Repository 'sortmerna'
hg clone https://toolshed.g2.bx.psu.edu/repos/rnateam/sortmerna

Changeset 9:eb35257d2e29 (2019-03-20)
Previous changeset 8:65c38d020fea (2017-09-24) Next changeset 10:10b84b577117 (2023-10-21)
Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
modified:
readme.md
sortmerna.xml
added:
test-data/forward_reads.fasta
test-data/reverse_reads.fasta
test-data/test5_aligned.fasta
test-data/test5_unaligned.fasta
test-data/test6_aligned_forward.fasta
test-data/test6_aligned_reverse.fasta
test-data/test6_unaligned_forward.fasta
test-data/test6_unaligned_reverse.fasta
removed:
macros.xml
b
diff -r 65c38d020fea -r eb35257d2e29 macros.xml
--- a/macros.xml Sun Sep 24 14:28:47 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
@@ -1,35 +0,0 @@
-<?xml version="1.0" ?>
-<macros>
-    <token name="@VERSION@">2.1b</token>
-    <xml name="db_prep">
-        <param name="seed_length" type="integer" min="0" max="100" value="18" label="Seed length for database indexing" help="(-L)"/>
-        <param name="max_pos" type="integer" min="0" max="100000" value="10000" label="Maximum number of positions to store for each k-mer for database indexing" help="With 0, all positions are stored (--max_pos)"/>
-    </xml>
-    <xml name="output_alignments">
-        <param name="print_all_reads" type="boolean" checked="false" truevalue="--print_all_reads" falsevalue="" label="Output null alignment strings for non-aligned reads"/>
-        <conditional name="blast">
-            <param name="blast_output" type="select" label="Output BLAST report?">
-                <option value="True">Yes</option>
-                <option value="False" selected="True">No</option>
-            </param>
-            <when value="True">
-                <param name="blast_format" type="select" label="BLAST-like format?">
-                    <option value="0">pairwise (--blast '0')</option>
-                    <option value="1">tabular BLAST -m 8 format (--blast '1')</option>
-                    <option value="1 cigar">tabular + column for CIGAR (--blast '1 cigar')</option>
-                    <option value="1 cigar qcov">tabular + columns for CIGAR and query coverage (--blast '1 cigar qcov')</option>
-                    <option value="1 cigar qcov qstrand">tabular + columns for CIGAR, query coverage and strand (--blast '1 cigar qcov qstrand')</option>
-                </param>
-            </when>
-            <when value="False"/>
-        </conditional>
-    </xml>
-    <token name="@ALIGNMENTS@">
-        $report.print_all_reads
-        --sam
-        --SQ
-        #if $report.blast.blast_output == 'True'
-            --blast '$report.blast.blast_format'
-        #end if
-    </token>
-</macros>
\ No newline at end of file
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diff -r 65c38d020fea -r eb35257d2e29 readme.md
--- a/readme.md Sun Sep 24 14:28:47 2017 -0400
+++ b/readme.md Wed Mar 20 03:03:08 2019 -0400
b
@@ -1,33 +1,27 @@
-=========
-SortMeRNA
-=========
+## SortMeRNA
 
 SortMeRNA, a fast and accurate filtering of ribosomal RNAs in metatranscriptomic data.
 
 For more information, please see http://bioinfo.lifl.fr/RNA/sortmerna/.
 
 
-============
-Installation
-============
+## Installation
 
 It is recommended to install this wrapper via the `Galaxy Tool Shed`.
 
-.. _`Galaxy Tool Shed`:  https://testtoolshed.g2.bx.psu.edu/view/bgruening/sortmerna
+.. _`Galaxy Tool Shed`:  https://toolshed.g2.bx.psu.edu/view/bgruening/sortmerna
 
 To install the databases, we recommend to use the dedicated data manager available in the `Galaxy Tool Shed`
 
 
-=======
-History
-=======
+## History
+
 - 0.1: First version of the wrapper from Jean-Frédéric
 - 1.9.0: First version with data tables, new dependency definition, generall restructuring
 
 
-===============================
-Wrapper Licence (MIT/BSD style)
-===============================
+## Wrapper Licence (MIT/BSD style)
+
 
 Permission to use, copy, modify, and distribute this software and its
 documentation with or without modifications and for any purpose and
b
diff -r 65c38d020fea -r eb35257d2e29 sortmerna.xml
--- a/sortmerna.xml Sun Sep 24 14:28:47 2017 -0400
+++ b/sortmerna.xml Wed Mar 20 03:03:08 2019 -0400
[
b'@@ -1,7 +1,38 @@\n-<tool id="bg_sortmerna" name="Filter with SortMeRNA" version="@VERSION@.5">\n+<tool id="bg_sortmerna" name="Filter with SortMeRNA" version="@VERSION@.6">\n     <description>of ribosomal RNAs in metatranscriptomic data</description>\n     <macros>\n-        <import>macros.xml</import>\n+        <token name="@VERSION@">2.1b</token>\n+        <xml name="db_prep">\n+            <param name="seed_length" type="integer" min="0" max="100" value="18" label="Seed length for database indexing" help="(-L)"/>\n+            <param name="max_pos" type="integer" min="0" max="100000" value="10000" label="Maximum number of positions to store for each k-mer for database indexing" help="With 0, all positions are stored (--max_pos)"/>\n+        </xml>\n+        <xml name="output_alignments">\n+            <param name="print_all_reads" type="boolean" checked="false" truevalue="--print_all_reads" falsevalue="" label="Output null alignment strings for non-aligned reads"/>\n+            <conditional name="blast">\n+                <param name="blast_output" type="select" label="Output BLAST report?">\n+                    <option value="True">Yes</option>\n+                    <option value="False" selected="True">No</option>\n+                </param>\n+                <when value="True">\n+                    <param name="blast_format" type="select" label="BLAST-like format?">\n+                        <option value="0">pairwise (--blast \'0\')</option>\n+                        <option value="1">tabular BLAST -m 8 format (--blast \'1\')</option>\n+                        <option value="1 cigar">tabular + column for CIGAR (--blast \'1 cigar\')</option>\n+                        <option value="1 cigar qcov">tabular + columns for CIGAR and query coverage (--blast \'1 cigar qcov\')</option>\n+                        <option value="1 cigar qcov qstrand">tabular + columns for CIGAR, query coverage and strand (--blast \'1 cigar qcov qstrand\')</option>\n+                    </param>\n+                </when>\n+                <when value="False"/>\n+            </conditional>\n+        </xml>\n+        <token name="@ALIGNMENTS@">\n+            $report.print_all_reads\n+            --sam\n+            --SQ\n+            #if $report.blast.blast_output == \'True\'\n+                --blast \'$report.blast.blast_format\'\n+            #end if\n+        </token>\n     </macros>\n     <requirements>\n         <requirement type="package" version="@VERSION@">sortmerna</requirement>\n@@ -49,9 +80,9 @@\n \n     #if str( $databases_type.databases_selector ) != \'cached\'\n         indexdb_rna \n-            --ref $ref \n-            -L $databases_type.seed_length \n-            --max_pos $databases_type.max_pos \n+            --ref \'$ref\'\n+            -L \'$databases_type.seed_length\'\n+            --max_pos \'$databases_type.max_pos\'\n         &&\n     #end if\n \n@@ -59,15 +90,15 @@\n         merge-paired-reads.sh\n             \'$sequencing_type.forward_reads\'\n             \'$sequencing_type.reverse_reads\'\n-            merged-reads.fastq\n+            merged-reads\n         &&\n     #end if\n \n     sortmerna \n-        --ref $ref\n-        --aligned aligned\n+        --ref \'$ref\'\n+        --aligned \'aligned\'\n         #if str( $sequencing_type.sequencing_type_selector ) == \'paired\'\n-            --reads merged-reads.fastq\n+            --reads \'merged-reads\'\n             $sequencing_type.paired_type\n         #else\n             --reads \'$sequencing_type.reads\'\n@@ -77,7 +108,7 @@\n         $aligned_fastx.aligned_fastx_selector\n         #if $aligned_fastx.aligned_fastx_selector == \'--fastx\'\n             #if $aligned_fastx.other\n-                --other unaligned\n+                --other \'unaligned\'\n             #end if\n         #end if\n         #if $report.report_type == \'best\'\n@@ -108,25 +139,34 @@\n         --mismatch \'$mismatch\'\n         --gap_open \'$gap_open\'\n         --gap_ext \'$gap_ext\'\n-        -N $ambiguous_letter\n+        -N \'$ambiguous_letter\'\n         -a \\${GALAXY_SLOTS:-1}\n     #if $report.report_type != \'None\'\n       '..b'="reverse_reads" value="reverse_reads.fasta" />\n+                <param name="paired_type" value=""/>\n+            </conditional>\n+            <param name="strand_search" value="" />\n+            <conditional name="databases_type">\n+                <param name="databases_selector" value="history" />\n+                <param name="database_name" value="ref_small.fasta" />\n+                <param name="seed_length" value="18" />\n+                <param name="max_pos" value="100000"/>\n+            </conditional>\n+            <conditional name="aligned_fastx">\n+                <param name="aligned_fastx_selector" value="--fastx" />\n+                <param name="other" value="True" />\n+            </conditional>\n+            <param name="log" value="False" />\n+            <conditional name="report">\n+                <param name="report_type" value="best" />\n+                <param name="report_num_alignments_type" value="1"/>\n+                <param name="print_all_reads" value="False" />\n+                <conditional name="blast">\n+                    <param name="blast_output" value="False"/>\n+                </conditional>\n+                <conditional name="otu">\n+                    <param name="otu_map" value="False"/>\n+                </conditional>\n+            </conditional>\n+            <param