Galaxy |

Changeset 0:dc70286127fe (2017-10-20)

Next changeset 1:c2d90cc4a063 (2017-11-24)

Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e

added:
discosnp_pp.xml
macros.xml
test-data/commet/A.fa
test-data/commet/B.fa
test-data/commet/C.fa
test-data/commet/D.fa
test-data/commet/dendrogram.png
test-data/commet/matrix_plain.csv
test-data/discosnp/multifasta.fa
test-data/discosnp/multifasta_paired.fa
test-data/discosnp/reads1
test-data/discosnp/reads2
test-data/discosnp/vcf_file.vcf
test-data/discosnp/vcf_file_paired.vcf
test-data/kissplice/alternative_splicing.fa
test-data/kissplice/reads1
test-data/kissplice/reads2
test-data/lordec/coli-pacbio-test-mini.fa
test-data/lordec/corrected_reads.fa
test-data/lordec/ill-test-5K-1.fa
test-data/lordec/ill-test-5K-2.fa
test-data/lordec/stat_file.txt
test-data/lordec/trimmed_reads.fa
test-data/mapsembler2/assembly.fa
test-data/mapsembler2/assembly_2.fa
test-data/mapsembler2/coherent.fa
test-data/mapsembler2/reads1
test-data/mapsembler2/reads2
test-data/mapsembler2/starter.fa
test-data/mapsembler2/starter_extremities.fa
test-data/takeabreak/inversion.fasta
test-data/takeabreak/inversion_list.fasta
test-data/takeabreak/toy_example_reads.fasta
test-data/takeabreak/toy_example_with_inv_reads.fasta

diff -r 000000000000 -r dc70286127fe discosnp_pp.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/discosnp_pp.xml Fri Oct 20 03:15:43 2017 -0400

[

b'@@ -0,0 +1,199 @@\n+<?xml version=\'1.0\' encoding=\'utf-8\'?>\n+<tool profile="16.04" id="discosnp_pp" name="DiscoSnp++" version="2.2.10">\n+ <description>is an efficient tool for detecting SNPs without a reference genome.</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <requirements>\n+ <requirement type="package" version="2.2.10">discosnp</requirement>\n+ </requirements>\n+ <command><![CDATA[\n+ ## simple option\n+ #if str( $input_type_options.input_type) == "single"\n+ @discosnp_single_reads@\n+ ## paired option\n+ #else if str( $input_type_options.input_type) == "paired"\n+ @discosnp_paired_reads@\n+ ## mix option\n+ #else\n+ @discosnp_single_reads@\n+ @discosnp_paired_reads@\n+ #end if\n+\n+ #if str($VCF_option.mapping) == \'reference\'\n+ #set $reference_file = str($VCF_option.G) + "." + $VCF_option.G.ext\n+ ln -sf \'${VCF_option.G}\' \'${reference_file}\' &&\n+ #end if\n+\n+ run_discoSnp++.sh\n+ -r input.lst\n+ -b ${b}\n+ -D ${D}\n+ -P ${P}\n+ ${low_complexity}\n+ -k ${k}\n+ ${t}\n+ ${T}\n+\n+ #if str($coverage_options_type.coverage_options) == \'auto\'\n+ -c auto\n+ #else\n+ -c \'${coverage_options_type.c}\'\n+ #end if\n+ -C ${C}\n+ -d ${d}\n+\n+ #if str($VCF_option.mapping) == \'reference\'\n+ -G \'${reference_file}\'\n+ -M ${VCF_option.M}\n+ ${VCF_option.R}\n+ #end if\n+\n+ ]]></command>\n+\n+ <inputs>\n+\n+ <conditional name="input_type_options">\n+ <param name="input_type" type="select" label="Input options">\n+ <option value="single">Single end reads</option>\n+ <option value="paired">Paired end reads</option>\n+ <option value="mix">Both single and paired reads</option>\n+ </param>\n+ <when value="single">\n+ <param name=\'list_reads\' argument="-r" format="fasta,fastq" type="data" multiple="true" label="Single read files" />\n+ </when>\n+ <when value="paired">\n+ <param name=\'list_paired_reads\' argument="-r" format="fasta,fastq" type="data_collection" collection_type="list:paired" multiple=\'true\' label="List of paired read files" />\n+ </when>\n+ <when value="mix">\n+ <param name=\'list_reads\' argument="-r" format="fasta,fastq" type="data" multiple="true" label="Single read files" />\n+ <param name=\'list_paired_reads\' argument="-r" format="fasta,fastq" type="data_collection" collection_type="list:paired" multiple=\'true\' label="List of paired read files"/>\n+ </when>\n+ </conditional>\n+\n+ <param argument="-b" type="select" label="Branching strategy">\n+ <option value="0">variants for which any of the two paths is branching are discarded</option>\n+ <option value="1">forbid SNPs for wich the two paths are branching</option>\n+ <option value="2">No limitation on branching</option>\n+ </param>\n+\n+ <param argument="-D" type="integer" label="Deletion size" value="0" help="If different of 0, discoSnp++ will search for deletions of size from 1 to D included"/>\n+ <param argument="-P" type="integer" label="Maximum SNPs per bubble" value="1" help="discoSnp++ will search up to P SNPs in a unique bubble"/>\n+ <param name="low_complexity" type="boolean" checked="false" truevalue="-l" falsevalue="" label="Remove low complexity bubbles" />\n+ <param argument="-k" type="integer" label="Size of kmers" value="31" />\n+\n+ <param argument="-t" type="boolean" checked="false" truevalue="-t" falsevalue="" label="Extends each polymorphism with left and right unitigs" />\n+ <param argument="-T" type="boolean" checked="false" truevalue="-T" falsevalue="" label="Extends each polymorphism with left and right contigs" />\n+\n+\n+ <conditional name="cover'..b'ference genome</option>\n+ <option value="reference">Mapping with a reference genome</option>\n+ </param>\n+ <when value="default"></when>\n+ <when value="reference">\n+ <param argument="-G" type="data" format="fasta,fastq" label="Reference genome file" />\n+ <param argument="-M" type="integer" value="4" label="Maximal number of mapping errors" help="during BWA mapping phase" />\n+ <param argument="-R" type="boolean" truevalue="-R" falsevalue="" checked="false" label="Use the reference genome also in the variant calling, not only for mapping results" />\n+ </when>\n+ </conditional>\n+\n+ </inputs>\n+\n+ <outputs>\n+ <data name="vcf" from_work_dir="*_coherent.vcf" format="vcf" label="VCF with ${tool.name} on $on_string"/>\n+ <data name="fasta" from_work_dir="*_coherent.fa" format="fasta" label="Multifasta with ${tool.name} on $on_string"/>\n+ </outputs>\n+\n+ <tests>\n+ <test>\n+ <conditional name="input_type_options">\n+ <param name="input_type" value="single"/>\n+ <param name="list_reads" value="discosnp/reads1,discosnp/reads2" ftype="fasta" />\n+ </conditional>\n+ <param name="k" value="25"/>\n+ <output name="fasta" file="discosnp/multifasta.fa"/>\n+ <output name="vcf" file="discosnp/vcf_file.vcf" compare="diff" lines_diff="2"/>\n+ </test>\n+ <test>\n+ <conditional name="input_type_options">\n+ <param name="input_type" value="paired"/>\n+ <param name="list_paired_reads">\n+ <collection type="list:paired">\n+ <element name="Pair1">\n+ <collection type="paired">\n+ <element name="forward" value="discosnp/reads1" ftype="fasta"/>\n+ <element name="reverse" value="discosnp/reads2" ftype="fasta"/>\n+ </collection>\n+ </element>\n+ </collection>\n+ </param>\n+ </conditional>\n+ <conditional name="VCF_option">\n+ <param name="mapping" value="reference"/>\n+ <param name="G" value="discosnp/reads1" ftype="fasta"/>\n+ </conditional>\n+ <output name="fasta" file="discosnp/multifasta_paired.fa"/>\n+ <output name="vcf" file="discosnp/vcf_file_paired.vcf" compare="diff" lines_diff="2"/>\n+ </test>\n+ </tests>\n+\n+ <help><![CDATA[\n+\n+**Description**\n+\n+Software discoSnp is designed for discovering Single Nucleotide Polymorphism (SNP) from raw set(s) of reads obtained with Next Generation Sequencers (NGS).\n+Note that number of input read sets is not constrained, it can be one, two, or more. Note also that no other data as reference genome or annotations are needed.\n+The software is composed by two modules. First module, kissnp2, detects SNPs from read sets. A second module, kissreads, enhance the kissnp2 results by computing per read set and for each found SNP i/ its mean read coverage and ii/ the (phred) quality of reads generating the polymorphism.\n+\n+Note that from release of DiscoSnp++-2.0.6, the tool also detects close SNPs and indels.\n+\n+-------\n+\n+.. class:: warningmark\n+\n+**Input parameters**\n+\n+-Sequences files in fasta or fastq each allele will be counted in each file individually\n+\n+-Use collections: data list and/or data list paired\n+\n+-Fasta sequence of a genome if case of you are willing to map the sequence extension on a reference in order to get a compliant VCF\n+\n+-------\n+\n+.. class:: warningmark\n+\n+**Ouput parameters**\n+\n+-VCF file with coordinates on the higher branch sequences or on a reference genome if provided\n+\n+-Fasta file with sequence extensions around the SNP.\n+\n+\n+-------\n+\n+**Web site**\n+\n+https://colibread.inria.fr/software/discosnp/\n+\n+ ]]></help>\n+ <expand macro="citations">\n+ <citation type="doi">10.1093/nar/gku1187</citation>\n+ </expand>\n+</tool>\n'

diff -r 000000000000 -r dc70286127fe macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Fri Oct 20 03:15:43 2017 -0400

