTACGTGATCTTTCCTGCAAATGGAACGCAAAATAAACACCTATTCCATAGGTTATATAATTTTCACAATGATTAATTTGTTTTTCTCAGGAAGAGATTTTATTTCTCTTCACGAATTAGTTCTTGTATCTTTATTAAACATTCGTAAAGGCTCATTTTTGTTCGGGAGATGTGCTTGTCATTCGAGCATAAGTTGGTTTCTCATCTTTAAAATATTTTACCATGATTGGATTATCAAGGACTGCTTAACAACTGAACTGGATCACTGCTCTTTTGATAGATACCCGCTCTTATACTTCTAAACCGATCGCCGAGAAACGCCGTTTTTCTGCTGTATTTATCAACTCCTGCAACGTTCCTTTGATGGCATATTTCATTAAGGCGTAGTGACCCGACGCAGATTGAGTCTCGCCCCGCTTGGTGTGAATTTAGTATTTTACATGTGCAGTTCTGTTTGCCAATAATACTCACCGATGTCCTCATTCTGATACCATCTCATGGCTTTATTATTTAAGACAGAAACCTTGGAAAAAATAGTACCCATAGCGAAAATAGTAAAACAATCCATGATCTTTAAAGCTTGTATTTCGCAATCAGCTATAACACCAAAACTAACAAATATCATCAGCAAAAAGAACAAAGCTCTTTTTCATTTTCTTATTCCTCTCGATGTTCTCTCTGTTTCATCTTAGCTAAAATTTCACCCAAATCATCTATCCTGCCGTTGCTGGCCCATCGGGTTTATTAATGTCCTGGGGAATAAATAGGGTTCTGCACAAGTATATCCTGGTGAGCCAATTGAGTTGTTGGCCAATTTGTCTGTGGCAGGTATTGCCCTTGCTGTCTTTGTATCCATCCCTGGATACCAGGAATCATCCTGTGGCGTACAAGTCCAGATTTGGTTTTACCCACTTCCTGCAATACAGTGTGTGGTCATGGGGCTTAATGCTCTGAAGAATGTTTTGAAAACATTAGGCGCACTACTGGCCTGGTCAATAGGATGTAAGCGGTCTTAATTGTTTCGCTATGTCCGGCAATTTTACTTGGATCGAAGTAGGCGGTTTGTTTTGAGTCTCGCTCCGCCCATCCGCCATTATTTAAGTGTCCATATTTTGATGCCAGTCCCATTGAATCTATATACTGAA\n-S\tS0000000023\t-\t5888\t2048\tATGACGTCTTTTATCATTTGATGAATGGCAATCACGCATCCAGTTAATAAAGCACTCGTGAAATTTTGCAGGACTGATACAGGATACAACCTGGCACAGTATCGTGAACAGGAATACCATTTCAAAATCACCATATTGCTCAAGAACGAGATGTTTCGAAATCCTCTATATCTTTCCTTAACTGGGTAATTAGAAATAACGGCAAAATAGTCAATAGTAGGATGCCTGGACAATTTATGCTCTACTTTCCAGGCTTATCTAGACCGGGAATAATAGAAATATGTTCCATCAATTTTTAAGTTCCATTTGTTCACCTTATTTATGTAAGGAGTATTTGATCATGTATGCTTATGAAAACAGCTTTAGGTAATAAGGAATATCAATTTTTAAAACATAAAATGCGAATTATTTAGTACAAAAAGTAGCGTTACGTGATCTTTTCCCTGATACAACTCTGGCAATGGTATCGTGAACAGGAATACCATTTTCAAAATCACCATATTGCTCAAAAAAATCGAGATGTGTTTCGAAATCCTCTTATATCTTCCCAACCTTCTGCACTATAGCCAATGGCACAAATAGTCAACAGTAGAATATCTGACAATTTATGCACCACTTTCCAGGCTTGTCTGTAATCGGGTGTAATTGTGAAATATGTTCCATCAATTTTTAAGTTCCATTTGTTCACCTTATTTATGTAAGGAGTATTTGATCAGCGTATGTTTAAGGAAAACAGCTTTAGACAACAAGTATCTCAATTGTTGAACTTTAAAATTGAATTATTTAGTACAAAAAGTAGCGTTACGTGATCTTTCCTGCAAATGGAACGCAAAACAAACACCTCTATTCCATGAGTTACAATTTTCACAATGATTAATTTGTTTTCAGGAAGAGATTTATTTCTCTTCACTACGAATTAGTTCATGCTGTATCTTTATTAAACATTCGTAAGACTCATATTTTGTTCGGGAGATGCTGTCATTCGAGAAGGGTTGGTTTCTCATCTTTAAATATTTTACCATGATTGAATTATCAAGGACTGCTGCAACAACTGAACTTGACTACTGCTCTTTTGATAGATACCCGCTCTTATAATCCCTAAAACCGATCGCCGAGAAACGCCGTTTTTTCTGGTTGTATTTATCAACTCCTGCAACGTTCCTTTGATGGCATGATTTTTCATTAAGGCGGTAGTGACCCGACGCGAATTAAGAGTCTCGCCCCGCTTGGTGTGAATTTTAATATTTTACATGTACCCAGTTCTGTTTCGCTATCAATACTCACCGATGTCCTCATTCTGATACCATCTCCACATGGCTTTATTATTTAAGACAGGAACGCGGAAAAATAGTACCCGAAGGAAAATAGTAAAACAACGTATGATCTTTAGCTTGTATTCTCGCAATCAATATGCAATTACCAAAACTACAAATATCATCAGCAAAAAGAACAAAATTTCTTTTCATTTTCTTTATTCCTCTCGATGTTCTGCTTCCATCTTACTAAAATTTCACCCAAATCATCTTATCCCCGTTGCCAGCCCATCGGGTTTATTAAATGTCTGGAATAAGTAGGGTTCTGTACGCATATCCTGGTGGTAATTGAGTTTGTTGGGCCAATTTGTCTGTGGCAGTGTAATCACTTCTTTTGCTGTCTTTGTATCCATCCCTGGATATCAGGGAATCATCCTGTGGCGTACAAGTCAGATTTGGTTTTACCCACTTCCTGCAATACAGTGTGTAGTCAAGTGGGCTTAATGCTCTGGAAGAACGTTTCTTTCTTTGAAACATTAGGCGCACTACTGGCCTGGTCAATAGGATATGGCAGTCTTAATTGTT'..b'CCCAGCGCCAGCACAGGCCACCGCCAGGCTTAAGCGCCAGCCAGACAATTAATAGCGACGGCGAACGCCATTCGCGCTGGGAACCAACGTGCAATCATGCTTCCTCCTGCAACTGCCCCGTTCACCAGCCCAATGGCAGCGGTCGCAGCGCCGCCAGTTGCAGGTCGTGGGTCACCATAATCAACGTGGTGCCATGTTTACGGTTGAGGAAAACAGCAGGTCGGCAATTTTATCGCCCGTCTGGCGGTCAAAGGTTGCCGGTTCGTCGGCAAACAGCATCAGGTCGACCATTAAAGGCTCGTGCCAGCATATCTTCCTCGTTGCTGTTCACCGCTGGAAAGCTGTGCCGGAAGATGATCAGACGTTTACCCAGCCCTAACTGTTTCGAGCAACGCTTTCGCCCCGTTACGACTTTCCGCTACTCTCCACCGCGCAGCAGGCCAGGAAGCTCGACGTTTTCCAGCGCGTTAAGGGTAGGAATTAACATAAATGACTGAAAAACAAAGCCGACGTGCTTCGCGCTTAACTTTGCCCGCGCTTCTTCGTCCATATTATGTGGCGGTTGTCCCTGGAGCTCACTTCGCCACTGCTGCCGTCATCAAGCCCGGCGAGGATCGCCAACAAGGTTGACTTACGATCCCGACTCGCCCACCAGTGCGATGGTCTCGCGCGTTTGACAACCAGCTCAACTCGGTGAGGATGGAGAGTTCATACTCCCTGACCGACGGACTTCTTAAGATGATGAACTTCAACAATGTTTTCGGCATTTGCCCTTCCTGTTCCTGGTCCTGTTAACCTTCCGTGCCGCCGCAGCCGTTATTGATTCTGGGTGATAGCCTGAGCCGGGTATCCAGATGTCTGCCAGCGCTGGCCTGGCCTGCCTGTTGAATGATAAGTGGCAGAGTAAACGTCGGTAATTAATGCCAGCATCAGCACGGCGACACCTCGCAACAAGGACTGGCGCCTTCCGGCTCTGCTGAAACAGCATCAGCCGCGTTGGGTGCTGGTTGAACTGGGCGGCAATGACGGTTTGCGTGGTTTTCGGCCGCAGCAAACCGGTGGCTGCGCCAGATTTTGCGGATGTCAAAGCGCCAACGCTGGACATTGTTAATGCAAAATACGTCTGCCTGCTGACGCTATGGTCGCCGTTATAATGAAGCCTTTAGCGCGCCATTTACCCCAAACTCGCCAAAGAGTTTGATGTTCCGCTGCTGCCCTTTTTTATGGAAAGGTCTGCCTCAAGCCACAATGGATGCGGGATGACCCAGGTATTCATCCCAACCGCGACGCCCAGCCGTTTATTGCCGACTGGATGGCGAAGCAGTTGCAGCCTTTAGTAAATCATGACTCATAAAGCAACGGAGATCCTGACAGGTAAAGTTATGCAAAATCATTAATTACCGGATGTTCCAGTGGAATTGACACCAGAGCGCTCGAATTAAAACGCCAGGGTTTTCATGCTGGCAGGTTGCCGGAAACCGGATGATGTTGAGCGCATGAACGGCATGGGATTTACCGGCGTGTTGATCGATCTGGATTCACCAGAAAGTGTTGATCGCGCAGCAACGAGGTGATCGCCTGACCGATAATTGTCTGTATGGGATCTTTAACAATGCCGGATTCAGCATGTATGGCCCCTTTCCTGCATCCAGCCCGTGCGCAGATGGAACAGCAGTTTCCGCCAACTTTTCGGCGCACCAGCTCTGTGCGCCTGTTACCCGCGATGTTACCGCACGGTGAGGGCGTATTGTGATGACATCATCGGTGATGGGATTAATCTCCACGCCAGGTCGTGGCGCTTACGCCGGCCAGTAAATATGCGCTGGAGGCGTGGTCAGATGCACTGCGCATGGGCTGCGCCACAGCGGAATTAAAGTCAGCCTGATCGAACCCGGTCCCATTCGTACTCGCTTCACCGACAA\n-S\tS0000000043\t+\t4096\t2048\tTGCGGTTTCAGGCCAGGGGATGGTTGCAGATCGCCATACATCGGGTAGATATCATCCACCGCTGACGTTCGCCAGCTGCGGTGTGTCGCCTGCAAAGGTCATTGTGGCGAAAGTCCGGCTGCTGCCGACTTTCAGGCCGCGCTTTGCGCTTCCTCCAGCCACGCTGCGGCACTTCACGCGTGAACCGCAACGCCCGATCGCCCGCCATAAACTCACGGCTTTGCTGGCTTAAGCCCTTCTCCATGCGATCGCTGATATTGCCCCAGCGCCAGCACGCAGGCCACCGCCGGAAGCTTAGCGCCAGCCAGACAATTAATAGCGACGGCGAACGCCATTCGCGCCAGAACCAACGATGCAATCATGCTTCCTCTGCAACTGCCCGTTCACCAGCCATGAAAGCAGCGGTCGCAGCGTGCCGCCAGTTGATTGCGGTGTGGAGTCACCATAATCAACGTGGTGCCATGTTCACGGTTGAGGAAAACAGCAGGTCCGGCAATTTTATCGCCCGTCTGGCGGTCAAGGTTGCCAGTGGGTTCAAATCGGCAAACAGCATCAGGTCGACCATTAAAGGCTCGTGCCAGCTCTTCCTCGTTGCTGTTCTGCGCCGGAAAGCTGTGCCGGAAGATGATCAGACGTTTACCCAGCCCTAACTGTTCGAGCAACGCTTTCGCCCCGTTACGACTTTCCGCACTTTCTCACCGCGCAGCAGGGCGGAAGCTCGACGCGTTTTCAACGCGTTAAGGTGGGAATTAACATAAATGACTGAAAAACAAAGCCGACGTGCTTCGCGCGCAACTTTGCCCGCTTCTTCGTCCATATTAATGGCGGTTGTCCCACCAGACTCACTTCGCCACTGCTGCCGTCATCAAGCCCGGCGAGGATCGCCAGCAGCAGGTTGACTTACCCGATCCCGACTCGCCCACCAGTGCGATGGTCTCGCCGTTTGATAACCAGCTCAACTCCGGTGAGGATGGAGAGTTCATGCTCCCCTGACCGACGGACCTTAAGATGATGAACCAGCAATGTTTTCCCGCTGGCATTTGCCCTTCCTGTTCCTGGTCACCATTAACCTTCCGTGCCGCCGCAGCGGCCGTTATTGATTCTGGGTGATAGCCTGAGCGCCGGGTATCGAATGTCTGCCAGCGCGGCTGGCCTGCCTTGTTGAATGATAAGTGGCAGAGTAAAGAGCATCGGTAGTTAATGCCAGCATCAGCGGCGACACCTCGCAACAAGGACTGGCGCGCCTTCCGGCTCTGCTGAAACAGCATCAGCCACGTTGGGTGCTGGTTGAACTAATGGGCAATGACGGTTTGCGTGGTTTCAGCCACAGCAAACCGAGCAAACGCTGCGCCCGGATTTTGCAGGATGTCAAAGCCGTAACGCTGAACCATTGTTAATGCAAATACGTCTGCCTGCAAACTATGGTCGCCGTTATAATGGAAGCCTTTAGCGCCATTTACCCCAAACTCGCCAAAAGAGTTTGATGTTCCGCTGCTGCCCATTTTTATGGAAGAGGTCTACCTCAAGCCACAATGGATGCAGGATGACGGTATTCATCCCAACCGCGACGCCCAGCCGTTTATTGCCGACTGGATGGCAGAAGCAGTTGCAGCCTTTAGTAAATCATGACTCATAAAGCAACGGAGATCCTGACAGGTAAAGTTATGCAAAAATCGGTCTTAATTACCGGATGTTCCAGTGGAATTGGCCTGGAAAGCGCGCTCGAATTAAAACGCCAGGGTTTCATGTGTGCTGGCAGGTTGCCGGAAACCGGATGATGTTGAGCGCGCGCAGACAGCATGGGATTTACCGGCGTGATCGATCTGGATTCACCAGAAAGTGTTGATCGCGCAGCCGACAGGAGGTGATCGCCCTGACCGATAGTGTCTGTATCGGGATCTTTAACAATGCCGGATTCGGCATGTATGGCTACTTTCCACCATCAGCCGTGCGCAGATGGAACAGCAGTTTCCGCCAACTTTTTCGGCGCACACCAGCTCACCATGCGCTGTTACCCGCGATATTACCGCACGGTGAAGGGCGTATTG\n' |
| b |