name="e_value" value="1"/>\n+            <param name="match" value="2"/>\n+            <param name="mismatch" value="-3" />\n+            <param name="gap_open" value="5"/>\n+            <param name="gap_ext" value="2"/>\n+            <param name="ambiguous_letter" value="-3"/>\n+            <output name="aligned_paired" file="test5_aligned.fasta" />\n+            <output name="unaligned_paired" file="test5_unaligned.fasta" />\n+        </test>\n+        <test>\n+            <conditional name="sequencing_type">\n+                <param name="sequencing_type_selector" value="paired" />\n+                <param name="forward_reads" value="forward_reads.fasta" />\n+                <param name="reverse_reads" value="reverse_reads.fasta" />\n+                <param name="paired_type" value="--paired_out"/>\n+            </conditional>\n+            <param name="strand_search" value="" />\n+            <conditional name="databases_type">\n+                <param name="databases_selector" value="history" />\n+                <param name="database_name" value="ref_small.fasta" />\n+                <param name="seed_length" value="18" />\n+                <param name="max_pos" value="100000"/>\n+            </conditional>\n+            <conditional name="aligned_fastx">\n+                <param name="aligned_fastx_selector" value="--fastx" />\n+                <param name="other" value="True" />\n+            </conditional>\n+            <param name="log" value="False" />\n+            <conditional name="report">\n+                <param name="report_type" value="best" />\n+                <param name="report_num_alignments_type" value="1"/>\n+                <param name="print_all_reads" value="False" />\n+                <conditional name="blast">\n+                    <param name="blast_output" value="False"/>\n+                </conditional>\n+                <conditional name="otu">\n+                    <param name="otu_map" value="False"/>\n+                </conditional>\n+            </conditional>\n+            <param name="e_value" value="1"/>\n+            <param name="match" value="2"/>\n+            <param name="mismatch" value="-3" />\n+            <param name="gap_open" value="5"/>\n+            <param name="gap_ext" value="2"/>\n+            <param name="ambiguous_letter" value="-3"/>\n+            <output name="aligned_forward" file="test6_aligned_forward.fasta" />\n+            <output name="aligned_reverse" file="test6_aligned_reverse.fasta" />\n+            <output name="unaligned_forward" file="test6_unaligned_forward.fasta" />\n+            <output name="unaligned_reverse" file="test6_unaligned_reverse.fasta" />\n+        </test>\n     </tests>\n     <help>\n <![CDATA[\n'
b
diff -r 65c38d020fea -r eb35257d2e29 test-data/forward_reads.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/forward_reads.fasta Wed Mar 20 03:03:08 2019 -0400
b
b'@@ -0,0 +1,2000 @@\n+>ERR1877483.1 M03099:23:000000000-APTLR:1:1101:19252:1849/1\n+CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCCATTCCCCGTGTGTGCTGCTTGCCTTCGGTTTGTATATCACTTTCTTTTTTGACGACTCTCTTTTTTTTATTACCTTTCTTTTTTTACTTTACCTACATTTTCTGCTCCGTCTTTCTTCTTTCCTTCTTCCTCTCTCATCCGTATGTTGCAACCTTTTTTCTTTTTTCCTTTTCTTTTATCTCTCTTTTTTGTTTCTTCACGTTTTCTTTTACCTCCCCTTTCTCTTCCTGTTAACTTCCTCCTAT\n+>ERR1877483.2 M03099:23:000000000-APTLR:1:1101:15851:1971/1\n+CCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGTGTTTTGGTTAATAACCGCAGCAATTTACGTTACCCGCAGAAGATGCACCGGCTACCTCCGTGCCAGCAGCCGCGTTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGTGCGTAACGCGCTCGCAGTCGTTCTGTCAAGTCGGTTGTTAAATCCCCGGGCTCAACCTGGGAACTGCATTCTAA\n+>ERR1877483.3 M03099:23:000000000-APTLR:1:1101:23102:1978/1\n+CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGCAAGCCTGATCCAGCCATGCCGCGTGTGTGATGAAGGCCCTAGGGTTGTAAAGCTCTTTCCCCGGATAAGATAATGACGTTATCCGTAGAAGAAGCCCCTGCTAACTTCGTGCCAGCATCCGCGGTAATACGACTGGCGCTAGCGTTGTTCGGTATTACTGGTCGTAAAGCTCACGTAGGCTGATCGATCAGTCATGGGTGCAATCCCATGTCTCACCCCTGGCTCTGCCTTTCATACTTTCCCTCTGGATTATGTCAGAG\n+>ERR1877483.4 M03099:23:000000000-APTLR:1:1101:22637:2119/1\n+CCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGGGAAACCCTGATGCAGCCATGCCGCGTGTGTGAAGAAGGCCTTCGGGTTGTAAAGCACTTTCAGTTGTGAGGAAAAGTTAGTAGTTAATACCTGCTAGCCGTGACGTTAACAACAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCGAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGCTAGATGTGAAAGCCCTGGGCTCAACCTGGGATGGTCATTTAGA\n+>ERR1877483.5 M03099:23:000000000-APTLR:1:1101:18265:2244/1\n+CCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGTGTTGTGGTTAATAACCGCAGCAATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTCTGTCAAGTCGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCGAA\n+>ERR1877483.6 M03099:23:000000000-APTLR:1:1101:12491:2265/1\n+CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGCAAGCCTGATCCAGCCATACCGCGTGGGTGAAGAAGGCCTTCGGGTTGTAAAGCCCTTTTGTTGGGAAAGAAATCCAGCCGGCTAATACCTGGTTGGGATGACGGTACCCAAAGAATAAGCACCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGGTGCAAGCGTTACTCGGAATTACTGGGCGTAAAGCGTGCGTAGGTGGTTGTTTAAGTCTGTTGTGAAAGCCCTGGGCTCAACCTGGGAACTGCAGTGGAA\n+>ERR1877483.7 M03099:23:000000000-APTLR:1:1101:8123:2395/1\n+ACTACGGGAGGCAGCAGTGGGGAATTTTGGACAATGGGCGCAAGCCTGATCCAGCCATGCCGCGTGTCTGAAGAAGGCCTTCGGGTTGTAAAGGACTTTTGTTCGGGAGGAAATCCCGCTGGTTAATAACTGGCGGGGATGACAGTACCGGAAGAATAAGCACCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTGAAAGCGTTAATCGGAATTACTGGGCGTAAAGCGTGCGCAGGCGGTTTTGCAAGTCTGATGTGAAAGCCCCGGGCTCAACCTGGGAACGGCATTGGCG\n+>ERR1877483.8 M03099:23:000000000-APTLR:1:1101:19895:2425/1\n+CCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGGGAAACCCTGATGCAGCCATGCCGCGTGTGTGAAGAAGGCCTTCGGGTTGTAAAGCACTTTCAGTTGTGAGGAAAAGTTAGTAGTTAATACCTGCTAGCCGTGACGTTAACAACAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCGAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGCTAGATGTGAAAGCCCCGGGCTCAACCTGGGATGGTCATTTAGA\n+>ERR1877483.9 M03099:23:000000000-APTLR:1:1101:24195:2452/1\n+CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCCATGCCGCGTGTGTGAAGAAGGTCTTCGGATTGTAAAGCACTTTAAGTTGGGAGGAAGGGTATTAATCTAATAAGTTAGTGTTTTGACGTTACCGACAGAATAAGCACCGGCTAACTCTGTGCCAGCAACCGCGGTAATAAAGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGGGCGTAGGTGGTTTGTTAAGTTGGGTTTGAAATTTACGGGGTTAACCTGGGAACTGTATTCTAA\n+>ERR1877483.10 M03099:23:000000000-APTLR:1:1101:8960:2646/1\n+CCTACGGGAGGCAGCAGTAGGGAATCTTCCGCAATGGACGAAAGTCTGACGGAGCAACGCCGCGTGAGTGATGAAGGTTTTCGGATCGTAAAGCTCTGTTGTTAGGGAAGAAAAAGTACCGTTCGAATAGGGCGGTACCTTGACGGTACCTAACCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGAAGGGTGCAAGCGTTACTCGGAATTACTGGGCGTAAAGCGTGCGTAGGTGGTTGGTTAAGTCTGTTGTGAAAGCCCTGGGCTCAACCTGGGAACTGCCGTGGA\n+>ERR1877483.11 M03099:23:000000000-APTLR:1:1101:17700:2703/1\n+CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCAACGCCGCGTGAGGGATGACGGCCTTCGGGTTGTAAACCTCTTTCAGCAGGGACGAAGCGAGAGTGACGGTACCTGCAGAAGAAGGACCGGCCAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTCCGAGCGTTGTCCGGAATTATTGGGCGTAAAGGGCTCGTAGGCGGTTTGTCGCGTCGGGAGTGAAAACTCAGGGCTCAACCCTGAGCGTGCTTCG'..b':24361/1\n+CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCCATGCCGCGTGTGTGAAGAAGGTCTTCGGATTGTAAAGCACTTTAAGTTGGGAGGAAGGGCAGTAAGTTAATACCTTGCTGTTTTGACGTTACCAACAGAATAAGCACCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTTGGTAAGATGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCCATA\n+>ERR1877483.32948 M03099:22:000000000-APTMA:1:2119:21559:24504/1\n+CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCCATGCCGCGTGTGTGAAGAAGGTCTTCGGATTGTAAAGCACTTTAAGTTGGGAGGAAGGGCAGTAAGTTAATACCTTGCTGTTTTGACGTTACCAACAGAATAAGCACCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTCAGCAAGTTGGAGGTGAAATCCCCGGGCTCACCCTGGGAACTGCCTCCAAA\n+>ERR1877483.32949 M03099:22:000000000-APTMA:1:2119:22063:24539/1\n+ACGGGCGGTGTGTACACATCTCCGAGCCCACGAGACAGCCCACGAGACATCCTACGAGACCGCCCGCAAGAAAGCCCCCGAGACATCCCACCCTCCGGCCCTCCAAGAGAACGACCACGCGGCCCACGTGCCCCGACACCTAAGCGGGTCCTAGAAGGCGCAAGCACGACTCCCTCCGTGCTAGGGTCAGCCCTCATACGACGGAAACCCGCGATCTTCTTAATCAACGTTCGCTAGAACACCCTAGGCTGACTCCGACGAACAGACTGCAGGACCGACGCTCGACCCCGCAACCACCACG\n+>ERR1877483.32950 M03099:22:000000000-APTMA:1:2119:8336:24549/1\n+CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGCAAGCCTGATCCAGCCATACCGCGTGGGTGATGAAGGCCTTCGGGTTGTAAAGCCCTTTTGTTGGGACAGAAATCCAGCCGGCTAATCCCTGGTTGGGATGACGGTACCCAAAGAATAAGCACCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGGTGCAAGCGTTACTCGGAATTACTGGGCGTAAAGCGTGCGTAGGTGGTTGTTTAAGTCTGTTGTTAAAGCCCTGGGCTCAACCTGGGAACTGCAGGGGAA\n+>ERR1877483.32951 M03099:22:000000000-APTMA:1:2119:14312:24605/1\n+CCTACGGGAGGCAGCAGTGGGGAATTTTGGACAATGGGCGCAAGCCTGATCCAGCCATGCCGCGTGTCTGAAGAAGGCCTTCGGGTTGTAAAGGACTTTTGTTCGGGAGGAAATCCCGCTGGTTAATACCTGGCGGGGATGACAGTACCGGAAGAATAAGCACCGGCTAACTACGTGCCAGCAGCCGCGGGAATACGTAGGGTGCAGGCGTTTACCGGATTTCTTGGGCGAAAGGCGTGCGCAGGCGGTTTGGCAGTCCGATGGTGAAGGCCCCGGCCCCAACCTGGGAACGGCATTGGAG\n+>ERR1877483.32952 M03099:22:000000000-APTMA:1:2119:20365:24795/1\n+CCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGAT\n+>ERR1877483.32953 M03099:22:000000000-APTMA:1:2119:9975:24853/1\n+CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCCATGCCGCGTGTGTGAAGAAGGTCTTCGGATTGTAAAGCACTTTAAGTTGGGAGGAAGGGCAGTAAGTTAATACCTTGCTGTTTTGACGTTACCAACAGAATAAGCACCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTCAGCAAGTTGGAGGTGAAATCCCCGGGCTCAACCTGGGAACTGCCTCCAAA\n+>ERR1877483.32954 M03099:22:000000000-APTMA:1:2119:11950:24861/1\n+CCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCAATGCCGCGTGTGTGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGGTTGTGGTTAATAACCGCAGCAATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTCTGTCAAGTCGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCGAA\n+>ERR1877483.32955 M03099:22:000000000-APTMA:1:2119:9959:24862/1\n+CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCCATGCCGCGTGTGTGAAGAAGGTCTTCGGATTGTAAAGCACTTTAAGTTGGGAGGAAGGGCAGTAAGTTAATACCTTGCTGTTTTGACGTTACCAACAGAATAAGCACCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTCAGCAAGTTGGAGGTGAAATCCCCGGGCTCAACCTGGGAACTGCCTCCAAA\n+>ERR1877483.32956 M03099:22:000000000-APTMA:1:2119:14880:24914/1\n+ACGGGCGGTAAGTAGAGCCGATTCGTTGACAAGGTTGGCAAGGTCAGCACCGGTAAACCCGGGAGTACCCCTTGCTATCACTTTGAGATCTACCTCCCGGGATAGAGGTATCTTCCCCGAGTGAACAGCACGTATCTTCTCCCTTCCCTTAACATCAGGAACATCAGCAATGACCTGCCGGTCGAATCTACCAGGCCTTAAAAGAGCCGGATACAGAACATCAGGCCTGTTTGTGGCAGCTATGATTATCAAACCCTCAGTGGTTTCAAAACCGTCCATCTCAACAAGAAGCTTGTTGAGA\n+>ERR1877483.32957 M03099:22:000000000-APTMA:1:2119:17520:25205/1\n+CCTCCGGGAGGCAGCAGTGGGGAATCTTAGACAATGGGGGCAACCCTGATCTAGCCATGCCGCGTGAGTGATGAAGGCCCTAGGGTTGTAAAGCTCTTTCAGCTGGGAAGATAATGACGGTACCAGCAGAAGAAGCCCCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGGGCTCGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGTAGGCGGACCGTAAAGTTGGGGGTGAAATCCCGGGGCTCAACCCCGGAACTGCCTTCAAAACTATCGGTCTGGATTTCGAGAGAG\n'
