# HG changeset patch # User iuc # Date 1526506482 14400 # Node ID 6ef10b28e967a1932b03b3310c7a781fdba59b06 planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86 diff -r 000000000000 -r 6ef10b28e967 bealign.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bealign.xml Wed May 16 17:34:42 2018 -0400 @@ -0,0 +1,117 @@ + + + to a reference using a codon alignment algorithm + + macros.xml + + + bealign --version + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + +
+
+ + + + advanced['discard'] + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
diff -r 000000000000 -r 6ef10b28e967 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed May 16 17:34:42 2018 -0400 @@ -0,0 +1,21 @@ + + + 0.18.6 + + + python-bioext + + + + + + @UNPUBLISHED{spond, + author = "Sergei Kosakovsky Pond", + title = "HyPhy: Hypothesis Testing using Phylogenies", + year = "2000", + note = "http://hyphy.org/", + url = "http://hyphy.org/"} + + + + \ No newline at end of file diff -r 000000000000 -r 6ef10b28e967 test-data/bam2msa-out1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bam2msa-out1.fa Wed May 16 17:34:42 2018 -0400 @@ -0,0 +1,196 @@ +>Z|JP|K03455|2036|DUPLICATE +CCTCAAATCACTCTTTGGCAACGACCCTTAGTTACAGCAAAAATAGGGGAACAGCTAATA +GAAGCCCTATTAGACACAGGAGCAGATGATACAGTATTAGAAGAAATAAATTTACCAGGG +AAATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGAT +CAGATACCTATAGAAATCTGTGGACATAAAACTATAGGTACGGTATTAATAGGACCTACA +CCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGCTTGGCTGCACTTTAAATTTTCCC +ATTAGCCCTATTGAAACCGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAGGTT +AAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAACAGAAATTTGTACAGAAATG +GAAAGGGAAGGAAAAATTTCAAAAATTGGGCCTGAGAATCCATACAATACTCCAATATTT +GCCATAAAGAAAAAAGATGGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAAT +AAAAGAACTCAAGACTTCTGGGAGGTCCAACTAGGAATACCTCATCCCGCAGGATTAAAA +AAGAAAAAATCAGTAACAGTACTAGATGTGGGGGATGCATATTTTTCAGTTCCCTTAGAT +AAAGACTTTAGAAAGTATACTGCATTCACTATACCTAGTATAAATAATGAAACACCGGGG +ATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTTCAG +GCTAGCATGACAAAAATCTTAGAGCCCTTTAGAGCAAAAAATCCAGAGATGGTGATTTAC +CAATACATGGATGATTTATATGTAGGATCTGACTTAGAGATAGGGCAGCATAGAACAAAA +ATACAAGAGTTGAGAGAACATCTACTGAAGTGGGGATTAACCACACCAGATAAAAAACAT +CAGAAAGAACCTCCATTTCTTTGGATGGGATATGAACTCCATCCTGACAAATGGACAGTC +CAGCCTATAAAGCTGCCAGAAAAAGACAGCTGGACTGTCAATGATATACAGAAATTAGTG +GGAAAGCTAAATTGGGCAAGTCAGATTTATGCAGGAATTAAAGTAAGGCARCTGTGTAAA +CTCCTCAGGGGAGCCAAAGCACTAACAGAGATAGTAACACTGACTGAGGAAGCAGAATTA +GAATTAGCAGAAAACAGAGAAATTCTAAAAGAACCTGTTCATGGRGTATATTATGATCCA +TTAAAAGACCTAGTAGCAGAAATACAGAAACAAGGGCAAGACCAATGGACATATCAAATT +TATCAAGAGCCATTTAAAAATTTAAAAACAGGAAAATATGCAAAAAAGAAGTCTGCCCAC +ACTAATGATGTAAAACAATTAACAGAGGTAGTGCAAAAGGTGTCTACAGAAAGCATAGTA +ATATGGGGAAAGACCCCTAAATTTAGACTACCCATACAAAAAGAAACATGGGAAGCA--- +------------------------------------------------------------ +--------------------------------------------------------- +>Z|JP|K03455|2036|DUPLICATE +CCTCAAATCACTCTTTGGCAACGACCCTTAGTTACAGCAAAAATAGGGGAACAGCTAATA +GAAGCCCTATTAGACACAGGAGCAGATGATACAGTATTAGAAGAAATAAATTTACCAGGG +AAATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGAT +CAGATACCTATAGAAATCTGTGGACATAAAACTATAGGTACGGTATTAGTAGGACCTACA +CCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGCTTGGCTGCACTTTAAATTTTCCC +ATTAGCCCTATTGAAACCGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCGAAAGTT +AAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAAATG +GAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTT +GCCATAAAGAAAAAGGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAAT +AAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGGATACCACATCCCGCAGGGTTAAAA +AAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGAT +AAAGACTTCCGGAAGTATACTGCATTCACTATACCTAGTACAAACAATGAGACACCAGGG +ATTAGATATCAATACAATGTGCTACCACAGGGCTGGAAAGGATCACCAGCAATATTTCAG +GCTAGCATGACAAAAATCTTAGAGCCCTTTAGAGCAAAAAATCCAGAGATGGTGATTTAC +CAATACATGGATGATTTATATGTAGGATCTGACTTAGAGATAGGGCAGCATAGAACAAAA +ATACAAGAGTTGAGAGAACATCTACTGAAGTGGGGATTAACCACACCAGATAAAAAACAT +CAGAAAGAACCTCCATTTCTTTGGATGGGATATGAACTCCATCCTGACAAATGGACAGTC +CAGCCTATAAAGCTGCCAGAAAAAGACAGCTGGACTGTCAATGATATACAGAAATTAGTG +GGAAAGCTAAATTGGGCAAGTCAGATTTATGCAGGAATTAAAGTAAGGCAACTGTGTAAA +CTCCTCAGGGGAGCCAAAGCACTAACAGAGATAGTAACACTGACTGAGGAAGCAGAATTA +GAATTAGCAGAAAACAGAGAAATTCTAAAAGAACCTGTTCATGGAGTATATTATGATCCA +TCAAAAGACCTAGTAGCAGAAATACAGAAACAAGGGCAAGACCAATGGACATATCAAATT +TATCAAGAGCCATTTAAAAATTTAAAAACAGGAAAATATGCAAAAAAGAAGTCTGCCCAC +ACTAATGATGTAAAACAATTAACAGAGGTAGTGCAAAAGGTGTCTACAGAAAGCATAGTA +ATATGGGGAAAGACCCCTAAATTTAGACTACCCATACAAAAAGAAACATGGGAAGCA--- +------------------------------------------------------------ +--------------------------------------------------------- +>Z|JP|K03455|2036|DUPLICATE +CCTCAAATCACTCTTTGGCAACGACCCTTAGTTACAGCAAAAATAGGGGAACAGCTAATA +GAAGCCCTATTAGACACAGGAGCAGATGATACAGTATTAGAAGAAATAAATTTAYCAGGG +AAATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGAT +CAGATACCTATAGAAATCTGTGGACATAAAACTATAGGTACGATATTAATAGGACCTACA +CCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGCTTGGCTGCACTTTAAATTTTCCC +ATTAGCCCTATTGAAACCGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCGAAAGTT +AAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAAATG +GAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTT +GCCATAAAGAAAAAGGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAAT +AAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGGATACCACATCCCGCAGGGTTAAAA +AAGAAAAAATCAGTAACAGTACTAGATGTGGGGGATGCATATTTTTCAGTTCCTTTAGAT +AAAGACTTTAGAAAGTATACTGCATTCACTATACCTAGTATAAATAATGAAACACCGGGG +ATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTTCAG +GCTAGCATGACAAAAATCTTAGAGCCCTTTAGAGCAAAAAATCCAGAGATGGTGATTTAC +CAATACATGGATGATTTATATGTAGGATCTGACTTAGAGATAGGGCAGCATAGAACAAAA +ATACAAGAGTTGAGAGAACATCTACTGAAGTGGGGATTAACCACACCAGATAAAAAACAT +CAGAAAGAACCTCCATTTCTTTGGATGGGATATGAACTCCATCCTGACAAATGGACAGTC +CAGCCTATAAAGCTGCCAGAAAAAGACAGCTGGACTGTCAATGATATACAGAAATTAGTG +GGAAAGCTAAATTGGGCAAGTCAGATTTATGCAGGAATTAAAGTAAGGCAACTGTGTAAA +CTCCTCAGGGGAGCCAAAGCACTAACAGAGATAGTAACACTGACTGAGGAAGCAGAATTA +GAATTAGCAGAAAACAGAGAAATTCTAAAAGAACCTGTTCATGGAGTATATTATGATCCA +TCAAAAGACCTAGTAGCAGAAATACAGAAACAAGGGCAAGACCAATGGACATATCAAATT +TATCAAGAGCCATTTAAAAATTTAAAAACAGGAAAATATGCAAAAAAGAAGTCTGCCCAC +ACTAATGATGTAAAACAATTAACAGAGGTAGTGCAAAAGGTGTCTACAGAAAGCATAGTA +ATATGGGGAAAGACCCCTAAATTTAGACTACCCATACAAAAAGAAACATGGGAAGCA--- +------------------------------------------------------------ +--------------------------------------------------------- +>Z|JP|K03455|2036|DUPLICATE +CCTCAAATCACTCTTTGGCAACGACCCTTAGTTACAGCAAAAATAGGGGAACAGCTAATA +GAAGCCCTATTAGACACAGGAGCAGATGATACAGTATTAGAAGAAATAAATTTACCAGGG +AAATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAGGTAAGACAATATGAT +CAGATACTTATAGAAATTTGTGGGAAAAAGGCTGTAGGTACAGTGTTAGTAGGACCTACA +CCTGTCAACATAATTGGACGAAATATGTTGACTCAGATTGGGTGTACTTTAAATCTTCCA +ATTAGTCCTATTGAAACTGTACCAGTAAAATTGAAGCCAGGAATGGATGGCCCAAAGGTT +AAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAACAGAAATTTGTACAGAAATG +GAAAGGGAAGGAAAAATTTCAAAAATTGGGCCTGAGAATCCATACAATACTCCAATATTT +GCCATAAAGAAAAAAGATGGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAAT +AAAAGAACTCAAGACTTCTGGGAGGTCCAACTAGGAATACCTCATCCCGCAGGATTAAAA +AAGAAAAAATCAGTAACAGTACTAGATGTGGGGGATGCATATTTTTCAGTTCCCTTAGAT +AAAGACTTTAGAAAGTATACTGCATTCACTATACCTAGTATAAATAATGAAACACCGGGG +ATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTTCAG +GCTAGCATGACAAAAATCTTAGAGCCCTTTAGAGCAAAAAATCCAGAGATGGTGATTTAC +CAATACATGGATGATTTATATGTAGGATCTGACTTAGAGATAGGGCAGCATAGAACAAAA +ATACAAGAGTTGAGAGAACATCTACTGAAGTGGGGATTAACCACACCAGATAAAAAACAT +CAGAAAGAACCTCCATTTCTTTGGATGGGATATGAACTCCATCCTGACAAATGGACAGTC +CAGCCTATAAAGCTGCCAGAAAAAGACAGCTGGACTGTCAATGATATACAGAAATTAGTG +GGAAAGCTAAATTGGGCAAGTCAGATTTATGCAGGAATTAAAGTAAGGCAACTGTGTAAA +CTCCTCAGGGGAGCCAAAGCACTAACAGAGATAGTAACACTGACTGAGGAAGCAGAATTA +GAATTAGCAGAAAACAGAGAAATTCTAAAAGAACCTGTTCATGGAGTATATTATGATCCA +TCAAAAGACCTAGTAGCAGAAATACAGAAACAAGGGCAAGAC------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------------------------------------- +>Z|JP|K03455|2036|DUPLICATE +CCTCAAATCACTCTTTGGCAACGACCCTTAGTTACAGCAAAAATAGGGGAACAGCTAATA +GAAGCCCTATTAGACACAGGAGCAGATGATACAGTATTAGAAGAAATAAATTTACCAGGG +AAATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAATATGAT +CAGATACTTATAGAAATTTGTGGGAAAAAGGCTGTAGGTACAGTGTTAGTAGGACCTACA +CCTGTCAACATAATTGGACGAAATATGTTGACTCAGATTGGGTGTACTTTAAATTTTCCA +ATTAGTCCTATTGAAACTGTACCAGTAAAATTGAAGCCAGGAATGGATGGCCCAAAGGTT +AAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAACAGAAATTTGTACAGAAATG +GAAAGGGAAGGAAAAATTTCAAAAATTGGGCCTGAGAATCCATACAATACTCCAATATTT +GCCATAAAGAAAAAAGATGGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAAT +AAAAGAACTCAAGACTTCTGGGAGGTCCAACTAGGAATACCTCATCCCGCAGGATTAAAA +AAGAAAAAATCAGTAACAGTACTAGATGTGGGGGATGCATATTTTTCAGTTCCCTTAGAT +AAAGACTTTAGAAAGTATACTGCATTCACTATACCTAGTATAAATAATGAAACACCGGGG +ATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTTCAG +GCTAGCATGACAAAAATCTTAGAGCCCTTTAGAGCAAAAAATCCAGAGATGGTGATTTAC +CAATACATGGATGATTTATATGTAGGATCTGACTTAGAGATAGGGCAGCATAGAACAAAA +ATACAAGAGTTGAGAGAACATCTACTGAAGTGGGGATTAACCACACCAGATAAAAAACAT +CAGAAAGAACCTCCATTTCTTTGGATGGGATATGAACTCCATCCTGACAAATGGACAGTC +CAGCCTATAAAGCTGCCAGAAAAAGACAGCTGGACTGTCAATGATATACAGAAATTAGTG +GGAAAGCTAAATTGGGCAAGTCAGATTTATGCAGGAATTAAAGTAAGGCAACTGTGTAAA +CTCCTCAGGGGAGCCAAAGCACTAACAGAGATAGTAACACTGACTGAGGAAGCAGAATTA +GAATTAGCAGAAAACAGAGAAATTCTAAAAGAACCTGTTCATGGAGTATATTATGATCCA +TCAAAAGACCTAGTAGCAGAAATACAGAAACAAGGGCAAGACCAATGGACATATCAAATT +TATCAAGAGCCATTTAAAAATTTAAAAACAGGAAAATATGCAAAAAAGAAGTCTGCCCAC +ACTAATGATGTAAAACAATTAACAGAGGTAGTGCAAAAGGTGTCTACAGAAAGCATAGTA +ATATGGGGAAAGACCCCTAAATTTAGACTACCCATACAAAAAGAAACATGGGAAGCA--- +------------------------------------------------------------ +--------------------------------------------------------- +>Z|JP|K03455|2036|DUPLICATE +CCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAG +GAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGA +AGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGAT +CAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACA +CCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCC +ATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTT +AAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATG +GAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTT +GCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAAT +AAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAA +AAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGAT +GAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGG +ATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAA +AGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTAT +CAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAA +ATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACAT +CAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTA +CAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTG +GGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAA +CTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTA +GAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCA +TCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATT +TATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCAC +ACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTA +ATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGG +TGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCC +TTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTC +>Z|JP|K03455|2036 +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------------------AAATATGTTGACTCAGATTGGTTGTACTTTAAATTTTCCA +ATTAGTCCTATTGAAACTGTACCAGTAAAATTGAAGCCAGGAATGGATGGCCCAAGGGTT +AAACAATGGCCATTGACAGAAGAAAAAATAAAGGCGTTAACAGAAATTTGTACAGAAATG +GAAAGGGAAGGAAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAATATTT +GCCATAAAGAAAAAAGATAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTCAAT +AAAAGAACTCAAGACTTCTGGGAGGTCCAACTAGGAATACCTCATCCCGCGGGATTAAAA +AAGAAAAAATCAGTAACAGTACTAGATGTGGGGGATGCATATTTTTCAGTTCCCTTAGAT +AAAGACTTTAGAAAGCATACTGCATTCACTATACCTAGTGTAAATAATGAAACACCGGGG +ATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTTCAG +GCTAGCATGACAAAAATCTTAGAACCCTTTAGAACAAACAATCCAGAGATGGTGATTTAC +CAATATATGGATGATTTATATGTAGGATCTGACTTAGAGATAGGACAGCATAGAGAAAAA +ATACAGGAGTTGAGAGAACATCTACTGAAATGGGGATTTACCACACCAGATAAAAAA--- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------------------------------------- diff -r 000000000000 -r 6ef10b28e967 test-data/bam2msa-out2.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bam2msa-out2.fa Wed May 16 17:34:42 2018 -0400 @@ -0,0 +1,23 @@ +>reads +CCTCAGATCACTCTTTGGCAACGACCCCTCGTCACAATAAAGGTAGGGGGGCAGCTAAAG +GAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATAAATTTGCCAGGA +AAATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGAT +CAGATACYTATAGAAATCWGYGGACATARAGCTATAGGTACAGTRTTAGTAGGACCTACA +CCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGCTGCACTTTAAATTTYCCC +ATTAGTCCTATTGAAACTGTACCAGTAAARTTAAAGCCAGGAATGGATGGCCCAAGAGTY +AAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAAATG +GAAAARGAAGGAAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTT +GCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGARCTTAAT +AAGAGAACTCAAGACTTCTGGGAAGTTCARTTAGGAATACCACATCCCGCAGGGTTAAAA +AAGAAAAAATCAGTRACAGTACTGGATGTAGGTGATGCATACTTTTCAGTTCCCTTAGAT +GAAGAKTTCAGGAAGTATACTGCATTTACCATACCTAGTACAAACAATGAGACACCAGGG +ATTAGATAYCAGTACAATGTGCTYCCACAGGGATGGAAAGGATCACCAGCAATATTCCAG +AGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAARCAAAATCCAGACATAGTKATYTAT +CAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAACATAGRGHAAAA +ATAGAGGAACTGAGACAACATCTGTTGAGGTGGGGATTTACCACACCAGACAARAAACAT +CAGAAAGAACCTCCATTYCTTTGGATGGGTTATGAACTCCATCCTGAYAAATGGACAGTA +CAGCCTATAATGCTGCCAGAAAAAGAAAGCTGGACTGTCAATGACATACAGAAGTTAGTG +GGAAAATTGAATTGGGCAAGTCAGATTTATGCAGGGATTAAAGTAAAGCAATTATGTAAA +CTCCTTAGGGGRACCAAAGCAYTAACAGAAGTAGTACCACTAACAGCAGAAGCAGAGCTA +GAACTAGCAGAGAACAGGGARATTCTAAAAGAACCAGTACATGGAGTATATTATGACCCA +TCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGC diff -r 000000000000 -r 6ef10b28e967 test-data/bealign-in-ref-1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bealign-in-ref-1.fa Wed May 16 17:34:42 2018 -0400 @@ -0,0 +1,22 @@ +>CUSTOM_JP_REFERENCE +cctcaggtcactctttggcaacgacccctcgtcacaataaagataggggggcaactaaaggaagctctattagatacagg +agcagatgatacagtattagaagaaatgagtttgccaggaagatggaaaccaaaaatgatagggggaattggaggtttta +tcaaagtaagacagtatgatcagatactcatagaaatctgtggacataaagctataggtacagtattagtaggacctaca +cctgtcaacataattggaagaaatctgttgactcagattggttgcactttaaattttcccattagccctattgagactgt +accagtaaaattaaagccaggaatggatggcccaaaagttaaacaatggccattgacagaagaaaaaataaaagcattag +tagaaatttgtacagagatggaaaaggaagggaaaatttcaaaaattgggcctgaaaatccatacaatactccagtattt +gccataaagaaaaaagacagtactaaatggagaaaattagtagatttcagagaacttaataagagaactcaagacttctg +ggaagttcaattaggaataccacatcccgcagggttaaaaaagaaaaaatcagtaacagtactggatgtgggtgatgcat +atttttcagttcccttagatgaagacttcaggaagtatactgcatttaccatacctagtataaacaatgagacaccaggg +attagatatcagtacaatgtgcttccacagggatggaaaggatcaccagcaatattccaaagtagcatgacaaaaatctt +agagccttttagaaaacaaaatccagacatagttatctatcaatacatggatgatttgtatgtaggatctgacttagaaa +tagggcagcatagaacaaaaatagaggagctgagacaacatctgttgaggtggggacttaccacaccagacaaaaaacat +cagaaagaacctccattcctttggatgggttatgaactccatcctgataaatggacagtacagcctatagtgctgccaga +aaaagacagctggactgtcaatgacatacagaagttagtggggaaattgaattgggcaagtcagatttacccagggatta +aagtaaggcaattatgtaaactccttagaggaaccaaagcactaacagaagtaataccactaacagaagaagcagagcta +gaactggcagaaaacagagagattctaaaagaaccagtacatggagtgtattatgacccatcaaaagacttaatagcaga +aatacagaagcaggggcaaggccaatggacatatcaaatttatcaagagccatttaaaaatctgaaaacaggaaaatatg +caagaatgaggggtgcccacactaatgatgtaaaacaattaacagaggcagtgcaaaaaataaccacagaaagcatagta +atatggggaaagactcctaaatttaaactgcccatacaaaaggaaacatgggaaacatggtggacagagtattggcaagc +cacctggattcctgagtgggagtttgttaatacccctcccttagtgaaattatggtaccagttagagaaagaacccatag +taggagcagaaaccttc diff -r 000000000000 -r 6ef10b28e967 test-data/bealign-in-ref-2.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bealign-in-ref-2.fa Wed May 16 17:34:42 2018 -0400 @@ -0,0 +1,18 @@ +>reference +CCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGG +AGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTA +TCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACA +CCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGT +ACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAG +TAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTT +GCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTG +GGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCAT +ATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGG +ATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTT +AGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAA +TAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACAT +CAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGA +AAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTA +AAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTA +GAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGA +AATACAGAAGCAGGGGCAAGGC diff -r 000000000000 -r 6ef10b28e967 test-data/bealign-in1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bealign-in1.fa Wed May 16 17:34:42 2018 -0400 @@ -0,0 +1,130 @@ +>Z|JP|K03455|2036 +aaatatgttgactcagattggttgtactttaaattttccaattagtcctattgaaactgtaccagtaaaattgaagccag +gaatggatggcccaagggttaaacaatggccattgacagaagaaaaaataaaggcgttaacagaaatttgtacagaaatg +gaaagggaaggaaaaatttcaaaaattgggcctgaaaatccatacaatactccaatatttgccataaagaaaaaagatag +tactaaatggagaaaattagtagatttcagagaactcaataaaagaactcaagacttctgggaggtccaactaggaatac +ctcatcccgcgggattaaaaaagaaaaaatcagtaacagtactagatgtgggggatgcatatttttcagttcccttagat +aaagactttagaaagcatactgcattcactatacctagtgtaaataatgaaacaccggggattagatatcagtacaatgt +gcttccacagggatggaaaggatcaccagcaatatttcaggctagcatgacaaaaatcttagaaccctttagaacaaaca +atccagagatggtgatttaccaatatatggatgatttatatgtaggatctgacttagagataggacagcatagagaaaaa +atacaggagttgagagaacatctactgaaatggggatttaccacaccagataaaaaa +>Z|JP|K03455|2036|DUPLICATE 2 +cctcaaatcactctttggcaacgacccttagttacagcaaaaataggggaacagctaatagaagccctattagacacagg +agcagatgatacagtattagaagaaataaatttaccagggaaatggaaaccaaaaatgatagggggaattggaggtttta +tcaaagtaagacagtatgatcagatacctatagaaatctgtggacataaaactataggtacggtattaataggacctaca +cctgtcaacataattggaagaaatctgttgactcagcttggctgcactttaaattttcccattagccctattgaaaccgt +accagtaaaattaaagccaggaatggatggcccaaaggttaaacaatggccattgacagaagaaaaaataaaagcattaa +cagaaatttgtacagaaatggaaagggaaggaaaaatttcaaaaattgggcctgagaatccatacaatactccaatattt +gccataaagaaaaaagatggtactaaatggagaaaattagtagatttcagagaacttaataaaagaactcaagacttctg +ggaggtccaactaggaatacctcatcccgcaggattaaaaaagaaaaaatcagtaacagtactagatgtgggggatgcat +atttttcagttcccttagataaagactttagaaagtatactgcattcactatacctagtataaataatgaaacaccgggg +attagatatcagtacaatgtgcttccacagggatggaaaggatcaccagcaatatttcaggctagcatgacaaaaatctt +agagccctttagagcaaaaaatccagagatggtgatttaccaatacatggatgatttatatgtaggatctgacttagaga +tagggcagcatagaacaaaaatacaagagttgagagaacatctactgaagtggggattaaccacaccagataaaaaacat +cagaaagaacctccatttctttggatgggatatgaactccatcctgacaaatggacagtccagcctataaagctgccaga +aaaagacagctggactgtcaatgatatacagaaattagtgggaaagctaaattgggcaagtcagatttatgcaggaatta +aagtaaggcarctgtgtaaactcctcaggggagccaaagcactaacagagatagtaacactgactgaggaagcagaatta +gaattagcagaaaacagagaaattctaaaagaacctgttcatggrgtatattatgatccattaaaagacctagtagcaga +aatacagaaacaagggcaagaccaatggacatatcaaatttatcaagagccatttaaaaatttaaaaacaggaaaatatg +caaaaaagaagtctgcccacactaatgatgtaaaacaattaacagaggtagtgcaaaaggtgtctacagaaagcatagta +atatggggaaagacccctaaatttagactacccatacaaaaagaaacatgggaagca +>Z|JP|K03455|2036|DUPLICATE 3 +cctcaaatcactctttggcaacgacccttagttacagcaaaaataggggaacagctaatagaagccctattagacacagg +agcagatgatacagtattagaagaaataaatttaccagggaaatggaaaccaaaaatgatagggggaattggaggtttta +tcaaagtaagacagtatgatcagatacctatagaaatctgtggacataaaactataggtacggtattagtaggacctaca +cctgtcaacataattggaagaaatctgttgactcagcttggctgcactttaaattttcccattagccctattgaaaccgt +accagtaaaattaaagccaggaatggatggcccgaaagttaaacaatggccattgacagaagaaaaaataaaagcattag +tagaaatttgtacagaaatggaaaaggaagggaaaatttcaaaaattgggcctgaaaatccatacaatactccagtattt +gccataaagaaaaaggacagtactaaatggagaaaattagtagatttcagagaacttaataagagaactcaagacttctg +ggaagttcaattagggataccacatcccgcagggttaaaaaagaaaaaatcagtaacagtactggatgtgggtgatgcat +atttttcagttcccttagataaagacttccggaagtatactgcattcactatacctagtacaaacaatgagacaccaggg +attagatatcaatacaatgtgctaccacagggctggaaaggatcaccagcaatatttcaggctagcatgacaaaaatctt +agagccctttagagcaaaaaatccagagatggtgatttaccaatacatggatgatttatatgtaggatctgacttagaga +tagggcagcatagaacaaaaatacaagagttgagagaacatctactgaagtggggattaaccacaccagataaaaaacat +cagaaagaacctccatttctttggatgggatatgaactccatcctgacaaatggacagtccagcctataaagctgccaga +aaaagacagctggactgtcaatgatatacagaaattagtgggaaagctaaattgggcaagtcagatttatgcaggaatta +aagtaaggcaactgtgtaaactcctcaggggagccaaagcactaacagagatagtaacactgactgaggaagcagaatta +gaattagcagaaaacagagaaattctaaaagaacctgttcatggagtatattatgatccatcaaaagacctagtagcaga +aatacagaaacaagggcaagaccaatggacatatcaaatttatcaagagccatttaaaaatttaaaaacaggaaaatatg +caaaaaagaagtctgcccacactaatgatgtaaaacaattaacagaggtagtgcaaaaggtgtctacagaaagcatagta +atatggggaaagacccctaaatttagactacccatacaaaaagaaacatgggaagca +>Z|JP|K03455|2036|DUPLICATE 4 +cctcaaatcactctttggcaacgacccttagttacagcaaaaataggggaacagctaatagaagccctattagacacagg +agcagatgatacagtattagaagaaataaatttaycagggaaatggaaaccaaaaatgatagggggaattggaggtttta +tcaaagtaagacagtatgatcagatacctatagaaatctgtggacataaaactataggtacgatattaataggacctaca +cctgtcaacataattggaagaaatctgttgactcagcttggctgcactttaaattttcccattagccctattgaaaccgt +accagtaaaattaaagccaggaatggatggcccgaaagttaaacaatggccattgacagaagaaaaaataaaagcattag +tagaaatttgtacagaaatggaaaaggaagggaaaatttcaaaaattgggcctgaaaatccatacaatactccagtattt +gccataaagaaaaaggacagtactaaatggagaaaattagtagatttcagagaacttaataagagaactcaagacttctg +ggaagttcaattagggataccacatcccgcagggttaaaaaagaaaaaatcagtaacagtactagatgtgggggatgcat +atttttcagttcctttagataaagactttagaaagtatactgcattcactatacctagtataaataatgaaacaccgggg +attagatatcagtacaatgtgcttccacagggatggaaaggatcaccagcaatatttcaggctagcatgacaaaaatctt +agagccctttagagcaaaaaatccagagatggtgatttaccaatacatggatgatttatatgtaggatctgacttagaga +tagggcagcatagaacaaaaatacaagagttgagagaacatctactgaagtggggattaaccacaccagataaaaaacat +cagaaagaacctccatttctttggatgggatatgaactccatcctgacaaatggacagtccagcctataaagctgccaga +aaaagacagctggactgtcaatgatatacagaaattagtgggaaagctaaattgggcaagtcagatttatgcaggaatta +aagtaaggcaactgtgtaaactcctcaggggagccaaagcactaacagagatagtaacactgactgaggaagcagaatta +gaattagcagaaaacagagaaattctaaaagaacctgttcatggagtatattatgatccatcaaaagacctagtagcaga +aatacagaaacaagggcaagaccaatggacatatcaaatttatcaagagccatttaaaaatttaaaaacaggaaaatatg +caaaaaagaagtctgcccacactaatgatgtaaaacaattaacagaggtagtgcaaaaggtgtctacagaaagcatagta +atatggggaaagacccctaaatttagactacccatacaaaaagaaacatgggaagca +>Z|JP|K03455|2036|DUPLICATE 5 +cctcaaatcactctttggcaacgacccttagttacagcaaaaataggggaacagctaatagaagccctattagacacagg +agcagatgatacagtattagaagaaataaatttaccagggaaatggaaaccaaaaatgatagggggaattggaggtttta +tcaaggtaagacaatatgatcagatacttatagaaatttgtgggaaaaaggctgtaggtacagtgttagtaggacctaca +cctgtcaacataattggacgaaatatgttgactcagattgggtgtactttaaatcttccaattagtcctattgaaactgt +accagtaaaattgaagccaggaatggatggcccaaaggttaaacaatggccattgacagaagaaaaaataaaagcattaa +cagaaatttgtacagaaatggaaagggaaggaaaaatttcaaaaattgggcctgagaatccatacaatactccaatattt +gccataaagaaaaaagatggtactaaatggagaaaattagtagatttcagagaacttaataaaagaactcaagacttctg +ggaggtccaactaggaatacctcatcccgcaggattaaaaaagaaaaaatcagtaacagtactagatgtgggggatgcat +atttttcagttcccttagataaagactttagaaagtatactgcattcactatacctagtataaataatgaaacaccgggg +attagatatcagtacaatgtgcttccacagggatggaaaggatcaccagcaatatttcaggctagcatgacaaaaatctt +agagccctttagagcaaaaaatccagagatggtgatttaccaatacatggatgatttatatgtaggatctgacttagaga +tagggcagcatagaacaaaaatacaagagttgagagaacatctactgaagtggggattaaccacaccagataaaaaacat +cagaaagaacctccatttctttggatgggatatgaactccatcctgacaaatggacagtccagcctataaagctgccaga +aaaagacagctggactgtcaatgatatacagaaattagtgggaaagctaaattgggcaagtcagatttatgcaggaatta +aagtaaggcaactgtgtaaactcctcaggggagccaaagcactaacagagatagtaacactgactgaggaagcagaatta +gaattagcagaaaacagagaaattctaaaagaacctgttcatggagtatattatgatccatcaaaagacctagtagcaga +aatacagaaacaagggcaagac +>Z|JP|K03455|2036|DUPLICATE 6 +cctcaaatcactctttggcaacgacccttagttacagcaaaaataggggaacagctaatagaagccctattagacacagg +agcagatgatacagtattagaagaaataaatttaccagggaaatggaaaccaaaaatgatagggggaattggaggtttta +tcaaagtaagacaatatgatcagatacttatagaaatttgtgggaaaaaggctgtaggtacagtgttagtaggacctaca +cctgtcaacataattggacgaaatatgttgactcagattgggtgtactttaaattttccaattagtcctattgaaactgt +accagtaaaattgaagccaggaatggatggcccaaaggttaaacaatggccattgacagaagaaaaaataaaagcattaa +cagaaatttgtacagaaatggaaagggaaggaaaaatttcaaaaattgggcctgagaatccatacaatactccaatattt +gccataaagaaaaaagatggtactaaatggagaaaattagtagatttcagagaacttaataaaagaactcaagacttctg +ggaggtccaactaggaatacctcatcccgcaggattaaaaaagaaaaaatcagtaacagtactagatgtgggggatgcat +atttttcagttcccttagataaagactttagaaagtatactgcattcactatacctagtataaataatgaaacaccgggg +attagatatcagtacaatgtgcttccacagggatggaaaggatcaccagcaatatttcaggctagcatgacaaaaatctt +agagccctttagagcaaaaaatccagagatggtgatttaccaatacatggatgatttatatgtaggatctgacttagaga +tagggcagcatagaacaaaaatacaagagttgagagaacatctactgaagtggggattaaccacaccagataaaaaacat +cagaaagaacctccatttctttggatgggatatgaactccatcctgacaaatggacagtccagcctataaagctgccaga +aaaagacagctggactgtcaatgatatacagaaattagtgggaaagctaaattgggcaagtcagatttatgcaggaatta +aagtaaggcaactgtgtaaactcctcaggggagccaaagcactaacagagatagtaacactgactgaggaagcagaatta +gaattagcagaaaacagagaaattctaaaagaacctgttcatggagtatattatgatccatcaaaagacctagtagcaga +aatacagaaacaagggcaagaccaatggacatatcaaatttatcaagagccatttaaaaatttaaaaacaggaaaatatg +caaaaaagaagtctgcccacactaatgatgtaaaacaattaacagaggtagtgcaaaaggtgtctacagaaagcatagta +atatggggaaagacccctaaatttagactacccatacaaaaagaaacatgggaagca +>Z|JP|K03455|2036|DUPLICATE 7 +cctcaggtcactctttggcaacgacccctcgtcacaataaagataggggggcaactaaaggaagctctattagatacagg +agcagatgatacagtattagaagaaatgagtttgccaggaagatggaaaccaaaaatgatagggggaattggaggtttta +tcaaagtaagacagtatgatcagatactcatagaaatctgtggacataaagctataggtacagtattagtaggacctaca +cctgtcaacataattggaagaaatctgttgactcagattggttgcactttaaattttcccattagccctattgagactgt +accagtaaaattaaagccaggaatggatggcccaaaagttaaacaatggccattgacagaagaaaaaataaaagcattag +tagaaatttgtacagagatggaaaaggaagggaaaatttcaaaaattgggcctgaaaatccatacaatactccagtattt +gccataaagaaaaaagacagtactaaatggagaaaattagtagatttcagagaacttaataagagaactcaagacttctg +ggaagttcaattaggaataccacatcccgcagggttaaaaaagaaaaaatcagtaacagtactggatgtgggtgatgcat +atttttcagttcccttagatgaagacttcaggaagtatactgcatttaccatacctagtataaacaatgagacaccaggg +attagatatcagtacaatgtgcttccacagggatggaaaggatcaccagcaatattccaaagtagcatgacaaaaatctt +agagccttttagaaaacaaaatccagacatagttatctatcaatacatggatgatttgtatgtaggatctgacttagaaa +tagggcagcatagaacaaaaatagaggagctgagacaacatctgttgaggtggggacttaccacaccagacaaaaaacat +cagaaagaacctccattcctttggatgggttatgaactccatcctgataaatggacagtacagcctatagtgctgccaga +aaaagacagctggactgtcaatgacatacagaagttagtggggaaattgaattgggcaagtcagatttacccagggatta +aagtaaggcaattatgtaaactccttagaggaaccaaagcactaacagaagtaataccactaacagaagaagcagagcta +gaactggcagaaaacagagagattctaaaagaaccagtacatggagtgtattatgacccatcaaaagacttaatagcaga +aatacagaagcaggggcaaggccaatggacatatcaaatttatcaagagccatttaaaaatctgaaaacaggaaaatatg +caagaatgaggggtgcccacactaatgatgtaaaacaattaacagaggcagtgcaaaaaataaccacagaaagcatagta +atatggggaaagactcctaaatttaaactgcccatacaaaaggaaacatgggaaacatggtggacagagtattggcaagc +cacctggattcctgagtgggagtttgttaatacccctcccttagtgaaattatggtaccagttagagaaagaacccatag +taggagcagaaaccttc diff -r 000000000000 -r 6ef10b28e967 test-data/bealign-in2.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bealign-in2.fa Wed May 16 17:34:42 2018 -0400 @@ -0,0 +1,18 @@ +>reads +CCTCAGATCACTCTTATGATGATGTGGCAACGACCCCTCGTCACAATAAAGGTAGGGGGGCAGCTAAAGGAAGCTCTATT +AGATACAGGAGCAGATGATACAGTATTAGAAGAAATAAATTTGCCAGGAAAATGGAAACCAAAAATGATAGGGGGAATTG +GAGGTTTTATCAAAGTAAGACAGTATGATCAGATACYTATAGAAATCWGYGGACATARAGCTATAGGTACAGTRTTAGTA +GGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGCTGCACTTTAAATTTYCCCATTAGTCCTAT +TGAAACTGTACCAGTAAARTTAAAGCCAGGAATGGATGGCCCAAGAGTYAAACAATGGCCATTGACAGAAGAAAAAATAA +AAGCATTAGTAGAAATTTGTACAGAAATGGAAAARGAAGGAAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACT +CCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGARCTTAATAAGAGAACTCA +AGACTTCTGGGAAGTTCARTTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTRACAGTACTGGATGTAG +GTGATGCATACTTTTCAGTTCCCTTAGATGAAGAKTTCAGGAAGTATACTGCATTTACCATACCTAGTACAAACAATGAG +ACACCAGGGATTAGATAYCAGTACAATGTGCTYCCACAGGGATGGAAAGGATCACCAGCAATATTCCAGAGTAGCATGAC +AAAAATCTTAGAGCCTTTTAGAAARCAAAATCCAGACATAGTKATYTATCAATACATGGATGATTTGTATGTAGGATCTG +ACTTAGAAATAGGGCAACATAGRGHAAAAATAGAGGAACTGAGACAACATCTGTTGAGGTGGGGATTTACCACACCAGAC +AARAAACATCAGAAAGAACCTCCATTYCTTTGGATGGGTTATGAACTCCATCCTGAYAAATGGACAGTACAGCCTATAAT +GCTGCCAGAAAAAGAAAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGAAAATTGAATTGGGCAAGTCAGATTTATG +CAGGGATTAAAGTAAAGCAATTATGTAAACTCCTTAGGGGRACCAAAGCAYTAACAGAAGTAGTACCACTAACAGCAGAA +GCAGAGCTAGAACTAGCAGAGAACAGGGARATTCTAAAAGAACCAGTACATGGAGTATATTATGACCCATCAAAAGACTT +AATAGCAGAAATACAGAAGCAGGGGCAAGGC diff -r 000000000000 -r 6ef10b28e967 test-data/bealign-out1.bam Binary file test-data/bealign-out1.bam has changed diff -r 000000000000 -r 6ef10b28e967 test-data/bealign-out2.bam Binary file test-data/bealign-out2.bam has changed diff -r 000000000000 -r 6ef10b28e967 test-data/bealign-out3.bam Binary file test-data/bealign-out3.bam has changed