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Changeset 0:13e98e2709b8 (2017-09-26)

Next changeset 1:d043b54b3bfb (2017-10-04)

Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 48012d1879395ecf1b4e6cd962f325c372164a33

added:
flash.xml
test-data/flash_forward_in1.fastq
test-data/flash_forward_in2.fastq
test-data/flash_hist_in_out2.tabular
test-data/flash_hist_in_out2.txt
test-data/flash_hist_out1.tabular
test-data/flash_hist_out1.txt
test-data/flash_hist_out2.tabular
test-data/flash_hist_out2.txt
test-data/flash_hist_out_out2.tabular
test-data/flash_hist_out_out2.txt
test-data/flash_merged_out1.fastq
test-data/flash_merged_out2.fastq
test-data/flash_reverse_in1.fastq
test-data/flash_reverse_in2.fastq
test-data/flash_unmerged_f_out1.fastq
test-data/flash_unmerged_f_out2.fastq
test-data/flash_unmerged_r_out1.fastq
test-data/flash_unmerged_r_out2.fastq

diff -r 000000000000 -r 13e98e2709b8 flash.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/flash.xml Tue Sep 26 16:42:09 2017 -0400

[

@@ -0,0 +1,89 @@
+<?xml version="1.0"?>
+<tool id="flash" name="FLASH" version="1.2.11">
+    <description>adjust length of short reads</description>
+    <requirements>
+        <requirement type="package" version="1.2.11">flash</requirement>
+    </requirements>
+    <version_command>flash --version | head -n 1</version_command>
+    <command detect_errors="aggressive">
+        <![CDATA[
+            flash --threads=\${GALAXY_SLOTS:-1}
+                -m $min_overlap
+                -M $max_overlap
+                -x $max_mismatch_density
+                $allow_outies
+                '$forward' '$reverse'
+        ]]>
+    </command>
+    <inputs>
+        <param format="fastq" name="forward" type="data" label="Forward reads" />
+        <param format="fastq" name="reverse" type="data" label="Reverse reads" />
+        <param name="min_overlap" argument="--min-overlap" type="integer" optional="true" value="10" label="Minimum overlap" help="The minimum required overlap length between two reads to provide a confident overlap." />
+        <param name="max_overlap" argument="--max-overlap" type="integer" optional="true" value="65" label="Maximum overlap" help="Maximum overlap length expected in approximately 90% of read pairs. Overlaps longer than the maximum overlap parameter are still considered as good overlaps, but the mismatch density is calculated over the first max_overlap bases in the overlapped region rather than the entire overlap." />
+        <param name="max_mismatch_density" argument="--max-mismatch-density" type="float" optional="true" value="0.25" label="Maximum mismatch density" help="Maximum allowed ratio between the number of mismatched base pairs and the overlap length. Two reads will not be combined with a given overlap if that overlap results in a mismatched base density higher than this value." />
+        <param name="allow_outies" argument="--allow-outies" type="boolean" truevalue="--allow-outies" falsevalue="" checked="false" label="Combine read pairs in both orientations" help="FLASH uses the same parameters when trying each orientation. If a read pair can be combined in either orientation, the better-fitting one will be chosen using the same scoring algorithm that FLASH normally uses." />
+    </inputs>
+    <outputs>
+        <data format="fastq" name="merged_reads" from_work_dir="out.extendedFrags.fastq" label="${tool.name} on ${on_string}: Merged reads" />
+        <data format="fastq" name="unmerged_reads_f" from_work_dir="out.notCombined_1.fastq" label="${tool.name} on ${on_string}: Unmerged forward reads" />
+        <data format="fastq" name="unmerged_reads_r" from_work_dir="out.notCombined_2.fastq" label="${tool.name} on ${on_string}: Unmerged reverse reads" />
+        <data format="tabular" name="hist" from_work_dir="out.hist" label="${tool.name} on ${on_string}: Unmerged reads tabular histogram" />
+        <data format="txt" name="histogram" from_work_dir="out.histogram" label="${tool.name} on ${on_string}: Unmerged reads histogram" />
+        <data format="tabular" name="hist_in" from_work_dir="out.hist.innie" label="${tool.name} on ${on_string}: Unmerged reads tabular histogram (in)" >
+            <filter>allow_outies</filter>
+        </data>
+        <data format="tabular" name="hist_out" from_work_dir="out.hist.outie" label="${tool.name} on ${on_string}: Unmerged reads tabular histogram (out)" >
+            <filter>allow_outies</filter>
+        </data>
+        <data format="txt" name="histogram_in" from_work_dir="out.histogram.innie" label="${tool.name} on ${on_string}: Unmerged reads histogram (in)" >
+            <filter>allow_outies</filter>
+        </data>
+        <data format="txt" name="histogram_out" from_work_dir="out.histogram.outie" label="${tool.name} on ${on_string}: Unmerged reads histogram (out)" >
+            <filter>allow_outies</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="forward" value="flash_forward_in1.fastq" />
+            <param name="reverse" value="flash_reverse_in1.fastq" />
+            <output name="merged_reads" file="flash_merged_out1.fastq" />
+            <output name="unmerged_reads_f" file="flash_unmerged_f_out1.fastq" />
+            <output name="unmerged_reads_r" file="flash_unmerged_r_out1.fastq" />
+            <output name="hist" file="flash_hist_out1.tabular" />
+            <output name="histogram" file="flash_hist_out1.txt" />
+        </test>
+        <test>
+            <param name="forward" value="flash_forward_in2.fastq" />
+            <param name="reverse" value="flash_reverse_in2.fastq" />
+            <param name="allow_outies" value="true" />
+            <output name="merged_reads" file="flash_merged_out2.fastq" />
+            <output name="unmerged_reads_f" file="flash_unmerged_f_out2.fastq" />
+            <output name="unmerged_reads_r" file="flash_unmerged_r_out2.fastq" />
+            <output name="hist" file="flash_hist_out2.tabular" />
+            <output name="histogram" file="flash_hist_out2.txt" />
+            <output name="hist_in" file="flash_hist_in_out2.tabular" />
+            <output name="histogram_in" file="flash_hist_in_out2.txt" />
+            <output name="hist_out" file="flash_hist_out_out2.tabular" />
+            <output name="histogram_out" file="flash_hist_out_out2.txt" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+FLASH (Fast Length Adjustment of SHort reads) is an accurate and fast tool
+to merge paired-end reads that were generated from DNA fragments whose
+lengths are shorter than twice the length of reads.  Merged read pairs result
+in unpaired longer reads, which are generally more desired in genome
+assembly and genome analysis processes.
+
+Briefly, the FLASH algorithm considers all possible overlaps at or above a
+minimum length between the reads in a pair and chooses the overlap that
+results in the lowest mismatch density (proportion of mismatched bases in
+the overlapped region).  Ties between multiple overlaps are broken by
+considering quality scores at mismatch sites.  When building the merged
+sequence, FLASH computes a consensus sequence in the overlapped region.
+]]>
+    </help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btr507</citation>
+    </citations>
+</tool>
\ No newline at end of file

diff -r 000000000000 -r 13e98e2709b8 test-data/flash_forward_in1.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/flash_forward_in1.fastq Tue Sep 26 16:42:09 2017 -0400