| diff -r e100f3f4d80e -r 2668027a533b test-data/ecoli-reads.fa --- a/test-data/ecoli-reads.fa Thu Sep 27 17:52:13 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,224 +0,0 @@\n->fa9ad683-35c5-4dad-a3af-de7a86b1ffa8\n-TTGGTATGCTTCGTTCCAGTTACGTATTACTTTCTGTTGGTGCTGATGTTGCGTCTGCTGATTGTTTAACCTGGCTGGATCGCTGCTGAATAACTTCGCCGCATGGCCGCTGAAATCTTTCACCCTCTGCGCCTGGCGGTTAGCCGCCTGTTACGTCAGCCGTGGTCAACGTTAAGTCAGCTTTTCGGCATTTCGCTCCGCTATGCTGGCACTGCTGCGGTGTGCATAGCGATCTGCTCGACCGCTGGCAGCAGCATCTCAAGCGAACTACTTGCATTCATCGCCACAGAACAGGTAACCATCGAGGCGTTCCTCGGAACATCAGATAGTCAGAATCGTTTTGTATCCGAGTGGGTACAGGCGCGGCTGACGGCGATTAACGATAAGCAACAAAAGGTAAATAGAAGATGCGGCGCTTAACCGCGAGCTCAATCTTACCTGGCAAAATACGCGGCTTGATCATGATCGATTGTAATGCCCGGTAACTGGCCGCCAAAGCCGATGAAGTGTCGATGGAAGGGGCTGGCCGAAACGCTTAAACGATTGCCCTCGGTGATACCGTGGCTTTGCGGGGCGATGCGCAGGAGTTTCCGCGCTAAAGTAGCCAGCCTGCGCAAGTGGACTGGAAAGTCACGGCCTAATTTCTATTTTATTTTTCCCTGAAGGGCATTCGTTAAGGCAACCGCAGAGCAACCACCCAGTTTCCGCTGGGAGAATGGCAACGGCATGATGACACCGGCTCTTCGCCAGTTCCCGACCATCAGCCTGATAGATATTGGCGCGATTTTTAAAACCGTCGGTCAGGTGCTGGAGCAGATGGGGTCGGGCGCTGGAAGTGATAAATTGGTACTGGTCACCGCCTGCGGTATATTTGCTGTTGCTAGCACAGGGGTACGGGCGAGACATCCAGCGTCATCAAGGCTAATTGGGTGTGGCGCACTCGGTGCGGAAAAAGGCTTTGCTGCGTACCACGTTGGCAAGTGTAGAGTTCGCCATACTTGGGTTTTGTTTTGTACCAAGTGGCCGCAAAATTAGTGCACAGAAACAGCGCTGGCGGCGGTGTGCAGGCGAAAGTGAACGATTTTCAAAGTAGGAGCCAAGACTGGCGATTGTGGATTATTCTACCGTGCAGCGGGCGGCTGCTGCTGTCGCTTTCCGGCGGCTGGCTGGGTGCGGTTGGGTAGGCGCTGTTCGAGGCAGTTTGCAGAAATGCGCAAGGTAAATAGGGGGCGTTCTGGTTTAGAATGAACGCGCCCAGCAATTTCGATGAATTCTACAATATGTTTCATTGATGATGTTATTGAATTGGTGATTTTATCTTTCTGTTGCTGTCGCTAATCACAAGATCGAGGTGGGTTTGTTGATTTTTAAATGTAGCCTACAATACTCCGTTCGTGAAATCATAAAAAGCCATATGCGTTGAATGGATGTCATCCTATGGTAATTTGTTGATGATGAATTCATCCTGTGTAAAAATGTTAGTTTAATAAAATATTAGTGACCTGTAACTAACGGTTTGTTTGTTGATTGAGAACCGTGGTTATATTGAAAAATATATAAATACATTGGCTGGTCTTGTATGTCGGTTTTATTTTTTGTTGCCTAAACACAGGGATATCGAACTAATAACTAAAGGGCACTTTATAGGCAGAAAAACCAACGCGTCGGGAGATATGAGCTCAAGTATGGCGGATCCCATTGTCCGGGGCTCGGCAGGTGTAAAATTGGCGCGCCCACCAGCGTGGCATGCTCGTTGTCGGGCGGGATGACTTCGGGCAACCCGGTAAATCCGCTGCTGGGGGCAGGTACGCTTGGCCGAGACGGACTTGCCGCTGCCCGTACGCTGCGTTCATTCTCTCCCGCACCTAAAAAGCCTTCTGGACGAAGACGCCTGCCGGTGGGCGTTTTCGGCCCCGGCACAAACGCTGATATCCGCTTACAACTGCGTGATGACGGACTGATACTCCAGCAACAACGGCAGACGAACATTCCGCTGAGCCGCTGCTGCCACATGAGGAGAGCGAAATTAATACAACCGCAGGGTACGAGTCAATGTGGCTGGTGCGGTAAGGCAGCGCAACTGGACGGCCATACTGCTAGCGCGCGGCTGTGGGGGCTATACCGCCGGATATCAGTTAAGCCCGCATCTTTACCTGGCGACCAACGCGCACAGGGGCCGTGGTGGATGCTGGGTGGTCTGAGCGGGTGCCGGGTGCTGAGGACGCTTGCTGCCAGCGCCGCTGCCGTACCAGGTGCCACCAGGATAGCGGACCGCTTCAGGCGGACGCTGACGCCTGCGGCGTAGAACATGGTGACCCTGGCCAGAAATCACCAGCGTGACGGACGGTGCCGGGCGGGGTTATTCTGATTTTGTCACGCAGGCGCGAGCGTTGCGGAAAAGGCCACTTACCTCTTCGCTATCTTAATACGACGTTCCCCGCCCTATATAGCCTCAGCGTTCCCCAACCTACCCAGTACCGAATACGGCCCCGTGGTGGCTGATCACGACCGGCATGCCAGAGAAACCCTGCCGCTGCGCCACTAGATTGCGGTACGTCTCTGGAAACCGAGTGAACTGCGGCGGTATATGAGCCGCAGCAATACGCAGGTGCGCTTTCATTATGACGCGCTTACCCGGGCAGATGTGGCGCACCGTTACACTTAGGAAAGGCCGGAGATGCGCTACCACTTCGACGATACAGGGCGGGTGGTGGAGCAACGACCAGCAGGGGTTAAGCTACACTATCTTTATAGGCAAGGACCATATCGTCACCGACGGCCTGAACCGGCGTGGGAGTGCTGCATACAGAAGGCAGGGCCGGGCTAAAACAAATTGGTGAAAAAGAACGAGCGGACGGCACAGAAGCGTTCCGCGCTGAAATTGCATCGACCGCGAAGCAGGAAGGCTCACGGCATGAACGGACGCGGCAGGGCAGGAGGATAAGTACGGTCTGAATGTGGTGTCCAGCGATATCGAATACCACCGGACGGGCGGGAGACGAAATTCCTATAACGACGGGAGCCAGCTGACGGCGGTGGTAATGCCGGACGAACTGGAGAAACCGCCAGGAATATGATGAACCGGGCAGGCTGGTGTCAGAACATCGCGCAGCGGGGACAGTACGCTACCGCTACGTGGCCGCCTGATAGTTACCGGCGACGACAACGGATGCGACGGGCGCTTACCAACAGATAATATAGACACGCTACGGGCGTTGCTGGCGTTCTGGCTTTTCGACACGGAGCCATTATGAATACGACCGCTTCGGCCAGATGACGGCGAAGTCCACCGCGAAGGCATCAAACGCTACCGCTATAATAACGTGGCGGTTAACCTCGATGAAAACCGCACAGGGCGATGAAACGCGACATGAGCCACAACGCCGCAGAGCAACCTATTTCGCCAATTATCTGCCCCGGACGCGGCCGGAGCGGAAGACACGAGGTACGATGCGTGGGGAAAGGCGGGTCAGCACCACACCAGGGCGGCTGACGCGCAGTATCATTACGGTGCTGCCGGATGTCATCGCCCTGACCAACGAGAACACGGCAGCCACGGCGTCTTCTGGTTACGATGCGCTGGACCGGCTGGTGGGACAAACACCAAGCAGACGCCGAAGATGAGAACGATGAGCAGTATACCCGTAATGACGCTTCCTC\n->a403a23e-20e7-43f7-a5fa-dae8ebc59a01\n-TTGACTGTGCTTCGTTCGGTTACGTATTGCTTTTTCTGTTGGTGCTGATATTGCGGCGTCTGTAGGTGTTTAACCTGCCAGCATCACACGAGATTGGTCAAGTGCGGTTGGGTTTTTCAAACGGATGCGACAGCAGTTGGCATTAAAGAAGCCACCGCCGTTAGGCGCCGAGCATCTTGATGCTTCCACGAAGCTACGATACCGCCGGGTAACAGCTGTTGCGCTCCTTCAACGGTATTC'..b'CCGGGGCTGAGGCTCCCCACCGGCGCGGGCGTTTTGTCCGGTAACTGCTGTAGGTGCGGGAGAGAATGAAAGACGGCAGCAGGCCGGGGCAGGGGGCGTCAGTTTCACCAGGAAGGACCTTTACCGAGCAGCGGATTGACCGGATGGCCGGACGTCACCCGCGGGGCACCGAACAGGCCACGCCGGTGGGGCACCGATGCGTACCCCGGCTGAACCCTGGACAATGCTGCCGCCATACCGTCATGTCGCCCTGACGCCGCCGGTTTTCCGCTCATCTGCTCATCCTTGTTTTATCGGGTTATTTGTCTGCTGACAGGCGAAACCCTACAGATTTATAAGAAACTAAGTGAGATATCTGTCAGATAAGAACAATTAGGAAAATATTTATATATATTTCCTTGAATATATGTTTCGATTGGTATAACGATGTCACAAATATTCCTCTGAACATCTTCCTGTTAAAAAACCGCCAGCGTTTCCCGCTGGCGGTTTCAATAATATTCAAACTCAGCAATCAATAAAATCACCAGTTGCCTTTTCGGCCTGATCCATCCGCACCGGTTTATCATGGTTTCGATGGAGCGCGATGCAAGGTAGCTGTAAAGCGGGCGCGGTCTTTCCAGAAAAGCATAAGAAAAGAGCCAGCGCCAGAACGCCCGCTGCAACCGCATAAGTACAGCGTAAAGATAAAGCCATGCAGGATATTCTCTGTAGAGTTCCATACTTTTCTCCCCTTTTATCTACCCGATTATGAATGGCACCGGAAAAATGAATTGTTTATCTGATGAAAATAGTACCGCCAGCACGTAGTTTTACTACTCATCCGACCACTTATTTTGCTTATTGATGGTTTATTTACATTCATCCGCAATTAAGTTACACAAAGTTAAATTAATACTAAACATTAGTTAAATCATGGCTTTTGCCATTTTTATACTTTACACCCCGCCCGCAGATTTTGCGAAATCTTTGCAGCCAGGTCTACCTTCGGTATCACTTTTAGGCCACTGGAGGTGCACTGTGAGTGCAGGCGTGATAACCGGCATTATTGCTGGTGTTTTATTACTGGGTTATCTGGTTTGTAACCTGATCCAAATGCGGAGCGTTCTGATGGCTGCGCAAAGGGTTCTTACTGATCGCCACGTTTTTACTGGTGTTATGGGTGCTGGCGCGTCCTTTAGGCAGCGGGCTGGCGCAGCTGATTAATGACATTCCCTTCCCGGTACAACGGGCGTTGAGCGCGTACTTTTTCCTTTGCCCAGCGTCTCTGACCGTGAGAGATGAACTGGAAGCAATATCTTTGTGCCATTCTCGGCCTGAACATGCTGGGGCTGGCGGTGCTGTTTTATGTTATCAGTCAGCACTATCTGCCGCCAATCCACAGCAGTTGCCAGGGCTGTCATTGGGATCTGGCGCTGAATACCGTCAGCTTTGTCACCAATACCAACTGGCAATCTTATAGCGGTGAAACCACGTTGACTTCTTCAGCCAGATGGCGGGCTTAACGGTGCAAACTTTCTTTCTGCCGCCAGCGGGATTGCGGTGATTTTGCCTCATCCGTGCAGTTTACCCGCCAGGTATGAGCACGCTCAAGAATGCCTGGGTCGATCTGCTACGCATCACGTTATGATTGCTAGTCCTGTGGCGTTGTTGATTGCGCTGTTTTTATTCAGCAAGGTGCGCTGCAAACTTTCTGCCTTATCGGGCTGTGAATACCGTTGAAGAGGCGCAACAGCTGTTACCATGGGGCCTGCTGCTTCTCAGGAAGCAGTCAAGATGCTCAGTACTAGCGAAGGCGGTGGCCTAACAATGCCAGCTCAAAATCGCATCCGTTTGAAAACAACCGCGCGGCAACTTCGTGCAGATGCTGGCGATCTTCTTGATCCCAACGGCGCTGGTAATACTTTGCCTTTGGTGAAGTGATGGGCGATCGCCGCCGAGAGCATGTTGCTTATGTGGGCGATGTCGGTAATTTTTTGTGTCATCTCTGCGTAGGCGTGGTGATGTGGGCAGAAGTTCAGGGTAATCCTCATCTGCTGGCACTGGGCACGGACGCTTGTATCAATATGGAAGGTAAAGAGAGCCGTTTCGGCGTGCTGGTCAGTAACCTGTTTGCGGTCGACGGCTGACGGCTTCCTGTGTTGCAGTGATTACGCGATGCATGATTCGTTTACCGCTCTCGGTGGCATGGTGCCGATGTGGCTGATGCTAAATTGGTGGTGGTAATTTCGGCGGTGTCGGTTCTGGTCTTTGGCATGATGCTGTTTGTCCTGCTGGCGGTGTTTTGTGCCGGGCTGATGATTGGGGTCGTACACCGGAATATCTGGGTAAAAAAATCGACGTACGCGAGATGAAGCTGACTGCGCACAGCAGTCTGGTTACCCCGACGCTGGTGCTGATGGGCGCGGCGTTGTGATATTGACCGACGCCGGACGTAGCGCCATGCTCAACCCCTGGCCCGCATGGTTTTAGCGAAGTGCTGCTACGCCATGTCATCACCGCCGCTAACAACAACGGCAGCGCCTTTGCCAGTTCGCGCCAACTCCGTTCTGGAACTGTTTACTGGCGTTCTGCATGTTTTGTCGGTCCTTCGGGGTGATTATCCCGGTGATGGCAGTGCCGGTTCGCTGGTGATAAAAAGAGCCAAACCGCCAGCTCGGCACGCTGCCAGCACACGGCCCGCTGTTTGTTGGCCTGTTAATCGCTGCTGTGTTGCTGGTTGGCACTGAAGCCTTTATCTGCTGGCGGTCAGTGGCGGGAATATCTCTCCTGATGATGTTGGTGAGCACTGGATATGAGTCGTAAACAAACTTCCGGCTATTCAAGACCAACACTTGTCGTTCAGGCGCTGAAAGAAGCGGTGAAAAATTAAACCCGCAGGCGCAATGGCGCAATCCGGTGATGTTATCGTCTGGATCGGCAGTCTGCTGACCACCTGTATTAGCATCGCGATGGCAAAAGCAGGTGCGATGCCCGGCAATGCTGTTTAGCGCGGCCATTAGCGGTTGGCTGTGGGATCACCGTACTGTTCCTTCAATTTCGCCGAGGCGCTGGCAGAAGGCCGCAGTAAGCCTGGGTAACAGTCTGAAGGTGAAAAAACTGCGCTTTGCCCACCAAGCTGCGTGAGCCGAAATATGGCGCTGCGGCAGACCAAAGTTCCTGCGACCAACTTCGTAAAGGCGATATCATGCTGGTAGAAGCTGGCGATATTATCCCCTGCGATGGTGAAGTTATTGAAGGAAATTGCATCGGTCGATAAACTATGCATCACTGCGAGAATCGGCACCGGTGATCCGTGAATCCGGCGGCGTTTTGCCTCGATCACCGGCGGCGCATATTCTTTCTGACTGGCTGGTGATTGGGTGTAGCGTTAACTTGGCAGACATTTCTGGATCGGATGATCGCGATGGTGGAAAGGCGCACAGCGGCGCAAAACGCCGAACGAAATTGCCCTGACCATTCTGCTGATTGCCCTGACTATCGTCACTGCTGGCAACCGCCGCACGCTGTAACCGTTTTCGCGTAGGGCGGTAATGCAGTCAGCGTAACGGTACTGGTGGCGCTGCTGGTCTGTCTGATCCCAAAAGCCACTATTGGCGGCCTGTTGTCAGCAGTCGTCGCCGGGATGAGCCGGATGCTAGGCGCCGAATGTGATTGCCACCAGCGGACGATGCAGTTGAAGCGGCAGGTGACGTTGACGTTCTGCTACTGGATAAAACCAGCACCATCACACTCGGTAACCGTCAGGCGTCGAGTTTATCCCACGCAGAGGGCGTGGATGAAAAAACGCTGGCTGACGCCGCTGGCAGCTTCGCTGGCTGATGAAACGCGGAAGGCCGCAGTATTGATCCTCGCCAAGCAGCGTTTTAACCTGCGCGAGCGCGATGTGCAGTCATCATGCCACCCTTTGTACCGTTTGCAAGCCGGATGAAGCCAGGATCAGCATCGACAACCGCAGGTTAAACACCCAAGCAGACGCCGAAGATGGGGAAACCGTA\n' |
