# HG changeset patch
# User iuc
# Date 1536836400 14400
# Node ID 9a0b65ad3c84e55a6fe62e04081c817f6deab702

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6

diff -r 000000000000 -r 9a0b65ad3c84 FilterUncorrectabledPEfastq.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/FilterUncorrectabledPEfastq.py	Thu Sep 13 07:00:00 2018 -0400
@@ -0,0 +1,85 @@
+"""
+author: adam h freedman
+afreedman405 at gmail.com
+data: Fri Aug 26 10:55:18 EDT 2016
+This script takes as an input Rcorrector error corrected Illumina paired-reads
+in fastq format and:
+1. Removes any reads that Rcorrector indentifes as containing an error,
+but can't be corrected, typically low complexity sequences. For these,
+the header contains 'unfixable'.
+2. Strips the ' cor' from headers of reads that Rcorrector fixed, to avoid
+issues created by certain header formats for downstream tools.
+3. Write a log with counts of (a) read pairs that were removed because one end
+was unfixable, (b) corrected left and right reads, (c) total number of
+read pairs containing at least one corrected read.
+Currently, this script only handles paired-end data, and handle either unzipped
+or gzipped files on the fly, so long as the gzipped files end with 'gz'.
+"""
+
+# import sys
+import argparse
+import gzip
+from itertools import izip_longest
+# izip
+from os.path import basename
+
+
+def get_input_streams(r1file, r2file):
+    if r1file[-2:] == 'gz':
+        r1handle = gzip.open(r1file, 'rb')
+        r2handle = gzip.open(r2file, 'rb')
+    else:
+        r1handle = open(r1file, 'r')
+        r2handle = open(r2file, 'r')
+    return r1handle, r2handle
+
+
+def grouper(iterable, n, fillvalue=None):
+    "Collect data into fixed-length chunks or blocks"
+    # grouper('ABCDEFG', 3, 'x') --> ABC DEF Gxx
+    args = [iter(iterable)] * n
+    return izip_longest(fillvalue=fillvalue, * args)
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description="options for filtering and logging rCorrector fastq outputs")
+    parser.add_argument('-1', '--left_reads', dest='leftreads', type=str, help='R1 fastq file')
+    parser.add_argument('-2', '--right_reads', dest='rightreads', type=str, help='R2 fastq file')
+    parser.add_argument('-o', '--out_prefix', dest='outprefix', type=str, help="prefix for filtered fastq output")
+    opts = parser.parse_args()
+    r1out = open(opts.outprefix + '_' + basename(opts.leftreads).replace('.gz', ''), 'w')
+    r2out = open(opts.outprefix + '_' + basename(opts.rightreads).replace('.gz', ''), 'w')
+    r1_cor_count = 0
+    r2_cor_count = 0
+    pair_cor_count = 0
+    unfix_count = 0
+    r1_stream, r2_stream = get_input_streams(opts.leftreads, opts.rightreads)
+    with r1_stream as f1, r2_stream as f2:
+        R1 = grouper(f1, 4)
+        R2 = grouper(f2, 4)
+        counter = 0
+        for entry in R1:
+            counter += 1
+            if counter % 100000 == 0:
+                print "%s reads processed" % counter
+            head1, seq1, placeholder1, qual1 = [i.strip() for i in entry]
+            head2, seq2, placeholder2, qual2 = [j.strip() for j in R2.next()]
+            if 'unfixable' in head1 or 'unfixable' in head2:
+                unfix_count += 1
+            else:
+                if 'cor' in head1:
+                    r1_cor_count += 1
+                if 'cor' in head2:
+                    r2_cor_count += 1
+                if 'cor' in head1 or 'cor' in head2:
+                    pair_cor_count += 1
+                head1 = head1.split('l:')[0][:-1]  # keeps all before the low kmer count statistic and removes the trailing whitespace character
+                head2 = head2.split('l:')[0][:-1]
+                # head1 = head1.replace(' cor', '')
+                # head2 = head2.replace(' cor', '')
+                r1out.write('%s\n' % '\n'.join([head1, seq1, placeholder1, qual1]))
+                r2out.write('%s\n' % '\n'.join([head2, seq2, placeholder2, qual2]))
+    unfix_log = open('rmunfixable.log', 'w')
+    unfix_log.write('total PE reads:%s\nremoved PE reads:%s\nretained PE reads:%s\nR1 corrected:%s\nR2 corrected:%s\npairs corrected:%s\n' % (counter, unfix_count, counter - unfix_count, r1_cor_count, r2_cor_count, pair_cor_count))
+    r1out.close()
+r2out.close()
diff -r 000000000000 -r 9a0b65ad3c84 rcorrector.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rcorrector.xml	Thu Sep 13 07:00:00 2018 -0400
@@ -0,0 +1,136 @@
+<tool id="rcorrector" name="RNA-seq Rcorrector" version="1.0.3">
+	<description>a kmer-based error correction method for RNA-seq data</description>
+    <requirements>
+        <requirement type="package" version="1.0.3">rcorrector</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        #if $library.lib == "single":
+            ln -s '$library.input1' input_1.fq &&
+        #end if
+        #if $library.lib == "paired":
+            ln -s '$library.input1' input_1.fq && ln -s '$library.input2' input_2.fq &&
+        #end if
+        run_rcorrector.pl
+        #if $library.lib == "single":
+            -s input_1.fq
+        #end if
+        #if $library.lib == "paired":
+            -1 input_1.fq -2 input_2.fq
+        #end if
+        -k '$advanced.kmers' -t \${GALAXY_SLOTS:-4} -maxcorK '$advanced.maxcorK' -wk '$advanced.wk' -ek '$advanced.ek' -od output_file_directory 
+        
+        #if $library.lib == "paired":
+            #if $library.filter:
+                && python '$__tool_directory__/FilterUncorrectabledPEfastq.py'
+                -1 output_file_directory/input_1.cor.fq -2 output_file_directory/input_2.cor.fq -o fixed 2>&1 > rmunfixable.log && cat rmunfixable.log
+            #end if
+        #end if
+    ]]></command>
+    <inputs>
+        <conditional name="library">
+            <param name="lib" type="select" label="Is this library paired- or single-end?">
+                <option value="single">single</option>
+                <option value="paired" selected="True">paired</option>
+            </param>
+            <when value="single">
+                <param type="data" name="input1" label="FastQ file" format="fastq,fastqsanger" />
+            </when>
+            <when value="paired">
+                <param type="data" name="input1" label="FastQ file R1 (left)" format="fastq,fastqsanger" />
+                <param type="data" name="input2" label="FastQ file R2 (right)" format="fastq,fastqsanger" />
+                <param name="filter" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Filter uncorrectable reads" help="This will run FilterUncorrectabledPEfastq and remove uncorrectable reads."/>
+            </when>
+        </conditional> 
+        <conditional name="advanced">
+            <param name="adv" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Additional options"/>
+            <when value="TRUE">
+                <param name="kmers" label="kmer length" value="23" max="32" type="integer" help="(smaller 33, default: 23)"/>
+                <param name="maxcorK" label="max correction within k-bp window" value="4" type="integer" help="the maximum number of correction within k-bp window (default: 4)"/>
+                <param name="wk" label="estimate weak kmer count" value="0.95" type="float" help="the proportion of kmers that are used to estimate weak kmer count threshold, lower for more divergent genome (default: 0.95)"/>
+                <param name="ek" label="expected number of kmers" value="100000000" type="integer" help="expected_number_of_kmers: does not affect the correctness of program but affect the memory usage (default: 100000000)"/>
+            </when>
+            <when value="FALSE">
+                <param name="kmers" value="23" type="hidden"/>
+                <param name="maxcorK" value="4" type="hidden"/>
+                <param name="wk" value="0.95" type="hidden"/>
+                <param name="ek" value="100000000" type="hidden"/>
+            </when>
+        </conditional> 
+    </inputs>
+    <outputs>
+        <data name="output1" format="fastq" label="${tool.name} on ${on_string}" from_work_dir="output_file_directory/input_1.cor.fq">
+            <filter>library['lib'] == 'single'</filter>
+        </data> 
+        <data name="output2" format="fastq" label="${tool.name} on ${on_string}: cor R1" from_work_dir="output_file_directory/input_1.cor.fq">
+            <filter>library['lib'] == 'paired' and library['filter'] is False</filter>
+        </data> 
+        <data name="output3" format="fastq" label="${tool.name} on ${on_string}: cor R2" from_work_dir="output_file_directory/input_2.cor.fq"> 
+            <filter>library['lib'] == 'paired' and library['filter'] is False</filter>
+        </data> 
+        <data name="output4" format="fastq" label="${tool.name} on ${on_string}: fixed R1" from_work_dir="fixed_input_1.cor.fq">
+            <filter>library['lib'] == 'paired' and library['filter']</filter>
+        </data> 
+        <data name="output5" format="fastq" label="${tool.name} on ${on_string}: fixed R2" from_work_dir="fixed_input_2.cor.fq"> 
+            <filter>library['lib'] == 'paired' and library['filter']</filter>
+        </data> 
+    </outputs>
+	<tests>
+        <test>
+            <conditional name="library">
+                <param name="lib" value="paired"/>
+                <param name="input1" value="sample_read1.fq" ftype="fastq"/>
+                <param name="input2" value="sample_read2.fq" ftype="fastq"/>
+            </conditional>
+            <conditional name="advanced">
+                <param name="kmers" value="23"/>
+                <param name="maxcorK" value="4"/>
+                <param name="wk" value="0.95"/>
+                <param name="ek" value="100000000"/>
+            </conditional>
+            <output name="output2" file="sample_read1.cor.fq" ftype="fastq"/>
+            <output name="output3" file="sample_read2.cor.fq" ftype="fastq"/>
+        </test>
+        <test>
+            <conditional name="library">
+                <param name="lib" value="paired"/>
+                <param name="input1" value="sample_read1.fq" ftype="fastq"/>
+                <param name="input2" value="sample_read2.fq" ftype="fastq"/>
+                <param name="filter" value="TRUE"/>
+            </conditional>
+            <conditional name="advanced">
+                <param name="kmers" value="23"/>
+                <param name="maxcorK" value="4"/>
+                <param name="wk" value="0.95"/>
+                <param name="ek" value="100000000"/>
+            </conditional>
+            <output name="output2" file="fixed_sample_read1.cor.fq" compare="sim_size"/>
+            <output name="output3" file="fixed_sample_read2.cor.fq" compare="sim_size"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+What is Rcorrector?
+
+Rcorrector (RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data.
+Rcorrector can also be applied to other type of sequencing data where the read coverage is non-uniform, such as single-cell sequencing.
+
+Uncorrectable paired-end reads can be removed using FilterUncorrectabledPEfastq.
+
+More informations, see citations.