b'@@ -0,0 +1,2000 @@\n+@chrM_460_919_3:0:0_1:0:0_0/1\n+CGACTCATCTAGGCATTTTCAGTGCCTTGCTTTATATGTTTAAGCTACATTAACTGGGATGTGGGGCTAACGTAGACATGTAAAATGTTGATCGATAGGGACGAATTAGAGTCAGGTCGGTATATCTATAGATAACTGCGAACAGAGTTATGATTTAGTATTAGTAGCTAGTAATAATAGGGGATTGGTAAGCTTATAAG\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_7564_8021_3:0:0_2:0:0_1/1\n+GAAATACGATTTCCTCAATGGGCTCTTTCCTCTCATTAACAGCAGACATGTTAATAGTTTTCATAGTGTGAGAAGCTTTCGCATCCAAGCTAGAAGTGGCCATAGTAGAACTAACCACAACTAATCTTGAATGATTGCATGGATGTCCTCCTCCGTACCACACATTTGAAGAGCCAACTTACGTACTATTAAAATAAGAA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_9159_9700_2:0:1_4:0:0_2/1\n+GGAATGTGCTTTCTCGGATAATGTCTCGTCATCATTGAAATATAGTTAGTAAGTTGGTAGTTATTCCAAGGGTTAACAGCAGTGTTAAGTTGTAGTGGAATCATATAGCCAGGCCTTAGGTTATTAAGAGGGCTGAAAGGGCTCCTGTAAGTGTCCATGGGCTAGGGTTGACTATGTGGTATGCATTGGTTTGGTGGGTC\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_1576_2102_2:1:0_1:0:0_3/1\n+TCTTTCATCTTTCCCTTGCGGTACTTTCTCTATAGCGCCAAGTTAAATTTCTATCTCCTATACTTTTATAAGGTGACTAAATGTTTTGTTTTATTATCTAGTGTTAGTTGTGTTTGTAGATGTTTGGGCTAGCTTTAGCTCAAGATGGTCAGTTTAATATGAAATCTTCTGGGTGTAAGCCAGATGCTTTGTTTAAGCTA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_2856_3324_2:0:0_6:0:0_4/1\n+AGCTGGTGCACCATCGGGATGTCCTGATCCAACATCGAGTTCGTAAACCCTATTGTCGATATGGACTCTGAAATAGGATTGCGCTGTTATCCCTAGGGTAACTTGTTCCGATGATCAATGTATTTGGATCAATACGTGATGTAGTACTTTCGACTGGTTAGTCTAGATTTAAATCACTCGGAGGTTGTTTTATTCTCCGA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_5342_5909_5:0:0_5:0:0_5/1\n+GGCTGAATGACAGCTATCATAATGTACCGCCCCACAATAATAATCTAAAACCTAACTATCTATATCATTATAACACTCACCACCTACATACTATTTATACACAACTCCACCACAACAACAGCATCCCTATCACAAACATGAAATAAAACCCCTCTAATCACCTCACTCATCCTAGTATTAATAATATCCGTGGGAGGCCT\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_11616_12104_4:0:0_7:0:0_6/1\n+CTGTAGCCCCCGGGGTCGGATTATTGTTCGGCTATGTACTCGTTCATAGTTTGAGTTTGCAAGGCAGAATCGCATAGATGAGGTCAGTCCATGAGCCATTATTAAGGCTGTAGCTCCTATATAGCTTCAGGGTGTTTGGATCAGAACTGGTACAATTACTAGGGCCCTGTGACTTACGGATGAGTATGCGATTAGGGATT\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_11745_12199_2:0:0_3:0:0_7/1\n+ACAAATAGCTCTCCGATTAGATTAATTGTGGGTGGTAGGGCTAGGTTTGCGAGGCTAGCTAGTAGTCATCAGGCAGCTATTAGGGTGAGGCTAGTCTGTAGCCCCCGGGCTAGGATTATTGTTCGGCTATGTACTCGTTCATAGTTTGAGTTTGCAAGGCAGAATCGCATAGATGAGGTCAGTCCATGAGCAATTATTAA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_4974_5463_3:0:0_4:0:0_8/1\n+GCTGTTGTTGTGGTGGAGTTGTGTCTAAATAGTATGAAGGTGGTTAGTGTTATACTGATATAGATAGTTAGGTTTAAGATTATTATTGTGGGGCTGTACATTATGATAGCTGTCATTCAGCCTATATGGGCGAATGAGGAGTATGCTATTATTTTTCGTAGTTGTGTTTGGTTTAGGCCTCCTCAGCCTCCGATTATGAC\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_9579_10013_'..b'2222222222222222\n+@chrM_13938_14449_2:0:0_6:0:0_1eb/1\n+CGTGGGAATTAAGTACGATTAGGCTGAGGGCTAGGGTGATTATGAAAGATAACAAGTAGAGTTTAACTAGTCGTTTCTGATTAGATACAGTAGTAGACATTTTTATTTGGAATAAGGAGATGGCTTTGGGTAATACATTTTCTAGTCAAATTATGTCTACTAGTATCGATGCGGACTTTTGGCTCATAGTTAGGCTCATT\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_7825_8191_3:0:0_2:0:0_1ec/1\n+ACTGTGAGGGAGGGGTTGTTTATTTCATCCATTATATAGAGAATTCGTAAGGAGGGTAGGGCGATAAGAATCAGGATAATAGCAGGTAGGATTGTTCAGATGGTTTCTACTTCTTGAGCATCTATTGTACTCGTGTGCGTGAGCTTGGTTGTTAGCATCAACGAGATAATATAAAGAACTAAAGAGCTGATTAAAAATAC\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_7570_8062_4:0:0_1:0:0_1ed/1\n+CTCGTGTGCGTGAGCTTGGTTGTTAGCATCAACGAGATAATATAAAGAACTAAAGAGCTGATTAAAAATACAATTATTAGTGTGTGGTCGTGAAAGTGTAGGAGTTCTACTATAATGGGGGATGTAGCATCTTGGAAACCTAGTTGAAAGGGGTACGCCATTGAAGCATATAGGATTCAAGCCTATAATTTAACTTCGAC\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_5184_5616_6:0:0_4:0:0_1ee/1\n+AAATTGCACCACTATCCATCCTCTACCAAATCTCATCCACCATTAACCCTAACCTAATCCTAACAATATCCATCATATCAGTCATAATCGGAGGCTGAGGCGGCCTAAAGCAAACACAACTACGAAAAATCCTAGCATACTCCTCAATCGCCCATATAGGCTGAATGACAGCTATCATAATGTACAGCCGCACAATAATA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_6011_6514_3:0:0_7:0:0_1ef/1\n+ATGTTGTTTATTGGGGGAAATGCTATGTCAGGAGCTCCAATTATTAATGGGACCAATCCGTTTCCGAACCCTCCACTTATAATAGGCATCACCAAAAAAAAGATCAATACAAAAGCATGGGCAGTGCCGATTACATTGTAAATCTGATCATCTCCTAGTAGTGTACCAGGTTGGCCCAGTTCGGCCCTGATTAGAAGACT\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_4160_4692_5:0:0_4:1:0_1f0/1\n+CATAATATGATTTATCTCAAGCCTAGCAGAGACCAACCGAGCCCCATTCGACCTGACAGAAGGAGAATCAGAACTAGTCTCGGGATTCGATGTAGAATATGCAGCAGGCCCCTTCGCCCTATTCTTCCTAGCAGAATATGCCCACATCATCATAATAAATATCCTCACAACAATCCTCATCTTCGGAGCATTCCACAGCC\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_7821_8285_3:0:0_3:0:0_1f1/1\n+TTTCTCAATTAAGAAGTATTAGTAAAACACTTACATAACTTTGTCGAAGTTAAATTATAGGCTTGAATCCTATATGCTTCAATGGCGTACCCCTTACAACTAGGTTTCCAAGATGCTACATCCCCCATTATAGAAGAACTCCTACACTTTCACGACCACACACTAATAATTGTATTTTTAATCAGCTCTTTAGTTCTTTC\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_11789_12313_6:0:0_5:0:0_1f2/1\n+GCGTATTACAGTCCTACTTAACCCCTCAACGAACCAAATGGCATACCCCTTTATAATACTATCCGTGTGAGGAATGGTTATAAGAAGCTCCATTTGCCTGCGCCAAACAGACCTAAAATCCCTAATCGCCTACTCATCCGTAATTCACATGGCCCTAGTAATTGTAGCAGTACTGAACCAAACACCCTGAAGCTATATAG\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_6047_6502_2:0:0_6:0:0_1f3/1\n+CCACTTCTCCCGCCGTCTATAAAAAAAAGGCGGGAGAAGCCCCGGCAGCGCCAAGCTGCTTCTTTGAATTTGCAATTCAACATGACATTCACCGCAGGACTTGGTAAAAAGAGGGCTCGAACCTCTGTCTTTAGATTTACAGTCTAATGCTTACTCAGCCATTTTACCTATGTTCATAAACCGGTGAGTATTTTCAACTA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n'

diff -r 000000000000 -r 13e98e2709b8 test-data/flash_forward_in2.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/flash_forward_in2.fastq Tue Sep 26 16:42:09 2017 -0400

diff -r 000000000000 -r 13e98e2709b8 test-data/flash_hist_in_out2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/flash_hist_in_out2.tabular Tue Sep 26 16:42:09 2017 -0400

@@ -0,0 +1,14 @@
+352 1
+367 1
+368 2
+370 1
+374 1
+375 1
+376 2
+377 1
+379 1
+382 1
+383 1
+385 1
+386 1
+388 3

diff -r 000000000000 -r 13e98e2709b8 test-data/flash_hist_in_out2.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/flash_hist_in_out2.txt Tue Sep 26 16:42:09 2017 -0400

@@ -0,0 +1,37 @@
+352 ************************
+353
+354
+355
+356
+357
+358
+359
+360
+361
+362
+363
+364
+365
+366
+367 ************************
+368 ************************************************
+369
+370 ************************
+371
+372
+373
+374 ************************
+375 ************************
+376 ************************************************
+377 ************************
+378
+379 ************************
+380
+381
+382 ************************
+383 ************************
+384
+385 ************************
+386 ************************
+387
+388 ************************************************************************

diff -r 000000000000 -r 13e98e2709b8 test-data/flash_hist_out1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/flash_hist_out1.tabular Tue Sep 26 16:42:09 2017 -0400

@@ -0,0 +1,14 @@
+352 1
+367 1
+368 2
+370 1
+374 1
+375 1
+376 2
+377 1
+379 1
+382 1
+383 1
+385 1
+386 1
+388 3

diff -r 000000000000 -r 13e98e2709b8 test-data/flash_hist_out1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/flash_hist_out1.txt Tue Sep 26 16:42:09 2017 -0400

diff -r 000000000000 -r 13e98e2709b8 test-data/flash_hist_out2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/flash_hist_out2.tabular Tue Sep 26 16:42:09 2017 -0400

@@ -0,0 +1,15 @@
+352 1
+367 1
+368 2
+370 1
+374 1
+375 1
+376 2
+377 1
+379 1
+382 1
+383 1
+385 1
+386 1
+388 3
+390 1

diff -r 000000000000 -r 13e98e2709b8 test-data/flash_hist_out2.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/flash_hist_out2.txt Tue Sep 26 16:42:09 2017 -0400

@@ -0,0 +1,39 @@
+352 ************************
+353
+354
+355
+356
+357
+358
+359
+360
+361
+362
+363
+364
+365
+366
+367 ************************
+368 ************************************************
+369
+370 ************************
+371
+372
+373
+374 ************************
+375 ************************
+376 ************************************************
+377 ************************
+378
+379 ************************
+380
+381
+382 ************************
+383 ************************
+384
+385 ************************
+386 ************************
+387
+388 ************************************************************************
+389
+390 ************************

diff -r 000000000000 -r 13e98e2709b8 test-data/flash_hist_out_out2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/flash_hist_out_out2.tabular Tue Sep 26 16:42:09 2017 -0400

@@ -0,0 +1,1 @@
+390 1

diff -r 000000000000 -r 13e98e2709b8 test-data/flash_hist_out_out2.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/flash_hist_out_out2.txt Tue Sep 26 16:42:09 2017 -0400