| b |
| diff -r e100f3f4d80e -r 2668027a533b test-data/ecoli-ref.fa --- a/test-data/ecoli-ref.fa Thu Sep 27 17:52:13 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,64860 +0,0 @@\n->gi|545778205|gb|U00096.3|:190-255 Escherichia coli str. K-12 substr. MG1655, complete genome\n-ATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGA\n->gi|545778205|gb|U00096.3|:337-2799 Escherichia coli str. K-12 substr. MG1655, complete genome\n-ATGCGAGTGTTGAAGTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTC\n-TGGAAAGCAATGCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCT\n-GGTGGCGATGATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATT\n-TTTGCCGAACTTTTGACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCGCAATTGAAAACTTTCG\n-TCGATCAGGAATTTGCCCAAATAAAACATGTCCTGCATGGCATTAGTTTGTTGGGGCAGTGCCCGGATAG\n-CATCAACGCTGCGCTGATTTGCCGTGGCGAGAAAATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCG\n-CGCGGTCACAACGTTACTGTTATCGATCCGGTCGAAAAACTGCTGGCAGTGGGGCATTACCTCGAATCTA\n-CCGTCGATATTGCTGAGTCCACCCGCCGTATTGCGGCAAGCCGCATTCCGGCTGATCACATGGTGCTGAT\n-GGCAGGTTTCACCGCCGGTAATGAAAAAGGCGAACTGGTGGTGCTTGGACGCAACGGTTCCGACTACTCT\n-GCTGCGGTGCTGGCTGCCTGTTTACGCGCCGATTGTTGCGAGATTTGGACGGACGTTGACGGGGTCTATA\n-CCTGCGACCCGCGTCAGGTGCCCGATGCGAGGTTGTTGAAGTCGATGTCCTACCAGGAAGCGATGGAGCT\n-TTCCTACTTCGGCGCTAAAGTTCTTCACCCCCGCACCATTACCCCCATCGCCCAGTTCCAGATCCCTTGC\n-CTGATTAAAAATACCGGAAATCCTCAAGCACCAGGTACGCTCATTGGTGCCAGCCGTGATGAAGACGAAT\n-TACCGGTCAAGGGCATTTCCAATCTGAATAACATGGCAATGTTCAGCGTTTCTGGTCCGGGGATGAAAGG\n-GATGGTCGGCATGGCGGCGCGCGTCTTTGCAGCGATGTCACGCGCCCGTATTTCCGTGGTGCTGATTACG\n-CAATCATCTTCCGAATACAGCATCAGTTTCTGCGTTCCACAAAGCGACTGTGTGCGAGCTGAACGGGCAA\n-TGCAGGAAGAGTTCTACCTGGAACTGAAAGAAGGCTTACTGGAGCCGCTGGCAGTGACGGAACGGCTGGC\n-CATTATCTCGGTGGTAGGTGATGGTATGCGCACCTTGCGTGGGATCTCGGCGAAATTCTTTGCCGCACTG\n-GCCCGCGCCAATATCAACATTGTCGCCATTGCTCAGGGATCTTCTGAACGCTCAATCTCTGTCGTGGTAA\n-ATAACGATGATGCGACCACTGGCGTGCGCGTTACTCATCAGATGCTGTTCAATACCGATCAGGTTATCGA\n-AGTGTTTGTGATTGGCGTCGGTGGCGTTGGCGGTGCGCTGCTGGAGCAACTGAAGCGTCAGCAAAGCTGG\n-CTGAAGAATAAACATATCGACTTACGTGTCTGCGGTGTTGCCAACTCGAAGGCTCTGCTCACCAATGTAC\n-ATGGCCTTAATCTGGAAAACTGGCAGGAAGAACTGGCGCAAGCCAAAGAGCCGTTTAATCTCGGGCGCTT\n-AATTCGCCTCGTGAAAGAATATCATCTGCTGAACCCGGTCATTGTTGACTGCACTTCCAGCCAGGCAGTG\n-GCGGATCAATATGCCGACTTCCTGCGCGAAGGTTTCCACGTTGTCACGCCGAACAAAAAGGCCAACACCT\n-CGTCGATGGATTACTACCATCAGTTGCGTTATGCGGCGGAAAAATCGCGGCGTAAATTCCTCTATGACAC\n-CAACGTTGGGGCTGGATTACCGGTTATTGAGAACCTGCAAAATCTGCTCAATGCAGGTGATGAATTGATG\n-AAGTTCTCCGGCATTCTTTCTGGTTCGCTTTCTTATATCTTCGGCAAGTTAGACGAAGGCATGAGTTTCT\n-CCGAGGCGACCACGCTGGCGCGGGAAATGGGTTATACCGAACCGGACCCGCGAGATGATCTTTCTGGTAT\n-GGATGTGGCGCGTAAACTATTGATTCTCGCTCGTGAAACGGGACGTGAACTGGAGCTGGCGGATATTGAA\n-ATTGAACCTGTGCTGCCCGCAGAGTTTAACGCCGAGGGTGATGTTGCCGCTTTTATGGCGAATCTGTCAC\n-AACTCGACGATCTCTTTGCCGCGCGCGTGGCGAAGGCCCGTGATGAAGGAAAAGTTTTGCGCTATGTTGG\n-CAATATTGATGAAGATGGCGTCTGCCGCGTGAAGATTGCCGAAGTGGATGGTAATGATCCGCTGTTCAAA\n-GTGAAAAATGGCGAAAACGCCCTGGCCTTCTATAGCCACTATTATCAGCCGCTGCCGTTGGTACTGCGCG\n-GATATGGTGCGGGCAATGACGTTACAGCTGCCGGTGTCTTTGCTGATCTGCTACGTACCCTCTCATGGAA\n-GTTAGGAGTCTGA\n->gi|545778205|gb|U00096.3|:2801-3733 Escherichia coli str. K-12 substr. MG1655, complete genome\n-ATGGTTAAAGTTTATGCCCCGGCTTCCAGTGCCAATATGAGCGTCGGGTTTGATGTGCTCGGGGCGGCGG\n-TGACACCTGTTGATGGTGCATTGCTCGGAGATGTAGTCACGGTTGAGGCGGCAGAGACATTCAGTCTCAA\n-CAACCTCGGACGCTTTGCCGATAAGCTGCCGTCAGAACCACGGGAAAATATCGTTTATCAGTGCTGGGAG\n-CGTTTTTGCCAGGAACTGGGTAAGCAAATTCCAGTGGCGATGACCCTGGAAAAGAATATGCCGATCGGTT\n-CGGGCTTAGGCTCCAGTGCCTGTTCGGTGGTCGCGGCGCTGATGGCGATGAATGAACACTGCGGCAAGCC\n-GCTTAATGACACTCGTTTGCTGGCTTTGATGGGCGAGCTGGAAGGCCGTATCTCCGGCAGCATTCATTAC\n-GACAACGTGGCACCGTGTTTTCTCGGTGGTATGCAGTTGATGATCGAAGAAAACGACATCATCAGCCAGC\n-AAGTGCCAGGGTTTGATGAGTGGCTGTGGGTGCTGGCGTATCCGGGGATTAAAGTCTCGACGGCAGAAGC\n-CAGGGCTATTTTACCGGCGCAGTATCGCCGCCAGGATTGCATTGCGCACGGGCGACATCTGGCAGGCTTC\n-ATTCACGCCTGCTATTCCCGTCAGCCTGAGCTTGCCGCGAAGCTGATGAAAGATGTTATCGCTGAACCCT\n-ACCGTGAACGGTTACTGCCAGGCTTCCGGCAGGCGCGGCAGGCGGTCGCGGAAATCGGCGCGGTAGCGAG\n-CGGTATCTCCGGCTCCGGCCCGACCTTGTTCGCTCTGTGTGACAAGCCGGAAACCGCCCAGCGCGTTGCC\n-GACTGGTTGGGTAAGAACTACCTGCAAAATCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGG\n-GCGCACGAGTACTGGAAAACTAA\n->gi|545778205|gb|U00096.3|:3734-5020 Escherichia coli str. K-12 substr. MG1655, complete genome\n-ATGAAACTCTACAATCTGAAAGATCACAA'..b'ACGCGAAGGTCCGCCGCCGGAAGTGGTGGCTCGTTTTACTGACAACATTCTGACGCAAAATGCGCGTA\n-TGCAGGCATTGGTAGAAACGTTACTACGCCAGGCAAGACTGGAGAATCGTCAGGAAGTCGTTCTGACTGC\n-TGTTGATGTGGCGGCATTATTCCGCCGCGTCAGCGAAGCGCGCACCGTGCAGTTGGCAGAAAAAAAAATC\n-ACTCTGCATGTTACGCCCACCGAGGTTAACGTTGCTGCTGAACCGGCGTTACTGGAGCAGGCGCTGGGAA\n-ATTTACTGGATAACGCCATCGATTTTACCCCCGAGAGCGGTTGCATCACGCTAAGCGCCGAAGTGGATCA\n-GGAACACGTCACGCTTAAGGTGCTGGATACCGGTAGTGGTATTCCTGACTACGCGCTTTCACGTATTTTT\n-GAACGCTTTTACTCTTTGCCTCGTGCAAATGGGCAAAAAAGCAGCGGTCTGGGGTTGGCGTTCGTCAGTG\n-AGGTCGCCCGTTTGTTTAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCT\n-TCGACTTCACCGTCACTTCACATAG\n->gi|545778205|gb|U00096.3|:4638178-4639530 Escherichia coli str. K-12 substr. MG1655, complete genome\n-ATGTTGAAATCCCCCCTGTTCTGGAAAATGACTAGCCTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGA\n-TAATGCTGATTCGGCAGGTGATTGTCGAACGTGCTGATTACCGTAGCGATGTGGAAGATGCGATTCGCCA\n-AAGTACCAGCGGGCCGCAAAAACTCGTTGGGCCGCTCATCGCTATTCCTGTGACCGAGCTTTATACGGTG\n-CAGGAAGAGGATAAAACCGTGGAGCGGAAACGAAGTTTTATCCATTTTTGGTTACCTGAGTCATTGATGG\n-TTGATGGCAATCAGAACGTGGAAGAACGCAAGATAGGGATTTATACCGGTCAGGTCTGGCACAGTGATTT\n-AACGTTAAAAGCCGATTTCGATGTTTCGCGTCTTAGCGAACTCAACGCGCCAAATATCACCTTAGGCAAG\n-CCATTTATTGTGATTAGCGTCGGGGATGCGCGTGGTATTGGTGTGGTGAAAGCGCCTGAAGTTAACGGAA\n-CGGCGCTGACCATTGAACCCGGCACCGGGTTAGAGCAAGGCGGGCAGGGCGTGCATATCCCTTTACCTGA\n-AGGGGACTGGCGGAAGCAGAACCTGAAGCTGAATATGGCCCTGAATTTAAGCGGTACCGGCGATCTTTCT\n-GTGGTGCCTGGCGGGCGTAATAGCGAAATGACCTTAACCAGCAACTGGCCGCATCCCAGTTTTTTAGGTG\n-ATTTTCTACCAGCCAAACGGGAAGTTAGCGAGTCAGGTTTTCAGGCGCACTGGCAAAGCAGCTGGTTTGC\n-TAATAATCTCGGTGAGCGTTTTGCTTCAGGCAATGATACCGGCTGGGAAAACTTCCCGGCGTTTAGCGTC\n-GCAGTAACGACGCCAGCCGATCAATACCAATTAACTGACCGGGCGACTAAGTACGCCATTCTGCTGATTG\n-CACTGACTTTTATGGCGTTCTTTGTTTTTGAAACGCTCACCGCGCAACGTTTACACCCAATGCAATATTT\n-GCTGGTGGGGCTTTCATTGGTGATGTTTTATTTGCTCTTGCTGGCGCTTTCTGAACATACCGGTTTTACC\n-GTGGCATGGATAATCGCCAGTCTGATTGGGGCGATAATGAACGGTATTTATTTGCAAGCGGTATTGAAAG\n-GTTGGTGCAACAGCATGTTGTTTACCCTCGCGCTGTTGTTGCTGGATGGTGTGATGTGGGGACTGCTCAA\n-CTCTGCCGATAGCGCGCTGTTGTTGGGAACCAGTGTGCTGGTGGTGGCGCTGGCCGGCATGATGTTTGTG\n-ACCCGTAATATCGACTGGTATGCGTTTTCACTGCCGAAAATGAAAGCCAGTAAAGAAGTTACAACGGACG\n-ATGAGTTACGTATCTGGAAATAA\n->gi|545778205|gb|U00096.3|:c4640306-4639590 