[

@@ -0,0 +1,42 @@
+<macros>
+    <token name="@discosnp_single_reads@"><![CDATA[
+        #for $input in $input_type_options.list_reads
+            #set $filename = str($input) + "." + $input.ext
+            ln -sf '${input}' '${filename}' &&
+            echo '${filename}' >> input.lst &&
+        #end for
+    ]]></token>
+    <token name="@discosnp_paired_reads@"><![CDATA[
+        #for $i, $paired in enumerate( $input_type_options.list_paired_reads )
+
+            #set $filenameFWD = str($paired.forward) + "." + $paired.forward.ext
+            ln -sf '${paired.forward}' '${filenameFWD}' &&
+
+            #set $filenameREV = str($paired.reverse) + "." + $paired.reverse.ext
+            ln -sf '${paired.reverse}' '${filenameREV}' &&
+
+            echo '${filenameFWD}' > "paired_${i}.lst" &&
+            echo '${filenameREV}' >> "paired_${i}.lst" &&
+            echo "paired_${i}.lst" >> input.lst &&
+
+        #end for
+    ]]></token>
+    <token name="@lordec_inputs@"><![CDATA[
+        -2 "${ ",".join(['%s' % file for file in $program_type_choice.inputs]) }"
+        -i '${program_type_choice.i}'
+        -k ${program_type_choice.k}
+        -s ${program_type_choice.s}
+    ]]></token>
+    <xml name="lordec_inputs">
+        <param name="inputs" argument="-2" type="data" format="fasta,fastq.gz,fastq" multiple="true" label="Short read FASTA/Q files" />
+        <param argument="-i" type="data" format="fasta,fastq.gz,fastq" label="Long read FASTA/Q file" help="PacBio reads files" />
+        <param argument="-k" type="integer" label="Size of kmers" value="31" help="Only uneven number"/>
+        <param argument="-s" type="integer" label="Solidity abundance threshold for k-mers" value="4" />
+    </xml>
+    <xml name="citations">
+        <citations>
+            <yield/>
+            <citation type="doi">10.1186/s13742-015-0105-2</citation>
+        </citations>
+    </xml>
+</macros>

diff -r 000000000000 -r dc70286127fe test-data/commet/A.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/commet/A.fa Fri Oct 20 03:15:43 2017 -0400

