# HG changeset patch
# User jdv
# Date 1518415090 18000
# Node ID 32cb27adeb341dbb10e7f5490d707ce85c3551ea
# Parent  36cc4ae4160e2093f7bdf69ba760e5ff6eb93184
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 2dabc22c3707cc87100b094b25705160b842e9f9-dirty

diff -r 36cc4ae4160e -r 32cb27adeb34 nanopolish_extract.py
--- a/nanopolish_extract.py	Mon Dec 04 02:03:21 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,58 +0,0 @@
-#!/usr/bin/env python3
-
-import sys, os
-import glob
-import subprocess
-import shutil
-import h5py
-import numpy as np
-
-def main():
-    tar_file = sys.argv[1]
-    out_file = sys.argv[2]
-    threads  = sys.argv[3] # currently unused
-
-    extract_fast5(tar_file)
-
-    subprocess.call([
-        "nanopolish",
-        "extract",
-        "--recurse",
-        "--fastq",
-        "--output", out_file,
-        "in_dir" ])
-
-def extract_fast5(fn):
-
-    try:
-        in_dir = "in_dir"
-        if not os.path.exists(in_dir):
-            os.makedirs(in_dir)
-
-        # python's tarfile interface does not sanitize file paths within
-        # tarballs, which can be a big security risk. GNU tar does sanitize by
-        # default, so it's easier/safer here just to call the system tar
-        subprocess.call([
-            "tar",
-            "-xf",
-            fn,
-            "-C",
-            "in_dir"])
-
-        files = glob.glob(
-            os.path.join(in_dir, "**", "*.fast5"),
-            recursive=True
-        )
-        if len(files) < 1:
-            raise ValueError('No FAST5 files found')
-
-    except OSError as e:
-        print("Unexpected error:", e.strerror)
-        raise
-
-    except:
-        print("Unexpected error:", sys.exc_info()[0])
-        raise
-
-if __name__ == "__main__" :
-    main()
diff -r 36cc4ae4160e -r 32cb27adeb34 nanopolish_extract.xml
--- a/nanopolish_extract.xml	Mon Dec 04 02:03:21 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,86 +0,0 @@
-<tool id="nanopolish_extract" name="Nanopolish::extract" version="0.8.2">
-
-    <description>FAST5 to FASTQ/A extraction</description>
-
-    <!-- ***************************************************************** -->
-   
-    <!--
-    <requirements>
-        <requirement type="package" version="0.7.2">nanopolish</requirement>
-    </requirements>
-    -->
-
-    <!-- ***************************************************************** -->
-
-    <version_command>nanopolish --version | perl -wnE'print "$1\n" for /^nanopolish version (.+)$/mg'</version_command>
-
-    <!-- ***************************************************************** -->
-
-    <command detect_errors="aggressive">
-    <![CDATA[
-
-    python3 $__tool_directory__/nanopolish_extract.py $input $output \${GALAXY_SLOTS:-1}
-
-    ]]>
-    </command>
-
-    <!-- ***************************************************************** -->
-
-    <inputs>
-
-        <param name="input" type="data" format="fast5.tar" label="Input reads" />
-        <param name="out_format" type="select" label="Output format">
-            <option value="fastq" selected="true">fastq</option>
-            <option value="fasta">fasta</option>
-        </param>
-
-    </inputs>
-
-    <!-- ***************************************************************** -->
-
-    <outputs>
-
-        <data name="output" format="fastqsanger" label="${tool.name} on ${on_string}">
-            <change_format>
-                <when input="out_format" value="fasta" format="fasta" />
-            </change_format>
-        </data>
-
-    </outputs>
-
-    <!-- ***************************************************************** -->
-
-    <tests>
-        <test>
-            <param name="input" value="test_data.fast5.tar.gz" ftype="fast5.tar.gz" />
-            <output name="output" file="test_data.fastq" compare="sim_size" delta="0"/>
-        </test>
-    </tests>
-
-    <!-- ***************************************************************** -->
-
-    <help>
-    <![CDATA[
-
-**Description**
-
-Nanopolish is a software package for signal-level analysis of Oxford Nanopore
-sequencing data. Nanopolish can calculate an improved consensus sequence for a
-draft genome assembly, detect base modifications, call SNPs and indels with
-respect to a reference genome and more.
-
-The Galaxy wrapper has modified nanopolish to take a gzip tarball of FAST5 reads
-as input, such as can be produced by `poretools combine`, and always outputs a
-single FASTQ file.
-
-This is the `extract` module.
-
-    ]]>
-    </help>
-
-    <!-- ***************************************************************** -->
-    
-    <citations>
-    </citations>
-
-</tool>
diff -r 36cc4ae4160e -r 32cb27adeb34 nanopolish_index.pl
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/nanopolish_index.pl	Mon Feb 12 00:58:10 2018 -0500
@@ -0,0 +1,74 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+use 5.012;
+
+use Cwd qw/getcwd abs_path/;
+use File::Copy qw/copy/;
+use Getopt::Long qw/:config pass_through/;
+use threads;
+use threads::shared;
+use BioX::Seq::Stream;
+
+my $fn_link = 'reads';
+
+my $fn_fast5;
+my $fn_reads;
+my $fn_outfile;
+
+# parse genome filename and add back to arg stack
+GetOptions(
+    'fast5=s'   => \$fn_fast5,
+    'reads=s'   => \$fn_reads,
+    'outfile=s' => \$fn_outfile,
+);
+
+my $ret;
+
+$fn_fast5   = abs_path($fn_fast5);
+$fn_reads   = abs_path($fn_reads);
+$fn_outfile = abs_path($fn_outfile);
+
+# extract FAST5 files to path where they are expected
+my $fast5_dir = 'fast5';
+if (-e $fast5_dir) {
+    warn "$fast5_dir exists, won't overwrite";
+    exit;
+}
+mkdir $fast5_dir;
+my $cwd = abs_path( getcwd() );
+chdir $fast5_dir;
+
+# use system 'tar' to transparently and safely handle absolute paths
+$ret = system(
+    'tar',
+    '-xf',
+    $fn_fast5
+);
+die "Failed to extract tarball: $!\n"
+    if ($ret);
+
+chdir $cwd;
+
+symlink( $fn_reads, $fn_link )
+    or die "Failed to create symlink: $@";
+
+# index reads
+$ret = system(
+    'nanopolish',
+    'index',
+    '--directory' => $fast5_dir,
+    $fn_link,
+);
+die "Failed nanopolish indexing: $!\n"
+    if ($ret);
+
+my @idx_fns = glob "$fn_link.*";
+$ret = system(
+    'tar',
+    '-cf' => $fn_outfile,
+    @idx_fns,
+);
+die "Failed tarball creation: $!\n"
+    if ($ret);
diff -r 36cc4ae4160e -r 32cb27adeb34 nanopolish_index.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/nanopolish_index.xml	Mon Feb 12 00:58:10 2018 -0500
@@ -0,0 +1,82 @@
+<tool id="nanopolish_index" name="Nanopolish::index" version="0.8.5">
+
+    <description>Index FASTQ reads in FAST5 file</description>
+
+    <!-- ***************************************************************** -->
+   
+    <requirements>
+        <requirement type="package" version="0.8.5">nanopolish</requirement>
+    </requirements>
+
+    <!-- ***************************************************************** -->
+
+    <version_command>nanopolish --version | perl -wnE'print "$1\n" for /^nanopolish version (.+)$/mg'</version_command>
+
+    <!-- ***************************************************************** -->
+
+    <command detect_errors="aggressive">
+    <![CDATA[
+
+    perl $__tool_directory__/nanopolish_index.pl
+
+        --reads $input_reads
+        --fast5 $input_fast5
+        --out   $out_index
+
+    ]]>
+    </command>
+
+    <!-- ***************************************************************** -->
+
+    <inputs>
+
+        <param name="input_reads" type="data" format="fasta,fastq" label="Input reads (FASTA/Q)" />
+        <param name="input_fast5" type="data" format="fast5.tar" label="Input reads (FAST5)" />
+
+    </inputs>
+
+    <!-- ***************************************************************** -->
+
+    <outputs>
+
+        <data name="out_index" format="tar" label="${tool.name} on ${on_string}" />
+
+    </outputs>
+
+    <!-- ***************************************************************** -->
+
+    <tests>
+        <test>
+            <param name="input_reads" value="called.fa" ftype="fasta" />
+            <param name="input_fast5" value="test.fast5.tar.gz" ftype="fast5.tar.gz" />
+            <output name="out_index" file="index.tar" compare="sim_size" delta="100"/>
+        </test>
+    </tests>
+
+    <!-- ***************************************************************** -->
+
+    <help>
+    <![CDATA[
+
+**Description**
+
+Nanopolish is a software package for signal-level analysis of Oxford Nanopore
+sequencing data. Nanopolish can calculate an improved consensus sequence for a
+draft genome assembly, detect base modifications, call SNPs and indels with
+respect to a reference genome and more.
+
+The Galaxy wrapper has modified nanopolish to take a gzip tarball of FAST5 reads
+as input, such as can be produced by `poretools combine`, and always outputs a
+single FASTQ file.
+
+This is the `index` module.
+
+    ]]>
+    </help>
+
+    <!-- ***************************************************************** -->
+    
+    <citations>
+    </citations>
+
+</tool>
diff -r 36cc4ae4160e -r 32cb27adeb34 nanopolish_variants.pl
--- a/nanopolish_variants.pl	Mon Dec 04 02:03:21 2017 -0500
+++ b/nanopolish_variants.pl	Mon Feb 12 00:58:10 2018 -0500
@@ -17,6 +17,7 @@
 my $fn_consensus;
 my $fn_fast5;
 my $fn_reads;
+my $fn_index;
 
 # remember full command string (with proper binary)
 
@@ -28,10 +29,12 @@
     'consensus=s' => \$fn_consensus,
     'fast5=s'     => \$fn_fast5,
     'reads=s'     => \$fn_reads,
+    'index=s'     => \$fn_index,
 );
 
 my $ret;
 
+my $fn_link = 'reads';
 my $tmp_dir = 'tmp_dir';
 mkdir $tmp_dir;
 
@@ -45,28 +48,42 @@
 chdir $fast5_dir;
 $ret = system(
     'tar',
-    '-xvf',
+    '-xf',
     $fn_fast5
 );
 die "Failed to extract tarball: $!\n"
     if ($ret);
 chdir $cwd;
 
+symlink( $fn_reads, $fn_link )
+    or die "Failed to create symlink";
+
 
 # index reads
-$ret = system(
-    'nanopolish',
-    'index',
-    '--directory' => $fast5_dir,
-    $fn_reads,
-);
-die "Failed nanopolish indexing: $!\n"
-    if ($ret);
+if (defined $fn_index) {
+    $ret = system(
+        'tar',
+        '-xf',
+        $fn_index
+    );
+    die "Failed to extract tarball: $!\n"
+        if ($ret);
+}
+else {
+    $ret = system(
+        'nanopolish',
+        'index',
+        '--directory' => $fast5_dir,
+        $fn_link,
+    );
+    die "Failed nanopolish indexing: $!\n"
+        if ($ret);
+}
 
 my @cmd = @ARGV;
 unshift @cmd, 'nanopolish';
 push @cmd, '--genome', $fn_genome;
-push @cmd, '--reads', $fn_reads;
+push @cmd, '--reads', $fn_link;
 
 my @regions :shared;
 
diff -r 36cc4ae4160e -r 32cb27adeb34 nanopolish_variants.xml
--- a/nanopolish_variants.xml	Mon Dec 04 02:03:21 2017 -0500
+++ b/nanopolish_variants.xml	Mon Feb 12 00:58:10 2018 -0500
@@ -1,14 +1,12 @@
-<tool id="nanopolish_variants" name="Nanopolish::variants" version="0.8.2">
+<tool id="nanopolish_variants" name="Nanopolish::variants" version="0.8.5">
 
     <description>Re-call consensus and variants from raw signal</description>
 
     <!-- ***************************************************************** -->
    
-    <!--
     <requirements>
-        <requirement type="package" version="0.7.2">nanopolish</requirement>
+        <requirement type="package" version="0.8.5">nanopolish</requirement>
     </requirements>
-    -->
 
     <!-- ***************************************************************** -->
 
@@ -35,6 +33,9 @@
         --min-candidate-depth $min_candidate_depth
         --min-candidate-frequency $min_candidate_frequency
         --fast5 $input_fast5
+    #if $input_index:
+        --index $input_index
+    #end if
         $fix_homopolymers
         $calculate_all_support
 
@@ -45,10 +46,11 @@
 
     <inputs>
 
-        <param name="input_reads" type="data" format="fasta" label="Input reads (FASTA)" />
+        <param name="input_reads" type="data" format="fasta,fastq" label="Input reads (FASTA/Q)" />
         <param name="input_fast5" type="data" format="fast5.tar" label="Input reads (FAST5)" />
         <param name="input_bam"   type="data" format="bam"   label="Alignment" />
         <param name="input_ref"   type="data" format="fasta" label="Reference" />
+        <param name="input_index" type="data" format="tar" label="Precalculated index (optional)" optional="True" />
         <param name="min_candidate_frequency" type="float" value="0.2" size="5" label="Minimum candidate frequency" />
         <param name="min_candidate_depth" type="integer" min="1" value="20" size="5" label="Minimum candidate depth" />
         <param name="max_haplotypes" type="integer" min="0" value="1000" size="5" label="Maximum haplotype combinations" />
@@ -69,13 +71,54 @@
     <!-- ***************************************************************** -->
 
