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Changeset 0:894eff01255b (2018-01-09)

Commit message:
planemo upload commit 3ad4270aabe37123987e91a178bd7d61778c849c-dirty

added:
kat_filter.xml
macros.xml
test-data/db.fasta
test-data/input.fastq
test-data/matched.fastq

diff -r 000000000000 -r 894eff01255b kat_filter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/kat_filter.xml Tue Jan 09 10:27:22 2018 -0500

[

@@ -0,0 +1,125 @@
+<?xml version='1.0' encoding='utf-8'?>
+<tool id="kat_@EXECUTABLE@" name="KAT @EXECUTABLE@" version="@VERSION@.2">
+  <description>Filtering reads or k-mer from fasta file</description>
+  <macros>
+    <token name="@EXECUTABLE@">filter_seq</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <expand macro="stdio" />
+  <expand macro="version_command" />
+  <command><![CDATA[
+
+
+  cp "$db" db.fasta &&
+
+  #if $single_or_paired.type == "single"
+  ln  "$input_se" read.fastq &&
+
+  kat filter seq
+
+  --seq read.fastq
+
+  #elif $single_or_paired.type == "paired"
+  ln  "$single_or_paired.forward_pe" read_1.fastq && ln  "$single_or_paired.reverse_pe" read_2.fastq &&
+
+  kat filter seq
+
+  --seq read_1.fastq --seq2 read_2.fastq
+
+  #else
+  ln "$single_or_paired.fastq_collection.forward" read_1.fastq && ln  "$single_or_paired.fastq_collection.reverse" read_2.fastq &&
+
+  kat filter seq
+
+  --seq read_1.fastq --seq2 read_2.fastq
+
+  #end if
+
+
+  @THREADS@
+
+  --mer_len $kmer
+
+  $stats
+
+  #if $invert_or_both.which == "invert":
+     $invert_or_both.invert
+  #elif $invert_or_both.which == "split":
+     $invert_or_both.separate
+  #end if
+
+  -o reads
+  'db.fasta'
+
+  ]]></command>
+  <inputs>
+    <expand macro="macro_input" />
+
+    <param name="db" type="data" format="fasta" label="Fasta file of targeted regions"/>
+    <expand macro="macro_kmers" />
+
+    <param name="threshold" type="float" value='0.10000000000000001' label="Target Threshold" help="What percentage of the sequence needs to be covered with target k-mers to keep the sequence"/>
+
+    <param name="stats" type="boolean" truevalue='--stats' falsevalue='' checked='False' label="Stats" help="Whether to emit statistics about quantity of found k-mers in each sequence."/>
+    <conditional name="invert_or_both">
+      <param name="which" type="select" label="Advance Options">
+        <option value="none">No Advance</option>
+        <option value="invert">Option 1</option>
+        <option value="split">Option 2</option>
+      </param>
+      <when value="invert">
+        <param name="invert" type="boolean" truevalue='--invert' falsevalue='' checked='True' label="Take k-mer not matching target" help="Whether to take k-mers outside region as selected content, rather than those inside."/>
+      </when>
+      <when value="split">
+        <param name="separate" type="boolean" truevalue='--separate' falsevalue='' checked='True' label="Keep inside and outside of target(s) region" help="Whether to partition the k-mers into two sets, those inside region and those outside."/>
