# HG changeset patch
# User iuc
# Date 1526506498 14400
# Node ID 12729213b4aeb5e50e06068321717acbe5ea22c6

planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86

diff -r 000000000000 -r 12729213b4ae bam2msa.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bam2msa.xml	Wed May 16 17:34:58 2018 -0400
@@ -0,0 +1,35 @@
+<?xml version="1.0"?>
+<tool id="bioext_bam2msa" name="Convert BAM" version="@VERSION@.0">
+  <description>to FASTA multiple sequence alignment</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <command detect_errors="exit_code"><![CDATA[
+    bam2msa
+        #if $region_start and $region_end:
+            -r $region_start:$region_end
+        #end if
+        '$input' '$output'
+    ]]></command>
+  <inputs>
+    <param name="input" type="data" format="bam,sam" label="Input BAM file"/>
+    <param name="region_start" type="integer" value="0" optional="True" label="Starting coordinate" help="Leave blank to extract all sequences"/>
+    <param name="region_end" type="integer" value="0" optional="True" label="End coordinate"/>
+  </inputs>
+  <outputs>
+    <data name="output" format="fasta"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="input" ftype="bam" value="bealign-out1.bam"/>
+      <output name="output" file="bam2msa-out1.fa"/>
+    </test>
+    <test>
+      <param name="input" ftype="bam" value="bealign-out2.bam"/>
+      <output name="output" file="bam2msa-out2.fa"/>
+    </test>
+  </tests>
+  <help>Extract MSA from a BAM file</help>
+  <expand macro="citations"/>
+</tool>
diff -r 000000000000 -r 12729213b4ae macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Wed May 16 17:34:58 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+                @UNPUBLISHED{spond,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 12729213b4ae test-data/bam2msa-out1.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bam2msa-out1.fa	Wed May 16 17:34:58 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 12729213b4ae test-data/bam2msa-out2.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bam2msa-out2.fa	Wed May 16 17:34:58 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 12729213b4ae 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 17:34:58 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 12729213b4ae 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 17:34:58 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 12729213b4ae test-data/bealign-in1.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bealign-in1.fa	Wed May 16 17:34:58 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 12729213b4ae test-data/bealign-in2.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bealign-in2.fa	Wed May 16 17:34:58 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 12729213b4ae test-data/bealign-out1.bam
Binary file test-data/bealign-out1.bam has changed
diff -r 000000000000 -r 12729213b4ae test-data/bealign-out2.bam
Binary file test-data/bealign-out2.bam has changed
diff -r 000000000000 -r 12729213b4ae test-data/bealign-out3.bam
Binary file test-data/bealign-out3.bam has changed