@@ -0,0 +1,1 @@
+390 ************************************************************************

diff -r 000000000000 -r 13e98e2709b8 test-data/flash_merged_out1.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/flash_merged_out1.fastq Tue Sep 26 16:42:09 2017 -0400

b'@@ -0,0 +1,72 @@\n+@chrM_200_695_6:0:0_2:0:0_5a\n+GTACGGTCTAGTCTTGTTAGTGGGGTTTGGCAAGACATAAATATGCACGTATTATTATAAATAAGGTTAACGGGGGGTAAGGGGGGTTTGATTAAGCTAGTTATTTACTTAAATTAAAGCGTTCGCGTGTATACGTGTGTACGTGTGTACGTGTGTACGTGTGTACGTGTACACGTGTGTACGTGTGTACGTGTGTACGTGTGTACGTGTGTACGTGTCTACGTGGGTACGTGTGTACGTGTGTACGTGTGTACGTGTGTACGTGTGTACGTGTGTACGTGTGTACGTGTGTTCGTGTACACGTGTGCACGCAAACGTGGGTGAGCGCAGCCCGTGTCCTGTGGAACAATAGGAATTTAAGTATATGTCCTGTGTC\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_149_684_2:0:0_2:0:0_6e\n+CTATGCGGGGTCTCCACACGCAGAGACAGTCAGGGTGCTATTCAGTCAATGGTCACAGGAGATATACTTAAATTCCTATTGTTCCACAGGACACGGGATGCGCGCACCCACGTTTGCGTGCACACGTGTACACGTACACACGTACACACGTACACACGTACACACGTACACACGTACACACGTACACACGTACACACGTACACACGTGTACACGTACACACGTACAAACGTACACACGTACACACGTATACACGCGAACGCTTTAATTTAAGTAAATAACTAGCTTAATCAAACCCCCCTTACCCCCCGTTAACCTTATTTATAATAATACGTGCATATTTATGTCTTGCCAAACCCCACAAACAAGA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_152_616_6:0:0_2:0:0_84\n+TGCGGGGTCTCCACACGCACAGAGAGTCAGGGTGCTATTCAGTCAATGGTCACAGGACATATACTTAAATTCCTATTGTTCCACAGGACACGGGATGCGCGCACCGACGTTTGCGTGCACACGTGTCCACGTACACACGTACACACGTAGACACTTACACACTTACACACGTACACACGTGTACACGTACACACGTACACACGTGTACACGTACACAAGTACACACGTACACACGTGTACACGTACACACGTACACACGTACACACGTACACACGTACACACGTGTACACGTACACACGTACACACGTACACACGTAAACACGTATACACGCGAACGCTTTAATTTAAGTAAATAACTAGCTTAATCAAACCCCCCT\n++\n+222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222##222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_11598_12060_3:0:0_5:0:0_89\n+CATAGTTTGAGTTTGCAAGGCAGAATAGCATAGATGAGGTCAGTCCATGATCAATTATAAAGGCTGTATCTCCTATATAGCTTCAGGGTGTTTTTATCAGTACTGCTACAATTACTAGGGCCATGTGACTTACGGATGAGTATGCGATTAGGGATTTTAGGTCTGTTTGGCGCAGGCAAATGGAGCTTGTAATACGCATTATCCCCTATCCCCCTAGTTTTAGTAATACGGCGGCAAGTACTATTGAACCTGCGATGGGAGCTTCAACATGTGCTTTTGGCAATCATAGGTGGAGTCCATATACAGGTATTTTTACTATAAATGCTATCATGCATGCTAGTCAGAGGAAAATATTGGACCAGGTGGTTGAGATGGGCTTGGCTCAGTA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222#222##222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_4705_5072_2:0:0_2:1:0_b7\n+ATTCTAAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTTATACCCTTCCCATACTAATCAACCCCCCTATCTTTATTATTATTCTATTAACCGTTATCTCAGGAACTATAATTGTAGTGACAACCTCCCACTGACTTCTAGTCTGAATTGGCTTTGAAATCAACCTATTAGCCATCATCCCCATCCTAATGAAAAAATACAACCCACGAGCCATAGAAGCAGCCACAAAATATTTCTTAACACAAGCAGCCGCCTCCATAATCCTAATAATATGATTCATTATCAATCTACTGCACTCGGGACAATGGACCGTACTAAAAGACCTTAATCCCATAGCATCAATCATAA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222#2#2222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_3253_3640_6:1:0_8:0:0_10a\n+AGT'..b'22222222222222\n+@chrM_209_705_3:0:0_2:0:0_1b3\n+TTATATTTAGGTACGGTCTAGTCTTGTTTGTGGGGTTTGGCAATACATAAATAGGCACGTATTATTATAAATAAGGTTAACGGGGGGTAAGGGGGGTTTGATTAAGCTAGTTATTTACTTAAATTACAGCGTTCGCGTGTATACGTGTGTACGTGTGTACGTGTGTACGTGTGTACGTGTACACGTGTGTACGTGTGTACGTGTGTACGTGTGTACGTGTGTACGTGTGTACGTGTGTACGTGTCTACGTGTGTACGTGTGTACGTGTGTACGTGGGTACGTGTGTACGTGTCTACGTGTGTACGTGTGTACGTGTACACGTGTGCACGCAAACGTGGGTGCGCGCATCCCGTGTCCTGTGGAACAATAGGAATTTAAGTATATG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_247_748_8:0:0_1:0:0_1b7\n+TGCGCGCACCCCCGTTTGCGTGCACACGTGTACACGTACACACGTACACACGTCCACACGTCCACACGAACACACGTACACACTTACACACGTACACACGTACACACGTACACACTTACACACGTACACACGTAGACACGTACACACGTACACACGTCCACACGTACACACGTGTACACGTACACACGTACACACGTATACACGCGAACGCTTTAATTTAAGTAAATAACTAGCTTAATCAAACCCCCCTTACCCCCCGTTAACCTTATTTATAATAATACGTGCCTATTTATGTCTTGCCATACCCCACAAACAAGACTAGACCGTACCTAAATATAAGGCCTAAGAAAACGCTTATAAGCTTACCAATCCCCTATTATTA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222#2222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_16370_16833_6:1:0_6:0:1_1bb\n+TACTGTGCTTGGCCAGTATGTCTTTATTTCCCACAAAAAAACGAAGTAAAAACCCCCAAACACCACAACCCAAAACACACACTGTAAAATCACTCTATTAACCACCAACTCACCCCAGGGGGAATTATACACCCATATACCTAAGACATACTATGTACATCGTGCATTAATTGCTAGTCCGCATGAATATTAAGCATGTACAGTAGTTTAGATATATTACATAAGACATACTATGGATATCGTGCATTAATTGCTAGTCCCCATGAATATTAAGCATGTACTGAGTAGTTTATATATATTACAGAAGACATAATAGTGCTTAAGCGTGCATTCACCTTAATTCTAGGACAGTCTGCTAGGGACCTCAACTATTCCAAAGAGCTTAA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_170_695_1:0:0_6:0:0_1e3\n+GTACGTTCTAGTCTTGTTAGTGGGGTTTGGCAAGACATAAATAGGCACGTATTAATATAAATAAGGTTAACGGGGGGTCAGGGGGGTTTGATTCAGCTAGTTATTTACTTAAATTAAAGCGTTCGCGTGTATACGTGTGTACGTGTGTACGTGTGTACGTGTGTACGTGAACACGTGTGTACGTGTGTACGTGTGTACGTGTGTACGTGTGTACGTGTGTACGTGTGTTCGTGTGTACGTGTGTACGTGTGTACGTGTGTACGTGTACACGTGTGCACGCAAACGTGGGTGCGCGCATCCCGTGTCCTGTGGAACAATAGGAATTTAAGTATATGTCCTGTGACCATTGACTGAATAGCACCCTGACTGTCTGT\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_7825_8191_3:0:0_2:0:0_1ec\n+ACTGTGAGGGAGGGGTTGTTTATTTCATCCATTATATAGAGAATTCGTAAGGAGGGTAGGGCGATAAGAATCAGGATAATAGCAGGTAGGATTGTTCAGATGGTTTCTACTTCTTGAGCATCTATTGTACTCGTGTGCGTGAGCTTGGTTGTTAGCATCAACGAGATAATATAAAGAACTAAAGAGCTGATTAAAAATACAATTATTAGTGTGTGGTCGTGATAGTGTAGGAGTTCTTCTATAATGGGGGATGTAGCATCTTGGTAACCTAGTTGAAAGGGGTACGCCATTGAAGCATATAGGATTCAAGCCTATAATTTAACTTCGACAAAGTTATGTAATTGTTTTACTAAGACTTCTTAATTGA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n'

diff -r 000000000000 -r 13e98e2709b8 test-data/flash_merged_out2.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/flash_merged_out2.fastq Tue Sep 26 16:42:09 2017 -0400