b
diff -r 65c38d020fea -r eb35257d2e29 test-data/reverse_reads.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/reverse_reads.fasta Wed Mar 20 03:03:08 2019 -0400
b
b'@@ -0,0 +1,2000 @@\n+>ERR1877483.1 M03099:23:000000000-APTLR:1:1101:19252:1849/2\n+CACTACCCGGTTTTCTTATCCTCTTTTCTCCCCCCCCTTTCCCCCCTCCTTCTCCGTTTTTTTCCCTTTCCTCCCCTTCCCCTCTTTTTTTCCTTCCTCTTTCTTCCCCTTTCCCCTCTTCCCCCCTTTTTCCCCCCTCCTCTTCCTTTCTCCTCCTCTCCCCTTTTCTTTTTCCTTTCCTTTTTTCTCCCCCTTCTTTCCCCTCCTCCTTTCTCTCCCCCCTTCCTTCCCTTTTCTCCCCGTTCTTCCCTTCCCCCCCTTCCCCCCTCTTTTTTCCCCCCCTTCTCTCCCCCTTTTTCC\n+>ERR1877483.2 M03099:23:000000000-APTLR:1:1101:15851:1971/2\n+CACTACAAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCTCCTGAGCGTCAGTCTTTGTCCAGTGGGCCGCCTTCGCCACCGGTTTTCCTCCAGATCTCTACGCATTTCACCGCTACACCTGGTATTCTCCCCCCCTCTACACTACTCAATCCTGCCAGTTTCGAATGCAGTTCCCAGGTTTAGCCCGTGGATTTCACATCCTACTTGCCATACCGCCTGCGTGCGCTTTACTCCCCGTAATTCCGATTTACGCTTGCCCCCTCCGTATTACCTCCGCTGCTGTCCCCTTCTTAGC\n+>ERR1877483.3 M03099:23:000000000-APTLR:1:1101:23102:1978/2\n+CACTACCGGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTCAGCGTCAGTATTGGACCAGTTCGCCGCCTTCGCCACTGGTTTTCCTCCGAATATCTACGCATTTCACCTCTACACTCGTTATTCCACTCACCTCTTCCATACTCCAGTTCGCCAGTTTCATTCGCAGTTCCACGGTTCATCCCTCGGCTTTCACTCCTTACTTATCGCTCCGCCTACCTTCGCTTTACGCCCAGTACTTCCTCTCACCGCTCTCCCCCCTCCTTTTTCGCCGCCTGCTTTCCCCTCTTTATC\n+>ERR1877483.4 M03099:23:000000000-APTLR:1:1101:22637:2119/2\n+GACTACTAGGGTATCTAATCCTGTTCGCTACCCACACTTTCGCACATGAGCGTCAGTCTTTGGCCAGGGAGTCGCCTTCGCCACTGATGTTCCTCCAGATATCTACGCATTTCACCGCTACACCTGGAATTCCACTCCCCTCTCCAAGACTCTAGTCTGCCAGTTCTACATGACCATCCCAGGTTGAGCCCAGGGCTTTCACACCTAGCTTAACAAACCGCCTGCGTGCGCTTTACGCCCAGTAATTCCGATCAACGATCGTCCCCTCCGTCTTACCGCGGCTGCTGGCACGGGGTTAGC\n+>ERR1877483.5 M03099:23:000000000-APTLR:1:1101:18265:2244/2\n+GACTACAAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTGAGCGTCAGTCTTTGTCCAGGGGGCCGCCTTCGCCACCGGTATTCCTCCAGATCTCTACGCATTTCACCGCTACACCTGGAATTCTACCCCCCTCTACAAGACTCAAGCCTGCCAGTTTCGAATGCAGTTCCCAGGTTGAGCCCGGGGATTTCACATCCGACTTGACAGACCGCCTGCGTGCGCTTTACGCCCAGTAATTCCGATTAACGATTGCACCCCCCGTATTACCGCGGCTGCTGGCACGGAGTTAGC\n+>ERR1877483.6 M03099:23:000000000-APTLR:1:1101:12491:2265/2\n+GACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGTGCCTCAGTGTCAGTGTTGGTCCAGGTAGCTGCCTTCGCCATGGATGTTCCTCCCGATCTCTACGCATTTCACTGCTACACCGGGAATTCCGCTACCCTCTACCACACTCTAGTTGTCCAGTTTCCACTGCAGTTCCCAGGTTGAGCCCAGGGCTTTCACAACAGACTTAAACAACCACCCACGCACGCCTTACGCCCAGTAAATCCGAGTACCGCTTGCACCCCTGCAACTTCCGCGGCCGCTGGCCCGAAGGAACC\n+>ERR1877483.7 M03099:23:000000000-APTLR:1:1101:8123:2395/2\n+GACTACACGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGTGCATGAGCGTCAGTGTCATCCCAGGGGGCTGCCTTCGCCATCGGTATTCCTCCGCATCTCTACGCATTTCACTGCTACACGCGGAATTCTACCCCACTCTGACGCACTCTAGTCTTGCCGTCTCCACTGCCGTTCCCAGGTTGAGCCCGGGGCTTTCCCATCAGCCTTGCACACACGCCTGCGCAAGCATCACGCCCAGTAATTCCGACTAACGCTTGCACCCTACGTATTTCATCCGCTGCTGGCCCGGCTTTAGCA\n+>ERR1877483.8 M03099:23:000000000-APTLR:1:1101:19895:2425/2\n+GACTACTCGGGTATCTAATCCTGTTCGCTACCCACACTTTCGCACATGAGCGTCAGTCTTTGGCCAGGGAGTCGCCTTCGCCACTGATGTTCCTCCAGATATCTACGCATTTCACCGCTACACCTGGAATTCCACTCCCCTCTCCAAGACTCTAGTCTGCCAGTTCTAAATGACCATCCCAGGTTGAGCCCGGGGCTTTCACATCTAGCTTAACAAACCGCCTGCGTGCGCTTTACGCCCAGTAATTCCGATTAACGCTCGCACCCTCCGTGTTACCGCGGCTGCGGGCCCGGAGAGAGC\n+>ERR1877483.9 M03099:23:000000000-APTLR:1:1101:24195:2452/2\n+GACTACTGGGGTATCCAATCCTGTTTGCTCCCCACGCTTTCGCACCTCAGTGTCAGTATTAGTCCAGGTGGTCGCCTTCGCCACTGGTGTTCCTTCCTATATCTACGCATTTCACCGCTACACAGGAAATTCCACTATCCTCTACCATACTCTAGTCAGTCAGTTTTGAATGAAGTTACCAGGTTGAGCCCGGGAATTTCACATCTAACTTAACAAACCACCTACGCGCGCTTTACGCCCAGTAATTCCGAATAACGCTTGCCCTCTACGTATTACCGCGGCTGCTGGCACAGAGTTAGC\n+>ERR1877483.10 M03099:23:000000000-APTLR:1:1101:8960:2646/2\n+GACTACCAGGGTATCTAATCCTGTTTGCTCCCCAAGCTTTCGTGCCTCAGTGTCAGTGTTGGTCCAGGTAGCTGCCTTCGCCATGGATGTTCCTCCCGATCACTACGCAATTCACTGCTACAACGGGAATTCCGCTACCCTCTACCACCCTCTAGTTGTCCAGTTTTCACTGCAGTTCCCAGGTTGAGCCCAGGGCTTTCAAAACAGACTTAAACAACCACCTACGCACGCATTACGCTCAGCACATCCGAGTAACGCTTGCACACCTCGTCTTACACGCGCTGCTGCCCCGGAGGTACC\n+>ERR1877483.11 M03099:23:000000000-APTLR:1:1101:17700:2703/2\n+GACTACAAGGGTATCTAATCCTGTTCGCTCCCCATGCTTTCGCTCCTCAGCGTCAGGTAATTCCCAGAGAACCGCCTTCGCCACCAGTGTTCCTCCTGATATCTGCGCATTCCACCGCTACACCAGGAATTCCGTTCTCCCCTGAATACCTCTAGTCTGCCCGTATCGGAAGCACGCTCAGGGTTGAGCCCTGAGTTTTCACTCCCGACGCGACAAACCGCCTACGAGCCCTTTACGTCCAATAATTCGGGACAACGCTCGGACCCTACGTATTACAGCGGCGCCTA'..b'1:2119:7531:24361/2\n+GACTACTAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTCAGTGTCAGTATCAGTCCAGGTGGTCGCCTTCGCCACTGGTGTTCCTTCCTATATCTACGCATTTCACCGCTACACAGGAAATTCCACCACCCTCTACCGTACTCTAGTCAGGCAGTTATGGATGCAATTCCCCGGTTTAGCCCGGGGATTTCACTCCCCTCTTACCCAACCACCTACGCGCCCTTTACGCCCAGTACTTCCGATTACCGCTTGCCCCCTTCGTATTACCGCGACTGCTGGCACGAAGTTAGC\n+>ERR1877483.32948 M03099:22:000000000-APTMA:1:2119:21559:24504/2\n+GACTACCGGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTCAGTGTCAGTATTAGTCCAGGTGGTCGCCTTCGCCACTGGTGTTCCTTCCTATATCTACGCATTTCACCGCTACACAGGAATTTCCACCACCCTCTACCATACTCTAGCCCAGTAGTTTTGGAGGCAGTTCCCAGGTTGAGCCCGGGGATTTCACCTCCAACTTGCTGAACCCCCTACGCGCGCTATACGCCCAGTAATTCCGATTAACGCTTGCACCCTGCGTATTACCGCGGCTGCTGGCACGCAGTTAGC\n+>ERR1877483.32949 M03099:22:000000000-APTMA:1:2119:22063:24539/2\n+CGCTACTGGCGTACCTAATCCCGTTCCCTACCCTCCCCTGCGTACCTACCCGCGATTAAGTGTGCTGCAGGCTTCATTCACCATAGGTCTTGCCCTCAATCCCAACGAATTTCACTGCTACAGCCATAGTTTAACCTGGCTCTCCATACCCCATGTCTACCATTCATTGCAGCCTTTGTCTATCTGCACTCTTGAATTGCAACATTAATTCACCTCATCCCCACCTTACTCTTTGTTCTCTACGTCAGTACCCACATCTGTCACCACTCGCTATGTACCACGCTCTCTCACCACTTCAGG\n+>ERR1877483.32950 M03099:22:000000000-APTMA:1:2119:8336:24549/2\n+GACTACCGGGGTATCTAATGCTGTTTGCTCCCCACGCTTTCGTGCCTCAGTGTCAGTGTTGGTCCAGGTAGCTGCCTTCGCCATGGATGTTCCTCCCGATCTCTACGCATTTCACTGCTACACCGGGAATTCCGCTACCCTCTACCACACTCTAGTTGTCCAGTTTCCACTGCAGTTCCCAGGTTGAGCCCAGGGCTTTCACAACAGACTTAAACAACCACCTCCGCACGCTTTAAGCACAGTCATTCCGAGTAACGCTTGCACCCTTCGTATTACCGCGGCTGCTGGCACGAAGTTACC\n+>ERR1877483.32951 M03099:22:000000000-APTMA:1:2119:14312:24605/2\n+GACTACCGGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGTGCATGAGCGTCAGTGTCATCCCAGGGGGCTGCCTTCGCCATCGGTATTCCTCCGCATCTCTACGCATTTCACTGCTACACGCGGAATTCTACCCCCCTCTGACGCACTCTAGTCTTGCAGTCTCCAATGCCGTTCCCAGGTTGAGCCCGGGGCTTTCCCATCAGACTTGCCAAACCGCCTGCGCACGCTTTACGCCCAGTAATTCCGATTAACGCTTGCACCCACCGATTCCTCCGGCCTCCTGGCACGGCGTTTCC\n+>ERR1877483.32952 M03099:22:000000000-APTMA:1:2119:20365:24795/2\n+GACTACAAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTGAGCGTCAGTCTTCGTCCAGGGGGCCGCCTTCGCCACCGGTATTCCTCCAGATCTCTACGCATTTCACCGCTACACCTGGAATTCTACCCCCCTCTACGAGACTCAAGCTTGCCAGTATCAGATGCAGTTCCCAGGTTGAGCCCGGGGATTTCACATCTGACTTAACAAACCGCCTGCGTGCGCTTTACGCCCAGTCATTCCGATTAACGCTTGCACCCTCCGTATTACCGCGGCTGCTGGCACGGAGTTAG\n+>ERR1877483.32953 M03099:22:000000000-APTMA:1:2119:9975:24853/2\n+GACTACAGGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGTGCATGAGCGTCAGTGTCATCCCAGGGGGCTGCCTTCGCCACTGGTGTTCCTTCCTATATCTACGCATTTCACCGCTACACAGGAAATTCCACCACCCTCTACCATACTCTAGCCCAGTAGTTTTGGAGGCAGTTCCCAGGTTGCGCCCGGGGATTTCTCCTCCAACTTCCTGACCCACCTACGCGCGCTTTACGCCCCGTAATTCCGATTACCGCTGTCACCCTTCGTATCACCGCGGCTGCTGCTACGACGTTAGC\n+>ERR1877483.32954 M03099:22:000000000-APTMA:1:2119:11950:24861/2\n+GGCTACTAGGGGTACTAATTCTCGTTTGTCCCCACGGTTTCGCACCTTCACGGTAGTCTTTATTCCGGCGACTCCCCTCGCCACCTGTAGTCCTCCAGGACTCTACGCAATTCACCGCCTCACCTGGAAATCTACCCCCCCCTTCCAGCATTCTACCTGCCCAGTTCCAATTCAGTTTCCCGGTTTAACCCCGGGGCTTCCACATCGACTTTACAGACCGCCCTCCTAGGCCTTACGCCCATTACATCCGATTAACGCCTTCACCCTCCGTATTCCCGCCTGCTCTGGCACCGTCTTAGG\n+>ERR1877483.32955 M03099:22:000000000-APTMA:1:2119:9959:24862/2\n+GACTACAGGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGTGCATGAGCGTCAGTGTCATCCCAGGGGGCTGCCTTCGCCACTGGTGTTCCTTCCTATATCTACGCATTTCACCGCTACACAGGAAATTCCACCACCCTCTACCATACTCTAGCCCAGTAGTTTTGGAGGCAGTTCCCAGGTTGAGCCCGGGGATTTCACCTCCAACTTGCTGAACCACCTACGCGCGCCTTACGACCAGTAATTCCGATTAACGCTTGCACCCTTCGTATTACCGCGGCAGCTGCTACTCTGTTAGC\n+>ERR1877483.32956 M03099:22:000000000-APTMA:1:2119:14880:24914/2\n+GCGACGGGTACGAGAGAGATCAGTGGGAATAGAAATGAAAGGAGGCGGAAGTAAGAACACAAACGAGTCGGTGTAATCTAAATGGAGAGGAGGACTAAGGTGCTGAATACGGCTGGAGCTAGGGGGGTGGCACATGGTCGATACTGACTGATCAACTGTGATGTCGCTCTTAGTAGTGGTGGAACAGGACTGGATATGGCTATTAGGACTGGGTATCATAAACATGCTACTATGGGTAACTTACTACGACAACACTTGGAGGCTAACATCACTATGTAACTATCGAAAGTGAGATTACGAT\n+>ERR1877483.32957 M03099:22:000000000-APTMA:1:2119:17520:25205/2\n+GACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTCAGCGTCAGTATCGAGCCAGTGAGCCGCCTTCGCCACTGGTGTTCCTCCGAATATCTACGAATCTCACCTCTACACTCGGACTTCCACTCACCTCTCTCGAACTCCCGACCGATAGTTTTGACGGCAGTTCCGGGGTTGAGCCCCGGGATTTCACCCCCAACTTTACGGTCCGCCTACGTGCGCTTTACGCCCGGTCCTTCCGATCACCGCTATCCCCCTCCGTACTACCGTGTCTGCTGGCCCGTACGTCGC\n'
b
diff -r 65c38d020fea -r eb35257d2e29 test-data/test5_aligned.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test5_aligned.fasta Wed Mar 20 03:03:08 2019 -0400
b