+      </when>
+      <when value="none">
+      </when>
+    </conditional>
+  </inputs>
+  <outputs>
+    <data format="fastqsanger" name="reads" label="Reads.fastq" from_work_dir="reads.in.fastq" >
+      <filter> single_or_paired['type'] == "single" </filter>
+    </data>
+    <data format="fastqsanger" name="forward" label="forward_R1.fastq" from_work_dir="reads.in.R1.fastq" >
+      <filter> single_or_paired['type'] == "paired"</filter>
+    </data>
+    <data format="fastqsanger" name="reverse" label="reverse_R2.fastq" from_work_dir="reads.in.R2.fastq" >
+      <filter> single_or_paired['type'] == "paired"</filter>
+    </data>
+
+
+    <collection name="paired_reads" type="paired" label="Reads">
+      <data name="forward" format="fastqsanger" from_work_dir="reads.in.R1.fastq" >
+        <filter> single_or_paired['type'] == "collection"</filter>
+      </data>
+      <data name="reverse" format="fastqsanger" from_work_dir="reads.in.R2.fastq" >
+        <filter> single_or_paired['type'] == "collection"</filter>
+      </data>
+    </collection>
+
+
+    <data format="fastqsanger" name="outside_reads" label='Outside reads' from_work_dir="reads.out.fastq">
+      <filter>invert_or_both['which'] == 'split' and invert_or_both['separate'] and single_or_paired['type'] == "single"</filter>
+    </data>
+    <data format="tabular" name="file_stats" label='Stats' from_work_dir="reads.stats">
+      <filter>stats</filter>
+    </data>
+
+  </outputs>
+  <tests>
+    <test>
+      <param name="input_se" value="input.fastq" />
+      <param name="db" value="db.fasta" />
+      <output file="matched.fastq" ftype="fastqsanger" name="reads" />
+    </test>
+  </tests>
+  <help><![CDATA[
+http://kat.readthedocs.io/en/latest/using.html#filtering-tools
+]]>
+
+  </help>
+  <citations>
+  </citations>
+</tool>

diff -r 000000000000 -r 894eff01255b macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Tue Jan 09 10:27:22 2018 -0500

@@ -0,0 +1,50 @@
+<macros>
+  <token name="@VERSION@">2.3</token>
+  <xml name="requirements">
+    <requirements>
+      <requirement type="package" version="2.3.1">kat</requirement>
+    </requirements>
+  </xml>
+  <xml name="stdio">
+    <stdio>
+      <exit_code range="1:" />
+      <exit_code range=":-1" />
+      <regex match="Error:" />
+      <regex match="Exception:" />
+    </stdio>
+  </xml>
+  <xml name="version_command">
+    <version_command>kat --version</version_command>
+  </xml>
+  <xml name="citations">
+    <citations>
+      <citation type="doi">10.1101/064733</citation>
+      <yield />
+    </citations>
+  </xml>
+  <token name="@THREADS@">
+    --threads \${GALAXY_SLOTS:-4}
+  </token>
+  <xml name="macro_input">
+    <conditional name="single_or_paired">
+      <param name="type" type="select" label="Read type">
+        <option value="single">Single-end</option>
+        <option value="paired">Paired-end</option>
