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Changeset 0:e1867440ed36 (2017-09-19)

Next changeset 1:f49992c79fe4 (2017-11-02)

Commit message:
planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 008f4667b70be22e9ddf496738b3f74bb942ed28

added:
seqtk_nml.pl
seqtk_nml.xml
test-data/inputforward.fastq
test-data/inputreverse.fastq
test-data/logdownsample.log
test-data/lognosample.log
test-data/outputdownsamepleforward.fastq
test-data/outputdownsameplereverse.fastq
test-data/outputforward.fastq
test-data/outputreverse.fastq
test-data/testref.fasta

diff -r 000000000000 -r e1867440ed36 seqtk_nml.pl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/seqtk_nml.pl Tue Sep 19 16:37:42 2017 -0400

[

@@ -0,0 +1,268 @@
+#!/usr/bin/env perl
+package seqtk_nml;
+use warnings;
+use strict;
+use Bio::SeqIO;
+use Getopt::Long;
+use Pod::Usage;
+use File::Copy;
+__PACKAGE__->run unless caller;
+
+
+my $rv;
+
+sub get_parameters {
+    my ($fastaref, $type, $coverage, $length,$log);
+    my ($for,$rev,$out_for,$out_rev);
+    #determine if our input are as sub arguments or getopt::long
+    if ( @_ && $_[0] eq __PACKAGE__ ) {
+        Getopt::Long::Configure('bundling');
+        GetOptions(
+            'ref=s' => \$fastaref,
+            'type=s' => \$type,
+            'forward=s'   => \$for,
+            'reverse=s'   => \$rev,
+            'out_forward=s'   => \$out_for,
+            'out_reverse=s'   => \$out_rev,
+            'log=s'=> \$log,
+            'cov=s' => \$coverage
+        );
+    }
+
+    if ( !$for || !( -e $for ) ) {
+        print "ERROR: Was not given or could not find fastq file: '$for'\n";
+        pod2usage( -verbose => 1 );
+    }
+
+    if ( !$out_for ) {
+        print "ERROR: Was not given output file path for fastq\n";
+        pod2usage( -verbose => 1 );
+    }
+
+    if ( $type eq 'paired') {
+        if ( !$rev || !( -e $rev ) ) {
+            print "ERROR: Was not given or could not find reverse fastq file: '$rev'\n";
+            pod2usage( -verbose => 1 );
+        }
+
+        if ( !$out_rev ) {
+            print "ERROR: Was not given output file path for reverse fastq\n";
+            pod2usage( -verbose => 1 );
+        }
+    }
+
+    if ( !$coverage ) {
+        print "ERROR: Was not given a coverage number\n";
+        pod2usage( -verbose => 1 );
+    }
+
+    if ( $coverage <=0  ) {
+        print "ERROR: Was given a coverage less than 0\n";
+        pod2usage( -verbose => 1 );
+    }
+
+
+
+    if ( !$log ) {
+        print "ERROR: Was not given a log file\n";
+        pod2usage( -verbose => 1 );
+    }
+
+
+    return ($fastaref, $type, $coverage, $length, $log,$for,$rev,$out_for,$out_rev);
+}
+
+
+sub run {
+    my ($fastaref, $type, $coverage, $length, $log,$for,$rev,$out_for,$out_rev) = get_parameters(@_);
+    my $subsample_size;
+
+
+    #open log fh here
+    open my $log_fh,">" ,"$log";
+
+
+    my @in_fastqs;
+    my @out_fastqs;
+
+
+    if ($type eq "single"){
+ $in_fastqs[0] = $for;
+        $out_fastqs[0] = $out_for;
+    }elsif ($type eq 'paired' ) {
+ $in_fastqs[0] = $for;
+ $in_fastqs[1] = $rev;
+        $out_fastqs[0] = $out_for;
+        $out_fastqs[1] = $out_rev;
+    }
+    else {
+        die "Given unknown read type of '$type'";
+    }
+
+    #get total read lengths from all fastq files given
+    my $total= get_total_length(@in_fastqs);
+
+
+    if (!($coverage)){
+ $coverage = 50;
+    }
+
+    my $seq_in  = Bio::SeqIO->new(
+        -format => 'fasta',
+        -file   => $fastaref,
+    );
+
+    while ( my $seq = $seq_in->next_seq()) {
+        $length += $seq->length();
+    }
+
+
+    print $log_fh "Downsampling to coverage of: $coverage\n";
+    print $log_fh "Total number of Basepairs: $total\n";
+    print $log_fh "Length of Reference: $length\n";
+
+    my $rawcoverage = $total/$length;
+    printf $log_fh "Raw Coverage: %.3f\n",$rawcoverage;
+
+    if($rawcoverage > $coverage){
+ #need to downsample
+ #calculate $subsample_size
+ $subsample_size = $coverage/$rawcoverage;
+ printf $log_fh "subsample: %.3f",$subsample_size;
+
+ foreach my $fastq (@in_fastqs){
+            my $out = shift @out_fastqs;
+            #seed always set to 42 for reproducibility
+            my $seqCommand = "seqtk sample -s42 $fastq $subsample_size > $out";
+            $rv = system($seqCommand);
+            #need to bit shift 8 bit because seqtk exit code for some reason are greater then standard 0-255 values that most unix application expect
+            die "Error when running '$seqCommand' command" if $rv >>8;
+ }
+    } else {
+ #no sampling needed, just copy the fastq's to the output
+ print "Subsampling not required\n";
+ foreach my $fastq (@in_fastqs){
+            my $out = shift @out_fastqs;
+            copy($fastq,$out) || die "Not able to copy '$fastq' to '$out' with error $!";
+ }
+    }
+
+
+
+}
+
+
+sub get_total_length {
+    my (@files) = @_;
+    my $total;
+    foreach my $fastq( @files) {
+
+        open my $in, "<",$fastq || die "Could not open file '$fastq'";
+        #skip first 3 lines
+        for ( 0..2) {
+            my $line = <$in>;
+        }
+
+        while ( <$in>) {
+            chomp;
+            $total+=length($_);
+            #skip first 3 lines
+            for ( 0..2) {
+                my $line = <$in>;
+            }
+        }
+        close $in;
+
+
+    }
+
+    return $total;
+
+}
+
+1;
+
+
+=head1 NAME
+
+
+
+seqtk_nml.pl - Down sample fastq(s) if raw coverage is above user provided level
+
+
+=head1 SYNOPSIS
+
+     seqtk_nml.pl --ref reference.fasta --forward first_R1.fastq --reverse --reverse_R2.fastq --out_forward answer_R1.fastq --out_reverse answer_R2.fastq --log log-file
+
+
+=head1 OPTIONS
+
+=over
+
+=item
+
+=item B<--ref>
+
+Reference fasta file that we getting the expected length [Required]
+
+
+=item B<--cov>
+
+Coverage desired i.e 50.0
+
+
+=item B<--forward>
+
+Forward fastq read file. [Required]
+
+=item B<--reverse>
+
+Reverse fastq read file. Can be optional
+
+
+=item B<--out_forward>
+
+Downsampled forward fastq read file. [Required]
+
+=item B<--out_reverse>
+
+Downsampled reverse fastq read file. Can be optional
+
+
+=item B<--log>
+
+Log file that indicate what has happen. [Required]
+
+=item B<--type>
+
+Indicate to application if we are receiving one or two fastq files [Required] ['paired','single']
+
+
+
+=back
+
+=head1 DESCRIPTION
+
+
+Downsample fastq(s) reads based on the raw coverage from reference fasta file. Needed when we have too much data to run correctly in downstream analyses tools. i.e spades , snvphyl , etc..
+
+
+=cut
+
+
+
+
+
+=back
+
+
+=head1 SYNOPSIS
+
+
+
+=head1 DESCRIPTION
+
+
+
+=cut
+

diff -r 000000000000 -r e1867440ed36 seqtk_nml.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/seqtk_nml.xml Tue Sep 19 16:37:42 2017 -0400

[

@@ -0,0 +1,113 @@
+<tool id="seqtk_nml_sample" name="seqTK Sample NML" version="1.0.0">
+  <description>Runs seqTK sample if raw coverage is above user defined threshold </description>
+  <requirements>
+    <requirement type="package" version="1.2">seqtk</requirement>
+    <requirement type="package" version="1.6.924">perl-bioperl</requirement>
+  </requirements>
+  <stdio>
+    <exit_code range="1:" level="fatal" description="Unknown error has occured"/>
+  </stdio>
+  <command>
+ perl  $__tool_directory__/seqtk_nml.pl --ref $fastar
+
+ #if $single_or_paired.type == "single"
+ --type single
+ --forward $input_se
+ --cov $coverage
+ --out_forward $output
+ --log $log
+ #elif $single_or_paired.type == "paired"
+         --type paired
+           --forward $single_or_paired.forward_pe
+ --reverse $single_or_paired.reverse_pe
+           --cov $coverage
+ --out_forward $output
+ --out_reverse $output_rev
+ --log $log
+        #else
+            collection
+            $single_or_paired.fastq_collection.forward $single_or_paired.fastq_collection.reverse
+            $coverage $output_collection.forward $output_collection.reverse
+        #end if
+
+  </command>
+  <inputs>
+    <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="txt" collection_type="paired" />
+      </when>
+    </conditional>
+    <param name="fastar" type="data" label="Fasta Reference File" format="fasta" />
+    <param name="coverage" type="integer" label="Desired Coverage" value="50" />
+  </inputs>
+  <outputs>
+    <data format="fastqsanger" name="output" label="SubSampled Fastq" >
+      <filter>single_or_paired['type']!="collection"</filter>
+    </data>
+    <data format="fastqsanger" name="output_rev" label="SubSampled Fastq Reverse">
+      <filter>single_or_paired['type']=="paired"</filter>
+    </data>
+    <collection name="output_collection" type="paired" label="SubSampled Fastqs">
+      <data name="forward" format="fastqsanger"/>
+      <data name="reverse" format="fastqsanger"/>
+      <filter>single_or_paired['type']=="collection"</filter>
+    </collection>
+    <data format="txt" name="log" label="Log file"/>
+  </outputs>
+
+  <tests>
+    <test>
+      <param name="type" value="paired" />
+      <param name="forward_pe" value="inputforward.fastq" />
+      <param name="reverse_pe" value="inputreverse.fastq" />
+      <param name="fastar" value="testref.fasta"/>
+      <param name="coverage" value="50" />
+      <output name="output" file="outputforward.fastq" />
+      <output name="output_rev" file="outputreverse.fastq" />
+      <output name="log" file="lognosample.log" />
+    </test>
+    <test>
+      <param name="type" value="paired" />
+      <param name="forward_pe" value="inputforward.fastq" />
+      <param name="reverse_pe" value="inputreverse.fastq" />
+      <param name="fastar" value="testref.fasta"/>
+      <param name="coverage" value="25" />
+      <output name="output" file="outputdownsamepleforward.fastq" />
+      <output name="output_rev" file="outputdownsameplereverse.fastq" />
+      <output name="log" file="logdownsample.log" />
+    </test>
+  </tests>
+  <help>
+What it does
+============
+
+Calculates raw coverage. If the raw coverage is greater than desired coverage, runs seqTK sample to generate downsampled reads.
+
+
+Usage
+=====
+
+**Parameters**
+ - Fastq reads (single end, paired end, or paired end collection)
+ - Fasta reference file
+
+**Options**
+ - Desired coverage (50)
+  </help>
+  <citations>
+    <citation type="doi">doi.org/10.1371/journal.pone.0163962</citation>
+  </citations>
+</tool>
+

diff -r 000000000000 -r e1867440ed36 test-data/inputforward.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/inputforward.fastq Tue Sep 19 16:37:42 2017 -0400

