| Next changeset 1:e100f3f4d80e (2018-09-27) |
|
Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit c97be39112be9dc6118a3e12e51dcb15ed554274 |
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added:
macros.xml 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 wtdbg.xml |
| b |
| diff -r 000000000000 -r 6a060928f7ff macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Jun 12 13:40:49 2018 -0400 |
| b |
| @@ -0,0 +1,22 @@ +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="1.2.8.1">wtdbg</requirement> + <yield/> + </requirements> + </xml> + <xml name="citations"> + <citations> + <citation type="bibtex"> +@misc{githubwtdbg-1.2.8, + author = {LastTODO, FirstTODO}, + year = {TODO}, + title = {wtdbg-1.2.8}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/ruanjue/wtdbg-1.2.8}, +}</citation> + <yield /> + </citations> + </xml> +</macros> \ No newline at end of file |
| b |
| diff -r 000000000000 -r 6a060928f7ff test-data/consensus_result1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/consensus_result1.fa Tue Jun 12 13:40:49 2018 -0400 |
| b |
| b'@@ -0,0 +1,231 @@\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 000000000000 -r 6a060928f7ff test-data/consensus_result2.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/consensus_result2.fa Tue Jun 12 13:40:49 2018 -0400 |
| b |
| b'@@ -0,0 +1,231 @@\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 000000000000 -r 6a060928f7ff test-data/consensus_result3.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/consensus_result3.fa Tue Jun 12 13:40:49 2018 -0400 |
| b |
| b'@@ -0,0 +1,231 @@\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 000000000000 -r 6a060928f7ff test-data/dbg.ctg.lay --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dbg.ctg.lay Tue Jun 12 13:40:49 2018 -0400 |
| b |
| b'@@ -0,0 +1,359 @@\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 000000000000 -r 6a060928f7ff test-data/ecoli-reads.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ecoli-reads.fa Tue Jun 12 13:40:49 2018 -0400 |
| b |
| b'@@ -0,0 +1,224 @@\n+>fa9ad683-35c5-4dad-a3af-de7a86b1ffa8\n+TTGGTATGCTTCGTTCCAGTTACGTATTACTTTCTGTTGGTGCTGATGTTGCGTCTGCTGATTGTTTAACCTGGCTGGATCGCTGCTGAATAACTTCGCCGCATGGCCGCTGAAATCTTTCACCCTCTGCGCCTGGCGGTTAGCCGCCTGTTACGTCAGCCGTGGTCAACGTTAAGTCAGCTTTTCGGCATTTCGCTCCGCTATGCTGGCACTGCTGCGGTGTGCATAGCGATCTGCTCGACCGCTGGCAGCAGCATCTCAAGCGAACTACTTGCATTCATCGCCACAGAACAGGTAACCATCGAGGCGTTCCTCGGAACATCAGATAGTCAGAATCGTTTTGTATCCGAGTGGGTACAGGCGCGGCTGACGGCGATTAACGATAAGCAACAAAAGGTAAATAGAAGATGCGGCGCTTAACCGCGAGCTCAATCTTACCTGGCAAAATACGCGGCTTGATCATGATCGATTGTAATGCCCGGTAACTGGCCGCCAAAGCCGATGAAGTGTCGATGGAAGGGGCTGGCCGAAACGCTTAAACGATTGCCCTCGGTGATACCGTGGCTTTGCGGGGCGATGCGCAGGAGTTTCCGCGCTAAAGTAGCCAGCCTGCGCAAGTGGACTGGAAAGTCACGGCCTAATTTCTATTTTATTTTTCCCTGAAGGGCATTCGTTAAGGCAACCGCAGAGCAACCACCCAGTTTCCGCTGGGAGAATGGCAACGGCATGATGACACCGGCTCTTCGCCAGTTCCCGACCATCAGCCTGATAGATATTGGCGCGATTTTTAAAACCGTCGGTCAGGTGCTGGAGCAGATGGGGTCGGGCGCTGGAAGTGATAAATTGGTACTGGTCACCGCCTGCGGTATATTTGCTGTTGCTAGCACAGGGGTACGGGCGAGACATCCAGCGTCATCAAGGCTAATTGGGTGTGGCGCACTCGGTGCGGAAAAAGGCTTTGCTGCGTACCACGTTGGCAAGTGTAGAGTTCGCCATACTTGGGTTTTGTTTTGTACCAAGTGGCCGCAAAATTAGTGCACAGAAACAGCGCTGGCGGCGGTGTGCAGGCGAAAGTGAACGATTTTCAAAGTAGGAGCCAAGACTGGCGATTGTGGATTATTCTACCGTGCAGCGGGCGGCTGCTGCTGTCGCTTTCCGGCGGCTGGCTGGGTGCGGTTGGGTAGGCGCTGTTCGAGGCAGTTTGCAGAAATGCGCAAGGTAAATAGGGGGCGTTCTGGTTTAGAATGAACGCGCCCAGCAATTTCGATGAATTCTACAATATGTTTCATTGATGATGTTATTGAATTGGTGATTTTATCTTTCTGTTGCTGTCGCTAATCACAAGATCGAGGTGGGTTTGTTGATTTTTAAATGTAGCCTACAATACTCCGTTCGTGAAATCATAAAAAGCCATATGCGTTGAATGGATGTCATCCTATGGTAATTTGTTGATGATGAATTCATCCTGTGTAAAAATGTTAGTTTAATAAAATATTAGTGACCTGTAACTAACGGTTTGTTTGTTGATTGAGAACCGTGGTTATATTGAAAAATATATAAATACATTGGCTGGTCTTGTATGTCGGTTTTATTTTTTGTTGCCTAAACACAGGGATATCGAACTAATAACTAAAGGGCACTTTATAGGCAGAAAAACCAACGCGTCGGGAGATATGAGCTCAAGTATGGCGGATCCCATTGTCCGGGGCTCGGCAGGTGTAAAATTGGCGCGCCCACCAGCGTGGCATGCTCGTTGTCGGGCGGGATGACTTCGGGCAACCCGGTAAATCCGCTGCTGGGGGCAGGTACGCTTGGCCGAGACGGACTTGCCGCTGCCCGTACGCTGCGTTCATTCTCTCCCGCACCTAAAAAGCCTTCTGGACGAAGACGCCTGCCGGTGGGCGTTTTCGGCCCCGGCACAAACGCTGATATCCGCTTACAACTGCGTGATGACGGACTGATACTCCAGCAACAACGGCAGACGAACATTCCGCTGAGCCGCTGCTGCCACATGAGGAGAGCGAAATTAATACAACCGCAGGGTACGAGTCAATGTGGCTGGTGCGGTAAGGCAGCGCAACTGGACGGCCATACTGCTAGCGCGCGGCTGTGGGGGCTATACCGCCGGATATCAGTTAAGCCCGCATCTTTACCTGGCGACCAACGCGCACAGGGGCCGTGGTGGATGCTGGGTGGTCTGAGCGGGTGCCGGGTGCTGAGGACGCTTGCTGCCAGCGCCGCTGCCGTACCAGGTGCCACCAGGATAGCGGACCGCTTCAGGCGGACGCTGACGCCTGCGGCGTAGAACATGGTGACCCTGGCCAGAAATCACCAGCGTGACGGACGGTGCCGGGCGGGGTTATTCTGATTTTGTCACGCAGGCGCGAGCGTTGCGGAAAAGGCCACTTACCTCTTCGCTATCTTAATACGACGTTCCCCGCCCTATATAGCCTCAGCGTTCCCCAACCTACCCAGTACCGAATACGGCCCCGTGGTGGCTGATCACGACCGGCATGCCAGAGAAACCCTGCCGCTGCGCCACTAGATTGCGGTACGTCTCTGGAAACCGAGTGAACTGCGGCGGTATATGAGCCGCAGCAATACGCAGGTGCGCTTTCATTATGACGCGCTTACCCGGGCAGATGTGGCGCACCGTTACACTTAGGAAAGGCCGGAGATGCGCTACCACTTCGACGATACAGGGCGGGTGGTGGAGCAACGACCAGCAGGGGTTAAGCTACACTATCTTTATAGGCAAGGACCATATCGTCACCGACGGCCTGAACCGGCGTGGGAGTGCTGCATACAGAAGGCAGGGCCGGGCTAAAACAAATTGGTGAAAAAGAACGAGCGGACGGCACAGAAGCGTTCCGCGCTGAAATTGCATCGACCGCGAAGCAGGAAGGCTCACGGCATGAACGGACGCGGCAGGGCAGGAGGATAAGTACGGTCTGAATGTGGTGTCCAGCGATATCGAATACCACCGGACGGGCGGGAGACGAAATTCCTATAACGACGGGAGCCAGCTGACGGCGGTGGTAATGCCGGACGAACTGGAGAAACCGCCAGGAATATGATGAACCGGGCAGGCTGGTGTCAGAACATCGCGCAGCGGGGACAGTACGCTACCGCTACGTGGCCGCCTGATAGTTACCGGCGACGACAACGGATGCGACGGGCGCTTACCAACAGATAATATAGACACGCTACGGGCGTTGCTGGCGTTCTGGCTTTTCGACACGGAGCCATTATGAATACGACCGCTTCGGCCAGATGACGGCGAAGTCCACCGCGAAGGCATCAAACGCTACCGCTATAATAACGTGGCGGTTAACCTCGATGAAAACCGCACAGGGCGATGAAACGCGACATGAGCCACAACGCCGCAGAGCAACCTATTTCGCCAATTATCTGCCCCGGACGCGGCCGGAGCGGAAGACACGAGGTACGATGCGTGGGGAAAGGCGGGTCAGCACCACACCAGGGCGGCTGACGCGCAGTATCATTACGGTGCTGCCGGATGTCATCGCCCTGACCAACGAGAACACGGCAGCCACGGCGTCTTCTGGTTACGATGCGCTGGACCGGCTGGTGGGACAAACACCAAGCAGACGCCGAAGATGAGAACGATGAGCAGTATACCCGTAATGACGCTTCCTC\n+>a403a23e-20e7-43f7-a5fa-dae8ebc59a01\n+TTGACTGTGCTTCGTTCGGTTACGTATTGCTTTTTCTGTTGGTGCTGATATTGCGGCGTCTGTAGGTGTTTAACCTGCCAGCATCACACGAGATTGGTCAAGTGCGGTTGGGTTTTTCAAACGGATGCGACAGCAGTTGGCATTAAAGAAGCCACCGCCGTTAGGCGCCGAGCATCTTGATGCTTCCACGAAGCTACGATACCGCCGGGTAACAGCTGTTGCGCTCCTTCAACGGTATTC'..b'CCGGGGCTGAGGCTCCCCACCGGCGCGGGCGTTTTGTCCGGTAACTGCTGTAGGTGCGGGAGAGAATGAAAGACGGCAGCAGGCCGGGGCAGGGGGCGTCAGTTTCACCAGGAAGGACCTTTACCGAGCAGCGGATTGACCGGATGGCCGGACGTCACCCGCGGGGCACCGAACAGGCCACGCCGGTGGGGCACCGATGCGTACCCCGGCTGAACCCTGGACAATGCTGCCGCCATACCGTCATGTCGCCCTGACGCCGCCGGTTTTCCGCTCATCTGCTCATCCTTGTTTTATCGGGTTATTTGTCTGCTGACAGGCGAAACCCTACAGATTTATAAGAAACTAAGTGAGATATCTGTCAGATAAGAACAATTAGGAAAATATTTATATATATTTCCTTGAATATATGTTTCGATTGGTATAACGATGTCACAAATATTCCTCTGAACATCTTCCTGTTAAAAAACCGCCAGCGTTTCCCGCTGGCGGTTTCAATAATATTCAAACTCAGCAATCAATAAAATCACCAGTTGCCTTTTCGGCCTGATCCATCCGCACCGGTTTATCATGGTTTCGATGGAGCGCGATGCAAGGTAGCTGTAAAGCGGGCGCGGTCTTTCCAGAAAAGCATAAGAAAAGAGCCAGCGCCAGAACGCCCGCTGCAACCGCATAAGTACAGCGTAAAGATAAAGCCATGCAGGATATTCTCTGTAGAGTTCCATACTTTTCTCCCCTTTTATCTACCCGATTATGAATGGCACCGGAAAAATGAATTGTTTATCTGATGAAAATAGTACCGCCAGCACGTAGTTTTACTACTCATCCGACCACTTATTTTGCTTATTGATGGTTTATTTACATTCATCCGCAATTAAGTTACACAAAGTTAAATTAATACTAAACATTAGTTAAATCATGGCTTTTGCCATTTTTATACTTTACACCCCGCCCGCAGATTTTGCGAAATCTTTGCAGCCAGGTCTACCTTCGGTATCACTTTTAGGCCACTGGAGGTGCACTGTGAGTGCAGGCGTGATAACCGGCATTATTGCTGGTGTTTTATTACTGGGTTATCTGGTTTGTAACCTGATCCAAATGCGGAGCGTTCTGATGGCTGCGCAAAGGGTTCTTACTGATCGCCACGTTTTTACTGGTGTTATGGGTGCTGGCGCGTCCTTTAGGCAGCGGGCTGGCGCAGCTGATTAATGACATTCCCTTCCCGGTACAACGGGCGTTGAGCGCGTACTTTTTCCTTTGCCCAGCGTCTCTGACCGTGAGAGATGAACTGGAAGCAATATCTTTGTGCCATTCTCGGCCTGAACATGCTGGGGCTGGCGGTGCTGTTTTATGTTATCAGTCAGCACTATCTGCCGCCAATCCACAGCAGTTGCCAGGGCTGTCATTGGGATCTGGCGCTGAATACCGTCAGCTTTGTCACCAATACCAACTGGCAATCTTATAGCGGTGAAACCACGTTGACTTCTTCAGCCAGATGGCGGGCTTAACGGTGCAAACTTTCTTTCTGCCGCCAGCGGGATTGCGGTGATTTTGCCTCATCCGTGCAGTTTACCCGCCAGGTATGAGCACGCTCAAGAATGCCTGGGTCGATCTGCTACGCATCACGTTATGATTGCTAGTCCTGTGGCGTTGTTGATTGCGCTGTTTTTATTCAGCAAGGTGCGCTGCAAACTTTCTGCCTTATCGGGCTGTGAATACCGTTGAAGAGGCGCAACAGCTGTTACCATGGGGCCTGCTGCTTCTCAGGAAGCAGTCAAGATGCTCAGTACTAGCGAAGGCGGTGGCCTAACAATGCCAGCTCAAAATCGCATCCGTTTGAAAACAACCGCGCGGCAACTTCGTGCAGATGCTGGCGATCTTCTTGATCCCAACGGCGCTGGTAATACTTTGCCTTTGGTGAAGTGATGGGCGATCGCCGCCGAGAGCATGTTGCTTATGTGGGCGATGTCGGTAATTTTTTGTGTCATCTCTGCGTAGGCGTGGTGATGTGGGCAGAAGTTCAGGGTAATCCTCATCTGCTGGCACTGGGCACGGACGCTTGTATCAATATGGAAGGTAAAGAGAGCCGTTTCGGCGTGCTGGTCAGTAACCTGTTTGCGGTCGACGGCTGACGGCTTCCTGTGTTGCAGTGATTACGCGATGCATGATTCGTTTACCGCTCTCGGTGGCATGGTGCCGATGTGGCTGATGCTAAATTGGTGGTGGTAATTTCGGCGGTGTCGGTTCTGGTCTTTGGCATGATGCTGTTTGTCCTGCTGGCGGTGTTTTGTGCCGGGCTGATGATTGGGGTCGTACACCGGAATATCTGGGTAAAAAAATCGACGTACGCGAGATGAAGCTGACTGCGCACAGCAGTCTGGTTACCCCGACGCTGGTGCTGATGGGCGCGGCGTTGTGATATTGACCGACGCCGGACGTAGCGCCATGCTCAACCCCTGGCCCGCATGGTTTTAGCGAAGTGCTGCTACGCCATGTCATCACCGCCGCTAACAACAACGGCAGCGCCTTTGCCAGTTCGCGCCAACTCCGTTCTGGAACTGTTTACTGGCGTTCTGCATGTTTTGTCGGTCCTTCGGGGTGATTATCCCGGTGATGGCAGTGCCGGTTCGCTGGTGATAAAAAGAGCCAAACCGCCAGCTCGGCACGCTGCCAGCACACGGCCCGCTGTTTGTTGGCCTGTTAATCGCTGCTGTGTTGCTGGTTGGCACTGAAGCCTTTATCTGCTGGCGGTCAGTGGCGGGAATATCTCTCCTGATGATGTTGGTGAGCACTGGATATGAGTCGTAAACAAACTTCCGGCTATTCAAGACCAACACTTGTCGTTCAGGCGCTGAAAGAAGCGGTGAAAAATTAAACCCGCAGGCGCAATGGCGCAATCCGGTGATGTTATCGTCTGGATCGGCAGTCTGCTGACCACCTGTATTAGCATCGCGATGGCAAAAGCAGGTGCGATGCCCGGCAATGCTGTTTAGCGCGGCCATTAGCGGTTGGCTGTGGGATCACCGTACTGTTCCTTCAATTTCGCCGAGGCGCTGGCAGAAGGCCGCAGTAAGCCTGGGTAACAGTCTGAAGGTGAAAAAACTGCGCTTTGCCCACCAAGCTGCGTGAGCCGAAATATGGCGCTGCGGCAGACCAAAGTTCCTGCGACCAACTTCGTAAAGGCGATATCATGCTGGTAGAAGCTGGCGATATTATCCCCTGCGATGGTGAAGTTATTGAAGGAAATTGCATCGGTCGATAAACTATGCATCACTGCGAGAATCGGCACCGGTGATCCGTGAATCCGGCGGCGTTTTGCCTCGATCACCGGCGGCGCATATTCTTTCTGACTGGCTGGTGATTGGGTGTAGCGTTAACTTGGCAGACATTTCTGGATCGGATGATCGCGATGGTGGAAAGGCGCACAGCGGCGCAAAACGCCGAACGAAATTGCCCTGACCATTCTGCTGATTGCCCTGACTATCGTCACTGCTGGCAACCGCCGCACGCTGTAACCGTTTTCGCGTAGGGCGGTAATGCAGTCAGCGTAACGGTACTGGTGGCGCTGCTGGTCTGTCTGATCCCAAAAGCCACTATTGGCGGCCTGTTGTCAGCAGTCGTCGCCGGGATGAGCCGGATGCTAGGCGCCGAATGTGATTGCCACCAGCGGACGATGCAGTTGAAGCGGCAGGTGACGTTGACGTTCTGCTACTGGATAAAACCAGCACCATCACACTCGGTAACCGTCAGGCGTCGAGTTTATCCCACGCAGAGGGCGTGGATGAAAAAACGCTGGCTGACGCCGCTGGCAGCTTCGCTGGCTGATGAAACGCGGAAGGCCGCAGTATTGATCCTCGCCAAGCAGCGTTTTAACCTGCGCGAGCGCGATGTGCAGTCATCATGCCACCCTTTGTACCGTTTGCAAGCCGGATGAAGCCAGGATCAGCATCGACAACCGCAGGTTAAACACCCAAGCAGACGCCGAAGATGGGGAAACCGTA\n' |