+
+    ]]>
+    </help>
+    <citations>
+        <citation type="doi">10.1186/s13742-015-0089-y</citation>
+        <citation type="bibtex">
+            @misc{githubFilterUncorrectabledPEfastq,
+            author = {Adam H. Freedman},
+            year = {2016},
+            title = {FilterUncorrectabledPEfastq},
+            publisher = {GitHub},
+            journal = {GitHub repository},
+            url = {https://github.com/harvardinformatics/TranscriptomeAssemblyTools/blob/master/FilterUncorrectabledPEfastq.py}
+            }
+        </citation>
+    </citations>
+</tool>
diff -r 000000000000 -r 9a0b65ad3c84 test-data/fixed_sample_read1.cor.fq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fixed_sample_read1.cor.fq	Thu Sep 13 07:00:00 2018 -0400
@@ -0,0 +1,80 @@
+@Id_4 Part1.fastq.000000008 contig=chr1:317720-453948W:ENST00000445840.1:2:180:5:85:S/1 haplotype=0 length=100 orig_begin=0 orig_end=76 haplotype_infix=GCAGGACAAGTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTG edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMEMMMMMM strand=forward exp=medium
+GCAGGACAAGTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTG
++
+EBHA>BE<<B?FG=9GB>ACGD;>B:C@@<A@;@7<:D084:H<;7::/5094=A169688=$=66B.0:A05169
+@Id_6 Part1.fastq.000000012 contig=chr1:317720-453948W:ENST00000445840.1:4:180:-6:131:S/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=GTTTCACAGCTGCAGGACAAGTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCA edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+GTTTCACAGCTGCAGGACAAGTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCA
++
+C>A=D=FJF><;DA@IGJ:I99>GC:>?<D8AB<;;C9=279<26<=-:E5?D;44@36=48.8=58F-:C524*0.C3)62M--,!%>/>,4-,04*.+
+@Id_8 Part1.fastq.000000016 contig=chr1:317720-453948W:ENST00000445840.1:6:180:12:230:S/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=AAGTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATAGATTTTTATAAAATGA edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+AAGTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATAGATTTTTATAAAATGA
++
+;HBDE@I=GB@ABAM9<>B;G><FD>D=CA?9EA=A:B;97:+?/7588:9@:39)4;;/2:48329651(.;A5/*2*5#:2@;!/*"42.,0C1)--&
+@Id_12 Part1.fastq.000000024 contig=chr1:317720-453948W:ENST00000445840.1:10:180:19:72:S/2 haplotype=0 length=100 orig_begin=0 orig_end=49 haplotype_infix=AGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGA edit_string=MMMMMMMMMMMMMMMMMMEMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+AGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGA
++
+GCLII<FH>DI=@EBFB5P@GBE8=89B9;G@IA<=B>A;879A;77;8
+@Id_13 Part1.fastq.000000026 contig=chr1:317720-453948W:ENST00000445840.1:11:180:3:115:S/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=CTGCAGGACAAGTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATAGATTTTT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMEMMMMMMMMMMMMMMEMMMMMMMEMMMEMM strand=forward exp=medium
+CTGCAGGACAAGTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATAGATTTTT
++
+H=ACCD?D7EBGCAGGHEEBA9?7<6=G@8;8??74?A@6A<6:74>1<37/>>E8<1<::7;3:5+8-A8*)9#+229633.0+1,.,7+*!!,0-!%+
+@Id_14 Part1.fastq.000000028 contig=chr1:317720-453948W:ENST00000445840.1:12:180:-11:166:S/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=CATTGGTTTCACAGCTGCAGGACAAGTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGA edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+CATTGGTTTCACAGCTGCAGGACAAGTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGA
++
+EHCHB?F?@G@FA8G>?D;5<8+=G;3F<@>7G7@<69@K2<1>??E46>6325A5@-D79176:5&,35M57))2*41:)>!4502!,!!(1)4&%3*'
+@Id_15 Part1.fastq.000000030 contig=chr1:317720-453948W:ENST00000445840.1:13:180:-25:144:S/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=GTGTCACAACTGCACATTGGTTTCACAGCTGCAGGACAAGTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAA edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMEMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+GTGTCACAACTGCACATTGGTTTCACAGCTGCAGGACAAGTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAA
++
+CA?B>BK@HKJ?C@DC;:9>9<@BC<>@B;C==8B>HO;94CB@72D97?4F<7>?GC8?,63)76981C9365?A->94#8)7+2!*/18%&3':,$&8
+@Id_18 Part1.fastq.000000036 contig=chr1:317720-453948W:ENST00000445840.1:16:180:26:182:S/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=TAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATAGATTTTTATAAAATGAAAGCTGCCTCTGAA edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+TAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATAGATTTTTATAAAATGAAAGCTGCCTCTGAA
++
+@B>FBB;A>?C=FAC;???B9=?::>;E?=>;?8A99?9,?66;;==0-9DH5;8EC,7*93A6.7&A056?(*&635)=:G1/74&5"./)&7?)5.*%
+@Id_19 Part1.fastq.000000038 contig=chr1:317720-453948W:ENST00000445840.1:17:180:-1:127:S/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=ACAGCTGCAGGACAAGTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATAGAT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMEM strand=forward exp=medium
+ACAGCTGCAGGACAAGTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATAGAT
++
+?CAEJHG<<E>:C?CAE>?9I;=E;;;9>:63;G=C:858<?G=:=5-/-05955E/E/J-53-=;+2?-?',31::;0/C5A.-.,-&7++4686297&
+@Id_20 Part1.fastq.000000040 contig=chr1:317720-453948W:ENST00000445840.1:18:180:1:173:S/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=AGCTGCAGGACAAGTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATAGATTT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+AGCTGCAGGACAAGTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATAGATTT
++
+@EACA@?>=EEI@AEB679J<96AJ:9=H2@<B?6D778;5B692>;9<B6?750(@:@5-)332=/154*6-.E6(,/.(>.+%+>&6E%4(./,14(4
+@Id_21 Part1.fastq.000000042 contig=chr1:317720-453948W:ENST00000445840.1:19:180:-19:117:S/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=CAACTGCACATTGGTTTCACAGCTGCAGGACAAGTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTG edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+CAACTGCACATTGGTTTCACAGCTGCAGGACAAGTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTG
++
+BE>EBH@F?=AD?DFG@=5<<?5=G<3>4@6<E>B-<>B:8>16.;7/;9>:4&::/249=?>64F">-/2<!?/9+58%2321?&805'!8/2#5$3!5
+@Id_26 Part1.fastq.000000052 contig=chr1:317720-453948W:ENST00000445840.1:24:180:50:207:S/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=AAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATAGATTTTTATAAAATGAAAGCTGCCTCTGAAGCACTGCAGACTCAGCTGAGCACC edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMEMMMMMMMMMMMMMMMMMMEMMMMMMMMMMMMMMMMMMMMEMMMMMMMMM strand=forward exp=medium
+AAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATAGATTTTTATAAAATGAAAGCTGCCTCTGAAGCACTGCAGACTCAGCTGAGCACC
++
+H@JADFG@;;8A@@B@@>:<9C?DA<><:=@5;5:?:987D5<AA??E;3)68J/<<?767=8;5:3='!*(%/+!,09)'&*&206*0+-B"!78;%!/
+@Id_27 Part1.fastq.000000054 contig=chr1:317720-453948W:ENST00000445840.1:25:180:14:194:S/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=GTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATAGATTTTTATAAAATGAAA edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+GTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATAGATTTTTATAAAATGAAA
++
+GD@C@I@HB><B@A;?@>:;7H;A03:=:A@A?=:?75H=?DB7@:?4;4118B13.54B/0-1:999')I:3.*4>492/"61365C!-<0%45104K#
+@Id_29 Part1.fastq.000000058 contig=chr1:317720-453948W:ENST00000445840.1:27:180:47:118:S/2 haplotype=0 length=100 orig_begin=0 orig_end=67 haplotype_infix=GATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATAGATTTTTATAAAATGAAA edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+GATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATAGATTTTTATAAAATGAAA
++
+M@C?AC<AEE;CB7?C:?E>@A9==?6BE:E57>:9-:5E7C2<15=-7+6/=?68>@)67.7.3E3
+@Id_32 Part1.fastq.000000064 contig=chr1:317720-453948W:ENST00000445840.1:30:180:32:142:S/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=GATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATAGATTTTTATAAAATGAAAGCTGCCTCTGAAGCACTG edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+GATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATAGATTTTTATAAAATGAAAGCTGCCTCTGAAGCACTG
++
+EGC>==@>HB@=;G8D8@;B:?@@=>47D6:8H2?<=6:>=@83/<749:4-6B)3@,(=:B<:+A5*9'!)"6;<'1=&)4-&)%!(7/+3*;$+'/2!
+@Id_33 Part1.fastq.000000066 contig=chr1:317720-453948W:ENST00000445840.1:31:180:-4:196:S/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=TTCACAGCTGCAGGACAAGTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATA edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMEMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+TTCACAGCTGCAGGACAAGTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATA
++
+IIJFD@DCA@>B?DBHEA6@BH>:5?8A;GC7>94B9;52=<E=9-?E@2(9+@951569>65*46=@.-:/';:4*;@%?*--+-*9,3(,&".(5"('
+@Id_34 Part1.fastq.000000068 contig=chr1:317720-453948W:ENST00000445840.1:32:180:44:221:S/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=GGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATAGATTTTTATAAAATGAAAGCTGCCTCTGAAGCACTGCAGACTCAGCTG edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+GGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATAGATTTTTATAAAATGAAAGCTGCCTCTGAAGCACTGCAGACTCAGCTG
++
+HG><DLADHBCG@?E??GDJC=@=CH@7>>=?>8E<=<B:577;0FE>@5A;>/,)988A/3255/+><A(0;+&/6*)7;9.-$3+:3+1+5./(:/!$
+@Id_36 Part1.fastq.000000072 contig=chr1:317720-453948W:ENST00000445840.1:34:180:24:196:S/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=CTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATAGATTTTTATAAAATGAAAGCTGCCTCTG edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+CTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATAGATTTTTATAAAATGAAAGCTGCCTCTG
++
+KLAD8@B;EA><;?<<DCE:;>5A;ABE<I?B;7=4-AB8D7.+A:?5>*2-23@75";4-7.9@3-<<B503!22(/4.(+65&6,2**,.-0,!,,*5
+@Id_37 Part1.fastq.000000074 contig=chr1:317720-453948W:ENST00000445840.1:35:180:87:166:S/2 haplotype=0 length=100 orig_begin=0 orig_end=75 haplotype_infix=GAAATCATAGATTTTTATAAAATGAAAGCTGCCTCTGAAGCACTGCAGACTCAGCTGAGCACCGATACAAAGAAA edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMEM strand=forward exp=medium
+GAAATCATAGATTTTTATAAAATGAAAGCTGCCTCTGAAGCACTGCAGACTCAGCTGAGCACCGATACAAAGAAA
++
+IJHHCLNF=?QG;<FEA@F6B9A7BBCBA?;DC:9:B6::9<7:<A,>I,@L>C8>0<=;07@1378')91;7)5
+@Id_38 Part1.fastq.000000076 contig=chr1:317720-453948W:ENST00000445840.1:36:180:-41:170:S/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=CAGCCACACTGCTTTGGTGTCACAACTGCACATTGGTTTCACAGCTGCAGGACAAGTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCT edit_string=MMMMMMMMMMMEMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+CAGCCACACTGATTTGGTGTCACAACTGCACATTGGTTTCACAGCTGCAGGACAAGTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCT
++
+ABGGMJFA?BCGQHD96JH>G4B9=1@??D@=4:2-B9=6<993:3C>1?:9<6:11B8A25.95<1/?'5D=5<8.5-)#6:+2@&5!F/.#4)!#1!(
diff -r 000000000000 -r 9a0b65ad3c84 test-data/fixed_sample_read2.cor.fq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fixed_sample_read2.cor.fq	Thu Sep 13 07:00:00 2018 -0400
@@ -0,0 +1,80 @@
+@Id_4 Part1.fastq.000000009 contig=chr1:317720-453948W:ENST00000445840.1:2:180:5:85:A/2 haplotype=0 length=100 orig_begin=0 orig_end=76 haplotype_infix=CCTTCCAGTTGTTTTTTCTCTTCCTCGAGCTTCCTTATCTCCTCCTGTTGAATCATTTTAAGATGCTCGAACTTGT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+CCTTCCAGTTGTTTTTTCTCTTCCTCGAGCTTCCTTATCTCCTCCTGTTGAATCATTTTAAGATGCTCGAACTTGT
++
+E8HCG>;DFBG?@CG@B?D:AQAD5.;9>7@>@:8=<20J;68<<706;B==:8505278D<64.F=02'5>0=1:
+@Id_6 Part1.fastq.000000013 contig=chr1:317720-453948W:ENST00000445840.1:4:180:-6:131:A/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=CAGTGCTTCAGAGGCAGCTTTCATTTTATAAAAATCTATGATTTCTCCTTCCAGTTGTTTTTTCTCTTCCTCGAGCTTCCTTATCTCCTCCTGTTGAATC edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+CAGTGCTTCAGAGGCAGCTTTCATTTTATAAAAATCTATGATTTCTCCTTCCAGTTGTTTTTTCTCTTCCTCGAGCTTCCTTATCTCCTCCTGTTGAATC
++
+HDLBAAACCA<K;=9<@@BC>@=JG>7<:A=BG@9+=6A8+<AB;339:6>6=49L<15<39+0&1:2.1/260('';1003=0)A*.-*,";$/61+"#
+@Id_8 Part1.fastq.000000017 contig=chr1:317720-453948W:ENST00000445840.1:6:180:12:230:A/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTCTTACGATGTTTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGC edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTCTTACGATGTTTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGC
++
+?ECI@F@IEAFF8F?9<@@:9@BA4@@??@C:1D89=><=58915P259+JE=:5719A,->0,-5125%@7(=1/>.-.!&60!/=5,6*8/5,*3'68
+@Id_12 Part1.fastq.000000025 contig=chr1:317720-453948W:ENST00000445840.1:10:180:19:72:A/1 haplotype=0 length=100 orig_begin=0 orig_end=49 haplotype_infix=TTTTCTCTTCCTCGAGCTTCCTTATCTCCTCCTGTTGAATCATTTTAAG edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+TTTTCTCTTCCTCGAGCTTCCTTATCTCCTCCTGTTGAATCATTTTAAG
++
+ADD@DDD@9GA=>M:DCG=:;>884==;>B;6;9;<@9<@/F=H@7=A9
+@Id_13 Part1.fastq.000000027 contig=chr1:317720-453948W:ENST00000445840.1:11:180:3:115:A/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=GCTTTCATTTTATAAAAATCTATGATTTCTCCTTCCAGTTGTTTTTTCTCTTCCTCGAGCTTCCTTATCTCCTCCTGTTGAATCATTTTAAGATGCTCGA edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+GCTTTCATTTTATAAAAATCTATGATTTCTCCTTCCAGTTGTTTTTTCTCTTCCTCGAGCTTCCTTATCTCCTCCTGTTGAATCATTTTAAGATGCTCGA
++
+GH@EIFABFCAC@H@:7?AH>9==::A9=:@;@D>?B;99;6:;BHA-2=55383<*-=C:4C98+/==!(*&:*=#0-315(45()=B36*+/+3%>36
+@Id_14 Part1.fastq.000000029 contig=chr1:317720-453948W:ENST00000445840.1:12:180:-11:166:A/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=TTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCATTTTATAAAAATCTATGATTTCTCCTTCCAGTTGTTTTTTCT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMEMMMMMMMMMMMMMMMMM strand=forward exp=medium
+TTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCATTTTATAAAAATCTATGATTTCTCCTTCCAGTTGTTTTTTCT
++
+FEEGE<IAGGDEBA:CB84>94FC?77EF9D8?<<D5::<=F5=@7??D9974??;C6*CE357+-2,26?D!2=/:#*/5&!.,2)%).#$&+1F4!)0
+@Id_15 Part1.fastq.000000031 contig=chr1:317720-453948W:ENST00000445840.1:13:180:-25:144:A/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=TCAGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCATTTTATAAAAATCTATGATTTCTCCTTCCAGTTGTTTTTTCTCTTCCTCGAGCTTCCTTATCTC edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+TCAGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCATTTTATAAAAATCTATGATTTCTCCTTCCAGTTGTTTTTTCTCTTCCTCGAGCTTCCTTATCTC
++
+@HBDE@C@G<:?K;@@<>>AE:8=;G;;BB9877<0I7=3<=?92FD::->BC39715+;-F840:=A5/;%<*853#")6%&4#1$).!631)3!$+!-
+@Id_18 Part1.fastq.000000037 contig=chr1:317720-453948W:ENST00000445840.1:16:180:26:182:A/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=TTTCTTCTTACGATGTTTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCATTTTATAAAAATCTATGATTTCTCCT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMEMMMMMMMMMMMM strand=forward exp=medium
+TTTCTTCTTACGATGTTTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCATTTTATAAAAATCTATGATTTCTCCT
++
+CIBLCIDCL>GBJ<BB;?=CC?@?=;@7:9=2EA<D<98/F@<;>33A<9111753@3806B4;B>(47368*,1!B6110,(&;/1/'->73*!4/)!+
+@Id_19 Part1.fastq.000000039 contig=chr1:317720-453948W:ENST00000445840.1:17:180:-1:127:A/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=GCTTCAGAGGCAGCTTTCATTTTATAAAAATCTATGATTTCTCCTTCCAGTTGTTTTTTCTCTTCCTCGAGCTTCCTTATCTCCTCCTGTTGAATCATTT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+GCTTCAGAGGCAGCTTTCATTTTATAAAAATCTATGATTTCTCCTTCCAGTTGTTTTTTCTCTTCCTCGAGCTTCCTTATCTCCTCCTGTTGAATCATTT
++
+LCNACHCG@>L;4>>@B=ACC;A<8E4<9<;9A;C=;??9B?<54E55<9G1:41=*;28?23-7A8>-.0302,-A+$.<2:)0@-0!51!,03)!.!:
+@Id_20 Part1.fastq.000000041 contig=chr1:317720-453948W:ENST00000445840.1:18:180:1:173:A/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=ACGATGTTTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCATTTTATAAAAATCTATGATTTCTCCTTCCAGTTGT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+ACGATGTTTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCATTTTATAAAAATCTATGATTTCTCCTTCCAGTTGT
++
+;BECDDH@AAKDK;>A6>D?7BEA===A;@F6A@:8=C9;8D8297?@,B..5:6,264262C'.:B844)0=C11-'4=.5!/!/4;7290"6/,1?7(
+@Id_21 Part1.fastq.000000043 contig=chr1:317720-453948W:ENST00000445840.1:19:180:-19:117:A/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=CAGCTTTCATTTTATAAAAATCTATGATTTCTCCTTCCAGTTGTTTTTTCTCTTCCTCGAGCTTCCTTATCTCCTCCTGTTGAATCATTTTAAGATGCTC edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+CAGCTTTCATTTTATAAAAATCTATGATTTCTCCTTCCAGTTGTTTTTTCTCTTCCTCGAGCTTCCTTATCTCCTCCTGTTGAATCATTTTAAGATGCTC
++
+C@BB?AB>CH>@86D>9A9DH??;6EDA9@;@:535@615?J?>0DIH3?A9?<839<8B859/,122-3*+254+7*5B/2:;1/&35&883)5%1(1>
+@Id_26 Part1.fastq.000000053 contig=chr1:317720-453948W:ENST00000445840.1:24:180:50:207:A/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=TTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTCTTACGATGTTTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCAT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+TTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTCTTACGATGTTTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCAT
++
+FA>CGDB?;HJ??EIDB>=D;;?6:9E:B@6;;>55<:@0:;EC:76-4<<+,=0=<9:;,/A7-<:3#+;?>5<05$3&$>.,'/9*7:B-%,:/3)+-
+@Id_27 Part1.fastq.000000055 contig=chr1:317720-453948W:ENST00000445840.1:25:180:14:194:A/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=TTTTTTTTTTTTTTTCTTCTTACGATGTTTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCATTTTATAAAAATCT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+TTTTTTTTTTTTTTTCTTCTTACGATGTTTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCATTTTATAAAAATCT
++
+DJ@DCE8LCFHGL?;<<OKF>AC?AE<<<=BC3A8@76C82;?9A7C;D==801?<;998639(-1819>1>42-3=7;(-*0<9/CA.10A0($)-//"
+@Id_29 Part1.fastq.000000059 contig=chr1:317720-453948W:ENST00000445840.1:27:180:47:118:A/1 haplotype=0 length=100 orig_begin=0 orig_end=67 haplotype_infix=GCAGCTTTCATTTTATAAAAATCTATGATTTCTCCTTCCAGTTGTTTTTTCTCTTCCTCGAGCTTCC edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+GCAGCTTTCATTTTATAAAAATCTATGATTTCTCCTTCCAGTTGTTTTTTCTCTTCCTCGAGCTTCC
++
+CF?CCDE>HDJGEF>5>?B8B<CF9CB6DF;<<@;.?9=>97F=;C614335<3;265)0:7+:@6=
+@Id_32 Part1.fastq.000000065 contig=chr1:317720-453948W:ENST00000445840.1:30:180:32:142:A/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=AGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCATTTTATAAAAATCTATGATTTCTCCTTCCAGTTGTTTTTTCTCTTCCTCGAGCTTCCTTATCTCCT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMEMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+AGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCATTTTATAAAAATCTATGATTTCTCCTTCCAGTTGTTTTTTCTCTTCCTCGAGCTTCCTTATCTCCT
++
+KCA;@8GA?5@<EA?AB@=>??8FG8CAD>?;B?D<246;8=F@C99/9@E8ACB4<1>++&H6621323/(9+:(A9D&(9124!-4..++3<-202/2
+@Id_33 Part1.fastq.000000067 contig=chr1:317720-453948W:ENST00000445840.1:31:180:-4:196:A/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=TTTTTTTTTTTTTTTTTCTTCTTACGATGTTTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCATTTTATAAAAAT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMEM strand=forward exp=medium
+TTTTTTTTTTTTTTTTTCTTCTTACGATGTTTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCATTTTATAAAAAT
++
+DLFJBEFIC@I5K;A;<=98:HE<+D6<>D=3<-1B/>;9248>88A:2822>A:<88B4,:1F)518>8>C%,=1A95:<>+/%,4-;5(98;G)($+!
+@Id_34 Part1.fastq.000000069 contig=chr1:317720-453948W:ENST00000445840.1:32:180:44:221:A/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTCTTACGATGTTTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGCAGTGCTTCA edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTCTTACGATGTTTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGCAGTGCTTCA
++
+HEFG@F=88?J<CBH;=:BAEF?GDH@<<6B=2QF><?>D6<7C7C=:;C87D5*:7%>9638+@;>+?0)!*29<;1+.6&7429*8%,:?0370'+((
+@Id_36 Part1.fastq.000000073 contig=chr1:317720-453948W:ENST00000445840.1:34:180:24:196:A/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=TTTTTTTTTTTTTTTTTCTTCTTACGATGTTTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCATTTTATAAAAAT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMEMM strand=forward exp=medium
+TTTTTTTTTTTTTTTTTCTTCTTACGATGTTTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCATTTTATAAAAAT
++
+FGF>E?DJGA<9B@EC<CKADE;7.FF75C>696<A6?2?6<5:=895<A00=B.>:536<16%+?9A48<0:,;(&088%.1)76$4(8433#.+*1,!
+@Id_37 Part1.fastq.000000075 contig=chr1:317720-453948W:ENST00000445840.1:35:180:87:166:A/1 haplotype=0 length=100 orig_begin=0 orig_end=75 haplotype_infix=TTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCATTTTATAAAAATCTATG edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+TTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCATTTTATAAAAATCTATG
++
+>E?ABEH@==G@;A8<J@?>@==CBDC;<?D8A=9?>9F:B8;A<47<231568BC0!??.26-49C(1B484.4
+@Id_38 Part1.fastq.000000077 contig=chr1:317720-453948W:ENST00000445840.1:36:180:-41:170:A/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=ATGTTTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCATTTTATAAAAATCTATGATTTCTCCTTCCAGTTGTTTT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMEMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+ATGTTTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCATTTTATAAAAATCTATGATTTCTCCTTCCAGTTGTTTT
++
+HHFIB?BF>:9=E7BC687F=?@;9>CBA==?;8C0I0E8C/5C/@669;=.71<092=846CG.%@5=A<:/*40!9.215==6'-&,717)!6'3".6
diff -r 000000000000 -r 9a0b65ad3c84 test-data/sample_read1.cor.fq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample_read1.cor.fq	Thu Sep 13 07:00:00 2018 -0400
@@ -0,0 +1,140 @@
+@Id_4 Part1.fastq.000000008 contig=chr1:317720-453948W:ENST00000445840.1:2:180:5:85:S/1 haplotype=0 length=100 orig_begin=0 orig_end=76 haplotype_infix=GCAGGACAAGTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTG edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMEMMMMMM strand=forward exp=medium l:10 m:19 h:23 cor
+GCAGGACAAGTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTG
++
+EBHA>BE<<B?FG=9GB>ACGD;>B:C@@<A@;@7<:D084:H<;7::/5094=A169688=$=66B.0:A05169
+@Id_5 Part1.fastq.000000010 contig=chr1:317720-453948W:ENST00000445840.1:3:180:158:302:S/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=GAAAGACAAACATCGTAAGAAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMEM strand=forward exp=medium l:3 m:1824 h:1824 unfixable_error
+GAAAGACAAACATCGTAAGAAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACA
++
+CG?FA?ACE56E?C=>?;B><:<9AJ=@>@7=8=@G0CE9E84?8:D4:A83@/<?226-A//?.7>)08+;):2A88/.*&&;+;)!/-3!!I!/!)5;
+@Id_6 Part1.fastq.000000012 contig=chr1:317720-453948W:ENST00000445840.1:4:180:-6:131:S/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=GTTTCACAGCTGCAGGACAAGTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCA edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium l:5 m:19 h:23
+GTTTCACAGCTGCAGGACAAGTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCA
++
+C>A=D=FJF><;DA@IGJ:I99>GC:>?<D8AB<;;C9=279<26<=-:E5?D;44@36=48.8=58F-:C524*0.C3)62M--,!%>/>,4-,04*.+
+@Id_7 Part1.fastq.000000014 contig=chr1:317720-453948W:ENST00000445840.1:5:180:321:438:S/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium l:1824 m:1824 h:1824 unfixable_error
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
++
+FIJC>CEAE<B=>CF?=E9CBD<F9E?B357AF548D9;<5<=+<E:,6=D0;2<33+9'96@'/082'5<-<2+,:-2,73&3528$*6+#7!#5<!1>
+@Id_8 Part1.fastq.000000016 contig=chr1:317720-453948W:ENST00000445840.1:6:180:12:230:S/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=AAGTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATAGATTTTTATAAAATGA edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium l:12 m:19 h:23
+AAGTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATAGATTTTTATAAAATGA
++
+;HBDE@I=GB@ABAM9<>B;G><FD>D=CA?9EA=A:B;97:+?/7588:9@:39)4;;/2:48329651(.;A5/*2*5#:2@;!/*"42.,0C1)--&
+@Id_9 Part1.fastq.000000018 contig=chr1:317720-453948W:ENST00000445840.1:7:180:245:432:S/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMEMMMMMMMEMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium l:1 m:1824 h:1824 unfixable_error
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
++
+EDAJ>J@=E8:=D<>A?ED?AB:<DFB6B>H7AE3;B;><(:84:D0D=836D)>+3C:3-004$B.?C4=7;32293:C+0+&&?.(!'+(,!10?.,&
+@Id_10 Part1.fastq.000000020 contig=chr1:317720-453948W:ENST00000445840.1:8:180:188:421:S/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium l:1824 m:1824 h:1824 unfixable_error
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
++
+?FCGICCB7HDKED8CBD=99?=BKF77A=:55>AI>9A8><0@;674/@::>,?9+<:*(763,A<8/0?&)+(!%)<';6,-(@&5%*'$%7#=0.&?