     <tests>
+        <!-- test defaults with FASTA input -->
         <test>
-            <param name="input_reads" value="variants.reads.fa" ftype="fasta" />
-            <param name="input_fast5" value="variants.in.fast5.tar.bz2" ftype="fast5.tar.bz2" />
-            <param name="input_bam"   value="variants.bam" ftype="bam" />
-            <param name="input_ref"   value="variants.ref.fa" ftype="fasta" />
+            <param name="input_reads" value="called.fa" ftype="fasta" />
+            <param name="input_fast5" value="test.fast5.tar.gz" ftype="fast5.tar.gz" />
+            <param name="input_bam"   value="called.bam" ftype="bam" />
+            <param name="input_ref"   value="ref.fa" ftype="fasta" />
+            <param name="fix_homopolymers" value="False"/>
+            <output name="out_consensus" file="consensus.fa" compare="diff" />
+            <output name="out_variants" file="consensus.vcf" compare="diff" />
+            <assert_command>
+                <not_has_text text="--index" />
+                <not_has_text text="--fix-homopolymers" />
+            </assert_command>
+        </test>
+        <!-- test FASTQ input -->
+        <test>
+            <param name="input_reads" value="called.fq" ftype="fastq" />
+            <param name="input_fast5" value="test.fast5.tar.gz" ftype="fast5.tar.gz" />
+            <param name="input_bam"   value="called.bam" ftype="bam" />
+            <param name="input_ref"   value="ref.fa" ftype="fasta" />
+            <param name="fix_homopolymers" value="False"/>
+            <output name="out_consensus" file="consensus.fa" compare="diff" />
+            <output name="out_variants" file="consensus.vcf" compare="diff" />
+        </test>
+        <!-- test homopolymer fixing -->
+        <test>
+            <param name="input_reads" value="called.fa" ftype="fasta" />
+            <param name="input_fast5" value="test.fast5.tar.gz" ftype="fast5.tar.gz" />
+            <param name="input_bam"   value="called.bam" ftype="bam" />
+            <param name="input_ref"   value="ref.fa" ftype="fasta" />
             <param name="fix_homopolymers" value="True"/>
-            <output name="out_consensus" file="variants.out.fa" compare="diff" />
+            <output name="out_consensus" file="consensus.hp.fa" compare="diff" />
+            <output name="out_variants" file="consensus.hp.vcf" compare="diff" />
+        </test>
+        <!-- test pre-calculated index input -->
+        <test>
+            <param name="input_reads" value="called.fa" ftype="fasta" />
+            <param name="input_fast5" value="test.fast5.tar.gz" ftype="fast5.tar.gz" />
+            <param name="input_bam"   value="called.bam" ftype="bam" />
+            <param name="input_ref"   value="ref.fa" ftype="fasta" />
+            <param name="input_index" value="index.tar" ftype="tar" />
+            <param name="fix_homopolymers" value="True"/>
+            <output name="out_consensus" file="consensus.hp.fa" compare="diff" />
+            <output name="out_variants" file="consensus.hp.vcf" compare="diff" />
+            <assert_command>
+                <has_text text="--index" />
+                <has_text text="--fix-homopolymers" />
+            </assert_command>
         </test>
     </tests>
 