| b |
| diff -r 000000000000 -r 6a060928f7ff test-data/ecoli-ref.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ecoli-ref.fa Tue Jun 12 13:40:49 2018 -0400 |
| b |
| b'@@ -0,0 +1,64860 @@\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 000000000000 -r 6a060928f7ff test-data/result1.alignments --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/result1.alignments Tue Jun 12 13:40:49 2018 -0400 |
| b |
| b'@@ -0,0 +1,507 @@\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 000000000000 -r 6a060928f7ff test-data/result1.ctg.lay --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/result1.ctg.lay Tue Jun 12 13:40:49 2018 -0400 |
| b |
| b'@@ -0,0 +1,361 @@\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 000000000000 -r 6a060928f7ff wtdbg.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/wtdbg.xml Tue Jun 12 13:40:49 2018 -0400 |
| [ |
| b'@@ -0,0 +1,167 @@\n+<tool id="wtdbg" name="WTDBG" version="1.2.8.1">\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>wtdbg -help | grep \'Version:\'</version_command>\n+ <command detect_errors="exit_code"><![CDATA[\n+ wtdbg\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="i'..b'L" type="integer" value="10" label="High coverage cutoff" />\n+ <param argument="-c" type="select" label="Candidate strategy">\n+ <option value="0" selected="true">best-kmers</option>\n+ <option value="1" >median length</option>\n+ <option value="2" >first (include)</option>\n+ <option value="3" >first (exclude)</option>\n+ <option value="4" >longest</option>\n+ <option value="5" >shortest</option>\n+ </param>\n+\n+ <param argument="-M" type="integer" value="2" label="Match score" />\n+ <param argument="-X" type="integer" value="-7" label="Mismatch score" />\n+ <param argument="-I" type="integer" value="-3" label="Insertion score" />\n+ <param argument="-D" type="integer" value="-4" label="Deletion score" />\n+ <param argument="-E" type="integer" value="-2" label="Gap extension score" />\n+ <param argument="-m" type="select" label="Correction mode">\n+ <option value="1" selected="true">DBG correction</option>\n+ <option value="2" >DAG correction</option>\n+ </param>\n+ <param argument="-S" type="integer" value="1" label="Correct structure before error correction" />\n+ </section>\n+\n+ </inputs>\n+ <outputs>\n+ <data name="output_alignments" format="fasta" label="${tool.name} alignments" from_work_dir="dbg.alignments" />\n+ <data name="output_ctglay" format="txt" label="${tool.name} contigs layout" from_work_dir="dbg.ctg.lay" />\n+ <data name="output_consensus" format="fasta" label="${tool.name} consensus" from_work_dir="dbg.ctg.lay.fa" />\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="i" value="ecoli-reads.fa"/>\n+ <output name="output_alignments" file="result1.alignments"/>\n+ <output name="output_ctglay" file="result1.ctg.lay"/>\n+ <output name="output_consensus" file="consensus_result1.fa"/>\n+ </test>\n+ <test>\n+ <param name="i" value="ecoli-reads.fa"/>\n+ <param name="tidy_reads" value="5000"/>\n+ <param name="edge_min" value="2"/>\n+ <param name="rescue_low_cov_edges" value="True"/>\n+ <output name="output_consensus" file="consensus_result2.fa"/>\n+ </test>\n+ <test>\n+ <param name="i" value="ecoli-reads.fa"/>\n+ <param name="cns.c" value="1"/>\n+ <param name="cns.E" value="-3"/>\n+ <param name="cns.j" value="500"/>\n+ <param name="cns.m" value="2"/>\n+ <param name="cns.k" value="5"/>\n+ <output name="output_consensus" file="consensus_result3.fa"/>\n+ </test>\n+ \n+ </tests>\n+ \n+ <help><![CDATA[\n+**What it does**\n+\n+WTDBG is a de novo assembler for long noisy sequences, based on fuzzy Bruijn graphs (FBG).\n+\n+**Alignment**\n+\n+KBM (Kmer-BIN-Mapping) groups k-mers from each non-overlapped sliding 256 bp fragments in long reads into bins.\n+Bins of which most k-mers are high frequency, are filtered as highly repetitive ones.\n+Then, KBM searches synteny of matched bin pairs in sequences in a dynamic programming way.\n+A matched bin pair in two sequences is defined as two bins different by original but share a set of k-mers.\n+The result of alignments in KBM have the same features of traditional sequence alignment, excepting the unit of\n+KBM alignments is 256 bp bin instead of single base.\n+\n+**Assembly**\n+\n+FBG (Fuzzy Bruijn Graph) is composed of vertices in length of 1024 bp from reads, and edges connecting vertices\n+in their order on read paths. Comparing with DBG, the size of vertices in FBG are much bigger, thus won\'t be\n+sensitive to small repeat. To tolerate high sequencing errors, FBG\'s vertices are found using gapped\n+sequence alignments from KBM or other aligners, comparing with searching identical k-mers in DBG.\n+\n+ ]]></help>\n+ <expand macro="citations" />\n+</tool>\n' |