Escherichia coli str. K-12 substr. MG1655, complete genome\n-ATGCAGACCCCGCACATTCTTATCGTTGAAGACGAGTTGGTAACACGCAACACGTTGAAAAGTATTTTCG\n-AAGCGGAAGGCTATGATGTTTTCGAAGCGACAGATGGCGCGGAAATGCATCAGATCCTCTCTGAATATGA\n-CATCAACCTGGTGATCATGGATATCAATCTGCCGGGTAAGAACGGTCTTCTGTTAGCGCGTGAACTGCGC\n-GAGCAGGCGAATGTTGCGTTGATGTTCCTGACTGGCCGTGACAACGAAGTCGATAAAATTCTCGGCCTCG\n-AAATCGGTGCAGATGACTACATCACCAAACCGTTCAACCCGCGTGAACTGACGATTCGTGCACGCAACCT\n-ACTGTCCCGTACCATGAATCTGGGTACTGTCAGCGAAGAACGTCGTAGCGTTGAAAGCTACAAGTTCAAT\n-GGTTGGGAACTGGACATCAACAGCCGTTCGTTGATCGGCCCTGATGGCGAGCAGTACAAGCTGCCGCGCA\n-GCGAGTTCCGCGCCATGCTTCACTTCTGTGAAAACCCAGGCAAAATTCAGTCCCGTGCTGAACTGCTGAA\n-GAAAATGACCGGCCGTGAGCTGAAACCGCACGACCGTACTGTAGACGTGACGATCCGCCGTATTCGTAAA\n-CATTTCGAATCTACGCCGGATACGCCGGAAATCATCGCCACCATTCACGGTGAAGGTTATCGCTTCTGCG\n-GTGATCTGGAAGATTAA\n->gi|545778205|gb|U00096.3|:4640402-4640542 Escherichia coli str. K-12 substr. MG1655, complete genome\n-ATGACTAAAGTACGTAATTGCGTTCTTGATGCACTTTCCATCAACGTCAACAACATCATTAGCTTGGTCG\n-TGGGTACTTTCCCTCAGGACCCGACAGTGTCAAAAACGGCTGTCATCCTAACCATTTTAACAGCAACATA\n-A\n->gi|545778205|gb|U00096.3|:4640942-4641628 Escherichia coli str. K-12 substr. MG1655, complete genome\n-ATGCGTATAACGATTATTCTGGTCGCACCCGCCAGAGCAGAAAATATTGGGGCAGCGGCGCGGGCAATGA\n-AAACGATGGGGTTTAGCGATCTGCGGATTGTCGATAGTCAGGCACACCTGGAGCCAGCCACCCGCTGGGT\n-CGCACATGGATCTGGTGATATTATTGATAATATTAAAGTTTTCCCGACATTGGCTGAATCGTTACACGAT\n-GTCGATTTCACTGTCGCCACCACTGCGCGCAGTCGGGCGAAATATCATTACTACGCCACGCCAGTTGAAC\n-TGGTGCCGCTGTTAGAGGAAAAATCTTCATGGATGAGCCATGCCGCGCTGGTGTTTGGTCGCGAAGATTC\n-CGGGTTGACTAACGAAGAGTTAGCGTTGGCTGACGTTCTTACTGGTGTGCCGATGGTGGCGGATTATCCT\n-TCGCTCAATCTGGGGCAGGCGGTGATGGTCTATTGCTATCAATTAGCAACATTAATACAACAACCGGCGA\n-AAAGTGATGCAACGGCAGACCAACATCAACTGCAAGCTTTACGCGAACGAGCCATGACATTGCTGACGAC\n-TCTGGCAGTGGCAGATGACATAAAACTGGTCGACTGGTTACAACAACGCCTGGGGCTTTTAGAGCAACGA\n-GACACGGCAATGTTGCACCGTTTGCTGCATGATATTGAAAAAAATATCACCAAATAA\n' |
| b |
| diff -r e100f3f4d80e -r 2668027a533b test-data/result1.alignments --- a/test-data/result1.alignments Thu Sep 27 17:52:13 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,507 +0,0 @@\n-3221ccdb-0395-4983-8a44-e5558664096f\t+\t12618\t3584\t10496\tc39789a3-7c1c-4b1e-bc6d-dc0df49e969c\t+\t6934\t0\t6912\t1798\t6912\t192\t1\t3MDIDIDIDIDIDIDIMDMIDMIDIDIDIdMIDIMDMIDMIDI\n-3221ccdb-0395-4983-8a44-e5558664096f\t+\t12618\t5120\t12544\t88b1797f-3a41-442f-bab4-cdfedf7ec597\t+\t8486\t0\t7424\t1765\t7424\t213\t4\t3MIDId3MIDMIDMIDIDMIDMIdMIDIDIdmMIDIDIDIDID\n-3221ccdb-0395-4983-8a44-e5558664096f\t-\t12618\t1536\t8960\tf58173f7-dbfb-4c47-92c1-0124626bf4c2\t+\t7462\t0\t7424\t1745\t7424\t184\t4\t3MDI2m2MDi7Mm2MDIDIDIMDI2MDI2M\n-3221ccdb-0395-4983-8a44-e5558664096f\t-\t12618\t6656\t12544\t95ff70e7-2b87-42d1-a957-21f9f276595c\t+\t10407\t4352\t10240\t1686\t5888\t174\t1\tMDIDIDIDIDIDIMDIMDIMDI2MDIDIDIDIDIDImM\n-3221ccdb-0395-4983-8a44-e5558664096f\t+\t12618\t3840\t12544\teaa48d4e-1945-4011-8bae-ded748af1fca\t+\t10149\t512\t9216\t1685\t8704\t175\t5\tMD4MIDmMm4MmMID2MIdMID3MIDIDIDIdMIDIDIDIDI\n-3221ccdb-0395-4983-8a44-e5558664096f\t-\t12618\t2560\t9216\t7f343574-f2bc-4388-91b9-84b99e39256a\t+\t6914\t256\t6912\t1664\t6656\t182\t2\tMI6Mm3MDIMm3MDIMDI2MDIMDID\n-3221ccdb-0395-4983-8a44-e5558664096f\t-\t12618\t6656\t12544\tbc5615d7-dc94-4315-9cf1-5112555c19d5\t+\t7174\t1536\t7168\t1621\t5632\t182\t0\t2MIDIMDID2MIDIDIDMID2MID2MIDIDMIDI\n-3221ccdb-0395-4983-8a44-e5558664096f\t+\t12618\t5632\t12544\tfb405411-031d-4447-8096-b603693b1fe7\t+\t8238\t0\t6912\t1616\t6912\t169\t2\t2MIDMIDMIDIDMIDID4MIDMIDIDIDi2MDm2MID\n-3221ccdb-0395-4983-8a44-e5558664096f\t+\t12618\t2560\t8704\t44b26523-eaf0-4f28-87ad-4cca044fabc8\t+\t6002\t0\t5888\t1583\t5888\t165\t1\tMIDIDMIDIDIDMIDIDIDIDIDIDID2MIDMmMIDIDI\n-3221ccdb-0395-4983-8a44-e5558664096f\t-\t12618\t1024\t8448\t1d5ccec9-296a-4afd-ad74-010ebd3732ec\t+\t7297\t0\t7168\t1571\t7168\t163\t4\tMIDMIDMI2mMDIDMIDMIdMi2MDI2MDIDIDIDIMDIDIDI\n-3221ccdb-0395-4983-8a44-e5558664096f\t-\t12618\t1024\t8192\t6a470b8f-d316-4d8c-b93f-ea7bd154775d\t+\t7009\t0\t6912\t1562\t6912\t169\t3\t10Mm3Mm4MID3Mm2MIDI\n-3221ccdb-0395-4983-8a44-e5558664096f\t+\t12618\t3584\t12032\t38f657d9-0701-44bb-8c13-d9446f8fe441\t+\t8686\t0\t8448\t1561\t8448\t156\t6\t2MDID2m2Mi2MDID3MImMD2MIDiMDiMDIDIDIDI2MDIMDI\n-3221ccdb-0395-4983-8a44-e5558664096f\t-\t12618\t3072\t10240\tc2ba4328-d217-4343-a959-874cf5addce4\t+\t7328\t0\t7168\t1482\t7168\t157\t2\t5MIDIDIDIDMId11MIDm4M\n-3221ccdb-0395-4983-8a44-e5558664096f\t-\t12618\t7424\t12544\tcdf5b34b-6170-45bb-9691-6fcdaadb4713\t+\t12467\t3328\t8448\t1368\t5120\t164\t2\tMDIDIDiMDMIMDIDIDIm3MDIDI2MDI\n-3221ccdb-0395-4983-8a44-e5558664096f\t+\t12618\t7936\t12544\tce4d48fa-9112-4aa8-b655-10c5064129db\t+\t5801\t256\t4608\t1365\t4352\t155\t1\tMI4Mm2MDIDI7M\n-3221ccdb-0395-4983-8a44-e5558664096f\t-\t12618\t5376\t12032\t29fcf315-e502-472c-8e1f-80e65e5b4972\t+\t6479\t0\t6400\t1364\t6400\t150\t4\tMId3MIDIDIDIDI2MDm4MmMIDIDIdMIDMI\n-3221ccdb-0395-4983-8a44-e5558664096f\t-\t12618\t7936\t12544\tbe16c798-0278-462a-b65b-6e77e03c7432\t+\t6756\t2048\t6656\t1332\t4608\t168\t1\t3Mm2MDI11M\n-3221ccdb-0395-4983-8a44-e5558664096f\t+\t12618\t5888\t11008\tbbe44e2d-c0b1-4a30-997b-7a077a66c189\t+\t5323\t0\t5120\t1330\t5120\t153\t2\t2MmMDIDIMDI3MDIDIMmMDIDI2M\n-3221ccdb-0395-4983-8a44-e5558664096f\t-\t12618\t2816\t10240\t380cc868-0f9e-478b-b1df-70cbe6602339\t+\t7681\t0\t7680\t1241\t7424\t131\t8\t2MmM3m2MDIMDIMm2MDiMmMDIm2MDIDIDIDIDID\n-3221ccdb-0395-4983-8a44-e5558664096f\t+\t12618\t6144\t11264\t10df3a9d-60a4-4cb5-ab3d-46483be7bb59\t+\t5183\t0\t5120\t1177\t5120\t135\t2\t3MDIDIMmMDI2MDI3MdMIDI2M\n-3221ccdb-0395-4983-8a44-e5558664096f\t-\t12618\t3584\t8704\tbec0a1f3-2776-4ace-b372-0a76a9cbed6b\t+\t5512\t256\t5376\t1122\t5120\t121\t3\tMIDIDIdMIDIDI2MDIMDmMIDMm3M\n-3221ccdb-0395-4983-8a44-e5558664096f\t+\t12618\t3072\t7936\t2c468ad4-194a-4af0-93d4-3fcbe17a9be7\t+\t5263\t0\t5120\t1115\t4864\t118\t3\tMDIDI3MDIMDIm5MDim2MD\n-3221ccdb-0395-4983-8a44-e5558664096f\t-\t12618\t6400\t12288\t60664444-cccc-41e7-b7a6-5c4c14343658\t+\t6020\t0\t5888\t1102\t5888\t117\t3\t2MDIMDi5Mm2Mm9M\n-3221ccdb-0395-4983-8a44-e5558664096f\t+\t12618\t6144\t12544\t1c935ec4-4503-44ea-be57-7201fc03eeb6\t+\t10879\t0\t6656\t1095\t6400\t116\t5\tMDMID3MID2MID2MmMm3MimMDIDIDmM\n-3221ccdb-0395-4983-8a44-e5558664096f\t+\t12618\t4352\t10752\t3048e786-5b3d-4587-b5d0-714b40192268\t+\t6628\t0\t6400\t1094\t6400\t108\t4\t2MDID2MIMDIdMmMiMDIm2MDI2MDIDIMDIDI\n-3221ccdb-0395-4983-8a44-e5558664096f\t+\t12618\t3072\t11008\t9388888e-4344-4e51-a'..b'0db853eaf2\t+\t6846\t2048\t4096\tce4d48fa-9112-4aa8-b655-10c5064129db\t+\t5801\t0\t2048\t508\t2048\t48\t0\tMIDIDIMDIDIMD\n-67ee25a0-86c1-44be-9b64-5a0db853eaf2\t-\t6846\t1536\t3840\tcc70a582-d0ee-47f5-890d-9d097df3619a\t+\t2710\t256\t2560\t507\t2304\t50\t1\tMIMDiMDMIDIDM\n-67ee25a0-86c1-44be-9b64-5a0db853eaf2\t+\t6846\t4096\t6656\t2a021335-d1c5-4881-93fc-a673d8960075\t+\t5964\t3072\t5376\t495\t2304\t51\t1\t5Mi4M\n-67ee25a0-86c1-44be-9b64-5a0db853eaf2\t-\t6846\t4096\t6400\t8b55f8dd-3fcb-478c-8384-6df32ed6400b\t+\t5296\t2048\t4352\t490\t2304\t54\t1\tMId2MID4M\n-67ee25a0-86c1-44be-9b64-5a0db853eaf2\t-\t6846\t0\t2560\t756abc44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|
| b |