diff -r 36cc4ae4160e -r 32cb27adeb34 test-data/called.bam
Binary file test-data/called.bam has changed
diff -r 36cc4ae4160e -r 32cb27adeb34 test-data/called.bam.bai
Binary file test-data/called.bam.bai has changed
diff -r 36cc4ae4160e -r 32cb27adeb34 test-data/called.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/called.fa	Mon Feb 12 00:58:10 2018 -0500
@@ -0,0 +1,174 @@
+>b420c1c9-a6c8-4473-b84f-66efa4615833 runid=f54935eaa7db14eeb8cd7e5a6f5a8fd32ad282c1 read=9985 ch=405 start_time=2017-08-29T09:24:12Z
+CCTCATTGTACTTGTTCAGTTACGTATTGCTGGGTGCTGAAGAAAGTTGTCAGATGTCTT
+TATTGTTAACCTTTCTGTTGGTGTGATATTGCGAGGTTACCTCCACTAAGCTAGAGAAAG
+GGGCACACCCTTACTTAAATACAATCCTTTAAGGAAATAAGCTGCGTCTCTGAGATTGCG
+CTCCGCCCTCCTTGAATCATCATGACAAAACAATCTGTCTTGATTATTTACAGTTAGTTT
+ACCTGTCTATCGAAGTTAGAAAAAACTTGGTGAAGATTCTGTGGATCCCGGTTGGCGCCC
+TCAGGGTGCAAGATGGGCTCCAGACCTTCTCAGAACTAGCACCTATGATGCTTGACTAGC
+CCGGGTTGCGCTGGTACTGGGGATTTGCATCTGTCCGGCAAACTCTCCATTGATAGCAGA
+CCCTCTCTTGCAGCTGCAGGAATTGTGGTTACAGGAGACAAAGCCGTCAACATATGCACC
+TCATCCCAGACCAGGATCAATCATAGTTAAGCTCCTCCACGAATCTGCCCAAGGATAAGG
+AGGCGTAGTGAAAGCCCCCCTTGGATGCATACAACGGGACATTGACCACTTTTGCTCACC
+TTGGTGACTCTATCAGGATACAAAGGTCTGTGACTACATCTGGAGACGGGGCGCCTTAGG
+CGCCCTGTCTCCCCCTCCGGATACCAAGAAGGCTATCTGGGCCAATATGCAAGGGCTTCA
+CACATGCTGAACCTTCGGAAACTGCTCCTGTTGATCCTGGCTCTGAGATAGTGCGCTGTC
+CTTATTCTGTTCCCGGCTGCCGGACGAATAACTCCATGCCAGCACAACGACAATCGGCAT
+CTGGAATAACTGAATTCGAAGGTCTGGGCCGCTACACCTGGGCAACATCCTCTACCGTTT
+CAACTTGACGAACGAACAAGCAATAATAATCGAGAGACGAATGATTTTGTCATGTCTGGA
+AGCTGAAATTGTCATTTAACGAAGTGTCTTCTCAG
+>82d06bd9-aca9-4fe2-9e73-b7a1b30973b2 runid=f54935eaa7db14eeb8cd7e5a6f5a8fd32ad282c1 read=9933 ch=405 start_time=2017-08-29T09:23:34Z
+AAGTATGCTTCGTTCAGTTACGTATTGCGGTGCTGGTTTCATCTATCGGAGGAATGGATT
+AACCTTTCTGTTGGTGCTGATATTGCGGGTTACCTCCACCCAAGCTGGAAGGAAAGATCA
+GGAGACTTGAATCTATCTGTTGGGCTCAGCAGTGTACTCGGACCCTCCATGCTTGTGAAG
+GCAGGGGTGCACGGACAGACTGCTGGCACCTTTCTTCTCTAGCAGTGGGACAGCCTGCTA
+TCCCCATAGCAAATGCACACCTCCTCAGGTAGCTAAGATACTCTGGAGTCAAACTGCACG
+CCTGCGGGTGTAAAGTCATCATTCAAGCAGACTTTTAACGTGCTGTTGCAGTGACTGCTG
+ACCATGAGGTCACCTCTACTAAAATAGAAAATACATACCATCGCTAAATACAATCCTTTC
+AAGAAATAAGCTGCACCCTGAGACTACCAACCGCCTGCTTCTCCTAATCACCATGATACT
+AGGTAATGATCTGTCTTAGTTGCTCACAGTTAGTTTACCTGTCATTAAATTAGAAAAAAC
+ACGGGTAGAAGAATTTGGATCCCGGTTGGCACATTGGGGTGCAAGATGGAAACCAGTCTT
+CTACAGGATCAGTATCTCCAATGCTGATCGTCCAGGTGCGCTGATGCTGAGTTGTATCCG
+TCTGACAAGCTCTCTCTTGATGTGGAGCCTCTCGCGGCTGCAGGGGATCGTGGTAACAGG
+TGATGAAGCAGTCAACATATACACCTCATCCCAGACAGGGTCAATCATAGTCAAGTTACT
+CCAAATATGCCCAAGGACAAAGAGGCGTGTGCAAGGCCCCATTGGAGGCAGCCTGGCAAG
+ACACTGACTACTTTGCTTACCCCATGGTGATTCTATCACCCAGGATGGGGAGTCTGTGAC
+TACTTCCGGAGGAAGGAGACAGAGACGCTTGGGGGTGCCATTATCGGCAGATTGTAGCTC
+TTGGGGTTGCAACAGCTGCACAGATAACAACAGCCACAGCCCTGATACAATAAACAGAAT
+GCTGTAACATCCTCCGGCTAAAGAGCATTGCTGCAACCAATGAAGCTGTGCAGGGTCACT
+GATGGATTATCACAATTAGCAGTGGCAGTTGGGAGGAGTAAGCAATTTGGAAATTTGAAA
+TGAAGATAGAGCGACAGGCAAGTAGGTTAATCCCATTCCCTCCGATAGATGCAT
+>576bfb49-03c7-4ba6-8d74-8bb886e5f3d3 runid=f54935eaa7db14eeb8cd7e5a6f5a8fd32ad282c1 read=9967 ch=405 start_time=2017-08-29T09:23:57Z
+ACGGTACTTCGTTCGAGGACACGTATTGCTGGTGCTGCATGCCAGCGACTACGCATTCTC
+ATTTAACCTTTCTGTTGGTGCTGATATTGCGGGTTACCTCTTACCAAGCTGGAAAACCAC
+ACCATCCGCCAAATACAATCCCTTCGAAATGGGTTTATCGAAGACTGTGATCACCGTTTT
+CCTGAATCGTACTGACAACAGACAATCTATCCTGATTGCCCCAGTTGATTCCGCTGTCTT
+TATAATTAGAAAAAACGGGTAGAAGAGTCTGGATCCCGGCTAACACATTTCTGGAAGGCG
+CAGTATGGAAAACCAAACGCTCACCGGGATCTTAGTACCTTGACACTGATCACTCGGATT
+GCATTGATACTAAAGTTGTATCTGCCTGACAAGCTCTCTGACGGCAGGTCACTTGCACAG
+CCACCAGGGATTATAAGTAACAGGATAAAGGCAATCAATATACCTCATCTCGAACAGGGT
+CCAATCATGAATCAAGTTGCTCCCGGAGCCAATGCCCAAGGACCAAAGGGCATGTGCAGA
+GCCCCATTAAGAGGCCTAACAGAACACTGACCTCACTCCAAGCCCCTTGGCGATTCCATC
+CCACCAGATACAAAGTCTGTGCCCTTCTGGAGGAAAGGAGGCAAACATAGGTGCTGTTAT
+CGGTAATTAGCTCTTGGGGTTTACAACAGCGGCGCAGATAACAGCAGCTGCAGCTAATAC
+AAGCCGCCGAGAATGCCGCCAGCATCCTCCGGCTTAAGGAGAACATTACCACAACCAATG
+AAGCTGTGCATGAGGTCGCAACGGATTGTCACAATAGCGGTAGGGAGAAGATCTACAACA
+GTTTGTTAATGAAGATGAGCGACAGGCAAGTGGGTTAAATGAATGCGTAGTCGCTGTACC
+TTTTCAACAATACGTAACTGA
+>3c97d255-57d0-4d02-8c8b-6d0c0d53e0df runid=f54935eaa7db14eeb8cd7e5a6f5a8fd32ad282c1 read=9989 ch=405 start_time=2017-08-29T09:24:15Z
+ACATTTTAGGTTAAGTTACGTGTGCTGGTGCTGTCGATTCCGTTTGCTTAGTCGTCTGTT
+TTAACCTACTTGCCTGTCGCTCTATCTTCCTCACATTAAATTGCTCATCTTCCCTACTGC
+CACTGCTGGTTGCAGATAATCCAAGTCAGTGACCCTCCTTCACGCAGCCTCATTGGTTGC
+GCAATGCTCTCTTTAAGTCCAGGAGGATGTTGGCAGCATTTTGTTTGGCTTGTATCAGAG
+CACGGCCACTGTGCAGCTGTGCGGCGATTTTAAAGGCCGCACATAATGAAAACAAACTAT
+AAGACGCCCTGTCTCCCCACCAGATGTGATACAGACTCTTGTATCCCGGTGGGAGGTCGC
+AAGGGGGCAAATTAATGTCCTGTTTAGCATGAGGGGGCTTTCGCACATTACCTCCCTTAT
+CCTTGGAATGATTCAGGGAGGAACTTAACTATGATTGGTCCCTGTCTGGGATGAAGGTGT
+ATATGTTATTCTACTTTGCAATGCTCCCTGTAACCCTACAGCTACAAGGCCTGCACCATC
+AATGAGTTTGGACAGATGCAACTCCAATACCAACACGACCCAGATAGTCAGCATCGCCGT
+TGCTGGGTTCTTGAGTAGAAAGGTCTGGAGCCCATCCACCTGCACCTGGAGGGGGCGCCA
+ACCGGGATCCAGAATCTTCCTACCCGTGACACAACGGTAGTTGGGTAAACTAACTTTGTA
+AATAATCAGACAATTGTTTTGCATGTCATGATGATCTGGGTGTTGAGTGGGCACGGAGCG
+CAATCAGGGAACACAACTTATTTCTTAAGAGGATTTCTTTATA
+>96868172-8a9c-4e05-9274-9135e30d1269 runid=f54935eaa7db14eeb8cd7e5a6f5a8fd32ad282c1 read=9957 ch=405 start_time=2017-08-29T09:23:51Z
+ACATTGTGCTTCGTTCAGTTACGTATTGCTGGTGCTGCGCTAGACACCTTGGTTGACAGA
+CCGCCAACCCTTTCTGTTGGTGCTGATATTGCGAGGTTACCTCTACTTAAGCTGGGTACA
+CCATTGCCAAACTCTCAATCCCCTTCAGGAAATAAGTTGCATCCTTAAGCCTGCGATTCA
+TTCGCTTTCCCTGCATCATTATGACATCAGATGCTTATAGTTAGTTCACCTACATCGCCA
+ATTAGAAAAACACGGGTAGAAAGAGTCTGGATCCCAACCAACACATTAAGAATCAATATG
+AACCAAACCTTCTACCAGGATCCCTGGTACCCTTGATGCGATCTCTGATTATGCTGATGC
+CAAACTTTCATATGTCAATAAACTCCCTTGACAGCATGAGCCTCTCTTGCAGCTTCCTGC
+GGGATTGGCAACAACAGGGGAATGGGCAATCAAGATATATACCTCATCTCAGACCCGGAT
+CCATCGCGCCAGTCAGTTGCTCCCAAACATACCCAGGGACAATAAGGAAGCGCGGCGAGC
+CCACTAGAGGCGCTTACCGGCAGAACACCATGCCTTACTCCACTCCTCTTGGTGATTCCA
+TCCACGCAGATACAAGGGGTCTGTCCACATCTGGAGGTGACGGAAGCACGTTTTGAGTGC
+AGTTGACGAGCAGTGTAGCTCTTGGGGTTGCAACAGCAGCACGGGTAGCAGCAACACGGC
+TCGGCCCTGAAGCTAACAGAATGCCAACATCCTCCGGCAGGAGCATTTTACAACCGGCCA
+GAGCTGCTGCAGTGCGCGACAGATTCCGCAACTGCGGCAGCGTTGAAGGTAACGTTTGTT
+AGAAATGACAAGTATTGGGGTTAAGTCCTGTCAGCAAGGTGTCTAACAGCACCAACCAAT
+ACGCCAACCCC
+>100dd03a-e91a-439a-b746-d1f2be90458d runid=f54935eaa7db14eeb8cd7e5a6f5a8fd32ad282c1 read=9995 ch=405 start_time=2017-08-29T09:24:20Z
+ACCTCCGGTGGCCTTCGTTCGGTTACGTATTGCTGGTGCTGGTAAGTTGGGTATGCAACA
+CCAATGTTAACCTACTTGCCTGTCGCTCTATCTTCTCATTAACAAATTGCTGCATCTTCC
+CAACGGCCACTGCGAGAGTTGCGATAATCCGTCAGTGACCTCATACGGCCTCATTGGTGC
+GGCAATGCTCTTCCCAAGCCGGAGGATGTTGGCAGCATTTTGGTTGAAAGAAGCAGCCTC
+AGAGCCAGGGCTGCTGTTATCTGTGCAGCAGTTGCAACCCCAAAGGGCTACACCGCCAAT
+AATGGCACCTATAAGACGCCCCTGTTTTCCCTCACTCCAGATGTGAGTGCAGACTCTTGT
+ATCCCTACGAATAGAGATACCAAGGGGTGAGCAGAGTGGTCAATGTCCTGTTGTATGCCT
+CTAAAGGTGCTTTTTTTGCACATGCCTCTTTATCCTTGGGCATGTTGGGAGTAACGACTA
+TGATTGACCCTGTCTGAGATGAGGTATATATGTTGGCTTCTGCCTTGTCCCCGTTACCAC
+AATTCCTGCAACTGCAGGAGGCCTGCCATCAAAGAGCTTGTCAGACGGATGCAACTTAGT
+GTCAGTGCGGCCGGACGGTCAGCATCAGGGCACGCTGGGATCCTGGTAGAAAGATCCGGA
+GTGGCATCCTGCACCCTGGAGGCATAACCGGGATCCAGAATCTTCTACCCGTGTTTTCTA
+ATCTGATGAACAGAGTAAACTAGTTATAAACTTAATCAAGACAGATCATTATTTAGTGTC
+ATGGTAATTCCGGGAAGGTGAACGGAGCTCAATCTCATAGATACAGCCTATTTCCTGAAA
+GAAAGGATTGTATTTAGCAATGGTATGCCCCTTCTCCAGCTTGGTGGAGGTAACCTCACG
+CAATATCAGCGCAACAGAAGGTTAACACGTTGCATACCCAACTTACCAGCACCAACAATA
+CACGTAACTTAC
+>89ae3497-c03e-4e48-b903-d00fc4851be1 runid=f54935eaa7db14eeb8cd7e5a6f5a8fd32ad282c1 read=9971 ch=405 start_time=2017-08-29T09:24:02Z
+ACGGTAGCACTTCGTTCAGTTACGTATTGCTGGTGCTGTGCGTACAGCAGCAATCAGTTA
+CATTGTTAACCTTTCTGTTGGTGCTGATATTGCGGTTACCTCTACTAAGCTGGAGAAAGA
+GGCACACCATTGCTAAGCTAATCTTTTGAAATAAGTTGCATCTCATGATGATTCTGCTTT
+CCTGAATCCTTATGACACTAGATAGTGATCCATTTCGATTGATATAGTTATTGCACCTGT
+CTATCTAATTAGAAAAAACACGGGTAGAAGAATTTGGATCCCGTACCAGGGCGCGGCATG
+GGCTCAACCTTCTACCAGGACTCCACATTATCCCTGATGCTTATTATCCAGATTATGCTG
+GTACACTAAGCTGTCTCTCGACAAGCTCGGCCTCTTGCGCTGCAGGAATTGGCTACACCT
+CGTCCCAGACAGGGTCGATCATAGTCAAGTTACTCGGGTAAAGGATAAAGGCGTGCAAGC
+CCCATTGAGGCATACAACAGAACATTAACCACCTGCTCACTCCTCGATTCCATCCACGGG
+ATACAAGGGTCTACATCTACATCTGGAGGAGGAGACGAAACGCTTTATAGGTGCCGGGTG
+GCAGTGTAGCTCTCTTGGGGTTGCAACAGCAGCACGGATAACAGCAGCTGCGGCCCTAAC
+CTGAAGACGCTGCCAACATCCTCCGGCTTAAGGAGAACATTGCTGCAACCAAGCTGTGTG
+AGGTCACCGACGGATTATCTACAAGTGATGCCCAGTGGCAGTACGGGAAGATGCGGCAGT
+TTGTTAATGAGAAGATAGAGCGACAGGCAAGTAGGTTAACAATGCAACTGATTGCTGTAC
+ACTTTGCTTCGCA
+>eb35cfa9-2726-4109-a157-398a32a4d5d8 runid=f54935eaa7db14eeb8cd7e5a6f5a8fd32ad282c1 read=9931 ch=405 start_time=2017-08-29T09:23:29Z
+CTGTACTTCGTTCAGTTACGTATTGCCTTTCAATTTGCTGTTTGCGTCCTGTTACGAGAA
+CTCAGCACATTTAACCTTTCTGTTGGTGCTGATGTGCAGGGTTACCTCTACTAAGCTGGA
+GAGACACACCATTGCCAAATACAATCCTTTCAGAAATAGAAGTTGCATCCCTAAGACTTG
+CGAGTTCACCTGCTTTTCCTGAATCAACACTTGAAGGCACCCAGATGAGTCATCTCAGCG
+CTGCTTATAGTTGGTTCTGTTTGCCAAATTAGAAAAACACGGGTAGAAGGGGTCTGGATC
+CCGACCGAAATCATCCAGGACAATGGAGGAAACCAAACCTTCTACCGGGAGGATCGCGCT
+TCGATGCAGTAACTCGGATTATGCTGATATTGAGCTGTATCGCGTCCCGACAGCTCCCAT
+GACGGCAGGCCTCTTGCTTCTTGAGATTGTAGTGACAGGAGATAAGGCAGTCCAATGTGT
+ACCTCGTCTCAGACGGGGTCAATCCTGGAGAATCAAATTGCTCCCGAGTATGCCAGGATA
+AGGAGGCGTGTGCAAAAGCCCCATTAGAGGCATGCTCCCAACAGAACACTGACTACTTTA
+TACACTCCTCTTGGCGATTCCATCCTGAAGATCCAAGGGTCTGTGTCCACGTCTGGAGGG
+AACTAAAAACATAGGTGCCATAGATTATTGGCAGTGTAGCGCTCAGGGTTGCAGCTGCGC
+TTGGCACAGATAACAGCTGCGGCTAATACAGGCCAACCAGAATGCTGCCAGCATCCTCCG
+GCTTAAGGGAGAGCATTGCTGCAACCAATGAGAGCTGTGCATGTGGGGAAGTCACCGACG
+GATTATGCAACTATCGAGGTAGCGGTTGGGAAGATGCAGCAATTTGTTAATGAAGATAGA
+GCGACAGGCAAAGTAGGTTGTTAAATGGAGTTCTCGTAACGCAGGACACCAACAGCACCA
+GCAATACGGCA
+>0b65a5bc-4672-48fd-b392-a96410a985d6 runid=f54935eaa7db14eeb8cd7e5a6f5a8fd32ad282c1 read=9935 ch=405 start_time=2017-08-29T09:23:38Z
+CGGTACTTCGTTCAGTTACGTATTACTGGTGCTGTTCGAGACAAACAAGTTACGATTTAA
+CCTACTTGCCTGTCGCTCTATCTTCTCTGCATTAACAAATTGCTGCATCTTTGCTACTGC
+TGCTGGTTACGATAATCCCGTCATTGACCTCATGCGGCCTCATTGGTTGCAGCAATGCTC
+TCTTTAGAATCGGAGGATATTGGCAGCATTTTGTTTTGGCTAGTGTCAGAGCTGCGGCCG
+CTGTTATTTGTGCAACAGTTGCAACCCCAAAACCCACACCGCCAACTAATGGCGCCTATA
+AAGCGTTCTGTCTCCTCCCTCCAGATGTAGTTACGGACTCTTGTATCCTACGGATAGGTC
+CTGAGGGGAGTGAGCAAGTGGTCAATGTCCTGTTGTATGCATCAAGGGGCTTTCGCACAT
+GCCTCCTTATCCTTGGGTGTGAGTTTGGGAGGAGGCAACTATGATTGATCCTGTCTGGGA
+TGAGGTGTATATGTTGACTGCTTTGTCCCCTGTTACCACAATTCCAGCAGCCGCAAAGGC