b'@@ -0,0 +1,24000 @@\n+>1\n+AAAAAACATTAGTTACGGAAGGTGGGTGGAGCGGGGGCCGCCAGTCTATATTCATACTAGAAAGGGGCTAAGGGCATCGCGCTCATGAAGTGGCACTTGCAGAGGTGAGT\n+>4\n+AAAAAATTGTCGTTAAGATGAGGAGCTCTTTCGCATTTGACCCATCAAATCTCGGAATGCACTTGAGATCGACCCGTTTGATACAAGCCTTCATCGTCGATAATATATCG\n+>6\n+AAAAACCGATGGGGCCGAGCTGTTCTTTGGCCGGGTTACTCTACGCCCACACGGGTACACAGCCGCGAAACGGGAGGCTCGTGCGCGGTCACCTAAGTCCCTGTGGCGGG\n+>7\n+AAAAACGGATGAGAAATAAAAGGGGAAATAGCGACATGTCAAATGGCCTCTTGGCTGGCGGTGTCTGGCTGGACTAACCCTCTTAAGGACTTAAAGCGTAGGCAAGGTTA\n+>10\n+AAAAAGCTTACAGTGTTCGTAGTTCTGCTCGTGTCGGTATTCTCATACTCACTCCAGGACTTCGGAAACATTAGTGAAAGTGTCACCGGCCGTGCATTTTCCGGAGTAAG\n+>12\n+AAAAAGTCTCACTTATTTACGCGCTTGATAGCCCAAACCGTTCACAGCATCTCCAGTAGTCGATTCCGGCTCCTCTCCATGTTGGAGATGTCAGCACGGCAGGTATATGA\n+>14\n+AAAAATATTTGAATCCGCTGCTGACTTTTTCAAAATTCGATTATCACTACGGCGGTCAGCATATTTCCTTGAACTTATAACGTATCTCAGTATTGCTGGTTTGGAAACGT\n+>15\n+AAAAATGCCCAGTTCGGCGATCCAACTCGTTAGTCTCAGGGTTCCCGCGGCGAACTCCCTTCGGTTGACTTTACGGCCTACACGCTCAGCCCTGTACCCGCATTGATGTC\n+>19\n+AAAACACGCATGTCCGACGGGCGCATTAAACGGCATTGTTGTTCTTGAACCGGAAGCAATAGTCTAGGACCGTTCATATTGACTTACTTTACGCGTGGGCCTTGGATGAA\n+>22\n+AAAACCATCTGTTTCCCAGAATGCTCCCGATACTTAATCACCTGCGCTTTGATCGTAGGCACTCACCCTCTCAAGTACCCTTGGACAGATTTAAGATCGATAGTTCGTAT\n+>26\n+AAAACGAACCGGACTACATTCCTCATAGGCTTGAGGGGCAAAAGTTACAGTACAGATTTCGGGACCCGTCGCTTTACAGTGTAGACTGTTTTCCGAGAGTGCCTAGTCCA\n+>28\n+AAAACGCTCGTGCCCAGTTCGAGCGCCCTGGAGTTTACCGCCCAAGTAAACGCTATTTTTTAAATGACATAGCTCCTTACAGGCGTGGGGGGACGCCTATAGGGCCGTCG\n+>29\n+AAAACGGTGCCAACCATTGAAGATAGAAGATTCAATACATTGCACAAACGAATATAACCGGTAGGTAAAGTCTCGTTTCAAAGCGGCTCTATTTGTGCACCTTTTGCTGA\n+>31\n+AAAACTCACCACCAGGACAGAAGCTAAAAGACAGGCCGATTCACGGGCGAGCGGTCGAAGCATACTTTTTAGGGCATCATGTGACCACACGTGTTGACCGTCCATCGTTT\n+>34\n+AAAACTTTACCGATTTGCAAGATGTAAACAGCACGGGGACGCTATATCGACTGAGTGTTGTAGTGGAATCTACCACCCCGGACATGGGGCTGGACTGATTATTGAACGCT\n+>38\n+AAAAGAGTTTGCAGGGTCACTAGCCCGGCTCTGCATACATTGGCAAAGAGGCGATAAGCTGTGAATTCCAGGCTGGGGACGAGCTTGAACCTACTGTGCGAAGTTACCAC\n+>40\n+AAAAGCCAGAAGGTATGCAGATCGATATCGCTCCAATGTGTCAGTAGCCCGGACGAAGGCCTGCTCGATGATGCGTCATATTAATGTCAGAGAACCTAGTAGCCATCGGT\n+>44\n+AAAAGGACAACGATGTGTGTGCTTCAAATATTCCTCCAATTCGTTACTGTCGCGGATGTTATGTCGGGCACTCTTAGCTTCCAAGGTGGGTGGATGTTAACGCGCATAGA\n+>46\n+AAAAGGGGTTTGCTGACCCACAGACAATAGATAGCGGATTACTTACTCCACTTACGAGACTAACGCAATGCTAATAACTTGACGTCTAAACGGGACCACATAAGCCTTTA\n+>47\n+AAAAGGTATTATATTGATGATTAGCCATTTAGGGAAGATCAACAAGATGAAGCATGACGCGAGAGGTAAGGGATCGACGAACGCTCCTGCCATGGGCAATCCAGGAGGGC\n+>49\n+AAAAGTCCCTGTCGTACCTCAATCCAGGCCACGTATACTCAGGGGGTACCGAAACCCTAATAACTCTCCCGTTGGTGACCAGATCTGAATCTGCACCGCACACAACTACA\n+>51\n+AAAAGTGGAAAATACCCTCACTAACAGGGTATCTTGCGTTGAGCTGGTAAGTGCACCAGGGAAAACTTGTTATCCTCGAGTCTGATCGATGCTATCTCATATTTCTGAGT\n+>54\n+AAAATAGAAATCGCAGCTTGAATGCTGTTACTCAATGTTTATGAACATAGCTCCCGCGTTACTCTGTTTCGACATAGGATGCGCGCACCGGAAGCCTGCTACCACAACAT\n+>57\n+AAAATCAAACTAGCTACTCCGAAGGCGGGATATTTGCCTGGTAGAGGGAAATGTAGCTCACGGGCCGTTTACTCTTCTTCAGAGCAACTAAGTATTCCGGAAAACCTCAG\n+>60\n+AAAATCGTGTTCAAGAAAGAGAGGGCCGGGCGCTGAATTGGGCCCGAATCACAAAAAAGTGAGTCGCGCTCCTACAAAGTCCTAATCTAATAGTGGATGATGTGTCTGGT\n+>62\n+AAAATGCCATACTAAATTAACGGTGTCTCATAGCGACATTGTTATTGTCACCTGACATAGCCAGAAGGTTAAAAGTAGTGCGCGACGCGAAATACCCATGCTGCGGAGTC\n+>67\n+AAAATTCAGCCTTTCTTACCCAAGGCCTCTCTCGGACAAGAACTATGAAAGCATGCCCTACAGCATACTTTCGCTGACATATGGAGCAGGGAGCCTAAAGGCCGTTTATC\n+>71\n+AAACAACCACAGATGGCCACTATGTGAAGTTTTGGACGAGTCCATACATTTTTCACTAAGTAAGAAGCTACCTTAATACGTGCACGCATCACATCCTAGACGCTCTGGCT\n+>72\n+AAACAAGCCGAGAATCTGGCGTGACAAATCCTCCGGAACGGGCTGACCCCACTGTACAAACAATGTAAATCACCGCAGTTTCACTGTACGTTTGGTCTTTTTGATAGACA\n+>74\n+AAACAATGGACGGAACCATGTTCTGTTACAAGCGCTGACCACACAAGCCGAGAGTACCCCAAGATGATGTCTTAGGATCGTATATACCCTCCATACCCGAGCTTTCCCCG\n+>77\n+AAACACGTCACCGAGCGCTTAGTGGATCGTACTCAACATGTTGAACAGACATTATCTACATTCGATTCTTCCCATTATGTATCATCGCAGTACACGCCGCTTTCCATTTT\n+>78\n+AAACACTCGCACAGACCGGTAACCGAGGGAATACAGAATTATAGCCCATATTCGCTGTCCCAAACTGCACCCATCGTTGGCAATTCCGAGACCTCTATTTCCGGTATGCG\n+>79\n+AAACAGAGACATGTACGTTTTGCGCGGTGGTAGCTCTGGAGTCGGAGGCAGGGTTTTTTGGCCGGCAAAATCAGTATCCGACCTCGTTGGATGACTCCGGAAAACCTTTT\n+>80\n+AAACAGATCGCTATTAGCACGCGTATGCTTTCACTAGCGAACAAAAGTGCCCCTTTGAGTCCTAGCAGCTACAGTGCCCGTAACTGATATTCTTAAGGCTATTTACAGTT\n+>81\n'..b'GCGAGCTAGCCTCGTTGACCCTCGGGAGGCTCTGCTGGCCCCAGGCTTCGCTACCCTATTTATAGATAGTA\n+>3825\n+ATCGCGGCCGGGTAAATCGGAACAGCTTCGACTCCAATAAAACAGGTGAACACGCCCATGGAAGTACAAGAATTGGCTCCGCGAGCCAAATGCGGCGCGTATAGCGTCCG\n+>3826\n+ATCGCGGGACGACTAGTCTGAGCATAGCTCGCTGTTGGCACATCCCCCACGAACACCATGTACGGCAAAATTGATCACCGGTACCCCTGTCAAGTTGGGAAGCGTGATGA\n+>3828\n+ATCGCTCATGAATCTCGTTGTAGACATTTTGACAGAACTCATGGCACTCACTTAAAAGGTTGTTTGGCGCGCGGAGGGAGGATGGTCCGGTAGACCAGCTCCGGATAAAT\n+>3829\n+ATCGCTCTCGAGATTTATAACTGCCAATTGCCCGTTGGCTAGGCCTTCAGACATTCTACGCAGGGTGGCTGGCTGACTCGTGGCAGTACTACTCTAACTTTAAGACGGGC\n+>3831\n+ATCGCTTCTTTCGCGGCGTACGTATCAATAACCTACCGGACGCATCCAAATTATCTTGTTTTTACATCATCACGTGCACCTAAAGGGTTACCACCTCTCTGAGGCAACTG\n+>3834\n+ATCGGAGAGACACTTCTCGGCGTGTGCTTCAGAGTTATGAGAGTTCTTTTTGGTTAACTCGGTCACTGAATCGCCCAATTTCTGACGCCAAGGCGGGTGGGTCTAGTCAT\n+>3836\n+ATCGGATTTATCACCCTGACTTACGGAAGAGTCCCGGTAGAATGCTGGTACAGGCACGTTGCGGCGTTTCCCTGTACGACAACCGGCTCATGATGGCGTGCTCTTAACTC\n+>3838\n+ATCGGCGCCCTGCTGCGCGCCTTCCCGTCAGCCTTGAGCATTTTCGTGCAGCTTCAGTTGCTATACTCTGTGTCAAAGATAGCTGACGCAAGTAAGGTAAGGAGAGATGG\n+>3841\n+ATCGGGACGGAGACTTCAAACAACGCCAGAAGCGGGAGGGTACCAGGAGCGGTTGATCAAAATCCAATCTCGTATGGGGAGTGGAGGTCGGACTATGAGGCCTTGGCGAA\n+>3844\n+ATCGGGTGTAATAATTCTCCAAAAGCGTGCCATTCGGGACCCGATCTTAACGATGGTGATATACCTATTTACTGATAAACACTCTCCGAGTGATGATGAAGCCGTGCATC\n+>3845\n+ATCGGTACGAGAAGTGTGTGTGCTGGTGACGGCGTGTGCAATTGAACCCGACCAGGAGCCCGGTTATGAACTCAAGTCCGCGGGGCTGACGCAAAAATTCCGTGTAATCT\n+>3846\n+ATCGGTATACCTTTATTTTGTCACTCATCGGTCGTGAGTTCCACTTCAGCCAGGATCGAACGACGTTGCGCGCTTGTGAAGTCGTCTTATGTACCACTTGGACGCGTAAC\n+>3847\n+ATCGGTCTAAGTTCCATCATTGCCGTACATGAGGAGTAAGAGTACGTTCCACTCTCTGTACGGTCCAGGTAGCTGCCGCTAGCCATCAATGTTGTTCCTGATATAAGATG\n+>3848\n+ATCGGTTATCGTATGGGAGTCGGACAGGAAGGCCAGTCACGAGGCTAAAAGCGCATTATAATACTCATTACAGGTAAGGTCTATTAATGACATTAAAGCTGCGATCGCCA\n+>3849\n+ATCGTAAAGCATGTTGTATTCATCGGGTCTGGTGATGTAGGGGAGAATTCCGGCGTTTCGACATGGGCTACATAGTACGTCAACATATAAGATTCTCCTCCGCTCTCGCG\n+>3852\n+ATCGTAGCTGAGCGTTGACGTATCGAATGGTCACTGAGCGGCAAGTTCCGGTCCAGTTCGTTGAGAAATCGCGATGCGCTTTCTGCTAATTTTGACGTCTAGCGGTCTTC\n+>3853\n+ATCGTATATTGATCGTTCGGCGGGCCATTGGTAGTTTTCTTTGGTCACGGTCGTTCACGACTAGGATAGGATGCCTTGCTCGGTGAGTGCTGTGGGTGCGGGGTACGCTT\n+>3856\n+ATCGTCGATTAATTTGGGTTATTGGACTGTAGATATGCGCGATATAATACGGCGGCCCGAGGGCTGTCTGTCTTTGCAGTCGGCACCATTATGGTGAACGAGCCAATATC\n+>3857\n+ATCGTCTCTGCGAGGCATCATCCTCCGTCCATATTATAATCTATACTTTACGTACCTTCGGCACGGGCTCTAATCTGTTACAAACTTGGGCCTCGGCTTTCTTGCAGTCT\n+>3859\n+ATCGTGCAGACTCCTATTCGACAATCCTGTGGGACAGACTTATTTTGTATGCCGGGTTGCCTACCTCCACTGTGGGAAGATCCTATCGAACGTAGGCGTCTCTGTATTGA\n+>3860\n+ATCGTGCTGAAAGCAGTCCTGACAGAATCAGATGAGATCGGCCGGGACGCCATAGCTGTTAGAGAGGTAAAAACCCCGAATCCTCAGGTAATACCCCACCACTCAATCAC\n+>3861\n+ATCGTGGCTTGTTGTTGCTATTAATCTCATCGCTGCTCCTTGAATCCATCATTGAGGTACCCTCCAATTTGGAGAGGGTAGACTCCTTCGATAAGCGGGAGGACATACTT\n+>3864\n+ATCGTTCGGGTGGACGGACCCCCGCCCATAGTTAGCTGTTGATGCAATAGGGTTGATAGGGGCAATCGGGGACGTACTTTACTGTCGCAGAGGTTTGTGGCAATAATCTG\n+>3865\n+ATCGTTGTAGGCTTAATTAGATTGACCGCGTTCTGGAAACCCCCGTTCTAGACACAACCACCGTGTCCGATGTAGTTACACTCGTATTAGAGCTGCGATGGCCAGCGATA\n+>3866\n+ATCGTTTCTGATTCTTGGCAGTAAGACGATCAGACGAGGACGGCCGACTCTAGCGGATCCATAGATAAGCACTCCTTACGCGAATGTCGATTCCGGTCAGCAGACAATAT\n+>3867\n+ATCTAAAACGGGGGTCCGATCCTAAGATTCGCCGAGAATTAGCGCGTCTTGGCAACTCTTTGGCTGCGACCGCCACCTATGACTGCACACACTCTCTCGGCGATAGCAAT\n+>3868\n+ATCTAACCAGGAAGTCACAGGAGTCTATGCGGTTTGGGAACGTTCCCCTCTTTTACGGTTACTTCGTACCATACGGATCCCAGATTGTCACTGACACCGCAGGCCACAAC\n+>3871\n+ATCTAATGTGGGCTGAATGGAGGGGTGTGTGAGTGCTGATAACTCGAAGGGTCTGCTACAGCTGTAATGGAACTATATATGCCAAGTTTGGTTAGCGAGCATAGGAGGTC\n+>3872\n+ATCTACAGGTCACGTCATCGTTCGAATGAGTAACTGGATTGCAGGGGGGCAACAGACCTAGACGCAAAACGTAACTTGGGACCGTAGTCCAATATATCGACCGATCCGGA\n+>3873\n+ATCTACGAATCGATCCGACCGTACATAGGCTTTCGTAGGGTTCCTTGGCGAACAGGGATGTACGTATTGATGTCCAAACGAACCCTTGAGATAGCCGGGAAGGCTGTCCT\n+>3878\n+ATCTAGGGCGTAAGCTCTAACGGATATGTCACCGATTGCTAGGCTGGCAGTATAACTGGTGGGGTGAGGTGAATAGCAAAATCACCGAATTTTTGTATAGGTGATTCTAC\n+>3879\n+ATCTAGTCATTAGCGGGGACGCGAATCTCGGTGCCCTGTTAGCTCCTTCAAAAGCATGGCGGACTAACGGCCAGCGACACGCCGAGGGGCGGAACGGACTTTAGTTGAGC\n+>3881\n+ATCTATATGTACGATGTAATCCACTGCTCTCCATTGAACAAAACCCACGCTTATTAAGCCCTATAGGCAAAGGCTCCGCGACCCGACAAAGCCATCTTGATGTATAGTCC\n'