+        <option value="collection">Collection Paired-end</option>
+      </param>
+      <when value="single">
+        <param name="input_se" type="data" format="fastqsanger" label="Single end read file(s)"/>
+      </when>
+      <when value="paired">
+        <param name="forward_pe" type="data" format="fastqsanger" label="Forward paired-end read file"/>
+        <param name="reverse_pe" type="data" format="fastqsanger" label="Reverse paired-end read file"/>
+      </when>
+      <when value="collection">
+        <param name="fastq_collection" type="data_collection" label="Paired-end reads collection" optional="false" format="fastqsanger" collection_type="paired" />
+      </when>
+    </conditional>
+  </xml>
+  <xml name="macro_kmers">
+    <param name="kmer" type="integer" value='27' label="Kmer size" help="The kmer length to use in the kmer hashes.  Larger values will provide more discriminating power between kmers but at the expense of additional memory and lower coverage."/>
+  </xml>
+</macros>

diff -r 000000000000 -r 894eff01255b test-data/db.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/db.fasta Tue Jan 09 10:27:22 2018 -0500

b'@@ -0,0 +1,13873 @@\n+>abcZ_1\n+AAATCGACGAACAGAATGCGTATAGGACTTTTCCGCAAGATGGAAAAACTATCAATCCGT\n+TTCTTCGATAGCCGCAATGATGGCGAAATGCTTAGTCGTTTCACTAGTGACTTAGATAAT\n+ATTTCCAACACACTAAACCAAGCATTGATCCAAGTACTATCCAACGTCGCGCTAATGATT\n+GGTGTTATCATCATGATGTTCCAACAAAACGTGGAACTAGCCTTCGTTACTCTAATATCT\n+GCTCCATTTGCGATTATTATTGCGACAGTGATTATTCGAAAAGCCCGCAAATTCGTTGAT\n+ATTCAACAAGATGAACTAGGCGTACTTAACGGCTACATTGACGAAAAAATCTCTGGTCAA\n+AAAATTATTATCACAAATGGCTTAGAAGAAGAAACAATTGACGGCTTTGTTAAACAAAAC\n+AATATCGTTAAAAACGCCACTTACAAAGGTCAAGTTTACTCCGGTTTACTTTTCCCAATG\n+ATGCAAGGTATTTCCCTATTAAATACAGCTATCGTTATCTTCTTCGGTGGATGGTTA\n+>abcZ_2\n+AAATCGACGAACAGAATGCGTATAGGGCTTTTCCGCAAGATGGAAAAACTATCAATCCGT\n+TTCTTCGATAGCCGCAATGATGGCGAAATGCTTAGTCGTTTCACTAGTGACTTAGATAAT\n+ATTTCCAACACACTAAACCAAGCATTGATCCAAGTACTATCCAACGTCGCGCTAATGATT\n+GGTGTTATCATCATGATGTTCCAACAAAACGTGGAACTAGCCTTCGTTACTCTAATATCT\n+GCTCCATTTGCGATTATTATTGCGACAGTGATTATTCGAAAAGCCCGCAAATTCGTTGAT\n+ATTCAACAAGATGAACTAGGCGTACTTAACGGCTACATTGACGAAAAAATCTCTGGTCAA\n+AAAATTATTATCACAAATGGCTTAGAAGAAGAAACAATTGACGGCTTTGTTAAACAAAAC\n+AATATCGTTAAAAACGCCACTTACAAAGGTCAAGTTTACTCCGGTTTACTTTTCCCAATG\n+ATGCAAGGTATTTCCCTATTAAATACAGCTATCGTTATCTTCTTCGGTGGATGGTTA\n+>abcZ_3\n+AAATCGACGAACAGAATGCGTATAGGACTTTTCCGCAAGATGGAAAAACTATCAATCCGT\n+TTCTTCGATAGTCGCAATGATGGCGAAATGCTTAGTCGTTTCACTAGTGACTTAGATAAT\n+ATTTCCAACACACTAAACCAAGCATTGATCCAAGTACTATCCAACGTCGCGCTAATGATT\n+GGTGTTATCATCATGATGTTCCAACAAAACGTGGAACTAGCCTTCGTTACTCTAATATCT\n+GCTCCATTTGCGATTATTATTGCGACAGTGATTATTCGAAAAGCCCGCAAATTCGTTGAT\n+ATTCAACAAGATGAACTAGGCGTACTTAACGGCTACATTGACGAAAAAATCTCTGGTCAA\n+AAAATTATTATCACAAATGGCTTAGAAGAAGAAACAATTGACGGCTTTGTTAAACAAAAC\n+AATATCGTTAAAAACGCAACTTACAAAGGTCAAGTTTACTCCGGTTTACTTTTCCCAATG\n+ATGCAAGGTATTTCCCTATTAAATACAGCTATTGTTATCTTCTTCGGTGGATGGTTA\n+>abcZ_4\n+AAATCGACGAACAGAATGCGTATAGGGCTTTTCCGCAAGATGGAAAAACTATCAATCCGT\n+TTCTTCGATAGCCGCAATGATGGCGAAATGCTTAGCCGCTTCACTAGTGACTTGGATAAT\n+ATTTCCAACACACTAAACCAAGCATTGATCCAAGTACTATCCAACGTCGCGCTAATGATT\n+GGTGTTATCATCATGATGTTCCAACAAAACGTGGAACTAGCCTTCGTTACTCTAATATCT\n+GCTCCATTTGCGATTATTATTGCGACAGTGATTATTCGAAAAGCCCGCAAATTCGTTGAT\n+ATTCAACAAGATGAACTAGGCGTACTTAACGGCTACATTGACGAAAAAATCTCTGGTCAA\n+AAAATTATTATCACAAATGGCTTAGAAGAAGAAACAATTGACGGCTTTGTTAAACAAAAC\n+AATATCGTTAAAAACGCCACTTACAAAGGTCAAGTTTACTCCGGTTTACTTTTCCCAATG\n+ATGCAAGGTATTTCCCTATTAAATACAGCTATCGTTATCTTCTTCGGTGGATGGCTA\n+>abcZ_5\n+AAATCAACGAACAGAATGCGTATAGGGCTTTTCCGCAAGATGGAAAAACTATCGATTCGT\n+TTCTTCGATAGCCGCAATGATGGCGAAATGCTTAGCCGCTTCACTAGCGACTTAGATAAT\n+ATTTCCAATACACTAAACCAAGCATTGATCCAAGTACTATCCAACGTCGCGCTAATGATT\n+GGTGTTATCATCATGATGTTCCAACAAAACGTGGAACTAGCCTTCGTTACTCTAATATCT\n+GCTCCATTTGCAATTATTATTGCGACAGTGATTATTCGAAAAGCACGTAAATTCGTTGAT\n+GTTCAACAAGATGAACTAGGCGTACTTAACGGCTACATTGACGAAAAAATCTCTGGACAA\n+AAAATCATTATCACAAATGGTTTAGAAGAAGAAACAATTGACGGCTTTGTTAAACAAAAC\n+AATATCGTTAAAAACGCCACTTATAAAGGGCAAGTTTACTCCGGTTTACTTTTCCCAATG\n+ATGCAAGGTATTTCCCTATTAAATACAGCTATCGTTATCTTCTTCGGTGGATGGTTA\n+>abcZ_6\n+AAATCGACGAACAGAATGCGTATAGGGCTTTTCCGCAAGATGGAAAAACTATCGATTCGT\n+TTCTTCGATAGCCGCAATGATGGCGAAATGCTTAGTCGTTTTACTAGTGACTTAGATAAT\n+ATTTCCAATACACTAAACCAAGCATTGATCCAGGTGCTATCCAACGTCGCGCTAATGATT\n+GGTGTTATCATCATGATGTTCCAACAAAACGTGGAACTAGCCTTCGTTACTTTAATATCT\n+GCTCCATTTGCGATTATTATTGCAACAGTGATTATTCGAAAAGCACGTAAATTCGTTGAT\n+GTTCAACAAGATGAACTAGGCGTACTTAACGGCTACATTGACGAAAAAATCTCTGGACAA\n+AAAATCATTATCACAAATGGTTTAGAAGAAGAAACAATTGACGGCTTTGTTAAACAAAAC\n+AATATCGTTAAAAACGCCACTTATAAAGGGCAAGTTTACTCCGGTTTACTTTTCCCAATG\n+ATGCAAGGTATTTCACTATTAAATACAGCTATCGTTATCTTCTTCGGTGGATGGTTA\n+>abcZ_7\n+AAATCGACGAACAGAATGCGTATAGGGCTTTTCCGCAAGATGGAAAAACTATCGATTCGT\n+TTCTTCGATAGCCGCAATGATGGCGAAATGCTTAGCCGCTTCACTAGTGACTTAGATAAT\n+ATTTCCAATACACTAAACCAAGCATTGATCCAAGTACTATCCAACGTCGCGCTAATGATT\n+GGTGTTATCATCATGATGTTCCAACAAAACGTGGAACTAGCCTTCGTTACTCTAATATCT\n+GCTCCATTTGCAATTATTATTGCGACAGTGATTATTCGAAAAGCACGTAAATTCGTTGAT\n+GTTCAACAAGATGAACTAGGCGTACTTAACGGCTACATTGACGAAAAAATCTCTGGACAA\n+AAAATCATTATCACAAATGGTTTAGAAGAAGAAACAATTGACGGCTTTGTTAAACAAAAC\n+AATATCGTTAAAAACGCCACTTATAAAGGGCAAGTTTACTCCGGTTTACTTTTCCCAATG\n+ATGCAAGGTATTTCCCTATTAAATACAGCTATCGTTATCTTCTTCGGTGGATGGTTA\n+>abcZ_8\n+AAATCGACGAACAGAATGCGT'..b'TCCGCAGAAGATAAG\n+AAAAAGTTGAAAAGTGGTGAAACGGTAAGTAAAAAAATTGATAATCGTTTTAATCAAGAA\n+ATGACCATTGTTTATGTCCCGTTGATGAATGGCGATAATTTTGTAGGATCCATCGTTTTG\n+AATTCTCCAATTAGTGGCACTGAACAAGTGATAGGAACAATTAATCAATATATGTTCTAT\n+ACTATTTTACTTTCGATCACAGTAGCACTTATTCTTAGCGCAATTATTTCCAAATTACAA\n+GTGAATCGGATAAACAAATTACGCGCCGCAACAAAAGATGTGATCGAAGGAAATTATCAA\n+ACTCGCTTAAAAGAAAATAACATTGATGAAATTGGTGCGCTCGCAGTCGATTTCAACAAA\n+ATGACAACGACGCTTGAAGCTTCCCAAGAAGAAATTGAGCGTCAAGAAAAACGGCGGCGT\n+>lhkA_158\n+TATCCAACACAAATGGACCAGCCTCTACCTAAAGACTTTTCGATTTCTTCAGAAGATAAG\n+AAAAAACTGGAAAGTGGCGAAACGGTTAGTAAGAAAATAGATAATCGATTTAATAGAGAA\n+ATGACGATTGTTTATGTGCCGATTATGGATGGTGATAAATTTGTCGGTTCTATCGTGCTG\n+AATTCACCTATTAGCGGGACCGAGCAAGTAATTGGTACTATTAATCGTTACATGTTCTAT\n+ACTATTTTACTTTCCATAACCGTAGCACTTATTCTTAGTGCGATTTTGTCCAAACTACAA\n+GTGAATCGAATCAACAAACTACGAGCAGCGACGAAAGATGTTATTCAAGGCAACTACAAA\n+GCCAGACTAAAAGAAAATAACTTTGATGAAATTGGCGCGCTTGCGATTGATTTCAATAAG\n+ATGACTCAAACACTGGAGATTTCTCAAGAAGAAATTGAAAGACAAGAAAAACGGCGCCGT\n+>lhkA_159\n+TATCCTACTCAGCTCAATCAGCCATTACCAAAAGATTTTTCGATTTCAAAAGATGATAAG\n+AAAAAATTAAAAAGTGGCGAAACAGTGAGTAAAAAAATCGACAATCGTTTTAATCGTGAA\n+ATGACTATTGTTTATGTGCCTATTATGGATGGCGATAAGTTTGTTGGCTCTATTGTCTTG\n+AATTCTCCAATTAGCGGAACTGAACAAGTGATTGGAACAATTAATCGCTATATGTTCTAT\n+ACTATTTTACTGTCGATTACAATTGCACTTATTTTGAGTGCTATTCTGTCCAAACTACAA\n+GTCAATCGGATTAATAAATTGCGTTCAGCGACAAAAGATGTAATCCAAGGCAATTATAAG\n+GCGCGGCTAAAAGAGAATAATTTTGATGAAATTGGCGCACTTGCCATTGATTTCAACAAA\n+ATGACGGAAACGCTTGAAACATCTCAAGAAGAAATTGAACGACAAGAAAAACGTCGGCGC\n+>lhkA_160\n+TATCCAACACAAATGGACCAGCCTCTACCTAAAGACTTTTCGATTTCTTCGGAAGATAAG\n+AAAAAACTGGAAAGTGGAGAAACGGTTAGCAAGAAAATAGATAATCGATTCAATAGAGAA\n+ATGACGATTGTTTATGTGCCGATTATGGATGGTGATAAATTTGTCGGTTCTATCGTGCTG\n+AATTCACCTATTAGCGGGACCGAGCAAGTAATTGGTACGATTAATCGTTACATGTTTTAT\n+ACTATTTTACTTTCCATAACCGTAGCACTTATTCTTAGTGCGATACTGTCCAAACTACAA\n+GTGAATCGAATCAACAAACTACGAGCAGCGACGAAAGATGTTATTCAAGGTAACTACAAA\n+GCCAGACTAAAAGAAAATAACTTTGATGAAATTGGCGCGCTTGCGATTGATTTCAATAAG\n+ATGACTCAAACACTGGAGATTTCTCAAGTAGAAATTGAAAGACAAGAAAAACGGCGCCGT\n+>lhkA_161\n+TATCCAACACAAATGGACCAGCCTCTACCTAAAGACTTTTCGATTTCTTCGGAAGATAAG\n+AAAAAACTGGAAAGTGGCGAAACGGTTAGCAAGAAAATAGATAATCGATTCAATAGAGAA\n+ATGACGATTGTTTATGTGCCGATTATGGATGGTGATAAATTTGTCGGTTCTATCGTGCTG\n+AATTCACCTATTAGCGGGACCGAGCAAGTAATTGGTACGATTAATCGTTACATGTTTTAT\n+ACTATTTTACTTTCCATAACCGTAGCACTTATTCTTAGTGCGATACTGTCCAAACTACAA\n+GTGAATCGAATCAACAAACTACGAGCAGCGACGAAAGATGTTATTCAAGGTAACTACAAA\n+GCCAGACTAAAAGAAAATAACTTTGATGAAATTGGCGCGCTTGCGATTGATTTCAATAAG\n+ATGACTCAAACACTGGAGATTTCTCAAGAAGAAATTGAAAGACAAGAAAAACGGCGCCGT\n+>lhkA_162\n+TATCCAACACAGATGAATCAGCCGTTACCAAAGGATTTCTCTATTTCTTTGGATGATAAG\n+AAAAAGCTTGAAAGTGGCGAAACAGTTAGTAAGAAAATAGATAATCGCTTTAATAAAGAA\n+ATGACAATTGTGTACGTCCCAATAATGAATGGCGACAAATTTGTCGGTTCTATCGTGCTC\n+AATTCACCTATTAGCGGTACGGAGCAAGTAATTGGTACGATTAACCGCTATATGTTCTAC\n+ACTATTTTACTTTCTATAACGGTAGCACTTATTCTTAGCGCAATCTTGTCCAAACTACAA\n+GTAAATCGAATCAACAAACTACGAGCAGCGACAAAAGACGTTATTCAAGGCAATTACAAA\n+GCTCGATTGAAGGAAAATAATTTTGATGAAATTGGTGCACTTGCCATTGATTTCAATAAA\n+ATGACACAAACCCTTGAAACATCTCAAGAAGAAATAGAACGACAAGAGAAGCGGAGACGC\n+>lhkA_163\n+TATCCAACACAGATGAATCAGCCTTTACCTAAGGATTTCTCTATTTCTGCGGATGATAAG\n+AAAAAGCTTGAAAGTGGTGAAACGGTTAGTAAGAAAATAGATAATCGCTTTAATAAAGAA\n+ATGACAATTGTGTACGTCCCAATAATGAATGGCGACAAATTTGTCGGTTCTATCGTGCTC\n+AATTCACCTATTAGCGGTACGGAGCAAGTAATTGGTACGATTAACCGCTATATGTTCTAC\n+ACTATTTTACTTTCTATAACGGTAGCACTTATTCTTAGCGCAATCTTGTCCAAACTACAA\n+GTAAATCGAATCAACAAACTACGAGCAGCGACAAAAGACGTTATTCAAGGCAATTACAAA\n+GCTCGCTTGAAGGAAAATAATTTTGATGAAATTGGTGCACTCGCCATTGATTTCAATAAA\n+ATGACACAAACCCTTGAAACATCTCAAGAAGAAATAGAACGACAAGAGAAGCGGAGACGC\n+>lhkA_164\n+TATCCAACACAGATGAATCAGCCTTTACCTAAGGATTTCTCTATTTCTGCGGATGATAAG\n+AAAAACCTTGAAAGTGGTGAAACGGTTAGTAAGAAAATAGATAATCGCTTTAACAAAGAA\n+ATGACAATTGTGTACGTCCCAATAATGAATGGCGATAAATTTGTCGGTTCTATCGTGCTG\n+AATTCACCCATTAGCGGTACGGAGCAAGTAATTGGCACGATTAACCGCTATATGTTCTAC\n+ACTATTTTACTTTCTATAACGGTAGCACTTATTCTTAGCGCAATCTTGTCCAAACTACAA\n+GTAAATCGAATCAACAAACTACGAGCAGCGACAAAAGACGTTATTCAAGGCAATTACAAC\n+GCTCGCTTGAAGGAAAATAATTTTGATGAAATTGGTGCACTCGCCATTGATTTCAATAAA\n+ATGACACAAACCCTTGAAACATCTCAAGAAGAAATTGAACGACAAGAGAAACGGAGACGC\n'