b'@@ -0,0 +1,3732 @@\n+>ERR1877483.1 M03099:23:000000000-APTLR:1:1101:19252:1849/1\n+CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCCATTCCCCGTGTGTGCTGCTTGCCTTCGGTTTGTATATCACTTTCTTTTTTGACGACTCTCTTTTTTTTATTACCTTTCTTTTTTTACTTTACCTACATTTTCTGCTCCGTCTTTCTTCTTTCCTTCTTCCTCTCTCATCCGTATGTTGCAACCTTTTTTCTTTTTTCCTTTTCTTTTATCTCTCTTTTTTGTTTCTTCACGTTTTCTTTTACCTCCCCTTTCTCTTCCTGTTAACTTCCTCCTAT\n+>ERR1877483.2 M03099:23:000000000-APTLR:1:1101:15851:1971/1\n+CCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGTGTTTTGGTTAATAACCGCAGCAATTTACGTTACCCGCAGAAGATGCACCGGCTACCTCCGTGCCAGCAGCCGCGTTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGTGCGTAACGCGCTCGCAGTCGTTCTGTCAAGTCGGTTGTTAAATCCCCGGGCTCAACCTGGGAACTGCATTCTAA\n+>ERR1877483.2 M03099:23:000000000-APTLR:1:1101:15851:1971/2\n+CACTACAAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCTCCTGAGCGTCAGTCTTTGTCCAGTGGGCCGCCTTCGCCACCGGTTTTCCTCCAGATCTCTACGCATTTCACCGCTACACCTGGTATTCTCCCCCCCTCTACACTACTCAATCCTGCCAGTTTCGAATGCAGTTCCCAGGTTTAGCCCGTGGATTTCACATCCTACTTGCCATACCGCCTGCGTGCGCTTTACTCCCCGTAATTCCGATTTACGCTTGCCCCCTCCGTATTACCTCCGCTGCTGTCCCCTTCTTAGC\n+>ERR1877483.3 M03099:23:000000000-APTLR:1:1101:23102:1978/1\n+CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGCAAGCCTGATCCAGCCATGCCGCGTGTGTGATGAAGGCCCTAGGGTTGTAAAGCTCTTTCCCCGGATAAGATAATGACGTTATCCGTAGAAGAAGCCCCTGCTAACTTCGTGCCAGCATCCGCGGTAATACGACTGGCGCTAGCGTTGTTCGGTATTACTGGTCGTAAAGCTCACGTAGGCTGATCGATCAGTCATGGGTGCAATCCCATGTCTCACCCCTGGCTCTGCCTTTCATACTTTCCCTCTGGATTATGTCAGAG\n+>ERR1877483.4 M03099:23:000000000-APTLR:1:1101:22637:2119/1\n+CCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGGGAAACCCTGATGCAGCCATGCCGCGTGTGTGAAGAAGGCCTTCGGGTTGTAAAGCACTTTCAGTTGTGAGGAAAAGTTAGTAGTTAATACCTGCTAGCCGTGACGTTAACAACAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCGAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGCTAGATGTGAAAGCCCTGGGCTCAACCTGGGATGGTCATTTAGA\n+>ERR1877483.3 M03099:23:000000000-APTLR:1:1101:23102:1978/2\n+CACTACCGGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTCAGCGTCAGTATTGGACCAGTTCGCCGCCTTCGCCACTGGTTTTCCTCCGAATATCTACGCATTTCACCTCTACACTCGTTATTCCACTCACCTCTTCCATACTCCAGTTCGCCAGTTTCATTCGCAGTTCCACGGTTCATCCCTCGGCTTTCACTCCTTACTTATCGCTCCGCCTACCTTCGCTTTACGCCCAGTACTTCCTCTCACCGCTCTCCCCCCTCCTTTTTCGCCGCCTGCTTTCCCCTCTTTATC\n+>ERR1877483.4 M03099:23:000000000-APTLR:1:1101:22637:2119/2\n+GACTACTAGGGTATCTAATCCTGTTCGCTACCCACACTTTCGCACATGAGCGTCAGTCTTTGGCCAGGGAGTCGCCTTCGCCACTGATGTTCCTCCAGATATCTACGCATTTCACCGCTACACCTGGAATTCCACTCCCCTCTCCAAGACTCTAGTCTGCCAGTTCTACATGACCATCCCAGGTTGAGCCCAGGGCTTTCACACCTAGCTTAACAAACCGCCTGCGTGCGCTTTACGCCCAGTAATTCCGATCAACGATCGTCCCCTCCGTCTTACCGCGGCTGCTGGCACGGGGTTAGC\n+>ERR1877483.5 M03099:23:000000000-APTLR:1:1101:18265:2244/1\n+CCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGTGTTGTGGTTAATAACCGCAGCAATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTCTGTCAAGTCGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCGAA\n+>ERR1877483.6 M03099:23:000000000-APTLR:1:1101:12491:2265/1\n+CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGCAAGCCTGATCCAGCCATACCGCGTGGGTGAAGAAGGCCTTCGGGTTGTAAAGCCCTTTTGTTGGGAAAGAAATCCAGCCGGCTAATACCTGGTTGGGATGACGGTACCCAAAGAATAAGCACCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGGTGCAAGCGTTACTCGGAATTACTGGGCGTAAAGCGTGCGTAGGTGGTTGTTTAAGTCTGTTGTGAAAGCCCTGGGCTCAACCTGGGAACTGCAGTGGAA\n+>ERR1877483.5 M03099:23:000000000-APTLR:1:1101:18265:2244/2\n+GACTACAAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTGAGCGTCAGTCTTTGTCCAGGGGGCCGCCTTCGCCACCGGTATTCCTCCAGATCTCTACGCATTTCACCGCTACACCTGGAATTCTACCCCCCTCTACAAGACTCAAGCCTGCCAGTTTCGAATGCAGTTCCCAGGTTGAGCCCGGGGATTTCACATCCGACTTGACAGACCGCCTGCGTGCGCTTTACGCCCAGTAATTCCGATTAACGATTGCACCCCCCGTATTACCGCGGCTGCTGGCACGGAGTTAGC\n+>ERR1877483.6 M03099:23:000000000-APTLR:1:1101:12491:2265/2\n+GACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGTGCCTCAGTGTCAGTGTTGGTCCAGGTAGCTGCCTTCGCCATGGATGTTCCTCCCGATCTCTACGCATTTCACTGCTACACCGGGAATTCCGCTACCCTCTACCACACTCTAGTTGTCCAGTTTCCACTGCAGTTCCCAGGTTGAGCCCAGGGCTTTCACAACAGACTTAAACAACCACCCACGCACGCCTTACGCCCAGTAAATCCGAGTACCGCTTGCACCCCTGCAACTTCCGCGGC'..b'119:8336:24549/2\n+GACTACCGGGGTATCTAATGCTGTTTGCTCCCCACGCTTTCGTGCCTCAGTGTCAGTGTTGGTCCAGGTAGCTGCCTTCGCCATGGATGTTCCTCCCGATCTCTACGCATTTCACTGCTACACCGGGAATTCCGCTACCCTCTACCACACTCTAGTTGTCCAGTTTCCACTGCAGTTCCCAGGTTGAGCCCAGGGCTTTCACAACAGACTTAAACAACCACCTCCGCACGCTTTAAGCACAGTCATTCCGAGTAACGCTTGCACCCTTCGTATTACCGCGGCTGCTGGCACGAAGTTACC\n+>ERR1877483.32951 M03099:22:000000000-APTMA:1:2119:14312:24605/2\n+GACTACCGGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGTGCATGAGCGTCAGTGTCATCCCAGGGGGCTGCCTTCGCCATCGGTATTCCTCCGCATCTCTACGCATTTCACTGCTACACGCGGAATTCTACCCCCCTCTGACGCACTCTAGTCTTGCAGTCTCCAATGCCGTTCCCAGGTTGAGCCCGGGGCTTTCCCATCAGACTTGCCAAACCGCCTGCGCACGCTTTACGCCCAGTAATTCCGATTAACGCTTGCACCCACCGATTCCTCCGGCCTCCTGGCACGGCGTTTCC\n+>ERR1877483.32952 M03099:22:000000000-APTMA:1:2119:20365:24795/1\n+CCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGAT\n+>ERR1877483.32953 M03099:22:000000000-APTMA:1:2119:9975:24853/1\n+CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCCATGCCGCGTGTGTGAAGAAGGTCTTCGGATTGTAAAGCACTTTAAGTTGGGAGGAAGGGCAGTAAGTTAATACCTTGCTGTTTTGACGTTACCAACAGAATAAGCACCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTCAGCAAGTTGGAGGTGAAATCCCCGGGCTCAACCTGGGAACTGCCTCCAAA\n+>ERR1877483.32952 M03099:22:000000000-APTMA:1:2119:20365:24795/2\n+GACTACAAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTGAGCGTCAGTCTTCGTCCAGGGGGCCGCCTTCGCCACCGGTATTCCTCCAGATCTCTACGCATTTCACCGCTACACCTGGAATTCTACCCCCCTCTACGAGACTCAAGCTTGCCAGTATCAGATGCAGTTCCCAGGTTGAGCCCGGGGATTTCACATCTGACTTAACAAACCGCCTGCGTGCGCTTTACGCCCAGTCATTCCGATTAACGCTTGCACCCTCCGTATTACCGCGGCTGCTGGCACGGAGTTAG\n+>ERR1877483.32953 M03099:22:000000000-APTMA:1:2119:9975:24853/2\n+GACTACAGGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGTGCATGAGCGTCAGTGTCATCCCAGGGGGCTGCCTTCGCCACTGGTGTTCCTTCCTATATCTACGCATTTCACCGCTACACAGGAAATTCCACCACCCTCTACCATACTCTAGCCCAGTAGTTTTGGAGGCAGTTCCCAGGTTGCGCCCGGGGATTTCTCCTCCAACTTCCTGACCCACCTACGCGCGCTTTACGCCCCGTAATTCCGATTACCGCTGTCACCCTTCGTATCACCGCGGCTGCTGCTACGACGTTAGC\n+>ERR1877483.32954 M03099:22:000000000-APTMA:1:2119:11950:24861/1\n+CCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCAATGCCGCGTGTGTGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGGTTGTGGTTAATAACCGCAGCAATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTCTGTCAAGTCGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCGAA\n+>ERR1877483.32955 M03099:22:000000000-APTMA:1:2119:9959:24862/1\n+CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCCATGCCGCGTGTGTGAAGAAGGTCTTCGGATTGTAAAGCACTTTAAGTTGGGAGGAAGGGCAGTAAGTTAATACCTTGCTGTTTTGACGTTACCAACAGAATAAGCACCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTCAGCAAGTTGGAGGTGAAATCCCCGGGCTCAACCTGGGAACTGCCTCCAAA\n+>ERR1877483.32955 M03099:22:000000000-APTMA:1:2119:9959:24862/2\n+GACTACAGGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGTGCATGAGCGTCAGTGTCATCCCAGGGGGCTGCCTTCGCCACTGGTGTTCCTTCCTATATCTACGCATTTCACCGCTACACAGGAAATTCCACCACCCTCTACCATACTCTAGCCCAGTAGTTTTGGAGGCAGTTCCCAGGTTGAGCCCGGGGATTTCACCTCCAACTTGCTGAACCACCTACGCGCGCCTTACGACCAGTAATTCCGATTAACGCTTGCACCCTTCGTATTACCGCGGCAGCTGCTACTCTGTTAGC\n+>ERR1877483.32957 M03099:22:000000000-APTMA:1:2119:17520:25205/1\n+CCTCCGGGAGGCAGCAGTGGGGAATCTTAGACAATGGGGGCAACCCTGATCTAGCCATGCCGCGTGAGTGATGAAGGCCCTAGGGTTGTAAAGCTCTTTCAGCTGGGAAGATAATGACGGTACCAGCAGAAGAAGCCCCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGGGCTCGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGTAGGCGGACCGTAAAGTTGGGGGTGAAATCCCGGGGCTCAACCCCGGAACTGCCTTCAAAACTATCGGTCTGGATTTCGAGAGAG\n+>ERR1877483.32957 M03099:22:000000000-APTMA:1:2119:17520:25205/2\n+GACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTCAGCGTCAGTATCGAGCCAGTGAGCCGCCTTCGCCACTGGTGTTCCTCCGAATATCTACGAATCTCACCTCTACACTCGGACTTCCACTCACCTCTCTCGAACTCCCGACCGATAGTTTTGACGGCAGTTCCGGGGTTGAGCCCCGGGATTTCACCCCCAACTTTACGGTCCGCCTACGTGCGCTTTACGCCCGGTCCTTCCGATCACCGCTATCCCCCTCCGTACTACCGTGTCTGCTGGCCCGTACGTCGC\n'
b
diff -r 65c38d020fea -r eb35257d2e29 test-data/test5_unaligned.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test5_unaligned.fasta Wed Mar 20 03:03:08 2019 -0400
b
b'@@ -0,0 +1,268 @@\n+>ERR1877483.1 M03099:23:000000000-APTLR:1:1101:19252:1849/2\n+CACTACCCGGTTTTCTTATCCTCTTTTCTCCCCCCCCTTTCCCCCCTCCTTCTCCGTTTTTTTCCCTTTCCTCCCCTTCCCCTCTTTTTTTCCTTCCTCTTTCTTCCCCTTTCCCCTCTTCCCCCCTTTTTCCCCCCTCCTCTTCCTTTCTCCTCCTCTCCCCTTTTCTTTTTCCTTTCCTTTTTTCTCCCCCTTCTTTCCCCTCCTCCTTTCTCTCCCCCCTTCCTTCCCTTTTCTCCCCGTTCTTCCCTTCCCCCCCTTCCCCCCTCTTTTTTCCCCCCCTTCTCTCCCCCTTTTTCC\n+>ERR1877483.46 M03099:23:000000000-APTLR:1:1101:21301:4734/2\n+GATACACGGGGATCTCTAACCGTTTGCGCCCCACGCGTTCGCTCCTCACCGCCAGATACAGGCCAGAGAAACGCCTTCGCCACAGGGGTTCCCCCACAGCTATACACATATCACCCCGACACGCCGGATTCCACACTCCACTCCTGCACTCACGATCCCCCGATTCCAATGAGCATTCCCGTGTGAGCCGGGAGCGTATACACAAACCATAGACACACCCCGCCACGCCCTCTGTGCCCCAAAGAACTGTAAAAGACGTTCCACCCCCGAGTAAACCCGCGTCTTCTAGCGCGGGGGTCGG\n+>ERR1877483.70 M03099:23:000000000-APTLR:1:1101:20716:6121/1\n+ACTACGGGAGGCAGCAGCGGGGAATCTTGGACAATGGGCGAAAGCCTGATCCAGCCAACCCGCGTGTGTGAAGAAGGCCTTCGGTTTGTAAACCACTTTAAGGTGGGAGGAAGGGCAGTAAGTTAATACCTTGATGGTTTGACGCTACCAACAGAATAAGCACCGGCGAACTTCGTGGCAGCAGCCGCGGGAAAACGGAGGGTGCCAGGGTTAATCGGAAGTAATGGGCGTAAAGCGCGAGTTGGGGGGTCAGCAAGTTGGAGGTGAAAGCCCCGGGCGCAGACGGGGAACAGCCGCCAAA\n+>ERR1877483.76 M03099:23:000000000-APTLR:1:1101:25401:6445/2\n+GCGCAGGGGGCTCACCGGGTTGCAGAAGAGAGACCGCACTACCAGGTAATATACTACTCGTTTGTCCCCCCGACTTTGTCACTCCACATCCACCCTACTCCCCCCCGCCCCCCTTGCCCCCCGCGCCCCCCCCCCCCCTTACGACTTGTCCCCCCCCAACCCGCCCTTTTCCTGCCCCTTCCCTCCCCCACCCTACCACACGCGCGCACACTGTCCTCCCCTGCCCTCCCCGCTTTCCGTACTACGTGTACTCCCACACCTCTCCCCTCTTCATCCCTCATTGACGCTATATTCCTCCCC\n+>ERR1877483.95 M03099:23:000000000-APTLR:1:1101:10309:7883/2\n+GACTACATGGGTTTTTAAATCCGGTTCCCTCCCCACGCTTTCCTCCTTAGCCGTCAGAATTAACCCATGAGCCTCCTTCCCCTTTTGTTGTTCCCCTACTTTCCAACAGTTTCTCCTCTTACATGCAAATTTCCGCCAACCCTTCCTTATCTCTAGTTTAACTGATCAAAGTACATTACTAGGGTTGCGCCGTAGCTTTCACCATTTGACTTTTTATCCACCCACCTGCCGCTTTACTCCCATATATCCCATCACCCTCTTCCCCCCTCCTCTTTCCACCGGCTGCGGCCACACACTTAT\n+>ERR1877483.107 