diff -r 000000000000 -r dc70286127fe test-data/commet/B.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/commet/B.fa Fri Oct 20 03:15:43 2017 -0400

b'@@ -0,0 +1,24000 @@\n+>0\n+AAAAAAACTCTACAGCGAGCAGTGTTAAAATCGTGGCGCACCCAGACAGCCACTTCGCCGTTCTAAGTGGCCGATCGTAGCACATCGGATGACCTTGGTTGGTACGACAT\n+>2\n+AAAAAAGAGACGAGCCACGCGGTGCGCCTGAACGTTGGGTCCAGACCACACTTATGGATTCGACGGGGCACCTATCAGGTTCTCCATCGTATAGTCGTCTGTAGGTCTGA\n+>3\n+AAAAAATCGCTAGGGGGGATGGCCATCAACCCCCCCTCCCGTACCTATGATAGTGGGATCAGATTTAAGCACGGGCCCTACGACTCCCCTTCATGGAATAGGCTAAGGTG\n+>4\n+AAAAAATTGTCGTTAAGATGAGGAGCTCTTTCGCATTTGACCCATCAAATCTCGGAATGCACTTGAGATCGACCCGTTTGATACAAGCCTTCATCGTCGATAATATATCG\n+>5\n+AAAAACATTGCGGACTACCGTCGTTGCAGTGGGTCGCCCATTCTAGGCTGCGAGTTCATATGTGTGCCTGTCGCTTAGGGCAATCCTCGGATTGGCTGTTTAACAGGGGT\n+>6\n+AAAAACCGATGGGGCCGAGCTGTTCTTTGGCCGGGTTACTCTACGCCCACACGGGTACACAGCCGCGAAACGGGAGGCTCGTGCGCGGTCACCTAAGTCCCTGTGGCGGG\n+>7\n+AAAAACGGATGAGAAATAAAAGGGGAAATAGCGACATGTCAAATGGCCTCTTGGCTGGCGGTGTCTGGCTGGACTAACCCTCTTAAGGACTTAAAGCGTAGGCAAGGTTA\n+>8\n+AAAAACTTTGACTTTTTCAAGACATGAAAGGATGCGGGCTCATACTGGACGGGTTCATTCCTACCGCGGAACGAAGGGCTATTTTTTGTTTGGGCGAGAGTACATCCGTC\n+>9\n+AAAAAGACTCAGCTTGACATGGCGGTCTGAGCTTTGCTTGGGCTCTTACTATGTCAGGGTTGGAAACTATGGCAGAAGGGCTTCTCGCATCCTCACGGCTCGAATTAGCT\n+>11\n+AAAAAGGCAAGGATCTTTGACCACGGCAGTTTGCAATAGTCAATTACGCTTCCCTGAGTACAAACAATGGTCTAATGCTGTTCAGTTGGGGTTAACTGGCCTGACGCTCT\n+>13\n+AAAAATAAAAATGGCCTAGGTCCAACTCGTCCCCGGGGTAAGTTAGTGTAAGAGCTTGGAGCAAGTCTGTTCCTCGTCTGTCCCAGTAACACTCGGGTCTACGGTCGCAG\n+>16\n+AAAAATTAGTCAGGTTACCCCCAATTAGGTGAAATACGTCGAAGGGTCGCGTCCAAGAAAGAATGATAGCTGACAGTTCTCTAGGTATTTATATTTGTTTGCATCGACTG\n+>17\n+AAAACAAATATCCTGAATTCATAGAGCCGTGACTTACAGTTCTATGAAAAGTGTCTGGCAAGGGAGATTTCACGTTTCCCTGTATAGGGTCGTCGTATTGCCCACCATTT\n+>18\n+AAAACAATGCTGAAGACCCTAATGCGTAACCAACAATGTAAGACTGGCACGTATTCTATGATATCTTATTGGCACTCCATCGCGAGGATACTAATAGACACCTAAAAGGA\n+>19\n+AAAACACGCATGTCCGACGGGCGCATTAAACGGCATTGTTGTTCTTGAACCGGAAGCAATAGTCTAGGACCGTTCATATTGACTTACTTTACGCGTGGGCCTTGGATGAA\n+>20\n+AAAACAGTCATTGTCTGATTTAGCATCGGGTGCACCGAAACGCTATCGCCTTCTCGTGAATTCGCAATTCAGCTCCAAGCATCAATCAGAATCACATGCCGCACACAGAA\n+>21\n+AAAACATAGTTATAATGTTTTGAGTGTAAATGCTTACATCGAAATATTCGACGTACTACACCGTGAGCCAAGACCCTGACTTCGAACCATGCGCTCCTGTGAGTGTGACG\n+>23\n+AAAACCCACCGTGCCGGTTTAAGAGCAGTAGCTGTTGGTGTTGTGTCCGCGTGGCATCGGAAAGTCGCTACAACGCCGGAAGCCGGGGATTTACAGAATACGTTATACGA\n+>24\n+AAAACCGGTTCGTGAAGTCCGAAGGAATTCCACAACGCACTGCATGACACCTGGAAGAAGAAGGCCTTTTCCACGCCCTGAACGTAATTTCTGGTAAAGCAAGTGCTCCA\n+>25\n+AAAACCTGATCGTGTTCATGAGTCTGGTATAGACGGATCCTTGGGCCAAAGTCTTCCGGTCTTCTGGCCGCCTTCAGGAGTCTAATTACCTGAACCTCATCGTAATTGCT\n+>27\n+AAAACGATTATTTATCATTTACCGCCTTAGAGTGTGGCTTATATAGCATGGGTTTGATTTGAGTGGGACAACAGATCCATTTGATGCAGTATGTATTAGCGGATCATGAC\n+>28\n+AAAACGCTCGTGCCCAGTTCGAGCGCCCTGGAGTTTACCGCCCAAGTAAACGCTATTTTTTAAATGACATAGCTCCTTACAGGCGTGGGGGGACGCCTATAGGGCCGTCG\n+>30\n+AAAACGTGATGTAATCGGACGCATTTGACCAGACGTAGCCACCTTATTCGGTGCGTGCCATGACCCGAGAGCGCCAGGGATGCTTCTCGTTCCGGGTCACTGATAAATAG\n+>31\n+AAAACTCACCACCAGGACAGAAGCTAAAAGACAGGCCGATTCACGGGCGAGCGGTCGAAGCATACTTTTTAGGGCATCATGTGACCACACGTGTTGACCGTCCATCGTTT\n+>32\n+AAAACTCCTCCGCCGAGGAGGCACTTAGCCTCGTATGGATGCTTAAGGCATGATCGAGCCGGCCGGAAATCTCCTACCGTCTAATTAGGGGCATTGAAGTCCGGTTCCGC\n+>33\n+AAAACTGTCAGCTCTAATCGAATGCTTGGAAGTTCTGTCCAAAGTGTTGCGAAGCCGAGCTTGAACGTATATAATAACTGCGGTCCTCATACCGGAACAAGTTTACTGCC\n+>35\n+AAAACTTTTGGATCGCCATGTGACTAATTCCTATAATTACAATCTGTCATTAGTCGGAGCGGTGCGAGATGTGAGTAGTATAGTCGACGCGGCTAATCGAGGCAGATTCC\n+>36\n+AAAAGACATCGCTAAGTAGTCGATAACTTTAGGTCTGGCTCAGCGAAGTCCGCGCACCGAGGTACGCGATGAACGTGTAGTAGCTGTGCTGCCGACTCTGAGGCGGTAGC\n+>37\n+AAAAGACGTGACAGAGGCGATGATACCGCAGACGATACGCCACTACAGCTAAAGAGTCTGTCTAGAAATGCCTAGCGGCACCTGGCGCCGCCGTCTAATGGAGTGCAAGC\n+>38\n+AAAAGAGTTTGCAGGGTCACTAGCCCGGCTCTGCATACATTGGCAAAGAGGCGATAAGCTGTGAATTCCAGGCTGGGGACGAGCTTGAACCTACTGTGCGAAGTTACCAC\n+>39\n+AAAAGATGCACCGGCTATCTTAGTTCGTTCCAGGCCAACGAGTGTGACTATAGACGAGTTCTGCTCAGAACGGACTAGGCTTCGGGTGTCACGCGGGATCATATTATCTT\n+>41\n+AAAAGCCTGGCCTTAACAAAATCTAGGTGCGTCTCGAATCGAACGGAAAACAACGTCTGGTTTACTGAGAAATCCTAGGATGCTGCTGGCTATTTGACCTCACGGGGGTT\n+>42\n+AAAAGCGTGCCGAAGATGCCGTAATTTCCGAGGATGCACTCTCGTGACATCTCTTTTTAACGAACAAATTGCAGAGGTCAAGGTGATCGAGGCACGCTATGCTAAGCACT\n+>43\n+AAAAGGAAAGGGAGAACGAATGATTGTTTCCAGGTATCAGGAAGCAACAAAATATAATCGATTCGTCACTGTGAGCCAACAGGCGTGTATGTCTGCGTCAAGCGTGCATC\n+>45\n+AAAA'..b'GCGAGCTAGCCTCGTTGACCCTCGGGAGGCTCTGCTGGCCCCAGGCTTCGCTACCCTATTTATAGATAGTA\n+>3825\n+ATCGCGGCCGGGTAAATCGGAACAGCTTCGACTCCAATAAAACAGGTGAACACGCCCATGGAAGTACAAGAATTGGCTCCGCGAGCCAAATGCGGCGCGTATAGCGTCCG\n+>3826\n+ATCGCGGGACGACTAGTCTGAGCATAGCTCGCTGTTGGCACATCCCCCACGAACACCATGTACGGCAAAATTGATCACCGGTACCCCTGTCAAGTTGGGAAGCGTGATGA\n+>3828\n+ATCGCTCATGAATCTCGTTGTAGACATTTTGACAGAACTCATGGCACTCACTTAAAAGGTTGTTTGGCGCGCGGAGGGAGGATGGTCCGGTAGACCAGCTCCGGATAAAT\n+>3829\n+ATCGCTCTCGAGATTTATAACTGCCAATTGCCCGTTGGCTAGGCCTTCAGACATTCTACGCAGGGTGGCTGGCTGACTCGTGGCAGTACTACTCTAACTTTAAGACGGGC\n+>3831\n+ATCGCTTCTTTCGCGGCGTACGTATCAATAACCTACCGGACGCATCCAAATTATCTTGTTTTTACATCATCACGTGCACCTAAAGGGTTACCACCTCTCTGAGGCAACTG\n+>3834\n+ATCGGAGAGACACTTCTCGGCGTGTGCTTCAGAGTTATGAGAGTTCTTTTTGGTTAACTCGGTCACTGAATCGCCCAATTTCTGACGCCAAGGCGGGTGGGTCTAGTCAT\n+>3836\n+ATCGGATTTATCACCCTGACTTACGGAAGAGTCCCGGTAGAATGCTGGTACAGGCACGTTGCGGCGTTTCCCTGTACGACAACCGGCTCATGATGGCGTGCTCTTAACTC\n+>3838\n+ATCGGCGCCCTGCTGCGCGCCTTCCCGTCAGCCTTGAGCATTTTCGTGCAGCTTCAGTTGCTATACTCTGTGTCAAAGATAGCTGACGCAAGTAAGGTAAGGAGAGATGG\n+>3841\n+ATCGGGACGGAGACTTCAAACAACGCCAGAAGCGGGAGGGTACCAGGAGCGGTTGATCAAAATCCAATCTCGTATGGGGAGTGGAGGTCGGACTATGAGGCCTTGGCGAA\n+>3844\n+ATCGGGTGTAATAATTCTCCAAAAGCGTGCCATTCGGGACCCGATCTTAACGATGGTGATATACCTATTTACTGATAAACACTCTCCGAGTGATGATGAAGCCGTGCATC\n+>3845\n+ATCGGTACGAGAAGTGTGTGTGCTGGTGACGGCGTGTGCAATTGAACCCGACCAGGAGCCCGGTTATGAACTCAAGTCCGCGGGGCTGACGCAAAAATTCCGTGTAATCT\n+>3846\n+ATCGGTATACCTTTATTTTGTCACTCATCGGTCGTGAGTTCCACTTCAGCCAGGATCGAACGACGTTGCGCGCTTGTGAAGTCGTCTTATGTACCACTTGGACGCGTAAC\n+>3847\n+ATCGGTCTAAGTTCCATCATTGCCGTACATGAGGAGTAAGAGTACGTTCCACTCTCTGTACGGTCCAGGTAGCTGCCGCTAGCCATCAATGTTGTTCCTGATATAAGATG\n+>3848\n+ATCGGTTATCGTATGGGAGTCGGACAGGAAGGCCAGTCACGAGGCTAAAAGCGCATTATAATACTCATTACAGGTAAGGTCTATTAATGACATTAAAGCTGCGATCGCCA\n+>3849\n+ATCGTAAAGCATGTTGTATTCATCGGGTCTGGTGATGTAGGGGAGAATTCCGGCGTTTCGACATGGGCTACATAGTACGTCAACATATAAGATTCTCCTCCGCTCTCGCG\n+>3852\n+ATCGTAGCTGAGCGTTGACGTATCGAATGGTCACTGAGCGGCAAGTTCCGGTCCAGTTCGTTGAGAAATCGCGATGCGCTTTCTGCTAATTTTGACGTCTAGCGGTCTTC\n+>3853\n+ATCGTATATTGATCGTTCGGCGGGCCATTGGTAGTTTTCTTTGGTCACGGTCGTTCACGACTAGGATAGGATGCCTTGCTCGGTGAGTGCTGTGGGTGCGGGGTACGCTT\n+>3856\n+ATCGTCGATTAATTTGGGTTATTGGACTGTAGATATGCGCGATATAATACGGCGGCCCGAGGGCTGTCTGTCTTTGCAGTCGGCACCATTATGGTGAACGAGCCAATATC\n+>3857\n+ATCGTCTCTGCGAGGCATCATCCTCCGTCCATATTATAATCTATACTTTACGTACCTTCGGCACGGGCTCTAATCTGTTACAAACTTGGGCCTCGGCTTTCTTGCAGTCT\n+>3859\n+ATCGTGCAGACTCCTATTCGACAATCCTGTGGGACAGACTTATTTTGTATGCCGGGTTGCCTACCTCCACTGTGGGAAGATCCTATCGAACGTAGGCGTCTCTGTATTGA\n+>3860\n+ATCGTGCTGAAAGCAGTCCTGACAGAATCAGATGAGATCGGCCGGGACGCCATAGCTGTTAGAGAGGTAAAAACCCCGAATCCTCAGGTAATACCCCACCACTCAATCAC\n+>3861\n+ATCGTGGCTTGTTGTTGCTATTAATCTCATCGCTGCTCCTTGAATCCATCATTGAGGTACCCTCCAATTTGGAGAGGGTAGACTCCTTCGATAAGCGGGAGGACATACTT\n+>3864\n+ATCGTTCGGGTGGACGGACCCCCGCCCATAGTTAGCTGTTGATGCAATAGGGTTGATAGGGGCAATCGGGGACGTACTTTACTGTCGCAGAGGTTTGTGGCAATAATCTG\n+>3865\n+ATCGTTGTAGGCTTAATTAGATTGACCGCGTTCTGGAAACCCCCGTTCTAGACACAACCACCGTGTCCGATGTAGTTACACTCGTATTAGAGCTGCGATGGCCAGCGATA\n+>3866\n+ATCGTTTCTGATTCTTGGCAGTAAGACGATCAGACGAGGACGGCCGACTCTAGCGGATCCATAGATAAGCACTCCTTACGCGAATGTCGATTCCGGTCAGCAGACAATAT\n+>3867\n+ATCTAAAACGGGGGTCCGATCCTAAGATTCGCCGAGAATTAGCGCGTCTTGGCAACTCTTTGGCTGCGACCGCCACCTATGACTGCACACACTCTCTCGGCGATAGCAAT\n+>3868\n+ATCTAACCAGGAAGTCACAGGAGTCTATGCGGTTTGGGAACGTTCCCCTCTTTTACGGTTACTTCGTACCATACGGATCCCAGATTGTCACTGACACCGCAGGCCACAAC\n+>3871\n+ATCTAATGTGGGCTGAATGGAGGGGTGTGTGAGTGCTGATAACTCGAAGGGTCTGCTACAGCTGTAATGGAACTATATATGCCAAGTTTGGTTAGCGAGCATAGGAGGTC\n+>3872\n+ATCTACAGGTCACGTCATCGTTCGAATGAGTAACTGGATTGCAGGGGGGCAACAGACCTAGACGCAAAACGTAACTTGGGACCGTAGTCCAATATATCGACCGATCCGGA\n+>3873\n+ATCTACGAATCGATCCGACCGTACATAGGCTTTCGTAGGGTTCCTTGGCGAACAGGGATGTACGTATTGATGTCCAAACGAACCCTTGAGATAGCCGGGAAGGCTGTCCT\n+>3878\n+ATCTAGGGCGTAAGCTCTAACGGATATGTCACCGATTGCTAGGCTGGCAGTATAACTGGTGGGGTGAGGTGAATAGCAAAATCACCGAATTTTTGTATAGGTGATTCTAC\n+>3879\n+ATCTAGTCATTAGCGGGGACGCGAATCTCGGTGCCCTGTTAGCTCCTTCAAAAGCATGGCGGACTAACGGCCAGCGACACGCCGAGGGGCGGAACGGACTTTAGTTGAGC\n+>3881\n+ATCTATATGTACGATGTAATCCACTGCTCTCCATTGAACAAAACCCACGCTTATTAAGCCCTATAGGCAAAGGCTCCGCGACCCGACAAAGCCATCTTGATGTATAGTCC\n'