b'@@ -0,0 +1,5024 @@\n+@M01649:56:000000000-A57BB:1:1101:15434:2015 1:N:0:1\n+GATGGTTACTTTGTTTGCTTTATGGCTGTTATATTTCTTTTCGTGGTAATCTTTTCCTGGCGTAAAGTTTCCTATCCTTTAGTTTGTATTTTAATGGGTGCGGTCTTTATTTTACTGACAAATTATTTATC\n++\n+>>>>ADD1@DFB131BB1FB3FF31EFFAA3333D333A112A00AB2222FAGB2F1100AAE//2DFF2212B10BBA1AAD21>22222DG221B0/>////EGHHGBG2G1B2@11BBG11BF22BF\n+@M01649:56:000000000-A57BB:1:1101:14542:2033 1:N:0:1\n+CTGTTGGCTCATCCATTAACACAATTGGACGATCCGTTAAGAATGCACGAGCCAGTGCGACACGCTGTTCTTGCC\n++\n+AA3AADAFFCCFGGFGGGGBGAFFHHDCBGAEGHGGFHGGHHCGHHHHGEEEGGHHHH?FG0EDGEFGHHFFGGG\n+@M01649:56:000000000-A57BB:1:1101:12538:2042 1:N:0:1\n+GGCTTCTACAGCAATCGTATGCAATTTTTCATTTGTGACGATATAAG\n++\n+>1>AAFFFFFFFB11A1AFGGFDBGHH33FGHHHFABGHCAFFGHGH\n+@M01649:56:000000000-A57BB:1:1101:15318:2049 1:N:0:1\n+ATTTAAATACTGCGCCCCCTCTAAAGAAGCTATATTGCTACTTTCTGCCGTTACTTCACTTATAGAATCTAGCTCTGCTTGTGAAACGTCAGATGTAGTACTAGGTTTATTTAAAGTTGCTTTTATTGCGTTTGCTAAATTCTCATCTGTAAAAATTTCATTAATTGGCGTCGGTTGATCAATTACTGCCGCCTGTACTTCCTCTTTTGAGCTAGTCCCTACCC\n++\n+AAABAFFFFFFBGG?EFGGGGGHHHFGHHHHHHHHHHGHHHHHHHHHGHGGGGGHHGHHHHHHGHGGGHGHGHHHHHHGHHHGHHHHGHHGGHGHHHHFHHGHHHGHHHGHGHHHHHHHHHHHHHHGHGGGGGGHHHHFHHHHHHHHHHHHHHHHHHHHHHGHHHHHGHGGGG?FGGHHHHGHHHHHHHHGGGGHHHHHHHHHHHHHHHGGHGHHHHHHGHHHH\n+@M01649:56:000000000-A57BB:1:1101:19885:2053 1:N:0:1\n+GGTTGGGTGGCTGACGATTGCAGATACGGAAATAGATTATCCAATTTTGCAAAGTACGGATAATGATTACTATTTACATCACAATTATAAAAATGAAAAAGCACGAGCGGGCAGTATTTTTAAAGATTATCGGAATACGAATGAGTTTTTGGATAAAAATACGATCATTTATGGGCATAATATGAAAGAC\n++\n+1AAAA11A1AFF11FEAFGEGGHFFFHGGCAEGHHFHHHHHHHFDFHHHHGGFHGDGFEAEGHGFGFFFHHHHGHHHGHHFHH1FGGGGFGBEFHHHFHHGFHFG?EEGGCGGGFGGHGHFG1D1GHHBGHECB/FHHHCGAFGHHGGHGGGGHGHHGHFFGEGHHCGFHFHHFFHEGGHHHHHHHHGHH\n+@M01649:56:000000000-A57BB:1:1101:17728:2054 1:N:0:1\n+CCATAAATCCAACTTCATACGCAACCTCCTTCCTATTCCACTTTTGTTGCCTTTAGTTCACCAGCATTTGTGACAGTTATTTTGAAATTAGAGCCATTTTCAGAAACCAAAATTGCGTCCTGTTTTTTATTCCAATTGGCAATATCGATTGCAGTCACATTATTTTTTTCTGCATTAGCTTCGATTCCATTTAATTTCGTTTTGTCGCTGGCGGGCATTAATCCAGATGTAGTAGTTGTAGCCGAGTCCAA\n++\n+AAAA?FFFFFFFGGGGGGGGGGGGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGHHHHHHHHHHHHHHHHHHHHHHHHGHHHHHHHHHHHHHHHHHHHHHHHHHHGHHHHGGGGGHHHHHGGGHHHHHHHHHHHHHHHHHGHHHGHHHHHHHHHHHHHHHHGGHHHHHHHHHHHHHGHHHHHHHHHHHHHHHHHHGGHHHGHGGGGGGGGFFGFGGFGGGGGFFF//:B;FBBFFFFFADFFFFF\n+@M01649:56:000000000-A57BB:1:1101:12508:2068 1:N:0:1\n+GTTGAAGAGGAACAACTTCTTTTTGCGTTGACCGATTTAAATGCAGAAATCATGGAAAATACTTCTATACCATTTTCCTCAGAGAAAAAACCAGAAGAAGCGATTGAGTTAATTGCTAAAAATGTGAAAAAGATGTGTGAAAACAGAGATATGAACCATTTGCTAGGAG\n++\n+AAA11@DD1ACCAGGCGGGGGGHHGHGGGGFGFGGGGC1GGHHHEFHHHHHHFHEFFFGGHEFGFFFHBGHHHHHHDGHFFHGCBB@CH/>>GGHHHG0CGGEFEGHEGHFHEFFHHGH1EGGHGFHFHHHGGGHHFGGHHDHFHHHGFFHHHHFHGHHFHHHHHGHGH\n+@M01649:56:000000000-A57BB:1:1101:11566:2074 1:N:0:1\n+GTTACAACCAATTCCGGAAACAAAAGCAACCCAGAAA\n++\n+AAAA13DCA?A1FGAGGGGGGBFHABGFHA000F0FG\n+@M01649:56:000000000-A57BB:1:1101:19846:2075 1:N:0:1\n+ATACTGACGAGGTGTGAATGTTAATGAAGTGGCACTAATATCGTTAAGAAACAGTTTGTTGTCCGCTTTAGAAGCTTGATAAGCAGTCTGGACAATCTCTTTGAATTTTGTTTTCACACTCGGACCATTGTAGTCATCTTGAATTACTTGGTTGGATGCGCCGAACTGCATGCCGAATTTGTGTGAATTAATGACTAATGGCTTTTTTGTGTGGTTCTCTGAAAGTAATAATATTTTTCCGCGGACATCTT\n++\n+ABABBBFFBBB@EGGGCGGGGGHHGGHGHFHHGHHHGGHHHHGGHHGHGHGHGHHHHEHGHFHHGGGGGHGHHHHGHHHGHHFHHHHHHHHHFFHHHHGHEHHHHFHHHHHHHHHHHHGHHGGGGGHHGHHHHHHHHHHHHHHHHHHHHHHHHGFHHHGGGGCDGGHHHHHHHHGG-FGHGHHHHHHHHHHHHHHHHGHHHHHHHHHGGFGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGFFFFFFFF\n+@M01649:56:000000000-A57BB:1:1101:18762:2076 1:N:0:1\n+GCAGTCAAGTCACTTGTACACCGCGATACCGAGCTTGCTAAACAAGTAG\n++\n+B@B@AFFFFFFBFGGGGGGGFGGGGGGGGHGGGGGHGHHHHHHFHHAGH\n+@M01649:56:000000000-A57BB:1:1101:13268:2078 1:N:0:1\n+GGACAGGTTAGTCCGGAAATGTTTCAATATATGCAAAAGGAACTTCCTTCAGCAGCGGAAATGCAAGATACAGAAAAACGTTTAGCATTTATGGACCAACATGGTATTGATATCCAAGTACTCTCT\n++\n+111>>A?FFBFFGGEEEG0GGFFHHHHHHHHHHHFFFFHCCGFHFDBGHBAGG1FBFEGFEFHFGGHHHFHHHGHHHHC?FGFHHHFFHGHGHHHFFGAEEGB0BBGGHFHGGHHFHHHGFHHHFH\n+@M01649:56:000000000-A57BB:1:1101:19034:2079 1:N:0:1\n+CTGCAACACAAATGCTTGATTCCATGCAACGCAACCC\n++\n+AAA1AFFFAAAFFGCGEGC1AAB3331BAAA000A0A\n+@M01649:56:000000000-A57BB:1:1101:19649:2081 1:N:0:1\n+GGAAACAGCCCAGACCACC'..b'GFGFF0CFFGGFFBBGBFF\n+@M01649:56:000000000-A57BB:1:1101:7843:4248 1:N:0:1\n+TGATTTCTTTGAAGTGATTGTGGCAGTGTTTAGTCCACTCGCGTCAATCGTACAATCTTATCCAGGCTTTGTGCTTTCGGTTTTCATTCCAGCATTTCTTTATACATTCGGGTTTTCTGGGCGGGTTATGATGCCCGCGATTTACCCGGTTTATATGGCAGGACTCGCAGAAAACTCACAAGCTGTAGCAAATGGCGCAAGTGC\n++\n+BBAB@FBFFFFFGBGD5E5FEGD44EG4ADGC5GGHHHFHDECAEA2EGEFCGGBGGFHHGH5FEGEFGHHHHBG5EGGGGDACGHHHHFGHHF3FF4@G@GHFF4BGFHH?11?F4F4FG/><C>FGH1@FG11?/AD-CHF1=FGA-<.EFHBHGHHHGGGE/GA-:.-/:;/C00CBB.990CB0;9B/CFFF??-;-///\n+@M01649:56:000000000-A57BB:1:1101:16655:4248 1:N:0:1\n+GGATCACACTTCCACGGCGGATTTGCTGAAAATGTCGTCATGAAAGCCGACAATGTCATTTCTATCGGCGACCTTGATTTTGAAGAAGGTGCGATGATTGAAC\n++\n+BBAABFFFFFFFGGGGGGGGEFGHHHHHHHHHHHGFHGGHHHHHHHHHGGGGGHHGHFHHHHHHHHGGGGGGGGHHHHHHHHFGHHHHHFFH?EHGHHHHFHH\n+@M01649:56:000000000-A57BB:1:1101:16286:4249 1:N:0:1\n+GTTTCATCTCATGAACACATATAGTATACTGGAAAAATAAGCGAAGAAACGGAGGCATATTCATATGATTAAACGAACTGGTGAGATAGTACTCGCT\n++\n+BBBBBFFFFFFFGGGGFGGGGGHHHCHFFDHFHHHHGHHHFHGGGGGHHHGGGGGGGHHHHFHHHHHGHHHHHHGGGGHHHGHGFHFHGGHHFHGFE\n+@M01649:56:000000000-A57BB:1:1101:13055:4250 1:N:0:1\n+CTGTTTGATATTTATTATACTGGCGTGATGGGCATTTATTTTGCTATCTTCCCGTTTACAGTGTATATCACAGATAAATTTATGAAAGTGTTGCAAAATAA\n++\n+CCCBCFFFFFFFGGGGGGGGGGHHGEGGHHHHGHHHHHHHHHGFFHHHHHHHHGFGHGHGFGHGHHHHHHHGHHHHHHGHHGHEFHHHGGFGEHHHHHHHG\n+@M01649:56:000000000-A57BB:1:1101:19334:4251 1:N:0:1\n+TGTCATCGCGAGCAAATGAGTAGCGTGACAATGCATAACAACGCGGTTTCCGGATCCACAGAAAGTCTTGCAATGTGACTCATAAAATGCGCTGGAAGTTCACTCGTTGGTAGTCCGCTGTCTGTATAGCCCCACAACAAATGAACTGCTTTCCCGTCTTCACTCACTTGAATTACACCTAAATTCACAGCTGGAGCTTCTTCAACATTTTTAAAATATTTACCCGAACCAGTTACTAAGAAATACTTGC\n++\n+A11A133F11ADGEB111DG3FEFE0AEAGHHHHBGD1FHGGEEC?E/EHH//E/EGFGEE1B@BFDF211@1GDFFHEFGFFDFH1BBDEEGGEAF0GBGFDHFFGFCGGBFHHGGGGCGFGFHGHHFHHFGGGGHGHFHHHGHHGGGHEHHHHGHGHGGGHGHHHHHHHHHHHHGHHHHHHHHHHHHHFHHHHHGGGGGGGGGGGGGGGGGGGGGGGBGFFFFGGGG@FFFFFFFFFFFFFFFFFFFF\n+@M01649:56:000000000-A57BB:1:1101:15543:4251 1:N:0:1\n+GGCTATAAGTGTAGGCGGATAAATACTTTTATCTACAGCCGATAGTGGAGAATAAATTGGCGATGCGGGATTTTCGTCTCTAACATAGGCCGTCCGCAGTAATTCGCCAGAGCTGTTCATTCCAATGATACCTGGCGCAACGAGCGGAAGTGTCT\n++\n+BBCCBFFFFFFFFGGGGGGGGGGHHHHHHHHHHGHHHHHHG?EEGFHHHFHHHHHHHHHHHGGGGGGGGGGHHHFGHGHHHGHHHHHHHHHGEEGGGGGGHHHHHGGGGGHHHHHHHFHHHGHHGHHGHHHHHHHHGGFFGGGGGGGGGGCGCFF\n+@M01649:56:000000000-A57BB:1:1101:18147:4252 1:N:0:1\n+CGCAGATTCACTAGAAGGAGACCAATAAACCGGTTTTTTACCTTTGTAAATGTAACCTTTTTTCGCCATTTCACCGAAGACTTTGATTTGCTCTGCTTCGTATTCTGGTAAAAGTGTAATGTAAGGATTTTCCCAGTCACCGTTAATTCCAAGTCGTTTGAATCCTGTACGTTGACCGTCTACTTGCGTCATTGCAT\n++\n+@A?AAB4DFFFFFGGGGGGCCCF44G445BEECEEGFAEFADGHHHH555AAFB5GFEFE3FEHGGGGEFHFFFFE0/>EGFFHE4GEF3@D3BFGDGFF2GGHG4F3BFFGBB34?B?GH4BFFG3BFGFDH2G2?B23BBFE/CGGGH2FFGHG/CF/FGH11FDHHGE0FAC1>->EFHG0DGF@EG?HFF0GG\n+@M01649:56:000000000-A57BB:1:1101:23733:4252 1:N:0:1\n+CTAAATGCATGGTTGTAAATATTTTGGACTAGGGTCATTGTCGCTCCACTTGGACCAACTTCTGTCATAATCATCACTTGGTCAAACACCTGGAATGAGTTGATAAGCGAAATTATCATCACAAAGAATGTAGTAGGAGTAAGAAGCGGGATAGTAATAGAGAATAATTGGCGAAGTTTTGATGCTCCGTCCATATTGGCAGCTTCGTAATACGATGGTGAAATATTTTGCAATCCACCAAGGAATAGTA\n++\n+1AAAABD113@F1FEEDGFGGGDB33011BA1EA0B0222DB00BAEC01111EGBA/BGGHFGGHGF222AFF2FGDFB1BD2AGDEHEBCGH1B@1@@2F2@2@@FC?E>EG1FFHB221E1>0GHFFFGGHFB1G<GBGH11<F@CCGGH1>22@D2@11@G1@GHFH0@C?<>GHFHEFGFBDGCHFF.D0DG00/<ECF0C?C/:CCGAEEE.0900;B9BBFFF00F0;/C/;A.A.9/0BB00\n+@M01649:56:000000000-A57BB:1:1101:17948:4253 1:N:0:1\n+GGTCAATATTCCCATGTTACTTGAAACGCTCTCAATGCGGGCTGCAAGTAATCAAAAAGATCTAGTTGAAACAGCTC\n++\n+AAABBFFFFFFFGGGGGGFGGGHHHGHGGGGHHHHHHGGGGGGGGGFHAEGHHFGFHFGGHHHFFGFHHFHHHHHHH\n+@M01649:56:000000000-A57BB:1:1101:20206:4254 1:N:0:1\n+GGCGACACACTATTGAATTTTCTGGAATGGACGAAAAAGAACAACAAATTAGTGGAAATAATGACTGTTTGGGACGAGCTAATTATCGGGACAATAGAAACGATTGAAGCAAATTTAGTAATGATTAATACCCTTGCACCAGAAGAATTTGCATCTGATGGGAAATGCTTTATAGAATGCGACAATATTGTTGATATTTGTATTGATACAGCGCGACTGAAATTTATTACTGCTTAACTATTTAACACTAA\n++\n+BBCCCCCCFBFFGGGGGGGGGGHHHHHHHGHGGGGGGHGGHHHGHHHGHHHHHHHGHHHHHHHHHHHGHHGGGHHGGGGGHHHHHHHHGGGGGHGFHHHHHGGHHEHHHHHGHHGHHHFGFHHFHHHHHHHHHHHHHHHHHHHGHFFHHHHHHHHHHHHHHHGHHHHHHHHHHHHGHHGHGGGGGHGHHHHHHHHHHHHHHGHHHGHHHHFHGGGGGGGGGGGGGGGGGGGGGGGGGFFFFFFFFFFFFFB\n'