+@Id_11 Part1.fastq.000000022 contig=chr1:317720-453948W:ENST00000445840.1:9:180:248:450:S/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium l:1824 m:1824 h:1824 unfixable_error
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
++
+@CEGCC@C=FM@?DDFD>?:6<>E=G9;6D9=6?:8>=2=.3:0?2/>4>585=34/;?-0)2>;46;.65??,+/(*6$91/'E750;/20*/=&4./;
+@Id_12 Part1.fastq.000000024 contig=chr1:317720-453948W:ENST00000445840.1:10:180:19:72:S/2 haplotype=0 length=100 orig_begin=0 orig_end=49 haplotype_infix=AGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGA edit_string=MMMMMMMMMMMMMMMMMMEMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium l:15 m:19 h:21 cor
+AGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGA
++
+GCLII<FH>DI=@EBFB5P@GBE8=89B9;G@IA<=B>A;879A;77;8
+@Id_13 Part1.fastq.000000026 contig=chr1:317720-453948W:ENST00000445840.1:11:180:3:115:S/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=CTGCAGGACAAGTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATAGATTTTT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMEMMMMMMMMMMMMMMEMMMMMMMEMMMEMM strand=forward exp=medium l:9 m:19 h:23 cor
+CTGCAGGACAAGTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATAGATTTTT
++
+H=ACCD?D7EBGCAGGHEEBA9?7<6=G@8;8??74?A@6A<6:74>1<37/>>E8<1<::7;3:5+8-A8*)9#+229633.0+1,.,7+*!!,0-!%+
+@Id_14 Part1.fastq.000000028 contig=chr1:317720-453948W:ENST00000445840.1:12:180:-11:166:S/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=CATTGGTTTCACAGCTGCAGGACAAGTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGA edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium l:4 m:18 h:23
+CATTGGTTTCACAGCTGCAGGACAAGTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGA
++
+EHCHB?F?@G@FA8G>?D;5<8+=G;3F<@>7G7@<69@K2<1>??E46>6325A5@-D79176:5&,35M57))2*41:)>!4502!,!!(1)4&%3*'
+@Id_15 Part1.fastq.000000030 contig=chr1:317720-453948W:ENST00000445840.1:13:180:-25:144:S/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=GTGTCACAACTGCACATTGGTTTCACAGCTGCAGGACAAGTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAA edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMEMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium l:2 m:13 h:23 cor
+GTGTCACAACTGCACATTGGTTTCACAGCTGCAGGACAAGTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAA
++
+CA?B>BK@HKJ?C@DC;:9>9<@BC<>@B;C==8B>HO;94CB@72D97?4F<7>?GC8?,63)76981C9365?A->94#8)7+2!*/18%&3':,$&8
+@Id_16 Part1.fastq.000000032 contig=chr1:317720-453948W:ENST00000445840.1:14:180:325:460:S/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMME strand=forward exp=medium l:1 m:1824 h:1824 unfixable_error
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAT
++
+NCB<?CEFDE??F>E?>AA>BCE;=9780B>??0A:@-A<C:D<D98808A5C6:<6@43@48=318221:A5A3D/*:)9"+(*8$!20,2$7-56.*4
+@Id_17 Part1.fastq.000000034 contig=chr1:317720-453948W:ENST00000445840.1:15:180:119:301:S/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=CTCTGAAGCACTGCAGACTCAGCTGAGCACCGATACAAAGAAAGACAAACATCGTAAGAAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium l:8 m:14 h:1824
+CTCTGAAGCACTGCAGACTCAGCTGAGCACCGATACAAAGAAAGACAAACATCGTAAGAAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
++
+FJFI>BCF??DKHC;>?A=>F?FAF;7>AA6@:N+:6B=8=:62A:/A@6@6A6:564B45;69F'.789)63:2+2*-<14*7;5'-)?@1%!39/03/
+@Id_18 Part1.fastq.000000036 contig=chr1:317720-453948W:ENST00000445840.1:16:180:26:182:S/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=TAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATAGATTTTTATAAAATGAAAGCTGCCTCTGAA edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium l:15 m:19 h:23
+TAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATAGATTTTTATAAAATGAAAGCTGCCTCTGAA
++
+@B>FBB;A>?C=FAC;???B9=?::>;E?=>;?8A99?9,?66;;==0-9DH5;8EC,7*93A6.7&A056?(*&635)=:G1/74&5"./)&7?)5.*%
+@Id_19 Part1.fastq.000000038 contig=chr1:317720-453948W:ENST00000445840.1:17:180:-1:127:S/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=ACAGCTGCAGGACAAGTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATAGAT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMEM strand=forward exp=medium l:7 m:19 h:23 cor
+ACAGCTGCAGGACAAGTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATAGAT
++
+?CAEJHG<<E>:C?CAE>?9I;=E;;;9>:63;G=C:858<?G=:=5-/-05955E/E/J-53-=;+2?-?',31::;0/C5A.-.,-&7++4686297&
+@Id_20 Part1.fastq.000000040 contig=chr1:317720-453948W:ENST00000445840.1:18:180:1:173:S/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=AGCTGCAGGACAAGTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATAGATTT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium l:8 m:19 h:23
+AGCTGCAGGACAAGTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATAGATTT
++
+@EACA@?>=EEI@AEB679J<96AJ:9=H2@<B?6D778;5B692>;9<B6?750(@:@5-)332=/154*6-.E6(,/.(>.+%+>&6E%4(./,14(4
+@Id_21 Part1.fastq.000000042 contig=chr1:317720-453948W:ENST00000445840.1:19:180:-19:117:S/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=CAACTGCACATTGGTTTCACAGCTGCAGGACAAGTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTG edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium l:3 m:15 h:23
+CAACTGCACATTGGTTTCACAGCTGCAGGACAAGTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTG
++
+BE>EBH@F?=AD?DFG@=5<<?5=G<3>4@6<E>B-<>B:8>16.;7/;9>:4&::/249=?>64F">-/2<!?/9+58%2321?&805'!8/2#5$3!5
+@Id_22 Part1.fastq.000000044 contig=chr1:317720-453948W:ENST00000445840.1:20:180:140:298:S/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=GCTGAGCACCGATACAAAGAAAGACAAACATCGTAAGAAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium l:8 m:15 h:1824 unfixable_error
+GCTGAGCACCGATACAAAGAAAGACAAACATCGTAAGAAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
++
+GCEHAIBFGDD><;M=H>?<IBAGC<>9G>=@@B4=;A6=9;9;E::;.5<5/33-2?.254/.8(+15623'0C5,%;/9/6/%766+!%$!&?!8!,9
+@Id_23 Part1.fastq.000000046 contig=chr1:317720-453948W:ENST00000445840.1:21:180:202:333:S/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium l:1824 m:1824 h:1824 unfixable_error
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
++
+BFBA<FFE<A>=?E:<=F:=@G37AB7K=65E8A87>CA>4.611@8E*<C92>84)1982=05)8/<,*5;@9!2)'58,0/.6@2/9)$%6/+2(%=6
+@Id_24 Part1.fastq.000000048 contig=chr1:317720-453948W:ENST00000445840.1:22:180:348:477:S/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium l:1824 m:1824 h:1824 unfixable_error
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
++
+G?CK><HEHDFBCLEDC7<CBGM<@GAA;2=>?@;7A>3D24<8B6F<3A=>:.>337-88,563/-8+8/70-8#(51.6-1D*&A01./10+(-.6#5
+@Id_25 Part1.fastq.000000050 contig=chr1:317720-453948W:ENST00000445840.1:23:180:100:267:S/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=TTTATAAAATGAAAGCTGCCTCTGAAGCACTGCAGACTCAGCTGAGCACCGATACAAAGAAAGACAAACATCGTAAGAAGAAAAAAAAAAAAAAAAAAAA edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMEEMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium l:8 m:15 h:19 cor
+TTTATAAAATGAAAGCTGCCTCTGAAGCACTGCAGACTCAGCTGAGCACCGATACAAAGAAAGACAAACATCGTAAGAAGAAAAAAAAAAAAAAAAAAAA
++
+GEG>CJ@GBIKC=AC;CAA78C=C:B@9@A:J:.9;=<>689>D>71;A4262"!)09(/.=G56'/6E06B5)''4<,;$&0"*3+:1&0.5(%1$15!
+@Id_26 Part1.fastq.000000052 contig=chr1:317720-453948W:ENST00000445840.1:24:180:50:207:S/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=AAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATAGATTTTTATAAAATGAAAGCTGCCTCTGAAGCACTGCAGACTCAGCTGAGCACC edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMEMMMMMMMMMMMMMMMMMMEMMMMMMMMMMMMMMMMMMMMEMMMMMMMMM strand=forward exp=medium l:14 m:17 h:23 cor
+AAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATAGATTTTTATAAAATGAAAGCTGCCTCTGAAGCACTGCAGACTCAGCTGAGCACC
++
+H@JADFG@;;8A@@B@@>:<9C?DA<><:=@5;5:?:987D5<AA??E;3)68J/<<?767=8;5:3='!*(%/+!,09)'&*&206*0+-B"!78;%!/
+@Id_27 Part1.fastq.000000054 contig=chr1:317720-453948W:ENST00000445840.1:25:180:14:194:S/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=GTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATAGATTTTTATAAAATGAAA edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium l:13 m:19 h:23
+GTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATAGATTTTTATAAAATGAAA
++
+GD@C@I@HB><B@A;?@>:;7H;A03:=:A@A?=:?75H=?DB7@:?4;4118B13.54B/0-1:999')I:3.*4>492/"61365C!-<0%45104K#
+@Id_28 Part1.fastq.000000056 contig=chr1:317720-453948W:ENST00000445840.1:26:180:188:430:S/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMEMMMMM strand=forward exp=medium l:1824 m:1824 h:1824 unfixable_error
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAANAAAAA
++
+AC?JC@DC=AB:?6A=?><BAH??C7<;@E2<GHB?2?5=;42087@2:C-:873=;3:44,6'<32582>067.=$2.457A2617<07/-/-!G5*@!
+@Id_29 Part1.fastq.000000058 contig=chr1:317720-453948W:ENST00000445840.1:27:180:47:118:S/2 haplotype=0 length=100 orig_begin=0 orig_end=67 haplotype_infix=GATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATAGATTTTTATAAAATGAAA edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium l:15 m:19 h:23
+GATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATAGATTTTTATAAAATGAAA
++
+M@C?AC<AEE;CB7?C:?E>@A9==?6BE:E57>:9-:5E7C2<15=-7+6/=?68>@)67.7.3E3
+@Id_30 Part1.fastq.000000060 contig=chr1:317720-453948W:ENST00000445840.1:28:180:126:304:S/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=GCACTGCAGACTCAGCTGAGCACCGATACAAAGAAAGACAAACATCGTAAGAAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMEMMMMMMMMMMEMMMMMMMMMMMMMMM strand=forward exp=medium l:1 m:11 h:15
+GCACTGCAGACTCAGCTGAGCACCGATACAAAGAAAGACAAACATCGTAAGAAGAAAAAAAAAAAAAAAAAAAGAAAAAAAAAAGAAAAAAAAAAAAAAA
++
+EB<>>H@G@@=B>BDA:H=99>?E<F@;8DC@M;9A;22;=88=0A5CA>>8;>><7,8379*F10/68(;44455*-7&,3,%.!+,#''00F()-0!7
+@Id_31 Part1.fastq.000000062 contig=chr1:317720-453948W:ENST00000445840.1:29:180:187:390:S/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium l:1824 m:1824 h:1824 unfixable_error
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
++
+?DDA>AHKHH:;>A=;=FD=6HA;@CADCC@>4F;=:9@;=/:;<DE?/5529<1/,18D,8>9=./:!/89G:<-4':8+!0)@54"!0:(-2!-C!72
+@Id_32 Part1.fastq.000000064 contig=chr1:317720-453948W:ENST00000445840.1:30:180:32:142:S/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=GATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATAGATTTTTATAAAATGAAAGCTGCCTCTGAAGCACTG edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium l:15 m:19 h:23
+GATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATAGATTTTTATAAAATGAAAGCTGCCTCTGAAGCACTG
++
+EGC>==@>HB@=;G8D8@;B:?@@=>47D6:8H2?<=6:>=@83/<749:4-6B)3@,(=:B<:+A5*9'!)"6;<'1=&)4-&)%!(7/+3*;$+'/2!
+@Id_33 Part1.fastq.000000066 contig=chr1:317720-453948W:ENST00000445840.1:31:180:-4:196:S/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=TTCACAGCTGCAGGACAAGTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATA edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMEMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium l:6 m:19 h:23 cor
+TTCACAGCTGCAGGACAAGTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATA
++
+IIJFD@DCA@>B?DBHEA6@BH>:5?8A;GC7>94B9;52=<E=9-?E@2(9+@951569>65*46=@.-:/';:4*;@%?*--+-*9,3(,&".(5"('
+@Id_34 Part1.fastq.000000068 contig=chr1:317720-453948W:ENST00000445840.1:32:180:44:221:S/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=GGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATAGATTTTTATAAAATGAAAGCTGCCTCTGAAGCACTGCAGACTCAGCTG edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium l:15 m:17 h:23
+GGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATAGATTTTTATAAAATGAAAGCTGCCTCTGAAGCACTGCAGACTCAGCTG
++
+HG><DLADHBCG@?E??GDJC=@=CH@7>>=?>8E<=<B:577;0FE>@5A;>/,)988A/3255/+><A(0;+&/6*)7;9.-$3+:3+1+5./(:/!$
+@Id_35 Part1.fastq.000000070 contig=chr1:317720-453948W:ENST00000445840.1:33:180:86:293:S/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=AGAAATCATAGATTTTTATAAAATGAAAGCTGCCTCTGAAGCACTGCAGACTCAGCTGAGCACCGATACAAAGAAAGACAAACATCGTAAGAAGAAAAAA edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium l:11 m:15 h:19
+AGAAATCATAGATTTTTATAAAATGAAAGCTGCCTCTGAAGCACTGCAGACTCAGCTGAGCACCGATACAAAGAAAGACAAACATCGTAAGAAGAAAAAA
++
+I?DH=?CBHDCA:D<;7:A?:=C:GBC;?E4>AIG8:A;A<CBFC44<<6A74=:947@6+5+=3*0.,E70;$59E/-/B,60$!.,$+11'%,*-0*%
+@Id_36 Part1.fastq.000000072 contig=chr1:317720-453948W:ENST00000445840.1:34:180:24:196:S/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=CTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATAGATTTTTATAAAATGAAAGCTGCCTCTG edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium l:15 m:19 h:23
+CTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATAGATTTTTATAAAATGAAAGCTGCCTCTG
++
+KLAD8@B;EA><;?<<DCE:;>5A;ABE<I?B;7=4-AB8D7.+A:?5>*2-23@75";4-7.9@3-<<B503!22(/4.(+65&6,2**,.-0,!,,*5
+@Id_37 Part1.fastq.000000074 contig=chr1:317720-453948W:ENST00000445840.1:35:180:87:166:S/2 haplotype=0 length=100 orig_begin=0 orig_end=75 haplotype_infix=GAAATCATAGATTTTTATAAAATGAAAGCTGCCTCTGAAGCACTGCAGACTCAGCTGAGCACCGATACAAAGAAA edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMEM strand=forward exp=medium l:14 m:15 h:19 cor
+GAAATCATAGATTTTTATAAAATGAAAGCTGCCTCTGAAGCACTGCAGACTCAGCTGAGCACCGATACAAAGAAA
++
+IJHHCLNF=?QG;<FEA@F6B9A7BBCBA?;DC:9:B6::9<7:<A,>I,@L>C8>0<=;07@1378')91;7)5
+@Id_38 Part1.fastq.000000076 contig=chr1:317720-453948W:ENST00000445840.1:36:180:-41:170:S/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=CAGCCACACTGCTTTGGTGTCACAACTGCACATTGGTTTCACAGCTGCAGGACAAGTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCT edit_string=MMMMMMMMMMMEMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium l:1 m:6 h:20
+CAGCCACACTGATTTGGTGTCACAACTGCACATTGGTTTCACAGCTGCAGGACAAGTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCT
++
+ABGGMJFA?BCGQHD96JH>G4B9=1@??D@=4:2-B9=6<993:3C>1?:9<6:11B8A25.95<1/?'5D=5<8.5-)#6:+2@&5!F/.#4)!#1!(
diff -r 000000000000 -r 9a0b65ad3c84 test-data/sample_read1.fq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample_read1.fq	Thu Sep 13 07:00:00 2018 -0400
@@ -0,0 +1,140 @@
+@Id_4 Part1.fastq.000000008 contig=chr1:317720-453948W:ENST00000445840.1:2:180:5:85:S/1 haplotype=0 length=100 orig_begin=0 orig_end=76 haplotype_infix=GCAGGACAAGTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTG edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMEMMMMMM strand=forward exp=medium
+GCAGGACAAGTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAATCAACTG
++
+EBHA>BE<<B?FG=9GB>ACGD;>B:C@@<A@;@7<:D084:H<;7::/5094=A169688=$=66B.0:A05169
+@Id_5 Part1.fastq.000000010 contig=chr1:317720-453948W:ENST00000445840.1:3:180:158:302:S/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=GAAAGACAAACATCGTAAGAAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMEM strand=forward exp=medium
+GAAAGACAAACATCGTAAGAAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACA
++
+CG?FA?ACE56E?C=>?;B><:<9AJ=@>@7=8=@G0CE9E84?8:D4:A83@/<?226-A//?.7>)08+;):2A88/.*&&;+;)!/-3!!I!/!)5;
+@Id_6 Part1.fastq.000000012 contig=chr1:317720-453948W:ENST00000445840.1:4:180:-6:131:S/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=GTTTCACAGCTGCAGGACAAGTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCA edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+GTTTCACAGCTGCAGGACAAGTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCA
++
+C>A=D=FJF><;DA@IGJ:I99>GC:>?<D8AB<;;C9=279<26<=-:E5?D;44@36=48.8=58F-:C524*0.C3)62M--,!%>/>,4-,04*.+
+@Id_7 Part1.fastq.000000014 contig=chr1:317720-453948W:ENST00000445840.1:5:180:321:438:S/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
++
+FIJC>CEAE<B=>CF?=E9CBD<F9E?B357AF548D9;<5<=+<E:,6=D0;2<33+9'96@'/082'5<-<2+,:-2,73&3528$*6+#7!#5<!1>
+@Id_8 Part1.fastq.000000016 contig=chr1:317720-453948W:ENST00000445840.1:6:180:12:230:S/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=AAGTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATAGATTTTTATAAAATGA edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+AAGTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATAGATTTTTATAAAATGA
++
+;HBDE@I=GB@ABAM9<>B;G><FD>D=CA?9EA=A:B;97:+?/7588:9@:39)4;;/2:48329651(.;A5/*2*5#:2@;!/*"42.,0C1)--&
+@Id_9 Part1.fastq.000000018 contig=chr1:317720-453948W:ENST00000445840.1:7:180:245:432:S/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMEMMMMMMMEMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
++
+EDAJ>J@=E8:=D<>A?ED?AB:<DFB6B>H7AE3;B;><(:84:D0D=836D)>+3C:3-004$B.?C4=7;32293:C+0+&&?.(!'+(,!10?.,&
+@Id_10 Part1.fastq.000000020 contig=chr1:317720-453948W:ENST00000445840.1:8:180:188:421:S/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
++
+?FCGICCB7HDKED8CBD=99?=BKF77A=:55>AI>9A8><0@;674/@::>,?9+<:*(763,A<8/0?&)+(!%)<';6,-(@&5%*'$%7#=0.&?