diff -r 000000000000 -r dc70286127fe test-data/commet/C.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/commet/C.fa Fri Oct 20 03:15:43 2017 -0400

b'@@ -0,0 +1,20000 @@\n+>0\n+AAAAAAACCGAAGTCTCTTGCAGTATGCACAGGAGATCGCGGAGAACCGGAATCCCCTGGTTCGACTGTGACTCTTGGAGCGTCGCTAATCGCGTCGGTAACTTTAATTT\n+>2\n+AAAAAAGCGGAATCACTGAAGACGTCATTTCCTCTTCAGAAAAAGTTTACCATGTTCTATTCTTGACCCTACGAATCAAGGTTCCGTTTAGCGTGTCGTTATAGAACAAT\n+>3\n+AAAAAATACAGTATATGCCCCGAACTAGCCATCCGGATCCCAATAATCAAATCACCGTGACTGATGGTCAGATATCTTCTCCGGGATTGTGGGGAACGCCTACTTCGTGG\n+>4\n+AAAAACAAGGGCTGAGCATCTGCGACATAAGTATCCCGTACATTATGTTCGATTGTAGTTAACTAAATTGTCCTACACTAGCGACCCTAAACCACCGTTACTCGAGGGCA\n+>7\n+AAAAACGGTGGTTTGCATGTTAGGCGGAAGATCCCAATCCCTTGAAGAATCACGGAAGTAAGTTACTAGTGAAGGTTACTTTGCGATCTAAGGCGCTCGTGGGTGTCACA\n+>8\n+AAAAACTGGCTACATTTAGACTTTTCCCAGCCTTGCCTACATGCCTAGCACTGAATCAAATACCCGGCTACCGGGTAGCGACCCCACAATATCAAGTTGCTTCTCTGAGT\n+>10\n+AAAAAGCAGTCGGAAGACCTTTAGCTGTCCTTTAGCAGTGACTCTCCGCCCGTCTCAATGCAAAGAGATTCTGCGCATTGCTCCTTGTCCTAAGACACCATTAAGCGAAT\n+>12\n+AAAAAGTTAGTCCTAAATTGTGGGCATCGGGTTGGCTGAATTAGACTGTGTGATCATATTCTACTTTTCGTCGACAGGATCTGGGCCGATTAGGGACATGTAAAGTGTCC\n+>13\n+AAAAATAAGAAGCCTTACGAGCGTTGCGGGTTCGTTCTATATAAGGGCAGTACGTTTAGTTTACCCATCTGGGGTTCTTGTTACAACATGGAGTCGACTGTGTCTTTTAC\n+>14\n+AAAAATCCGTTTAAGTCCACACCCCATATCTTTTGCAAGTTACGTCTTCACTTGTGTACTGTAGACTGCTGGGGACTAGAGTCCATCGTTGTGACTTAAAGGACGCTTTC\n+>15\n+AAAAATGAATGATCCACGCCCGGTCAGTGTAGATCACTGAGCCTCGGCTATTCAGCCCATAAAACACAAAGCCTGCGGAGCGGCGGCCTACTAGAAATGCGATCCATCCT\n+>17\n+AAAACAAAAGCAATTAGCAACGGACGCGAACTCTCGATCTTACAAGGATACCAGAATAGTTCACCCTGGCTGCGCAATGCCGATATTAAGTGTAGGCTTCGGCCCATTGT\n+>18\n+AAAACAAGCGATTGAGATTCTAATCCAGCTTGCGACATACTTTGTCAGCGATCTGCGCTGTCTAATTTGCATCAAGTGTCTATACACGGTCCCTCCTCAGGGCGGGCACG\n+>19\n+AAAACACTCCCGTATTCATGTCTACGTACCGTTATCCACTATTAAATGTACACTAGCTAACAGTGGTCATTGAGTAATCAAGATCAAGCGCGAGATGGGGGAGGATTGCT\n+>23\n+AAAACCCAAGATGACGAATATCTGGTTACTGGGTTGACGGGATATAATCATTGCAAAACCTTTTGGGAAGGGACCTTAAAGCCTAGTCTGTCTTTTAGTTGCCCTCGTGG\n+>25\n+AAAACCTGACGTGTAGATTAGTTACGTCCCCCGGCGCATGCAATCGTCCCACACGGCAGATGTGTTCGGACTGGAGACAATAGTGCTAGTTGGACTACGGCCTATTGGCG\n+>26\n+AAAACGAAGTAGCGGGTTACGTGAATGGTGCCCACTTACGATAGGTTCGAGGCTGAGGGCTGTACCACGCCGGACGATTCGTGTTCGCCTCCTTGAATCTGATTCCCCGT\n+>29\n+AAAACGGGACCTGCTTTTTTGCTTTGCGGAGGTCAATGGTTAAGTACGAACCAGCATGCGGGATGTGGCCCCGCCAATGTGGTACCGTTTGGTACTGGATCAGTCCTTTT\n+>38\n+AAAAGATACCTACGCTCCATCTAGAGGTTAATAGCGAACCTCTCGCTTCTAGAGCGAGGTGGCATTCAGCGAGATGAACCTCTAATCTAAGCCCCGAATATCTGACGCAG\n+>39\n+AAAAGATTGCGTCTCAGGCGGGCTCTAAACACGCTTCGCCGGACCAACTTTCTGACATTCTGGGACTGTCACTTGCAAGGCCTTATAGCTTTACGGCATTCTCCTTCGCC\n+>40\n+AAAAGCACTACTCCGTTTGGACCATTTGCGCAAACATGATCCCCGCGCGGTACGGAACTTTTTTACAACGCAGGATCTTCTGACCCGGTAACATGCTACCTGGCGCCTGT\n+>41\n+AAAAGCCGGGATGGGTAACTCTTTTACTATTTGGGGACAAAGCTGCATAGTGACCGGCACTCAAACATACATTGTAATAGTGAAATCGGAGAGCACCATGCGCCAGTCGG\n+>42\n+AAAAGCGATTTGAGCGGAGGAGGCGTTGAGGAGATCAGAAGGGGGCACACCGCAACGGTCTTCAACACACACTGGCAGTCTTTAAGACGTTTGAAGTTTAGCTTAGTTAT\n+>43\n+AAAAGCTGGTCCTGCCATTGATGTCCGATGAGCGACTCTTACCCTTGCAAAGAGCACAAAAGTTATATTCTGATCAATGTCATGCATTTAACATTACTGACAGGGTGGCG\n+>44\n+AAAAGGAAGATCACAGGAGAAGTAGACACCTCATCGATGGCACGGACCCAGTTCACATATAGGGTGGGGAGCTATCCAGAAGTGGCCATGGTTTTGTAACTTCGCGTTAG\n+>46\n+AAAAGGGGGAAACAACTGAAGGTCGGTGCCGCGATAAGCCCGTTAACAGGGACGGGCCAAAGCATTAGCTTGTTAAGAACCGATGCTATGTTTATCCGATTGGATGTTGT\n+>50\n+AAAAGTGACGAATTCCTGCATCGAGAGGATGGCGTCTCTCGCATCGCCGGTCCAAGAAGACCACAGGAAACAGATCGGAGAAGGCCGCAGGTATTCAGGAAGTTCATATA\n+>51\n+AAAAGTTCCATTGGGGGCACGCCTAAGTTACGGCACCCGAGTTTCGCCAGGAAGTGGAAATTTATTCTTTTGAATCCGCAGAAGTGTAAAATGCCGTCCAATAAAATTAC\n+>53\n+AAAATAAGGCTTTGGTGCCAAGACCAAACTCGCTTTGATGTCGTCTTGGCCAAAAAGATACCTTCGGATGGGCCCACCCCTATGCTTCCTCATGCTTTCACTAGGGAGAC\n+>55\n+AAAATAGTAGGCCGAATGGATTGGGTGACGTGTGGCACAGTAAGGGAGGACTATCAGGTGATTCTCTACCTGGAGCCACCATGAACCTCATGAGTAGAGGCGGAACAAGG\n+>58\n+AAAATCCGTACCTCGAGCGGTTGGAGAACGCTCGCGCTGAATGCCCGTAAGATGTTGACAGTGAAGTGATTTTGCAATCGATGTATTCGTGTCGAATCATCATGCCCGCT\n+>60\n+AAAATCTATTAGGAGATCAACTGTCCGAGTATTGTGGGGTTGGCTCTACTTACGCAACCCGCGATACAGCAATACGATCCTCGAGCTCTCCTCAACCCCGATTGCGTATG\n+>62\n+AAAATGCACGAAAATAGGAGCATTCGTCCCAGTAGTGATTGAAAGTCCTTAGGCATAATTCAATACATTCGTTTGGACCCCAAGTGTTGGGCGTTCAACGCGCGAGATTG\n+>64\n+AAAATGGCGGAATCTGTTGGATCCTGGCCGGTAGAGTGTGCCTACAGATTTGTCGAGGCGGGTAGTCTGCCTGCGGCCTGCACGTTAGAGTACTACCTCATAGTGTTAAG\n+>65\n+A'..b'ATACACTTGCTTGGAATAGGTTGTAGGAAATTGCACTC\n+>17967\n+TTTTGAGATACATCTGAATGCGCGTTGCGAATACCTCTTTAGCAAGATATACCTGCAGGGTCCGCCTCGCCGATATCCTCCGGTCCAGACCGCGATATCCACCCGAATCT\n+>17968\n+TTTTGATACGCTCTCTGGGGGGTCTGTCTTGCCTTAAGTGGGCTCATGCAGTCTTGCAAGGCTTAGCAACAGAATCAGAACCAAACTTAGGAGTTGGTTATTATCAGGTA\n+>17969\n+TTTTGCACCCCGCGCCGTACAATCAGATCGTGGGCCCCCGATGGGGCCGGACACGACGCAGTCAACCTAATGGTTTTAGGAGGAGTGAGGAGTGGATGTCAGAATTGGAG\n+>17970\n+TTTTGCCGAGGATCCTATCAGGATACTCCACCCGTTACAATACGTCAATAAAACTAAGTCTACGTATCACGCTTTCGACGCTCCGATCATACCCTCACCAGGTGAGTACT\n+>17971\n+TTTTGCGCCTTTAAGACCTCAGCTAAAACACTTCGTGCCTCTAATTGACTTGTTGAATGCGACATATGTAGTGCCGTGACATTGTAGCCTGTCCATTGCAATACTGCACG\n+>17972\n+TTTTGCGGACCCTGAGGATAATTTGAGGTTCAGGACCGCACCCGGCTACATCACCACACGCCTACTTGCACGCTCCTCAGAAGTCCATATACGGGTGCTACTCCCGTCTA\n+>17973\n+TTTTGCTGCTTGGAGAGAAGGACGAAAGAATTTTAAGGACTTTCGTTTCCTTATTACCGTCGTGTTATACATAGTATCTATGTTTATGCATGTCAAGAGTGGCTAAAAGC\n+>17974\n+TTTTGGAGATTACCGGTGAATCTCTCCTAAGATACCATAACAGTACTTGTATTAATCGCTGTCGTTGCTTGCAACCGACGGGATAAACCTCTACTTGTTGCGGTTGATGG\n+>17975\n+TTTTGGCTGAAAATTCGCTCTATAATTTACTTTGAAGCTGGCTGCCATCAAGCGTAGAACTGAACGTTATTGACCGAACCCACTATTCTACCGTGTGGACCTAATAGTAA\n+>17976\n+TTTTGGGCGAATATGAACGAGGTGCGTAAAGGAATCCTCCCAGCTAAACTTCATCGCGTATCGTAAGCGTTATGGCGTATCACGTTTTTATTATCGTTAGAAGAAAAAAG\n+>17977\n+TTTTGGTGAGATTACCCCTTAACCCATATGTACACGTCAAACACTGGTGACATGCCCGATCTTATCAGCACAAATGTACCCGCATGGGTCCTCTTGTCTTGGTGTTAGAA\n+>17978\n+TTTTGTAGGCATAAGTGGTACTCCATGCGTTCACCATTTCAATATGCGATAGGATTGCCAGGTCCAGGAGAGTCAGGCCCCTGCGGCATAATCTGCATATCATCATTGCC\n+>17979\n+TTTTGTCATCGGCTCGGCGAGTGCTTTAGTTTGCCGATCTCCACGCACATGGCTAAAGGTCTAGAGGGTACAATGTCTTCTAGCTCTCGCTCATTCCGCATGTATCGTTC\n+>17980\n+TTTTGTGCGAGCCAAAAATGAGGCTAAAGAAGAACTTGGTGTCCTGGGTGCACTGCTTGCATAAGCGGTTGCTTTAGCTAGGTTGGGTCACCCCTCTCGAACGTTCCGCT\n+>17981\n+TTTTGTGTCATTATACTTACAGCACCTGTCTTCGGCTAGAAATTAGGTTCGTAATCGACGCGAAGCTTTGGGATGACGGGAACTAGGGCCAACATGCAGAGGCTTTTGTC\n+>17982\n+TTTTGTTTACGTCCGCTTCGTTTTCGAATGTCCTTTTAGTACCTTAGTGTCCTCACAACACATGCCCCTTGTAGCGGGAAGCAAAGTGCGAACACAGGGGAACCGCAATA\n+>17983\n+TTTTTAAGCACACCCTTGCATCTTTAGTCGTCACACTGCGTTGTAGTGTTGTCACAAATCGGAGCCAACGTCACCAAGCAGTTATTAAGATTAAGTTTGAATCCTTCCCT\n+>17984\n+TTTTTAGACTTTCACATACTGCTCTGGTTACTAGTAAGCTCGACTACTTGATGGGTAAGCGCACCCGGTCACACTACCAATACTCCCCAGCACATCTAGCTTACTTAGAC\n+>17985\n+TTTTTAGGGAAGTCGCCCATGGACGGGCGCTGGGACACTCCATGGGCATATGTTGTAATGAGCCCAGGGCCCTGCCGAGGGGATTGCGTATGCTTGTGACGTTCCTACTT\n+>17986\n+TTTTTATGACAAGACGGCTACTGTGTCTTTGGGAGTTCTGCTCGCTCTACTCTCCCGCGGAGTCAGACTCGGCGGCAACGTTGCGCGGACATAAGACTGTGTAGCCCTAC\n+>17987\n+TTTTTCACCCCATGAGACAGGCGCTGTTTTCCTTGGGAGCGTAACGTTGACTCCTAAGTATCGGGCACGATGTAACATTGTCCGGCATCTGTTTCTCTCTTTCGTGCTTC\n+>17988\n+TTTTTCCCAGTACCTGTGCACGGACAGCGAGCTAAAGTATGCCACCTCAAGCAATCACGTTAACGCCTGTGGAGGTAGATTTCTGGGAGATCCAATTAATAGGCCAGCAT\n+>17989\n+TTTTTCGTACTAACTTTTATAGATATGAAATTGCTCACTGCGCTCCGACCCGCTTCTATACTGGCTAGTCAGCTTCGTGTACAGCAGCTTGCGAGTACTTTGAGACTAAT\n+>17990\n+TTTTTCTCCCTGGCTCACTCCGGGGGAGCCCAGAAACTGTGTAGACACCAGCGCTGCCGACGAAAGTGGAGAATGGTCACGTGTCACCGTGATATCCAGACATCATCCCA\n+>17991\n+TTTTTGACGCCGCTGCAGAACGCCGCTCAACGCCATTTTGCTCGTTTGCCATAAATCTGGCTTAAAGCGTTACGCGACGGTCCAATGAACGATTGCCAGCCAGTCTTTCC\n+>17992\n+TTTTTGCAGGCTTGTAGCTGCTATACAATTCATGGTGTGTGAAGCCTATCGAGGGTATCCTTTCGATTTAACGTATGTCAACACACTCCTCTATACGAATACTGTCGTGG\n+>17993\n+TTTTTGCTTGCCATACTTGGTTCCGATGGCAATGAGGTAATCGACAGAGCAAACGTCGGACTTTAATCAAATATTAATCGCAACACCAAGTTTGTACACAGATCGATCAA\n+>17994\n+TTTTTGGGTGGGGACGCAGATCTATCTGTTAAGCTATCCATGTAAGTTACGTGTAAGTTGTACAAAAGGATGTGTCACGAATTAACTCAGAGAAACGCGACAGTGAGTGC\n+>17995\n+TTTTTGTTCGGTAAACGACGTTGTCCGCACCGTACCCGCCGCAGTCATAGTTCTATGAGTCCTAACGTTACCGCTGTTATCGACAAGGAGCTCGCAAATATCAGAAGATG\n+>17996\n+TTTTTTAGATGTAGTTTCCGTGACTAACTGCAAGACCTCATATTTTTTTTTCGCTCCTTCCGCTGAGGTCGCTAAAGATTAAAGTCTCCCACAACCAATGCTACCCTCCC\n+>17997\n+TTTTTTCGAAGAGGTTACCAACACTTTTTCGCTGGCCATGTACCGGATTAGCAACCATCATCTCATGAGTCCGATAATTCGTGACTGCCATGTTAGTGGAGACCGTCAAA\n+>17998\n+TTTTTTGGTTTCTCTCCGCTGTTCAATGTTATAGGCTCCTCGGATAGTGGCGCCAAAAGTGGGTGAAACCTCATCTAAGCACCGACTAACACAAGGGTAAGTCGCGGGCG\n+>17999\n+TTTTTTTTCACTTAGATCATATAGTCTTGTATAGCTGCACTTCTCTGTCTCAGCAAAACTGTGATCTTAGGCAGAGCCACTAAAAGATTGGCTGAAGAACGACATAGTGG\n'

diff -r 000000000000 -r dc70286127fe test-data/commet/D.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/commet/D.fa Fri Oct 20 03:15:43 2017 -0400

diff -r 000000000000 -r dc70286127fe test-data/commet/dendrogram.png

Binary file test-data/commet/dendrogram.png has changed

diff -r 000000000000 -r dc70286127fe test-data/commet/matrix_plain.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/commet/matrix_plain.csv Fri Oct 20 03:15:43 2017 -0400