b'@@ -0,0 +1,76 @@\n+@chrM_200_695_6:0:0_2:0:0_5a\n+GTACGGTCTAGTCTTGTTAGTGGGGTTTGGCAAGACATAAATATGCACGTATTATTATAAATAAGGTTAACGGGGGGTAAGGGGGGTTTGATTAAGCTAGTTATTTACTTAAATTAAAGCGTTCGCGTGTATACGTGTGTACGTGTGTACGTGTGTACGTGTGTACGTGTACACGTGTGTACGTGTGTACGTGTGTACGTGTGTACGTGTGTACGTGTCTACGTGGGTACGTGTGTACGTGTGTACGTGTGTACGTGTGTACGTGTGTACGTGTGTACGTGTGTACGTGTGTTCGTGTACACGTGTGCACGCAAACGTGGGTGAGCGCAGCCCGTGTCCTGTGGAACAATAGGAATTTAAGTATATGTCCTGTGTC\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_149_684_2:0:0_2:0:0_6e\n+CTATGCGGGGTCTCCACACGCAGAGACAGTCAGGGTGCTATTCAGTCAATGGTCACAGGAGATATACTTAAATTCCTATTGTTCCACAGGACACGGGATGCGCGCACCCACGTTTGCGTGCACACGTGTACACGTACACACGTACACACGTACACACGTACACACGTACACACGTACACACGTACACACGTACACACGTACACACGTGTACACGTACACACGTACAAACGTACACACGTACACACGTATACACGCGAACGCTTTAATTTAAGTAAATAACTAGCTTAATCAAACCCCCCTTACCCCCCGTTAACCTTATTTATAATAATACGTGCATATTTATGTCTTGCCAAACCCCACAAACAAGA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_152_616_6:0:0_2:0:0_84\n+TGCGGGGTCTCCACACGCACAGAGAGTCAGGGTGCTATTCAGTCAATGGTCACAGGACATATACTTAAATTCCTATTGTTCCACAGGACACGGGATGCGCGCACCGACGTTTGCGTGCACACGTGTCCACGTACACACGTACACACGTAGACACTTACACACTTACACACGTACACACGTGTACACGTACACACGTACACACGTGTACACGTACACAAGTACACACGTACACACGTGTACACGTACACACGTACACACGTACACACGTACACACGTACACACGTGTACACGTACACACGTACACACGTACACACGTAAACACGTATACACGCGAACGCTTTAATTTAAGTAAATAACTAGCTTAATCAAACCCCCCT\n++\n+222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222##222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_11598_12060_3:0:0_5:0:0_89\n+CATAGTTTGAGTTTGCAAGGCAGAATAGCATAGATGAGGTCAGTCCATGATCAATTATAAAGGCTGTATCTCCTATATAGCTTCAGGGTGTTTTTATCAGTACTGCTACAATTACTAGGGCCATGTGACTTACGGATGAGTATGCGATTAGGGATTTTAGGTCTGTTTGGCGCAGGCAAATGGAGCTTGTAATACGCATTATCCCCTATCCCCCTAGTTTTAGTAATACGGCGGCAAGTACTATTGAACCTGCGATGGGAGCTTCAACATGTGCTTTTGGCAATCATAGGTGGAGTCCATATACAGGTATTTTTACTATAAATGCTATCATGCATGCTAGTCAGAGGAAAATATTGGACCAGGTGGTTGAGATGGGCTTGGCTCAGTA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222#222##222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_4705_5072_2:0:0_2:1:0_b7\n+ATTCTAAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTTATACCCTTCCCATACTAATCAACCCCCCTATCTTTATTATTATTCTATTAACCGTTATCTCAGGAACTATAATTGTAGTGACAACCTCCCACTGACTTCTAGTCTGAATTGGCTTTGAAATCAACCTATTAGCCATCATCCCCATCCTAATGAAAAAATACAACCCACGAGCCATAGAAGCAGCCACAAAATATTTCTTAACACAAGCAGCCGCCTCCATAATCCTAATAATATGATTCATTATCAATCTACTGCACTCGGGACAATGGACCGTACTAAAAGACCTTAATCCCATAGCATCAATCATAA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222#2#2222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_11067_11640_2:0:0_7:0:0_d2\n+CA'..b'22222222222222\n+@chrM_209_705_3:0:0_2:0:0_1b3\n+TTATATTTAGGTACGGTCTAGTCTTGTTTGTGGGGTTTGGCAATACATAAATAGGCACGTATTATTATAAATAAGGTTAACGGGGGGTAAGGGGGGTTTGATTAAGCTAGTTATTTACTTAAATTACAGCGTTCGCGTGTATACGTGTGTACGTGTGTACGTGTGTACGTGTGTACGTGTACACGTGTGTACGTGTGTACGTGTGTACGTGTGTACGTGTGTACGTGTGTACGTGTGTACGTGTCTACGTGTGTACGTGTGTACGTGTGTACGTGGGTACGTGTGTACGTGTCTACGTGTGTACGTGTGTACGTGTACACGTGTGCACGCAAACGTGGGTGCGCGCATCCCGTGTCCTGTGGAACAATAGGAATTTAAGTATATG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_247_748_8:0:0_1:0:0_1b7\n+TGCGCGCACCCCCGTTTGCGTGCACACGTGTACACGTACACACGTACACACGTCCACACGTCCACACGAACACACGTACACACTTACACACGTACACACGTACACACGTACACACTTACACACGTACACACGTAGACACGTACACACGTACACACGTCCACACGTACACACGTGTACACGTACACACGTACACACGTATACACGCGAACGCTTTAATTTAAGTAAATAACTAGCTTAATCAAACCCCCCTTACCCCCCGTTAACCTTATTTATAATAATACGTGCCTATTTATGTCTTGCCATACCCCACAAACAAGACTAGACCGTACCTAAATATAAGGCCTAAGAAAACGCTTATAAGCTTACCAATCCCCTATTATTA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222#2222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_16370_16833_6:1:0_6:0:1_1bb\n+TACTGTGCTTGGCCAGTATGTCTTTATTTCCCACAAAAAAACGAAGTAAAAACCCCCAAACACCACAACCCAAAACACACACTGTAAAATCACTCTATTAACCACCAACTCACCCCAGGGGGAATTATACACCCATATACCTAAGACATACTATGTACATCGTGCATTAATTGCTAGTCCGCATGAATATTAAGCATGTACAGTAGTTTAGATATATTACATAAGACATACTATGGATATCGTGCATTAATTGCTAGTCCCCATGAATATTAAGCATGTACTGAGTAGTTTATATATATTACAGAAGACATAATAGTGCTTAAGCGTGCATTCACCTTAATTCTAGGACAGTCTGCTAGGGACCTCAACTATTCCAAAGAGCTTAA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_170_695_1:0:0_6:0:0_1e3\n+GTACGTTCTAGTCTTGTTAGTGGGGTTTGGCAAGACATAAATAGGCACGTATTAATATAAATAAGGTTAACGGGGGGTCAGGGGGGTTTGATTCAGCTAGTTATTTACTTAAATTAAAGCGTTCGCGTGTATACGTGTGTACGTGTGTACGTGTGTACGTGTGTACGTGAACACGTGTGTACGTGTGTACGTGTGTACGTGTGTACGTGTGTACGTGTGTACGTGTGTTCGTGTGTACGTGTGTACGTGTGTACGTGTGTACGTGTACACGTGTGCACGCAAACGTGGGTGCGCGCATCCCGTGTCCTGTGGAACAATAGGAATTTAAGTATATGTCCTGTGACCATTGACTGAATAGCACCCTGACTGTCTGT\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_7825_8191_3:0:0_2:0:0_1ec\n+ACTGTGAGGGAGGGGTTGTTTATTTCATCCATTATATAGAGAATTCGTAAGGAGGGTAGGGCGATAAGAATCAGGATAATAGCAGGTAGGATTGTTCAGATGGTTTCTACTTCTTGAGCATCTATTGTACTCGTGTGCGTGAGCTTGGTTGTTAGCATCAACGAGATAATATAAAGAACTAAAGAGCTGATTAAAAATACAATTATTAGTGTGTGGTCGTGATAGTGTAGGAGTTCTTCTATAATGGGGGATGTAGCATCTTGGTAACCTAGTTGAAAGGGGTACGCCATTGAAGCATATAGGATTCAAGCCTATAATTTAACTTCGACAAAGTTATGTAATTGTTTTACTAAGACTTCTTAATTGA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n'

diff -r 000000000000 -r 13e98e2709b8 test-data/flash_reverse_in1.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/flash_reverse_in1.fastq Tue Sep 26 16:42:09 2017 -0400

b'@@ -0,0 +1,2000 @@\n+@chrM_460_919_3:0:0_1:0:0_0/2\n+ACACACGTACACACGTGTACACGTACACACGTACACACGTCCACACGTACACACGTACACACGTGTACCCGTACACACGTACACACGTACACACGTACACACGTATACACGCGAACGCTTTAATTTAAGTAAATAACTAGCTTAATCAAACCCCCCTTACCGCCCGTTAACCTTATTTATAATAATACGTGCCTATTTAT\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_7564_8021_3:0:0_2:0:0_1/2\n+ATAAAGAACTAAAGAGCTGATTAAAAATACAATTATTAGTGTGTGGTCGTGAAAGTGTAGGAGTTGTTCTATAATGGGGGATGTAGCATCTTGGAAACCTATTTGAAAGGGGTACGCCATTGAAGCATATAGGATTCAAGCCTATAATTTAACTTCGACAAAGTTATGTAATTGTTTTACTAATACTTCTTAATTGAGAA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_9159_9700_2:0:1_4:0:0_2/2\n+TTACCGGGTTACGCCACAAGACTAAAGCATCTCTGGCCCACTTTCTACCACAAGTAACACCTGTCCCCCTAATTCCTATGCTTGTAGTCATTAGAGACTATCAGCCTCTTTATCCAACCTATAGCTCTCGCCGTACGACTTACAGCCAACATCACCGCAGGTCACTTATTAATACATCTAATTGGAGGGGCCGCCCTAGC\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_1576_2102_2:1:0_1:0:0_3/2\n+TAAAAAGGAAGAAAAGTAAGCACAAGTATGTAAACATAAAAAAGTTAGGTCAAGGTGTAGCTCATGAGATGGGAAGCAATGGGCTACATTTTCTAAAATTAGAACACTCACGAAGATCCTTACGAAACTAAGTATTAAAGGAGGATTTAGTAGTAAATTTGAGAATAGAGAGCTCAATTGAATCGGGCCATGAAGCACGC\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_2856_3324_2:0:0_6:0:0_4/2\n+CTAGTTAAACGGCCGCGGTATCCTGACCGTGCAAAGGTCGCATAATCATTTGTTCCCTAAATAGGGACTTGTATGAACGGCCACACGAGGGCTTTACTGTCTCTTACTTCCAATCCGTGAAATTGACCTTCCCGTGAAGAGGCGGGAATATAATAATAAGACGAGAAGACCCTATGGAGCTTTCATTAACCGACCCAAAG\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_5342_5909_5:0:0_5:0:0_5/2\n+TTAGAATGGTTTAGATGTGCAGAAGTTAAGTCTGTAGGCCTTGCTTAGAGCTTTGAAGGCTCTTGGTCTAGTTTAACCTAAACTTCAAAACCAGGATAGATAGTATAGGTGCGAGTGGAAGTAGTCTGGTTGATATTACAACTAGAGGGGGTAGGAAGGTTATTTTTTTTGTGCATTCAAATCGTCATTTTATTTTTATA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_11616_12104_4:0:0_7:0:0_6/2\n+TCAACCACCTGGTCCAATAATTTCCTCTGACTAGCATGCATGATAGCATTTATAGTAAAAATACCTCTATATGGACTCCACCTATGATTGCCAAAAGGACATGTTGAAGCTCCCATCGCTGGATCAATAGTACTTTCCGCCGTATTACTAAAACTAGGGGGATACGGGATAATGCGTATTACAGTCCTACTTAACCCCGC\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_11745_12199_2:0:0_3:0:0_7/2\n+GTACTTGCCGCCGTATTACTAAAACTAGGGGGATACGGGATAATGCGTATTACAGTCCTACTTAACCCCGCAACGAACCAAATGGCATACCCCTTTATAATACTATCCCTGTGAGGAATGGTTATAACACGCTCCATTTGCCTGCGCCAAACAGACCAAAAATCCCTAATCGCATACTCATCCGTAAGTCACATGGCCCT\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_4974_5463_3:0:0_4:0:0_8/2\n+CCGCCTCCATAATCCTAATAATATGAATCATTATCAATCTACTGCACTCGGGACAATGGACCGTACTAAAAGACCTTAATCCCATAGCATCAATCATAATAACAACCGCTCTAGCAATAAAACTAGGAGTAGCCCCATTCCACTTCAGAGTACCGGAAGTTACACAAGGAATTTCTATATCATCAGGCTTAATTCTACTA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_9579_10013_'..b'2222222222222222\n+@chrM_13938_14449_2:0:0_6:0:0_1eb/2\n+ACGATTCAATACCTTGAATCTAATCAATGAAAATAATACCCACCTCATCAACTCCATTAAACGTCTCTTAATCGGAAGTATCTTTGCAGGATATCTAATTTCTTACAACATCCCCCCAACAACTATCCCACAAATAACTATCCCCTACTATCAAAAACTAACTGCTCTTGCCGTGACTATCGCAGGCTTCATCCTAGCAT\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_7825_8191_3:0:0_2:0:0_1ec/2\n+TCAATTAAGAAGTCTTAGTAAAACAATTACATAACTTTGTCGAAGTTAAATTATAGGCTTGAATCCTATATGCTTCAATGGCGTACCCCTTTCAACTAGGTTACCAAGATGCTACATCCCCCATTATAGAAGAACTCCTACACTATCACGACCACACACTAATAATTGTATTTTTAATCAGCTCTTTAGTTCTTTATATT\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_7570_8062_4:0:0_1:0:0_1ed/2\n+CGATTTCCTCAATGGGCTCTTTGATCTCATTAACAGCAGTCATGTTAATAGTTTTCATAGTGTGAGAAGCTTTCGCATCCAAGCGAGAAGTGGCCATAGTAGAACTAACCACAACTAATCATGAATGATTGCATGGATGTCCTCCTCCGTACCACACAATTGAAGAGCCAACTTACGTACTATTAAAATAAGAACGGAAG\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_5184_5616_6:0:0_4:0:0_1ee/2\n+GGCCTTATGCTTAATTCATTTTTAGTCAATTCTTGGATGATTATTCATTTTGGGATAAATCCGGAGAGTGGGGGGAGGCCTCCCAGGGAAATTATTAATACTAGGATGAGTGAGGTGATTAGAGGGGTTTTATTTCATGTTTGTGATAGGGATGCTGTAGTTGTGGTGGAGTTGTGTATAAATAGTATGAAGGTGGTTAG\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_6011_6514_3:0:0_7:0:0_1ef/2\n+GTTAACAGCTAAATGCCCTAATCAACTGGCTTCAATCCACTTCTCCCGCCGTCTAGAAAAAAAAGGCGGGATAAGCCCCGGCAGCGCCAAGCTGCTTCTTTGAATTTGCAATTCAACATGACATTCACCGCAGGACTTGGTAAAAAGAGGGCTCGAACCTCTGTCTTTAGATTTCCAGTCTAATGCTTACTCAGGCATTT\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_4160_4692_5:0:0_4:1:0_1f0/2\n+TGGTAGCACGAAGATTTATGGATTCTTAGGCTTAGGTTCGATTCCTGTTATTCTAGAAATAAGAGGGTTTCAACCTCTATGTTTTACTCTATCAAAGTAACTCTTTTGTCAGACATATTTCTTATGTTTGAGGTGGGATGCATGCTGTGATGATAGGTAGGGATACATGTCATATGCATAGGGGTAGGGTGAGAGGCAGA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_7821_8285_3:0:0_3:0:0_1f1/2\n+TAGCTCTTGGGTAGGAATTATGTAAGAGTCAAAATTCAAGACTTCGTAATCAGTGTACTCATAACTTCAATATCATTGATGTCCTATGGTTTTTACTTTGAGGGAGGGGTTGTTGATTTCATCCATTATATAGAGAATTCGTAAGGAGGGTAGGGCGATACGAATCAGGATAATAGCAGGTAGGATGGTTCAGATGGTTT\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_11789_12313_6:0:0_5:0:0_1f2/2\n+TATTTGCCTCGTTGAGTTATAATAAGTATGTAGAGGTAGTATAGGGCTGTACTGATGATATTAGTACCCCTTAGGATACTGGTTATGTTTGATCATGAGAAGGAGGCTATTACTACAAATAGCTCTCCGATTAGATTAATTGTGGGTGGTAGGGCTAGGATTGCGAGGCTAGCTAGTAGTCATCAGGCAGCTATTAGGGG\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_6047_6502_2:0:0_6:0:0_1f3/2\n+CGGGGCAATGCTATGTCAGGAGCTCCAATTATTAATGGGACCAATCAGTTTCCGACCCCTCCAATTATCATAGGCATCACCATACAAAAGATCATTACAAAAGCATGGGCAGTGACGATTACATTGTAAATCTGATCATCTCCTAGTAGTGTACCAGGTTGGCGCATTTCGGCCCGGATTAGAAGACTAAGAGCAGTCCC\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n'