+@Id_11 Part1.fastq.000000022 contig=chr1:317720-453948W:ENST00000445840.1:9:180:248:450:S/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
++
+@CEGCC@C=FM@?DDFD>?:6<>E=G9;6D9=6?:8>=2=.3:0?2/>4>585=34/;?-0)2>;46;.65??,+/(*6$91/'E750;/20*/=&4./;
+@Id_12 Part1.fastq.000000024 contig=chr1:317720-453948W:ENST00000445840.1:10:180:19:72:S/2 haplotype=0 length=100 orig_begin=0 orig_end=49 haplotype_infix=AGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGA edit_string=MMMMMMMMMMMMMMMMMMEMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+AGCATCTTAAAATGATTCGACAGGAGGAGATAAGGAAGCTCGAGGAAGA
++
+GCLII<FH>DI=@EBFB5P@GBE8=89B9;G@IA<=B>A;879A;77;8
+@Id_13 Part1.fastq.000000026 contig=chr1:317720-453948W:ENST00000445840.1:11:180:3:115:S/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=CTGCAGGACAAGTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATAGATTTTT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMEMMMMMMMMMMMMMMEMMMMMMMEMMMEMM strand=forward exp=medium
+CTGCAGGACAAGTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAGACAACTGGAAGGAGTAATCATANATTNTT
++
+H=ACCD?D7EBGCAGGHEEBA9?7<6=G@8;8??74?A@6A<6:74>1<37/>>E8<1<::7;3:5+8-A8*)9#+229633.0+1,.,7+*!!,0-!%+
+@Id_14 Part1.fastq.000000028 contig=chr1:317720-453948W:ENST00000445840.1:12:180:-11:166:S/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=CATTGGTTTCACAGCTGCAGGACAAGTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGA edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+CATTGGTTTCACAGCTGCAGGACAAGTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGA
++
+EHCHB?F?@G@FA8G>?D;5<8+=G;3F<@>7G7@<69@K2<1>??E46>6325A5@-D79176:5&,35M57))2*41:)>!4502!,!!(1)4&%3*'
+@Id_15 Part1.fastq.000000030 contig=chr1:317720-453948W:ENST00000445840.1:13:180:-25:144:S/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=GTGTCACAACTGCACATTGGTTTCACAGCTGCAGGACAAGTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAA edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMEMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+GTGTCACAACTGCACATTGGTTTCACAGCTGCAGGACAAGTTCGAGCATCTTAAAATGATTCAACAGGAGGAGGTAAGGAAGCTCGAGGAAGAGAAAAAA
++
+CA?B>BK@HKJ?C@DC;:9>9<@BC<>@B;C==8B>HO;94CB@72D97?4F<7>?GC8?,63)76981C9365?A->94#8)7+2!*/18%&3':,$&8
+@Id_16 Part1.fastq.000000032 contig=chr1:317720-453948W:ENST00000445840.1:14:180:325:460:S/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMME strand=forward exp=medium
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAT
++
+NCB<?CEFDE??F>E?>AA>BCE;=9780B>??0A:@-A<C:D<D98808A5C6:<6@43@48=318221:A5A3D/*:)9"+(*8$!20,2$7-56.*4
+@Id_17 Part1.fastq.000000034 contig=chr1:317720-453948W:ENST00000445840.1:15:180:119:301:S/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=CTCTGAAGCACTGCAGACTCAGCTGAGCACCGATACAAAGAAAGACAAACATCGTAAGAAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+CTCTGAAGCACTGCAGACTCAGCTGAGCACCGATACAAAGAAAGACAAACATCGTAAGAAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
++
+FJFI>BCF??DKHC;>?A=>F?FAF;7>AA6@:N+:6B=8=:62A:/A@6@6A6:564B45;69F'.789)63:2+2*-<14*7;5'-)?@1%!39/03/
+@Id_18 Part1.fastq.000000036 contig=chr1:317720-453948W:ENST00000445840.1:16:180:26:182:S/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=TAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATAGATTTTTATAAAATGAAAGCTGCCTCTGAA edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+TAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATAGATTTTTATAAAATGAAAGCTGCCTCTGAA
++
+@B>FBB;A>?C=FAC;???B9=?::>;E?=>;?8A99?9,?66;;==0-9DH5;8EC,7*93A6.7&A056?(*&635)=:G1/74&5"./)&7?)5.*%
+@Id_19 Part1.fastq.000000038 contig=chr1:317720-453948W:ENST00000445840.1:17:180:-1:127:S/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=ACAGCTGCAGGACAAGTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATAGAT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMEM strand=forward exp=medium
+ACAGCTGCAGGACAAGTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATAGGT
++
+?CAEJHG<<E>:C?CAE>?9I;=E;;;9>:63;G=C:858<?G=:=5-/-05955E/E/J-53-=;+2?-?',31::;0/C5A.-.,-&7++4686297&
+@Id_20 Part1.fastq.000000040 contig=chr1:317720-453948W:ENST00000445840.1:18:180:1:173:S/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=AGCTGCAGGACAAGTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATAGATTT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+AGCTGCAGGACAAGTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATAGATTT
++
+@EACA@?>=EEI@AEB679J<96AJ:9=H2@<B?6D778;5B692>;9<B6?750(@:@5-)332=/154*6-.E6(,/.(>.+%+>&6E%4(./,14(4
+@Id_21 Part1.fastq.000000042 contig=chr1:317720-453948W:ENST00000445840.1:19:180:-19:117:S/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=CAACTGCACATTGGTTTCACAGCTGCAGGACAAGTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTG edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+CAACTGCACATTGGTTTCACAGCTGCAGGACAAGTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTG
++
+BE>EBH@F?=AD?DFG@=5<<?5=G<3>4@6<E>B-<>B:8>16.;7/;9>:4&::/249=?>64F">-/2<!?/9+58%2321?&805'!8/2#5$3!5
+@Id_22 Part1.fastq.000000044 contig=chr1:317720-453948W:ENST00000445840.1:20:180:140:298:S/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=GCTGAGCACCGATACAAAGAAAGACAAACATCGTAAGAAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+GCTGAGCACCGATACAAAGAAAGACAAACATCGTAAGAAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
++
+GCEHAIBFGDD><;M=H>?<IBAGC<>9G>=@@B4=;A6=9;9;E::;.5<5/33-2?.254/.8(+15623'0C5,%;/9/6/%766+!%$!&?!8!,9
+@Id_23 Part1.fastq.000000046 contig=chr1:317720-453948W:ENST00000445840.1:21:180:202:333:S/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
++
+BFBA<FFE<A>=?E:<=F:=@G37AB7K=65E8A87>CA>4.611@8E*<C92>84)1982=05)8/<,*5;@9!2)'58,0/.6@2/9)$%6/+2(%=6
+@Id_24 Part1.fastq.000000048 contig=chr1:317720-453948W:ENST00000445840.1:22:180:348:477:S/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
++
+G?CK><HEHDFBCLEDC7<CBGM<@GAA;2=>?@;7A>3D24<8B6F<3A=>:.>337-88,563/-8+8/70-8#(51.6-1D*&A01./10+(-.6#5
+@Id_25 Part1.fastq.000000050 contig=chr1:317720-453948W:ENST00000445840.1:23:180:100:267:S/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=TTTATAAAATGAAAGCTGCCTCTGAAGCACTGCAGACTCAGCTGAGCACCGATACAAAGAAAGACAAACATCGTAAGAAGAAAAAAAAAAAAAAAAAAAA edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMEEMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+TTTATAAAATGAAAGCTGCCTCTGAAGCACTGCAGACTCAGCTGAGCACCGATTNAAAGAAAGACAAACATCGTAAGAAGAAAAAAAAAAAAAAAAAAAA
++
+GEG>CJ@GBIKC=AC;CAA78C=C:B@9@A:J:.9;=<>689>D>71;A4262"!)09(/.=G56'/6E06B5)''4<,;$&0"*3+:1&0.5(%1$15!
+@Id_26 Part1.fastq.000000052 contig=chr1:317720-453948W:ENST00000445840.1:24:180:50:207:S/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=AAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATAGATTTTTATAAAATGAAAGCTGCCTCTGAAGCACTGCAGACTCAGCTGAGCACC edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMEMMMMMMMMMMMMMMMMMMEMMMMMMMMMMMMMMMMMMMMEMMMMMMMMM strand=forward exp=medium
+AAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATAGATTCTTATAAAATGAAAGCTGCNTCTGAAGCACTGCAGACTCATCTGAGCACC
++
+H@JADFG@;;8A@@B@@>:<9C?DA<><:=@5;5:?:987D5<AA??E;3)68J/<<?767=8;5:3='!*(%/+!,09)'&*&206*0+-B"!78;%!/
+@Id_27 Part1.fastq.000000054 contig=chr1:317720-453948W:ENST00000445840.1:25:180:14:194:S/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=GTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATAGATTTTTATAAAATGAAA edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+GTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATAGATTTTTATAAAATGAAA
++
+GD@C@I@HB><B@A;?@>:;7H;A03:=:A@A?=:?75H=?DB7@:?4;4118B13.54B/0-1:999')I:3.*4>492/"61365C!-<0%45104K#
+@Id_28 Part1.fastq.000000056 contig=chr1:317720-453948W:ENST00000445840.1:26:180:188:430:S/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMEMMMMM strand=forward exp=medium
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAANAAAAA
++
+AC?JC@DC=AB:?6A=?><BAH??C7<;@E2<GHB?2?5=;42087@2:C-:873=;3:44,6'<32582>067.=$2.457A2617<07/-/-!G5*@!
+@Id_29 Part1.fastq.000000058 contig=chr1:317720-453948W:ENST00000445840.1:27:180:47:118:S/2 haplotype=0 length=100 orig_begin=0 orig_end=67 haplotype_infix=GATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATAGATTTTTATAAAATGAAA edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+GATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATAGATTTTTATAAAATGAAA
++
+M@C?AC<AEE;CB7?C:?E>@A9==?6BE:E57>:9-:5E7C2<15=-7+6/=?68>@)67.7.3E3
+@Id_30 Part1.fastq.000000060 contig=chr1:317720-453948W:ENST00000445840.1:28:180:126:304:S/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=GCACTGCAGACTCAGCTGAGCACCGATACAAAGAAAGACAAACATCGTAAGAAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMEMMMMMMMMMMEMMMMMMMMMMMMMMM strand=forward exp=medium
+GCACTGCAGACTCAGCTGAGCACCGATACAAAGAAAGACAAACATCGTAAGAAGAAAAAAAAAAAAAAAAAAAGAAAAAAAAAAGAAAAAAAAAAAAAAA
++
+EB<>>H@G@@=B>BDA:H=99>?E<F@;8DC@M;9A;22;=88=0A5CA>>8;>><7,8379*F10/68(;44455*-7&,3,%.!+,#''00F()-0!7
+@Id_31 Part1.fastq.000000062 contig=chr1:317720-453948W:ENST00000445840.1:29:180:187:390:S/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
++
+?DDA>AHKHH:;>A=;=FD=6HA;@CADCC@>4F;=:9@;=/:;<DE?/5529<1/,18D,8>9=./:!/89G:<-4':8+!0)@54"!0:(-2!-C!72
+@Id_32 Part1.fastq.000000064 contig=chr1:317720-453948W:ENST00000445840.1:30:180:32:142:S/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=GATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATAGATTTTTATAAAATGAAAGCTGCCTCTGAAGCACTG edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+GATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATAGATTTTTATAAAATGAAAGCTGCCTCTGAAGCACTG
++
+EGC>==@>HB@=;G8D8@;B:?@@=>47D6:8H2?<=6:>=@83/<749:4-6B)3@,(=:B<:+A5*9'!)"6;<'1=&)4-&)%!(7/+3*;$+'/2!