diff -r 000000000000 -r 894eff01255b test-data/input.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input.fastq Tue Jan 09 10:27:22 2018 -0500

b'@@ -0,0 +1,24288 @@\n+@HWI-ST1348:99:H0D4GADXX:1:1101:12325:8854/1\n+CTTATAATGAACACATTGATCGCTTATATGCTAGTGCAGCAAAAATTGACTTAGTTATTCCTTATTCCAAAGAAGAGCTACGTGAATTACTTGAAAAATTA\n++\n+CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJJJIIJJJJJJJJJJJJJJJJJJIJJJJJJJJJJJJJJJJJJJJJJHHHHHFFFFEEEEEEEDDDDDDDD\n+@HWI-ST1348:99:H0D4GADXX:1:1101:16009:11807/1\n+TTTCCGTACTTCCATCGCTTGGTCCCGTATCTTCCCAAATGGTGACGAAACTGAGCCAAACGAAGCAGGACTACAATTTTACGATGATTTATTCGATGAAC\n++\n+CCCFFFFFHHHHHJJJJJJJJJIIJJJHIJJJJJJJJJJJJJFHIIJJJJJJJJJJJJJIJHHFFFEEDDDDDDDDDDDDFDDBDDDFEEDEDDDEEEDDD\n+@HWI-ST1348:99:H0D4GADXX:1:1101:13122:12268/1\n+GAAAAGGACTTTCCGTTCAAGATGTTACTCCAAAAGGCGGATTCGGTCACATTACTGACGGTCCAACACCAGATAACTTAAAATTAGAAGGAATCGACTTC\n++\n+CCCFFFFFHHHHHJJIJJJJJJJJIJJJJJJJJJJJJJJJJJJJJJHIIJJJJHHHHHHFFCDDEDDDDDDDDDDDDDEDDDDEDDDDDDDDDDDDDDDDD\n+@HWI-ST1348:99:H0D4GADXX:1:1101:3847:12540/1\n+CTTGGTTTAGTGTATTGGAAATATTATCTAAGTCGCTAGTGAAGCGGCTAAGCATTTCGCCATCATTGCGGCTATCGAAGAAACGAATCGATAGTTTTTCC\n++\n+CCCFFDDFHHHHHJJJIIJJJJJJJJJIJJJJIHJIIIJDHGJJJJJJJJJJJJJJJJIJJIGHHHHFFFDDDDDDDDDDDDDDDDDDDDDDDD:BDDDCD\n+@HWI-ST1348:99:H0D4GADXX:1:1101:15695:12654/1\n+GGCAGTTACAACAACTAGGTCCGCATCGTGGCAGTCGCTATAATTTGCTGAGTAGATTTTCTTCGGTGTAGAAAATGGAACGGCATGGCTTAAATCCATTG\n++\n+CCCFFFFFHHHHHJJJJJJHHIJJJJJJJIJJJJIJIIIJJJJJJJJJJJGIIJJGJJJJJHHHHF?DDEEEEEEDDDCDDDDDDDDDDDDDDDECDDDED\n+@HWI-ST1348:99:H0D4GADXX:1:1101:11189:13900/1\n+GTTTAGTGTATTGGAAATATTATCTAAGTCGCTAGTGAAGCGGCTAAGCATTTCGCCATCATTGCGGCTATCGAAGAAACGAATCGATAGTTTTTCCATCT\n++\n+CCCFFFEFHHHHHJGJIJJJJJJJJJJIHJJJJJJGGHIIJJJJJJJJJJJJJIIIIIJJJJIHHHFFDDDDDDDDDDDDDBDBDDDDDDCEEDDDDEEDD\n+@HWI-ST1348:99:H0D4GADXX:1:1101:10723:17926/1\n+TCTCTATTTCTGCGGATGATAAGAAAAAGCTTGAAAGTGGTGAAACGGTTAGTAAGAAAATAGATAATCGCTTTAACAAAGAAATGACAATTGTGTACGTC\n++\n+CCCFFFFFHHHHHJJJJJJJJJJIJJJIJJJIJJJJIFHIIJJIJJJJIIGIFHIJJJJJJJJJHGHHHHFFFDDEDEDEDDDDDDDDDDDDDDDDEEDDD\n+@HWI-ST1348:99:H0D4GADXX:1:1101:20826:19324/1\n+GTTCACCGATGATTAAACCATCTAAATCATCTGCGTAACCTTTTTGTGTTAGTTGTTCTGCTCCAAGTTCACCGATTTCTTCCCCAACTGTTGCTAATAAT\n++\n+CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJJJJIJJJJJJJJJJHIJJIJIJJJJJJJJIJJJJHHHHHHFFEDDDDEDDDDDDDDDDDDDDDEDDDDE\n+@HWI-ST1348:99:H0D4GADXX:1:1101:11646:21325/1\n+GAGTAACGAAGGCTAGTTCCACGTTTTGTTGGAACATCATGATGATAACACCAATCATTAGCGCGACGTTGGATAGTACTTGGATCAATGCTTGGTTTAGT\n++\n+@@@?DEFFHHHGHIJIIJIGIIJFGIJJJJJIIGIIJJJJIEGGIJJJJJIJJJJJJIIIIIHIGDDDDBDDCCEDDEDEEDDDDDDDDDDDECD@BDCDC\n+@HWI-ST1348:99:H0D4GADXX:1:1101:13141:21911/1\n+AGCCTTGATACAGCACGTTTCCGTATGTCAATTGCTGACTATCTAAAAGTAGATGCTCGTAACGTCCATGGTTACATCCTTGGCGAACACGGCGATACAGA\n++\n+CCCFFFFFHGHGHJJJJJJJJJJIIGIJI:::?CGHIJJJJJJJJJIJJDHHIJGHIIJBGHIGHIIJJJHEHHHHFFFFFFEEDDDBDDDDDDDDDDDDD\n+@HWI-ST1348:99:H0D4GADXX:1:1101:10800:28631/1\n+CTAGTGAAGCGGCTAAGCATTTCGCCATCATTGCGGCTATCGAAGAAACGAATCGATAGTTTTTCCATCTTGCGGAAAAGCCCTATACGCATTCTGTTCGT\n++\n+@CCFDFFFHHHHHJJJIJJJJJJJJJJJJJJJJJJJJJIJJJIJJJJJJHHHHFFFFDDEEEDDDDEEDDDDDDDDDDDDDDDDDDDDDDDDDDEEEDDDB\n+@HWI-ST1348:99:H0D4GADXX:1:1101:20491:28620/1\n+ATTCAAGGCAATTACAACGCTCGCTTGAAGGAAAATAATTTTGATGAAATTGGTGCACTCGCCATTGATTTCAATAAAATGACACAAACCCTTGAAACATC\n++\n+CCCFFFFFHHHHHJJIJIJJIJJJJJJJJJJJJIJJJJIJJJJJJJJJJIJJJFHIIJJJIHHHFFFFFFEEEEEEDDDEDCDDDDDDBDDDDDDDDDDDC\n+@HWI-ST1348:99:H0D4GADXX:1:1101:7329:32108/1\n+ATAGTATCCATTGCACCTTGTTCATCTTCGCTAATCCATTCAGTAATTGGAAGGCCGCCGACAGTTGTGTGCCTCCATGCTGGGAATTCTGTATCGCCGTG\n++\n+BCCFDFFFHHHHHJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJIIIJJJJJIJJJJJJJJHHFFFEEEDEDDDDDDDDDDDDDDDDDDDEEEEEEDDDDDD\n+@HWI-ST1348:99:H0D4GADXX:1:1101:6537:33082/1\n+AGTTCAATCATTGCAATAACCATCGCCGCTAGACCTGACTTCATATCCGTTGCGCCGCGTCCGTATAGTTTCCCTTCATGCTCTGTCGCTTCAAAAGGTGG\n++\n+BCBFFFFFHHHHHJJJJJJJJJJJIIJIJJJIJJJJJIJJJJJJJJJJJIJIJJIJHFDDDDDBDDDEDFEEDDDDDDEDDDDDDDDDDDDDDDDDDD@CB\n+@HWI-ST1348:99:H0D4GADXX:1:1101:8396:34357/1\n+CCGCATGCGTCCATAATACACCATCTTTAATAATAGAAACGTTTGAAGCAGAACATTCTGTTACTTGTTCCCCGCGATGTAAAATAGCTTCCAAAGCATTT\n++\n+CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJJJJJIJJJJJJJJJJJJJJJJIJJJJJJJJJJJJJJJJJHHHFDDDDDE@C@;ACDDDDDDDDDDDDDD\n+@HWI-ST1348:99:H0D4GADXX:1:1101:4455:40892/1\n+GGTAAATATTGATTCGACTAATGGGCATGAAGAACAAGTTGCGAACTATTTGCAAAAGTTGTTAGCTGAACACGGTATTGAGTCCGAAAAGGTACAA'..b'CTTGAAACATCTCAAGAAGAAATTGAACGACAAGAGAAACGGAGACGCCAGTTTATTGCTGA\n++\n+BB1BDFFFFHHHFHIJJJIJJJJJJIJJJIGHIIIJJJJJEIJJJJGGFEGIGIIIJJIJGHIGGIIGHGFFFED@CECDD?@???BDDDCDEECDCDCC@\n+@HWI-ST1348:99:H0D4GADXX:2:2216:7148:70790/1\n+CTTGTCCAAACTACAAGTAAATCGAATCAACAAACTACGAGCAGCGACAAAAGACGTTATTCAAGGCAATTACAACGCTCGCTTGAAGGAAAATAATTTTG\n++\n+?@@DFFFEDFDBHEHGGGGIIIGHGFGIJGIJGGGACHH@GGGHGIG6FEF=A1CEAEEFFFFEFC?AACCDCCDC;;??;@?BBDDDD8>><CCDDDDD:\n+@HWI-ST1348:99:H0D4GADXX:2:2216:3356:73770/1\n+AACGATAGCTGTATTTAATAGGGAAATACCTTGCATCATTGGGAAAAGTAAACCGGAGTAAACTTGCCCTTTATAAGTGGCGTTTTTAACGATATTGTTTT\n++\n+CCCFFFFFHHHHHJJJJJJJJJJIJJJJJIJJJJJJJJJIJJJJJJJIFHIJJJJJJJGHHIJIJJJHHHHHFFFFFADEDDDDDDDDDDDDDDDEEDDDD\n+@HWI-ST1348:99:H0D4GADXX:2:2216:5940:75462/1\n+GCTGAAATGGGCTTCAAGGTTTTCCGTACTTCCATCGCTTGGTCCCGTATCTTCCCAAATGGTGACGAAACTGAGCCAAACGAAGCAGGACTACAATCTGT\n++\n+@@@FDDDDHGHHGJIIIJJHIGIIJJFFHIEHJIJIIJGGIJDDHGIGIJJIIJJJIJJIHI7@CHHEEFFFEACCCCDDDD=BB@ACDBBCACCCADCD:\n+@HWI-ST1348:99:H0D4GADXX:2:2216:16564:76685/1\n+GTATTGGAAATATTATCTAAGTCGCTAGTGAAGCGGCTAAGCATTTCGCCATCATTGCGGCTATCGAAGAAACGAATCGATAGTTTTTCCATCTTGCGGAA\n++\n+C@@FFFFFHFBFDIIGGIJDHIIGIIIIHIG9GHIIGGEFHEEIIIGGGEGGJIJEGGHEEBBCCDDCBBDCCBBD??BBB25:@CCD?A@ACCCD@BB>>\n+@HWI-ST1348:99:H0D4GADXX:2:2216:11696:77729/1\n+TTCGATGAACTTCTAGCACATAATATCGAACCACTAATCACTTTATCTCACTATGAAACACCACTTCACTTATCGAAAACTTACGACGGCTGGGTAAATAG\n++\n+CCCFFFFFHHHHHJJJJJJJJJJJJJJIJJJJJJJJJJIJJJJJIJJIJJJJIIJIJJJJJJJIJJJJJIJJJJHHHHFFFFDEDDDDDDDBDDA@9::@>\n+@HWI-ST1348:99:H0D4GADXX:2:2216:1712:78154/1\n+CAATGATGGCGAAATGCTTAGCCGCTTCACTAGCGACTTAGATAATATTTCCAATACACTAAACCAAGCATTGATCCAAGTACTATCCAACGTCGCGCTAA\n++\n+CCCFFEFFHHHHHIJJIJIJJJIJJJJIJJJGIIJGIIIIIJJJIIIIJJIIIIJJIFHGHHHFFFFECEEEDDEDDDDDDDDEEDDDDCCBBBDDDDDDB\n+@HWI-ST1348:99:H0D4GADXX:2:2216:8423:78377/1\n+GTTGATGCGGGTGATGTATCTAAGTGGAAGTTCCCACCTTTTGAAGCGACAGAGCATGAAGGGAAACTATACGGACGCGGCGCAACGGATATGAAGTCAGG\n++\n+CBCFFFFFHHH@FGIJHJJJJJJJIHIIJJHJJJJIJJJJJIJJJJIJIJJJIIHHHHFFFFFDEDEEEDDDDDDDDDDDBDDBDDDDDDDDDEEDDDEDD\n+@HWI-ST1348:99:H0D4GADXX:2:2216:4026:81369/1\n+CTGTATCGCCGTGTTCGCCAAGGATGTAACCATGGACGTTACGAGCATCTACTTTTAGATAGTCAGCAATTGACATACGGAAACGTGCTGTATCAAGGCTT\n++\n+CCCFFFFFHHHHHJJJJJJJJJJIJJJJJJJJJJJIJIJJJJJJIJJJIIJHHHHHHDEEFFFFEEEEEEDDDDDDDDDDDDDDDADDDDDDEEEDDDDDD\n+@HWI-ST1348:99:H0D4GADXX:2:2216:9367:83208/1\n+CATCTAAATCATCTGCGTAACCTTTTTGTGTTAGTTGTTCTGCCCCAAGTTCACCGATTTCTTCCCCAACTGTTGCTAATAATCTGATCTTGCCGTTTAGT\n++\n+CCCFFFFFHHHGHIJJJGGJJJJJJJIIFHGHIIIJJJJIJIJJJJJJJJJIIJJJHHIGIJJJHHHHFFFFDEEEDEDDCDEDDECCDDDDDDDDDDDDD\n+@HWI-ST1348:99:H0D4GADXX:2:2216:9137:83619/1\n+ATTAAATACGGTGCGGACATAGTTTTCATAGAAGTCGATCATTTTTCTATTTACCCAGCCGTCGTAAGTTTTCGATAAGTGAAGTGGTGTTTCATAGTGAG\n++\n+@@CDFFDFHFHFDHHHGJIJJGGGIIGIJG?BFDFEDGIIIJJJIIIGIJIJJIIIIGHHIBEEFDECBCECCBBFBDDDCDEDCDDC@ABDCBCDDEEEC\n+@HWI-ST1348:99:H0D4GADXX:2:2216:4540:85153/1\n+GTGTTTCATAGTGAGATAAAGTGATTAGTGGTTCGATATTATGTGCTAGAAGTTCATCGAATAAATCATCGTAAAATTGTAGTCCTGCTTCGTTTGGCTCA\n++\n+BB@FFFFFHHHHHGIJIGIJJ?FHIIJJEGHIJIJIIIJJHHIFGIJJJGGIGGIJJIJJJIJJJJIJJIJJJJJJJHHEHHHHFFFFFEEDEEDDDDCDD\n+@HWI-ST1348:99:H0D4GADXX:2:2216:14434:93168/1\n+GTTTTTCCATCTTGCGGAAAAGCCCTATACGCATTCTGTTCGTTGATTTACCAGCTACCCCTGTCATAATGATACTTTGAATAAAAGTGGCAGCAGCGAGC\n++\n+CCCFFFFFHHHHHJIJJJJJJIJJJJJIIJJJJJJJJJJJJJIIJJJJJJJJIJIIJJJJHHGEFFFFFFFEDDEEEEDADDEDDDDACDD?BBDDDDBDD\n+@HWI-ST1348:99:H0D4GADXX:2:2216:8036:96051/1\n+CATCTGGAAACTTAATCGCATCACGAATGAAGAATACTGGCAAATTATTTCCGACAAAGTCATAATTTCCCTCTTCCGTATAAAACTTAACGGAGAAACCG\n++\n+@CCFFFFFHHHHHJJJJJJJJJJJIJJJJJJJJIJJJJIIHGIJIIIIJJJJGIIIJJHC@EGHHHHHHHFFFFFFEDEEDDEEDDDCDDDBBDBDDDDDD\n+@HWI-ST1348:99:H0D4GADXX:2:2216:6952:98103/1\n+ATTTGTGATAATGATTTTTTGTCCAGAGATTTTTTCGTCAATGTAGCCGTTAAGTACGCCTAGTTCATCTTGTTGAACATCAACGAATTTACGTGCTTTTC\n++\n++18BD,2AC>DDDDAEEICE??49C@D?)41?C4?BDDDD6BC<9*/8:7;;;;77@DDD25?;>?>@A;;>AA?AAAAAA3:,3==59A###########\n+@HWI-ST1348:99:H0D4GADXX:2:2216:11200:100390/1\n+AACGTGCTGTATCAAGGCTTGTTCCAGAACCGATAACACGTTCTTTTGGAAGACCTGAGAATTTCCATGTAGCGTAAGTTAAGATGTCTACTGGGTTAGAA\n++\n+:?14ADDFHHHHHJJJJJJJJJJJJJJJJJJJHJJJJEGIHHIJJJJJJJJIIJJIJIGHHHHHFFFFFFFEEDDDDDDDEEDDDDCCCDDDDDDCBDDDC\n'

diff -r 000000000000 -r 894eff01255b test-data/matched.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/matched.fastq Tue Jan 09 10:27:22 2018 -0500