diff -r 000000000000 -r 13e98e2709b8 test-data/flash_reverse_in2.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/flash_reverse_in2.fastq Tue Sep 26 16:42:09 2017 -0400

diff -r 000000000000 -r 13e98e2709b8 test-data/flash_unmerged_f_out1.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/flash_unmerged_f_out1.fastq Tue Sep 26 16:42:09 2017 -0400

b'@@ -0,0 +1,1928 @@\n+@chrM_460_919_3:0:0_1:0:0_0/1\n+CGACTCATCTAGGCATTTTCAGTGCCTTGCTTTATATGTTTAAGCTACATTAACTGGGATGTGGGGCTAACGTAGACATGTAAAATGTTGATCGATAGGGACGAATTAGAGTCAGGTCGGTATATCTATAGATAACTGCGAACAGAGTTATGATTTAGTATTAGTAGCTAGTAATAATAGGGGATTGGTAAGCTTATAAG\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_7564_8021_3:0:0_2:0:0_1/1\n+GAAATACGATTTCCTCAATGGGCTCTTTCCTCTCATTAACAGCAGACATGTTAATAGTTTTCATAGTGTGAGAAGCTTTCGCATCCAAGCTAGAAGTGGCCATAGTAGAACTAACCACAACTAATCTTGAATGATTGCATGGATGTCCTCCTCCGTACCACACATTTGAAGAGCCAACTTACGTACTATTAAAATAAGAA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_9159_9700_2:0:1_4:0:0_2/1\n+GGAATGTGCTTTCTCGGATAATGTCTCGTCATCATTGAAATATAGTTAGTAAGTTGGTAGTTATTCCAAGGGTTAACAGCAGTGTTAAGTTGTAGTGGAATCATATAGCCAGGCCTTAGGTTATTAAGAGGGCTGAAAGGGCTCCTGTAAGTGTCCATGGGCTAGGGTTGACTATGTGGTATGCATTGGTTTGGTGGGTC\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_1576_2102_2:1:0_1:0:0_3/1\n+TCTTTCATCTTTCCCTTGCGGTACTTTCTCTATAGCGCCAAGTTAAATTTCTATCTCCTATACTTTTATAAGGTGACTAAATGTTTTGTTTTATTATCTAGTGTTAGTTGTGTTTGTAGATGTTTGGGCTAGCTTTAGCTCAAGATGGTCAGTTTAATATGAAATCTTCTGGGTGTAAGCCAGATGCTTTGTTTAAGCTA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_2856_3324_2:0:0_6:0:0_4/1\n+AGCTGGTGCACCATCGGGATGTCCTGATCCAACATCGAGTTCGTAAACCCTATTGTCGATATGGACTCTGAAATAGGATTGCGCTGTTATCCCTAGGGTAACTTGTTCCGATGATCAATGTATTTGGATCAATACGTGATGTAGTACTTTCGACTGGTTAGTCTAGATTTAAATCACTCGGAGGTTGTTTTATTCTCCGA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_5342_5909_5:0:0_5:0:0_5/1\n+GGCTGAATGACAGCTATCATAATGTACCGCCCCACAATAATAATCTAAAACCTAACTATCTATATCATTATAACACTCACCACCTACATACTATTTATACACAACTCCACCACAACAACAGCATCCCTATCACAAACATGAAATAAAACCCCTCTAATCACCTCACTCATCCTAGTATTAATAATATCCGTGGGAGGCCT\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_11616_12104_4:0:0_7:0:0_6/1\n+CTGTAGCCCCCGGGGTCGGATTATTGTTCGGCTATGTACTCGTTCATAGTTTGAGTTTGCAAGGCAGAATCGCATAGATGAGGTCAGTCCATGAGCCATTATTAAGGCTGTAGCTCCTATATAGCTTCAGGGTGTTTGGATCAGAACTGGTACAATTACTAGGGCCCTGTGACTTACGGATGAGTATGCGATTAGGGATT\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_11745_12199_2:0:0_3:0:0_7/1\n+ACAAATAGCTCTCCGATTAGATTAATTGTGGGTGGTAGGGCTAGGTTTGCGAGGCTAGCTAGTAGTCATCAGGCAGCTATTAGGGTGAGGCTAGTCTGTAGCCCCCGGGCTAGGATTATTGTTCGGCTATGTACTCGTTCATAGTTTGAGTTTGCAAGGCAGAATCGCATAGATGAGGTCAGTCCATGAGCAATTATTAA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_4974_5463_3:0:0_4:0:0_8/1\n+GCTGTTGTTGTGGTGGAGTTGTGTCTAAATAGTATGAAGGTGGTTAGTGTTATACTGATATAGATAGTTAGGTTTAAGATTATTATTGTGGGGCTGTACATTATGATAGCTGTCATTCAGCCTATATGGGCGAATGAGGAGTATGCTATTATTTTTCGTAGTTGTGTTTGGTTTAGGCCTCCTCAGCCTCCGATTATGAC\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_9579_10013_'..b'2222222222222222\n+@chrM_1605_2128_3:1:0_4:1:0_1ea/1\n+CTTAACATAACAAAGTTAGGTCAAGGTGTAGCTCATGAGATGGGAAGCAATGGGCTACATTTTCTAAAATTAGAACACTCACGAAGATCCTTACGAAACTAAGTATTAAAGGAGGATTTAGTAGTAAATTTGAGAATAGAGAGCTCAATTGAATCTGGCCATGAAGCACGCACACACCGCCCGTCCCCCTCCTCAAGTGG\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_13938_14449_2:0:0_6:0:0_1eb/1\n+CGTGGGAATTAAGTACGATTAGGCTGAGGGCTAGGGTGATTATGAAAGATAACAAGTAGAGTTTAACTAGTCGTTTCTGATTAGATACAGTAGTAGACATTTTTATTTGGAATAAGGAGATGGCTTTGGGTAATACATTTTCTAGTCAAATTATGTCTACTAGTATCGATGCGGACTTTTGGCTCATAGTTAGGCTCATT\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_7570_8062_4:0:0_1:0:0_1ed/1\n+CTCGTGTGCGTGAGCTTGGTTGTTAGCATCAACGAGATAATATAAAGAACTAAAGAGCTGATTAAAAATACAATTATTAGTGTGTGGTCGTGAAAGTGTAGGAGTTCTACTATAATGGGGGATGTAGCATCTTGGAAACCTAGTTGAAAGGGGTACGCCATTGAAGCATATAGGATTCAAGCCTATAATTTAACTTCGAC\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_5184_5616_6:0:0_4:0:0_1ee/1\n+AAATTGCACCACTATCCATCCTCTACCAAATCTCATCCACCATTAACCCTAACCTAATCCTAACAATATCCATCATATCAGTCATAATCGGAGGCTGAGGCGGCCTAAAGCAAACACAACTACGAAAAATCCTAGCATACTCCTCAATCGCCCATATAGGCTGAATGACAGCTATCATAATGTACAGCCGCACAATAATA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_6011_6514_3:0:0_7:0:0_1ef/1\n+ATGTTGTTTATTGGGGGAAATGCTATGTCAGGAGCTCCAATTATTAATGGGACCAATCCGTTTCCGAACCCTCCACTTATAATAGGCATCACCAAAAAAAAGATCAATACAAAAGCATGGGCAGTGCCGATTACATTGTAAATCTGATCATCTCCTAGTAGTGTACCAGGTTGGCCCAGTTCGGCCCTGATTAGAAGACT\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_4160_4692_5:0:0_4:1:0_1f0/1\n+CATAATATGATTTATCTCAAGCCTAGCAGAGACCAACCGAGCCCCATTCGACCTGACAGAAGGAGAATCAGAACTAGTCTCGGGATTCGATGTAGAATATGCAGCAGGCCCCTTCGCCCTATTCTTCCTAGCAGAATATGCCCACATCATCATAATAAATATCCTCACAACAATCCTCATCTTCGGAGCATTCCACAGCC\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_7821_8285_3:0:0_3:0:0_1f1/1\n+TTTCTCAATTAAGAAGTATTAGTAAAACACTTACATAACTTTGTCGAAGTTAAATTATAGGCTTGAATCCTATATGCTTCAATGGCGTACCCCTTACAACTAGGTTTCCAAGATGCTACATCCCCCATTATAGAAGAACTCCTACACTTTCACGACCACACACTAATAATTGTATTTTTAATCAGCTCTTTAGTTCTTTC\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_11789_12313_6:0:0_5:0:0_1f2/1\n+GCGTATTACAGTCCTACTTAACCCCTCAACGAACCAAATGGCATACCCCTTTATAATACTATCCGTGTGAGGAATGGTTATAAGAAGCTCCATTTGCCTGCGCCAAACAGACCTAAAATCCCTAATCGCCTACTCATCCGTAATTCACATGGCCCTAGTAATTGTAGCAGTACTGAACCAAACACCCTGAAGCTATATAG\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_6047_6502_2:0:0_6:0:0_1f3/1\n+CCACTTCTCCCGCCGTCTATAAAAAAAAGGCGGGAGAAGCCCCGGCAGCGCCAAGCTGCTTCTTTGAATTTGCAATTCAACATGACATTCACCGCAGGACTTGGTAAAAAGAGGGCTCGAACCTCTGTCTTTAGATTTACAGTCTAATGCTTACTCAGCCATTTTACCTATGTTCATAAACCGGTGAGTATTTTCAACTA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n'