+@Id_33 Part1.fastq.000000066 contig=chr1:317720-453948W:ENST00000445840.1:31:180:-4:196:S/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=TTCACAGCTGCAGGACAAGTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATA edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMEMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+TTCACAGCTGCAGGACAAGTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCTAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATA
++
+IIJFD@DCA@>B?DBHEA6@BH>:5?8A;GC7>94B9;52=<E=9-?E@2(9+@951569>65*46=@.-:/';:4*;@%?*--+-*9,3(,&".(5"('
+@Id_34 Part1.fastq.000000068 contig=chr1:317720-453948W:ENST00000445840.1:32:180:44:221:S/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=GGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATAGATTTTTATAAAATGAAAGCTGCCTCTGAAGCACTGCAGACTCAGCTG edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+GGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATAGATTTTTATAAAATGAAAGCTGCCTCTGAAGCACTGCAGACTCAGCTG
++
+HG><DLADHBCG@?E??GDJC=@=CH@7>>=?>8E<=<B:577;0FE>@5A;>/,)988A/3255/+><A(0;+&/6*)7;9.-$3+:3+1+5./(:/!$
+@Id_35 Part1.fastq.000000070 contig=chr1:317720-453948W:ENST00000445840.1:33:180:86:293:S/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=AGAAATCATAGATTTTTATAAAATGAAAGCTGCCTCTGAAGCACTGCAGACTCAGCTGAGCACCGATACAAAGAAAGACAAACATCGTAAGAAGAAAAAA edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+AGAAATCATAGATTTTTATAAAATGAAAGCTGCCTCTGAAGCACTGCAGACTCAGCTGAGCACCGATACAAAGAAAGACAAACATCGTAAGAAGAAAAAA
++
+I?DH=?CBHDCA:D<;7:A?:=C:GBC;?E4>AIG8:A;A<CBFC44<<6A74=:947@6+5+=3*0.,E70;$59E/-/B,60$!.,$+11'%,*-0*%
+@Id_36 Part1.fastq.000000072 contig=chr1:317720-453948W:ENST00000445840.1:34:180:24:196:S/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=CTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATAGATTTTTATAAAATGAAAGCTGCCTCTG edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+CTTAAAATGATTCAACAGGAGGAGATAAGGAAGCTCGAGGAAGAGAAAAAACAACTGGAAGGAGAAATCATAGATTTTTATAAAATGAAAGCTGCCTCTG
++
+KLAD8@B;EA><;?<<DCE:;>5A;ABE<I?B;7=4-AB8D7.+A:?5>*2-23@75";4-7.9@3-<<B503!22(/4.(+65&6,2**,.-0,!,,*5
+@Id_37 Part1.fastq.000000074 contig=chr1:317720-453948W:ENST00000445840.1:35:180:87:166:S/2 haplotype=0 length=100 orig_begin=0 orig_end=75 haplotype_infix=GAAATCATAGATTTTTATAAAATGAAAGCTGCCTCTGAAGCACTGCAGACTCAGCTGAGCACCGATACAAAGAAA edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMEM strand=forward exp=medium
+GAAATCATAGATTTTTATAAAATGAAAGCTGCCTCTGAAGCACTGCAGACTCAGCTGAGCACCGATACAAAGAGA
++
+IJHHCLNF=?QG;<FEA@F6B9A7BBCBA?;DC:9:B6::9<7:<A,>I,@L>C8>0<=;07@1378')91;7)5
+@Id_38 Part1.fastq.000000076 contig=chr1:317720-453948W:ENST00000445840.1:36:180:-41:170:S/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=CAGCCACACTGCTTTGGTGTCACAACTGCACATTGGTTTCACAGCTGCAGGACAAGTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCT edit_string=MMMMMMMMMMMEMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+CAGCCACACTGATTTGGTGTCACAACTGCACATTGGTTTCACAGCTGCAGGACAAGTTCGAGCATCTTAAAATGATTCAACAGGAGGAGATAAGGAAGCT
++
+ABGGMJFA?BCGQHD96JH>G4B9=1@??D@=4:2-B9=6<993:3C>1?:9<6:11B8A25.95<1/?'5D=5<8.5-)#6:+2@&5!F/.#4)!#1!(
diff -r 000000000000 -r 9a0b65ad3c84 test-data/sample_read2.cor.fq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample_read2.cor.fq	Thu Sep 13 07:00:00 2018 -0400
@@ -0,0 +1,140 @@
+@Id_4 Part1.fastq.000000009 contig=chr1:317720-453948W:ENST00000445840.1:2:180:5:85:A/2 haplotype=0 length=100 orig_begin=0 orig_end=76 haplotype_infix=CCTTCCAGTTGTTTTTTCTCTTCCTCGAGCTTCCTTATCTCCTCCTGTTGAATCATTTTAAGATGCTCGAACTTGT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium l:11 m:19 h:23
+CCTTCCAGTTGTTTTTTCTCTTCCTCGAGCTTCCTTATCTCCTCCTGTTGAATCATTTTAAGATGCTCGAACTTGT
++
+E8HCG>;DFBG?@CG@B?D:AQAD5.;9>7@>@:8=<20J;68<<706;B==:8505278D<64.F=02'5>0=1:
+@Id_5 Part1.fastq.000000011 contig=chr1:317720-453948W:ENST00000445840.1:3:180:158:302:A/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium l:1824 m:1824 h:1824 unfixable_error
+TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
++
+FH<CLFG:?A@@C@A@E=AD0D9<>B>=C;5<?9DA397=94B;>)1-55,+?:7C1*1)0192:?>3:8/37/761)7:412,(.<5!*>5/%*,/2*!
+@Id_6 Part1.fastq.000000013 contig=chr1:317720-453948W:ENST00000445840.1:4:180:-6:131:A/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=CAGTGCTTCAGAGGCAGCTTTCATTTTATAAAAATCTATGATTTCTCCTTCCAGTTGTTTTTTCTCTTCCTCGAGCTTCCTTATCTCCTCCTGTTGAATC edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium l:15 m:19 h:23
+CAGTGCTTCAGAGGCAGCTTTCATTTTATAAAAATCTATGATTTCTCCTTCCAGTTGTTTTTTCTCTTCCTCGAGCTTCCTTATCTCCTCCTGTTGAATC
++
+HDLBAAACCA<K;=9<@@BC>@=JG>7<:A=BG@9+=6A8+<AB;339:6>6=49L<15<39+0&1:2.1/260('';1003=0)A*.-*,";$/61+"#
+@Id_7 Part1.fastq.000000015 contig=chr1:317720-453948W:ENST00000445840.1:5:180:321:438:A/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMEMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMEMMMMMMMMMMMMMMMMMM strand=forward exp=medium l:1 m:9 h:1824 unfixable_error
+TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTTTTTTTTTTTTTTTTT
++
+LHFDDLK=CE@B>@>GDF@=@>=@5<J;=7@G:;::67<:;2>8@G.5</8A41<1=1=.*,7/49;A8--=201++7+'3#29!$500!%<@!1!-:4$
+@Id_8 Part1.fastq.000000017 contig=chr1:317720-453948W:ENST00000445840.1:6:180:12:230:A/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTCTTACGATGTTTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGC edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium l:8 m:15 h:1824
+TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTCTTACGATGTTTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGC
++
+?ECI@F@IEAFF8F?9<@@:9@BA4@@??@C:1D89=><=58915P259+JE=:5719A,->0,-5125%@7(=1/>.-.!&60!/=5,6*8/5,*3'68
+@Id_9 Part1.fastq.000000019 contig=chr1:317720-453948W:ENST00000445840.1:7:180:245:432:A/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium l:1824 m:1824 h:1824 unfixable_error
+TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
++
+GIA@DJE?<HG>@LD:BD?6B7A>F=A@<?C?BAAJ:A773)FD8<;9+ID5454>.?16J936I-60A-,B5$.:(D%1.-!-%);018/-&,-?">05
+@Id_10 Part1.fastq.000000021 contig=chr1:317720-453948W:ENST00000445840.1:8:180:188:421:A/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium l:1824 m:1824 h:1824 unfixable_error
+TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
++
+CG@??@A;EDADHBE>C?A>:=CC4<2@=7<>F:7C2D3:HHFDC>;/-CD,=B26A>1..4,8=>587D2199=282?=6;49/"14/3!!+8/*"()(
+@Id_11 Part1.fastq.000000023 contig=chr1:317720-453948W:ENST00000445840.1:9:180:248:450:A/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium l:1824 m:1824 h:1824 unfixable_error
+TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
++
+ALB@AG<>O@CD?<9D@B7;;=?<;BD=C3C>955<3E4B1973<1<)47;28938=6P4.;,,:/CB0:+<:8.A'F@37*7-,.(0<*!=.,237!*3
+@Id_12 Part1.fastq.000000025 contig=chr1:317720-453948W:ENST00000445840.1:10:180:19:72:A/1 haplotype=0 length=100 orig_begin=0 orig_end=49 haplotype_infix=TTTTCTCTTCCTCGAGCTTCCTTATCTCCTCCTGTTGAATCATTTTAAG edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium l:17 m:19 h:23
+TTTTCTCTTCCTCGAGCTTCCTTATCTCCTCCTGTTGAATCATTTTAAG
++
+ADD@DDD@9GA=>M:DCG=:;>884==;>B;6;9;<@9<@/F=H@7=A9
+@Id_13 Part1.fastq.000000027 contig=chr1:317720-453948W:ENST00000445840.1:11:180:3:115:A/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=GCTTTCATTTTATAAAAATCTATGATTTCTCCTTCCAGTTGTTTTTTCTCTTCCTCGAGCTTCCTTATCTCCTCCTGTTGAATCATTTTAAGATGCTCGA edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium l:14 m:19 h:23
+GCTTTCATTTTATAAAAATCTATGATTTCTCCTTCCAGTTGTTTTTTCTCTTCCTCGAGCTTCCTTATCTCCTCCTGTTGAATCATTTTAAGATGCTCGA
++
+GH@EIFABFCAC@H@:7?AH>9==::A9=:@;@D>?B;99;6:;BHA-2=55383<*-=C:4C98+/==!(*&:*=#0-315(45()=B36*+/+3%>36
+@Id_14 Part1.fastq.000000029 contig=chr1:317720-453948W:ENST00000445840.1:12:180:-11:166:A/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=TTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCATTTTATAAAAATCTATGATTTCTCCTTCCAGTTGTTTTTTCT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMEMMMMMMMMMMMMMMMMM strand=forward exp=medium l:14 m:15 h:20 cor
+TTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCATTTTATAAAAATCTATGATTTCTCCTTCCAGTTGTTTTTTCT
++
+FEEGE<IAGGDEBA:CB84>94FC?77EF9D8?<<D5::<=F5=@7??D9974??;C6*CE357+-2,26?D!2=/:#*/5&!.,2)%).#$&+1F4!)0
+@Id_15 Part1.fastq.000000031 contig=chr1:317720-453948W:ENST00000445840.1:13:180:-25:144:A/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=TCAGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCATTTTATAAAAATCTATGATTTCTCCTTCCAGTTGTTTTTTCTCTTCCTCGAGCTTCCTTATCTC edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium l:15 m:17 h:23
+TCAGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCATTTTATAAAAATCTATGATTTCTCCTTCCAGTTGTTTTTTCTCTTCCTCGAGCTTCCTTATCTC
++
+@HBDE@C@G<:?K;@@<>>AE:8=;G;;BB9877<0I7=3<=?92FD::->BC39715+;-F840:=A5/;%<*853#")6%&4#1$).!631)3!$+!-
+@Id_16 Part1.fastq.000000033 contig=chr1:317720-453948W:ENST00000445840.1:14:180:325:460:A/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium l:1824 m:1824 h:1824 unfixable_error
+TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
++
+DHEC=ACH?D@I99C>DB;=EE>8:=A@D=C>>>@;6?6;4<>D7768B-6?@B2.@2:*921:71.5.'(-3(894)=:731+-6'2;/.67)18#7!0
+@Id_17 Part1.fastq.000000035 contig=chr1:317720-453948W:ENST00000445840.1:15:180:119:301:A/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT edit_string=EMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMEMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMEMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium l:1 m:1824 h:1824 unfixable_error
+CTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTNTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTATTTTTTTTTTTTTTTTTTTT
++
+JGKA@FGADJF:?==<C;D@7?6<=?D@=:C:BDIB!@9:><;=163;<<.:;:-?30997/0+12=9)<44/,2,6**20:9+=(:(7:8&.5)4(3%2
+@Id_18 Part1.fastq.000000037 contig=chr1:317720-453948W:ENST00000445840.1:16:180:26:182:A/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=TTTCTTCTTACGATGTTTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCATTTTATAAAAATCTATGATTTCTCCT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMEMMMMMMMMMMMM strand=forward exp=medium l:11 m:15 h:19 cor
+TTTCTTCTTACGATGTTTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCATTTTATAAAAATCTATGATTTCTCCT
++
+CIBLCIDCL>GBJ<BB;?=CC?@?=;@7:9=2EA<D<98/F@<;>33A<9111753@3806B4;B>(47368*,1!B6110,(&;/1/'->73*!4/)!+
+@Id_19 Part1.fastq.000000039 contig=chr1:317720-453948W:ENST00000445840.1:17:180:-1:127:A/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=GCTTCAGAGGCAGCTTTCATTTTATAAAAATCTATGATTTCTCCTTCCAGTTGTTTTTTCTCTTCCTCGAGCTTCCTTATCTCCTCCTGTTGAATCATTT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium l:15 m:19 h:23
+GCTTCAGAGGCAGCTTTCATTTTATAAAAATCTATGATTTCTCCTTCCAGTTGTTTTTTCTCTTCCTCGAGCTTCCTTATCTCCTCCTGTTGAATCATTT
++
+LCNACHCG@>L;4>>@B=ACC;A<8E4<9<;9A;C=;??9B?<54E55<9G1:41=*;28?23-7A8>-.0302,-A+$.<2:)0@-0!51!,03)!.!:
+@Id_20 Part1.fastq.000000041 contig=chr1:317720-453948W:ENST00000445840.1:18:180:1:173:A/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=ACGATGTTTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCATTTTATAAAAATCTATGATTTCTCCTTCCAGTTGT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium l:12 m:15 h:19
+ACGATGTTTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCATTTTATAAAAATCTATGATTTCTCCTTCCAGTTGT
++
+;BECDDH@AAKDK;>A6>D?7BEA===A;@F6A@:8=C9;8D8297?@,B..5:6,264262C'.:B844)0=C11-'4=.5!/!/4;7290"6/,1?7(
+@Id_21 Part1.fastq.000000043 contig=chr1:317720-453948W:ENST00000445840.1:19:180:-19:117:A/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=CAGCTTTCATTTTATAAAAATCTATGATTTCTCCTTCCAGTTGTTTTTTCTCTTCCTCGAGCTTCCTTATCTCCTCCTGTTGAATCATTTTAAGATGCTC edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium l:15 m:19 h:23
+CAGCTTTCATTTTATAAAAATCTATGATTTCTCCTTCCAGTTGTTTTTTCTCTTCCTCGAGCTTCCTTATCTCCTCCTGTTGAATCATTTTAAGATGCTC
++
+C@BB?AB>CH>@86D>9A9DH??;6EDA9@;@:535@615?J?>0DIH3?A9?<839<8B859/,122-3*+254+7*5B/2:;1/&35&883)5%1(1>
+@Id_22 Part1.fastq.000000045 contig=chr1:317720-453948W:ENST00000445840.1:20:180:140:298:A/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium l:1824 m:1824 h:1824 unfixable_error
+TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
++
+=DINIJBFAAJ@GCFA@@><F=BGK=:>@0,9BE/95<;71447>J+6;274=+?565/64,70-G6@2(//,4364<-916=&3-!+?C&#;!!(*.+<
+@Id_23 Part1.fastq.000000047 contig=chr1:317720-453948W:ENST00000445840.1:21:180:202:333:A/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium l:1824 m:1824 h:1824 unfixable_error
+TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
++
+FBIB@:B?;DMJA<=;5D<GM9:BBBAB;D>>26<;7>@26:D59D2;><I:/59/5<22.;877G3-9345/33(3"6)>/'2/07)*3%)-!+1!<>#
+@Id_24 Part1.fastq.000000049 contig=chr1:317720-453948W:ENST00000445840.1:22:180:348:477:A/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium l:1824 m:1824 h:1824 unfixable_error
+TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
++
+@BDJ@GHBKA>:?ABDAB?;88@<EAB;;EJ8@A?@56597:41E3992<40-=3'9,B/8=9<#8<(17/-,.;2027+38'5/6<+:-*-!"6+%#)!