M03099:23:000000000-APTLR:1:1101:20082:8248/2\n+GACTACTGGGGTATCTAATCCTGTTCGCTACCCAAACTTTCCCACATTATCGTCCGCTTATGGCCAGGGCGTCGCCTTCGCCACTGATTTTCCTCCACGTATCTACCCATTTCACCTCTCCCCCTGGCAATCCCCCCCCCTCTCCACGCCTCCAGTCTGCCTTTTCTAAATTACCATTCCCGGTTCCCCCCGGGGCCTTCACCTCTCGCTTAACCAACCTCCCCCACGTGCTTTTCCTCCCATACTTCCGCTTAACCCTCCTCCCCCCCGTCATACCCCGGCCTCGCGCCCCGCCTTGTC\n+>ERR1877483.116 M03099:23:000000000-APTLR:1:1101:28087:8411/2\n+GACCACAAGGGTATCCAAATCCTTTCGGCTCCCACCCCTTTGGCCCCCAACCTCAGTTACAGATCAGGCGGTCCGCCTCCCCACCTGTGTTCCCCCCCGACACTTCCCATTTCACCCCCACACCCGGGACTCCCCCCTCCTCCTCCGCACCTCACGCCCCCAGTTTTCAATTACACTCCCCGGTTTGCCCCCGGGCCTTTCCCTCCCACTTTACAACACGCCCTCCAGCCCCTTTACCCCAACTATTCCCGCCACCCGTTCGCACCCACCGTGTTCCTCGTACTCTGCGCCGTAGTTAGC\n+>ERR1877483.127 M03099:23:000000000-APTLR:1:1101:12005:9181/2\n+GCCTACTGGGGTATCTTATACACATCTGACGTTGCCGACGACTTAATAGGTGTAGGATTCCGAGGGAGCCGAACTACTAAAATTAGGATTGAAGACTCAGATCCGAACTGAGACCTACTTTGTAGATTTGCATCCTGTCACCAGGTAGCTGCCCTCTGTATCGGCCCTTGTAGCACGTTTGTAGCCCTTGACGTACGGGCCCTTCTGAGTTTACGTCCTCCCTGCCTTCCTCACTTCTTTCGTCGGCAGTCCCTTTAGAGTCCCCAGCTTAACCTGCTGTCAACTACAGGCAAGCGTTTC\n+>ERR1877483.149 M03099:23:000000000-APTLR:1:1101:6596:10202/1\n+ACTACGGGAGGCAGCAGCTAGGAATCTTCCGCAATGGGCGCAAGCCTGACGGAGCGACGCCGACTGGAGGAAGAAGACCTTCGGGGTGTAAACTCCTGAACCCGGGACGAAACCACCGAGGCGGGGACGGACGGTACCGGGGCAATCGCGCCGGCCAACGCCGAGCCAGCAGGCGCGGTTATACGGAGGGCGCGAGCGTCACCCGGATTAACTGGGTGTAAAGGGCGCGAAGGCGTCCTGGGCCGTACCACGTGGAAGACCACGGGTCAACCGTGGAGGAGCGGGGGATAAGCTCAGGCAA\n+>ERR1877483.167 M03099:23:000000000-APTLR:1:1101:22979:11600/2\n+GACCACTAGGGTTTCTAATCCCGTTTGCTCCCCACCCTTTCCCGTCTTAGTCTCAATTCCGTCCCCGCGAGCCGCCCTCGCCATCGGTTGTCCCCCTCGTTTCTGCGCATTTCCCCCCTTCACCCGGAATTCCCCCCTCCCCTTCCGGCCTCCAGCCAGACCGTTTCCACCGGCATTTCATGGTTGGGGCCCGGGCTTTCCACACGGACCTAGCGAGCCCCCCCAACGCCGCTTAACCCCCATTCATCCCGACCAACGCTTCCCCCCACCTATGTCCCCCGCCTCCTGCCCGCACTTTAC\n+>ERR1877483.183 M03099:23:000000000-APTLR:1:1101:27013:12199/2\n+GACTACAGGGTATCTATTACTGTTTGCGCCCCACACGTTCGCAACTGAGCGTCAGTCTTTGTGCAGGGGGCCGCCCTCTCCACCGGTATGCCCCCCGCTCTCTACGCATTTCACCCCTACACCCGGAATTCTACCCCCCTCTACCAGACTCAATCCTGCCCGTTTCGCAGGCAGTTCCCAGGTTTTGGCCGCTGACTTTTCATCCCCGTTTACCTACCCCCCCCGCGCGCGCTACGCCCCGCAATTCCCATCACCGCTTGTGCCCCCC'..b'9:13774:21033/2\n+GACCCTCTGAGTAACCAGTCCCGGTTGCTTACCACACGTGCCAACCCGAGCGGATCAACCAAGCCAGTGCGCCCACTCCCACACCGCATCCCCTCCGAAATTCCAACACTCACACCTCCACTCTCATGATTCCCGCCTCCTACCTCTGTCTCCACTCGACCCGCACACACGGAACCGAGTCGATCCATCCCCGTCATACCACTTATACCTCAATGATCCACCTAAGTTCCCCTGATTCCCCGTCCTAGCGATCATCTCACTGCCCCTCCCGTACCTCATGTCTCCACTTCCCAGCATAGA\n+>ERR1877483.32898 M03099:22:000000000-APTMA:1:2119:24030:22105/1\n+ACGGGCGTCGGAAGCATCAGGGCCCGACAGTGCCAGTCCTGCCATGGGATGGGCGGCAACGAACCGCGCCCTGCCGGGATGGTTCTCAATGCTGCGGCAAACGGCGTCTTTTACCGAACCGGCATCTATCACCACGGTCTGATCTCCGGTGCGGTCAAGAATACCGGGAAGAATAGCGATGGTGGTATCGACCGGGACGGTGATCAGGACCAGCGAGGCATCACTGAGTGAGTTCTCCAGTGAGGTGCTCCTGTCAACCCGTCCCCTTGAAAGCGCCTGCTGCAAATGGCCGGCATTTGTT\n+>ERR1877483.32898 M03099:22:000000000-APTMA:1:2119:24030:22105/2\n+ACGGCCGATTTGTGCATGGCACGGCAATATATTCCCCCCCTCATATATGGGCCGCGAGCACTACCCATTCCGTCTTCATCGGGTCGGGGGGCACATCCCACACTCAACGTCCCACACGCTTTTGCGCTGCCCACTCGATCACGTGATCGACTCGCTCCTTAGTGGGCATTTTAGCACTTGTCTCCCCATGGCGGCTAGGCTGTAGGTGAGCCGAGTGCGGACTCATCTTTCACCGACTTGCGCAGCGAGTACTCGTAGCAGACCCGGCGCTGACCACCAGCCACTGCAGTGTACGACCGT\n+>ERR1877483.32900 M03099:22:000000000-APTMA:1:2119:9095:22203/2\n+GACTACTGGGGTATCTAATACTGTTTTCTCCCCCCGGTTTCGCACCTTAGTGGTAGTTTAAGTCCCGGAGGTCGGCCTCGCCACCTGTTTTTCTTCCTATTTTCTCGCATTTTACCGCCTAACAAGACATTCCACCACTCTCTACCGTACCTTAATCAGGCAGGTATGGGTGCAGTTCCCAGGTTGAGCCCGGGGATTTCACCTCCTTCCTACCATACCACCTTCGCGAGCGTTACGACCAGCAACTGCCTATAACACTTGCACCCTTTGTAATACCGCTGACGTTGGCACGTAGTTAGT\n+>ERR1877483.32926 M03099:22:000000000-APTMA:1:2119:7498:23338/1\n+ACGGGCGGTGGCGATCTCGTGGACGATGACGTTGATCCTCGTCTCCCCGGATACGGGGATGAAGCTGCAGCCGGTGCCGTCTCTGACCAGCTGGGCCTCCAGCTGCCTGCCCGCAAAGCCGGCGATGAAGCCGCGGGCCCGGTTCTCGGCGCCGAGGGCGGTCAGGACCTTCGATACGTCGATCCCCTTCCCTCCGGCGTAGCTCTCCTCCCGGATTATCCTGTTGGGGACGTCCTCCCTCATCACGTCGATGAGGAGGGTCCGATCGAGGGCTGGGTTGATGGTTATGGTGTAAATCATC\n+>ERR1877483.32926 M03099:22:000000000-APTMA:1:2119:7498:23338/2\n+GCCCAGTCCCCCCCTACTGCCAGCTGCGCCGTTAAGTCAGGCGGGCCAGCTCCGAATCTAGAGGATAACGACTACAACAGAAATAAGCAGAATGATTAAAGCCCCACATCACGGCGGCTAACCTGCATGCACACTACTCTCGTCTAAACCCATGGCCGACACGTTCCAATGACCTCACCAGCTGCCCACCATTAATAACTGCCTCGATCTCATGTGCTAGCCTCGAGCTCCTCACACACTTCAGCGTAACGCCGCCTCACCCACCCACCACATACCTTCAACATCCTGTGCTTCTTCTA\n+>ERR1877483.32949 M03099:22:000000000-APTMA:1:2119:22063:24539/1\n+ACGGGCGGTGTGTACACATCTCCGAGCCCACGAGACAGCCCACGAGACATCCTACGAGACCGCCCGCAAGAAAGCCCCCGAGACATCCCACCCTCCGGCCCTCCAAGAGAACGACCACGCGGCCCACGTGCCCCGACACCTAAGCGGGTCCTAGAAGGCGCAAGCACGACTCCCTCCGTGCTAGGGTCAGCCCTCATACGACGGAAACCCGCGATCTTCTTAATCAACGTTCGCTAGAACACCCTAGGCTGACTCCGACGAACAGACTGCAGGACCGACGCTCGACCCCGCAACCACCACG\n+>ERR1877483.32949 M03099:22:000000000-APTMA:1:2119:22063:24539/2\n+CGCTACTGGCGTACCTAATCCCGTTCCCTACCCTCCCCTGCGTACCTACCCGCGATTAAGTGTGCTGCAGGCTTCATTCACCATAGGTCTTGCCCTCAATCCCAACGAATTTCACTGCTACAGCCATAGTTTAACCTGGCTCTCCATACCCCATGTCTACCATTCATTGCAGCCTTTGTCTATCTGCACTCTTGAATTGCAACATTAATTCACCTCATCCCCACCTTACTCTTTGTTCTCTACGTCAGTACCCACATCTGTCACCACTCGCTATGTACCACGCTCTCTCACCACTTCAGG\n+>ERR1877483.32954 M03099:22:000000000-APTMA:1:2119:11950:24861/2\n+GGCTACTAGGGGTACTAATTCTCGTTTGTCCCCACGGTTTCGCACCTTCACGGTAGTCTTTATTCCGGCGACTCCCCTCGCCACCTGTAGTCCTCCAGGACTCTACGCAATTCACCGCCTCACCTGGAAATCTACCCCCCCCTTCCAGCATTCTACCTGCCCAGTTCCAATTCAGTTTCCCGGTTTAACCCCGGGGCTTCCACATCGACTTTACAGACCGCCCTCCTAGGCCTTACGCCCATTACATCCGATTAACGCCTTCACCCTCCGTATTCCCGCCTGCTCTGGCACCGTCTTAGG\n+>ERR1877483.32956 M03099:22:000000000-APTMA:1:2119:14880:24914/1\n+ACGGGCGGTAAGTAGAGCCGATTCGTTGACAAGGTTGGCAAGGTCAGCACCGGTAAACCCGGGAGTACCCCTTGCTATCACTTTGAGATCTACCTCCCGGGATAGAGGTATCTTCCCCGAGTGAACAGCACGTATCTTCTCCCTTCCCTTAACATCAGGAACATCAGCAATGACCTGCCGGTCGAATCTACCAGGCCTTAAAAGAGCCGGATACAGAACATCAGGCCTGTTTGTGGCAGCTATGATTATCAAACCCTCAGTGGTTTCAAAACCGTCCATCTCAACAAGAAGCTTGTTGAGA\n+>ERR1877483.32956 M03099:22:000000000-APTMA:1:2119:14880:24914/2\n+GCGACGGGTACGAGAGAGATCAGTGGGAATAGAAATGAAAGGAGGCGGAAGTAAGAACACAAACGAGTCGGTGTAATCTAAATGGAGAGGAGGACTAAGGTGCTGAATACGGCTGGAGCTAGGGGGGTGGCACATGGTCGATACTGACTGATCAACTGTGATGTCGCTCTTAGTAGTGGTGGAACAGGACTGGATATGGCTATTAGGACTGGGTATCATAAACATGCTACTATGGGTAACTTACTACGACAACACTTGGAGGCTAACATCACTATGTAACTATCGAAAGTGAGATTACGAT\n'
b
diff -r 65c38d020fea -r eb35257d2e29 test-data/test6_aligned_forward.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test6_aligned_forward.fasta Wed Mar 20 03:03:08 2019 -0400
b
b'@@ -0,0 +1,1740 @@\n+>ERR1877483.1 M03099:23:000000000-APTLR:1:1101:19252:1849/1\n+CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCCATTCCCCGTGTGTGCTGCTTGCCTTCGGTTTGTATATCACTTTCTTTTTTGACGACTCTCTTTTTTTTATTACCTTTCTTTTTTTACTTTACCTACATTTTCTGCTCCGTCTTTCTTCTTTCCTTCTTCCTCTCTCATCCGTATGTTGCAACCTTTTTTCTTTTTTCCTTTTCTTTTATCTCTCTTTTTTGTTTCTTCACGTTTTCTTTTACCTCCCCTTTCTCTTCCTGTTAACTTCCTCCTAT\n+>ERR1877483.2 M03099:23:000000000-APTLR:1:1101:15851:1971/1\n+CCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGTGTTTTGGTTAATAACCGCAGCAATTTACGTTACCCGCAGAAGATGCACCGGCTACCTCCGTGCCAGCAGCCGCGTTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGTGCGTAACGCGCTCGCAGTCGTTCTGTCAAGTCGGTTGTTAAATCCCCGGGCTCAACCTGGGAACTGCATTCTAA\n+>ERR1877483.3 M03099:23:000000000-APTLR:1:1101:23102:1978/2\n+CACTACCGGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTCAGCGTCAGTATTGGACCAGTTCGCCGCCTTCGCCACTGGTTTTCCTCCGAATATCTACGCATTTCACCTCTACACTCGTTATTCCACTCACCTCTTCCATACTCCAGTTCGCCAGTTTCATTCGCAGTTCCACGGTTCATCCCTCGGCTTTCACTCCTTACTTATCGCTCCGCCTACCTTCGCTTTACGCCCAGTACTTCCTCTCACCGCTCTCCCCCCTCCTTTTTCGCCGCCTGCTTTCCCCTCTTTATC\n+>ERR1877483.4 M03099:23:000000000-APTLR:1:1101:22637:2119/2\n+GACTACTAGGGTATCTAATCCTGTTCGCTACCCACACTTTCGCACATGAGCGTCAGTCTTTGGCCAGGGAGTCGCCTTCGCCACTGATGTTCCTCCAGATATCTACGCATTTCACCGCTACACCTGGAATTCCACTCCCCTCTCCAAGACTCTAGTCTGCCAGTTCTACATGACCATCCCAGGTTGAGCCCAGGGCTTTCACACCTAGCTTAACAAACCGCCTGCGTGCGCTTTACGCCCAGTAATTCCGATCAACGATCGTCCCCTCCGTCTTACCGCGGCTGCTGGCACGGGGTTAGC\n+>ERR1877483.5 M03099:23:000000000-APTLR:1:1101:18265:2244/2\n+GACTACAAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTGAGCGTCAGTCTTTGTCCAGGGGGCCGCCTTCGCCACCGGTATTCCTCCAGATCTCTACGCATTTCACCGCTACACCTGGAATTCTACCCCCCTCTACAAGACTCAAGCCTGCCAGTTTCGAATGCAGTTCCCAGGTTGAGCCCGGGGATTTCACATCCGACTTGACAGACCGCCTGCGTGCGCTTTACGCCCAGTAATTCCGATTAACGATTGCACCCCCCGTATTACCGCGGCTGCTGGCACGGAGTTAGC\n+>ERR1877483.6 M03099:23:000000000-APTLR:1:1101:12491:2265/2\n+GACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGTGCCTCAGTGTCAGTGTTGGTCCAGGTAGCTGCCTTCGCCATGGATGTTCCTCCCGATCTCTACGCATTTCACTGCTACACCGGGAATTCCGCTACCCTCTACCACACTCTAGTTGTCCAGTTTCCACTGCAGTTCCCAGGTTGAGCCCAGGGCTTTCACAACAGACTTAAACAACCACCCACGCACGCCTTACGCCCAGTAAATCCGAGTACCGCTTGCACCCCTGCAACTTCCGCGGCCGCTGGCCCGAAGGAACC\n+>ERR1877483.7 M03099:23:000000000-APTLR:1:1101:8123:2395/2\n+GACTACACGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGTGCATGAGCGTCAGTGTCATCCCAGGGGGCTGCCTTCGCCATCGGTATTCCTCCGCATCTCTACGCATTTCACTGCTACACGCGGAATTCTACCCCACTCTGACGCACTCTAGTCTTGCCGTCTCCACTGCCGTTCCCAGGTTGAGCCCGGGGCTTTCCCATCAGCCTTGCACACACGCCTGCGCAAGCATCACGCCCAGTAATTCCGACTAACGCTTGCACCCTACGTATTTCATCCGCTGCTGGCCCGGCTTTAGCA\n+>ERR1877483.8 M03099:23:000000000-APTLR:1:1101:19895:2425/2\n+GACTACTCGGGTATCTAATCCTGTTCGCTACCCACACTTTCGCACATGAGCGTCAGTCTTTGGCCAGGGAGTCGCCTTCGCCACTGATGTTCCTCCAGATATCTACGCATTTCACCGCTACACCTGGAATTCCACTCCCCTCTCCAAGACTCTAGTCTGCCAGTTCTAAATGACCATCCCAGGTTGAGCCCGGGGCTTTCACATCTAGCTTAACAAACCGCCTGCGTGCGCTTTACGCCCAGTAATTCCGATTAACGCTCGCACCCTCCGTGTTACCGCGGCTGCGGGCCCGGAGAGAGC\n+>ERR1877483.9 M03099:23:000000000-APTLR:1:1101:24195:2452/2\n+GACTACTGGGGTATCCAATCCTGTTTGCTCCCCACGCTTTCGCACCTCAGTGTCAGTATTAGTCCAGGTGGTCGCCTTCGCCACTGGTGTTCCTTCCTATATCTACGCATTTCACCGCTACACAGGAAATTCCACTATCCTCTACCATACTCTAGTCAGTCAGTTTTGAATGAAGTTACCAGGTTGAGCCCGGGAATTTCACATCTAACTTAACAAACCACCTACGCGCGCTTTACGCCCAGTAATTCCGAATAACGCTTGCCCTCTACGTATTACCGCGGCTGCTGGCACAGAGTTAGC\n+>ERR1877483.10 