+CACCATCAATAGAGTTTGCCGGACAGATTAGCTCAGTACCAGCGCGACTCTGACGGTCAG
+CATCATAGGTGCTGGGTTCTTGGTAGAAGGTCTGGGGCCCATCTTGCACCCTAGAAGGCG
+CCAACCGGGATCCAGAATCTTCTACCCGTGTTTTCTAATTTGATGAACAGAATTGAAACT
+AACTGTAAATAATCAAGACAGATTAGTTTTGTGTCATGATACTCCAGGTGAGAGTGAGCA
+GGTCTCAGAGACGCAACTTATTTCTTAAAAAGTTGTATTTGGCAAAGGGTGTGTGCCCCT
+TCTCAACAGTGGGGTAACCTCGCAATATCAGCACCAACAGAAGGTTAAACGTAGCTTGGT
+TTGTTCCTGAACAGCACCAGCAATACGGCAGCTTCA
+>9ac4d524-83af-4bac-a4c7-76be1b9cb92c runid=f54935eaa7db14eeb8cd7e5a6f5a8fd32ad282c1 read=9939 ch=405 start_time=2017-08-29T09:23:40Z
+ACGGTACTTCGTTCAGTTACATTATTGCTGGTGCTGGTAGACCCTGTTACGAGAACTCAT
+TTAATACTGCCTGTCGCTCTATCTTCTCATTAACAAATTGCGTCTTCCTACTACTACTGA
+TGGTTGTGATGGCTCCGTCGGTGACTTCATTACACAGCTTCGTGGTTGCAACAATGCTCT
+CTAACAAACCAGATGTTGGCATTCTGGTTGGCCACATATTGGGGCCGCAGCTGCTTTCTG
+TTATCTCTGTACCCTTGCTATTCCCATTTACCCAAGAGCTACCAATAACGGCACCTGCTC
+AAACGCTTTTATTCCTCCAGACGTGGACACAAGACCCTTGGATCTTGCGGATGGAGTCAT
+AGAAAGTGAGCAAGTGGTCAGTGTTCTGCCATGCCTCTAATGGAGACTTTTGCACACCTC
+ACCCATCCTTGGGCATATTCGGGGCAATTTGACTATGATTGACCCTTCTGAGACGAGGTG
+GCATAGCCATTGACTGCCTTATCTCTATCATAATTCACCCAGCTACGGAGGCCTGCGATC
+GAGAGCTGTCAGGCTGGATACAGCTCAATATCAATCCCGAGTTATCAGCATCAAGTGCCT
+GGATCTGGTAGAGGTTGGAGCCCATATTGGGCATCCTGAGTGAGCTGGTCGGGATCCAGG
+CCCTTCCCTGCTGTTTTTCTAATTTGCTAAACAATTGTGAACTAACTATAAGCAGTTGAG
+ATGGATCATTATCTGGTGTCCTATTTGATTCAGGAAAGCAGGTGAACTGCAGTCTTAGGG
+ATGCAACTTATTTTCGAGTTGTATTTGGCAATAGGTGTCTCTTCTCTCCAGCTTGGTGAA
+GGTAACCTCGCAATATCAGCACCAACAGAAAGGTTAAATGAGTTCTGCCTCGTAACAGGA
+CTGGCACAAACAATGCAATAACTAC
diff -r 36cc4ae4160e -r 32cb27adeb34 test-data/called.fq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/called.fq	Mon Feb 12 00:58:10 2018 -0500
@@ -0,0 +1,174 @@
+>b420c1c9-a6c8-4473-b84f-66efa4615833 runid=f54935eaa7db14eeb8cd7e5a6f5a8fd32ad282c1 read=9985 ch=405 start_time=2017-08-29T09:24:12Z
+CCTCATTGTACTTGTTCAGTTACGTATTGCTGGGTGCTGAAGAAAGTTGTCAGATGTCTT
+TATTGTTAACCTTTCTGTTGGTGTGATATTGCGAGGTTACCTCCACTAAGCTAGAGAAAG
+GGGCACACCCTTACTTAAATACAATCCTTTAAGGAAATAAGCTGCGTCTCTGAGATTGCG
+CTCCGCCCTCCTTGAATCATCATGACAAAACAATCTGTCTTGATTATTTACAGTTAGTTT
+ACCTGTCTATCGAAGTTAGAAAAAACTTGGTGAAGATTCTGTGGATCCCGGTTGGCGCCC
+TCAGGGTGCAAGATGGGCTCCAGACCTTCTCAGAACTAGCACCTATGATGCTTGACTAGC
+CCGGGTTGCGCTGGTACTGGGGATTTGCATCTGTCCGGCAAACTCTCCATTGATAGCAGA
+CCCTCTCTTGCAGCTGCAGGAATTGTGGTTACAGGAGACAAAGCCGTCAACATATGCACC
+TCATCCCAGACCAGGATCAATCATAGTTAAGCTCCTCCACGAATCTGCCCAAGGATAAGG
+AGGCGTAGTGAAAGCCCCCCTTGGATGCATACAACGGGACATTGACCACTTTTGCTCACC
+TTGGTGACTCTATCAGGATACAAAGGTCTGTGACTACATCTGGAGACGGGGCGCCTTAGG
+CGCCCTGTCTCCCCCTCCGGATACCAAGAAGGCTATCTGGGCCAATATGCAAGGGCTTCA
+CACATGCTGAACCTTCGGAAACTGCTCCTGTTGATCCTGGCTCTGAGATAGTGCGCTGTC
+CTTATTCTGTTCCCGGCTGCCGGACGAATAACTCCATGCCAGCACAACGACAATCGGCAT
+CTGGAATAACTGAATTCGAAGGTCTGGGCCGCTACACCTGGGCAACATCCTCTACCGTTT
+CAACTTGACGAACGAACAAGCAATAATAATCGAGAGACGAATGATTTTGTCATGTCTGGA
+AGCTGAAATTGTCATTTAACGAAGTGTCTTCTCAG
+>82d06bd9-aca9-4fe2-9e73-b7a1b30973b2 runid=f54935eaa7db14eeb8cd7e5a6f5a8fd32ad282c1 read=9933 ch=405 start_time=2017-08-29T09:23:34Z
+AAGTATGCTTCGTTCAGTTACGTATTGCGGTGCTGGTTTCATCTATCGGAGGAATGGATT
+AACCTTTCTGTTGGTGCTGATATTGCGGGTTACCTCCACCCAAGCTGGAAGGAAAGATCA
+GGAGACTTGAATCTATCTGTTGGGCTCAGCAGTGTACTCGGACCCTCCATGCTTGTGAAG
+GCAGGGGTGCACGGACAGACTGCTGGCACCTTTCTTCTCTAGCAGTGGGACAGCCTGCTA
+TCCCCATAGCAAATGCACACCTCCTCAGGTAGCTAAGATACTCTGGAGTCAAACTGCACG
+CCTGCGGGTGTAAAGTCATCATTCAAGCAGACTTTTAACGTGCTGTTGCAGTGACTGCTG
+ACCATGAGGTCACCTCTACTAAAATAGAAAATACATACCATCGCTAAATACAATCCTTTC
+AAGAAATAAGCTGCACCCTGAGACTACCAACCGCCTGCTTCTCCTAATCACCATGATACT
+AGGTAATGATCTGTCTTAGTTGCTCACAGTTAGTTTACCTGTCATTAAATTAGAAAAAAC
+ACGGGTAGAAGAATTTGGATCCCGGTTGGCACATTGGGGTGCAAGATGGAAACCAGTCTT
+CTACAGGATCAGTATCTCCAATGCTGATCGTCCAGGTGCGCTGATGCTGAGTTGTATCCG
+TCTGACAAGCTCTCTCTTGATGTGGAGCCTCTCGCGGCTGCAGGGGATCGTGGTAACAGG
+TGATGAAGCAGTCAACATATACACCTCATCCCAGACAGGGTCAATCATAGTCAAGTTACT
+CCAAATATGCCCAAGGACAAAGAGGCGTGTGCAAGGCCCCATTGGAGGCAGCCTGGCAAG
+ACACTGACTACTTTGCTTACCCCATGGTGATTCTATCACCCAGGATGGGGAGTCTGTGAC
+TACTTCCGGAGGAAGGAGACAGAGACGCTTGGGGGTGCCATTATCGGCAGATTGTAGCTC
+TTGGGGTTGCAACAGCTGCACAGATAACAACAGCCACAGCCCTGATACAATAAACAGAAT
+GCTGTAACATCCTCCGGCTAAAGAGCATTGCTGCAACCAATGAAGCTGTGCAGGGTCACT
+GATGGATTATCACAATTAGCAGTGGCAGTTGGGAGGAGTAAGCAATTTGGAAATTTGAAA
+TGAAGATAGAGCGACAGGCAAGTAGGTTAATCCCATTCCCTCCGATAGATGCAT
+>576bfb49-03c7-4ba6-8d74-8bb886e5f3d3 runid=f54935eaa7db14eeb8cd7e5a6f5a8fd32ad282c1 read=9967 ch=405 start_time=2017-08-29T09:23:57Z
+ACGGTACTTCGTTCGAGGACACGTATTGCTGGTGCTGCATGCCAGCGACTACGCATTCTC
+ATTTAACCTTTCTGTTGGTGCTGATATTGCGGGTTACCTCTTACCAAGCTGGAAAACCAC
+ACCATCCGCCAAATACAATCCCTTCGAAATGGGTTTATCGAAGACTGTGATCACCGTTTT
+CCTGAATCGTACTGACAACAGACAATCTATCCTGATTGCCCCAGTTGATTCCGCTGTCTT
+TATAATTAGAAAAAACGGGTAGAAGAGTCTGGATCCCGGCTAACACATTTCTGGAAGGCG
+CAGTATGGAAAACCAAACGCTCACCGGGATCTTAGTACCTTGACACTGATCACTCGGATT
+GCATTGATACTAAAGTTGTATCTGCCTGACAAGCTCTCTGACGGCAGGTCACTTGCACAG
+CCACCAGGGATTATAAGTAACAGGATAAAGGCAATCAATATACCTCATCTCGAACAGGGT
+CCAATCATGAATCAAGTTGCTCCCGGAGCCAATGCCCAAGGACCAAAGGGCATGTGCAGA
+GCCCCATTAAGAGGCCTAACAGAACACTGACCTCACTCCAAGCCCCTTGGCGATTCCATC
+CCACCAGATACAAAGTCTGTGCCCTTCTGGAGGAAAGGAGGCAAACATAGGTGCTGTTAT
+CGGTAATTAGCTCTTGGGGTTTACAACAGCGGCGCAGATAACAGCAGCTGCAGCTAATAC
+AAGCCGCCGAGAATGCCGCCAGCATCCTCCGGCTTAAGGAGAACATTACCACAACCAATG
+AAGCTGTGCATGAGGTCGCAACGGATTGTCACAATAGCGGTAGGGAGAAGATCTACAACA
+GTTTGTTAATGAAGATGAGCGACAGGCAAGTGGGTTAAATGAATGCGTAGTCGCTGTACC
+TTTTCAACAATACGTAACTGA
+>3c97d255-57d0-4d02-8c8b-6d0c0d53e0df runid=f54935eaa7db14eeb8cd7e5a6f5a8fd32ad282c1 read=9989 ch=405 start_time=2017-08-29T09:24:15Z
+ACATTTTAGGTTAAGTTACGTGTGCTGGTGCTGTCGATTCCGTTTGCTTAGTCGTCTGTT
+TTAACCTACTTGCCTGTCGCTCTATCTTCCTCACATTAAATTGCTCATCTTCCCTACTGC
+CACTGCTGGTTGCAGATAATCCAAGTCAGTGACCCTCCTTCACGCAGCCTCATTGGTTGC
+GCAATGCTCTCTTTAAGTCCAGGAGGATGTTGGCAGCATTTTGTTTGGCTTGTATCAGAG
+CACGGCCACTGTGCAGCTGTGCGGCGATTTTAAAGGCCGCACATAATGAAAACAAACTAT
+AAGACGCCCTGTCTCCCCACCAGATGTGATACAGACTCTTGTATCCCGGTGGGAGGTCGC
+AAGGGGGCAAATTAATGTCCTGTTTAGCATGAGGGGGCTTTCGCACATTACCTCCCTTAT
+CCTTGGAATGATTCAGGGAGGAACTTAACTATGATTGGTCCCTGTCTGGGATGAAGGTGT
+ATATGTTATTCTACTTTGCAATGCTCCCTGTAACCCTACAGCTACAAGGCCTGCACCATC
+AATGAGTTTGGACAGATGCAACTCCAATACCAACACGACCCAGATAGTCAGCATCGCCGT
+TGCTGGGTTCTTGAGTAGAAAGGTCTGGAGCCCATCCACCTGCACCTGGAGGGGGCGCCA
+ACCGGGATCCAGAATCTTCCTACCCGTGACACAACGGTAGTTGGGTAAACTAACTTTGTA
+AATAATCAGACAATTGTTTTGCATGTCATGATGATCTGGGTGTTGAGTGGGCACGGAGCG
+CAATCAGGGAACACAACTTATTTCTTAAGAGGATTTCTTTATA
+>96868172-8a9c-4e05-9274-9135e30d1269 runid=f54935eaa7db14eeb8cd7e5a6f5a8fd32ad282c1 read=9957 ch=405 start_time=2017-08-29T09:23:51Z
+ACATTGTGCTTCGTTCAGTTACGTATTGCTGGTGCTGCGCTAGACACCTTGGTTGACAGA
+CCGCCAACCCTTTCTGTTGGTGCTGATATTGCGAGGTTACCTCTACTTAAGCTGGGTACA
+CCATTGCCAAACTCTCAATCCCCTTCAGGAAATAAGTTGCATCCTTAAGCCTGCGATTCA
+TTCGCTTTCCCTGCATCATTATGACATCAGATGCTTATAGTTAGTTCACCTACATCGCCA
+ATTAGAAAAACACGGGTAGAAAGAGTCTGGATCCCAACCAACACATTAAGAATCAATATG
+AACCAAACCTTCTACCAGGATCCCTGGTACCCTTGATGCGATCTCTGATTATGCTGATGC
+CAAACTTTCATATGTCAATAAACTCCCTTGACAGCATGAGCCTCTCTTGCAGCTTCCTGC
+GGGATTGGCAACAACAGGGGAATGGGCAATCAAGATATATACCTCATCTCAGACCCGGAT
+CCATCGCGCCAGTCAGTTGCTCCCAAACATACCCAGGGACAATAAGGAAGCGCGGCGAGC
+CCACTAGAGGCGCTTACCGGCAGAACACCATGCCTTACTCCACTCCTCTTGGTGATTCCA
+TCCACGCAGATACAAGGGGTCTGTCCACATCTGGAGGTGACGGAAGCACGTTTTGAGTGC
+AGTTGACGAGCAGTGTAGCTCTTGGGGTTGCAACAGCAGCACGGGTAGCAGCAACACGGC
+TCGGCCCTGAAGCTAACAGAATGCCAACATCCTCCGGCAGGAGCATTTTACAACCGGCCA
+GAGCTGCTGCAGTGCGCGACAGATTCCGCAACTGCGGCAGCGTTGAAGGTAACGTTTGTT
+AGAAATGACAAGTATTGGGGTTAAGTCCTGTCAGCAAGGTGTCTAACAGCACCAACCAAT
+ACGCCAACCCC
+>100dd03a-e91a-439a-b746-d1f2be90458d runid=f54935eaa7db14eeb8cd7e5a6f5a8fd32ad282c1 read=9995 ch=405 start_time=2017-08-29T09:24:20Z
+ACCTCCGGTGGCCTTCGTTCGGTTACGTATTGCTGGTGCTGGTAAGTTGGGTATGCAACA
+CCAATGTTAACCTACTTGCCTGTCGCTCTATCTTCTCATTAACAAATTGCTGCATCTTCC
+CAACGGCCACTGCGAGAGTTGCGATAATCCGTCAGTGACCTCATACGGCCTCATTGGTGC
+GGCAATGCTCTTCCCAAGCCGGAGGATGTTGGCAGCATTTTGGTTGAAAGAAGCAGCCTC
+AGAGCCAGGGCTGCTGTTATCTGTGCAGCAGTTGCAACCCCAAAGGGCTACACCGCCAAT
+AATGGCACCTATAAGACGCCCCTGTTTTCCCTCACTCCAGATGTGAGTGCAGACTCTTGT
+ATCCCTACGAATAGAGATACCAAGGGGTGAGCAGAGTGGTCAATGTCCTGTTGTATGCCT
+CTAAAGGTGCTTTTTTTGCACATGCCTCTTTATCCTTGGGCATGTTGGGAGTAACGACTA
+TGATTGACCCTGTCTGAGATGAGGTATATATGTTGGCTTCTGCCTTGTCCCCGTTACCAC
+AATTCCTGCAACTGCAGGAGGCCTGCCATCAAAGAGCTTGTCAGACGGATGCAACTTAGT
+GTCAGTGCGGCCGGACGGTCAGCATCAGGGCACGCTGGGATCCTGGTAGAAAGATCCGGA
+GTGGCATCCTGCACCCTGGAGGCATAACCGGGATCCAGAATCTTCTACCCGTGTTTTCTA
+ATCTGATGAACAGAGTAAACTAGTTATAAACTTAATCAAGACAGATCATTATTTAGTGTC
+ATGGTAATTCCGGGAAGGTGAACGGAGCTCAATCTCATAGATACAGCCTATTTCCTGAAA
+GAAAGGATTGTATTTAGCAATGGTATGCCCCTTCTCCAGCTTGGTGGAGGTAACCTCACG
+CAATATCAGCGCAACAGAAGGTTAACACGTTGCATACCCAACTTACCAGCACCAACAATA
+CACGTAACTTAC
+>89ae3497-c03e-4e48-b903-d00fc4851be1 runid=f54935eaa7db14eeb8cd7e5a6f5a8fd32ad282c1 read=9971 ch=405 start_time=2017-08-29T09:24:02Z
+ACGGTAGCACTTCGTTCAGTTACGTATTGCTGGTGCTGTGCGTACAGCAGCAATCAGTTA
+CATTGTTAACCTTTCTGTTGGTGCTGATATTGCGGTTACCTCTACTAAGCTGGAGAAAGA
+GGCACACCATTGCTAAGCTAATCTTTTGAAATAAGTTGCATCTCATGATGATTCTGCTTT
+CCTGAATCCTTATGACACTAGATAGTGATCCATTTCGATTGATATAGTTATTGCACCTGT
+CTATCTAATTAGAAAAAACACGGGTAGAAGAATTTGGATCCCGTACCAGGGCGCGGCATG
+GGCTCAACCTTCTACCAGGACTCCACATTATCCCTGATGCTTATTATCCAGATTATGCTG
+GTACACTAAGCTGTCTCTCGACAAGCTCGGCCTCTTGCGCTGCAGGAATTGGCTACACCT
+CGTCCCAGACAGGGTCGATCATAGTCAAGTTACTCGGGTAAAGGATAAAGGCGTGCAAGC
+CCCATTGAGGCATACAACAGAACATTAACCACCTGCTCACTCCTCGATTCCATCCACGGG
+ATACAAGGGTCTACATCTACATCTGGAGGAGGAGACGAAACGCTTTATAGGTGCCGGGTG
+GCAGTGTAGCTCTCTTGGGGTTGCAACAGCAGCACGGATAACAGCAGCTGCGGCCCTAAC
+CTGAAGACGCTGCCAACATCCTCCGGCTTAAGGAGAACATTGCTGCAACCAAGCTGTGTG
+AGGTCACCGACGGATTATCTACAAGTGATGCCCAGTGGCAGTACGGGAAGATGCGGCAGT
+TTGTTAATGAGAAGATAGAGCGACAGGCAAGTAGGTTAACAATGCAACTGATTGCTGTAC
+ACTTTGCTTCGCA
+>eb35cfa9-2726-4109-a157-398a32a4d5d8 runid=f54935eaa7db14eeb8cd7e5a6f5a8fd32ad282c1 read=9931 ch=405 start_time=2017-08-29T09:23:29Z
+CTGTACTTCGTTCAGTTACGTATTGCCTTTCAATTTGCTGTTTGCGTCCTGTTACGAGAA
+CTCAGCACATTTAACCTTTCTGTTGGTGCTGATGTGCAGGGTTACCTCTACTAAGCTGGA
+GAGACACACCATTGCCAAATACAATCCTTTCAGAAATAGAAGTTGCATCCCTAAGACTTG
+CGAGTTCACCTGCTTTTCCTGAATCAACACTTGAAGGCACCCAGATGAGTCATCTCAGCG
+CTGCTTATAGTTGGTTCTGTTTGCCAAATTAGAAAAACACGGGTAGAAGGGGTCTGGATC
+CCGACCGAAATCATCCAGGACAATGGAGGAAACCAAACCTTCTACCGGGAGGATCGCGCT