| diff -r e100f3f4d80e -r 2668027a533b test-data/result1.ctg.lay --- a/test-data/result1.ctg.lay Thu Sep 27 17:52:13 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,361 +0,0 @@\n->ctg1 nodes=15 len=14848\n-E\t0\tN20\t+\tN18\t+\n-S\tbdfab7a9-1792-4c9a-9428-261e109cdfae\t-\t5376\t2304\tAGCTTTTTACTCAGTAATATAAAAATATTGAATTGTTAGCTTTTGTGTGTTGTTTTGTGAAGATAAAAGCCGCTTTATTATTACGGCTTTAATTAATAAAGGCAGCTGTATTAAAATTAATATTCAAAAGCATAAACCGATGTTTTCAATACGGTTTCCCAGTAATGAAATGGCGGGCGGGCGGGATCCTGTTCCAGTTTTTGTCGCAGATGTCCCATATAAATACGCAAATAGTGACTGTGTTCGACCGCGTTTGGCCCCCACACCTGGTTAAGGAAAGCTGGCGCTGGGTGAGTACTTCTTCCGGCATTGTTACAGCACCGCCAGCAGGCGGAACTCAATTGGTGTGAGATGCACCTCTTCCTCACCCTGGCAATCACGCGGCGGTTAACCGGACGGTAACATCGGAAAATTTTACAGCAGCGGATCGGGCGCGGTGGTGGCAGAGTATAGGTGTAATGCGACGCGCAGACGGGCCCGTAATTCGCCACGCCAAACGGTTTACTCAGAGAATCATCCGCTCCGGCATCCAGCGGCGATTTTGGTCGCTCTTCGCTGCGTGCGGAAAGCACAACTGCGGCACTGCGCTCCACTGGCGCAGGTCGCGGATAAACCAATCTCATCACCATCGGGCAGGCCGCCGAGATCGAGAATAATCAAATCTGGCTTACGGGTTGCTGCTTCCATAAGCCGCGTTGCAGCGTTTCGGCCTCAAAGATCGTGCATCCCGTCGTTCTCCAGCGCGTGCGCGCAGAAAGCGACGAATACGCCTGTTCATTCGAATAACCAGAACGTTTGTCATATATCCCGCGAAATTCTTCAGTTCAGGGCAGTTTGGCTGTGAAGCGTAATAATGAAAAACAGGCACCACCTTCCAATGGTTGAACGCAGGTAATAGTGCCCTTCGTGTACATCCACTATCGCCTGACAAATTGCCAGTCCGCCCCACTCTGGTACTTCCGCTTCGACTCTTTATTCCCGCGAGCAAACTTATCAAATATCAAAGTCCGCTCCTGGCCTGGCGGAAGACCGGGGCCAAGTATTATCCCAGACATCCAGTTGCAGATTTTCGCCCTCAACGTGGGCACGATACCAATTCGGCCTGCGCAATCCGCATATTTCACCCGGGCGTTCTCTGTAGATTAATCAGCACCTCGTTCAAAAGAGTGCGGCCTGTCAACGTGGATCGAGGTCATGGTTCGGCAGAGAAAGATTGATGGGTAGACGATAAAACCCGGTTCCAGCATTTGCAGCGCTGCCGACTACTTCTTTCCGTAGCGTTAACCACTTTTCCAAATTAAAGCCGCCGGACTGAATTCGCGCCATACTCCAGTAGATTATTCACCAGTCGGTAGTGTTCGCTACTATGCTGGACGGATCTCGCCGGCCTTGGCGGGCGTGGGGTGATCCTCTGCGTTTGCCAGATCGACAAGCTGGGCGATTGGCCTGACCAAACAGCACCGTAAGCGGCGTGCGTAAATCATGTGCAGCGCTGCCAGTGGGCGTTGCGATCTGTTCACGTTCGTTTGCCATCCGCCTGTTCTTCGCTGCTGGCGGTTAGCGTCAGCCGCCCATGATAAGAGACCAACAGCGAACGTTCCAGCAGCGCTGCTGGTTCCGGATCATCAACTGGCGCAGACTCCCCGGCTCCACCACACCAACAGCCCGTAGAGCTTTCGCCGCTTTTAGCGGCGAAAATCTGGCACGGTACACCGGGTAACGCGTCAGTGCCCGCGCCCGCAGGCAGGCCTTTACCGCAAACCTCCACTGCGCGATGGTACTTTGTCCCCACTGGCGTCATTCCCAGGATGTTAACGGCTGCAATTTCTACCGTTGTCATCGGGCAACAACACCCGACTGCGGGCATGAAACGTGGAGGCGTAAATTGTTCGCTGGTGAAGATATCCCTGCGGACTGCGGCCCACCGCCAGAGCTGATGATTTCATATGGTGCCGCGTGCGTTGCCTGCGGTAACGGGCTACCTCCGCGCCTGATAACGCACGCCAGCAGTAAGGTTCTGATCAGCCTGACGGTTAACACCGCGAAGCGTCAGCAGATATTGCACATCAGAGACGGCGAGCGTGCCGTGTGGGCGATAAAAGAGATCGAAACTCACTACACACGACGGCGGCAACCACTGAAGGCCAGCAGTCCATAAAATAGCGCCACCACACACCACGCCAAGCAGATATTGCTGTTACCAGGTTGGCGGCATCAACGCCATCAGCCACGCATGGCAATTAAGGTGATAACGGCGCATAACGCGGCGGCAACCACGCATCCCCTGAATTTGTACACGCCACT\n-S\t1d5ccec9-296a-4afd-ad74-010ebd3732ec\t-\t5120\t2048\tGCGGAACTCAATTGGTGTGGAGATGCACCTTCCTCACCCCGGTGAATCACGCGGGCGGCTAAATCGACGGTAACATCGGAAAAATTTTACCAGCGGATCGGGCGCGGTGGTGGCAGAGTGGCGGCGTAATGCGACGCGCAGACGGGCCTGGCATCTGCCACGCCAAAACGGCTTTACTCAGATAGCTAATCATCCGCCTGGCATCCAGCGCGCGGCGATTTTGTCGCTCTTCTGCTGCGTGCGGAAAGTCAATCACCGGCACCGCGCCCCACTGGCGCAGGTCGCGTGATAAACTCAATCCCATCACCATCGGGCAGGCCGAGATCGAGAATAATCAAATCTGGCTTACGGGTTGCCGCTTCCAGCAAGCCGCGTTGCAGCGTTTCGGCCTCAAAGATCGCATCCGTCGCCTCCTCCAGCGCCGTGCGCAGAAAGGACGAATAGCCTGTTCATCTTCAAGAATCAGAACGTTTGTCAAGCATATCCCGCTGAAATCTTTCCGTTCAGGGCAGTTTGGTTGGGGAAGTGTAACACGAAAAACAGGCACCACCTTCCGGTCGGTTGAACGCGGTAATAGTGCCCCCGTGTACATCCACTATCGCCCGACAAATTGCCAGTCCAAGCCCTACCCCCGGTACTGCCGCCGACTCTTTATTCCCGCGAGCAAACTTATCAAATATCGTCTGTCTTGGCCTGGCGGAAGACCGCCGCTATCCCAGACATCCAGTTGTAGATTTTCGCCTCAACGTGGGCATCGATAATTAATTTCGGCCTGCGCACCCGCATATTTCACCGCGTTCTCCAGCAGATTAATCAGCACCCGTTCAAAGAGGCCCGTCAACGTGGATTAAGGTCAGCGGTTCTGGCAGAGAAAGATTGATGGGCGACGATAAACCCGGTTCCAGACGGCAGCGCGCTGCTGACTACTTCTTTCCAGCGTTAACCACTCTTTCTTCCCCAAATTAAAGCCGCCGGACTGAATTCGCGCCATATCCAGTAGATTATTCACCAGTCGGGTAGTAAGAAGTTAATACGCTACCTGATCTCGCTGGCCTGGCGGGCGGGTGATCCTCGCTTCGCCGGTAGGATCGAGGTTAAGATTTCTGCCTGACCTCGCAGCACCGTAAGCGGCGTGCGTAAATCATGCGAAAGCGCCGCCAGCAGGGCATTGCGGATCTGGTTCACGTTCGCTTGCCATCCGCGCCTGTTCTTCGCTGGCGGTTAGCGTCACGCTCAAGGGTGATATGACTAACAGCGTAACGGTTCCAGCAGGCGCTGCTGTTCCGGGATCATCAACTGGCGCAGATTCCCCGGCTCCACCACCACCAGCCCGTAGGTTTTCTCGCCGCTTTACGCAAAATCTGGTACGGTACACCGGGTAACGTCGGTGCCCGCGCCCGCAGGCAGGCCTTTATCAAAACTCCACTGCAAGGATGGCATCGTCCCACGGCGTCATTCCCTTGCGGATGTGTTAACGGCTGCAATTTACCGCTGCCATCGGGCAACAACACCTGACTGCGGGCATGAAA'..b'AGGCTTAAGCGCCAGCCAGACAATTAATAGCGACGGCGAACGCCATTCGCGCTGGGAACCAACGTGCAATCATGCTTCCTCCTGCAACTGCCCCGTTCACCAGCCCAATGGCAGCGGTCGCAGCGCCGCCAGTTGCAGGTCGTGGGTCACCATAATCAACGTGGTGCCATGTTTACGGTTGAGGAAAACAGCAGGTCGGCAATTTTATCGCCCGTCTGGCGGTCAAAGGTTGCCGGTTCGTCGGCAAACAGCATCAGGTCGACCATTAAAGGCTCGTGCCAGCATATCTTCCTCGTTGCTGTTCACCGCTGGAAAGCTGTGCCGGAAGATGATCAGACGTTTACCCAGCCCTAACTGTTTCGAGCAACGCTTTCGCCCCGTTACGACTTTCCGCTACTCTCCACCGCGCAGCAGGCCAGGAAGCTCGACGTTTTCCAGCGCGTTAAGGGTAGGAATTAACATAAATGACTGAAAAACAAAGCCGACGTGCTTCGCGCTTAACTTTGCCCGCGCTTCTTCGTCCATATTATGTGGCGGTTGTCCCTGGAGCTCACTTCGCCACTGCTGCCGTCATCAAGCCCGGCGAGGATCGCCAACAAGGTTGACTTACGATCCCGACTCGCCCACCAGTGCGATGGTCTCGCGCGTTTGACAACCAGCTCAACTCGGTGAGGATGGAGAGTTCATACTCCCTGACCGACGGACTTCTTAAGATGATGAACTTCAACAATGTTTTCGGCATTTGCCCTTCCTGTTCCTGGTCCTGTTAACCTTCCGTGCCGCCGCAGCCGTTATTGATTCTGGGTGATAGCCTGAGCCGGGTATCCAGATGTCTGCCAGCGCTGGCCTGGCCTGCCTGTTGAATGATAAGTGGCAGAGTAAACGTCGGTAATTAATGCCAGCATCAGCACGGCGACACCTCGCAACAAGGACTGGCGCCTTCCGGCTCTGCTGAAACAGCATCAGCCGCGTTGGGTGCTGGTTGAACTGGGCGGCAATGACGGTTTGCGTGGTTTTCGGCCGCAGCAAACCGGTGGCTGCGCCAGATTTTGCGGATGTCAAAGCGCCAACGCTGGACATTGTTAATGCAAAATACGTCTGCCTGCTGACGCTATGGTCGCCGTTATAATGAAGCCTTTAGCGCGCCATTTACCCCAAACTCGCCAAAGAGTTTGATGTTCCGCTGCTGCCCTTTTTTATGGAAAGGTCTGCCTCAAGCCACAATGGATGCGGGATGACCCAGGTATTCATCCCAACCGCGACGCCCAGCCGTTTATTGCCGACTGGATGGCGAAGCAGTTGCAGCCTTTAGTAAATCATGACTCATAAAGCAACGGAGATCCTGACAGGTAAAGTTATGCAAAATCATTAATTACCGGATGTTCCAGTGGAATTGACACCAGAGCGCTCGAATTAAAACGCCAGGGTTTTCATGCTGGCAGGTTGCCGGAAACCGGATGATGTTGAGCGCATGAACGGCATGGGATTTACCGGCGTGTTGATCGATCTGGATTCACCAGAAAGTGTTGATCGCGCAGCAACGAGGTGATCGCCTGACCGATAATTGTCTGTATGGGATCTTTAACAATGCCGGATTCAGCATGTATGGCCCCTTTCCTGCATCCAGCCCGTGCGCAGATGGAACAGCAGTTTCCGCCAACTTTTCGGCGCACCAGCTCTGTGCGCCTGTTACCCGCGATGTTACCGCACGGTGAGGGCGTATTGTGATGACATCATCGGTGATGGGATTAATCTCCACGCCAGGTCGTGGCGCTTACGCCGGCCAGTAAATATGCGCTGGAGGCGTGGTCAGATGCACTGCGCATGGGCTGCGCCACAGCGGAATTAAAGTCAGCCTGATCGAACCCGGTCCCATTCGTACTCGCTTCACCGACAA\n-S\tb1594985-30ce-4f59-9230-dff6ec966710\t+\t4096\t2048\tTGCGGTTTCAGGCCAGGGGATGGTTGCAGATCGCCATACATCGGGTAGATATCATCCACCGCTGACGTTCGCCAGCTGCGGTGTGTCGCCTGCAAAGGTCATTGTGGCGAAAGTCCGGCTGCTGCCGACTTTCAGGCCGCGCTTTGCGCTTCCTCCAGCCACGCTGCGGCACTTCACGCGTGAACCGCAACGCCCGATCGCCCGCCATAAACTCACGGCTTTGCTGGCTTAAGCCCTTCTCCATGCGATCGCTGATATTGCCCCAGCGCCAGCACGCAGGCCACCGCCGGAAGCTTAGCGCCAGCCAGACAATTAATAGCGACGGCGAACGCCATTCGCGCCAGAACCAACGATGCAATCATGCTTCCTCTGCAACTGCCCGTTCACCAGCCATGAAAGCAGCGGTCGCAGCGTGCCGCCAGTTGATTGCGGTGTGGAGTCACCATAATCAACGTGGTGCCATGTTCACGGTTGAGGAAAACAGCAGGTCCGGCAATTTTATCGCCCGTCTGGCGGTCAAGGTTGCCAGTGGGTTCAAATCGGCAAACAGCATCAGGTCGACCATTAAAGGCTCGTGCCAGCTCTTCCTCGTTGCTGTTCTGCGCCGGAAAGCTGTGCCGGAAGATGATCAGACGTTTACCCAGCCCTAACTGTTCGAGCAACGCTTTCGCCCCGTTACGACTTTCCGCACTTTCTCACCGCGCAGCAGGGCGGAAGCTCGACGCGTTTTCAACGCGTTAAGGTGGGAATTAACATAAATGACTGAAAAACAAAGCCGACGTGCTTCGCGCGCAACTTTGCCCGCTTCTTCGTCCATATTAATGGCGGTTGTCCCACCAGACTCACTTCGCCACTGCTGCCGTCATCAAGCCCGGCGAGGATCGCCAGCAGCAGGTTGACTTACCCGATCCCGACTCGCCCACCAGTGCGATGGTCTCGCCGTTTGATAACCAGCTCAACTCCGGTGAGGATGGAGAGTTCATGCTCCCCTGACCGACGGACCTTAAGATGATGAACCAGCAATGTTTTCCCGCTGGCATTTGCCCTTCCTGTTCCTGGTCACCATTAACCTTCCGTGCCGCCGCAGCGGCCGTTATTGATTCTGGGTGATAGCCTGAGCGCCGGGTATCGAATGTCTGCCAGCGCGGCTGGCCTGCCTTGTTGAATGATAAGTGGCAGAGTAAAGAGCATCGGTAGTTAATGCCAGCATCAGCGGCGACACCTCGCAACAAGGACTGGCGCGCCTTCCGGCTCTGCTGAAACAGCATCAGCCACGTTGGGTGCTGGTTGAACTAATGGGCAATGACGGTTTGCGTGGTTTCAGCCACAGCAAACCGAGCAAACGCTGCGCCCGGATTTTGCAGGATGTCAAAGCCGTAACGCTGAACCATTGTTAATGCAAATACGTCTGCCTGCAAACTATGGTCGCCGTTATAATGGAAGCCTTTAGCGCCATTTACCCCAAACTCGCCAAAAGAGTTTGATGTTCCGCTGCTGCCCATTTTTATGGAAGAGGTCTACCTCAAGCCACAATGGATGCAGGATGACGGTATTCATCCCAACCGCGACGCCCAGCCGTTTATTGCCGACTGGATGGCAGAAGCAGTTGCAGCCTTTAGTAAATCATGACTCATAAAGCAACGGAGATCCTGACAGGTAAAGTTATGCAAAAATCGGTCTTAATTACCGGATGTTCCAGTGGAATTGGCCTGGAAAGCGCGCTCGAATTAAAACGCCAGGGTTTCATGTGTGCTGGCAGGTTGCCGGAAACCGGATGATGTTGAGCGCGCGCAGACAGCATGGGATTTACCGGCGTGATCGATCTGGATTCACCAGAAAGTGTTGATCGCGCAGCCGACAGGAGGTGATCGCCCTGACCGATAGTGTCTGTATCGGGATCTTTAACAATGCCGGATTCGGCATGTATGGCTACTTTCCACCATCAGCCGTGCGCAGATGGAACAGCAGTTTCCGCCAACTTTTTCGGCGCACACCAGCTCACCATGCGCTGTTACCCGCGATATTACCGCACGGTGAAGGGCGTATTG\n' |