M03099:23:000000000-APTLR:1:1101:8960:2646/2\n+GACTACCAGGGTATCTAATCCTGTTTGCTCCCCAAGCTTTCGTGCCTCAGTGTCAGTGTTGGTCCAGGTAGCTGCCTTCGCCATGGATGTTCCTCCCGATCACTACGCAATTCACTGCTACAACGGGAATTCCGCTACCCTCTACCACCCTCTAGTTGTCCAGTTTTCACTGCAGTTCCCAGGTTGAGCCCAGGGCTTTCAAAACAGACTTAAACAACCACCTACGCACGCATTACGCTCAGCACATCCGAGTAACGCTTGCACACCTCGTCTTACACGCGCTGCTGCCCCGGAGGTACC\n+>ERR1877483.11 M03099:23:000000000-APTLR:1:1101:17700:2703/2\n+GACTACAAGGGTATCTAATCCTGTTCGCTCCCCATGCTTTCGCTCCTCAGCGTCAGGTAATTCCCAGAGAACCGCCTTCGCCACCAGTGTTCCTCCTGATATCTGCGCATTCCACCGCTACACCAGGAATTCCGTTCTCCCCTGAATACCTCTAGTCTGCCCGTATCGGAAGCACGCTCAGGGTTGAGCCCTGAGTTTTCACTCCCGACGCGACAAACCGCCTACGAGCCCTTTACGTCCAATAATTCGGGACAACGCTCGGACCCTACGTATTACAGCGGCGCC'..b':2119:21316:24023/2\n+GACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTCAGCGTCAGTAATGGACCAGTGAGCCGCCTTCGCCACTGGTGTTCCTCCGAATATCTACGAATTTCACCTCTACACTCGGAATTCCACTCACCTCTTCCATACTCCAGATCGACAGTATCAAAGGCAGTTCCAGGGTTGAGCCCTGGGATTTCACCCCTGACTGATCGATCCGCCTACGTGCGCTTTACGCCCAGTAATTCCGTACAACGCTCGCCCCCTTCGTATTACCGCGTCTGCTGGCACGTATTTAGC\n+>ERR1877483.32942 M03099:22:000000000-APTMA:1:2119:22743:24096/2\n+GACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACATCAGTGTCAGTATTAGTCCAGTAGGTCGCCTTCGCCACTGGTGTTCCTTCCTATATCTACGCATTTCCCCGCTCCACAGGAAATTCCACCCCCCTCTACCATACTCTCGCCCAGTAGTTTTGGAGGAAGTCTCCAGGTTTAGCCCCGTGATTTCCCCTCCCACTTGCTGAACCACCTACGCCCCCTTTACGCCCAGTCATTCCGCTTAACGCTTGCACCCTTCGTATTACCGCGGCGTGTGCCACGACGTTACC\n+>ERR1877483.32943 M03099:22:000000000-APTMA:1:2119:20410:24202/2\n+GACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTCAGTGTCAGTATCAGTCCAGGTGGTCGCCTTCGCCACTGGTGTTCCTTCCTCTATCTACGCATTTCACCGCTACACAGGAAATTCCACCACCCTCTACCGTACTCTAGTCAGGCAGTTATGGATGCAGTTCCCAGGTTGAGCCCGGGGATTTCACATCCATCTTACCAAACCACCTACGCGCGCTTTACGCCCATTACTTCCGCTTAACGCTTGCACCCTTCGTATTACCACGGCTGCTTGCACGAACTTAGCG\n+>ERR1877483.32944 M03099:22:000000000-APTMA:1:2119:18061:24218/2\n+GACTACAGGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTGAGCGTCAGTCTTCGTCCAGGGGGCCGCCTTCGCCACCGGTATTCCTCCAGATCTCTACGCATTTCACCGCTACACCTGGAATTCTACCCCCCTCTACGAGACTCAAGCTTGCCAGTATCAGATGCAGTTCCCAGGTTGAGCCCGGGGATTTCACATCTGACTTAACAAACCGCCTGCGTGCGCTTTACGCCCAGTAATTCCTATTAACGCTTGCACCCTCCGTATTACCGCTGCTACTGGCACGGATTTAGC\n+>ERR1877483.32945 M03099:22:000000000-APTMA:1:2119:18837:24311/2\n+GACTACAGGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTCAGTGTCAGTATTAGTCCAGGTGGTCGCCTTCGCCACTGGTGTTCCTTCCTATATCTACGCATTTCACCGCTACACAGGAAATTCCACCACCCTCTACCATACTCTAGTCAGTCAGTTTTGAATGCAGTTCCCAGGTTGAGCCCGGGGATTTCACATCCAACTTAACAAACCACCTACGCGCGCTTTACGCCCAGTAATTCCGATTAACGCTTGCACCCTCTGTATTACCGCGGCTGCTGGCACAGAGTTAGC\n+>ERR1877483.32946 M03099:22:000000000-APTMA:1:2119:18816:24311/2\n+GACTACAGGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTCAGTGTCAGTATTAGTCCAGGTGGTCGCCTTCGCCACTGGTGTTCCTTCCTATATCTACGCATTTCACCGCTACACAGGAAATTCCACCATCCTCTACCATACTCTAGTCAGTCAGTTTTGAATGCATTTCCCAGGTTGAGCCCGGGGATTTCACCTCCAACTTAACAAACCACCTACGCCCCCTTTACCCCCAGTAATTCCGATTCACGCTTTCACCCTCTGTATTACCTCGGCTGCTAGCACAGCCATAGC\n+>ERR1877483.32947 M03099:22:000000000-APTMA:1:2119:7531:24361/2\n+GACTACTAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTCAGTGTCAGTATCAGTCCAGGTGGTCGCCTTCGCCACTGGTGTTCCTTCCTATATCTACGCATTTCACCGCTACACAGGAAATTCCACCACCCTCTACCGTACTCTAGTCAGGCAGTTATGGATGCAATTCCCCGGTTTAGCCCGGGGATTTCACTCCCCTCTTACCCAACCACCTACGCGCCCTTTACGCCCAGTACTTCCGATTACCGCTTGCCCCCTTCGTATTACCGCGACTGCTGGCACGAAGTTAGC\n+>ERR1877483.32950 M03099:22:000000000-APTMA:1:2119:8336:24549/2\n+GACTACCGGGGTATCTAATGCTGTTTGCTCCCCACGCTTTCGTGCCTCAGTGTCAGTGTTGGTCCAGGTAGCTGCCTTCGCCATGGATGTTCCTCCCGATCTCTACGCATTTCACTGCTACACCGGGAATTCCGCTACCCTCTACCACACTCTAGTTGTCCAGTTTCCACTGCAGTTCCCAGGTTGAGCCCAGGGCTTTCACAACAGACTTAAACAACCACCTCCGCACGCTTTAAGCACAGTCATTCCGAGTAACGCTTGCACCCTTCGTATTACCGCGGCTGCTGGCACGAAGTTACC\n+>ERR1877483.32951 M03099:22:000000000-APTMA:1:2119:14312:24605/2\n+GACTACCGGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGTGCATGAGCGTCAGTGTCATCCCAGGGGGCTGCCTTCGCCATCGGTATTCCTCCGCATCTCTACGCATTTCACTGCTACACGCGGAATTCTACCCCCCTCTGACGCACTCTAGTCTTGCAGTCTCCAATGCCGTTCCCAGGTTGAGCCCGGGGCTTTCCCATCAGACTTGCCAAACCGCCTGCGCACGCTTTACGCCCAGTAATTCCGATTAACGCTTGCACCCACCGATTCCTCCGGCCTCCTGGCACGGCGTTTCC\n+>ERR1877483.32952 M03099:22:000000000-APTMA:1:2119:20365:24795/2\n+GACTACAAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTGAGCGTCAGTCTTCGTCCAGGGGGCCGCCTTCGCCACCGGTATTCCTCCAGATCTCTACGCATTTCACCGCTACACCTGGAATTCTACCCCCCTCTACGAGACTCAAGCTTGCCAGTATCAGATGCAGTTCCCAGGTTGAGCCCGGGGATTTCACATCTGACTTAACAAACCGCCTGCGTGCGCTTTACGCCCAGTCATTCCGATTAACGCTTGCACCCTCCGTATTACCGCGGCTGCTGGCACGGAGTTAG\n+>ERR1877483.32953 M03099:22:000000000-APTMA:1:2119:9975:24853/2\n+GACTACAGGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGTGCATGAGCGTCAGTGTCATCCCAGGGGGCTGCCTTCGCCACTGGTGTTCCTTCCTATATCTACGCATTTCACCGCTACACAGGAAATTCCACCACCCTCTACCATACTCTAGCCCAGTAGTTTTGGAGGCAGTTCCCAGGTTGCGCCCGGGGATTTCTCCTCCAACTTCCTGACCCACCTACGCGCGCTTTACGCCCCGTAATTCCGATTACCGCTGTCACCCTTCGTATCACCGCGGCTGCTGCTACGACGTTAGC\n'
b
diff -r 65c38d020fea -r eb35257d2e29 test-data/test6_aligned_reverse.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test6_aligned_reverse.fasta Wed Mar 20 03:03:08 2019 -0400
b
b'@@ -0,0 +1,1740 @@\n+>ERR1877483.3 M03099:23:000000000-APTLR:1:1101:23102:1978/1\n+CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGCAAGCCTGATCCAGCCATGCCGCGTGTGTGATGAAGGCCCTAGGGTTGTAAAGCTCTTTCCCCGGATAAGATAATGACGTTATCCGTAGAAGAAGCCCCTGCTAACTTCGTGCCAGCATCCGCGGTAATACGACTGGCGCTAGCGTTGTTCGGTATTACTGGTCGTAAAGCTCACGTAGGCTGATCGATCAGTCATGGGTGCAATCCCATGTCTCACCCCTGGCTCTGCCTTTCATACTTTCCCTCTGGATTATGTCAGAG\n+>ERR1877483.4 M03099:23:000000000-APTLR:1:1101:22637:2119/1\n+CCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGGGAAACCCTGATGCAGCCATGCCGCGTGTGTGAAGAAGGCCTTCGGGTTGTAAAGCACTTTCAGTTGTGAGGAAAAGTTAGTAGTTAATACCTGCTAGCCGTGACGTTAACAACAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCGAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGCTAGATGTGAAAGCCCTGGGCTCAACCTGGGATGGTCATTTAGA\n+>ERR1877483.5 M03099:23:000000000-APTLR:1:1101:18265:2244/1\n+CCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGTGTTGTGGTTAATAACCGCAGCAATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTCTGTCAAGTCGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCGAA\n+>ERR1877483.6 M03099:23:000000000-APTLR:1:1101:12491:2265/1\n+CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGCAAGCCTGATCCAGCCATACCGCGTGGGTGAAGAAGGCCTTCGGGTTGTAAAGCCCTTTTGTTGGGAAAGAAATCCAGCCGGCTAATACCTGGTTGGGATGACGGTACCCAAAGAATAAGCACCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGGTGCAAGCGTTACTCGGAATTACTGGGCGTAAAGCGTGCGTAGGTGGTTGTTTAAGTCTGTTGTGAAAGCCCTGGGCTCAACCTGGGAACTGCAGTGGAA\n+>ERR1877483.7 M03099:23:000000000-APTLR:1:1101:8123:2395/1\n+ACTACGGGAGGCAGCAGTGGGGAATTTTGGACAATGGGCGCAAGCCTGATCCAGCCATGCCGCGTGTCTGAAGAAGGCCTTCGGGTTGTAAAGGACTTTTGTTCGGGAGGAAATCCCGCTGGTTAATAACTGGCGGGGATGACAGTACCGGAAGAATAAGCACCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTGAAAGCGTTAATCGGAATTACTGGGCGTAAAGCGTGCGCAGGCGGTTTTGCAAGTCTGATGTGAAAGCCCCGGGCTCAACCTGGGAACGGCATTGGCG\n+>ERR1877483.8 M03099:23:000000000-APTLR:1:1101:19895:2425/1\n+CCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGGGAAACCCTGATGCAGCCATGCCGCGTGTGTGAAGAAGGCCTTCGGGTTGTAAAGCACTTTCAGTTGTGAGGAAAAGTTAGTAGTTAATACCTGCTAGCCGTGACGTTAACAACAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCGAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGCTAGATGTGAAAGCCCCGGGCTCAACCTGGGATGGTCATTTAGA\n+>ERR1877483.9 M03099:23:000000000-APTLR:1:1101:24195:2452/1\n+CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCCATGCCGCGTGTGTGAAGAAGGTCTTCGGATTGTAAAGCACTTTAAGTTGGGAGGAAGGGTATTAATCTAATAAGTTAGTGTTTTGACGTTACCGACAGAATAAGCACCGGCTAACTCTGTGCCAGCAACCGCGGTAATAAAGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGGGCGTAGGTGGTTTGTTAAGTTGGGTTTGAAATTTACGGGGTTAACCTGGGAACTGTATTCTAA\n+>ERR1877483.10 M03099:23:000000000-APTLR:1:1101:8960:2646/1\n+CCTACGGGAGGCAGCAGTAGGGAATCTTCCGCAATGGACGAAAGTCTGACGGAGCAACGCCGCGTGAGTGATGAAGGTTTTCGGATCGTAAAGCTCTGTTGTTAGGGAAGAAAAAGTACCGTTCGAATAGGGCGGTACCTTGACGGTACCTAACCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGAAGGGTGCAAGCGTTACTCGGAATTACTGGGCGTAAAGCGTGCGTAGGTGGTTGGTTAAGTCTGTTGTGAAAGCCCTGGGCTCAACCTGGGAACTGCCGTGGA\n+>ERR1877483.11 M03099:23:000000000-APTLR:1:1101:17700:2703/1\n+CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCAACGCCGCGTGAGGGATGACGGCCTTCGGGTTGTAAACCTCTTTCAGCAGGGACGAAGCGAGAGTGACGGTACCTGCAGAAGAAGGACCGGCCAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTCCGAGCGTTGTCCGGAATTATTGGGCGTAAAGGGCTCGTAGGCGGTTTGTCGCGTCGGGAGTGAAAACTCAGGGCTCAACCCTGAGCGTGCTTCGGATACGGGCAGACTAGAGGTATT\n+>ERR1877483.12 M03099:23:000000000-APTLR:1:1101:9100:2742/1\n+ACTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGAGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGTGTTGTGGTTAATAACCGCAGCAATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGCTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGGCTGTCAAGTCGGATGTGAAATCCACGGGCTCAACCTGGGCACTGCATTCGAA\n+>ERR1877483.13 M03099:23:000000000-APTLR:1:1101:15854:2768/1\n+CCTACGGGAGGCAGCAGTAGGGAATCTTCCGCAATGGACGAAAGTCTGACGGAGCAACGCCGCGTGAGTGATGAAGGTTTTCGGATCGTAAAGCTCTGTTGTTAGGGAAGAACAAGTACCGTTCGAATAGGGCGGTACCTTGACGGTACCTAACCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGCTCGCAGGCGGTTTCTTAAGTCTGATGTGAAAGCCCCCG'..b'0:24202/1\n+CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCCATGCCGCGTGTGTGAAGAAGGTCTTCGGATTGTAAAGCACTTTAAGTTGGGAGGAAGGGCAGTAAGTTAATACCTTGCTGTTTTGACGTTACCAACAGAATAAGCACCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTTGGTACGATGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCCATA\n+>ERR1877483.32944 M03099:22:000000000-APTMA:1:2119:18061:24218/1\n+CCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGTAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGAT\n+>ERR1877483.32945 M03099:22:000000000-APTMA:1:2119:18837:24311/1\n+CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCCATGCCGCGTGTGTGAAGAAGGTCTTCGGATTGTAAAGCACTTTAAGTTGGGAGGAAGGGCATTAACCTAATACGTTAGTGTTTTGACGTTACCGACAGAATAAGCACCGGCTAACTCTGTGCCAGCAGCCGCGGTAATACAGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTTGTTAAGTTGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCAAA\n+>ERR1877483.32946 