+TCGATGCAGTAACTCGGATTATGCTGATATTGAGCTGTATCGCGTCCCGACAGCTCCCAT
+GACGGCAGGCCTCTTGCTTCTTGAGATTGTAGTGACAGGAGATAAGGCAGTCCAATGTGT
+ACCTCGTCTCAGACGGGGTCAATCCTGGAGAATCAAATTGCTCCCGAGTATGCCAGGATA
+AGGAGGCGTGTGCAAAAGCCCCATTAGAGGCATGCTCCCAACAGAACACTGACTACTTTA
+TACACTCCTCTTGGCGATTCCATCCTGAAGATCCAAGGGTCTGTGTCCACGTCTGGAGGG
+AACTAAAAACATAGGTGCCATAGATTATTGGCAGTGTAGCGCTCAGGGTTGCAGCTGCGC
+TTGGCACAGATAACAGCTGCGGCTAATACAGGCCAACCAGAATGCTGCCAGCATCCTCCG
+GCTTAAGGGAGAGCATTGCTGCAACCAATGAGAGCTGTGCATGTGGGGAAGTCACCGACG
+GATTATGCAACTATCGAGGTAGCGGTTGGGAAGATGCAGCAATTTGTTAATGAAGATAGA
+GCGACAGGCAAAGTAGGTTGTTAAATGGAGTTCTCGTAACGCAGGACACCAACAGCACCA
+GCAATACGGCA
+>0b65a5bc-4672-48fd-b392-a96410a985d6 runid=f54935eaa7db14eeb8cd7e5a6f5a8fd32ad282c1 read=9935 ch=405 start_time=2017-08-29T09:23:38Z
+CGGTACTTCGTTCAGTTACGTATTACTGGTGCTGTTCGAGACAAACAAGTTACGATTTAA
+CCTACTTGCCTGTCGCTCTATCTTCTCTGCATTAACAAATTGCTGCATCTTTGCTACTGC
+TGCTGGTTACGATAATCCCGTCATTGACCTCATGCGGCCTCATTGGTTGCAGCAATGCTC
+TCTTTAGAATCGGAGGATATTGGCAGCATTTTGTTTTGGCTAGTGTCAGAGCTGCGGCCG
+CTGTTATTTGTGCAACAGTTGCAACCCCAAAACCCACACCGCCAACTAATGGCGCCTATA
+AAGCGTTCTGTCTCCTCCCTCCAGATGTAGTTACGGACTCTTGTATCCTACGGATAGGTC
+CTGAGGGGAGTGAGCAAGTGGTCAATGTCCTGTTGTATGCATCAAGGGGCTTTCGCACAT
+GCCTCCTTATCCTTGGGTGTGAGTTTGGGAGGAGGCAACTATGATTGATCCTGTCTGGGA
+TGAGGTGTATATGTTGACTGCTTTGTCCCCTGTTACCACAATTCCAGCAGCCGCAAAGGC
+CACCATCAATAGAGTTTGCCGGACAGATTAGCTCAGTACCAGCGCGACTCTGACGGTCAG
+CATCATAGGTGCTGGGTTCTTGGTAGAAGGTCTGGGGCCCATCTTGCACCCTAGAAGGCG
+CCAACCGGGATCCAGAATCTTCTACCCGTGTTTTCTAATTTGATGAACAGAATTGAAACT
+AACTGTAAATAATCAAGACAGATTAGTTTTGTGTCATGATACTCCAGGTGAGAGTGAGCA
+GGTCTCAGAGACGCAACTTATTTCTTAAAAAGTTGTATTTGGCAAAGGGTGTGTGCCCCT
+TCTCAACAGTGGGGTAACCTCGCAATATCAGCACCAACAGAAGGTTAAACGTAGCTTGGT
+TTGTTCCTGAACAGCACCAGCAATACGGCAGCTTCA
+>9ac4d524-83af-4bac-a4c7-76be1b9cb92c runid=f54935eaa7db14eeb8cd7e5a6f5a8fd32ad282c1 read=9939 ch=405 start_time=2017-08-29T09:23:40Z
+ACGGTACTTCGTTCAGTTACATTATTGCTGGTGCTGGTAGACCCTGTTACGAGAACTCAT
+TTAATACTGCCTGTCGCTCTATCTTCTCATTAACAAATTGCGTCTTCCTACTACTACTGA
+TGGTTGTGATGGCTCCGTCGGTGACTTCATTACACAGCTTCGTGGTTGCAACAATGCTCT
+CTAACAAACCAGATGTTGGCATTCTGGTTGGCCACATATTGGGGCCGCAGCTGCTTTCTG
+TTATCTCTGTACCCTTGCTATTCCCATTTACCCAAGAGCTACCAATAACGGCACCTGCTC
+AAACGCTTTTATTCCTCCAGACGTGGACACAAGACCCTTGGATCTTGCGGATGGAGTCAT
+AGAAAGTGAGCAAGTGGTCAGTGTTCTGCCATGCCTCTAATGGAGACTTTTGCACACCTC
+ACCCATCCTTGGGCATATTCGGGGCAATTTGACTATGATTGACCCTTCTGAGACGAGGTG
+GCATAGCCATTGACTGCCTTATCTCTATCATAATTCACCCAGCTACGGAGGCCTGCGATC
+GAGAGCTGTCAGGCTGGATACAGCTCAATATCAATCCCGAGTTATCAGCATCAAGTGCCT
+GGATCTGGTAGAGGTTGGAGCCCATATTGGGCATCCTGAGTGAGCTGGTCGGGATCCAGG
+CCCTTCCCTGCTGTTTTTCTAATTTGCTAAACAATTGTGAACTAACTATAAGCAGTTGAG
+ATGGATCATTATCTGGTGTCCTATTTGATTCAGGAAAGCAGGTGAACTGCAGTCTTAGGG
+ATGCAACTTATTTTCGAGTTGTATTTGGCAATAGGTGTCTCTTCTCTCCAGCTTGGTGAA
+GGTAACCTCGCAATATCAGCACCAACAGAAAGGTTAAATGAGTTCTGCCTCGTAACAGGA
+CTGGCACAAACAATGCAATAACTAC
diff -r 36cc4ae4160e -r 32cb27adeb34 test-data/consensus.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/consensus.fa	Mon Feb 12 00:58:10 2018 -0500
@@ -0,0 +1,2 @@
+>ref:0-921
+ACGGTACTTCGTTCGAGGACACGTATTGCTGGTGCTGCATGCCAGCGACTACGCATTCTCATTTAACCTTTCTGTTGGTGCTGATATTGCGAGGTTACCTCTACCAAGCTGGAGAAGCCACACCATCCGCCAAATACAATCCTTTCGAAATGGGTTTATCGAAGACTGTGATCACCGTTTTCCTGAATCGTACTGACAACAGACAATCTATCCTGATTGCCCCAGTTGATTCCGCTGTCTTTAAAATTAGAAAAACACGGGTAGAAGAGTCTGGATCCCGGCTAACACATTTCTGGAAGGCGCAGTATGGAAAACCAAACGCTCACCGGGATCTTAGTACCTTGACACTGATCACTCGGATTGCACTTGATACTAAAGTTGTATCTGCCTGACAAGCTCTCTGACGGCAGGTCACTTGCACACCACCAGGGATTATAAGTAACAGGATAAAGGCAATCAATATACCTCATCTCGAACAGGGTCCAATCATGAACCAAGTTGCTCCCGGAGCCATGCCCAAGGACCAAAGAGGGCATGTGCAAGAGCCCCATTAGAGGCATAACAGAACACTGACCTCACTCCAAGCCCCTTGGCGATTCCATCCCACCAGATACAAAGTCTGTGCCCTTCTGGAGGAAAGGAGGCAAACATAGGTGCTGTTATCGGTAGTGTAGCTCTTGGGGTTTGCAACAGCGGCGCAGATAACAGCAGCTGCAGCCCTAATACAAGCCGCCGAGAATGCCGCCAGCATCCTCCGGCTTAAGGAGAGCATTGCTGCAACCAATGAAGCTGTGCATGAGGTCGCAACGGATTGTCACAATAGCGGTAGGGAGAAGATCTACAGCAATTTGTTAATGAGAAGATAGAGCGACAGGCAAGTGGGTTAAATGAATGCGTAGTCGCTGTACCTTTTCAACAATACGTAACTGA
diff -r 36cc4ae4160e -r 32cb27adeb34 test-data/consensus.hp.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/consensus.hp.fa	Mon Feb 12 00:58:10 2018 -0500
@@ -0,0 +1,2 @@
+>ref:0-921
+ACGGTACTTCGTTCGAGGACACGTATTGCTGGTGCTGCATGCCAGCGACTACGCATTCTCATTTAACCTTTCTGTTGGTGCTGATATTGCGAGGTTACCTCTACCAAGCTGGAGAAGCCACACCATCCGCCAAATACAATCCTTTCGAAATGGGGTTTATCGAAGACTGTGATCACCGTTTTTCCTGAATCGTACTGACAACAGACAATCTATCCTGATTGCCCCAGTTGATTCCGCTGTCTTTAAAATTAGAAAAACACGGGTAGAAGAGTCTGGATCCCGGCTAACACATTTCTGGAAGGCGCAGTATGGAAACCAAACGCTCACCGGGATCTTAGTACCTTGACACTGATCACTCGGATTGCACTTGATACTAAAGTTGTATCTGCCTGACAAGCTCTCTGACGGCAGGTCACTTGCACACCACCAGGGATTATAAGTAACAGGATAAAGGCAATCAATATACCTCATCTCGAACAGGGTCCAATCATGAACCAAGTTGCTCCCGGAGCCATGCCCAAGGACCAAAGAGGGCATGTGCAAGAGCCCCATTAGAGGCATAACAGAACACTGACCTCACTCCAAGCCCCTTGGCGATTCCATCCCACCAGATACAAAGTCTGTGCCCTTCTGGAGGAAAGGAGGCAAAACATAGGTGCTGTTATCGGTAGTGTAGCTCTTGGGGTTTGCAACAGCGGCGCAGATAACAGCAGCTGCAGCCCTAATACAAGCCGCCGAGAATGCCGCCAGCATCCTCCGGCTTAAGGAGAGCATTGCTGCAACCAATGAAGCTGTGCATGAGGTCGCAACGGATTGTCACAATAGCGGTAGGGAGAAGATCTACAGCAATTTGTTAATGAGAAGATAGAGCGACAGGCAAGTGGGTTAAATGAATGCGTAGTCGCTGTACCTTTTCAACAATACGTAACTGA
diff -r 36cc4ae4160e -r 32cb27adeb34 test-data/consensus.hp.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/consensus.hp.vcf	Mon Feb 12 00:58:10 2018 -0500
@@ -0,0 +1,83 @@
+##fileformat=VCFv4.2
+##INFO=<ID=TotalReads,Number=1,Type=Integer,Description="The number of event-space reads used to call the variant">
+##INFO=<ID=SupportFraction,Number=1,Type=Float,Description="The fraction of event-space reads that support the variant">
+##INFO=<ID=BaseCalledReadsWithVariant,Number=1,Type=Integer,Description="The number of base-space reads that support the variant">
+##INFO=<ID=BaseCalledFraction,Number=1,Type=Float,Description="The fraction of base-space reads that support the variant">
+##INFO=<ID=AlleleCount,Number=1,Type=Integer,Description="The inferred number of copies of the allele">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	sample
+ref	91	.	G	GA	76.8	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.472064	GT	1
+ref	100	.	CT	C	76.8	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.600762	GT	1
+ref	113	.	A	AG	20.3	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.62332	GT	1
+ref	116	.	A	G	20.3	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.568855	GT	1
+ref	142	.	C	T	28.0	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.215363	GT	1
+ref	254	.	A	AC	57.6	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.435726	GT	1
+ref	456	.	CA	C	48.4	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.0291696	GT	1
+ref	510	.	CA	C	48.4	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.352106	GT	1
+ref	528	.	G	GA	23.8	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.542136	GT	1
+ref	537	.	C	CA	23.8	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.520509	GT	1
+ref	548	.	TA	T	43.0	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.299671	GT	1
+ref	556	.	C	A	43.0	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.120227	GT	1
+ref	599	.	TC	T	21.7	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.0689728	GT	1
+ref	638	.	GA	G	21.7	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.0753427	GT	1
+ref	666	.	A	G	35.1	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.172919	GT	1
+ref	667	.	T	TG	35.1	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.29952	GT	1
+ref	683	.	A	G	39.0	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.695758	GT	1
+ref	694	.	G	A	39.0	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.679033	GT	1
+ref	713	.	G	GC	41.5	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.288257	GT	1
+ref	728	.	CG	C	41.5	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.223589	GT	1
+ref	742	.	G	A	41.5	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.455935	GT	1
+ref	763	.	A	G	92.3	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.783764	GT	1
+ref	768	.	A	G	92.3	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.835095	GT	1
+ref	770	.	C	T	92.3	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.605993	GT	1
+ref	771	.	A	G	92.3	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.845481	GT	1
+ref	838	.	A	G	29.3	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.139648	GT	1
+ref	841	.	G	A	29.3	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.366238	GT	1
+ref	852	.	A	AG	37.7	PASS	TotalReads=5;AlleleCount=1;SupportFraction=0.796436	GT	1
+ref	856	.	T	TA	37.7	PASS	TotalReads=5;AlleleCount=1;SupportFraction=0.874709	GT	1
+ref	91	.	G	GA	78.7	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.50089	GT	1
+ref	100	.	CT	C	78.7	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.374252	GT	1
+ref	113	.	A	AG	20.1	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.635287	GT	1
+ref	116	.	A	G	20.1	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.744199	GT	1
+ref	142	.	C	T	36.6	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.703642	GT	1
+ref	254	.	A	AC	65.0	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.803838	GT	1
+ref	510	.	CA	C	33.4	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.513822	GT	1
+ref	528	.	G	GAG	24.6	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.408269	GT	1
+ref	537	.	C	CA	24.6	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.338892	GT	1
+ref	548	.	TA	T	46.0	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.351277	GT	1
+ref	556	.	C	A	46.0	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.709209	GT	1
+ref	666	.	A	G	47.6	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.829231	GT	1
+ref	667	.	T	TG	47.6	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.6682	GT	1
+ref	683	.	A	G	27.0	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.88787	GT	1
+ref	713	.	G	GCC	32.2	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.530639	GT	1
+ref	763	.	A	G	89.9	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.774073	GT	1
+ref	768	.	A	G	89.9	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.876258	GT	1
+ref	770	.	C	T	89.9	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.555854	GT	1
+ref	771	.	A	G	89.9	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.852648	GT	1
