Mercurial > repos > iuc > bioext_bealign
changeset 0:6ef10b28e967 draft
planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
| author | iuc |
|---|---|
| date | Wed, 16 May 2018 17:34:42 -0400 |
| parents | |
| children | f9b72a376ec9 |
| files | bealign.xml macros.xml test-data/bam2msa-out1.fa test-data/bam2msa-out2.fa test-data/bealign-in-ref-1.fa test-data/bealign-in-ref-2.fa test-data/bealign-in1.fa test-data/bealign-in2.fa test-data/bealign-out1.bam test-data/bealign-out2.bam test-data/bealign-out3.bam |
| diffstat | 11 files changed, 545 insertions(+), 0 deletions(-) [+] |
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--- /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 @@ +<?xml version="1.0"?> +<tool id="bioext_bealign" name="Align sequences" version="@VERSION@.0"> + <description>to a reference using a codon alignment algorithm</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <version_command>bealign --version</version_command> + <command detect_errors="exit_code"> + <![CDATA[ + bealign --reference '$select_reference.reference' --alphabet $advanced.alphabet + #if $advanced.expected_identity: + --expected-identity $advanced.expected_identity + #end if + --score-matrix $advanced.score_matrix $advanced.reverse_complement $advanced.keep_reference + #if $advanced.discard: + $advanced.discard '$advanced.discarded_reads' + #end if + '$input' '$output' + ]]> + </command> + <inputs> + <param name="input" type="data" format="fasta" label="Input reads" /> + <conditional name="select_reference"> + <param name="reference_type" type="select"> + <option value="preset">Select preset</option> + <option value="dataset">Use a history dataset</option> + </param> + <when value="preset"> + <param argument="--reference" type="select"> + <option value="HXB2_tat">HXB2 tat</option> + <option value="HXB2_gag">HXB2 gag</option> + <option value="HXB2_pol">HXB2 polymerase</option> + <option value="HXB2_int">HXB2 integrase</option> + <option value="HXB2_vif">HXB2 vif</option> + <option value="HXB2_pr">HXB2 protease</option> + <option value="HXB2_vpr">HXB2 vpr</option> + <option value="NL4-3_prrt">NL4-3 protease and reverse transcriptase</option> + <option value="HXB2_nef">HXB2 nef</option> + <option value="HXB2_env">HXB2 envelope</option> + <option value="HXB2_rt">HXB2 reverse transcriptase</option> + <option value="HXB2_prrt">HXB2 protease and reverse transcriptase</option> + <option value="HXB2_rev">HXB2 rev</option> + <option value="HXB2_vpu">HXB2 vpu</option> + </param> + </when> + <when value="dataset"> + <param argument="--reference" type="data" format="fasta" label="Reference sequences" /> + </when> + </conditional> + <section name="advanced" title="Advanced options" expanded="False"> + <param name="expected_identity" argument="--expected-identity" type="float" min="0" max="1" optional="True" label="Discard sequences that are insufficiently identical to the reference" /> + <param argument="--alphabet" type="select" label="Alphabet to use for alignment"> + <option value="codon" selected="True">Codon</option> + <option value="dna">DNA</option> + <option value="amino">Amino acids</option> + </param> + <param name="score_matrix" argument="--score-matrix" type="select" label="Parametrize using score matrix"> + <option value="BLOSUM62" selected="True">Blocks substitution</option> + <option value="DNA65">DNA, 65% expected identity</option> + <option value="DNA70">DNA, 70% expected identity</option> + <option value="DNA88">DNA, 88% expected identity</option> + <option value="DNA80">DNA, 80% expected identity</option> + <option value="DNA95">DNA, 95% expected identity</option> + <option value="PAM200">PAM 200 substitution</option> + <option value="PAM250">PAM 250 substitution</option> + <option value="HIV_BETWEEN_F">HIV between+F</option> + </param> + <param argument="--discard" type="boolean" checked="False" truevalue="--discard" falsevalue="" label="Output discarded sequences to a separate dataset" /> + <param name="reverse_complement" argument="--reverse-complement" type="boolean" checked="False" truevalue="--reverse-complement" falsevalue="" label="Also try to align against reverse complement of reference" /> + <param name="keep_reference" argument="--keep-reference" type="boolean" checked="False" truevalue="--keep-reference" falsevalue="" label="Include reference as first sequence in aligned BAM" /> + </section> + </inputs> + <outputs> + <data name="output" format="bam" /> + <data name="discarded_reads" format="fasta"> + <filter>advanced['discard']</filter> + </data> + </outputs> + <tests> + <test> + <param name="input" ftype="fasta" value="bealign-in1.fa" /> + <param name="reference_type" value="dataset" /> + <param name="score_matrix" value="HIV_BETWEEN_F" /> + <param name="reference" ftype="fasta" value="bealign-in-ref-1.fa" /> + <output name="output" file="bealign-out1.bam" /> + </test> + <test> + <param name="input" ftype="fasta" value="bealign-in2.fa" /> + <param name="reference_type" value="dataset" /> + <param name="score_matrix" value="BLOSUM62" /> + <param name="reference" ftype="fasta" value="bealign-in-ref-2.fa" /> + <output name="output" file="bealign-out2.bam" /> + </test> + <test> + <param name="input" ftype="fasta" value="bealign-in2.fa" /> + <param name="reference_type" value="dataset" /> + <param name="expected_identity" value="0.9" /> + <param name="score_matrix" value="BLOSUM62" /> + <param name="reference" ftype="fasta" value="bealign-in-ref-2.fa" /> + <output name="output" file="bealign-out3.bam" /> + </test> + </tests> + <help> + <![CDATA[ +bealign +------- + +Align sequences to a reference using a codon alignment algorithm. + +NOTES +----- + +Reference can be one of the presets or a custom history reference. + ]]></help> + <expand macro="citations"/> +</tool>
--- /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 @@ +<?xml version="1.0"?> +<macros> + <token name="@VERSION@">0.18.6</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@VERSION@">python-bioext</requirement> + </requirements> + </xml> + <xml name="citations"> + <citations> + <citation type="bibtex"> + @UNPUBLISHED{spond, + author = "Sergei Kosakovsky Pond", + title = "HyPhy: Hypothesis Testing using Phylogenies", + year = "2000", + note = "http://hyphy.org/", + url = "http://hyphy.org/"} + </citation> + </citations> + </xml> +</macros> \ No newline at end of file
--- /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--- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +---------------------------------------------------------
--- /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
--- /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
--- /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
--- /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
--- /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