| b |
| diff -r e100f3f4d80e -r 2668027a533b test-data/test1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test1.fastq Sat Jan 29 12:49:28 2022 +0000 |
| b |
| b"@@ -0,0 +1,400 @@\n+@SRR7477814.1.9 1bbf88d-8c8b-4221-bfb9-953eaba39a83_Basecall_1D length=719\r\n+TCGGTATTGCTTCGTTCCAGTTGCGTATTGCTGAAGTCTTGTGTCCCAGTTACCAGGGTTTTCGCATTTATCGTGAAACAGCTTTCGCGTTTTCGTGCGCCGCTTCAACTGATAAATAATTTTCAAATACTAAAAGCGACTGCCAGATTATTTTTATTGCTTCTGGTGAAGTTATTAACTCAGCAACTTCGGTGAGTTCGATTATAAATTTCGCCATTGTAAATAACGCTTTGCTGACCGATGGAATATCCATCATACTGGTGGGAGTAAATTCCATCAGTATTGTTCCCCGGAACTAAACCTTCACAGTGATAAGAGTGAATATCCATTGGCTTTAAAAATATAATACAGTTGCCATGCAGTGTTATTTGTTCGCCATTCTTTAAAGAATCTTCCCACATCCTTGTACGGTATACACCGCAACCCATGAGTTGGCGATAAGCGGTTTCTTCTTGTCCGTGGCCAGATCGCCCGGTAATGCTCCGTCGGCGTAGGTATGCCAGAGGCGAGATCAGAAGAATTCCGCTGGAATCACATTTCGTTAATCAATAAAGGAATATTGTATGGAGTTTCGTTTTTTTCCATCTGAAGTTGCAATTTTCCATTCATTTAATATCCCTCCGGCGAATTATGCTCACAACTAGGCAACGAAGAAAACAATCCGTTCAGGGATACGACGTTTGTATTTTAAGGAAATCTGACTGCCTGACCCGACATAG\r\n++SRR7477814.1.9 1bbf88d-8c8b-4221-bfb9-953eaba39a83_Basecall_1D length=719\r\n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r\n+@SRR7477814.1.21 a06b716-0986-4eb6-955f-051804824165_Basecall_1D length=2884\r\n+TTGTTGTACTTCGTTCAGTTGCGTATTGCTGAGTCTTGTGTCCCAGTTACCAGGGTTTCGCATTTATCGTGAAACGCTTTCGCGTTTTCGTGCGCCGCTTCAACAACATCATCATCATGACCGATGCGGACGTCGACGGCTCGCACATTCGTACGCTGCTGTTGACAACTGGCTATCGTCAGATGCCGGAAATTGTTGAACGCGGTCGTCTCTGCATCGCTCAGCCGCCGCTGTACAAAGTGAAGAAGAGCAAAGCAGGAACGGTACAGTAAAGACAGCGACGAAGCGATGGATCAGTACCCAGATCTCTATCGCGCTGGACGGCGCAACGCACGCACACACCAACGCCAGCTGCCGGCATTGGCTGGCGAAGCGTTAAACACAGTGTCTGAGTACAACGACGCAGAAAATGATCAGCCACGTGGAGCGTCGTTATCCGAAAGCAATGCTGAAAGGCTTATCTGTAATGAAGCGCTGACCGACCTCTCTGATGAGCAGACCGTTACCCGGTGGGTGAACGCTGGTCAGCGAACTGAACGACAAAAGAACTGGCGGCAGCCAGTGGAAGTTTGATGTCACGCAATGCCGAACAAAACCTGTCGAGCGATTGTTCGCGTGCGTACCCACGGTGTGGATACTGACTATCCGCTGGATCACGAGTTTATCACTGGTGGCGAATATCGTCGTATCTGCACGCTGGGTGAAACTGCGTGGCTTGCTGGAAGAAAGATGCGTTTATCGAACGTGGCGAGCGTCGTCAGCCCGGTAGCCAGCTTCGAGCGAGCGCTGGACTGGCTGTTAGAAAGTCCCGTCGCGGCCTCTCCATCCAGCGTTATAAAGGTCTGGGCGAATGAACCCGGAACAGCGGGAAACCACCATGGACCCGGAAAGCCGTCGTATGCTGCGTTGCCGTTAGGATGCGATTGCCGCTGACCAGTTGTTCACCACGCTGATGGGCGACGCCGTTGAACCGCGCCGTGCGTTTATTGAAAGGAGAACGCCCACAAGAAAGCGGCGAATATTGATATTTAATGGCGTTAACAATGCGAGCGTGCTGATGCGCTACGCTTATCAGGCCTGGGGATCCTGCAATATATTGATTTGCATGTTTTGTAGGCCGGATAAAGGCGTTCCGCCGCATCCGGCAAACTATAAGAAAAGACGGAGATCATCTCCGCCCTTTTTATTCTACAATCTGAAATTATCATCCCGCAGTTCTATACTTTTGGGTCAACGTAACGCTTTACAGGTGATTATCATGGGGCTTTTGATGAAGTTGTCGGCGCCTTTCTGAAAGGCGATGCGGGAAAATATCAGGCGATTTTAAGTTGGGTTGAGCAGGGTGGCATTCAGGTGCTGCTGGAAAAACTGCAAAGTGGCGGCAGGGGCCATTCTCTCCAACTTTGGCTGAGTAATCAACAGAACGTCAACCAGTTAGCGGCGAGCAACTGGAATCAGCACTCGGCACAAACGCGGTATCCGATCTTGGACAAAACTTGGCGTGGATACCGAGTACGGCTTCCTGTTTACTGGCAGAACAGTGCCGAAGATTATTGATGCGCTCTCACCGCAAGGTGAAGTGTCACCACAACCAATAACGATCTGCTTTCCGCAGGCATGGAACTGCTACGAAGGAAACTCTTCCGCTAAGCAAATGGGGAGCATGCAGCCCGCGTTTCATCCCCTTTCCCTCAGGTGTTGTACTGATTTTTGAGCGGAATCGCGTTGCTGGAGTCAGGAACCAATCACCGGGGGAACTCGATCTTATCAAACTCATTGCTATCGATATGGATGGCGCCTTCTGCTGCCGATCACACCATTTCACCTGCCGTTAAAAATGCGATTGCCGCAGCTCGCCCGCCCGTGGCGTGAATGCTAACGACAGGTCGCCATATGCAGGTGTTCACAATTACCTGAAAAAGAACGCATGTGGAACAACCGGGCATTCTGCATTACTTATAACGGCGCGCTGGTACAGAGGCCGCTGATGGTAACACCGTGGCGCAAACTGCTCTCAGCTATGACGACTATCGTTTCACGGAAAAACTCTCTCGCGAAAGAGTCGGTTCTCATTCCACGCCACCGGACCGCACCACGCTGTACCGCCAGCCATTGATATCAAAGCTACTACGGTGCATGAATCATCGTTGCCACCATTCGCTGGTGTTCTGCGGAAAGCGAGGAGAAAATGGACCCCAATACCCAGTTCCTGAAAGTGATGATGATTGATGAACCCGCCATCCTCGACGGGCTATCGCGTATTCCGCAGGAAGTGAAAGAAATATACCGTGCTGAAAAGTGCG"..b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r\n" |
| b |
| diff -r e100f3f4d80e -r 2668027a533b test-data/test1_head.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test1_head.fa Sat Jan 29 12:49:28 2022 +0000 |
| b |
| b'@@ -0,0 +1,100 @@\n+>SRR7477814.1.9 1bbf88d-8c8b-4221-bfb9-953eaba39a83_Basecall_1D length=719\n+TCGGTATTGCTTCGTTCCAGTTGCGTATTGCTGAAGTCTTGTGTCCCAGTTACCAGGGTTTTCGCATTTATCGTGAAACAGCTTTCGCGTTTTCGTGCGCCGCTTCAACTGATAAATAATTTTCAAATACTAAAAGCGACTGCCAGATTATTTTTATTGCTTCTGGTGAAGTTATTAACTCAGCAACTTCGGTGAGTTCGATTATAAATTTCGCCATTGTAAATAACGCTTTGCTGACCGATGGAATATCCATCATACTGGTGGGAGTAAATTCCATCAGTATTGTTCCCCGGAACTAAACCTTCACAGTGATAAGAGTGAATATCCATTGGCTTTAAAAATATAATACAGTTGCCATGCAGTGTTATTTGTTCGCCATTCTTTAAAGAATCTTCCCACATCCTTGTACGGTATACACCGCAACCCATGAGTTGGCGATAAGCGGTTTCTTCTTGTCCGTGGCCAGATCGCCCGGTAATGCTCCGTCGGCGTAGGTATGCCAGAGGCGAGATCAGAAGAATTCCGCTGGAATCACATTTCGTTAATCAATAAAGGAATATTGTATGGAGTTTCGTTTTTTTCCATCTGAAGTTGCAATTTTCCATTCATTTAATATCCCTCCGGCGAATTATGCTCACAACTAGGCAACGAAGAAAACAATCCGTTCAGGGATACGACGTTTGTATTTTAAGGAAATCTGACTGCCTGACCCGACATAG\n+>SRR7477814.1.21 a06b716-0986-4eb6-955f-051804824165_Basecall_1D length=2884\n+TTGTTGTACTTCGTTCAGTTGCGTATTGCTGAGTCTTGTGTCCCAGTTACCAGGGTTTCGCATTTATCGTGAAACGCTTTCGCGTTTTCGTGCGCCGCTTCAACAACATCATCATCATGACCGATGCGGACGTCGACGGCTCGCACATTCGTACGCTGCTGTTGACAACTGGCTATCGTCAGATGCCGGAAATTGTTGAACGCGGTCGTCTCTGCATCGCTCAGCCGCCGCTGTACAAAGTGAAGAAGAGCAAAGCAGGAACGGTACAGTAAAGACAGCGACGAAGCGATGGATCAGTACCCAGATCTCTATCGCGCTGGACGGCGCAACGCACGCACACACCAACGCCAGCTGCCGGCATTGGCTGGCGAAGCGTTAAACACAGTGTCTGAGTACAACGACGCAGAAAATGATCAGCCACGTGGAGCGTCGTTATCCGAAAGCAATGCTGAAAGGCTTATCTGTAATGAAGCGCTGACCGACCTCTCTGATGAGCAGACCGTTACCCGGTGGGTGAACGCTGGTCAGCGAACTGAACGACAAAAGAACTGGCGGCAGCCAGTGGAAGTTTGATGTCACGCAATGCCGAACAAAACCTGTCGAGCGATTGTTCGCGTGCGTACCCACGGTGTGGATACTGACTATCCGCTGGATCACGAGTTTATCACTGGTGGCGAATATCGTCGTATCTGCACGCTGGGTGAAACTGCGTGGCTTGCTGGAAGAAAGATGCGTTTATCGAACGTGGCGAGCGTCGTCAGCCCGGTAGCCAGCTTCGAGCGAGCGCTGGACTGGCTGTTAGAAAGTCCCGTCGCGGCCTCTCCATCCAGCGTTATAAAGGTCTGGGCGAATGAACCCGGAACAGCGGGAAACCACCATGGACCCGGAAAGCCGTCGTATGCTGCGTTGCCGTTAGGATGCGATTGCCGCTGACCAGTTGTTCACCACGCTGATGGGCGACGCCGTTGAACCGCGCCGTGCGTTTATTGAAAGGAGAACGCCCACAAGAAAGCGGCGAATATTGATATTTAATGGCGTTAACAATGCGAGCGTGCTGATGCGCTACGCTTATCAGGCCTGGGGATCCTGCAATATATTGATTTGCATGTTTTGTAGGCCGGATAAAGGCGTTCCGCCGCATCCGGCAAACTATAAGAAAAGACGGAGATCATCTCCGCCCTTTTTATTCTACAATCTGAAATTATCATCCCGCAGTTCTATACTTTTGGGTCAACGTAACGCTTTACAGGTGATTATCATGGGGCTTTTGATGAAGTTGTCGGCGCCTTTCTGAAAGGCGATGCGGGAAAATATCAGGCGATTTTAAGTTGGGTTGAGCAGGGTGGCATTCAGGTGCTGCTGGAAAAACTGCAAAGTGGCGGCAGGGGCCATTCTCTCCAACTTTGGCTGAGTAATCAACAGAACGTCAACCAGTTAGCGGCGAGCAACTGGAATCAGCACTCGGCACAAACGCGGTATCCGATCTTGGACAAAACTTGGCGTGGATACCGAGTACGGCTTCCTGTTTACTGGCAGAACAGTGCCGAAGATTATTGATGCGCTCTCACCGCAAGGTGAAGTGTCACCACAACCAATAACGATCTGCTTTCCGCAGGCATGGAACTGCTACGAAGGAAACTCTTCCGCTAAGCAAATGGGGAGCATGCAGCCCGCGTTTCATCCCCTTTCCCTCAGGTGTTGTACTGATTTTTGAGCGGAATCGCGTTGCTGGAGTCAGGAACCAATCACCGGGGGAACTCGATCTTATCAAACTCATTGCTATCGATATGGATGGCGCCTTCTGCTGCCGATCACACCATTTCACCTGCCGTTAAAAATGCGATTGCCGCAGCTCGCCCGCCCGTGGCGTGAATGCTAACGACAGGTCGCCATATGCAGGTGTTCACAATTACCTGAAAAAGAACGCATGTGGAACAACCGGGCATTCTGCATTACTTATAACGGCGCGCTGGTACAGAGGCCGCTGATGGTAACACCGTGGCGCAAACTGCTCTCAGCTATGACGACTATCGTTTCACGGAAAAACTCTCTCGCGAAAGAGTCGGTTCTCATTCCACGCCACCGGACCGCACCACGCTGTACCGCCAGCCATTGATATCAAAGCTACTACGGTGCATGAATCATCGTTGCCACCATTCGCTGGTGTTCTGCGGAAAGCGAGGAGAAAATGGACCCCAATACCCAGTTCCTGAAAGTGATGATGATTGATGAACCCGCCATCCTCGACGGGCTATCGCGTATTCCGCAGGAAGTGAAAGAAATATACCGTGCTGAAAAGTGCGCCGTACTTCCTCGAATCATGATAAACGCGTTAACAAGGTACGGGTGTGAAATCACTGGCCGACGTGTTTAGGTATTAAACGGAAAATCATGGCGATTGGCGATCAGGAAAACGACATCGCAATGATTGAATATGCAGGCATCGGTGTGGCAATGGATAATGCTATTCCTTCGGTGAAAGAGTGGCGAACTTTGTCACCAAATCCAACCTGCATTCGATGGCGTGGCGTTTGCTATTGAAGTATGTGCTGAATTAATCTGTGGGCGGGCAAACGCGCCAAACGCGTTTGCCCGCTTATATTTCAATGGTTTTACTGCATATACAACCAGAAATTGCAGCGGCACCCAGTAATGATGTCCAGCGTAACAGTCACTGGCAGTAATGCTGCGGAAACACCATCGGAATGCCTCTGGGTGAATAGTATTCGCCAAAATCGCACTTTAAATGGATGGTAGAACGCCATCACTTGCTGGTAATCATGTTTTATTTTCTCATGGTTATTGCCTTTTAGGTTTTCCAGTGACACGAGCACGGTGTTGAACACCACAGGCAAAACCATAATGCGTTGCCGGTACGCCCGCA\n+>SRR7477814.1.50 44ae57b-47f5-4355-9b59-62e590dec286_Basecall_1D length=3437\n+TTGTTGTACTTCGTTCAGTTACGTATTGCTAGTCTTGTGTCCCAGTTACCAGGGTTTTCGCATTTATCGTGAAACGCTTTCGCGTTTTCGTGCCTGCAACATAATCATTATTCTCTTTTTCTAATGGTAAAATACGTATCG'..b'GACGTGAACGCCTTATCCACCCTACAGGTCAGGCGCGGTCTGTAGGCTGATAAAGATGGTGGTTTTAATGCAGCCAGTGAACGCCCTCGGCAGGCTGAAGAACGCGTTATGGCGCATCCTGAAAAGCAATTAATATCCTGCATTTCAGGTTCGGTTTCGCGCGAAACCAGCGCCAGCCTGGCCTGAGCATCCAGTAATGGGGAGCGGCAAGGCGGGCTTTTTGTAAAATCCGATGCCATTGCGGCAGTTCTGTTCGCTACCATCGACAATGACAATTTGCCAGATGAGCAACACCTGCGCGGCGTTTTGCAGGTGCGACTCATCCGGACGATGCAAATAACGTAAAAATTCGTCGCAGAAGCTGACTTTCCCGGTGATCGACCATCGACTCCACGGGTACGACTTCGATATTCAGCCGATCGCTGAGACGGCGATCGCTTTTCTGGCCCCGGATGTCAGCACCCGAAAACCAACCACAAACACTACCGCCAGCGTGGCGAGCATTATCAGATCATGAGTTCTCCTGCGTAATCAGAACTCATGATATCACAAAACTCTCGCCAGTTGCTAATCCGCAGAATAATCTTCGATTACTGCAAACCCCGATCGACCACCACCACACAGGTTCGAATCGCGCCAGCGCCAATTTTACTTTCGCTGATGCAGTACGGGCATAAAGCCAGAGTGCAATCCCTTCGGTGATCGAGAAGTAAAGGGCATCATCACCGTGGTATCGACGCAGGCACCGATTCGGTAAAATCATCCCGGATAACGCGCGCCAGACTTGAGGTCATCAACACGCCAACAAAGATTAACGCTCCGGCGGTTGCGTAAAGGAAGGAACCATCGCCACCAGCGGTGAGAAAGAACATAACCAACAGGAACATAACGCCGACCACAACCGCAGTCAGCCGCGTGCGACCACCGACTGCCGCACCAGAGGTACTTTCAATATGGCCGGTAACAGACGAGGTGCCGATAAACGCGCCCGCCACCGAACACTATCAACATGGCACGCTATTCATATTGGGGAATTTACCGTTACTATCTATTAAGCCAGCTTTATCAGTTACGCAATTAATGTTCCTGATGATGAATCAAATAGGTTGATCAGCATAAAGGAAAATGATACCGGCGAGTTCAAGTCTTAACGCGCCGCTCAAAATCTGCTTCACCAATGACGCCGCTAATATCAGGCGGAATGGAATAGACACTAAAATGAACATCACCGAAAAATAATCATAGAACGTCACCACAATAGAAGCAAACACCGCGGCATGAAAATGACGTGATGACAACACGGTTATAATAAAACCTAAAATACCTAACAACACGCCGTGAGGGCAAATCATGAAATCATCACCAGAGTGTCTTTATTGGCGGCAATAACGCCAGTATTTTTAATCCCATTAAGGCGACCGTAATCCGATTCCGCTGGTGATACCAATACGGCGTAAACTTAATGCAGATGTGGAAGTCATCCCGGTACCGGATACGAAATAGCGTGAGCAAAATAGCCCAATTGCGCCCCAGAATATCGCGCCCATCCCGGTCTGCCGGGGAGATGCCCATCACGACCACAGCGAGAACGCAAAGAGGCGTTCAGCCCCCGTGCCGGAGCCAGCGCCACGGGTAAGTTAGCAAATATCCCCATCGCAATACTGCCGATACCGGCAATCAAACAGGTGGTAACAAACACCACTTTCGGGTCCATTTATTGCCGCGCCGAGGATTTGCGGGTTCACAAAACGATAACACCATGGTTAAAAATTAATTCATCCCGCAATCAATTCTGTTACGGACGGTGGTTACATGCTGAGGTAGTTTAAAATAATCGCGAAAGCGTCCCTGATTCATTACTCACGTAATCCCGGTATTGTCATTATTCGTTTTGTCCATTGGAGGAATTTAATCCTTGCTTTTGTAAAACAAATGACAACAACAGTTCAGTGATAATTATCACATTCAATTGCACATTAATGGATATTCTTTAATAATCTTGCGACATTTCTTTATGATAAATAACAATCAAATTAATAAAATCAAAATGAAAAATATGAATAATTCATTAACCGCCGATTTCATCACATTAGCCGGGCGGAATACCGGGGAATTGTTAATGCGTTTCCCGTGGCGACGCTGTTGCCGATTATGAAATTCAATTGATAATGTCTCTATTCTCGACCTGATTAATGACGGAGAAATTTCCGGCCCAATTGTGATTAAAAGGGCGTTACATTGCCGGTGTTGGCGCAGAATGCACTGATGCTCCGGCTTTGCAGCGGATTGATGCCCACGGCGCGGCTTGGCAGTGCCGGGGTTTATTGATGCTCACCTGCATATTGAATCAACATGATGACGCCGGTCACCTTTAAACCGCCACCCTGCCTCGCGGCCTGACAACTGTTATTTGCGATCCTCATGAAATCGTCAACGTGATGGGCGAAGCCGGTTTCGCTGGTTTGCCCGCTGTGCCGAACAGGCGGAAGGCAAAACCAGTACTTACAGGTCAACTCTTGCGTTACCCGCTCTGGAAGGCTGCGATGTTAACGGTGCAGTTTTGCCTTGAACAGATGCTCGCACGGCGGGACCATCCGCAGGATACCGGCCTTGCAGAAATGATGGGCCCTACGGCGTAATTAGCGGGCAGAATGCGCTGCTCGATAAACTGGATGCATTTCGCCACCTGGCGCTGGACGGTCACTGCTGCCGGGTTTGGGTGGTAAGAACTTAACGCCTATATTGCTGCGGGTATTGAAAACTGCCGCGAAGTTATCAGCTGGAAGAAGGACGCCGGAAATTACAACTCGGCATGTTGATGATCCGCGAAGGGTCCGCTGCCCGCAATCTCAACACTTAACAGTTGATAAACGAGATTTAACAGCTTCCCGCAATGCATGCTCTGTACTGATGACCGTAACCCGTGGGGAGATCGCCCATGAAGGTTACATCGATGCCTTAATTCGCCGCCTGATCGAACAACACAATGTGCCGCTGCGTGTGGCATATCCGCGTCGCCAATGGTCGACGGCGCACTTTTGGTCTGAAATCACCTCGGCTTACTGGCACTGGTAAGCAGGCTGATATCGTCCTGTTGAGCGATGCGCGTAAAGGTCACGGTGCAGCAGGTACTGGTGAAAGGCAGACGATTGACGCGCAAACCTTACGAGCGGAAGAGTCGGCAGAAACTGGCACAATCCCGCTCCGCCATGGCAACACCATTGCCCGCCAGCCAGTTTCCGCCAGCGACTTTACCACCAATTTACGCCCGGAAAACGCTATCGGGTCATTGACGTCATCCATAACAGGTGATTACGCACTCCCACTCCAGCGTCTACAGCGAAAATGGTTTGAGCGCAATGATGTGTCTTTATTGCCATTAGCGGGCGTTACGGGCAACGTCTGGCTCCGGCAGTTTGCTCGGCGGCACGGTCTGAATGAAGGCGCGCTGGCTGCGACGGTCAGCCATGACAGCCGCAATATTGTGGTGATCGATTCGCGGTGCCCAGAGGATGGCGCTAAGCGAGTCAATCAGGTGATTCAGGATGGCGGCGGGTTGTGCGTGGTACGTAACGGCCGGGTCCAAAACCATCTGCCGTTACCCATTGCCGGGCTGATGAGCACCGACACGGCGCAGTCGCTGGCGGAGCAAATTGACATGAAAACCGCCGCCGTGAATTACGGTCCGTACGATGAGCCGTTTATTCAGATGGCGTTTCTTTCCCTGCCAGTGATCCCCGCGCTGAAACTAACCAGCCTTGGGGGCTGTTTGATGGCGAGTTTGCCTTCACCACGCTGAAGTCACTGAATAATAAAAAAGCCCGGCGTCATGCGGGCAAAATCTGGTGCACGTTTATGCCACTGTCAGCTTTGTGAATTTTTTTCTCGCGGCGGATTTGCGTTCTTCCATGCCGCCACTATCGCCATCAGGCAGATACAACCAATCGCGGCGATATCAGCGCAGCGAAAGTTGCATACTACCCAGCCGGTAGGCCATA\n' |
| b |
| diff -r e100f3f4d80e -r 2668027a533b test-data/test1_tail.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test1_tail.fastq Sat Jan 29 12:49:28 2022 +0000 |
| b |
| b'@@ -0,0 +1,200 @@\n+@SRR7477814.1.2571 b5e73e2-8615-42ad-8bea-18038a843554_Basecall_1D length=1499\r\n+TCTCGGTATGCGTTCAGTTACGTATTGGCGATCTTGTGTCCCCAGTTACACCGGGTTTTCGCGATTTAAATCATTGAAACGCTTTCCTGCGTTTTCGTGCGCCACTTCATCCACCATCACCAAATGGACGCCGTCGTAAACGCGGGACGTTCCTCAGTTTCTGGAACATTTCTCACAACCTTGGCGGTGCAGGCGCAACTGATTACTGGCACTGTTCGGCGCAAATTACTGTTCGATAATACATGTCATCCCGGCATGTTTATCTTCCGTCGATTATCGCGCTGATTGTCGGTTTTATCGGCCTGCGTTACGGCAGCGACTCCCCGGAATCTTATGGCCTCAGCAAAGCAGAGAGCTGTTCGGCGAGGAGATCAGCGAAAGGACAAAGAGACAGAATCTACCGTGCCGACCAAATGGCGGATTTTGTTGAGTATGTGCTGAAAAACAAAGTGATCTGGCTGCTGTGCTTCGCCAACATTTTCCTCATGTGGTGCGTGGTATCGACCAGTAGTTAACTGTGTACGCGTTCAGGAACTAAGAACTCTCTAAAACGGTGGCATTCAGGGCTTTACGCTGTTTGAAGCTGGTGCGCTGGTCGAATTTTTGCTGCTGTGGGGCTGGCTCTCTGACCTAGCGACGGTCGCCGTAGCTGGTGTACCATCGCGCTGGCGCTGATTATCGCCACGCTCGGTATTGTACCAACATACCTTAACGGAATATATCTATCTGGCTTCTCTCTTTGCGTTTAGGTTTCACGGTCTTTGGCCCTGGTGTTGATTGGTGTGGCTGCTGTTGGCTTGTACCTAAAAAAGGTTAATCTGCCGATGGTATTAAAGAGCACCTTCGCTTACCTGATTGGTGACAGCTTTTGCCAATTAGGTCTGCAGAATGATTGCCGATGGGACGCCAGTATTCGGCCCACCGGCTGGGCTGACACCTTCGCTGCGCTGGATATCGCCGCGATTGGTTGTATCTGCCTGATGGCGATAGTGGCGGTGATGGAAGAACGCAAAATCCGCCGCGAGAAAAAAATTCAGCAGTTGACAGTGGCATAAACGTAACTGGTGACTTTGGCATGACGCCAGGCTTTTTATTATTCAGTGACCAGCGTGGTGAGCAAACTTCTCGCCATCAAGCAGCCCGGCTGGTTAGTTTCAGCGAGGGATCCGCGGCAGGGAAAACGCCATCTGAATAAAGCGGCTCATCGGGTAACGGACCGCATTCACGGGCGGCGGCTTTCAGGCGTCAATTTGCTCCGCAACGACTGCGCCGTGTCGATTATCATCAGCCCGGCAATGGGTAACGGCAAGATGGCTGGACTGTGCGTTACGTACCACGCACAACCGCGCCGCCATCCTGAATCACCTGATTGACCGCTAGCGCCATCTCTTCGGCACTGCGACCGATCACCACAATATTATGGCTGTCATGGCTGACCGTCACCCAGCCAGCGCGCCTTCATTCAGACCAAACCGCCAGGCAAACCACAAGCCGGGCAG\r\n++SRR7477814.1.2571 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|