+ref	838	.	A	G	45.1	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.773069	GT	1
+ref	841	.	G	A	45.1	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.701949	GT	1
+ref	852	.	A	AGA	60.2	PASS	TotalReads=5;AlleleCount=1;SupportFraction=0.791628	GT	1
+ref	856	.	T	TA	60.2	PASS	TotalReads=5;AlleleCount=1;SupportFraction=0.672761	GT	1
+ref	91	.	G	GA	78.7	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.50089	GT	1
+ref	100	.	CT	C	78.7	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.374252	GT	1
+ref	113	.	A	AG	20.1	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.635287	GT	1
+ref	116	.	A	G	20.1	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.744199	GT	1
+ref	142	.	C	T	36.6	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.703642	GT	1
+ref	254	.	A	AC	65.0	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.803838	GT	1
+ref	510	.	CA	C	33.4	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.513822	GT	1
+ref	528	.	G	GAG	24.6	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.268594	GT	1
+ref	537	.	C	CA	24.6	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.340399	GT	1
+ref	548	.	TA	T	46.0	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.351277	GT	1
+ref	556	.	C	A	46.0	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.709209	GT	1
+ref	666	.	A	G	47.6	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.829231	GT	1
+ref	667	.	T	TG	47.6	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.6682	GT	1
+ref	683	.	A	G	27.0	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.88787	GT	1
+ref	713	.	G	GCC	32.2	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.31882	GT	1
+ref	763	.	A	G	89.9	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.774073	GT	1
+ref	768	.	A	G	89.9	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.876258	GT	1
+ref	770	.	C	T	89.9	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.555854	GT	1
+ref	771	.	A	G	89.9	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.852648	GT	1
+ref	838	.	A	G	45.1	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.773069	GT	1
+ref	841	.	G	A	45.1	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.701949	GT	1
+ref	852	.	A	AGA	60.2	PASS	TotalReads=5;AlleleCount=1;SupportFraction=0.752959	GT	1
+ref	856	.	T	TA	60.2	PASS	TotalReads=5;AlleleCount=1;SupportFraction=0.672828	GT	1
diff -r 36cc4ae4160e -r 32cb27adeb34 test-data/consensus.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/consensus.vcf	Mon Feb 12 00:58:10 2018 -0500
@@ -0,0 +1,83 @@
+##fileformat=VCFv4.2
+##INFO=<ID=TotalReads,Number=1,Type=Integer,Description="The number of event-space reads used to call the variant">
+##INFO=<ID=SupportFraction,Number=1,Type=Float,Description="The fraction of event-space reads that support the variant">
+##INFO=<ID=BaseCalledReadsWithVariant,Number=1,Type=Integer,Description="The number of base-space reads that support the variant">
+##INFO=<ID=BaseCalledFraction,Number=1,Type=Float,Description="The fraction of base-space reads that support the variant">
+##INFO=<ID=AlleleCount,Number=1,Type=Integer,Description="The inferred number of copies of the allele">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	sample
+ref	91	.	G	GA	76.8	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.472064	GT	1
+ref	100	.	CT	C	76.8	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.600762	GT	1
+ref	113	.	A	AG	20.3	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.62332	GT	1
+ref	116	.	A	G	20.3	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.568855	GT	1
+ref	142	.	C	T	28.0	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.215363	GT	1
+ref	254	.	A	AC	57.6	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.435726	GT	1
+ref	456	.	CA	C	48.4	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.0291696	GT	1
+ref	510	.	CA	C	48.4	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.352106	GT	1
+ref	528	.	G	GA	23.8	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.542136	GT	1
+ref	537	.	C	CA	23.8	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.520509	GT	1
+ref	548	.	TA	T	43.0	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.299671	GT	1
+ref	556	.	C	A	43.0	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.120227	GT	1
+ref	599	.	TC	T	21.7	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.0689728	GT	1
+ref	638	.	GA	G	21.7	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.0753427	GT	1
+ref	666	.	A	G	35.1	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.172919	GT	1
+ref	667	.	T	TG	35.1	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.29952	GT	1
+ref	683	.	A	G	39.0	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.695758	GT	1
+ref	694	.	G	A	39.0	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.679033	GT	1
+ref	713	.	G	GC	41.5	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.288257	GT	1
+ref	728	.	CG	C	41.5	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.223589	GT	1
+ref	742	.	G	A	41.5	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.455935	GT	1
+ref	763	.	A	G	92.3	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.783764	GT	1
+ref	768	.	A	G	92.3	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.835095	GT	1
+ref	770	.	C	T	92.3	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.605993	GT	1
+ref	771	.	A	G	92.3	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.845481	GT	1
+ref	838	.	A	G	29.3	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.139648	GT	1
+ref	841	.	G	A	29.3	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.366238	GT	1
+ref	852	.	A	AG	37.7	PASS	TotalReads=5;AlleleCount=1;SupportFraction=0.796436	GT	1
+ref	856	.	T	TA	37.7	PASS	TotalReads=5;AlleleCount=1;SupportFraction=0.874709	GT	1
+ref	91	.	G	GA	78.7	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.50089	GT	1
+ref	100	.	CT	C	78.7	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.374252	GT	1
+ref	113	.	A	AG	20.1	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.635287	GT	1
+ref	116	.	A	G	20.1	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.744199	GT	1
+ref	142	.	C	T	36.6	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.703642	GT	1
+ref	254	.	A	AC	65.0	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.803838	GT	1
+ref	510	.	CA	C	33.4	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.513822	GT	1
+ref	528	.	G	GAG	24.6	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.408269	GT	1
+ref	537	.	C	CA	24.6	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.338892	GT	1
+ref	548	.	TA	T	46.0	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.351277	GT	1
+ref	556	.	C	A	46.0	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.709209	GT	1
+ref	666	.	A	G	47.6	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.829231	GT	1
+ref	667	.	T	TG	47.6	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.6682	GT	1
+ref	683	.	A	G	27.0	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.88787	GT	1
+ref	713	.	G	GCC	32.2	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.530639	GT	1
+ref	763	.	A	G	89.9	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.774073	GT	1
+ref	768	.	A	G	89.9	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.876258	GT	1
+ref	770	.	C	T	89.9	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.555854	GT	1
+ref	771	.	A	G	89.9	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.852648	GT	1
+ref	838	.	A	G	45.1	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.773069	GT	1
+ref	841	.	G	A	45.1	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.701949	GT	1
+ref	852	.	A	AGA	60.2	PASS	TotalReads=5;AlleleCount=1;SupportFraction=0.791628	GT	1
+ref	856	.	T	TA	60.2	PASS	TotalReads=5;AlleleCount=1;SupportFraction=0.672761	GT	1
+ref	91	.	G	GA	78.7	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.50089	GT	1
+ref	100	.	CT	C	78.7	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.374252	GT	1
+ref	113	.	A	AG	20.1	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.635287	GT	1
+ref	116	.	A	G	20.1	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.744199	GT	1
+ref	142	.	C	T	36.6	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.703642	GT	1
+ref	254	.	A	AC	65.0	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.803838	GT	1
+ref	510	.	CA	C	33.4	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.513822	GT	1
+ref	528	.	G	GAG	24.6	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.268594	GT	1
+ref	537	.	C	CA	24.6	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.340399	GT	1
+ref	548	.	TA	T	46.0	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.351277	GT	1
+ref	556	.	C	A	46.0	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.709209	GT	1
+ref	666	.	A	G	47.6	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.829231	GT	1
+ref	667	.	T	TG	47.6	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.6682	GT	1
+ref	683	.	A	G	27.0	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.88787	GT	1
+ref	713	.	G	GCC	32.2	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.31882	GT	1
+ref	763	.	A	G	89.9	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.774073	GT	1
+ref	768	.	A	G	89.9	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.876258	GT	1
+ref	770	.	C	T	89.9	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.555854	GT	1
+ref	771	.	A	G	89.9	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.852648	GT	1
+ref	838	.	A	G	45.1	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.773069	GT	1
+ref	841	.	G	A	45.1	PASS	TotalReads=8;AlleleCount=1;SupportFraction=0.701949	GT	1
+ref	852	.	A	AGA	60.2	PASS	TotalReads=5;AlleleCount=1;SupportFraction=0.752959	GT	1
+ref	856	.	T	TA	60.2	PASS	TotalReads=5;AlleleCount=1;SupportFraction=0.672828	GT	1
diff -r 36cc4ae4160e -r 32cb27adeb34 test-data/index.tar
Binary file test-data/index.tar has changed
diff -r 36cc4ae4160e -r 32cb27adeb34 test-data/ref.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ref.fa	Mon Feb 12 00:58:10 2018 -0500
@@ -0,0 +1,17 @@
+>ref
+ACGGTACTTCGTTCGAGGACACGTATTGCTGGTGCTGCATGCCAGCGACTACGCATTCTC
+ATTTAACCTTTCTGTTGGTGCTGATATTGCGGGTTACCTCTTACCAAGCTGGAAAACCAC
+ACCATCCGCCAAATACAATCCCTTCGAAATGGGTTTATCGAAGACTGTGATCACCGTTTT