diff -r 000000000000 -r e1867440ed36 test-data/inputreverse.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/inputreverse.fastq Tue Sep 19 16:37:42 2017 -0400

b'@@ -0,0 +1,5024 @@\n+@M01649:56:000000000-A57BB:1:1101:15434:2015 2:N:0:1\n+TATAAATAATTTGTCAGTAAAATAAAGGCTGCACCCATTAAAATAACAACTAAAAGATACGAAACTTTACGCCAGGAAAAGATTACCACTAGAAGAAATATAACAGCCATAAAGCATGCAAAGTAACCATC\n++\n+1>1>ADFFFFFFF3BFDFEGEFGDEH1EA1BF0ABEFHHEAF1BA1BAA0B11111/BFEAC/EE11DBE/EEEE/EAEA>/@@@11DFGHGBG11GH1GEGFHGB0/>GGFF1DE1D11GFB>BBE1EG1\n+@M01649:56:000000000-A57BB:1:1101:14542:2033 2:N:0:1\n+GGCAAGAACAGCGTGTCGCACTGGCTCGTGCATTCTTAACGGATCGTCCAAATGGGGTAATTGATGCGCCAACAACTGTCCCTTTTACACCACCTACGCCGCCGGCCACTCCTTACAGGCTAATCTTCGGGGGCCCCTGTACCTTATTAAAAAAAAAAACAACGCTCTGCTGATGTTCTACACCATCCGTAACTAATAGAATAAAAGCCTAGGAACCCTGACCGGTCTTGTGACATGCAGCTCAACAACA\n++\n+?>AABABFFBFFGGGGGGGGGGHHHHHGGHDADH55D5A5AA11AAB1AA55B5311BAF55D5@5501B1/B11?334B3@3B3343F33///033?/>///<///>/2?2221<110/011?1111..>------..0:00000000;000A-----....--...//9//////9////9/.//:...9.9/;///9////9//;9/////:......9/9---.////9/;9/9/////9/./.9.\n+@M01649:56:000000000-A57BB:1:1101:12538:2042 2:N:0:1\n+CTTATATCGTCACAAATGAAAAATTGCATACGATTGCTGTAGAAGCC\n++\n+AABABDFFAFA?EFFGGGG55FCGFHAGHFFHGGDFHCG55DFFHHH\n+@M01649:56:000000000-A57BB:1:1101:15318:2049 2:N:0:1\n+GGGTAGGGACTAGCTCAAAAGAGGAAGTACAGGCGGCAGTAATTGATCAACCGACGCCAATTAATGAAATTTTTACAGATGAGAATTTAGCAAACGCAATAAAAGCAACTTTAAATAAACCTAGTACTACATCTGACGTTTCACAAGCAGAGCTAGATTCTATAAGTGAAGTAACGGCAGAAAGTAGCAATATAGCTTCTTTAGAGGGGGCGCAGTATTTAAAT\n++\n+>AA>3>AAFBFFGGGGGGGGFFFHGFFFGHHGGGGGCGGGFHFHHFFHFF3B0EEGGGCEFFHHHHHHGEHHHHHHGHBFHFFHHFHBEGEHHFFGGCEEBGFHFHHHAFFHHHGHGHHFEGHHFHHHHGGHHHHHHG?FHFBGHHAHC<0GHHHGHHHFFHHHBG1FFHHGFHHCGGCFGHFHGFHFHHHGFHHFHHFHFGBBFGGGGGGFFFFDFFFFFFBB\n+@M01649:56:000000000-A57BB:1:1101:19885:2053 2:N:0:1\n+GTCTTTCATATTATGCCCATAAATGATCGTATTTTTATCCAAAAACTCATTCGTATTCCGATAATCTTTAAAAATACTGCCCGCTCGTGCTTTTTCATTTTTATAATTGTGATGTAAATAGTAATCATTATCCGTACTTTGCAAAATTGGATAATCTATTTCCGTATCTGCAATCGTCAGCCACCCAACC\n++\n+>>>AAFFFF3DFGDB1F1FGGGHHCGBFG0CGCGHF0FEFFGG0AEGFBAFAGHGHFHHHCEEGHHBDGE2F11BGGHBHHCAE?E@>FFAFFFHFHGHFHHGHFHGFBBGGH2@FF2FGDHGGHB1F>FHHDEFACGHHEHBGFFHHHHDGHHGBGBFHHFHAFGHHHHHHHHHGHHH/GGHHHGGH?E\n+@M01649:56:000000000-A57BB:1:1101:17728:2054 2:N:0:1\n+ATCCGAAGACACATGTAACGGCTGTGGAAGGTTTGGACTCGGCTACAACTACTACATCTGGATTAATGCCCGCCAGCGACAAAACGAAATTAAATGGAATCGAAGCTAATGCAGAAAAAAATAATGTGACTGCAATCGATATTGCCAATTGGAATAAAAAACAGGACGCAATTTTGGTTTCTGAAAATGGCTCTAATTTCAAAATAACTGTCACAAATGCTGGTGAACTAAAGGCAACAAAAGTGGAATAG\n++\n+AAACABBCBFFFGGGGGGGGGGGGGHGDGHGGHH2FBBGGGGGDGFBGHHHHFHEEHFHGHGBFHHHHEFHG0E?ECE?EEGHGGGDEGAHHHHHHHHHGHFFGGGHHHHHG4GDCHFHGGHHHDFHHHFGBGGHFHAFEHCHFGGFHHHBGHHHHHHHHG?GCGHGGGGCGHEHHGCGHHFGFFFGGGGGGFFGGGGGGGGGFBFGFFGFGGGGGGGFFFBFFBBFBFFFFFEE9A.:EFFF;BFBB///\n+@M01649:56:000000000-A57BB:1:1101:12508:2068 2:N:0:1\n+CTCCTAGCAAATGGTTCATATCTCTGTTTTCACACATCTTTTTCACATTTTTAGCAATTAACTCAATCGCTTCTTCTGGTTTTTTCTCTGAGGAAAATGGTATAGAAGTATTTTCCATGATTTCTGCATTTAAATCGGTCAACGCAAAAAGAAGTTGTTCCTCTTCAAC\n++\n+?3AAADFBDFFFFFGGGGGGGGDGHHFHGHHHHHHFHFHHFGHHBHBFGHHFAGHHBGHFHHEHHGHHGAAFEHHHGHHABEAFEHH5FD5BF3FB?FGFBGHDGB3BF4BGHHHHHHFFGHHHFDBDFHHHHGBGCGGFE3EEGGE@FFDGFF1?DGG1G2DHHHHHH\n+@M01649:56:000000000-A57BB:1:1101:11566:2074 2:N:0:1\n+TTTCTGGGTTGCTTTTGTTTCCGGAATTGGTTGTAAC\n++\n+AAAAAB1C>ADFG1BG1FFCB3AEA0AFF11A00DG2\n+@M01649:56:000000000-A57BB:1:1101:19846:2075 2:N:0:1\n+TCCCAGAACTGACACGAGCAATAAAATCCCTACATTAAAAGATGTCCGCGGAAAAATATTATTACTTTCAGAGAACCACACAAAAAAGCCATTAGTCATTAATTCACACAAATTCGGCATGCAGTTCGGCGCATCCAACCAAGTAATTCAAGATGACTACAATGGTCCGAGTGTGAAAACAAAATTCAAAGAGATTGTCCAGACTGCTTATCAAGCTTCTAAAGCGGACAACAAACTGTTTCTTAACGATA\n++\n+BAABBFA4FFFFGFGGGGGEFGGHHHHHHHHFHHHHHHHGFEHHFHHGGGGECE2CHFHHGHHHHFBGHHGHEHFHHHGHGGGHGHEFFFHFHHHHHHHHHFHHHHHHHGEHGHHGFGGCHHHHHFGG?DGGGGGHHHHGGHHHHHHHHHGGHHHGHHHHGHHEFGHHGGGGHCFFFHFHEGCGHHGHGFHFGGGGGFGFGGGGGGGGGFBFFGGGFGGGGFFGF?DBFFFEFEFFFFFFFFFFFFFFEF.\n+@M01649:56:000000000-A57BB:1:1101:18762:2076 2:N:0:1\n+CTACTTGTTTAGCAAGCTCGGTATCGCGGTGTACAAGTGACTTGACTGC\n++\n+BBCCCFFFFFBFGGGGGGGGGGHGHGGGGGGGHHHHHGHHHGHHHHHGH\n+@M01649:56:000000000-A57BB:1:1101:13268:2078 2:N:0:1\n+AGAGAGTACTTGGATATCAATACCATGTTGGTCCATAAATGCTAAACGTTTTTCTGTATCTTGCATTTCCGCTGCTGAAGGAAGTTCCTTTTGCATATATTGAAACATTTCCGGACT'..b'FFGGGGGGGGEFFBEFB\n+@M01649:56:000000000-A57BB:1:1101:7843:4248 2:N:0:1\n+GCACTTGCGCCATTTGCTACAGCTTGTGAGTTTTCTGCGAGTCCTGCCATATAAACCGGGTAAATCGCGGGCATCATAACCCACCCAGAAATCCCGAATGTATAAAGAAATGCTGGAATGAAAACCGAAAGCACAAAGCCTGGATAAGATTGTACGATTGACGCGAGTGGACTAAACACTGCCACAATCACTTCAAAGAAATCA\n++\n+>AAA1CDF??