| b |
| diff -r e100f3f4d80e -r 2668027a533b wtdbg.xml --- a/wtdbg.xml Thu Sep 27 17:52:13 2018 -0400 +++ b/wtdbg.xml Sat Jan 29 12:49:28 2022 +0000 |
| [ |
| b'@@ -1,167 +1,211 @@\n-<tool id="wtdbg" name="WTDBG" version="2.0">\n- <description>De novo assembler AND consensuser for long noisy sequences</description>\n- <macros>\n- <import>macros.xml</import>\n- </macros>\n- <expand macro="requirements" />\n- <version_command>wtdbg2 -help | grep \'Version:\'</version_command>\n- <command detect_errors="exit_code"><![CDATA[\n- wtdbg2\n- -t \\${GALAXY_SLOTS:-4} \n- -i \'$i\'\n- -o \'dbg\' \n- #if $I:\n- -I \'$I\'\n- #end if\n- #if $load_alignments:\n- --load-alignments \'$load_alignments\'\n- #end if\n-\n- -k $k\n- -p $p\n- -K $K\n- -E $E\n- $F\n- -S $S\n- -X $X\n- -Y $Y\n- -x $x\n- -y $y\n- -l $l\n- -m $m\n- -s $s\n- --tidy-reads $tidy_reads \n- --edge-min $edge_min \n- $rescue_low_cov_edges\n- && \n- wtdbg-cns \n- -t \\${GALAXY_SLOTS:-4} \n- -o dbg.ctg.lay.fa\n- -i dbg.ctg.lay\n- -j $cns.j\n- -k $cns.k\n- -Z $cns.Z\n- -W $cns.W\n- -H $cns.H\n- -L $cns.L\n- -c $cns.c\n- -M $cns.M\n- -X $cns.X\n- -I $cns.I\n- -D $cns.D\n- -E $cns.E\n- -m $cns.m\n- -S $cns.S\n-\n- ]]></command>\n- <inputs>\n- <param type="data" argument="-i" format="fasta,fasta.gz" label="Long reads sequences file"/>\n- <param type="data" argument="-I" format="fasta,fasta.gz" optional="True" label="Error-free sequences file"/>\n- <param type="data" argument="--load-alignments" name="load_alignments" format="tabular" optional="True" label="Load pre-computed alignments"/>\n-\n- <param argument="k" type="integer" value="0" min="0" max="25" label="Kmer fsize" />\n- <param argument="p" type="integer" value="21" min="0" max="25" label="Kmer psize" />\n- <param argument="K" type="float" value="1000" min="0" max="65535" label="Filter high frequency kmers" />\n- <param argument="E" type="integer" value="2" label="Min kmer frequency" />\n- <param argument="F" type="boolean" truevalue="-F" falsevalue="" checked="False" label="Filter low frequency kmers by a 4G-bytes array" />\n- <param argument="S" type="integer" value="4" label="Subsampling kmers, 1/S kmers are indexed" />\n- <param argument="X" type="integer" value="4" label="Max number of bin (256bp) in one gap" />\n- <param argument="Y" type="integer" value="4" label="Max number of bin (256bp) in one deviation" />\n- <param argument="x" type="integer" value="-7" label="penalty for BIN gap" />\n- <param argument="y" type="integer" value="-21" label="penalty for BIN deviation" />\n- <param argument="l" type="float" value="2048" min="1" label="Min length of alignment" />\n- <param argument="m" type="float" value="200" label="Min matched" />\n- <param argument="s" type="float" value="0.2" label="Max length variation of two aligned fragments" />\n-\n- <param argument="--tidy-reads" name="tidy_reads" type="integer" value="0" label="Filter reads less than tidy-reads" />\n- <param argument="--edge-min" name="edge_min" type="integer" value="3" label="The minimal depth of a valid edge set to" />\n- <param argument="--rescue-low-cov-edges" name="rescue_low_cov_edges" type="boolean" truevalue="--rescue-low-cov-edges" \n- falsevalue="" label="Try to rescue low coverage edges" />\n-\n- <section name="cns" title="Consensus options">\n- <!-- optional inputs -->\n- <!-- <param argument="-i" type="data" format="utg.cns" label="Input file(s) *.utg.cns" /> -->\n-\n- <param argument="-j" type="integer" value="1000" label="Expected length of node" />\n- <param argument="-k" type="integer" value="15" label="Kmer size for long reads" />\n- <param argument="-Z" type="integer" value="4" label="Z-cutoff, drop the lower" />\n- <param argument="-W" type='..b' <has_text text=">ctg2 " />\r\n+ <has_text text=">ctg3 " />\r\n+ <has_size value="70000" delta="10000" />\r\n+ </assert_contents>\r\n+ </output>\r\n+ </test>\r\n+ <test expect_num_outputs="1">\r\n+ <param name="input_reads" value="test1.fastq" />\r\n+ <param name="sequencing_technology" value="ont" />\r\n+ <param name="genome_size" value="60k" />\r\n+ <section name="asm">\r\n+ <param name=\'X\' value="10.0" />\r\n+ <param name=\'L\' value="2000" />\r\n+ <param name=\'k\' value="15" />\r\n+ <param name=\'p\' value="0" />\r\n+ <param name=\'K\' value="500" />\r\n+ <param name=\'l\' value="1024" />\r\n+ <param name=\'m\' value="200" />\r\n+ <param name=\'s\' value="0.1" />\r\n+ <param name=\'e\' value="5" />\r\n+ </section>\r\n+ <output name="out_assembly">\r\n+ <assert_contents>\r\n+ <has_text text=">ctg1 " />\r\n+ <has_text text=">ctg2 " />\r\n+ <has_text text=">ctg3 " />\r\n+ <has_size value="50000" delta="10000" />\r\n+ </assert_contents>\r\n+ </output>\r\n+ </test>\r\n+ </tests>\r\n+ <help><![CDATA[\r\n+\r\n+**Wtdbg2**\r\n+\r\n+|\r\n+\r\n+**What it does**\r\n+\r\n+WTDBG is a de novo assembler for long noisy sequences, based on fuzzy Bruijn graphs (FBG).\r\n+\r\n+"Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy.\r\n+\r\n+**Alignment**\r\n+\r\n+KBM (Kmer-BIN-Mapping) groups k-mers from each non-overlapped sliding 256 bp fragments in long reads into bins.\r\n+Bins of which most k-mers are high frequency, are filtered as highly repetitive ones.\r\n+Then, KBM searches synteny of matched bin pairs in sequences in a dynamic programming way.\r\n+A matched bin pair in two sequences is defined as two bins different by original but share a set of k-mers.\r\n+The result of alignments in KBM have the same features of traditional sequence alignment, excepting the unit of\r\n+KBM alignments is 256 bp bin instead of single base.\r\n+\r\n+**Assembly**\r\n+\r\n+FBG (Fuzzy Bruijn Graph) is composed of vertices in length of 1024 bp from reads, and edges connecting vertices\r\n+in their order on read paths. Comparing with DBG, the size of vertices in FBG are much bigger, thus won\'t be\r\n+sensitive to small repeat. To tolerate high sequencing errors, FBG\'s vertices are found using gapped\r\n+sequence alignments from KBM or other aligners, comparing with searching identical k-mers in DBG.\r\n+\r\n+See the github (https://github.com/ruanjue/wtdbg2) and paper (https://doi.org/10.1038/s41592-019-0669-3) for more information. \r\n+\r\n+|\r\n+\r\n+**Input**\r\n+\r\n+One or more fastq or fasta files. Can be in any fastq/fasta format with any valid exension. \r\n+\r\n+|\r\n+\r\n+**Output**\r\n+\r\n+Assembled contigs (the assembled genome).\r\n+To polish, use external tools such as pilon, racon, medaka, nextpolish etc.\r\n+\r\n+|\r\n+\r\n+**Sequencing Technology Preset Information**\r\n+\r\n+- Oxford Nanopore (ont) (genome size < 1G): -p 0 -k 15 -AS 2 -s 0.05 -L 5000\r\n+- Oxford Nanopore (ont) (genome size >= 1G): -p 19 -AS 2 -s 0.05 -L 5000\r\n+- PacBio CCS (ccs): -p 21 -k 0 -AS 4 -K 0.05 -s 0.5\r\n+- PacBio RSII (rs): -p 21 -S 4 -s 0.05 -L 5000\r\n+- PacBio Sequel (sq) (genome size < 1G): -p 0 -k 15 -AS 2 -s 0.05 -L 5000\r\n+- PacBio Sequel (sq) (genome size >= 1G): -p 19 -AS 2 -s 0.05 -L 5000\r\n+\r\n+|\r\n+ ]]></help>\r\n+ <expand macro="citations" />\r\n+</tool>\n\\ No newline at end of file\n' |