diff -r 000000000000 -r 13e98e2709b8 test-data/flash_unmerged_f_out2.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/flash_unmerged_f_out2.fastq Tue Sep 26 16:42:09 2017 -0400

b'@@ -0,0 +1,1924 @@\n+@chrM_460_919_3:0:0_1:0:0_0/1\n+CGACTCATCTAGGCATTTTCAGTGCCTTGCTTTATATGTTTAAGCTACATTAACTGGGATGTGGGGCTAACGTAGACATGTAAAATGTTGATCGATAGGGACGAATTAGAGTCAGGTCGGTATATCTATAGATAACTGCGAACAGAGTTATGATTTAGTATTAGTAGCTAGTAATAATAGGGGATTGGTAAGCTTATAAG\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_7564_8021_3:0:0_2:0:0_1/1\n+GAAATACGATTTCCTCAATGGGCTCTTTCCTCTCATTAACAGCAGACATGTTAATAGTTTTCATAGTGTGAGAAGCTTTCGCATCCAAGCTAGAAGTGGCCATAGTAGAACTAACCACAACTAATCTTGAATGATTGCATGGATGTCCTCCTCCGTACCACACATTTGAAGAGCCAACTTACGTACTATTAAAATAAGAA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_9159_9700_2:0:1_4:0:0_2/1\n+GGAATGTGCTTTCTCGGATAATGTCTCGTCATCATTGAAATATAGTTAGTAAGTTGGTAGTTATTCCAAGGGTTAACAGCAGTGTTAAGTTGTAGTGGAATCATATAGCCAGGCCTTAGGTTATTAAGAGGGCTGAAAGGGCTCCTGTAAGTGTCCATGGGCTAGGGTTGACTATGTGGTATGCATTGGTTTGGTGGGTC\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_1576_2102_2:1:0_1:0:0_3/1\n+TCTTTCATCTTTCCCTTGCGGTACTTTCTCTATAGCGCCAAGTTAAATTTCTATCTCCTATACTTTTATAAGGTGACTAAATGTTTTGTTTTATTATCTAGTGTTAGTTGTGTTTGTAGATGTTTGGGCTAGCTTTAGCTCAAGATGGTCAGTTTAATATGAAATCTTCTGGGTGTAAGCCAGATGCTTTGTTTAAGCTA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_2856_3324_2:0:0_6:0:0_4/1\n+AGCTGGTGCACCATCGGGATGTCCTGATCCAACATCGAGTTCGTAAACCCTATTGTCGATATGGACTCTGAAATAGGATTGCGCTGTTATCCCTAGGGTAACTTGTTCCGATGATCAATGTATTTGGATCAATACGTGATGTAGTACTTTCGACTGGTTAGTCTAGATTTAAATCACTCGGAGGTTGTTTTATTCTCCGA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_5342_5909_5:0:0_5:0:0_5/1\n+GGCTGAATGACAGCTATCATAATGTACCGCCCCACAATAATAATCTAAAACCTAACTATCTATATCATTATAACACTCACCACCTACATACTATTTATACACAACTCCACCACAACAACAGCATCCCTATCACAAACATGAAATAAAACCCCTCTAATCACCTCACTCATCCTAGTATTAATAATATCCGTGGGAGGCCT\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_11616_12104_4:0:0_7:0:0_6/1\n+CTGTAGCCCCCGGGGTCGGATTATTGTTCGGCTATGTACTCGTTCATAGTTTGAGTTTGCAAGGCAGAATCGCATAGATGAGGTCAGTCCATGAGCCATTATTAAGGCTGTAGCTCCTATATAGCTTCAGGGTGTTTGGATCAGAACTGGTACAATTACTAGGGCCCTGTGACTTACGGATGAGTATGCGATTAGGGATT\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_11745_12199_2:0:0_3:0:0_7/1\n+ACAAATAGCTCTCCGATTAGATTAATTGTGGGTGGTAGGGCTAGGTTTGCGAGGCTAGCTAGTAGTCATCAGGCAGCTATTAGGGTGAGGCTAGTCTGTAGCCCCCGGGCTAGGATTATTGTTCGGCTATGTACTCGTTCATAGTTTGAGTTTGCAAGGCAGAATCGCATAGATGAGGTCAGTCCATGAGCAATTATTAA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_4974_5463_3:0:0_4:0:0_8/1\n+GCTGTTGTTGTGGTGGAGTTGTGTCTAAATAGTATGAAGGTGGTTAGTGTTATACTGATATAGATAGTTAGGTTTAAGATTATTATTGTGGGGCTGTACATTATGATAGCTGTCATTCAGCCTATATGGGCGAATGAGGAGTATGCTATTATTTTTCGTAGTTGTGTTTGGTTTAGGCCTCCTCAGCCTCCGATTATGAC\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_9579_10013_'..b'2222222222222222\n+@chrM_1605_2128_3:1:0_4:1:0_1ea/1\n+CTTAACATAACAAAGTTAGGTCAAGGTGTAGCTCATGAGATGGGAAGCAATGGGCTACATTTTCTAAAATTAGAACACTCACGAAGATCCTTACGAAACTAAGTATTAAAGGAGGATTTAGTAGTAAATTTGAGAATAGAGAGCTCAATTGAATCTGGCCATGAAGCACGCACACACCGCCCGTCCCCCTCCTCAAGTGG\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_13938_14449_2:0:0_6:0:0_1eb/1\n+CGTGGGAATTAAGTACGATTAGGCTGAGGGCTAGGGTGATTATGAAAGATAACAAGTAGAGTTTAACTAGTCGTTTCTGATTAGATACAGTAGTAGACATTTTTATTTGGAATAAGGAGATGGCTTTGGGTAATACATTTTCTAGTCAAATTATGTCTACTAGTATCGATGCGGACTTTTGGCTCATAGTTAGGCTCATT\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_7570_8062_4:0:0_1:0:0_1ed/1\n+CTCGTGTGCGTGAGCTTGGTTGTTAGCATCAACGAGATAATATAAAGAACTAAAGAGCTGATTAAAAATACAATTATTAGTGTGTGGTCGTGAAAGTGTAGGAGTTCTACTATAATGGGGGATGTAGCATCTTGGAAACCTAGTTGAAAGGGGTACGCCATTGAAGCATATAGGATTCAAGCCTATAATTTAACTTCGAC\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_5184_5616_6:0:0_4:0:0_1ee/1\n+AAATTGCACCACTATCCATCCTCTACCAAATCTCATCCACCATTAACCCTAACCTAATCCTAACAATATCCATCATATCAGTCATAATCGGAGGCTGAGGCGGCCTAAAGCAAACACAACTACGAAAAATCCTAGCATACTCCTCAATCGCCCATATAGGCTGAATGACAGCTATCATAATGTACAGCCGCACAATAATA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_6011_6514_3:0:0_7:0:0_1ef/1\n+ATGTTGTTTATTGGGGGAAATGCTATGTCAGGAGCTCCAATTATTAATGGGACCAATCCGTTTCCGAACCCTCCACTTATAATAGGCATCACCAAAAAAAAGATCAATACAAAAGCATGGGCAGTGCCGATTACATTGTAAATCTGATCATCTCCTAGTAGTGTACCAGGTTGGCCCAGTTCGGCCCTGATTAGAAGACT\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_4160_4692_5:0:0_4:1:0_1f0/1\n+CATAATATGATTTATCTCAAGCCTAGCAGAGACCAACCGAGCCCCATTCGACCTGACAGAAGGAGAATCAGAACTAGTCTCGGGATTCGATGTAGAATATGCAGCAGGCCCCTTCGCCCTATTCTTCCTAGCAGAATATGCCCACATCATCATAATAAATATCCTCACAACAATCCTCATCTTCGGAGCATTCCACAGCC\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_7821_8285_3:0:0_3:0:0_1f1/1\n+TTTCTCAATTAAGAAGTATTAGTAAAACACTTACATAACTTTGTCGAAGTTAAATTATAGGCTTGAATCCTATATGCTTCAATGGCGTACCCCTTACAACTAGGTTTCCAAGATGCTACATCCCCCATTATAGAAGAACTCCTACACTTTCACGACCACACACTAATAATTGTATTTTTAATCAGCTCTTTAGTTCTTTC\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_11789_12313_6:0:0_5:0:0_1f2/1\n+GCGTATTACAGTCCTACTTAACCCCTCAACGAACCAAATGGCATACCCCTTTATAATACTATCCGTGTGAGGAATGGTTATAAGAAGCTCCATTTGCCTGCGCCAAACAGACCTAAAATCCCTAATCGCCTACTCATCCGTAATTCACATGGCCCTAGTAATTGTAGCAGTACTGAACCAAACACCCTGAAGCTATATAG\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_6047_6502_2:0:0_6:0:0_1f3/1\n+CCACTTCTCCCGCCGTCTATAAAAAAAAGGCGGGAGAAGCCCCGGCAGCGCCAAGCTGCTTCTTTGAATTTGCAATTCAACATGACATTCACCGCAGGACTTGGTAAAAAGAGGGCTCGAACCTCTGTCTTTAGATTTACAGTCTAATGCTTACTCAGCCATTTTACCTATGTTCATAAACCGGTGAGTATTTTCAACTA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n'