+CCTGAATCGTACTGACAACAGACAATCTATCCTGATTGCCCCAGTTGATTCCGCTGTCTT
+TAAAATTAGAAAAAACGGGTAGAAGAGTCTGGATCCCGGCTAACACATTTCTGGAAGGCG
+CAGTATGGAAAACCAAACGCTCACCGGGATCTTAGTACCTTGACACTGATCACTCGGATT
+GCACTTGATACTAAAGTTGTATCTGCCTGACAAGCTCTCTGACGGCAGGTCACTTGCACA
+CCACCAGGGATTATAAGTAACAGGATAAAGGCAATCAATATACCTCATCTCGAACAGGGT
+CCAATCATGAACCAAGTTGCTCCCGGAGCCAATGCCCAAGGACCAAAGGGCATGTGCAGA
+GCCCCATTAAGAGGCCTAACAGAACACTGACCTCACTCCAAGCCCCTTGGCGATTCCATC
+CCACCAGATACAAAGTCTGTGCCCTTCTGGAGGAAAGGAGGCAAACATAGGTGCTGTTAT
+CGGTAATTAGCTCTTGGGGTTTACAACAGCGGCGCAGATAACAGCAGCTGCAGCTAATAC
+AAGCCGCCGAGAATGCCGCCAGCATCCTCCGGCTTAAGGAGAACATTACCACAACCAATG
+AAGCTGTGCATGAGGTCGCAACGGATTGTCACAATAGCGGTAGGGAGAAGATCTACAACA
+GTTTGTTAATGAAGATGAGCGACAGGCAAGTGGGTTAAATGAATGCGTAGTCGCTGTACC
+TTTTCAACAATACGTAACTGA
diff -r 36cc4ae4160e -r 32cb27adeb34 test-data/ref.fa.fai
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ref.fa.fai	Mon Feb 12 00:58:10 2018 -0500
@@ -0,0 +1,1 @@
+ref	921	5	60	61
diff -r 36cc4ae4160e -r 32cb27adeb34 test-data/test.fast5.tar.gz
Binary file test-data/test.fast5.tar.gz has changed
diff -r 36cc4ae4160e -r 32cb27adeb34 test-data/test_data.fast5.tar.gz
Binary file test-data/test_data.fast5.tar.gz has changed
diff -r 36cc4ae4160e -r 32cb27adeb34 test-data/test_data.fastq
--- a/test-data/test_data.fastq	Mon Dec 04 02:03:21 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,32 +0,0 @@
-@3030a28d-1f16-4086-9ba1-ff31a97f434d_Basecall_1D_template:1D_001:template macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12068_ch_399_strand in_dir/out_dir/workspace/macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12068_ch_399_strand.fast5
-TCGTGTAGCCTGAATTCGATGCGTATCGCTTGAGAAAATAAACTCGCTGGCGTGACGAAACGTAATGAATTACGACGCTGTCGAAATGAAACTCTTCGCCGGCATGTCGCAGGCATTAGCGGGCCGAAACTAGTGATAGCACATTATCGATAAAAACTGGCGAATCTCATCTAAAGAGGCGGCGCTGTTCGTGAATAAGGGCAGCAATGGCTGCGAAGCGTGTTCAGGCAGAATTGCCAGAGAGAATCATCGAAGGCATCGAAAATGATATGCTCTTCTTTCGCTGGCGATATGAGAATGTCGAGAGCTTCGTTCGTAATAAATGGCGAGGCAATGTGAGCTCTCGTATAAAGATGGGCGGGCGTCTTGAATGGCATCGCGAAAGCCAAGCTTCGGTATGACTCGGTAGAAGCTGACGTGTTATCGAGGCATAGCGAGAGA
-+
-"%(()""#2.,$.*->,,,,*-27,1,#"&"($&+6:0/$+.&)*&,0>E(,(($/.39'$""$'((+).%"&/'<&$&"($"$$#*&+'"#-$')""(&0.<+=0:?7C&'MN%K'&"*/),/9,/1&#"%#-##1"(*&*#4,,/=%%&,8:=27'*&"%-(-+-+&(("&*%)'-7D>FEE=<&*'(%'*'%%"$,)&$%"&))(**$"#")$$&#(,+%/#(6.'%0'(1)&*(#()()',(/6-))%&(--47?:&02@,%$)),-""$"#($%+(&*4+6)%'$#""&')+01/;C2.2$&:5>.&/71)B*.*(*"""$(&%(%)*1&(2.*((%''%"$"%.7.-$,/6*'-?/352&'&'*=0(+'),+$&+6EB35:2.&+2)--#%'--""#$(+#&&-+"$$'",&*"%""$=-0959&+'%#$+&&(%
-@86fd3e14-b5ee-4453-98fa-084d75821456_Basecall_1D_template:1D_001:template macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12091_ch_399_strand in_dir/out_dir/workspace/macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12091_ch_399_strand.fast5
-ATATTATGCTAAATTGGAAGTGCGTATGAATACAGAAGCTGACGCGAGAGTGAGCGAAAGCGAAATGACGAAGCATGTCAAAAATTACAACTTTAATATCGGCTAGAATGAGCTGCTAAGCATGTCGCAAGCGTGGGCCGAAACTAAAGATGATATTTGATATCATTAAGCTGGCATAGAATCAGAAAGCGGCGTAAAGTCTCGGCATCGAGCATTATAGTGCGAAAGCGGGAAATGATGAAGCGGTGAGAATACATCAAAGGCGCTCAAAGTAAATGTAGAATGCGCGATATCAATGATATATTAATGAAAGAAATATCGAAATCAGTGTATAAACGACACGGCTGGCGAATTCACTAATATCGAAATGGGCCGAGGCGGTAATGAGCCGAGCGCATCGCTGAGGCAGTATAGTGTAATCCTGATATAAATTCCAGGGCGCAATATACTCGAAGCTTTGCGAAGAGAGCGTGGAAACACAATGGCATATATGAGGGGCGTAGCAATGAGATATAAAGTAACGATGAAATTCTCATCGAGAGCTCAAATGAAATAATCGGCGCGGTCGTCCTGCCTCGAAGCCCTAAAGAGGTAATGAAGGCGAAATGATGAGGCATATCTCCCAAGCGAAAGCGAGAAAATGGAGAGCAATCAGGCCGAAGTGGCTCGGTATTGATCGAAAGTGCGCGATCGAAACGAGAGAGCGACGGGCGATCAGCCAGCGCTTGGTATAACGTAGCTCAATGGGCGAAACCGAAACACCGACAATAGTGATAAAGAAACGCGCCATTTC
-+
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
-@2dd21811-c9af-4c4a-aaa0-4fd1f605abf8_Basecall_1D_template:1D_001:template macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12153_ch_399_strand in_dir/out_dir/workspace/macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12153_ch_399_strand.fast5
-CAAGTAATGTAATTGGATGTCCAACATGGTGGCGGTAGATGACGAGATAATTCCTAAAATTAAACGTGATGATGATAAAATTGCTAAGTAAACATTCTGGCTGTCAAATAGTAATAACGATGCATTTTAAGATTTAATGCTGACGCTGTATTATGCATAACATCGGCATCGGCATATGCATAGCGAGAATATTTGATGGAGTCGATAACCGTGAGATGGCATCTTTGTCTCTTCTGGCGCTGAGAGAATCAGAAGCCTCTCATCCAATAAACCATCATTTCAATGATAAATTTTAAGTAAGCGATAGTATTTAATTTGCTGGTGAAGATTATTATGTCGCGTAACTAACGATAATATCAATGGCGGCGGCGCTGGTACGGTAATTTTGTCATTATCTCTCATGATGCCGAGCTTCAATGACATCGTCTCTCGGTAACTTTTCGTATATCGCTATTTTATTGTATTTATTTTGCTTTTTGGCGCCGCGCCGTGTTTAATGAGTGGTATTAGCA
-+
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
-@28daae22-d0dc-4fee-8453-3a2178b331c8_Basecall_1D_template:1D_001:template macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12175_ch_399_strand in_dir/out_dir/workspace/macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12175_ch_399_strand.fast5
-TCGTATGCTAGATCGTCGCATATCAGCGAATCCTGAGCGTAGCGTGAGTAGAGGCGAGGCCGGTAATGAGAGAGAATGAGTAGCCTGGCAGTCGAGCGTAGCGTCTCCTATCGTCATCGAGGCCTCCAGAAGCCGAAATCGCGCGAAGCTCGGTATTTTAGAAGAAACGCGAATGTGAAGCTCTCGTGAGTATTCGAGGCAAGGCCAATCTGTCGCTCTATTCAAAGAAATCCCTGAAATTGTGTTGCGTCGCCGTGGTTGTCGGCGAGGGAGCCTGCGTATGAGCCGTGGCAAAAATAGCCTAAATGAAATGAAGGCTGAAACGGCATGTTGAGGCGGTAAAGGCTATGCGAAGCTGAAATGAGCATTCATCAGGCGAAAGTAGCGCTCGTTACGCTCGACTAATTTGGCGCTTGCTGGTATGATATATGCGTAGGGTAAGGCGTGACGCGTGAAAACTGTGGCTATTATGTGCCGCTCAATGAAGCCGAGTAGCACGGCATCGTCACGAGCGAATGGCATTGCAGCCCGCTAATCGAGCATGAAACGAAATGGCCCGATAGCAAGGCGCGTAGGCGAAATGGCCTGAATCGATGGTGACGGCGAAGCCATGAAATGCGCGTAGAGCTGGGCGGAAATGCGCGGCCAATGAGAGCAGTGAGCTCGCCTAAAGCTCGATGCTGAATCTGAAACGTCTCAATAATGCGGCTCGCCCGAAAGCAATAATTGCCGAAATGGCAGCATTCGAAATGTCTCTCAAATGTGCGGCGGCATCGTGAATAATAAGCAATATCTGAATTATGATAAAATGCTAAAATGCGTATCAAATAAACAAATAGGTACAAGGCGCTGAAGAGTAACTCGAATCTATGAAGTATCGGCGAAGCGTAACAATGAGTATTGACGATATTCATTGTCGGCATAGGCTGGAAATGAAATACTCTTTGCTCGCATAAATGACTGG
-+
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
-@15bdfe23-0646-4c89-b523-185bc14c3a2a_Basecall_1D_template:1D_001:template macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12081_ch_399_strand in_dir/out_dir/workspace/macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12081_ch_399_strand.fast5
-CATTGTAACTTGCATTCAAATTGCATGTCAGCCTAGGAAAATGCAGCCATCTAGTAGAGTAGAGTGTGTATTCAGGTAAATATATGGCTAAAAGCTAGGCCTAGTTAGCAGGAACTCATAGATGTATTATTTCAAATATACTACTGATCTCTTTGATCACAACAAACTCTTTAATCATTTGTTTCTGAAGCTTATAGACTCAGAACATTTATAAGCCGTACAAATTTTCTAAATTTGAGTAGAAATTATAAAATGCTGGTGGCTTTCTTAATAAGGCCGAGATGTAACCAAAGGACTCTAGAACTCGAGCTGTTACATAAACATTTGAAATTTTGGCTGGGAGACCGTACGGCATCATCATTGTAATGCCTCAGGAAATTGTAGGTACGTGCTTCTAGCCTACAAATGAAACCACTATGATGGCATCAGCCTTCCGCAGTGATCGAAATCACTTCAGAATTTCTTGATAATGTATGGTTTGAAGGCCTCGCGCCTGCCAGGCATCAGCTCGGCGTCCTCGGCCTCGTACCATAGGCTCAAATCGGCAAGAAGAATAAGAGGTAATGTCCTTCAGTACTCATCAAATTCTCTCCTGGGGAATGCAGCCTGCTTCTTCAAGCGCGATGGCCCTGATATACATTTGAAATAACTGCTCACCATGCTCGAGGCTTTCAGATAAAGCGCAGGCAAAAGCCTCGAAATGGTATCAAATTATATGTAAATCGTCGCAGGCACTTCTGCTGAAACGCGTATGCAGAGGCTCATCTCATTTTGCCTCACTGCTCTAGGGGTGCTCAATATGGCGGCATCAGCAGCTTATGGCCAACAAAATAACTCTGCAGGTGGGCCAGGCATGAAACAGTGGCGTGGCGCGCGGTGCATCGCGGGGAGAGTGTCAGGCTGGTATCATGGCGAGGCTGATCAATAATCGGGGCATCGCAGGTAACTGGCATGTTTTTGAAGTCAAATGGCGGTGGTACTGATGCGCCGGAAATAAAGGAAGAACTACTCGAAGCTAAGTAGAAGTATAAAATTGGCGGGGGCCATGCGGTATCAAGGCTCTCATATAAAATGCCATATAAGTGTTTCTCGGCTCGCATAGAGGTGTGCATATCAGCGGCGAAAAGTAAACACCTTCTGGAATCTCCTCATGTCTGTGCCACAAACCATACCGACAGGCGTCATCTGTGAAATCGACATCAATGCGCAAAAAGTACTTCGATACTAATCCGGTAGCTTCAGTACCTAAATCAGAGTAACTCCAGCAAATATCCCC
-+
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
-@310f7b48-a3e0-4cdc-b396-09f4b86081dd_Basecall_1D_template:1D_001:template macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12113_ch_399_strand in_dir/out_dir/workspace/macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12113_ch_399_strand.fast5
-TCTTTCATTTGTGGCAGGTGGAGCGTATTCGAATCTCGAAACTGGCGCGGTGATGAAACTTGAGGTATTTTATCGCTAAATAATTTGGCCGAGGTTACTCGCTCAACTCTGCTTCGGCTGATAATTGAAACAATAAAGCGTCATCTGTTGACTGATGCTCTGTGTTGCTGTCGTGGCAGCGATCATTGTTCTTAGAGCTTTAGCGACAAGTGTTATAAACAAGAACAACGGAGGTAGGAATGCTCGTATGGCGGCGAAGTGTATGAATTTCATGAGAGGGCTCGACTATTGATGCAATAAAATTGCATTCGAGTCTCGTCAGGGGCTTTTGATAGCCCTGACGTCTCGTCGGTATATGAGAGAAATGGCGATGAAATTTCTCGCGATTCAACCATAACTATAAAGTACAATGGCCATCAGGTTTCGGCGTCAGTCGCTGAAAGTAAAACACCGACCATATGATATTTGTAAATGCGTTATTAACAATTCGTGCAATGCCGAGGCGCAAGCACCTGTTGGTATGGCGCATCAGGCAATCATCGATATTCTTCAATAGTCATATCGGTCGATATGGTGGCAGGCAGGCAATAGTCGTACCGAGTGGCACTCCATCGTTAACTACTCTCGAAATCGCTCATATCATTTTACGCGTCTTCTTCGTGTCCGGGCCGAAATTAGCCTGCTCTTGCATAAGAACCTGATGCGGCGCGGCCATCGAGGTCTCCGATGCTGCCGTCGTGCATGCTTGAAAACTTGTCTACTCGAAAGCTCGACGCGTGTCAAAGCTAAAATTATGTTTTTTATTGGCATATTTATCGCTT
-+
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
-@921ea44a-1215-4f98-9f38-bf36b1bdf69c_Basecall_1D_template:1D_001:template macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12085_ch_399_strand in_dir/out_dir/workspace/macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12085_ch_399_strand.fast5
-TCTTTCGGTAGCAAATTAAATCCAACGGTAACCGGCTTCATTCTGAAATGAAATTAAATAGAAGCGAAATAACCCTGAGGCAGTATGGTGTGACGTGGCATTCGCATTAGCCCTAAGTGCGTAATGAAGATGGTAGTGCGTCAGCAAGGCCCGGGGAGATAAATAATCCTCGATACATGGCCTTGGCTGAAAGATAGAAATTTAGAATTCATTGACCAAGTAACTCGAGCAATAGAGGCATTTCCCTCGTCGGCCTGAAGCCTCGGTGTGGAAATGGCATATAGTATTAATGCAGTAACTAATGAAATTGCCAAATGGGCATATAAGCATTGCGATGAGGGCCGTATTTGCATTGGGCTGAGGTGCGTGTGTCCTTATGGGCGAGGTAGGCTCGTCATGCCTCCGGTGAGGGGTGAGGTAGAAATATTACCGTAGAAGTGCTGAAAGCTAACCAATGAAATGGGTAAAACCATCGGAAGCGCCTAGCGATGGGCTATACAATTTCATTCGACAATCCAGCTATAAATGATGAGGCATCAGGGCGCATTCTAGAGAGGCGTGACAGCATTGATAGCATTTCGATGCAAACCATCTTCTGCGTAATGACACTGACACTATTCAGTGACAGCTCATC
-+
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
-@aabaf035-7aa8-439b-8773-523c69a350ca_Basecall_1D_template:1D_001:template macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12103_ch_399_strand in_dir/out_dir/workspace/macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12103_ch_399_strand.fast5