>1FFGGGGBFD1FA1FGFHHDGGBD12FG?EGHF2GGHFHHF2FGHBE?EEEFHHHGGGGCCEHGHFB2BF///E>///BB1F1B<E/FHFFGHDFDDFBD<GFHFF1FFGGHF0C?@G/<FGFHHHEH0<G.0>GDF1DFD<1GEEC<<DDAE@-@:..GCGFF0/;FG9FBFFF.CFBFFGG9FBBFABFBB\n+@M01649:56:000000000-A57BB:1:1101:16655:4248 2:N:0:1\n+GTTCAATCATCGCACCTTCTTCAAAATCAAGGTCGCCGATAGAAATGACATTGTCGGCTTTCATGACGACATTTTCAGCAAATCCGCCGTGGAAGTGTGATCC\n++\n+BB?AAFFFFFFFEFGCGGGGGGHHHHHHHCFGFFEGFGGCFFFDDGFHHHHHBGGEGGGGGFHGHHHDCEFGGGBFDDHHHGHHHE1>>>EC/FGFG4F4F4?\n+@M01649:56:000000000-A57BB:1:1101:16286:4249 2:N:0:1\n+AGCGAGTACTATCTCACCAGTTCGTTTAATCATATGAATATGCCTCCGTTTCTTCGCTTATTTTTCCAGTATACTATATGTGTTCATGAGATGAAAC\n++\n+BABBCCBFFFFFGGGGGGGGGGHGGHGGHHHHFGHHFBHHGHHHFHHGGFHHFHHHGGHGHHHHHHGFHHHHHEHHHHGFGFGFHFHHHHGHHHFBG\n+@M01649:56:000000000-A57BB:1:1101:13055:4250 2:N:0:1\n+TTATTTTGCAACACTTTCATAAATTTATCTGTGATATACACTGTAAACGGGAAGATAGCAAAATAAATGCCCATCACGCCAGTATAATAAATATCAAACAG\n++\n+CCCCCFFFFFFFGGGGGGGGGGHHHHHHHHHHFHGHHHHHHHHHHFHFEAEGGGHHHHHIHHHGHHHHGHHHHHGHGGHGGGGHHFHHHHFHHHGHHHHHG\n+@M01649:56:000000000-A57BB:1:1101:19334:4251 2:N:0:1\n+AAAAAGAAGTTGTGGAATATTTAGATGTAAAGCAAATCATTCGCACAATTCCAATGGACTTTGACGGTAAAAAGCTTGCTGGCAAGTATTTCTTAGTAACTGGTTCGGGTAAATATTTTAAAAATGTTGAAGAAGCTCCAGCTGTGAATTTAGGTGTAATTCAAGTGAGTGAAGACGGGAAAGCAGTTCATTTGTTGTGGGGCTATACAGACAGCGGACTACCAACGAGTGAACTTCCAGCGCATTTTATG\n++\n+1AAA>AA1>3BFGAE1FFGFFBDD1FFGGF3B1ABCG11222BEEEGGFH1D2DAE1FGFGD12B//EH/D21BF11FGHH1F0G/D2DG2GHFGHGHFHFFBFHGCEGEEHHHGHHGHHBGFHCF2GGHHHF001FFGHHHGGFFBGFEBGHHGGHFBGHHHF2@GHFGHHGHHFFGG/CEHHHHGHEHHHHGFHHHGCGCCCHHHHFHGFFGACGGG?B9CFCBBEGBEFGFGB09FFFG@?A-/BF/9\n+@M01649:56:000000000-A57BB:1:1101:15543:4251 2:N:0:1\n+AGACACTTCCGCTCGTTGCGCCAGGTATCATTGGAATGAACAGCTCTGGCGAATTACTGCGGACGGCCTATGTTAGAGACGAAAATCCCGCATCGCCAATTTATTCTCCACTATCGGCTGTAGATAAAAGTATTTATCCGCCTACACTTATAGCC\n++\n+AABCBFFFFFCCGGGGGGGGGGGGHHHHHHHHHHHHHHHHHHHGGHFHHFFGFGHHGHGHGGGGFGEEGHGHHHHHHHHHGGGGFHHHHGGFGFGGGGGHHHHFHFFHFHHHFFHGCCGGFHHHFGBGHFFD1FGFHHHGEGDDH0CGHHHGFHH\n+@M01649:56:000000000-A57BB:1:1101:18147:4252 2:N:0:1\n+ATGCAATGACGCAAGTAGACGGTCAACGTACAGGATTCAAACGACTTGGAATTAACGGTGACTGGGAAAATCCTTACATTACACTTTTACCAGAATACGAAGCAGAGCAAATCAAAGTCTTCGGTGAAATGGCGAAAAAAGGTTACATTTACAAAGGCAAAAAACCGGTTTATTGGTCTCCTTCTAGTGAATCTGCG\n++\n+A1A?11B11@AAGECEGG3F00BAEBFEGFG0FBFCAF1GGH/EC/EGGBBGFGEDEEAAFGDA/GCE/GHEF1D2GFGFFBGFB1BF2@GFFB0BFFHCFC/CGG?0EGCGDD11G1>GGBE/FFAGHHHFFCGCCCH/?/<?DGHHGHHFB1?00.>000FCGCC-<.<CCC00<0C00;:GGFB0:00<CB00-\n+@M01649:56:000000000-A57BB:1:1101:23733:4252 2:N:0:1\n+ATGCTTATTCTGGCTACTCAATTTACTAGGTTTTCTCATTTTTCTTGCAATCCCAATCCTTGGCTCGCTTGGTATTCGTTTTACAGATTGGGACTTCGTGAGTACTATTCACATTACTGGAATTGAGCATTATAAAAGGCTGTTTAATGACCCAGAGTTTTGGAAATCGATTAGAAATCCAATCACGTTCATCATCGGTTTTTTGCCTAGAGTAATGTGTCTTGTCCTAGTGTGTTACTTGATGTTGAAT\n++\n+>11>1D313B3311BBG111B3DF3A331AF1FFG1333A32D011D1B12BF110AF0DBF1BCF/EFG//1AA22000/A2@21@1@1>/?0BG1/BE0/F2DDB22BGG2BF11221011B1B11>B2122B211/?10011>BB221B<?G//BB1BC/1<1@>/0?>/1@1??1<<11<FF<0F01=D><D1AC..<.<-<0=0<000:<0000;:;C00:;0C000:0:/0;C0000;000000\n+@M01649:56:000000000-A57BB:1:1101:17948:4253 2:N:0:1\n+GAGCTGTTTCAACTAGATCTTTTTGATTACTTGCAGCCCGCATTGAGAGCGTTTCAAGTAACATGGGAATATTGACC\n++\n+BBBBAFDFFFFFGGGGGGGGGGHHGDHCHFFFFFGCHAEGGGGEFG3GFEGFGCFHHHFFFFFFF2FEGGEGGBFFG\n+@M01649:56:000000000-A57BB:1:1101:20206:4254 2:N:0:1\n+GAATTATTAATTTTATTAATTATAATTAGTGTTAAATAGTTAAGCAGTAATAAATTTCAGTCGCGCTGTATCAATACAAATATCAACAATATTGTCGCATTCTATAAAGCATTTCCCATCAGATGCAAATTCTTCTGGTGCAAGGGTATTAATCATTACTAAATTTGCTTCAATCGTTTCTATTGTCCCGATAATTAGCTCGTCCCAAACAGTCATTATTTCCACTAATTTGTTGTTCTTTTTCGTCCATT\n++\n+AA@AAFFFFFFFGGGGGGGGGGHGFGHCH5FGHFHGGBGFHGFFHHFGGDGHHHHHHH5BGF2?2E00EHGGHHGFHHGBGHHFHHGHHHHHHGHHFGCGFGHFBGEGFGHHHHHGFHHHHHHHGGHFFG4FFHHEHBGGHG3?/?GHFHH?HFGHHHHHHHHHHHFHGFFD3FFACGEFGHGHHHDFFC?CFEHHHF0GHGGGDABG.C./=GHFHFFHHH0D<G:/CFGBGGACGGHHHHHE@CDGGG0\n'

diff -r 000000000000 -r e1867440ed36 test-data/logdownsample.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/logdownsample.log Tue Sep 19 16:37:42 2017 -0400

@@ -0,0 +1,5 @@
+Downsampling to coverage of: 25
+Total number of Basepairs: 451843
+Length of Reference: 9120
+Raw Coverage: 49.544
+subsample: 0.505

diff -r 000000000000 -r e1867440ed36 test-data/lognosample.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/lognosample.log Tue Sep 19 16:37:42 2017 -0400

@@ -0,0 +1,4 @@
+Downsampling to coverage of: 50
+Total number of Basepairs: 451843
+Length of Reference: 9120
+Raw Coverage: 49.544

diff -r 000000000000 -r e1867440ed36 test-data/outputdownsamepleforward.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/outputdownsamepleforward.fastq Tue Sep 19 16:37:42 2017 -0400