diff -r 000000000000 -r 13e98e2709b8 test-data/flash_unmerged_r_out1.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/flash_unmerged_r_out1.fastq Tue Sep 26 16:42:09 2017 -0400

b'@@ -0,0 +1,1928 @@\n+@chrM_460_919_3:0:0_1:0:0_0/2\n+ACACACGTACACACGTGTACACGTACACACGTACACACGTCCACACGTACACACGTACACACGTGTACCCGTACACACGTACACACGTACACACGTACACACGTATACACGCGAACGCTTTAATTTAAGTAAATAACTAGCTTAATCAAACCCCCCTTACCGCCCGTTAACCTTATTTATAATAATACGTGCCTATTTAT\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_7564_8021_3:0:0_2:0:0_1/2\n+ATAAAGAACTAAAGAGCTGATTAAAAATACAATTATTAGTGTGTGGTCGTGAAAGTGTAGGAGTTGTTCTATAATGGGGGATGTAGCATCTTGGAAACCTATTTGAAAGGGGTACGCCATTGAAGCATATAGGATTCAAGCCTATAATTTAACTTCGACAAAGTTATGTAATTGTTTTACTAATACTTCTTAATTGAGAA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_9159_9700_2:0:1_4:0:0_2/2\n+TTACCGGGTTACGCCACAAGACTAAAGCATCTCTGGCCCACTTTCTACCACAAGTAACACCTGTCCCCCTAATTCCTATGCTTGTAGTCATTAGAGACTATCAGCCTCTTTATCCAACCTATAGCTCTCGCCGTACGACTTACAGCCAACATCACCGCAGGTCACTTATTAATACATCTAATTGGAGGGGCCGCCCTAGC\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_1576_2102_2:1:0_1:0:0_3/2\n+TAAAAAGGAAGAAAAGTAAGCACAAGTATGTAAACATAAAAAAGTTAGGTCAAGGTGTAGCTCATGAGATGGGAAGCAATGGGCTACATTTTCTAAAATTAGAACACTCACGAAGATCCTTACGAAACTAAGTATTAAAGGAGGATTTAGTAGTAAATTTGAGAATAGAGAGCTCAATTGAATCGGGCCATGAAGCACGC\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_2856_3324_2:0:0_6:0:0_4/2\n+CTAGTTAAACGGCCGCGGTATCCTGACCGTGCAAAGGTCGCATAATCATTTGTTCCCTAAATAGGGACTTGTATGAACGGCCACACGAGGGCTTTACTGTCTCTTACTTCCAATCCGTGAAATTGACCTTCCCGTGAAGAGGCGGGAATATAATAATAAGACGAGAAGACCCTATGGAGCTTTCATTAACCGACCCAAAG\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_5342_5909_5:0:0_5:0:0_5/2\n+TTAGAATGGTTTAGATGTGCAGAAGTTAAGTCTGTAGGCCTTGCTTAGAGCTTTGAAGGCTCTTGGTCTAGTTTAACCTAAACTTCAAAACCAGGATAGATAGTATAGGTGCGAGTGGAAGTAGTCTGGTTGATATTACAACTAGAGGGGGTAGGAAGGTTATTTTTTTTGTGCATTCAAATCGTCATTTTATTTTTATA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_11616_12104_4:0:0_7:0:0_6/2\n+TCAACCACCTGGTCCAATAATTTCCTCTGACTAGCATGCATGATAGCATTTATAGTAAAAATACCTCTATATGGACTCCACCTATGATTGCCAAAAGGACATGTTGAAGCTCCCATCGCTGGATCAATAGTACTTTCCGCCGTATTACTAAAACTAGGGGGATACGGGATAATGCGTATTACAGTCCTACTTAACCCCGC\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_11745_12199_2:0:0_3:0:0_7/2\n+GTACTTGCCGCCGTATTACTAAAACTAGGGGGATACGGGATAATGCGTATTACAGTCCTACTTAACCCCGCAACGAACCAAATGGCATACCCCTTTATAATACTATCCCTGTGAGGAATGGTTATAACACGCTCCATTTGCCTGCGCCAAACAGACCAAAAATCCCTAATCGCATACTCATCCGTAAGTCACATGGCCCT\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_4974_5463_3:0:0_4:0:0_8/2\n+CCGCCTCCATAATCCTAATAATATGAATCATTATCAATCTACTGCACTCGGGACAATGGACCGTACTAAAAGACCTTAATCCCATAGCATCAATCATAATAACAACCGCTCTAGCAATAAAACTAGGAGTAGCCCCATTCCACTTCAGAGTACCGGAAGTTACACAAGGAATTTCTATATCATCAGGCTTAATTCTACTA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_9579_10013_'..b'2222222222222222\n+@chrM_1605_2128_3:1:0_4:1:0_1ea/2\n+TTTGCTGTGTGGTGCTTTTAATTTTATCTTTCATCTTTCCCCTGCGGTACTTTCTCTATAGCGCCAAGTTAAATTTCTATCTCCTATACTTTTATAAGGTGACTAAATGTTTTTTTTTATTTTCTAGTGTTAGTTGTGTTTGAAGATGATTGGGCTAGCTTTAGCTCAAGATGGTCAGTTTAATATGACATCTTCTGGGT\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_13938_14449_2:0:0_6:0:0_1eb/2\n+ACGATTCAATACCTTGAATCTAATCAATGAAAATAATACCCACCTCATCAACTCCATTAAACGTCTCTTAATCGGAAGTATCTTTGCAGGATATCTAATTTCTTACAACATCCCCCCAACAACTATCCCACAAATAACTATCCCCTACTATCAAAAACTAACTGCTCTTGCCGTGACTATCGCAGGCTTCATCCTAGCAT\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_7570_8062_4:0:0_1:0:0_1ed/2\n+CGATTTCCTCAATGGGCTCTTTGATCTCATTAACAGCAGTCATGTTAATAGTTTTCATAGTGTGAGAAGCTTTCGCATCCAAGCGAGAAGTGGCCATAGTAGAACTAACCACAACTAATCATGAATGATTGCATGGATGTCCTCCTCCGTACCACACAATTGAAGAGCCAACTTACGTACTATTAAAATAAGAACGGAAG\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_5184_5616_6:0:0_4:0:0_1ee/2\n+GGCCTTATGCTTAATTCATTTTTAGTCAATTCTTGGATGATTATTCATTTTGGGATAAATCCGGAGAGTGGGGGGAGGCCTCCCAGGGAAATTATTAATACTAGGATGAGTGAGGTGATTAGAGGGGTTTTATTTCATGTTTGTGATAGGGATGCTGTAGTTGTGGTGGAGTTGTGTATAAATAGTATGAAGGTGGTTAG\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_6011_6514_3:0:0_7:0:0_1ef/2\n+GTTAACAGCTAAATGCCCTAATCAACTGGCTTCAATCCACTTCTCCCGCCGTCTAGAAAAAAAAGGCGGGATAAGCCCCGGCAGCGCCAAGCTGCTTCTTTGAATTTGCAATTCAACATGACATTCACCGCAGGACTTGGTAAAAAGAGGGCTCGAACCTCTGTCTTTAGATTTCCAGTCTAATGCTTACTCAGGCATTT\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_4160_4692_5:0:0_4:1:0_1f0/2\n+TGGTAGCACGAAGATTTATGGATTCTTAGGCTTAGGTTCGATTCCTGTTATTCTAGAAATAAGAGGGTTTCAACCTCTATGTTTTACTCTATCAAAGTAACTCTTTTGTCAGACATATTTCTTATGTTTGAGGTGGGATGCATGCTGTGATGATAGGTAGGGATACATGTCATATGCATAGGGGTAGGGTGAGAGGCAGA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_7821_8285_3:0:0_3:0:0_1f1/2\n+TAGCTCTTGGGTAGGAATTATGTAAGAGTCAAAATTCAAGACTTCGTAATCAGTGTACTCATAACTTCAATATCATTGATGTCCTATGGTTTTTACTTTGAGGGAGGGGTTGTTGATTTCATCCATTATATAGAGAATTCGTAAGGAGGGTAGGGCGATACGAATCAGGATAATAGCAGGTAGGATGGTTCAGATGGTTT\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_11789_12313_6:0:0_5:0:0_1f2/2\n+TATTTGCCTCGTTGAGTTATAATAAGTATGTAGAGGTAGTATAGGGCTGTACTGATGATATTAGTACCCCTTAGGATACTGGTTATGTTTGATCATGAGAAGGAGGCTATTACTACAAATAGCTCTCCGATTAGATTAATTGTGGGTGGTAGGGCTAGGATTGCGAGGCTAGCTAGTAGTCATCAGGCAGCTATTAGGGG\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_6047_6502_2:0:0_6:0:0_1f3/2\n+CGGGGCAATGCTATGTCAGGAGCTCCAATTATTAATGGGACCAATCAGTTTCCGACCCCTCCAATTATCATAGGCATCACCATACAAAAGATCATTACAAAAGCATGGGCAGTGACGATTACATTGTAAATCTGATCATCTCCTAGTAGTGTACCAGGTTGGCGCATTTCGGCCCGGATTAGAAGACTAAGAGCAGTCCC\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n'