+@Id_25 Part1.fastq.000000051 contig=chr1:317720-453948W:ENST00000445840.1:23:180:100:267:A/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTCTTACGATG edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMEMMMMMMMMMMM strand=forward exp=medium l:1 m:1824 h:1824 unfixable_error
+TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTACGATG
++
+@@C>F<@?@@C?D=:7<EE>KA<@B<=C<9A9@<280<51:A64564>=8>F(<72697+%/=./(4+3<28,6'5!48.8)?(.)746<!/*&.%/.*,
+@Id_26 Part1.fastq.000000053 contig=chr1:317720-453948W:ENST00000445840.1:24:180:50:207:A/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=TTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTCTTACGATGTTTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCAT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium l:8 m:14 h:1824
+TTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTCTTACGATGTTTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCAT
++
+FA>CGDB?;HJ??EIDB>=D;;?6:9E:B@6;;>55<:@0:;EC:76-4<<+,=0=<9:;,/A7-<:3#+;?>5<05$3&$>.,'/9*7:B-%,:/3)+-
+@Id_27 Part1.fastq.000000055 contig=chr1:317720-453948W:ENST00000445840.1:25:180:14:194:A/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=TTTTTTTTTTTTTTTCTTCTTACGATGTTTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCATTTTATAAAAATCT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium l:11 m:15 h:19
+TTTTTTTTTTTTTTTCTTCTTACGATGTTTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCATTTTATAAAAATCT
++
+DJ@DCE8LCFHGL?;<<OKF>AC?AE<<<=BC3A8@76C82;?9A7C;D==801?<;998639(-1819>1>42-3=7;(-*0<9/CA.10A0($)-//"
+@Id_28 Part1.fastq.000000057 contig=chr1:317720-453948W:ENST00000445840.1:26:180:188:430:A/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMEMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMEMMMMMMMMMMMMMM strand=forward exp=medium l:1824 m:1824 h:1824 unfixable_error
+TTTTTTTTTTTTTTTTTTTTTTTTTTNTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTNTTTTTTTTTTTTTT
++
+>EBDBHCCG@?F=@JCC>?BF?B9DC!5=;.F9227;@3-;76448?.>::/<4'4<+?=?7*+*1>5>90.?02+-33;*-;55!&193-417!/*51!
+@Id_29 Part1.fastq.000000059 contig=chr1:317720-453948W:ENST00000445840.1:27:180:47:118:A/1 haplotype=0 length=100 orig_begin=0 orig_end=67 haplotype_infix=GCAGCTTTCATTTTATAAAAATCTATGATTTCTCCTTCCAGTTGTTTTTTCTCTTCCTCGAGCTTCC edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium l:15 m:18 h:21
+GCAGCTTTCATTTTATAAAAATCTATGATTTCTCCTTCCAGTTGTTTTTTCTCTTCCTCGAGCTTCC
++
+CF?CCDE>HDJGEF>5>?B8B<CF9CB6DF;<<@;.?9=>97F=;C614335<3;265)0:7+:@6=
+@Id_30 Part1.fastq.000000061 contig=chr1:317720-453948W:ENST00000445840.1:28:180:126:304:A/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMEMMMMMMMMMMMMEM strand=forward exp=medium l:1 m:1824 h:1824 unfixable_error
+TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTTTTTTTTTTTTCT
++
+FF??BDCBI>?C9>>FDBA=B?ABA<;?DD;C9;79=04;>@2;87.A7B:-MC=59<=5/(<68:>+=8/6?&2353B65)!5<398:'7-7'00,!21
+@Id_31 Part1.fastq.000000063 contig=chr1:317720-453948W:ENST00000445840.1:29:180:187:390:A/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium l:1824 m:1824 h:1824 unfixable_error
+TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
++
+LKGK?=G;E?D>@E@@<C?;A;53@63G=89J=;E4FBC?>2<50*EE9;88*;7@0E49,C9)4?>2:0920*18>3<,07)!34)@3%+9-./)-.#*
+@Id_32 Part1.fastq.000000065 contig=chr1:317720-453948W:ENST00000445840.1:30:180:32:142:A/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=AGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCATTTTATAAAAATCTATGATTTCTCCTTCCAGTTGTTTTTTCTCTTCCTCGAGCTTCCTTATCTCCT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMEMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium l:15 m:18 h:23 cor
+AGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCATTTTATAAAAATCTATGATTTCTCCTTCCAGTTGTTTTTTCTCTTCCTCGAGCTTCCTTATCTCCT
++
+KCA;@8GA?5@<EA?AB@=>??8FG8CAD>?;B?D<246;8=F@C99/9@E8ACB4<1>++&H6621323/(9+:(A9D&(9124!-4..++3<-202/2
+@Id_33 Part1.fastq.000000067 contig=chr1:317720-453948W:ENST00000445840.1:31:180:-4:196:A/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=TTTTTTTTTTTTTTTTTCTTCTTACGATGTTTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCATTTTATAAAAAT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMEM strand=forward exp=medium l:10 m:15 h:19 cor
+TTTTTTTTTTTTTTTTTCTTCTTACGATGTTTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCATTTTATAAAAAT
++
+DLFJBEFIC@I5K;A;<=98:HE<+D6<>D=3<-1B/>;9248>88A:2822>A:<88B4,:1F)518>8>C%,=1A95:<>+/%,4-;5(98;G)($+!
+@Id_34 Part1.fastq.000000069 contig=chr1:317720-453948W:ENST00000445840.1:32:180:44:221:A/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTCTTACGATGTTTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGCAGTGCTTCA edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium l:8 m:14 h:1824
+TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTCTTACGATGTTTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGCAGTGCTTCA
++
+HEFG@F=88?J<CBH;=:BAEF?GDH@<<6B=2QF><?>D6<7C7C=:;C87D5*:7%>9638+@;>+?0)!*29<;1+.6&7429*8%,:?0370'+((
+@Id_35 Part1.fastq.000000071 contig=chr1:317720-453948W:ENST00000445840.1:33:180:86:293:A/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMEMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMEM strand=forward exp=medium l:1 m:1824 h:1824 unfixable_error
+TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGT
++
+CAGKCFJF<@<DHC=@C>=>?<=C9;<C6;DC5;;><@76=77287AB/7570,@:9?41,1<94<:79-105+118/77/1.,.4%(;663616',!+(
+@Id_36 Part1.fastq.000000073 contig=chr1:317720-453948W:ENST00000445840.1:34:180:24:196:A/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=TTTTTTTTTTTTTTTTTCTTCTTACGATGTTTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCATTTTATAAAAAT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMEMM strand=forward exp=medium l:10 m:15 h:19 cor
+TTTTTTTTTTTTTTTTTCTTCTTACGATGTTTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCATTTTATAAAAAT
++
+FGF>E?DJGA<9B@EC<CKADE;7.FF75C>696<A6?2?6<5:=895<A00=B.>:536<16%+?9A48<0:,;(&088%.1)76$4(8433#.+*1,!
+@Id_37 Part1.fastq.000000075 contig=chr1:317720-453948W:ENST00000445840.1:35:180:87:166:A/1 haplotype=0 length=100 orig_begin=0 orig_end=75 haplotype_infix=TTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCATTTTATAAAAATCTATG edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium l:14 m:15 h:19
+TTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCATTTTATAAAAATCTATG
++
+>E?ABEH@==G@;A8<J@?>@==CBDC;<?D8A=9?>9F:B8;A<47<231568BC0!??.26-49C(1B484.4
+@Id_38 Part1.fastq.000000077 contig=chr1:317720-453948W:ENST00000445840.1:36:180:-41:170:A/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=ATGTTTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCATTTTATAAAAATCTATGATTTCTCCTTCCAGTTGTTTT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMEMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium l:13 m:15 h:20 cor
+ATGTTTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCATTTTATAAAAATCTATGATTTCTCCTTCCAGTTGTTTT
++
+HHFIB?BF>:9=E7BC687F=?@;9>CBA==?;8C0I0E8C/5C/@669;=.71<092=846CG.%@5=A<:/*40!9.215==6'-&,717)!6'3".6
diff -r 000000000000 -r 9a0b65ad3c84 test-data/sample_read2.fq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample_read2.fq	Thu Sep 13 07:00:00 2018 -0400
@@ -0,0 +1,140 @@
+@Id_4 Part1.fastq.000000009 contig=chr1:317720-453948W:ENST00000445840.1:2:180:5:85:A/2 haplotype=0 length=100 orig_begin=0 orig_end=76 haplotype_infix=CCTTCCAGTTGTTTTTTCTCTTCCTCGAGCTTCCTTATCTCCTCCTGTTGAATCATTTTAAGATGCTCGAACTTGT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+CCTTCCAGTTGTTTTTTCTCTTCCTCGAGCTTCCTTATCTCCTCCTGTTGAATCATTTTAAGATGCTCGAACTTGT
++
+E8HCG>;DFBG?@CG@B?D:AQAD5.;9>7@>@:8=<20J;68<<706;B==:8505278D<64.F=02'5>0=1:
+@Id_5 Part1.fastq.000000011 contig=chr1:317720-453948W:ENST00000445840.1:3:180:158:302:A/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
++
+FH<CLFG:?A@@C@A@E=AD0D9<>B>=C;5<?9DA397=94B;>)1-55,+?:7C1*1)0192:?>3:8/37/761)7:412,(.<5!*>5/%*,/2*!