M03099:22:000000000-APTMA:1:2119:18816:24311/1\n+CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCCATGCCGCGTGTGTGAAGAAGGTCTTCGGATTGTAAAGCACTTTAAGTTGGGAGGAAGGGCATTAACCTAATACGTTAGTGTTTTGACGTTACCGACAGAATAAGCACCGGCTAACTCTGTGCCAGCAGCCGCGGTAATACAGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTTGTTAAGTTGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCAAA\n+>ERR1877483.32947 M03099:22:000000000-APTMA:1:2119:7531:24361/1\n+CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCCATGCCGCGTGTGTGAAGAAGGTCTTCGGATTGTAAAGCACTTTAAGTTGGGAGGAAGGGCAGTAAGTTAATACCTTGCTGTTTTGACGTTACCAACAGAATAAGCACCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTTGGTAAGATGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCCATA\n+>ERR1877483.32950 M03099:22:000000000-APTMA:1:2119:8336:24549/1\n+CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGCAAGCCTGATCCAGCCATACCGCGTGGGTGATGAAGGCCTTCGGGTTGTAAAGCCCTTTTGTTGGGACAGAAATCCAGCCGGCTAATCCCTGGTTGGGATGACGGTACCCAAAGAATAAGCACCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGGTGCAAGCGTTACTCGGAATTACTGGGCGTAAAGCGTGCGTAGGTGGTTGTTTAAGTCTGTTGTTAAAGCCCTGGGCTCAACCTGGGAACTGCAGGGGAA\n+>ERR1877483.32951 M03099:22:000000000-APTMA:1:2119:14312:24605/1\n+CCTACGGGAGGCAGCAGTGGGGAATTTTGGACAATGGGCGCAAGCCTGATCCAGCCATGCCGCGTGTCTGAAGAAGGCCTTCGGGTTGTAAAGGACTTTTGTTCGGGAGGAAATCCCGCTGGTTAATACCTGGCGGGGATGACAGTACCGGAAGAATAAGCACCGGCTAACTACGTGCCAGCAGCCGCGGGAATACGTAGGGTGCAGGCGTTTACCGGATTTCTTGGGCGAAAGGCGTGCGCAGGCGGTTTGGCAGTCCGATGGTGAAGGCCCCGGCCCCAACCTGGGAACGGCATTGGAG\n+>ERR1877483.32952 M03099:22:000000000-APTMA:1:2119:20365:24795/1\n+CCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGAT\n+>ERR1877483.32953 M03099:22:000000000-APTMA:1:2119:9975:24853/1\n+CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCCATGCCGCGTGTGTGAAGAAGGTCTTCGGATTGTAAAGCACTTTAAGTTGGGAGGAAGGGCAGTAAGTTAATACCTTGCTGTTTTGACGTTACCAACAGAATAAGCACCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTCAGCAAGTTGGAGGTGAAATCCCCGGGCTCAACCTGGGAACTGCCTCCAAA\n+>ERR1877483.32954 M03099:22:000000000-APTMA:1:2119:11950:24861/1\n+CCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCAATGCCGCGTGTGTGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGGTTGTGGTTAATAACCGCAGCAATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTCTGTCAAGTCGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCGAA\n+>ERR1877483.32955 M03099:22:000000000-APTMA:1:2119:9959:24862/1\n+CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCCATGCCGCGTGTGTGAAGAAGGTCTTCGGATTGTAAAGCACTTTAAGTTGGGAGGAAGGGCAGTAAGTTAATACCTTGCTGTTTTGACGTTACCAACAGAATAAGCACCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTCAGCAAGTTGGAGGTGAAATCCCCGGGCTCAACCTGGGAACTGCCTCCAAA\n'
b
diff -r 65c38d020fea -r eb35257d2e29 test-data/test6_unaligned_forward.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test6_unaligned_forward.fasta Wed Mar 20 03:03:08 2019 -0400
b
b'@@ -0,0 +1,260 @@\n+>ERR1877483.1 M03099:23:000000000-APTLR:1:1101:19252:1849/2\n+CACTACCCGGTTTTCTTATCCTCTTTTCTCCCCCCCCTTTCCCCCCTCCTTCTCCGTTTTTTTCCCTTTCCTCCCCTTCCCCTCTTTTTTTCCTTCCTCTTTCTTCCCCTTTCCCCTCTTCCCCCCTTTTTCCCCCCTCCTCTTCCTTTCTCCTCCTCTCCCCTTTTCTTTTTCCTTTCCTTTTTTCTCCCCCTTCTTTCCCCTCCTCCTTTCTCTCCCCCCTTCCTTCCCTTTTCTCCCCGTTCTTCCCTTCCCCCCCTTCCCCCCTCTTTTTTCCCCCCCTTCTCTCCCCCTTTTTCC\n+>ERR1877483.2 M03099:23:000000000-APTLR:1:1101:15851:1971/2\n+CACTACAAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCTCCTGAGCGTCAGTCTTTGTCCAGTGGGCCGCCTTCGCCACCGGTTTTCCTCCAGATCTCTACGCATTTCACCGCTACACCTGGTATTCTCCCCCCCTCTACACTACTCAATCCTGCCAGTTTCGAATGCAGTTCCCAGGTTTAGCCCGTGGATTTCACATCCTACTTGCCATACCGCCTGCGTGCGCTTTACTCCCCGTAATTCCGATTTACGCTTGCCCCCTCCGTATTACCTCCGCTGCTGTCCCCTTCTTAGC\n+>ERR1877483.69 M03099:23:000000000-APTLR:1:1101:26536:6120/1\n+CCTACGGGAGGCAGCAGCGGGGAATATTGCACAATGGGCGAAAGCCTGATCCAGCCATACCGCGTGCGTGATGACGGCCTTAGGGTTGTAAACCGCTTTCAGTTGGGAAGAAGATCACTATCCTTCCAGAAGAGTCTTCGGCCGTCTCCGTGCCAGCAGCCGCGGTCATACGTAGGGAGCACACGTTGTCCGGCATTGTTGGGCGTAACGTGCTCGTAGGCGACTGAGCAAGTCGGGCGTGAAAGTCTGGGGCTCAACCCCAGGAAGACGCTCGAGGCTGTTTTCGCTAACGTCAGTTAAA\n+>ERR1877483.70 M03099:23:000000000-APTLR:1:1101:20716:6121/1\n+ACTACGGGAGGCAGCAGCGGGGAATCTTGGACAATGGGCGAAAGCCTGATCCAGCCAACCCGCGTGTGTGAAGAAGGCCTTCGGTTTGTAAACCACTTTAAGGTGGGAGGAAGGGCAGTAAGTTAATACCTTGATGGTTTGACGCTACCAACAGAATAAGCACCGGCGAACTTCGTGGCAGCAGCCGCGGGAAAACGGAGGGTGCCAGGGTTAATCGGAAGTAATGGGCGTAAAGCGCGAGTTGGGGGGTCAGCAAGTTGGAGGTGAAAGCCCCGGGCGCAGACGGGGAACAGCCGCCAAA\n+>ERR1877483.95 M03099:23:000000000-APTLR:1:1101:10309:7883/2\n+GACTACATGGGTTTTTAAATCCGGTTCCCTCCCCACGCTTTCCTCCTTAGCCGTCAGAATTAACCCATGAGCCTCCTTCCCCTTTTGTTGTTCCCCTACTTTCCAACAGTTTCTCCTCTTACATGCAAATTTCCGCCAACCCTTCCTTATCTCTAGTTTAACTGATCAAAGTACATTACTAGGGTTGCGCCGTAGCTTTCACCATTTGACTTTTTATCCACCCACCTGCCGCTTTACTCCCATATATCCCATCACCCTCTTCCCCCCTCCTCTTTCCACCGGCTGCGGCCACACACTTAT\n+>ERR1877483.96 M03099:23:000000000-APTLR:1:1101:10292:7893/2\n+GACTACAGGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTCAGCGTCAGTAATGGACCAGTGAGCCGCCTTCTCCACTGGTGTTCCTCCGAATATCTACGAATTTCACCTCTACACTCGGAATTCCACTCACCTCTTCCATACTCCAGATCGACAGTATCAAAGGCAGTTCCAGGTTTGAGCCCTGGGCTTTCACCCCTGACTGATCGATCCGCCTACGTGCGCTTTACGCCCAGTAATCCCGAAAAACGCTAGCCCCCTTCGTATTCCCGCGCCAGCTGGCCCGCAGGTGCC\n+>ERR1877483.115 M03099:23:000000000-APTLR:1:1101:28104:8405/2\n+GACTACAAGGGTATCTAATCCTGTTCGCTCCCCACGCTTTCGCTCCTCAGCGTCAGTTACAGACCAGAGAGTCGCCTTCGCCACTGGTGTTCCTCCACATCTCTACGCATTTCACCGCTACACGTGGAATTCCACTCTCCTCTTCTGCACTCAAGTTCCCCAGTTTCCAATGACCCTCCCCGGTTGAGCCGGGGGCTTTCACATCAGACTTAAGAAACCGCCCGCGAGCCCTTTACGCCCAATACTTCCGGACAACGCTTGCCCCCTCCGTCTTACCGCCGCTGCTGGCCCGTCGTTAGC\n+>ERR1877483.116 M03099:23:000000000-APTLR:1:1101:28087:8411/2\n+GACCACAAGGGTATCCAAATCCTTTCGGCTCCCACCCCTTTGGCCCCCAACCTCAGTTACAGATCAGGCGGTCCGCCTCCCCACCTGTGTTCCCCCCCGACACTTCCCATTTCACCCCCACACCCGGGACTCCCCCCTCCTCCTCCGCACCTCACGCCCCCAGTTTTCAATTACACTCCCCGGTTTGCCCCCGGGCCTTTCCCTCCCACTTTACAACACGCCCTCCAGCCCCTTTACCCCAACTATTCCCGCCACCCGTTCGCACCCACCGTGTTCCTCGTACTCTGCGCCGTAGTTAGC\n+>ERR1877483.149 M03099:23:000000000-APTLR:1:1101:6596:10202/1\n+ACTACGGGAGGCAGCAGCTAGGAATCTTCCGCAATGGGCGCAAGCCTGACGGAGCGACGCCGACTGGAGGAAGAAGACCTTCGGGGTGTAAACTCCTGAACCCGGGACGAAACCACCGAGGCGGGGACGGACGGTACCGGGGCAATCGCGCCGGCCAACGCCGAGCCAGCAGGCGCGGTTATACGGAGGGCGCGAGCGTCACCCGGATTAACTGGGTGTAAAGGGCGCGAAGGCGTCCTGGGCCGTACCACGTGGAAGACCACGGGTCAACCGTGGAGGAGCGGGGGATAAGCTCAGGCAA\n+>ERR1877483.150 M03099:23:000000000-APTLR:1:1101:18892:10219/1\n+CCTACGGGAGGCAGCAGTGGGGAATTTTGGACAATGGGCGCAAGCCTGATCCAGCCATGCCGCGTGTCTGAAGAAGGCCTTCGGGTTGTAAAGGACTTTTGTTCGGGAGGAAATCCCGCTGGTTAATACCTGGCGGGGATGACAGTACCGGAAGAATAAGCACCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGTGCGCAGGCGGTTTTGCAAGTCTGATGTGAAAGCCCCGGGCTCAACCTGGGAACGGCATTGGAG\n+>ERR1877483.183 M03099:23:000000000-APTLR:1:1101:27013:12199/2\n+GACTACAGGGTATCTATTACTGTTTGCGCCCCACACGTTCGCAACTGAGCGTCAGTCTTTGTGCAGGGGGCCGCCCTCTCCACCGGTATGCCCCCCGCTCTCTACGCATTTCACCCCTACACCCGGAATTCTACCCCCCTCTACCAGACTCAATCCTGCCCGTTTCGCAGGCAGTTCCCAGGTTTTGGCCGCTGACTTTTCATCCCCGTTTACCTACCCCCCCCGCGCGCGCTACGCCCCGCAATTCCCATCACCGCTTGTGCCCCCCG'..b'19:16207:20617/2\n+GACTACAAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTCAGTGTCAGTATCAGTCCAGGTGGTCGCCTTCGCCACTGGTGTTCCTTCCTATATCTACGCATTTCACCGCTACACAGGAAATTCCACCACCCTCTACCGTACTCTAGTCAGGCAGTTATGGATGCAGTTCCCAGGTTGAGCCCGGGGATTTCACATCCATCTTACCAAACCACCTACGCGCGCTTTACGCCCAGTAATTCCGATTACCGCTTGCACCCTTCGTATCACCGCGTCGGCTGGCACGAACTTAGC\n+>ERR1877483.32898 M03099:22:000000000-APTMA:1:2119:24030:22105/1\n+ACGGGCGTCGGAAGCATCAGGGCCCGACAGTGCCAGTCCTGCCATGGGATGGGCGGCAACGAACCGCGCCCTGCCGGGATGGTTCTCAATGCTGCGGCAAACGGCGTCTTTTACCGAACCGGCATCTATCACCACGGTCTGATCTCCGGTGCGGTCAAGAATACCGGGAAGAATAGCGATGGTGGTATCGACCGGGACGGTGATCAGGACCAGCGAGGCATCACTGAGTGAGTTCTCCAGTGAGGTGCTCCTGTCAACCCGTCCCCTTGAAAGCGCCTGCTGCAAATGGCCGGCATTTGTT\n+>ERR1877483.32899 M03099:22:000000000-APTMA:1:2119:20673:22173/1\n+CCTACGGGAGGCAGCAGCGGGGAATATTGGACAATGGGCGAAAGCCTGATACAGCCACGCCGCGTGGGTGAAGAAGGCCCTCGGATTGTAAAGCACTGTTAGGTGGGAGGAAGGGCAGTAAGTTAATAACTCGCTGTTTTCAGGTTATCCACAGAATTAGTACCCGCTAACTTTGTGCTAGCAGACGCGGTCATACAAAGGGTGCAAGCGTTTATCTGAGTTACTGGGAGGAAAGAGCGCGTAGGTGGGTTGGTAAGATGGATGTGAAATGTCCGGGCGCAACACGGGAACAGCATCCATA\n+>ERR1877483.32900 M03099:22:000000000-APTMA:1:2119:9095:22203/2\n+GACTACTGGGGTATCTAATACTGTTTTCTCCCCCCGGTTTCGCACCTTAGTGGTAGTTTAAGTCCCGGAGGTCGGCCTCGCCACCTGTTTTTCTTCCTATTTTCTCGCATTTTACCGCCTAACAAGACATTCCACCACTCTCTACCGTACCTTAATCAGGCAGGTATGGGTGCAGTTCCCAGGTTGAGCCCGGGGATTTCACCTCCTTCCTACCATACCACCTTCGCGAGCGTTACGACCAGCAACTGCCTATAACACTTGCACCCTTTGTAATACCGCTGACGTTGGCACGTAGTTAGT\n+>ERR1877483.32901 M03099:22:000000000-APTMA:1:2119:9107:22299/2\n+GCCTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTGAGCGTCAGTCTTTGTCCAGGGGGCCGCCTTCGCCACCGGTATTCCTCCAGATCTCTACGCATTTCACCGCTACACCTGGAATTCTACCCCCCTCTACAAGACTCAAGCCTGCCAGTTTCGAATGCAGTTCCCAGGTTGAGCCCGGGGATGTCACATCCGACTTGACAGACCGCCTGCGTGCGCTTTACTCCCAGTCATTCGGCTTAACGCTTGCACCCTCCGTATTACCGCGGCTGCTCGCACGGAGGTAGC\n+>ERR1877483.32926 M03099:22:000000000-APTMA:1:2119:7498:23338/2\n+GCCCAGTCCCCCCCTACTGCCAGCTGCGCCGTTAAGTCAGGCGGGCCAGCTCCGAATCTAGAGGATAACGACTACAACAGAAATAAGCAGAATGATTAAAGCCCCACATCACGGCGGCTAACCTGCATGCACACTACTCTCGTCTAAACCCATGGCCGACACGTTCCAATGACCTCACCAGCTGCCCACCATTAATAACTGCCTCGATCTCATGTGCTAGCCTCGAGCTCCTCACACACTTCAGCGTAACGCCGCCTCACCCACCCACCACATACCTTCAACATCCTGTGCTTCTTCTA\n+>ERR1877483.32927 M03099:22:000000000-APTMA:1:2119:15956:23349/2\n+GACTACGCGGGGATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTCAGTGTCAGTATTAGTCCAGGTGGTCGCCTTCGCAACTGGTGTTCCTTCCTATATCTACGCATTTCACCGCTACACAGGAAATTCCACCACCCTCTACCATACTCTAGTCAGTCAGTTTTGAATGCAGTTCCCAGGTTGAGCCCGTGGATTTCACATCAAACTTAACATACCACCTACGCGCGCTCTACGCCCATTAATCCCGACTAACGCATGCACCCTCTGTATTACCGCGGCTGCTGGGACAGAGTTAGC\n+>ERR1877483.32948 M03099:22:000000000-APTMA:1:2119:21559:24504/2\n+GACTACCGGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTCAGTGTCAGTATTAGTCCAGGTGGTCGCCTTCGCCACTGGTGTTCCTTCCTATATCTACGCATTTCACCGCTACACAGGAATTTCCACCACCCTCTACCATACTCTAGCCCAGTAGTTTTGGAGGCAGTTCCCAGGTTGAGCCCGGGGATTTCACCTCCAACTTGCTGAACCCCCTACGCGCGCTATACGCCCAGTAATTCCGATTAACGCTTGCACCCTGCGTATTACCGCGGCTGCTGGCACGCAGTTAGC\n+>ERR1877483.32949 M03099:22:000000000-APTMA:1:2119:22063:24539/2\n+CGCTACTGGCGTACCTAATCCCGTTCCCTACCCTCCCCTGCGTACCTACCCGCGATTAAGTGTGCTGCAGGCTTCATTCACCATAGGTCTTGCCCTCAATCCCAACGAATTTCACTGCTACAGCCATAGTTTAACCTGGCTCTCCATACCCCATGTCTACCATTCATTGCAGCCTTTGTCTATCTGCACTCTTGAATTGCAACATTAATTCACCTCATCCCCACCTTACTCTTTGTTCTCTACGTCAGTACCCACATCTGTCACCACTCGCTATGTACCACGCTCTCTCACCACTTCAGG\n+>ERR1877483.32956 M03099:22:000000000-APTMA:1:2119:14880:24914/1\n+ACGGGCGGTAAGTAGAGCCGATTCGTTGACAAGGTTGGCAAGGTCAGCACCGGTAAACCCGGGAGTACCCCTTGCTATCACTTTGAGATCTACCTCCCGGGATAGAGGTATCTTCCCCGAGTGAACAGCACGTATCTTCTCCCTTCCCTTAACATCAGGAACATCAGCAATGACCTGCCGGTCGAATCTACCAGGCCTTAAAAGAGCCGGATACAGAACATCAGGCCTGTTTGTGGCAGCTATGATTATCAAACCCTCAGTGGTTTCAAAACCGTCCATCTCAACAAGAAGCTTGTTGAGA\n+>ERR1877483.32957 M03099:22:000000000-APTMA:1:2119:17520:25205/1\n+CCTCCGGGAGGCAGCAGTGGGGAATCTTAGACAATGGGGGCAACCCTGATCTAGCCATGCCGCGTGAGTGATGAAGGCCCTAGGGTTGTAAAGCTCTTTCAGCTGGGAAGATAATGACGGTACCAGCAGAAGAAGCCCCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGGGCTCGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGTAGGCGGACCGTAAAGTTGGGGGTGAAATCCCGGGGCTCAACCCCGGAACTGCCTTCAAAACTATCGGTCTGGATTTCGAGAGAG\n'