-TTTTTTTTTTTTTTTTGCACTCATTTGGCCGCTAATTCGTCCGTATTGATCTAGTGACGCAGTGAGTAAGCAGGTATTTTCATCATCAAATAGTGAGCGAGGATTATATCTCGGCTCTGCTCGATGGTGGCGAGCAGGCATCGCTGACTGAAACATACCATGTGCCGATACCGCGTGAAACTGGCCGTGGCGCTTCGCTTTGTAGAACTTGCATTGAGGTATTTACCAAGACACCGTTTGCGGAGGTGATTGCTCGCACTCAGGTGCAGCCTATGCAGAAACGTGTAATTTAAGAGCTCATTAATGATATCATTAAAATTCGCGAGTGCTCGTCGAGGGGCTGATGCATTTCGACTCTCTGTGACATGTCTCAAGTGGCCGTGAAGTATCGCAGTAATATATGAAATATAATTAATGTCAGAGATTTCTGGCCGTCGAAATGCGCTAAAGTAAACAATATGATGTTAGCCGATAAAATTATTATAGTGCATTATTCTGATACTTGAAGCCTCGCTGATATTGAGGAAGTATGAAATATTATCGATATTCGACGTCATATCGATTAAATATGTCGAGAGCGAAATAGTCGTACAAGTATATCAAGGGCAACTTGCCGAATAAATGCTCGCTCTTATTTTTAAAAAAATTCGGCTGTTTCGTGGCCGGTGGTAGCACTCTTACTCTGGTAGCGGCCCATCAATCGGGCATCACTTTAAATTATCAGTCTGCCGATAATTGGCGGGCATGCGAAAACGTCTACTCGAAACCCGGCGACAGTGAATCGTAGCCTTTGTCGCACCAGCTTTTGCGACTCATAAGTATTC
-+
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
diff -r 36cc4ae4160e -r 32cb27adeb34 test-data/variants.bam
Binary file test-data/variants.bam has changed
diff -r 36cc4ae4160e -r 32cb27adeb34 test-data/variants.in.fast5.tar.bz2
Binary file test-data/variants.in.fast5.tar.bz2 has changed
diff -r 36cc4ae4160e -r 32cb27adeb34 test-data/variants.out.fa
--- a/test-data/variants.out.fa	Mon Dec 04 02:03:21 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
->cluster_0:0-783
-TCATTAACAAATGCTGCATCTTCCCTACTGCTACTGATAGTTGTGATAATCCGTCGGTGACTTCATGCACAGCTTCATTGGTTGCAGCAATGCTCTCCTTAAGCCGGAGGATGTTGGCAGCATTCTGGTTGGCCTGTATTAGGGCCGCAGCTGCTGTTATCTGTGCCGCTGTTGCAACCCCAAGAGCTACACTGCCAATAACGGCACCTATAAAGCGCTTTTGTCTCCTTCCTCAGACGTGGACACAGACCCTTGGATCTTGCGGATGGAATCGCCAAGAGGAGTGAGCAAAGTAGTCAGTGTTCTGTTATATGCCTCTAATGGGGCTTTTGCACACGCCTCCTTATCCTTGGGCATATTCGGGAGCAATTTGACTATGATTGACCCTGTCTGAGACGAGGTGTATACATTGACTGCCTTATCTCCTGTCACTACAATTCCTGCAGCTGCANGAGGCCTGCCGTCAAGGGAGCTTGTCAGACGGATACAGCTCAATATCAGCATAATCCGAGTTATCAGCATCNGAAGTGCTGGGATCCTGGTGAAGGTTTGGAGCCCATATTGCGTCCTGGATGAGCTGGTCGGGATCCAGACCCTTCTACCCGTGTGTTTTTCTAATTTGCTAAACAGGTGAACTAACTATAAGCAGTTGAGATGGATCATTATCTGGTGTCATGTTGATTCAGGAAAGCAGGTGAACTGCAGTCTTAGGGATGCAACTTATTTTCTGAAAGGATTGTATTTGGCAATGGTGTGTCTCTTCTCCAGCTTAGTAGAGGTAACCTC
diff -r 36cc4ae4160e -r 32cb27adeb34 test-data/variants.reads.fa
--- a/test-data/variants.reads.fa	Mon Dec 04 02:03:21 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,121 +0,0 @@
->88bad4e9-c28f-4b9c-8011-6b07bace6d29
-ACGGTATTGCTTCGTTCAGTTACGTATTGCTGGTGCTGTTGCGTCCTGTACGAGAACTCA
-TTTAACCTACTTGCCTGTCGCTCTATCTTCTCATTAACAACTGCTGCATCTTCCCAACTA
-CTGATGATTTGTGATAATCGTCAGTGACTTCATGCACAACTTCATTGAGTTGCAACAATG
-CTCTCCTTAAACCGGAGGATGTTGGCAGCATTCTGGATGGCCAGCCTGTATTAGGGCCGC
-AGCTGCTGTTATCTGTGCCACTGTTGCAACCCCAGAGCTACACTGCCAATAACAGCTATA
-AAGCGCTTTTGTCTCCTTCACTCCCAGACGGACACAGACCCTTGGATCTTGCGGATGGAA
-TCGCCAAGAAGGAGTGAAGAAGTAGTCAGTGGATGTTGCTTAGCCTCTAATGGGGCTTTT
-ACACGCCTCTTGCTTAGTCGGAGCAATTTGACTATGATTGACCTGTCTGAGACAGATGTA
-TACATTGACTGCCTTATCTCCCTGTCACTGTTCCTGCAGCTGCAAGGCCTGCCGTCAAGG
-GAGCTTGTCAGACGGATACATCTCCAATATATCAGCATAATCGAGTTATCAGCATCAAGA
-ATTCTTTGGGATCCTGTGAAAGGTTTGGAGCCCATATTGCGTCCTGGATGAGCTGGTCAG
-ACCCTTCTACCGATGTTTTTCTAATTTGCTAAACAGACACAACTATAAGCGGATGGATCG
-TATCTGGTGTCGCATGTGTTGATTCAGGAAAGCAGGTGAACTGCAGTCTTAGGGATGCAA
-CTTATTTTCTGTGAAGGATTGTGTACAACTTGTGGTATTGTCTCTTCTCCAACGGTGGAG
-TACTCATATCAGCACCAACAGAAAGGTTAAATGAGTTCTCGTAACAGGACACAACAGCAC
-CAACAATACATGAAAAAAAAAAAAGA
->307ec816-d48a-46c5-93dd-4035dde1d324
-ACATCGGTACTTCCGTTCAGTTACGTATTGCTGGTGCTGTTGCGTCCTGTTACGAGAACT
-CATTTAACCTACTTGCCTGTCAGCTCCTCTTCTCATTAACAAACTGCATCTTCCCTACTG
-CTACTGATAGTTGTAGGTAATCCGTCGTTGACTGTACACAGCTTCATTAGTTTTGCAATA
-CTCCGCAAGCCGGAGGATGTTGACATTCTGGTTGGCCTGTAGTGGGGCCACGGCTATATT
-GTCTGTTGCCGCTATTTACTAACCCAAAACTACACTGCCAATAACGGCACCTATAAAAGC
-GCTTTGTCTCCCTTCCCCTCAGACGTGGACACAGACCCTTGGATCTTGGGATGGAATCGC
-CAAGAAGAATTGAACAAAGTAGTCAGTGTTCACAGTATGCCTCTAAGCTGGGGCTTTTGC
-ACACGCCTCCTTGTCCTTGGGCATATTCAGGGAGCAATTTGACTATGATTGACCCTGTCT
-GAGACAGTGTATACATTGACACCTTATCTCCTGTCACTACAATTTCCTGCAGCTACAGGC
-CTGCCAAATCCAAGGGAGCTTGTCAGACGGATACAACAATATCAGCATAATCCGAGTTAT
-CCAGCATCAAGTGCTGGGATCTGGTGAAGGTTTGGTGGAGCCCATATTGCGTCCTGGATG
-GCTGGTCGGGATCAGACCCTTCTACCAAATGTTTTCTAATTTGCTAAACAGGTGAACTAA
-CTTAAGCAGTTGAGATGGATCATTATCTGAGTGTCATGTTGGATTCAGGAAGCAGGTGAA
-CACCACAGTCTTAGGGATGCAACTTATTTTCTGAAGGATTGTATTTGGCAATGTTGTGTC
-TCTTCTCTAGCTTAGGGTAACCTCTGCAATATCAGCACCAACAGAAAGGTTAAATGAGTT
-CTCGTAACAGGACGCAACAACTCCAGCACAACTCCCCTTCAACTCCCA
->8b9c1924-15ee-4da4-960b-c1f9de201685
-ACGGTATGCTTGCTTCGTTCAGTTACATGTTACTGAATTGCTGTTGCGTGTCCTGTTACG
-AGAACTTTCGATTGCTCCTACTTGCCTGTCGCTCTATCCTTCTCATTAACAAACTGCTGC
-ATCTTCCCTACTGCTACTGATAGTTTGTGATAATCCGTCCCATTTGACTTCATACACAAC
-TTCATTGGTTGCAACAATATATAACCGGAGGAGGATGTTCGGCAGCATTCTGGTTGGCCT
-GTATTGGGCCGCAGCTGCTGGTATCTATTATATGTTACCCAACCCAAAACTACTGTATGG
-CACCTATAAAGCGCTTTTGTCTCCTTCCTCAGACTTTTGGACACGGGCCCTTGAGATCTT
-GCCGGATGGAATCGCCAAGGAGTGGTACAAAGTAGTCAGTGTTCTGTTATGTATGCCTCT
-AATGGAGACTTTTGCACACACCTCCTTATCACTTGGGCATATTCGGGAACATTTGACTAC
-CAATTGACCCTATGCGAGACGGTGTATACGATGACTGCCTTATCTCCTGTCACTACAGGT
-TCCTGCAGCTGCAAGGAGGTACCGTCAAGGAGCTTGTGTCAGACCGGATACAGCTCCAAT
-ATCAACATAATCCGAGTTACATCAGCATCAAGAGTGCTGGGATCCTATTGGTGAAGGTTT
-GGAGCCCATATTGCGTCCTGGATGAGCTGGTCGGGACCAGACCCTTCTACCACTATTTTA
-TTTGCTAAACGGGTGAACTAACATAAGCCGGTTGAGATGGATCATTATCTGGTGTCATGT
-TGATTCCAGGAAAACAGGTGAACTGCAGTCTTAGGGATGCAACTTAGTACTGAAAGAGTT
-GTATTTGGCAATGGTGTCTCTTCTCCAGCGGAAAAGTAGAGGTAACCTCGCAACCATCCT
-TTCCAAACAGAAAGGTTAAATGAGTTCTCGTAACAGGACGCAACAGCACCAAACAGCCCA
-TGAG
->a6f90ea9-42d4-47c2-b988-f805ca7a154b
-ACGGTAACGCTTCGTTCAGTTTACGTATTGCTGGTGCTGTTGCGTCCTGTACGAGAACTC
-AATTTAACCTACTTGCCTGTCGCTCTATCTTCTCATTAACAAACTGCATCTTCCCAACTG
-CTACTGATAGTTGTGATAATCCGTCAGTGACTTCATGCAGCTTCATTGGTTTAACCAATG
-CTCTCCCTTACAGCCTTGGAGGGATGCTGGCAGCATTCTGGTTGGCCTGTGTGGGGCCGC
-AGCTGCTGTTATCTGTGCCGCTGTTGCAACCCCAAAACTACTGCCAATAGCGGCACCTAT
-AAAGCGCTTTTGTCTCCTTCCTCAGACGTGGACACAGACCCTTGGATCTTGGATGGAATC
-GCCAAGAGGAGTGAGCAAGTGATCGGTGTTCTGTTATATGCCTCTAATGGAGACTTTTGC
-ACACCTCCTTATCCTTGGGCATATTCGGGAGCAATTTGATATGGTGACCCTGTCTGAGAC
-GAGGTGTATACATTGACTGCACTTATCTCCTGTCACCAATTCCTGCAGCTGCAAGGCCTG
-CCGTCAAAGGGGAGCTTGTCAGACGGATACAGCTCAATATCAGCATAATCGAGTTATCAG
-CATCAGAAGTGCTGGGATCCTGGTGAAGGTTTGGAGGCCCATATTGCGTCCTGGATGAGC
-TAGCGGTCGGGATCTCCAGACCCTTCTACTGATGTTTTTCTAATTTCATGGTGAACCCCT
-TTATAAGCAGTTGAGATGGATCATTATCTGGTGTCATGTTGATTCAGAGCCAGGTGGAGC
-ACAGTCTTAGGGATGCAACTTATTTTCTGAAAGGATTGTATTTGGCAATGGTGTGTCTTC
-TCAGCTTAGTGAAACACCTCGCAATATCAGCACCAACAGAAGGTTAAATAGGTTCTGTAA
-CAGGACGCAACAGCACCAGCAATACGTAGCA
->eb35cfa9-2726-4109-a157-398a32a4d5d8
-CTGTACTTCGTTCAGTTACGTATTGCCTTTCAATTTGCTGTTTGCGTCCTGTTACGAGAA
-CTCAGCACATTTAACCTTTCTGTTGGTGCTGATGTGCAGGGTTACCTCTACTAAGCTGGA
-GAGACACACCATTGCCAAATACAATCCTTTCAGAAATAGAAGTTGCATCCCTAAGACTTG
-CGAGTTCACCTGCTTTTCCTGAATCAACACTTGAAGGCACCCAGATGAGTCATCTCAGCG
-CTGCTTATAGTTGGTTCTGTTTGCCAAATTAGAAAAACACGGGTAGAAGGGGTCTGGATC
-CCGACCGAAATCATCCAGGACAATGGAGGAAACCAAACCTTCTACCGGGAGGATCGCGCT
-TCGATGCAGTAACTCGGATTATGCTGATATTGAGCTGTATCGCGTCCCGACAGCTCCCAT
-GACGGCAGGCCTCTTGCTTCTTGAGATTGTAGTGACAGGAGATAAGGCAGTCCAATGTGT
-ACCTCGTCTCAGACGGGGTCAATCCTGGAGAATCAAATTGCTCCCGAGTATGCCAGGATA
-AGGAGGCGTGTGCAAAAGCCCCATTAGAGGCATGCTCCCAACAGAACACTGACTACTTTA
-TACACTCCTCTTGGCGATTCCATCCTGAAGATCCAAGGGTCTGTGTCCACGTCTGGAGGG
-AACTAAAAACATAGGTGCCATAGATTATTGGCAGTGTAGCGCTCAGGGTTGCAGCTGCGC
-TTGGCACAGATAACAGCTGCGGCTAATACAGGCCAACCAGAATGCTGCCAGCATCCTCCG
-GCTTAAGGGAGAGCATTGCTGCAACCAATGAGAGCTGTGCATGTGGGGAAGTCACCGACG
-GATTATGCAACTATCGAGGTAGCGGTTGGGAAGATGCAGCAATTTGTTAATGAAGATAGA
-GCGACAGGCAAAGTAGGTTGTTAAATGGAGTTCTCGTAACGCAGGACACCAACAGCACCA
-GCAATACGGCA
->9ac4d524-83af-4bac-a4c7-76be1b9cb92c
-ACGGTACTTCGTTCAGTTACATTATTGCTGGTGCTGGTAGACCCTGTTACGAGAACTCAT
-TTAATACTGCCTGTCGCTCTATCTTCTCATTAACAAATTGCGTCTTCCTACTACTACTGA
-TGGTTGTGATGGCTCCGTCGGTGACTTCATTACACAGCTTCGTGGTTGCAACAATGCTCT
-CTAACAAACCAGATGTTGGCATTCTGGTTGGCCACATATTGGGGCCGCAGCTGCTTTCTG
-TTATCTCTGTACCCTTGCTATTCCCATTTACCCAAGAGCTACCAATAACGGCACCTGCTC
-AAACGCTTTTATTCCTCCAGACGTGGACACAAGACCCTTGGATCTTGCGGATGGAGTCAT
-AGAAAGTGAGCAAGTGGTCAGTGTTCTGCCATGCCTCTAATGGAGACTTTTGCACACCTC
-ACCCATCCTTGGGCATATTCGGGGCAATTTGACTATGATTGACCCTTCTGAGACGAGGTG
-GCATAGCCATTGACTGCCTTATCTCTATCATAATTCACCCAGCTACGGAGGCCTGCGATC
-GAGAGCTGTCAGGCTGGATACAGCTCAATATCAATCCCGAGTTATCAGCATCAAGTGCCT
-GGATCTGGTAGAGGTTGGAGCCCATATTGGGCATCCTGAGTGAGCTGGTCGGGATCCAGG
-CCCTTCCCTGCTGTTTTTCTAATTTGCTAAACAATTGTGAACTAACTATAAGCAGTTGAG
-ATGGATCATTATCTGGTGTCCTATTTGATTCAGGAAAGCAGGTGAACTGCAGTCTTAGGG
-ATGCAACTTATTTTCGAGTTGTATTTGGCAATAGGTGTCTCTTCTCTCCAGCTTGGTGAA
-GGTAACCTCGCAATATCAGCACCAACAGAAAGGTTAAATGAGTTCTGCCTCGTAACAGGA
-CTGGCACAAACAATGCAATAACTAC
->2751bdce-4bb4-4d0a-ba04-6fcaaa1b7f93
-TTTAACATCAGTATGCTTCGTTCAGTTACGTATTGCTGGTGCTATTTGCGTCCTGTTACG
-AGAACTCATTTAACACTCTGTTGGTGCTGATGGCCCGAGGTTACCTCTACTAAGCTGGAG
-AAAAGAGACACACCATTGCCAAATACAATCACTTTCCAGAAAATAAAGTTGCATCCTAAG
-ACTGCAGTTCACCTGCTTTCCTGAATCAACATGACACCAGATAATGATCCATCTCAACTG
-CCCATAGTTGGATTCTTGTTTAGCAAATTAGAAAAACACGGGTAGAAGGGTCTGGATCCC
-GACCAGCTCATCAGACGCAATATGGGCTCCAAACCTTCTACCAGGATCCCAGCACTTCTG
-ATGCTGATAACTCTCCCGGATTATGCTGATGATGAGCTTTGTATCCGTCCTGACAAGCTC
-CCTTGACGGCGAGCCTCTTGCAGCTGGGAATTGTAGTGACGGGGAGATAAGGCAGTCAAT
-GTATACACCTCGCCTCAGACAGGGTCAATCTTAGTCAAATTGCTCCCAGGCCATGCCCAA
-GGATAGGAGCGTGTGCAAAGCCCCCATTAGAGGCATATAACAGAACACTGACTACTTTGC
-TCACTCCTCTTGGCGATTCATCCACCAAGATCAGGGTCTATGTCCACGTCTGGAGGGGAA
-CCAAAAAGCGCTTTATAGGTGCCGTTATTGGCAGTGTAGCTCTTGGGGTTGCAACAACGC
-ACAAATAACAGCAACTGCGGCCCTAATACAGGCCAACCAGAATACTTAACATCCTCGGCT
-TAAGGAGAGCATTGCTGCAACCAATGAAGCTGTGCATGAAGTCACCGACAGTTATCACAA
-CGCTATCAGTAGCAGTAGGGAAGATGCAGCAATTTGTTAATGAGAAGATAGAGCGACAGT
-AGAGTAGGTTAAATGAGTTCTCGTAACAGGACATAACAACTTTTTCAACAATAAG
diff -r 36cc4ae4160e -r 32cb27adeb34 test-data/variants.ref.fa
--- a/test-data/variants.ref.fa	Mon Dec 04 02:03:21 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,15 +0,0 @@
->cluster_0
-TCATTAACAAATGCTGCATCTTCCCTACTGCTACTGATAGTTGTGATAATCCGTCGGTGA
-CTTCATGCACAGCTTCATTGGTTGCAACAATGCTCTCCTTAAGCCGGAGGATGTTGGCAG
-CATTCTGGTTGGCCTGTATTGGGGCCGCAGCTGCTGTTATCTGTGCCGCTGTTGCAACCC
-CAAAGCTACACTGCCAATAACGGCACCTATAAAGCGCTTTTGTCTCCTTCCTCAGACGTG
-GACACAGACCCTTGGATCTTGCGGATGGAATCGCCAAGAGGAGTGANCAAAGTAGTCAGT
-GTTCTGTTATATGCCTCTAATGGNGGCTTTTGCACACGCCTCCTTATCCTTGGGCATATT
-CGGGAGCAATTTGACTATGATTGACCCTGTCTGAGACGAGGTGTATACATTGACTGCCTT
-ATCTCCTGTCACTACAATTCCTGCAGCTGCANGAGGCCTGCCGTCAAGGGAGCTTGTCAG
-ACGGATACAGCTCAATATCAGCATAATCCGAGTTATCAGCATCNAAGTGCTGGGATCCTG
-GTGAAGGTTTGGAGCCCATATTGCGTCCTGGATGAGCTGGTCGGGATCCAGACCCTTCTA
-CCGATGTTTTTCTAATTTGCTAAACAGGTGAACNAACTATAAGCAGTTGAGATGGATCAT
-TATCTGGTGTCATGTTGATTCAGGAAAGCAGGTGAACTGCAGTCTTAGGGATGCAACTTA
-TTTTCTGAAAGGATTGTATTTGGCAATGGTGTGTCTCTTCTCCAGCTTAGTAGAGGTAAC
-CTC