+@Id_6 Part1.fastq.000000013 contig=chr1:317720-453948W:ENST00000445840.1:4:180:-6:131:A/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=CAGTGCTTCAGAGGCAGCTTTCATTTTATAAAAATCTATGATTTCTCCTTCCAGTTGTTTTTTCTCTTCCTCGAGCTTCCTTATCTCCTCCTGTTGAATC edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+CAGTGCTTCAGAGGCAGCTTTCATTTTATAAAAATCTATGATTTCTCCTTCCAGTTGTTTTTTCTCTTCCTCGAGCTTCCTTATCTCCTCCTGTTGAATC
++
+HDLBAAACCA<K;=9<@@BC>@=JG>7<:A=BG@9+=6A8+<AB;339:6>6=49L<15<39+0&1:2.1/260('';1003=0)A*.-*,";$/61+"#
+@Id_7 Part1.fastq.000000015 contig=chr1:317720-453948W:ENST00000445840.1:5:180:321:438:A/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMEMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMEMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTTTTTTTTTTTTTTTTT
++
+LHFDDLK=CE@B>@>GDF@=@>=@5<J;=7@G:;::67<:;2>8@G.5</8A41<1=1=.*,7/49;A8--=201++7+'3#29!$500!%<@!1!-:4$
+@Id_8 Part1.fastq.000000017 contig=chr1:317720-453948W:ENST00000445840.1:6:180:12:230:A/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTCTTACGATGTTTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGC edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTCTTACGATGTTTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGC
++
+?ECI@F@IEAFF8F?9<@@:9@BA4@@??@C:1D89=><=58915P259+JE=:5719A,->0,-5125%@7(=1/>.-.!&60!/=5,6*8/5,*3'68
+@Id_9 Part1.fastq.000000019 contig=chr1:317720-453948W:ENST00000445840.1:7:180:245:432:A/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
++
+GIA@DJE?<HG>@LD:BD?6B7A>F=A@<?C?BAAJ:A773)FD8<;9+ID5454>.?16J936I-60A-,B5$.:(D%1.-!-%);018/-&,-?">05
+@Id_10 Part1.fastq.000000021 contig=chr1:317720-453948W:ENST00000445840.1:8:180:188:421:A/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
++
+CG@??@A;EDADHBE>C?A>:=CC4<2@=7<>F:7C2D3:HHFDC>;/-CD,=B26A>1..4,8=>587D2199=282?=6;49/"14/3!!+8/*"()(
+@Id_11 Part1.fastq.000000023 contig=chr1:317720-453948W:ENST00000445840.1:9:180:248:450:A/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
++
+ALB@AG<>O@CD?<9D@B7;;=?<;BD=C3C>955<3E4B1973<1<)47;28938=6P4.;,,:/CB0:+<:8.A'F@37*7-,.(0<*!=.,237!*3
+@Id_12 Part1.fastq.000000025 contig=chr1:317720-453948W:ENST00000445840.1:10:180:19:72:A/1 haplotype=0 length=100 orig_begin=0 orig_end=49 haplotype_infix=TTTTCTCTTCCTCGAGCTTCCTTATCTCCTCCTGTTGAATCATTTTAAG edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+TTTTCTCTTCCTCGAGCTTCCTTATCTCCTCCTGTTGAATCATTTTAAG
++
+ADD@DDD@9GA=>M:DCG=:;>884==;>B;6;9;<@9<@/F=H@7=A9
+@Id_13 Part1.fastq.000000027 contig=chr1:317720-453948W:ENST00000445840.1:11:180:3:115:A/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=GCTTTCATTTTATAAAAATCTATGATTTCTCCTTCCAGTTGTTTTTTCTCTTCCTCGAGCTTCCTTATCTCCTCCTGTTGAATCATTTTAAGATGCTCGA edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+GCTTTCATTTTATAAAAATCTATGATTTCTCCTTCCAGTTGTTTTTTCTCTTCCTCGAGCTTCCTTATCTCCTCCTGTTGAATCATTTTAAGATGCTCGA
++
+GH@EIFABFCAC@H@:7?AH>9==::A9=:@;@D>?B;99;6:;BHA-2=55383<*-=C:4C98+/==!(*&:*=#0-315(45()=B36*+/+3%>36
+@Id_14 Part1.fastq.000000029 contig=chr1:317720-453948W:ENST00000445840.1:12:180:-11:166:A/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=TTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCATTTTATAAAAATCTATGATTTCTCCTTCCAGTTGTTTTTTCT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMEMMMMMMMMMMMMMMMMM strand=forward exp=medium
+TTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCATTTTATAAAAATCTATGATTTCTCTTTCCAGTTGTTTTTTCT
++
+FEEGE<IAGGDEBA:CB84>94FC?77EF9D8?<<D5::<=F5=@7??D9974??;C6*CE357+-2,26?D!2=/:#*/5&!.,2)%).#$&+1F4!)0
+@Id_15 Part1.fastq.000000031 contig=chr1:317720-453948W:ENST00000445840.1:13:180:-25:144:A/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=TCAGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCATTTTATAAAAATCTATGATTTCTCCTTCCAGTTGTTTTTTCTCTTCCTCGAGCTTCCTTATCTC edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+TCAGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCATTTTATAAAAATCTATGATTTCTCCTTCCAGTTGTTTTTTCTCTTCCTCGAGCTTCCTTATCTC
++
+@HBDE@C@G<:?K;@@<>>AE:8=;G;;BB9877<0I7=3<=?92FD::->BC39715+;-F840:=A5/;%<*853#")6%&4#1$).!631)3!$+!-
+@Id_16 Part1.fastq.000000033 contig=chr1:317720-453948W:ENST00000445840.1:14:180:325:460:A/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
++
+DHEC=ACH?D@I99C>DB;=EE>8:=A@D=C>>>@;6?6;4<>D7768B-6?@B2.@2:*921:71.5.'(-3(894)=:731+-6'2;/.67)18#7!0
+@Id_17 Part1.fastq.000000035 contig=chr1:317720-453948W:ENST00000445840.1:15:180:119:301:A/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT edit_string=EMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMEMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMEMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+CTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTNTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTATTTTTTTTTTTTTTTTTTTT
++
+JGKA@FGADJF:?==<C;D@7?6<=?D@=:C:BDIB!@9:><;=163;<<.:;:-?30997/0+12=9)<44/,2,6**20:9+=(:(7:8&.5)4(3%2
+@Id_18 Part1.fastq.000000037 contig=chr1:317720-453948W:ENST00000445840.1:16:180:26:182:A/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=TTTCTTCTTACGATGTTTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCATTTTATAAAAATCTATGATTTCTCCT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMEMMMMMMMMMMMM strand=forward exp=medium
+TTTCTTCTTACGATGTTTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCATTTTATAAAAATCGATGATTTCTCCT
++
+CIBLCIDCL>GBJ<BB;?=CC?@?=;@7:9=2EA<D<98/F@<;>33A<9111753@3806B4;B>(47368*,1!B6110,(&;/1/'->73*!4/)!+
+@Id_19 Part1.fastq.000000039 contig=chr1:317720-453948W:ENST00000445840.1:17:180:-1:127:A/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=GCTTCAGAGGCAGCTTTCATTTTATAAAAATCTATGATTTCTCCTTCCAGTTGTTTTTTCTCTTCCTCGAGCTTCCTTATCTCCTCCTGTTGAATCATTT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+GCTTCAGAGGCAGCTTTCATTTTATAAAAATCTATGATTTCTCCTTCCAGTTGTTTTTTCTCTTCCTCGAGCTTCCTTATCTCCTCCTGTTGAATCATTT
++
+LCNACHCG@>L;4>>@B=ACC;A<8E4<9<;9A;C=;??9B?<54E55<9G1:41=*;28?23-7A8>-.0302,-A+$.<2:)0@-0!51!,03)!.!:
+@Id_20 Part1.fastq.000000041 contig=chr1:317720-453948W:ENST00000445840.1:18:180:1:173:A/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=ACGATGTTTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCATTTTATAAAAATCTATGATTTCTCCTTCCAGTTGT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+ACGATGTTTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCATTTTATAAAAATCTATGATTTCTCCTTCCAGTTGT
++
+;BECDDH@AAKDK;>A6>D?7BEA===A;@F6A@:8=C9;8D8297?@,B..5:6,264262C'.:B844)0=C11-'4=.5!/!/4;7290"6/,1?7(
+@Id_21 Part1.fastq.000000043 contig=chr1:317720-453948W:ENST00000445840.1:19:180:-19:117:A/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=CAGCTTTCATTTTATAAAAATCTATGATTTCTCCTTCCAGTTGTTTTTTCTCTTCCTCGAGCTTCCTTATCTCCTCCTGTTGAATCATTTTAAGATGCTC edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+CAGCTTTCATTTTATAAAAATCTATGATTTCTCCTTCCAGTTGTTTTTTCTCTTCCTCGAGCTTCCTTATCTCCTCCTGTTGAATCATTTTAAGATGCTC
++
+C@BB?AB>CH>@86D>9A9DH??;6EDA9@;@:535@615?J?>0DIH3?A9?<839<8B859/,122-3*+254+7*5B/2:;1/&35&883)5%1(1>
+@Id_22 Part1.fastq.000000045 contig=chr1:317720-453948W:ENST00000445840.1:20:180:140:298:A/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
++
+=DINIJBFAAJ@GCFA@@><F=BGK=:>@0,9BE/95<;71447>J+6;274=+?565/64,70-G6@2(//,4364<-916=&3-!+?C&#;!!(*.+<
+@Id_23 Part1.fastq.000000047 contig=chr1:317720-453948W:ENST00000445840.1:21:180:202:333:A/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
++
+FBIB@:B?;DMJA<=;5D<GM9:BBBAB;D>>26<;7>@26:D59D2;><I:/59/5<22.;877G3-9345/33(3"6)>/'2/07)*3%)-!+1!<>#
+@Id_24 Part1.fastq.000000049 contig=chr1:317720-453948W:ENST00000445840.1:22:180:348:477:A/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
++
+@BDJ@GHBKA>:?ABDAB?;88@<EAB;;EJ8@A?@56597:41E3992<40-=3'9,B/8=9<#8<(17/-,.;2027+38'5/6<+:-*-!"6+%#)!
+@Id_25 Part1.fastq.000000051 contig=chr1:317720-453948W:ENST00000445840.1:23:180:100:267:A/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTCTTACGATG edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMEMMMMMMMMMMM strand=forward exp=medium
+TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTACGATG
++
+@@C>F<@?@@C?D=:7<EE>KA<@B<=C<9A9@<280<51:A64564>=8>F(<72697+%/=./(4+3<28,6'5!48.8)?(.)746<!/*&.%/.*,
+@Id_26 Part1.fastq.000000053 contig=chr1:317720-453948W:ENST00000445840.1:24:180:50:207:A/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=TTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTCTTACGATGTTTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCAT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+TTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTCTTACGATGTTTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCAT
++
+FA>CGDB?;HJ??EIDB>=D;;?6:9E:B@6;;>55<:@0:;EC:76-4<<+,=0=<9:;,/A7-<:3#+;?>5<05$3&$>.,'/9*7:B-%,:/3)+-
+@Id_27 Part1.fastq.000000055 contig=chr1:317720-453948W:ENST00000445840.1:25:180:14:194:A/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=TTTTTTTTTTTTTTTCTTCTTACGATGTTTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCATTTTATAAAAATCT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+TTTTTTTTTTTTTTTCTTCTTACGATGTTTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCATTTTATAAAAATCT
++
+DJ@DCE8LCFHGL?;<<OKF>AC?AE<<<=BC3A8@76C82;?9A7C;D==801?<;998639(-1819>1>42-3=7;(-*0<9/CA.10A0($)-//"
+@Id_28 Part1.fastq.000000057 contig=chr1:317720-453948W:ENST00000445840.1:26:180:188:430:A/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMEMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMEMMMMMMMMMMMMMM strand=forward exp=medium
+TTTTTTTTTTTTTTTTTTTTTTTTTTNTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTNTTTTTTTTTTTTTT
++
+>EBDBHCCG@?F=@JCC>?BF?B9DC!5=;.F9227;@3-;76448?.>::/<4'4<+?=?7*+*1>5>90.?02+-33;*-;55!&193-417!/*51!
+@Id_29 Part1.fastq.000000059 contig=chr1:317720-453948W:ENST00000445840.1:27:180:47:118:A/1 haplotype=0 length=100 orig_begin=0 orig_end=67 haplotype_infix=GCAGCTTTCATTTTATAAAAATCTATGATTTCTCCTTCCAGTTGTTTTTTCTCTTCCTCGAGCTTCC edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+GCAGCTTTCATTTTATAAAAATCTATGATTTCTCCTTCCAGTTGTTTTTTCTCTTCCTCGAGCTTCC
++
+CF?CCDE>HDJGEF>5>?B8B<CF9CB6DF;<<@;.?9=>97F=;C614335<3;265)0:7+:@6=
+@Id_30 Part1.fastq.000000061 contig=chr1:317720-453948W:ENST00000445840.1:28:180:126:304:A/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMEMMMMMMMMMMMMEM strand=forward exp=medium
+TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTTTTTTTTTTTTCT
++
+FF??BDCBI>?C9>>FDBA=B?ABA<;?DD;C9;79=04;>@2;87.A7B:-MC=59<=5/(<68:>+=8/6?&2353B65)!5<398:'7-7'00,!21
+@Id_31 Part1.fastq.000000063 contig=chr1:317720-453948W:ENST00000445840.1:29:180:187:390:A/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
++
+LKGK?=G;E?D>@E@@<C?;A;53@63G=89J=;E4FBC?>2<50*EE9;88*;7@0E49,C9)4?>2:0920*18>3<,07)!34)@3%+9-./)-.#*
+@Id_32 Part1.fastq.000000065 contig=chr1:317720-453948W:ENST00000445840.1:30:180:32:142:A/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=AGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCATTTTATAAAAATCTATGATTTCTCCTTCCAGTTGTTTTTTCTCTTCCTCGAGCTTCCTTATCTCCT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMEMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+AGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCATTTTATAAAAATCTATGATTTCTCCTTCCAGTTGTTTTTTCTCTCCCTCGAGCTTCCTTATCTCCT
++
+KCA;@8GA?5@<EA?AB@=>??8FG8CAD>?;B?D<246;8=F@C99/9@E8ACB4<1>++&H6621323/(9+:(A9D&(9124!-4..++3<-202/2
+@Id_33 Part1.fastq.000000067 contig=chr1:317720-453948W:ENST00000445840.1:31:180:-4:196:A/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=TTTTTTTTTTTTTTTTTCTTCTTACGATGTTTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCATTTTATAAAAAT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMEM strand=forward exp=medium
+TTTTTTTTTTTTTTTTTCTTCTTACGATGTTTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCATTTTATAAAATT
++
+DLFJBEFIC@I5K;A;<=98:HE<+D6<>D=3<-1B/>;9248>88A:2822>A:<88B4,:1F)518>8>C%,=1A95:<>+/%,4-;5(98;G)($+!
+@Id_34 Part1.fastq.000000069 contig=chr1:317720-453948W:ENST00000445840.1:32:180:44:221:A/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTCTTACGATGTTTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGCAGTGCTTCA edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTCTTACGATGTTTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGCAGTGCTTCA
++
+HEFG@F=88?J<CBH;=:BAEF?GDH@<<6B=2QF><?>D6<7C7C=:;C87D5*:7%>9638+@;>+?0)!*29<;1+.6&7429*8%,:?0370'+((
+@Id_35 Part1.fastq.000000071 contig=chr1:317720-453948W:ENST00000445840.1:33:180:86:293:A/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMEMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMEM strand=forward exp=medium
+TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGT
++
+CAGKCFJF<@<DHC=@C>=>?<=C9;<C6;DC5;;><@76=77287AB/7570,@:9?41,1<94<:79-105+118/77/1.,.4%(;663616',!+(
+@Id_36 Part1.fastq.000000073 contig=chr1:317720-453948W:ENST00000445840.1:34:180:24:196:A/2 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=TTTTTTTTTTTTTTTTTCTTCTTACGATGTTTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCATTTTATAAAAAT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMEMM strand=forward exp=medium
+TTTTTTTTTTTTTTTTTCTTCTTACGATGTTTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCATTTTATAAAGAT
++
+FGF>E?DJGA<9B@EC<CKADE;7.FF75C>696<A6?2?6<5:=895<A00=B.>:536<16%+?9A48<0:,;(&088%.1)76$4(8433#.+*1,!
+@Id_37 Part1.fastq.000000075 contig=chr1:317720-453948W:ENST00000445840.1:35:180:87:166:A/1 haplotype=0 length=100 orig_begin=0 orig_end=75 haplotype_infix=TTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCATTTTATAAAAATCTATG edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+TTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCATTTTATAAAAATCTATG
++
+>E?ABEH@==G@;A8<J@?>@==CBDC;<?D8A=9?>9F:B8;A<47<231568BC0!??.26-49C(1B484.4
+@Id_38 Part1.fastq.000000077 contig=chr1:317720-453948W:ENST00000445840.1:36:180:-41:170:A/1 haplotype=0 length=100 orig_begin=0 orig_end=100 haplotype_infix=ATGTTTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCATTTTATAAAAATCTATGATTTCTCCTTCCAGTTGTTTT edit_string=MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMEMMMMMMMMMMMMMMMMMMMMMMM strand=forward exp=medium
+ATGTTTGTCTTTCTTTGTATCGGTGCTCAGCTGAGTCTGCAGTGCTTCAGAGGCAGCTTTCATTTTATAAAAATCTNTGATTTCTCCTTCCAGTTGTTTT
++
+HHFIB?BF>:9=E7BC687F=?@;9>CBA==?;8C0I0E8C/5C/@669;=.71<092=846CG.%@5=A<:/*40!9.215==6'-&,717)!6'3".6