diff -r 000000000000 -r 13e98e2709b8 test-data/flash_unmerged_r_out2.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/flash_unmerged_r_out2.fastq Tue Sep 26 16:42:09 2017 -0400

b'@@ -0,0 +1,1924 @@\n+@chrM_460_919_3:0:0_1:0:0_0/2\n+ACACACGTACACACGTGTACACGTACACACGTACACACGTCCACACGTACACACGTACACACGTGTACCCGTACACACGTACACACGTACACACGTACACACGTATACACGCGAACGCTTTAATTTAAGTAAATAACTAGCTTAATCAAACCCCCCTTACCGCCCGTTAACCTTATTTATAATAATACGTGCCTATTTAT\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_7564_8021_3:0:0_2:0:0_1/2\n+ATAAAGAACTAAAGAGCTGATTAAAAATACAATTATTAGTGTGTGGTCGTGAAAGTGTAGGAGTTGTTCTATAATGGGGGATGTAGCATCTTGGAAACCTATTTGAAAGGGGTACGCCATTGAAGCATATAGGATTCAAGCCTATAATTTAACTTCGACAAAGTTATGTAATTGTTTTACTAATACTTCTTAATTGAGAA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_9159_9700_2:0:1_4:0:0_2/2\n+TTACCGGGTTACGCCACAAGACTAAAGCATCTCTGGCCCACTTTCTACCACAAGTAACACCTGTCCCCCTAATTCCTATGCTTGTAGTCATTAGAGACTATCAGCCTCTTTATCCAACCTATAGCTCTCGCCGTACGACTTACAGCCAACATCACCGCAGGTCACTTATTAATACATCTAATTGGAGGGGCCGCCCTAGC\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_1576_2102_2:1:0_1:0:0_3/2\n+TAAAAAGGAAGAAAAGTAAGCACAAGTATGTAAACATAAAAAAGTTAGGTCAAGGTGTAGCTCATGAGATGGGAAGCAATGGGCTACATTTTCTAAAATTAGAACACTCACGAAGATCCTTACGAAACTAAGTATTAAAGGAGGATTTAGTAGTAAATTTGAGAATAGAGAGCTCAATTGAATCGGGCCATGAAGCACGC\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_2856_3324_2:0:0_6:0:0_4/2\n+CTAGTTAAACGGCCGCGGTATCCTGACCGTGCAAAGGTCGCATAATCATTTGTTCCCTAAATAGGGACTTGTATGAACGGCCACACGAGGGCTTTACTGTCTCTTACTTCCAATCCGTGAAATTGACCTTCCCGTGAAGAGGCGGGAATATAATAATAAGACGAGAAGACCCTATGGAGCTTTCATTAACCGACCCAAAG\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_5342_5909_5:0:0_5:0:0_5/2\n+TTAGAATGGTTTAGATGTGCAGAAGTTAAGTCTGTAGGCCTTGCTTAGAGCTTTGAAGGCTCTTGGTCTAGTTTAACCTAAACTTCAAAACCAGGATAGATAGTATAGGTGCGAGTGGAAGTAGTCTGGTTGATATTACAACTAGAGGGGGTAGGAAGGTTATTTTTTTTGTGCATTCAAATCGTCATTTTATTTTTATA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_11616_12104_4:0:0_7:0:0_6/2\n+TCAACCACCTGGTCCAATAATTTCCTCTGACTAGCATGCATGATAGCATTTATAGTAAAAATACCTCTATATGGACTCCACCTATGATTGCCAAAAGGACATGTTGAAGCTCCCATCGCTGGATCAATAGTACTTTCCGCCGTATTACTAAAACTAGGGGGATACGGGATAATGCGTATTACAGTCCTACTTAACCCCGC\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_11745_12199_2:0:0_3:0:0_7/2\n+GTACTTGCCGCCGTATTACTAAAACTAGGGGGATACGGGATAATGCGTATTACAGTCCTACTTAACCCCGCAACGAACCAAATGGCATACCCCTTTATAATACTATCCCTGTGAGGAATGGTTATAACACGCTCCATTTGCCTGCGCCAAACAGACCAAAAATCCCTAATCGCATACTCATCCGTAAGTCACATGGCCCT\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_4974_5463_3:0:0_4:0:0_8/2\n+CCGCCTCCATAATCCTAATAATATGAATCATTATCAATCTACTGCACTCGGGACAATGGACCGTACTAAAAGACCTTAATCCCATAGCATCAATCATAATAACAACCGCTCTAGCAATAAAACTAGGAGTAGCCCCATTCCACTTCAGAGTACCGGAAGTTACACAAGGAATTTCTATATCATCAGGCTTAATTCTACTA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_9579_10013_'..b'2222222222222222\n+@chrM_1605_2128_3:1:0_4:1:0_1ea/2\n+TTTGCTGTGTGGTGCTTTTAATTTTATCTTTCATCTTTCCCCTGCGGTACTTTCTCTATAGCGCCAAGTTAAATTTCTATCTCCTATACTTTTATAAGGTGACTAAATGTTTTTTTTTATTTTCTAGTGTTAGTTGTGTTTGAAGATGATTGGGCTAGCTTTAGCTCAAGATGGTCAGTTTAATATGACATCTTCTGGGT\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_13938_14449_2:0:0_6:0:0_1eb/2\n+ACGATTCAATACCTTGAATCTAATCAATGAAAATAATACCCACCTCATCAACTCCATTAAACGTCTCTTAATCGGAAGTATCTTTGCAGGATATCTAATTTCTTACAACATCCCCCCAACAACTATCCCACAAATAACTATCCCCTACTATCAAAAACTAACTGCTCTTGCCGTGACTATCGCAGGCTTCATCCTAGCAT\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_7570_8062_4:0:0_1:0:0_1ed/2\n+CGATTTCCTCAATGGGCTCTTTGATCTCATTAACAGCAGTCATGTTAATAGTTTTCATAGTGTGAGAAGCTTTCGCATCCAAGCGAGAAGTGGCCATAGTAGAACTAACCACAACTAATCATGAATGATTGCATGGATGTCCTCCTCCGTACCACACAATTGAAGAGCCAACTTACGTACTATTAAAATAAGAACGGAAG\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_5184_5616_6:0:0_4:0:0_1ee/2\n+GGCCTTATGCTTAATTCATTTTTAGTCAATTCTTGGATGATTATTCATTTTGGGATAAATCCGGAGAGTGGGGGGAGGCCTCCCAGGGAAATTATTAATACTAGGATGAGTGAGGTGATTAGAGGGGTTTTATTTCATGTTTGTGATAGGGATGCTGTAGTTGTGGTGGAGTTGTGTATAAATAGTATGAAGGTGGTTAG\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_6011_6514_3:0:0_7:0:0_1ef/2\n+GTTAACAGCTAAATGCCCTAATCAACTGGCTTCAATCCACTTCTCCCGCCGTCTAGAAAAAAAAGGCGGGATAAGCCCCGGCAGCGCCAAGCTGCTTCTTTGAATTTGCAATTCAACATGACATTCACCGCAGGACTTGGTAAAAAGAGGGCTCGAACCTCTGTCTTTAGATTTCCAGTCTAATGCTTACTCAGGCATTT\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_4160_4692_5:0:0_4:1:0_1f0/2\n+TGGTAGCACGAAGATTTATGGATTCTTAGGCTTAGGTTCGATTCCTGTTATTCTAGAAATAAGAGGGTTTCAACCTCTATGTTTTACTCTATCAAAGTAACTCTTTTGTCAGACATATTTCTTATGTTTGAGGTGGGATGCATGCTGTGATGATAGGTAGGGATACATGTCATATGCATAGGGGTAGGGTGAGAGGCAGA\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_7821_8285_3:0:0_3:0:0_1f1/2\n+TAGCTCTTGGGTAGGAATTATGTAAGAGTCAAAATTCAAGACTTCGTAATCAGTGTACTCATAACTTCAATATCATTGATGTCCTATGGTTTTTACTTTGAGGGAGGGGTTGTTGATTTCATCCATTATATAGAGAATTCGTAAGGAGGGTAGGGCGATACGAATCAGGATAATAGCAGGTAGGATGGTTCAGATGGTTT\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_11789_12313_6:0:0_5:0:0_1f2/2\n+TATTTGCCTCGTTGAGTTATAATAAGTATGTAGAGGTAGTATAGGGCTGTACTGATGATATTAGTACCCCTTAGGATACTGGTTATGTTTGATCATGAGAAGGAGGCTATTACTACAAATAGCTCTCCGATTAGATTAATTGTGGGTGGTAGGGCTAGGATTGCGAGGCTAGCTAGTAGTCATCAGGCAGCTATTAGGGG\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n+@chrM_6047_6502_2:0:0_6:0:0_1f3/2\n+CGGGGCAATGCTATGTCAGGAGCTCCAATTATTAATGGGACCAATCAGTTTCCGACCCCTCCAATTATCATAGGCATCACCATACAAAAGATCATTACAAAAGCATGGGCAGTGACGATTACATTGTAAATCTGATCATCTCCTAGTAGTGTACCAGGTTGGCGCATTTCGGCCCGGATTAGAAGACTAAGAGCAGTCCC\n++\n+22222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n'