b'@@ -0,0 +1,2588 @@\n+@M01649:56:000000000-A57BB:1:1101:15318:2049 1:N:0:1\n+ATTTAAATACTGCGCCCCCTCTAAAGAAGCTATATTGCTACTTTCTGCCGTTACTTCACTTATAGAATCTAGCTCTGCTTGTGAAACGTCAGATGTAGTACTAGGTTTATTTAAAGTTGCTTTTATTGCGTTTGCTAAATTCTCATCTGTAAAAATTTCATTAATTGGCGTCGGTTGATCAATTACTGCCGCCTGTACTTCCTCTTTTGAGCTAGTCCCTACCC\n++\n+AAABAFFFFFFBGG?EFGGGGGHHHFGHHHHHHHHHHGHHHHHHHHHGHGGGGGHHGHHHHHHGHGGGHGHGHHHHHHGHHHGHHHHGHHGGHGHHHHFHHGHHHGHHHGHGHHHHHHHHHHHHHHGHGGGGGGHHHHFHHHHHHHHHHHHHHHHHHHHHHGHHHHHGHGGGG?FGGHHHHGHHHHHHHHGGGGHHHHHHHHHHHHHHHGGHGHHHHHHGHHHH\n+@M01649:56:000000000-A57BB:1:1101:17728:2054 1:N:0:1\n+CCATAAATCCAACTTCATACGCAACCTCCTTCCTATTCCACTTTTGTTGCCTTTAGTTCACCAGCATTTGTGACAGTTATTTTGAAATTAGAGCCATTTTCAGAAACCAAAATTGCGTCCTGTTTTTTATTCCAATTGGCAATATCGATTGCAGTCACATTATTTTTTTCTGCATTAGCTTCGATTCCATTTAATTTCGTTTTGTCGCTGGCGGGCATTAATCCAGATGTAGTAGTTGTAGCCGAGTCCAA\n++\n+AAAA?FFFFFFFGGGGGGGGGGGGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGHHHHHHHHHHHHHHHHHHHHHHHHGHHHHHHHHHHHHHHHHHHHHHHHHHHGHHHHGGGGGHHHHHGGGHHHHHHHHHHHHHHHHHGHHHGHHHHHHHHHHHHHHHHGGHHHHHHHHHHHHHGHHHHHHHHHHHHHHHHHHGGHHHGHGGGGGGGGFFGFGGFGGGGGFFF//:B;FBBFFFFFADFFFFF\n+@M01649:56:000000000-A57BB:1:1101:11566:2074 1:N:0:1\n+GTTACAACCAATTCCGGAAACAAAAGCAACCCAGAAA\n++\n+AAAA13DCA?A1FGAGGGGGGBFHABGFHA000F0FG\n+@M01649:56:000000000-A57BB:1:1101:19846:2075 1:N:0:1\n+ATACTGACGAGGTGTGAATGTTAATGAAGTGGCACTAATATCGTTAAGAAACAGTTTGTTGTCCGCTTTAGAAGCTTGATAAGCAGTCTGGACAATCTCTTTGAATTTTGTTTTCACACTCGGACCATTGTAGTCATCTTGAATTACTTGGTTGGATGCGCCGAACTGCATGCCGAATTTGTGTGAATTAATGACTAATGGCTTTTTTGTGTGGTTCTCTGAAAGTAATAATATTTTTCCGCGGACATCTT\n++\n+ABABBBFFBBB@EGGGCGGGGGHHGGHGHFHHGHHHGGHHHHGGHHGHGHGHGHHHHEHGHFHHGGGGGHGHHHHGHHHGHHFHHHHHHHHHFFHHHHGHEHHHHFHHHHHHHHHHHHGHHGGGGGHHGHHHHHHHHHHHHHHHHHHHHHHHHGFHHHGGGGCDGGHHHHHHHHGG-FGHGHHHHHHHHHHHHHHHHGHHHHHHHHHGGFGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGFFFFFFFF\n+@M01649:56:000000000-A57BB:1:1101:18762:2076 1:N:0:1\n+GCAGTCAAGTCACTTGTACACCGCGATACCGAGCTTGCTAAACAAGTAG\n++\n+B@B@AFFFFFFBFGGGGGGGFGGGGGGGGHGGGGGHGHHHHHHFHHAGH\n+@M01649:56:000000000-A57BB:1:1101:13268:2078 1:N:0:1\n+GGACAGGTTAGTCCGGAAATGTTTCAATATATGCAAAAGGAACTTCCTTCAGCAGCGGAAATGCAAGATACAGAAAAACGTTTAGCATTTATGGACCAACATGGTATTGATATCCAAGTACTCTCT\n++\n+111>>A?FFBFFGGEEEG0GGFFHHHHHHHHHHHFFFFHCCGFHFDBGHBAGG1FBFEGFEFHFGGHHHFHHHGHHHHC?FGFHHHFFHGHGHHHFFGAEEGB0BBGGHFHGGHHFHHHGFHHHFH\n+@M01649:56:000000000-A57BB:1:1101:17969:2101 1:N:0:1\n+GTTGGTTGGAGTCGTTTTGACCGTCCAACCAGAAAGACTTTTAGCGGTAGTTTGATAAGGAGCATCAATTTTGCCGTTCAGTGTGTCGGAAGTAGCTAATTCGTTGCCATCCACGTCGACATATTTCACGGTAACAGGAGCGCCGTCCGCTTTTTCGTACACATAAGTGACCGTTTGGTTAGCGTTTGTGAATACGCC\n++\n+>AA>AAAABFFCG?EEGGGGFGGE2AEGFEGFHH3AGCGGHGHHHEE1BEBFFF5BAFDFEE11BF3F@FEG5E3>E1BGBGH4F?BEEEF>344@FED4FFEBFFEEGGE0F?/FG</>/C1DGFHHGEDFGCHFDH<FHGGCD@?EGG?GCFHHCCGC.DGHHGCCGCGFCAEHDEHAGFFBGGGGCFFFGGGGGG\n+@M01649:56:000000000-A57BB:1:1101:17879:2105 1:N:0:1\n+ACGAAAATCTGGTTCGTTTCGTAGTTTAAGAACTGATCTTTTTGGAGCTTATCAACAATCGCTTGTTTTAGCTCGATGATTCCACTAGAAGGAGTATATTTGGTGAATCCTTTGTTCATGGACTCAATTGCTG\n++\n+AAABAB3DFFFFADGEFGGGGGHDFEHHGHGFHHHHHHGHHHHGGHFHHHHHGHHHGHHHGGHHGHHHHHHHHHGGGHGHHHHHHHFHHFHHHEHHHHHHHFG1FFGHHHHHHHHGHHHHHEHHHHGGHHGHH\n+@M01649:56:000000000-A57BB:1:1101:13768:2106 1:N:0:1\n+CATAAAGGCGATCATTCAATTTATCTGCGCGAACCCAGCCGATTACTTTCTCGCCTTCTGAAATTCGGAAC\n++\n+BBBBBDFFBDDBGCGGGGGGGGHFFGFFCGCGGGGGFHFFGGGGGHHHFHFHGCEFDGGGHHFHGFEFGEG\n+@M01649:56:000000000-A57BB:1:1101:16607:2111 1:N:0:1\n+GTGCAGATAGCATTCCAGCTGATGAAATGGGACTAGATATTGGTCAAGCTACAATTGACTTATTTACAAAAGAACTTCAAGGCGCTAAAACAGTTGTATGGAATGGTCCAATAGGCGTATTCGAACTTAGCAACTTTGCTAAAGGTACAATTGGCGTTTGTGAAGCTATTGCAAACTTAACGGATGCAACAACAATCATCGGTGGTGGGG\n++\n+BBBBAFB4DFFF5FGGGGGFGGFHF5F5EFC4FGHHHHFHH5FGGHHHFHFFDFF5FGGHFHHHHFFHFDGGFHFEGHBFFE1EEEGG5FFH2GFFHHHG2FFFHBGHHFHH3B@@>EEEEHFHFGHH3EGHHHFFGHEHHFHFHGGHFBGHHHHGGGCGHGHEHGHHHHHGGHHHHGHHHGGGGGHHHEHHFHGHEHHHHGCAFGGGGG\n+@M01649:56:000000000-A57BB:1:1101:13666:2113 1:N:0:1\n+TACCTACGATTGCTGGATTCATCGAACCATTTGGACGTAAGATGAATTTACCAAGTTGAACAGCTTCTGCATCGGATAAGAAGTGTGCTCCTTGTTTTCTAAATTCAGCAATGACAGCTTCTTTATTCACACGTTCCACAACGACAGATTGCTCAGATGCGCAAATTGTTCCGTTATCGAATGTTTTGGAATCAAGAATATGTTTCACTGCGCGA'..b'AATGAGTGAGGCGGCTGATTTTTACTATGATGGCGAAACGACAAAATGGCTGACGAGCGAGCGCTTTGATACGCCGCATACGCACGGAACTGGTTGCACTTTTTCGGCATGTATTGCAGCTGAACTTGCGAAAGGGAATTCGCTTTTGGATAGTGT\n++\n+ACCCBFFFFFFAGGGGGGGGGGGHHHHHHHHHHHGGGGGGGGGGHHHHHHHGGHGGFFF@EGGGGGGHHHHHGGGGGGGGHHGFFGCCFGHHHFGGHBHHHHHHHGGGGGHHFHHHG1GHHEDFHHHHHCCGGGHGE.FHHFGGHGGGGFGGGGFF\n+@M01649:56:000000000-A57BB:1:1101:22094:4235 1:N:0:1\n+AATCTCCCGCGCCGAATGTTTTGAGCACTTTTGTTTTATATGCTTTTGCTTGGAATGTTTCTCCCGCTTTTGTATATGCGAATGAGCCTTCCACCCCATGCTTAATGACAACAATTTCTGCTTGATGTTGGAAAAGATGCGCTTTTGTTGCTTCATTTTTGCCACCGACTTGATTTTCCATCATATCAAAT\n++\n+AABBBFFFB@DBGGEEFGGGGGHCGFHHHFHHHHHHHHHHHHHHHHHHFFHHGHHFHGGGHHHFGGGGEGHHFHHGHHHDEFGHHFHHHGFGFHHGGGHHHHHGEHGHHHGHHHHHHHGFHHHHHGFHGHHHHFHHGEHHGGGGGHGHHGHHHHFGHGHHCFBGHHGGGGGHHHGFHGGHGHHHHHHHGHH\n+@M01649:56:000000000-A57BB:1:1101:19966:4235 1:N:0:1\n+GAAGTACTTTTTTCCTTTAAAGAAAAAGTGAAATGAATCCAACATAAATGACCGCGTGTAATCAAATTGATTTCAGGCGGTTTTTGTTTTAAAAACTTTACTGTTTCGCCTTCCTTTGCTATTCTACTAAGAGAGCAGGAGGAGAAAGATGACAAAGAAATTAGTAATCTGTATAAGTTTAATCGCGATATTTTTAAGCGGTTGTAGTT\n++\n+B@BBBFFFFFFFGGFGGGGGFFFGHHHG4DFGGFHHHHFFHHHDHHFDGHFGEEGGGGEEBGHFFBFHHEGHFHHF3FFGGGGFGGGGHHHHHHHGHHFBGHHHHHGGGEGGHHHGHHHHGGG4GGHHHHHFGH?HHFHGGGGFGHHHHFGHHHGHHGHHGHHHGHHHFHGHHHFHHFFGHHHHGGGCCGGGHHHHHHHGGGGGGGGGG\n+@M01649:56:000000000-A57BB:1:1101:12372:4238 1:N:0:1\n+GTTGGAGATGTGTTTAATGTGTTAAAAGGAGTTACTGCGAAAGATAACGAAGATGGTGATTTAACAGCAAAAATCAAAGTGACCAAGGATACAGTGAATAATTCGAAAAAAGGTGTTTATCAAGTTACATATAC\n++\n+BBB@BFFFFFFFGGGGGGGGGGHFFGHHCFFHFHHHHHGGGGGGHGGHGGGGGHHHHHHHHHHHHGFHHHHHHHHHHHHHHHGHHHGGGFGHHHGHGGHFHHGHGHHGGHGGG?FGGFFHGHHHFGHHHHHHGH\n+@M01649:56:000000000-A57BB:1:1101:8767:4246 1:N:0:1\n+CTGGGGATTAGAGGCATAAATATTCAAATCGCGCTCATCTAAAAATGTATACTGCGCTATGTTAATATTGTTCGCTTCTGAAAATTGCTTTATAG\n++\n+AA?A?DABFFFFDB2FGGGGGGHFFHFEEGEGG2AEEHHHHHFFGHHGHHHHFGFDGGGGHHFFHHHHHHHFHGGGHGHHFBBGHHHHHHHGFHH\n+@M01649:56:000000000-A57BB:1:1101:14394:4246 1:N:0:1\n+CGTCTAGACAGCGTCATTGAATTTAAATCTCTAGAAAAAGACGAT\n++\n+BBBBCCFFFFFDGGGGGGGGGGHHHHHHHHHHHHGHHHHGGHGGG\n+@M01649:56:000000000-A57BB:1:1101:7843:4248 1:N:0:1\n+TGATTTCTTTGAAGTGATTGTGGCAGTGTTTAGTCCACTCGCGTCAATCGTACAATCTTATCCAGGCTTTGTGCTTTCGGTTTTCATTCCAGCATTTCTTTATACATTCGGGTTTTCTGGGCGGGTTATGATGCCCGCGATTTACCCGGTTTATATGGCAGGACTCGCAGAAAACTCACAAGCTGTAGCAAATGGCGCAAGTGC\n++\n+BBAB@FBFFFFFGBGD5E5FEGD44EG4ADGC5GGHHHFHDECAEA2EGEFCGGBGGFHHGH5FEGEFGHHHHBG5EGGGGDACGHHHHFGHHF3FF4@G@GHFF4BGFHH?11?F4F4FG/><C>FGH1@FG11?/AD-CHF1=FGA-<.EFHBHGHHHGGGE/GA-:.-/:;/C00CBB.990CB0;9B/CFFF??-;-///\n+@M01649:56:000000000-A57BB:1:1101:16655:4248 1:N:0:1\n+GGATCACACTTCCACGGCGGATTTGCTGAAAATGTCGTCATGAAAGCCGACAATGTCATTTCTATCGGCGACCTTGATTTTGAAGAAGGTGCGATGATTGAAC\n++\n+BBAABFFFFFFFGGGGGGGGEFGHHHHHHHHHHHGFHGGHHHHHHHHHGGGGGHHGHFHHHHHHHHGGGGGGGGHHHHHHHHFGHHHHHFFH?EHGHHHHFHH\n+@M01649:56:000000000-A57BB:1:1101:16286:4249 1:N:0:1\n+GTTTCATCTCATGAACACATATAGTATACTGGAAAAATAAGCGAAGAAACGGAGGCATATTCATATGATTAAACGAACTGGTGAGATAGTACTCGCT\n++\n+BBBBBFFFFFFFGGGGFGGGGGHHHCHFFDHFHHHHGHHHFHGGGGGHHHGGGGGGGHHHHFHHHHHGHHHHHHGGGGHHHGHGFHFHGGHHFHGFE\n+@M01649:56:000000000-A57BB:1:1101:13055:4250 1:N:0:1\n+CTGTTTGATATTTATTATACTGGCGTGATGGGCATTTATTTTGCTATCTTCCCGTTTACAGTGTATATCACAGATAAATTTATGAAAGTGTTGCAAAATAA\n++\n+CCCBCFFFFFFFGGGGGGGGGGHHGEGGHHHHGHHHHHHHHHGFFHHHHHHHHGFGHGHGFGHGHHHHHHHGHHHHHHGHHGHEFHHHGGFGEHHHHHHHG\n+@M01649:56:000000000-A57BB:1:1101:23733:4252 1:N:0:1\n+CTAAATGCATGGTTGTAAATATTTTGGACTAGGGTCATTGTCGCTCCACTTGGACCAACTTCTGTCATAATCATCACTTGGTCAAACACCTGGAATGAGTTGATAAGCGAAATTATCATCACAAAGAATGTAGTAGGAGTAAGAAGCGGGATAGTAATAGAGAATAATTGGCGAAGTTTTGATGCTCCGTCCATATTGGCAGCTTCGTAATACGATGGTGAAATATTTTGCAATCCACCAAGGAATAGTA\n++\n+1AAAABD113@F1FEEDGFGGGDB33011BA1EA0B0222DB00BAEC01111EGBA/BGGHFGGHGF222AFF2FGDFB1BD2AGDEHEBCGH1B@1@@2F2@2@@FC?E>EG1FFHB221E1>0GHFFFGGHFB1G<GBGH11<F@CCGGH1>22@D2@11@G1@GHFH0@C?<>GHFHEFGFBDGCHFF.D0DG00/<ECF0C?C/:CCGAEEE.0900;B9BBFFF00F0;/C/;A.A.9/0BB00\n+@M01649:56:000000000-A57BB:1:1101:17948:4253 1:N:0:1\n+GGTCAATATTCCCATGTTACTTGAAACGCTCTCAATGCGGGCTGCAAGTAATCAAAAAGATCTAGTTGAAACAGCTC\n++\n+AAABBFFFFFFFGGGGGGFGGGHHHGHGGGGHHHHHHGGGGGGGGGFHAEGHHFGFHFGGHHHFFGFHHFHHHHHHH\n'