b
diff -r 65c38d020fea -r eb35257d2e29 test-data/test6_unaligned_reverse.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test6_unaligned_reverse.fasta Wed Mar 20 03:03:08 2019 -0400
b
b'@@ -0,0 +1,260 @@\n+>ERR1877483.45 M03099:23:000000000-APTLR:1:1101:24920:4667/2\n+GACTACTCGGGTATCTAATCCTGTTTGCTCCCCAAGCTTTCGTGCATGAGCGTCAGTGTTATCCCAGGGGGCTGCCTTCGCCATCGGTATTCCTCCGCATATCTACGCATTTCACTGCTACACGCGGAATTCTACTTCCCTCTGACGCACTCTAGTCTTGCAGTATCGAATGCCGTTTCCCGGTTGAGCCCGGGGATTTCACATCAGACTTACAAAACCGCCTGCACACGCTTTACGCCCAGTAATTCCGATTAACGCTTGCATCCTACGTATTACCGCGTCTGCTGTAACGTAGTTAGC\n+>ERR1877483.46 M03099:23:000000000-APTLR:1:1101:21301:4734/2\n+GATACACGGGGATCTCTAACCGTTTGCGCCCCACGCGTTCGCTCCTCACCGCCAGATACAGGCCAGAGAAACGCCTTCGCCACAGGGGTTCCCCCACAGCTATACACATATCACCCCGACACGCCGGATTCCACACTCCACTCCTGCACTCACGATCCCCCGATTCCAATGAGCATTCCCGTGTGAGCCGGGAGCGTATACACAAACCATAGACACACCCCGCCACGCCCTCTGTGCCCCAAAGAACTGTAAAAGACGTTCCACCCCCGAGTAAACCCGCGTCTTCTAGCGCGGGGGTCGG\n+>ERR1877483.75 M03099:23:000000000-APTLR:1:1101:20308:6281/2\n+GACACAAGGGTATCTCATCCTGTTTGCTCCCCACGCTTTCGCCCCCCAGTGCCAGTATTTGTCTAGTTGGTCGCCTTCTCCACTGTGTTACCTCCCTTTATCTACGCATTTCACCCCTCCACACCAAATTTCCCACTCCCCTACCCTACTCTATTCCTTCCCTTTTGCGAATGTTTCCCCCTTTTTGCCCCCGGTTCTTTCACCTCCCTTAAAAAACCCCCCCACCGCGCCTTTCACCCCTAAATTCCCATTAACCCTTTCACCCACTCTATTACCCCGGCTCTGCGCACATAGTTTTCT\n+>ERR1877483.76 M03099:23:000000000-APTLR:1:1101:25401:6445/2\n+GCGCAGGGGGCTCACCGGGTTGCAGAAGAGAGACCGCACTACCAGGTAATATACTACTCGTTTGTCCCCCCGACTTTGTCACTCCACATCCACCCTACTCCCCCCCGCCCCCCTTGCCCCCCGCGCCCCCCCCCCCCCTTACGACTTGTCCCCCCCCAACCCGCCCTTTTCCTGCCCCTTCCCTCCCCCACCCTACCACACGCGCGCACACTGTCCTCCCCTGCCCTCCCCGCTTTCCGTACTACGTGTACTCCCACACCTCTCCCCTCTTCATCCCTCATTGACGCTATATTCCTCCCC\n+>ERR1877483.107 M03099:23:000000000-APTLR:1:1101:20082:8248/2\n+GACTACTGGGGTATCTAATCCTGTTCGCTACCCAAACTTTCCCACATTATCGTCCGCTTATGGCCAGGGCGTCGCCTTCGCCACTGATTTTCCTCCACGTATCTACCCATTTCACCTCTCCCCCTGGCAATCCCCCCCCCTCTCCACGCCTCCAGTCTGCCTTTTCTAAATTACCATTCCCGGTTCCCCCCGGGGCCTTCACCTCTCGCTTAACCAACCTCCCCCACGTGCTTTTCCTCCCATACTTCCGCTTAACCCTCCTCCCCCCCGTCATACCCCGGCCTCGCGCCCCGCCTTGTC\n+>ERR1877483.108 M03099:23:000000000-APTLR:1:1101:28179:8259/2\n+GACTACTAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGTGCATGAGCGTCAGTGTCATCCCAGGGGGCTGCCTTCGCCATCGGTATTCCTCCGCATCTCTACGCATTTCACTGCTACACGCGGAATTCTACCCCCCTCTGACGCACTCTAGTCTTGCAGTCTCCAATGCCGTTCCCAGGTTGAGCCCGGGGCTTTCACATCAGACTTGCAAAACCGCCTGCGCCCGCTTTACGCCCAGTAATTCCGATTAACGCTTGCACCCTACGTATTACCGCGCCTGCTGGCACGTAGTTAGC\n+>ERR1877483.127 M03099:23:000000000-APTLR:1:1101:12005:9181/2\n+GCCTACTGGGGTATCTTATACACATCTGACGTTGCCGACGACTTAATAGGTGTAGGATTCCGAGGGAGCCGAACTACTAAAATTAGGATTGAAGACTCAGATCCGAACTGAGACCTACTTTGTAGATTTGCATCCTGTCACCAGGTAGCTGCCCTCTGTATCGGCCCTTGTAGCACGTTTGTAGCCCTTGACGTACGGGCCCTTCTGAGTTTACGTCCTCCCTGCCTTCCTCACTTCTTTCGTCGGCAGTCCCTTTAGAGTCCCCAGCTTAACCTGCTGTCAACTACAGGCAAGCGTTTC\n+>ERR1877483.128 M03099:23:000000000-APTLR:1:1101:17447:9215/2\n+GACTACTCGGGTATCTAATCCTGTCTACTCCCCACGCTTTCGCACCTGAGCGTCAGTCTTTGTCCAGGGGGCCGCCTTCGCCACCGGTATTCCTCCAGATCTCTACGCATTTCACCGCTACACCTGGAATTCTACCCCCCTCTACAAGACTCAAGCCTGCCAGTTTCGAATGCAGTTCCCAGGTTGAGCCCGGGGATTTCAAATCCGACTTGACAGACCGCCCGCGTGCGCCTTACGCCCAGTAATTCCGATTAACGCTTGCCCCCTCCGTATTACCCCGGCCTCTGGCCCGGGGTTAGC\n+>ERR1877483.167 M03099:23:000000000-APTLR:1:1101:22979:11600/2\n+GACCACTAGGGTTTCTAATCCCGTTTGCTCCCCACCCTTTCCCGTCTTAGTCTCAATTCCGTCCCCGCGAGCCGCCCTCGCCATCGGTTGTCCCCCTCGTTTCTGCGCATTTCCCCCCTTCACCCGGAATTCCCCCCTCCCCTTCCGGCCTCCAGCCAGACCGTTTCCACCGGCATTTCATGGTTGGGGCCCGGGCTTTCCACACGGACCTAGCGAGCCCCCCCAACGCCGCTTAACCCCCATTCATCCCGACCAACGCTTCCCCCCACCTATGTCCCCCGCCTCCTGCCCGCACTTTAC\n+>ERR1877483.168 M03099:23:000000000-APTLR:1:1101:26900:11613/2\n+GACTACAGGGGTATCTAATTCTGTTTGCTCCCCACGCTTTCGCACCTCAGTGTCAGTATTAGTCCAGGTGGTCGCCTTCGCCACTTGTGTTCCTTCCTATATCTACGCATTTCACCGCTACCCCGGAAATTCCACCACCCTCTACCATACTCTAGCCCAGTAGTTTTCGAGTCAGTTCCCAGGGTGAGCCCGGGGATTTCACCTCCCACTTGCTGAACCACCTACGCGCCCTTTACCACCAGTAATTCCCATTTACTATTGCACCCCTCGTATTATCGCGGCTGCGCGCACCCAGTTCGC\n+>ERR1877483.191 M03099:23:000000000-APTLR:1:1101:15859:12475/2\n+GACCACAAGGGTATCCAATCCTGTTCGCTCCCCACGCCTTCGCTCCTCAGCCTCAGTTACAGACCAGAGAGTCGCCTTCGCCCCTGGTGTTCCTCCACATCTCTACGCATTTCACCGCTACACGTGGAATTCCACTCACCTCCTCTGCACCCAAGTTCCCCAGTTTCCAATGACCCTCCCCGGGTGAGCCGCGGGCCTTCCCCTCAGACTTAAGAAACCGCCTGCGCGCCCTTTACGCCCCATAAATCCGCACAACGCTTGCCCCCC'..b'20965:21047/2\n+ACTACAAGGGTATCTAATCCTGTTCGCTCCCCACGCTTTCGCTCCTCAGCGTCAGTTACAGACCAGAGAGTCGCCTTCGCCACTGGTGTTCCTCCACATCTCTACGCATTTCACCGCTACACGTGGAATTCCACTCTCCTCTTCTGCACTCAAGTTCCCCAGTTTCCAATGACCCTCCCCGGTTGAGCCGGGGGCTTTCACATCAGACTTAAGCAACCGCCTGCGAGCCCTTTACGCCCAATCATTCCGTACAACGCTTGACACCTCCGTATTACCGCGCCTGCTGGCGCGTCGTTAGC\n+>ERR1877483.32898 M03099:22:000000000-APTMA:1:2119:24030:22105/2\n+ACGGCCGATTTGTGCATGGCACGGCAATATATTCCCCCCCTCATATATGGGCCGCGAGCACTACCCATTCCGTCTTCATCGGGTCGGGGGGCACATCCCACACTCAACGTCCCACACGCTTTTGCGCTGCCCACTCGATCACGTGATCGACTCGCTCCTTAGTGGGCATTTTAGCACTTGTCTCCCCATGGCGGCTAGGCTGTAGGTGAGCCGAGTGCGGACTCATCTTTCACCGACTTGCGCAGCGAGTACTCGTAGCAGACCCGGCGCTGACCACCAGCCACTGCAGTGTACGACCGT\n+>ERR1877483.32899 M03099:22:000000000-APTMA:1:2119:20673:22173/2\n+GACTACTAGGGTATCTAATCCTGGTTGCTCCCCACGCTTTAGCACCTCAGTGTCAGTAACAGGTCAGGTGGTCGCCTTCGCCACTGGTGTTCTTTCCCATATCGAACCAGTTCAGCGCTACACAGGAAATTCCACCACTCCCTGCTGGACTCTAGTTGGGCAGTTATGGTTGCAGTTCGTAGGTTCAGCCCGGTGATTTCACTTCCTATTTACCGACCCACCTACTCGCCTCATAATCCCCCACACTCGGTTTTACGCTGCCACCTGTCTTATAACCACGGTAGTGATGACAACGTTACGG\n+>ERR1877483.32926 M03099:22:000000000-APTMA:1:2119:7498:23338/1\n+ACGGGCGGTGGCGATCTCGTGGACGATGACGTTGATCCTCGTCTCCCCGGATACGGGGATGAAGCTGCAGCCGGTGCCGTCTCTGACCAGCTGGGCCTCCAGCTGCCTGCCCGCAAAGCCGGCGATGAAGCCGCGGGCCCGGTTCTCGGCGCCGAGGGCGGTCAGGACCTTCGATACGTCGATCCCCTTCCCTCCGGCGTAGCTCTCCTCCCGGATTATCCTGTTGGGGACGTCCTCCCTCATCACGTCGATGAGGAGGGTCCGATCGAGGGCTGGGTTGATGGTTATGGTGTAAATCATC\n+>ERR1877483.32927 M03099:22:000000000-APTMA:1:2119:15956:23349/1\n+CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCCATGCCGCGTGTGTGAAGAAGGTCTTCGGATTGTAAAGCACTTTAAGTTGGGAGGAAGGGCATTAACCTAATACGTTAGTGTTTTGACGTTACCGACAGAATAAGCACCGGCTAACTCTGTGCCAGCAGCCGCGGTAATACAGAGGGTGCAAGCGTTAATCGTAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTTGTTAAGTTGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCAAA\n+>ERR1877483.32948 M03099:22:000000000-APTMA:1:2119:21559:24504/1\n+CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCCATGCCGCGTGTGTGAAGAAGGTCTTCGGATTGTAAAGCACTTTAAGTTGGGAGGAAGGGCAGTAAGTTAATACCTTGCTGTTTTGACGTTACCAACAGAATAAGCACCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTCAGCAAGTTGGAGGTGAAATCCCCGGGCTCACCCTGGGAACTGCCTCCAAA\n+>ERR1877483.32949 M03099:22:000000000-APTMA:1:2119:22063:24539/1\n+ACGGGCGGTGTGTACACATCTCCGAGCCCACGAGACAGCCCACGAGACATCCTACGAGACCGCCCGCAAGAAAGCCCCCGAGACATCCCACCCTCCGGCCCTCCAAGAGAACGACCACGCGGCCCACGTGCCCCGACACCTAAGCGGGTCCTAGAAGGCGCAAGCACGACTCCCTCCGTGCTAGGGTCAGCCCTCATACGACGGAAACCCGCGATCTTCTTAATCAACGTTCGCTAGAACACCCTAGGCTGACTCCGACGAACAGACTGCAGGACCGACGCTCGACCCCGCAACCACCACG\n+>ERR1877483.32954 M03099:22:000000000-APTMA:1:2119:11950:24861/2\n+GGCTACTAGGGGTACTAATTCTCGTTTGTCCCCACGGTTTCGCACCTTCACGGTAGTCTTTATTCCGGCGACTCCCCTCGCCACCTGTAGTCCTCCAGGACTCTACGCAATTCACCGCCTCACCTGGAAATCTACCCCCCCCTTCCAGCATTCTACCTGCCCAGTTCCAATTCAGTTTCCCGGTTTAACCCCGGGGCTTCCACATCGACTTTACAGACCGCCCTCCTAGGCCTTACGCCCATTACATCCGATTAACGCCTTCACCCTCCGTATTCCCGCCTGCTCTGGCACCGTCTTAGG\n+>ERR1877483.32955 M03099:22:000000000-APTMA:1:2119:9959:24862/2\n+GACTACAGGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGTGCATGAGCGTCAGTGTCATCCCAGGGGGCTGCCTTCGCCACTGGTGTTCCTTCCTATATCTACGCATTTCACCGCTACACAGGAAATTCCACCACCCTCTACCATACTCTAGCCCAGTAGTTTTGGAGGCAGTTCCCAGGTTGAGCCCGGGGATTTCACCTCCAACTTGCTGAACCACCTACGCGCGCCTTACGACCAGTAATTCCGATTAACGCTTGCACCCTTCGTATTACCGCGGCAGCTGCTACTCTGTTAGC\n+>ERR1877483.32956 M03099:22:000000000-APTMA:1:2119:14880:24914/2\n+GCGACGGGTACGAGAGAGATCAGTGGGAATAGAAATGAAAGGAGGCGGAAGTAAGAACACAAACGAGTCGGTGTAATCTAAATGGAGAGGAGGACTAAGGTGCTGAATACGGCTGGAGCTAGGGGGGTGGCACATGGTCGATACTGACTGATCAACTGTGATGTCGCTCTTAGTAGTGGTGGAACAGGACTGGATATGGCTATTAGGACTGGGTATCATAAACATGCTACTATGGGTAACTTACTACGACAACACTTGGAGGCTAACATCACTATGTAACTATCGAAAGTGAGATTACGAT\n+>ERR1877483.32957 M03099:22:000000000-APTMA:1:2119:17520:25205/2\n+GACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTCAGCGTCAGTATCGAGCCAGTGAGCCGCCTTCGCCACTGGTGTTCCTCCGAATATCTACGAATCTCACCTCTACACTCGGACTTCCACTCACCTCTCTCGAACTCCCGACCGATAGTTTTGACGGCAGTTCCGGGGTTGAGCCCCGGGATTTCACCCCCAACTTTACGGTCCGCCTACGTGCGCTTTACGCCCGGTCCTTCCGATCACCGCTATCCCCCTCCGTACTACCGTGTCTGCTGGCCCGTACGTCGC\n'