# 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 @@
+<?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>
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 @@
+<?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
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