diff -r 000000000000 -r e1867440ed36 test-data/outputdownsameplereverse.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/outputdownsameplereverse.fastq Tue Sep 19 16:37:42 2017 -0400

b'@@ -0,0 +1,2588 @@\n+@M01649:56:000000000-A57BB:1:1101:15318:2049 2:N:0:1\n+GGGTAGGGACTAGCTCAAAAGAGGAAGTACAGGCGGCAGTAATTGATCAACCGACGCCAATTAATGAAATTTTTACAGATGAGAATTTAGCAAACGCAATAAAAGCAACTTTAAATAAACCTAGTACTACATCTGACGTTTCACAAGCAGAGCTAGATTCTATAAGTGAAGTAACGGCAGAAAGTAGCAATATAGCTTCTTTAGAGGGGGCGCAGTATTTAAAT\n++\n+>AA>3>AAFBFFGGGGGGGGFFFHGFFFGHHGGGGGCGGGFHFHHFFHFF3B0EEGGGCEFFHHHHHHGEHHHHHHGHBFHFFHHFHBEGEHHFFGGCEEBGFHFHHHAFFHHHGHGHHFEGHHFHHHHGGHHHHHHG?FHFBGHHAHC<0GHHHGHHHFFHHHBG1FFHHGFHHCGGCFGHFHGFHFHHHGFHHFHHFHFGBBFGGGGGGFFFFDFFFFFFBB\n+@M01649:56:000000000-A57BB:1:1101:17728:2054 2:N:0:1\n+ATCCGAAGACACATGTAACGGCTGTGGAAGGTTTGGACTCGGCTACAACTACTACATCTGGATTAATGCCCGCCAGCGACAAAACGAAATTAAATGGAATCGAAGCTAATGCAGAAAAAAATAATGTGACTGCAATCGATATTGCCAATTGGAATAAAAAACAGGACGCAATTTTGGTTTCTGAAAATGGCTCTAATTTCAAAATAACTGTCACAAATGCTGGTGAACTAAAGGCAACAAAAGTGGAATAG\n++\n+AAACABBCBFFFGGGGGGGGGGGGGHGDGHGGHH2FBBGGGGGDGFBGHHHHFHEEHFHGHGBFHHHHEFHG0E?ECE?EEGHGGGDEGAHHHHHHHHHGHFFGGGHHHHHG4GDCHFHGGHHHDFHHHFGBGGHFHAFEHCHFGGFHHHBGHHHHHHHHG?GCGHGGGGCGHEHHGCGHHFGFFFGGGGGGFFGGGGGGGGGFBFGFFGFGGGGGGGFFFBFFBBFBFFFFFEE9A.:EFFF;BFBB///\n+@M01649:56:000000000-A57BB:1:1101:11566:2074 2:N:0:1\n+TTTCTGGGTTGCTTTTGTTTCCGGAATTGGTTGTAAC\n++\n+AAAAAB1C>ADFG1BG1FFCB3AEA0AFF11A00DG2\n+@M01649:56:000000000-A57BB:1:1101:19846:2075 2:N:0:1\n+TCCCAGAACTGACACGAGCAATAAAATCCCTACATTAAAAGATGTCCGCGGAAAAATATTATTACTTTCAGAGAACCACACAAAAAAGCCATTAGTCATTAATTCACACAAATTCGGCATGCAGTTCGGCGCATCCAACCAAGTAATTCAAGATGACTACAATGGTCCGAGTGTGAAAACAAAATTCAAAGAGATTGTCCAGACTGCTTATCAAGCTTCTAAAGCGGACAACAAACTGTTTCTTAACGATA\n++\n+BAABBFA4FFFFGFGGGGGEFGGHHHHHHHHFHHHHHHHGFEHHFHHGGGGECE2CHFHHGHHHHFBGHHGHEHFHHHGHGGGHGHEFFFHFHHHHHHHHHFHHHHHHHGEHGHHGFGGCHHHHHFGG?DGGGGGHHHHGGHHHHHHHHHGGHHHGHHHHGHHEFGHHGGGGHCFFFHFHEGCGHHGHGFHFGGGGGFGFGGGGGGGGGFBFFGGGFGGGGFFGF?DBFFFEFEFFFFFFFFFFFFFFEF.\n+@M01649:56:000000000-A57BB:1:1101:18762:2076 2:N:0:1\n+CTACTTGTTTAGCAAGCTCGGTATCGCGGTGTACAAGTGACTTGACTGC\n++\n+BBCCCFFFFFBFGGGGGGGGGGHGHGGGGGGGHHHHHGHHHGHHHHHGH\n+@M01649:56:000000000-A57BB:1:1101:13268:2078 2:N:0:1\n+AGAGAGTACTTGGATATCAATACCATGTTGGTCCATAAATGCTAAACGTTTTTCTGTATCTTGCATTTCCGCTGCTGAAGGAAGTTCCTTTTGCATATATTGAAACATTTCCGGACTAACCTGTCC\n++\n+AA?A@ABB1BFBBFFG3GFG3FGHHEBDE3FEFFHHHHDDHFFFGFHGFHHGGFHFHHHGFFB1GGFFGGGFGCFHEFGF1GFFFEFDGFEGHBBGFGDGHHG1@1>BGHHD?//>EGFEGHH11G\n+@M01649:56:000000000-A57BB:1:1101:17969:2101 2:N:0:1\n+GGCGTATTCACAAACGCTAACCAAACGGTCACTTATGTGTACGAAAAAGCGGACGGCGCTCCTGTTACCGTGAAATATGTCGACGTGGATGGCAACGAATTAGCTACTTCCGACACACTGAACGGCAAAATTGATGCTCCTTATCAAACTACCGCTAAAAGTCTTTCTGGTTGGACGGTCAAAACGACTCCAACCAAC\n++\n+1111A1ACFBFFFGFFGGEEBGHHCECAFGFHGHFFHAAGHFEF//EF/AF/E/A//EGGGGGHGFFHFG/CEEDGHHHGGGE/><?//GCFH0BACA<FGHFGHEHHGB1C/><C0CB<1<<<.-->0GHFF=0<D000<0<0DDG0DBGGHGGG-.GGF0CGGFGFFF09.?BFG@9AEGFGGGE@FFFFFFFFEF\n+@M01649:56:000000000-A57BB:1:1101:17879:2105 2:N:0:1\n+CAGCAATTGAGTCCATGAACAAAGGATTCACCAACTATACTCCTTCTAGTGGAATCATCGAGCTAAAACAAGCGATTGTTGATAAGCTCCAAAAAGATCAGTTCTTAAACTACGAAACGAACCAGATTTTCGT\n++\n+BBBBAFFFFFFFGFFGGGGGC4FCEHFHFGHHHF2BGHGHFHHHHHD5D5DAAFGHHGFF3AEEHFHHGEFHHGGHHGHHH5GGHEGEGHFFDCGGAFDGGEGD4FGHFGFHHGGEEEG/FGGHHHHHGGHG0\n+@M01649:56:000000000-A57BB:1:1101:13768:2106 2:N:0:1\n+GTTCCGAATTTCAGAAGGCGAGAAAGTAATCGGCTGGGTTCGCGCAGATAAATTGAATGATCGCCTTTATG\n++\n+A11AAAAAA13@GB3BGGG0EEGGCCHHHFHE0EFCC/BAFEEGG/AA1FFHH2DFDHH1@@FA/>E1GGB\n+@M01649:56:000000000-A57BB:1:1101:16607:2111 2:N:0:1\n+CCCCACCACCGATGATTGTTGTTGCATCCGTTAAGTTTGCAATAGCTTCACACACGCCAATTGTACCTTTAGCAAAGTTGCTAAGTTCGAATACGCCCATTGGACCATTCCATACAACTGTTTTAGCGCCTTGAAGTTCTTTTGTAAATAAGTCAATTGTAGCTTGACCAATATCTAGTCCCATTTCATCAGCTGGAATGCTATCTGCAC\n++\n+1A?AAAAAAAA1EAGGCGGGGGC0DGGFHGGHGCDAGGFFGHHF1GHHHHHG1EEGCECAHHHDGF2FHH1FF1@EG1BF11F2GBFGE/0F>BGCE>>0111F1FGHFH22GFGBFC1FBGFFGBGE@?CGHFFGGHHHHHHHBF22FDDDDGGFFFDDHHHHHHHHGFGHFHGHHHHHGHDGHGHBFGFDHGHHFHHHHHGHHBFGHH\n+@M01649:56:000000000-A57BB:1:1101:13666:2113 2:N:0:1\n+TCATTAGTGAAGCAGCAGAAAAAGCTGGTTGTCCAAAAGGCGCTATCAGCTGTATGACTGTTCCAACCATCCAAGGAACAGATCAACTGATGAAACACAAAGATACAGCAGTTATCCTTGCAACAGGTGGATCTGCAATGGTAAAAGCGGCTTATTCATCTGGTACTCCAGCAATTGGAGTTGGTCCAGGTAATGGCCCAGCATTTATCGAACGC'..b'ACACTATCCAAAAGCGAATTCCCTTTCGCAAGTTCAGCTGCAATACATGCCGAAAAAGTGCAACCAGTTCCGTGCGTATGCGGCGTATCAAAGCGCTCGCTCGTCAGCCATTTTGTCGTTTCGCCATCATAGTAAAAATCAGCCGCCTCACTCATT\n++\n+CCCCCFFFFFFFGGGGGGGGGGHGHHHGGGGGHHHGGHHHHHHHHHHHFHHGGGGGHGEFHFFHHCGHHHHGHGGGGGGFHGGGGGGGHHGGHGEEGFGCFHGGDEGHHHHHHHHGHGGGGHGGGGGHFHHHHHHHHHHHHHHHCGGGFHHHHHHH\n+@M01649:56:000000000-A57BB:1:1101:22094:4235 2:N:0:1\n+ATTTGATATGATGGAAAATCAAGTCGGTGGCAAAAATGAAGCAACAAAAGCGCATCTTTTCCAACATCAAGCAGAAATTGTTGTCATTAAGCATGGGGTGGAAGGCTCATTCGCATATACAAAAGCGGGAGAAACATTCCAAGCAAAAGCATATAACACAAAAGTGCTCAAAACATTCGGCGCGGGAGATT\n++\n+AAAB?FFFFFFDGGGGF4DFEGFGHGCF2EFFGHGFFHHHHHHHFHEG2FF?20A0BGFFGGGHHFFFGHHFHFHHHFHE@5B2@EDGHHEHHGFEEE1/>1@CEEHHFGFFHGDGGB?443F0GFG?C/@EFHHHGHFHHGEEHF1FGAGHHHHH11GEFGHHFGEHHFFFECG00<0GC@CGG-DCDFF\n+@M01649:56:000000000-A57BB:1:1101:19966:4235 2:N:0:1\n+AACTACAACCGCTTAAAAATATCGCGATTAAACTTATACAGATTACTAATTTCTTTGTCATCTTTCTCCTCCTGCTCTCTTAGTAGAATAGCAAAGGAAGGCGAAACAGTAAAGTTTTTAAAACAAAAACCGCCTGAAATCAATTTGATTACACGCGGTCATTTATGTTGGATTCATTTCACTTTTTCTTTAAAGGAAAAAAGTACTTC\n++\n+3>AB@FFFF@DDGGEGGGGFEGFF?GEEE2BEGFHDGFFFFHBDGHHE5FAGHHHGGBGFHHHHHHHGDGHHF3FHHHHH5GFHFEFDG5FGGH3F?2FGCHGFGGGHEHF44DFHHHGEHGFG/FGHHEEGGGDEGHEGFHEHHHHHHHHHHHFGGGCDGGHHHHHHHGFBGHHHHHHHHHFHGHHHHHHHBGHGFGHHHCGFHGFGG\n+@M01649:56:000000000-A57BB:1:1101:12372:4238 2:N:0:1\n+GTATATGTAACTTGATAAACACCTTTTTTCGAATTATTCACTGTATCCTTGGTCACTTTGATTTTTGCTGTTAAATCACCATCTTCGTTATCTTTCGCAGTAACTCCTTTTAACACATTAAACACATCTCCAAC\n++\n+BBBBBFBFFFFFGGBGDGGGGGGHHHHHEHGGHHD5GHHHHFHHBGHHHHFF3EGHHHHHHHHHHHGHHGHHGHHHHHHHHHHHGHHHHHHHGHHHGGEEEFGHHHFG3GHHHBHHHFHHGDHFHFHHGHGFFH\n+@M01649:56:000000000-A57BB:1:1101:8767:4246 2:N:0:1\n+CTATAAAGCAATTTTCAGAAGCGAACAATATTAACATAGCGCAGTATACATTTTTAGATGAACGCGATTTGAATATTTATGCCTCTAATCCCCAG\n++\n+1AAAA33D1FFFGGGGGGGGGGCCGEEHHHHHHHHHHFHHAAECEGFHHHHFFHHGFFFHHHFC?EEEEFFHFEHHFGDHHHEDGHHHHHHGFHC\n+@M01649:56:000000000-A57BB:1:1101:14394:4246 2:N:0:1\n+ATCGTCTTTTTCTAGAGATTTAAATTCAATGACGCTGTCTAGACG\n++\n+ABCAAABCFFFFGGFGGGGGGGHHHGHHHHHHHGGGGGHGHHHHG\n+@M01649:56:000000000-A57BB:1:1101:7843:4248 2:N:0:1\n+GCACTTGCGCCATTTGCTACAGCTTGTGAGTTTTCTGCGAGTCCTGCCATATAAACCGGGTAAATCGCGGGCATCATAACCCACCCAGAAATCCCGAATGTATAAAGAAATGCTGGAATGAAAACCGAAAGCACAAAGCCTGGATAAGATTGTACGATTGACGCGAGTGGACTAAACACTGCCACAATCACTTCAAAGAAATCA\n++\n+>AAA1CDF??>1FFGGGGBFD1FA1FGFHHDGGBD12FG?EGHF2GGHFHHF2FGHBE?EEEFHHHGGGGCCEHGHFB2BF///E>///BB1F1B<E/FHFFGHDFDDFBD<GFHFF1FFGGHF0C?@G/<FGFHHHEH0<G.0>GDF1DFD<1GEEC<<DDAE@-@:..GCGFF0/;FG9FBFFF.CFBFFGG9FBBFABFBB\n+@M01649:56:000000000-A57BB:1:1101:16655:4248 2:N:0:1\n+GTTCAATCATCGCACCTTCTTCAAAATCAAGGTCGCCGATAGAAATGACATTGTCGGCTTTCATGACGACATTTTCAGCAAATCCGCCGTGGAAGTGTGATCC\n++\n+BB?AAFFFFFFFEFGCGGGGGGHHHHHHHCFGFFEGFGGCFFFDDGFHHHHHBGGEGGGGGFHGHHHDCEFGGGBFDDHHHGHHHE1>>>EC/FGFG4F4F4?\n+@M01649:56:000000000-A57BB:1:1101:16286:4249 2:N:0:1\n+AGCGAGTACTATCTCACCAGTTCGTTTAATCATATGAATATGCCTCCGTTTCTTCGCTTATTTTTCCAGTATACTATATGTGTTCATGAGATGAAAC\n++\n+BABBCCBFFFFFGGGGGGGGGGHGGHGGHHHHFGHHFBHHGHHHFHHGGFHHFHHHGGHGHHHHHHGFHHHHHEHHHHGFGFGFHFHHHHGHHHFBG\n+@M01649:56:000000000-A57BB:1:1101:13055:4250 2:N:0:1\n+TTATTTTGCAACACTTTCATAAATTTATCTGTGATATACACTGTAAACGGGAAGATAGCAAAATAAATGCCCATCACGCCAGTATAATAAATATCAAACAG\n++\n+CCCCCFFFFFFFGGGGGGGGGGHHHHHHHHHHFHGHHHHHHHHHHFHFEAEGGGHHHHHIHHHGHHHHGHHHHHGHGGHGGGGHHFHHHHFHHHGHHHHHG\n+@M01649:56:000000000-A57BB:1:1101:23733:4252 2:N:0:1\n+ATGCTTATTCTGGCTACTCAATTTACTAGGTTTTCTCATTTTTCTTGCAATCCCAATCCTTGGCTCGCTTGGTATTCGTTTTACAGATTGGGACTTCGTGAGTACTATTCACATTACTGGAATTGAGCATTATAAAAGGCTGTTTAATGACCCAGAGTTTTGGAAATCGATTAGAAATCCAATCACGTTCATCATCGGTTTTTTGCCTAGAGTAATGTGTCTTGTCCTAGTGTGTTACTTGATGTTGAAT\n++\n+>11>1D313B3311BBG111B3DF3A331AF1FFG1333A32D011D1B12BF110AF0DBF1BCF/EFG//1AA22000/A2@21@1@1>/?0BG1/BE0/F2DDB22BGG2BF11221011B1B11>B2122B211/?10011>BB221B<?G//BB1BC/1<1@>/0?>/1@1??1<<11<FF<0F01=D><D1AC..<.<-<0=0<000:<0000;:;C00:;0C000:0:/0;C0000;000000\n+@M01649:56:000000000-A57BB:1:1101:17948:4253 2:N:0:1\n+GAGCTGTTTCAACTAGATCTTTTTGATTACTTGCAGCCCGCATTGAGAGCGTTTCAAGTAACATGGGAATATTGACC\n++\n+BBBBAFDFFFFFGGGGGGGGGGHHGDHCHFFFFFGCHAEGGGGEFG3GFEGFGCFHHHFFFFFFF2FEGGEGGBFFG\n'

diff -r 000000000000 -r e1867440ed36 test-data/outputforward.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/outputforward.fastq Tue Sep 19 16:37:42 2017 -0400

diff -r 000000000000 -r e1867440ed36 test-data/outputreverse.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/outputreverse.fastq Tue Sep 19 16:37:42 2017 -0400

diff -r 000000000000 -r e1867440ed36 test-data/testref.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/testref.fasta Tue Sep 19 16:37:42 2017 -0400

b'@@ -0,0 +1,115 @@\n+>gi|360034408|ref|NC_016445.1|_2000000_2400000\n+CCCGCTCGCCACGCTTTGGCCATAGTGCTGCCTTCTACGATGTGTAAACCGTGCAACTTAATGCCATCGGTGCCTACCTT\n+CAGTACTTGCTGTAACGTGGTGAGGTTTTCAGTGCGCTCTTCACCGGGTAACCCAACAATCAAGTGAGTACACACTTTGA\n+TACCTAACGCTCTAGCTTTGGCAGTGATCTCTGCGTAGCAGGCAAAATCGTGCCCGCGGTTAATGCGTTTTAAAGTCTGG\n+TCGTGCGCCGTCTGTAAACCCAATTCAAGCCAAATTTCATAACCTTGCTGCACATAATCGGCGAGCAACTTAAGCACCGC\n+ATCCGGTACACAATCAGGACGAGTGCCAACACACAACCCCACAATATCCGCTTCTTCTAGGGCTTGTTCGTACATGGATT\n+TCAGCACTTGCACTTCCGCATACGTGCTGGTGTAAGCTTGAAAATAAGCGAGGTATTTTTTGGCGCGTTTGATCTCCCCC\n+GCCCGATCTTTCAACTGCGCTTGAATACTCTGCTGCTGAGTATTTTCATCGGCAAACGACGCCACATTACAGAAAGTGCA\n+GCCGCCACGGCCTATCGTGCCATCGCGATTCGGACAACTGAATCCACCATGCAGCGTTAACTTATGGACCTTCTCTCCAT\n+AACGGCGTTGTAAATCTTGACCTATGGTGTTCACCAGTTGATGTAAATGCATCGGCTCGCTCAATCTAAATACAAATATC\n+TCTCACTACCATCCGTGTAATTTAATTACATTTCCAATCGAATTGGTCACAAATTTTAATCCCTCGCGTTTGATTTCAAA\n+CAGCGTCAAATCAATAAATAGGCATAAAATAAACACTATTTGCATTTTGTTTCTAGTTTGTTAAACAAAACATTCATCTA\n+GCTGTAAAAAAATAAACCAAACCGCAGACTTTTCGTTGGAATTTGCGCCAGCAAAATTGTAGGATACTTTCAGTTTTCCG\n+TGCTTTTTTGCTCAATTAATTACAAAAAACGCGGCAGACTATCGGTGATATTCCACACCTACCAAAAGAATCCACTAGTA\n+AAGTGGCTCGACAACAGGAATGTCACTAAGGATTGTCTTTCTCACAATATATTTCCTGTGAGAGACGGAAAGGACGCGGA\n+TCTGCTCCCTAAGCAGATTTCACTCAAAACAAAAAGGACAGGACGTATCGCCCAAGCGACTCATTCAGCGGATGCTGCTT\n+GATGCGTGGCGGGAATAACTGAGTGCACACTCAGTGCGGTTGCGTCCTCAATAACTGGAAGGATGTATCTATGGTAGATA\n+AAGCGCAACGTTCGCGTGGTCTTTATACGCCTGAGCTGGAGCATGATGCTTGTGGCATCGGCTTTGTCGCTCACCTGAAA\n+AATCGCAAGTCTCATCAGGTGGTCACTCAAGCTTTGGACATGCTCGCACGCATGGAACACCGTGGCGGTCAGGGTTGTGA\n+CCCTTGCAGCGGTGACGGTGCGGGTATTTTGTTGCAAAAACCTCACGAATTTTTACTCGAAGAAGCGGTTAAACTGGGGA\n+TCAAGCTGCCTTCATTCGAAAAGTACGGTGTTGGTGTGGTGCTGTTCCCGAAAGATGAACATAAACGCGCCCAATGCCGC\n+GACATTCTAGAACGCAATGCCAAACGCCTTGATCTGGATGTGATTGGCTACCGCGTTTTACCGACCAATAACAGCATGTT\n+GGGTGCCGACCCCCTCAGTACCGAACCACAATTTGAACACGTGTTTATTTCTGGCGGCCCGGGTATGCAGCCTGACGAGC\n+TAGAACGCAAGCTGTACGTGCTGCGTAACTACACCGTTCGCGTCTGCCTTGAGAGCGTGTCGAACATCGGTGATGATTTT\n+TATATCAACTCGATGTCGTACAAAACCTTGGTCTATAAAGGTCAGTTGACTACAGAGCAAGTACCGCAATACTTCCTCGA\n+CTTGCAAAATCCGACCATGGTGACAGCGTTAGCACTGGTGCACTCGCGTTTTTCGACCAACACCTTCCCGAAATGGCGAC\n+TGGCTCAACCTTTCCGCTACATCGCGCACAACGGTGAGATCAACACGGTTCGCGGTAACTTGAACTGGATGAAAGCGCGC\n+GAAGCGATTTTACAATCCAAGCTGTTTACTCAAGCTGAAATCGATATGCTGCTGCCTATCTGCCAAGAAGGCGCATCCGA\n+TTCGGCTAACTTTGACATGGTACTCGAACTGCTGGTGCTTTCCGGTCGCAGCTTGCCTCACGCTCTGATGATGATGATCC\n+CAGAAGCATGGCAAGAAAACAAAGCGATGGATCCTAAGCGCCGCGCCTTCTATCAATACCACGCTAACGTCATGGAACCT\n+TGGGACGGCCCAGCATCAGTGTGCTTTACCGATGGGGTACAAGTAGGCGCCACACTGGATCGTAACGGTCTGCGTCCGTC\n+TCGTTATACCGTGACCAAAGACGATTTTCTGATCATGGCTTCCGAATCTGGCGTCGTGGAAATTGATCCGGCCAATGTGG\n+AATACCGTGGTCGTCTGCAACCGGGACGTATCTTTGTTGCCGACTTAGAACAAGGCCGTATTATCTCAGATGAAGAGGTG\n+AAAGACGGTATCGCTTCGGCGCAGCCTTATGAAAAATGGGTAGAAGAAAACCTACTCAGTTTGAAAAAACTGCCGGATGC\n+CGACAACGTACATAGCCAACCGTCGCCAGAGCGTCTCCTCCATCGCCAACAAGCGTTTGGGGTGAGTAGCGAAGAGGTCA\n+ATGACATCATTCTGACTCTCGCGCAAACTGGTTATGAGCCGCTCGGTTCGATGGGGGCAGACTGGCCGGTCGCCGTGCTG\n+TCACACCAATCTCAGCATCTCTCCAACTACTTCAAGCAGTTGTTTGCCCAAGTGACCAACCCACCGATCGACCCGATCCG\n+TGAACGCATGGTGATGTCGCTCAACACTTATATCGGCCGCGATCAAAACTTGCTAGCAGAAACCCCTGCGCACTGTCGTA\n+AGGTCGAATTGGAATCGCCGGTCATTTCTAATGCTGAGCTTGAGAAAATCCGGGCAATCGATAACGAGCACTTGCAAGCC\n+AAAACCTTAGACATCGTATTTCGTGCCAGCGATGAACCGGGCAAGCTCGAACGCGCTCTGAAACGTATTTGCCAATACGC\n+GGAAGATGCGGTGATTGATGGCTATTCGATCATTTTGCTGACCGACCGCGCGGTAAACTCCAACCACGCCGCCATCCCAG\n+CCATGCTGGCTGTAGGCGCGGTGCACCATCACCTGATCCGCAAAGGTCTGCGTTCGAAATGCGGCATTGTGGTGGAAACT\n+GGTGATGCGCGTGAAACGCACCACTTTGCAACCCTACTCGGCTACGGTGCAAACGCAGTCAACCCGTATCTAGTGGTGGA\n+AACCATCGTCGATCTCAAGCGTCAGAAGAAACTCGATGCCGATGTTTCGGTAGAGAAATACTTCGAGAATTACCGTAAAG\n+GCGTGAACGGCGGTCTGTTGAAGATCTTCTCTAAAATGGGGATTTCGACGCTGCAGTCTTATCACGGTGCACAGATTTTT\n+GAAGCGCTCGGGATCAGTAAAGCGGTGGTCGATAAATACTTCACTGGCACCATCACCCGTATTCAAGGTTTGACCCTCGA\n+CGACATCGCTAAAGAAGTGTTGGTTCGTCATCGCATTGGTTACCCAACGCGTGAAATCCCACTGCAAGTGCTGGATGTCG\n+GCGGCGTGTATCAATGGAAACAGCGTGGTGAGCAGCATCTGTTTAACCCAGAAACGATTCACCTGCTGCAAGAATCGACT\n+CGCCACAAAAATTATCAGCAGTTCAAGAAGTACGCAGCCGCGGTGGATAGCCAAGGCGATAAAGCCGTTACTCTGCGC'..b'TACTTTGAAGTGGAAGGCGATGCTAACGACTACTGGGGCAAAGGTCTTTCTGGTGGCACGCT\n+GGTGCTCTACCCGAACCGTAACGCCACCATAGTTCCGGAAGAGAACATTGTGGTCGGTAACGTCTGTTTCTACGGCGCAA\n+CCTCTGGCGAATCTTACATTCGCGGCCTAGCGGGCGAGCGTTTCTGCGTGCGTAACTCAGGTGCCAAAGTGGTGGTGGAA\n+GGTATCGGCGATCACGGCTGTGAATACATGACCGGCGGTGTCGCAGTGATCCTCGGTTCAACCGGCCGTAACTTCGCCGC\n+AGGTATGAGTGGCGGTGTGGCTTACGTGTGGGATAAATCTGGCGACTTCCAATCTAAGCTCAATGCAGAATTGGTTGATC\n+TGGACCCTATCGAAGCGGAAGACAGAGCCCTACTCAAAGAGATGTTAACCAAGCATGTTCAATTCACAGGAAGTGAAGTG\n+GCCAAAGCTTTCCTTGCCAACTTTGACGCAAGCCTAGCCACTATGGTCAAGGTCATGCCGCGTGATTACAAAGCGGTACT\n+GCAAAAGCGTAAAGCACAGGAGCAACAAGCCACATTAGCAGCGGAGGCGGTATAAATGGGTAAAGCAACCGGATTTTTAG\n+AATTTGGTCGTGAACTGCCGAAAAAAATCGACCCGGCAGAGCGCATCAAAAACAACAAAGAGTTTGTCCTTAACCAAGAG\n+TTTGGTAAGAAGATCAATCAGCAAGCTTCACGTTGTATGGATTGTGGCGTGCCGTTTTGTCATAACGGCTGCCCGATTGG\n+CAACATCATTCCCGAGTTTAACGATGCAGTGTATCGCGACAGTTGGGAAGAGGCTTGGAATATTCTGAGCTCGACCAACA\n+ACTTCCCAGAGTTTACCGGTCGTGTCTGCCCTGCACCTTGTGAAACCGCCTGTGTGCTTGGCATCAACCAAGATCCGATC\n+ACCATCTGTAACATTGAAAAAACCATTGTGGAACGTGCTTACCAAGAAGGCTATGCCAAGCCGAAAACGCCACGTTCACG\n+CACCGGAAAAACGGTCGCGATCATTGGCTCAGGCCCTGCGGGGCTGGCCGCGGCGGAGCAGTTGAATGCCGCGGGTCATA\n+GCGTCACCGTGTTTGAGCGGGATGAAAAAGTCGGCGGCTTGCTGCGCTTTGGCATTCCCGATTTCAAACTCGGTATGGAT\n+GTGATTGATCGCAAAATCAATCTGATGGAACAAGCGGGCGTTAAGTTCGTGGTCAATGCGCATATCGGTGTAGACATCAA\n+CGCTCAACAGTTGCGTCAGGAGTTTGATGCGGTATTGCTGACGGGCGGCTCAACCGTACCACGTGATCTGAGCATTCCCG\n+GACGTGATCTGAAAGGCGTTTACTTCGCGATGCAGTTCCTCGCGCAAAATAACCGCCGAGCCAATGGCATGGATCTGAAA\n+GGTGAAGAGATCCACGCTAAAGGCAAACATGTGGTAGTGATCGGAGGCGGCGATACTGGCTCCGACTGTGTCGGCACCTC\n+TAACCGCCACGGCGCTGCGAGTATCACTCAAGTGGAGATCATGCCGATCCCACCGCAAAAGCGCCCAGTGAATATGCCTT\n+GGCCGCAATATCCGATGATTCTGCGCACCTCTACCTCTCATGAAGAAGGCTGTGAGCGTCATTGGAACATCCTCACCAAA\n+GAGTTCATTGGTAATGAACAAGGTGAAGTGACGGGTCTACGCATCGCTGACATCGTTTGGAAAGATGCAGCCCCCGGTGA\n+GCGACCAAGCTTTGACGAAGTGGTGGGCAGTGAACGCGTCATTCCTTGTGATATGGCATTTCTGGCGATGGGCTTCTTGC\n+ATCCAGAGCCACACGGCGTGCTTGCTCAGTTGGGGATTAAGCTTGATGAGCGCGGCAATGTGGCGACGCAAGATTTTGCG\n+ACCAACCAAAAAGGCGTATTCGCCGCAGGTGATATGCGCACAGGCCAATCCTTGGTGGTGCGCTGTATCAACGAAGGTCG\n+CGAATGTGCGCGAGCCGTTGACACCTTCTTGATGGGCAATACCCATCTTGAGGCAAAAGCGGACTCACTCATGCTGTCAG\n+CATAATCCTCTGTTGGCGCGGGTGATGCATCCTCATCCGTGTCAACACAACCGTTTCCTTCCATATTGTTTTACTTCGGC\n+CAGCACTCCCTGCTGGCCTTTTTTATGCCTATTCTCATCACACGGGATAAAACCTTGAGTTATCTGTAACTGAGAGAAAA\n+CTATCCCATTGAATATAATGACATTATTTGAAGTATTCCTCGGCAAATACCCTGCAAACCCTATTTTCAACCAATAACTT\n+GACCTTTTGTACAATAAGCTATAGGTTGTGAATTCGGTGAAAATAAAATCCCGCAAAAATGTTAATTAATTAACCTGAAA\n+TGTTAGTTAATTATTCAAATTATAAAGATTTAAATGAATAGTTATACCCAAGCTACTTGAAGCCATCGTTAAACGGAAGT\n+GGATGAATCCCCATCAGCATAGATAACTATGTGATTGGAGTAGACAGACACCGCCCATACCGAGGCTGTTTCAAGGAGTA\n+AGGGAATTGTCATTTACTGTCTGGATGACAGAGATGCAAAGGGAGAATTGCAATGGCTCTATACGATCCAAGTCTTGAAA\n+AAGACAACTGTGGATTCGGCTTGATCGCGCACATGGAAGGGCAAGCCAGTCACAAACTCGTTCGTACCGCGATTTCAGCA\n+CTTGATCGCATGACTCACCGTGGCGGTATCGCCGCCGATGGTAAAACTGGTGATGGCTGTGGTCTGTTGCTGCAAAAACC\n+TGACTCTTATTTGCGCCTGATCGCAGAAGAGCAACATTGGAAACTCAGCAAACAGTACGCGATTGGCATGCTGTTTCTCA\n+GCCGAGATCCACACAAAGCGCAGCTGGCACAGCAAATTGTTAACCAAGAACTCGCTAAAGAAACCTTAAGCGTGGCAGGT\n+TGGCGCAAAGTGCCCACCAACCCGAAAGTGCTTGGCCCGATAGCCCTCGACTCTTTGCCCGATATTCAACAAGTCTTCAT\n+CTCCGCCCCGGCCGGTTGGCGTGAGCGCGATGTTGAGCGCCGTCTGTATATTGCGCGTCGTCGCATTGAAAAACAGATTA\n+CGGATGATCGCGATTTCTACATCTGCTCGCTCTCGACTCAAGTGTTGGTTTACAAAGGCCTGTGTATGCCCGCAGACCTA\n+CCACGCTTTTATCTCGACTTAGCCGATCTGCGTATGGAATCGGCGATTTGCTTGTTCCACCAACGTTTCTCCACCAATAC\n+TCAGCCACGCTGGCCGCTGGCTCAGCCGTTTCGCTATCTGGCGCACAATGGCGAAATCAACACCATTGAAGGTAACCGCC\n+AGTGGGCACGCGCTCGGGCTTATAAGTTCGCGTCACCGCTGCTGCCCGATTTGCAAAGCGCTGCCCCTTTTGTGAATGAA\n+ACCGGTTCGGACTCTTCGAGCCTAGACAACATGCTGGATCTGTTTTTAGCCGGCGGGATGGATATCTTCCGTGCGATGCG\n+CATGCTGGTTCCGCCCGCATGGCAAAACCATCCGGATATGGATCCGGATCTGCGTGCTTTCTACGATTTCAACTCCAAAC\n+ACATGGAGCCTTGGGATGGCCCGGCGGGGATCGTGCTGTCCGATGGTCGTTACGCCGCGTGTAACCTTGACCGTAACGGC\n+CTGCGTCCTGCGCGTTATGTGATCACCAAAGATAAGCTCATCACCCTCGCTTCAGAAGTCGGGATTTGGGATTACGCACC\n+AGATGAAGTGTCTGAAAAAGGTCGGGTTGGCCCCGGCGAGCTGCTGGTGATCGACACTCGCAAAGGCAAAATTTGGCAAT\n+CGAGCGAAATTGATAACGACCTAAAAAGCCGTCACCCCTATCGTGAGTGGATGGAAAATAACGTTCATAAACTCACGCCC\n'