@@ -0,0 +1,4 @@
+;set0;set1;set2
+set0;12000;3000;3000
+set1;3000;12000;12000
+set2;3000;12000;12000

diff -r 000000000000 -r dc70286127fe test-data/discosnp/multifasta.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/discosnp/multifasta.fa Fri Oct 20 03:15:43 2017 -0400

@@ -0,0 +1,12 @@
+>SNP_higher_path_3|P_1:24_A/T|high|nb_pol_1|C1_74|C2_0|Q1_0|Q2_0|G1_0/0:8,227,1484|G2_1/1:1724,263,8|rank_1
+AGGGCCGGGCTACATGTTAACTACAAGGCTATAACCTATTGATGACCCG
+>SNP_lower_path_3|P_1:24_A/T|high|nb_pol_1|C1_0|C2_86|Q1_0|Q2_0|G1_0/0:8,227,1484|G2_1/1:1724,263,8|rank_1
+AGGGCCGGGCTACATGTTAACTACTAGGCTATAACCTATTGATGACCCG
+>SNP_higher_path_2|P_1:24_C/G|high|nb_pol_1|C1_0|C2_134|Q1_0|Q2_0|G1_1/1:2484,378,10|G2_0/0:10,408,2684|rank_1
+ATTACAGAGCTGCCGGGTGGATGACTCTCTACCGCGCTCTGTGGAAGTG
+>SNP_lower_path_2|P_1:24_C/G|high|nb_pol_1|C1_124|C2_0|Q1_0|Q2_0|G1_1/1:2484,378,10|G2_0/0:10,408,2684|rank_1
+ATTACAGAGCTGCCGGGTGGATGAGTCTCTACCGCGCTCTGTGGAAGTG
+>SNP_higher_path_1|P_1:24_A/T|high|nb_pol_1|C1_0|C2_114|Q1_0|Q2_0|G1_1/1:2204,335,9|G2_0/0:9,347,2284|rank_1
+CAACAACGCAACAGCTCGAGGTGTACTTCGCAGAGAAACCGCACGTCCA
+>SNP_lower_path_1|P_1:24_A/T|high|nb_pol_1|C1_110|C2_0|Q1_0|Q2_0|G1_1/1:2204,335,9|G2_0/0:9,347,2284|rank_1
+CAACAACGCAACAGCTCGAGGTGTTCTTCGCAGAGAAACCGCACGTCCA

diff -r 000000000000 -r dc70286127fe test-data/discosnp/multifasta_paired.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/discosnp/multifasta_paired.fa Fri Oct 20 03:15:43 2017 -0400

@@ -0,0 +1,12 @@
+>SNP_higher_path_3|P_1:30_C/G|high|nb_pol_1|C1_124|Q1_0|G1_0/1:1927,18,1727|rank_0
+CAAGTGCACTTCCACAGAGCGCGGTAGAGACTCATCCACCCGGCAGCTCTGTAATAGGGAC
+>SNP_lower_path_3|P_1:30_C/G|high|nb_pol_1|C1_134|Q1_0|G1_0/1:1927,18,1727|rank_0
+CAAGTGCACTTCCACAGAGCGCGGTAGAGAGTCATCCACCCGGCAGCTCTGTAATAGGGAC
+>SNP_higher_path_2|P_1:30_A/T|high|nb_pol_1|C1_74|Q1_0|G1_0/1:1260,18,1020|rank_0
+ACTAATAGGGCCGGGCTACATGTTAACTACAAGGCTATAACCTATTGATGACCCGGTCCAT
+>SNP_lower_path_2|P_1:30_A/T|high|nb_pol_1|C1_86|Q1_0|G1_0/1:1260,18,1020|rank_0
+ACTAATAGGGCCGGGCTACATGTTAACTACTAGGCTATAACCTATTGATGACCCGGTCCAT
+>SNP_higher_path_1|P_1:30_A/T|high|nb_pol_1|C1_114|Q1_0|G1_0/1:1548,17,1628|rank_0
+GCAGCGCAACAACGCAACAGCTCGAGGTGTACTTCGCAGAGAAACCGCACGTCCAGTTCTA
+>SNP_lower_path_1|P_1:30_A/T|high|nb_pol_1|C1_110|Q1_0|G1_0/1:1548,17,1628|rank_0
+GCAGCGCAACAACGCAACAGCTCGAGGTGTTCTTCGCAGAGAAACCGCACGTCCAGTTCTA

diff -r 000000000000 -r dc70286127fe test-data/discosnp/reads1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/discosnp/reads1 Fri Oct 20 03:15:43 2017 -0400

b'@@ -0,0 +1,2000 @@\n+>read0_contig0_position268_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n+TGGTGTCGGATCAGAGCGGTCTTACGACCAGTCGTATGCCTTCTCGAGTTCCGTCCGGTTAAGCGTGACAGTCCCAGTGAACCCACAAACCGTGATGGCT\n+>read1_contig0_position729_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n+CCACTGCCAAAATTCTGTCCACAAGCGTTTTAGTTCGCCCCAGTAAAGTTGTCTATAACGACTACCAAATCCGCATGTTACGGGACTTCTTATTAATTCT\n+>read2_contig0_position653_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n+CGGATCCCCTTGTCCAATCTAACTCACCGAATTCTTACATTTTAGACCCTAATATCACATCATTAGAGATTAATTGCCACTGCCAAAATTCTGTCCACAA\n+>read3_contig0_position190_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n+GCGGTAGAGACTCATCCACCCGGCAGCTCTGTAATAGGGACTAAAAAAGTGATGATAATCATGAGTGCCGCGTTATGGTGGTGTCGGATCAGAGCGGTCT\n+>read4_contig0_position530_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n+CAGTGTCGCACATATCACTTTTGCTTCAACGACTGCCGCTTTCGCTGTATCCCTAGACAGTCAACAGTAAGCGCTTTTTGTAGGCAGGGGCTCCCCCTGT\n+>read5_contig0_position177_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n+ACTTCCACAGAGCGCGGTAGAGACTCATCCACCCGGCAGCTCTGTAATAGGGACTAAAAAAGTGATGATAATCATGAGTGCCGCGTTATGGTGGTGTCGG\n+>read6_contig0_position84_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n+GTAGTTAACATGTAGCCCGGCCCTATTAGTACAGTAGTGCCTTCATCGGCATTCTGTTTATTAAGTTTTTTCTACAGCAAAACGATCAAGTGCACTTCCA\n+>read7_contig0_position522_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+AGCCCCTGCCTACAAAAAGCGCTTACTGTTGACTGTCTAGGGATACAGCGAAAGCGGCAGTCGTTGAAGCAAAAGTGATATGTGCGACACTGCATCTAGG\n+>read8_contig0_position15_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+TACTAATAGGGCCGGGCTACATGTTAACTACAAGGCTATAACCTATTGATGACCCGGTCCATACATAACTTGGTATCGTGCATGTAGCGTTCAAGGGCTA\n+>read9_contig0_position654_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n+GGATCCCCTTGTCCAATCTAACTCACCGAATTCTTACATTTTAGACCCTAATATCACATCATTAGAGATTAATTGCCACTGCCAAAATTCTGTCCACAAG\n+>read10_contig0_position309_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n+TCTCGAGTTCCGTCCGGTTAAGCGTGACAGTCCCAGTGAACCCACAAACCGTGATGGCTGTCCTTGGAGTCATACGCAAGAAGGATGGTCTCCAGACACC\n+>read11_contig0_position487_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+TCTAGGGATACAGCGAAAGCGGCAGTCGTTGAAGCAAAAGTGATATGTGCGACACTGCATCTAGGCAGCGCAACAACGCAACAGCTCGAGGTGTTCTTCG\n+>read12_contig0_position449_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n+CATATGAGAGTGTTAGAACTGGACGTGCGGTTTCTCTGCGAAGAACACCTCGAGCTGTTGCGTTGTTGCGCTGCCTAGATGCAGTGTCGCACATATCACT\n+>read13_contig0_position520_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+CCCCTGCCTACAAAAAGCGCTTACTGTTGACTGTCTAGGGATACAGCGAAAGCGGCAGTCGTTGAAGCAAAAGTGATATGTGCGACACTGCATCTAGGCA\n+>read14_contig0_position882_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n+TAATAGCGCGGGTGAGAGGGTAATCAGCCGTGTCCACCAACACAACGCTATCGGGCGATTCTATAAGATTCCGCATTGCGTCTACTTATAAGATGTCTCA\n+>read15_contig0_position696_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+TGGTAGTCGTTATAGACAACTTTACTGGGGCGAACTAAAACGCTTGTGGACAGAATTTTGGCAGTGGCAATTAATCTCTAATGATGTGATATTAGGGTCT\n+>read16_contig0_position642_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+ATTTTGGCAGTGGCAATTAATCTCTAATGATGTGATATTAGGGTCTAAAATGTAAGAATTCGGTGAGTTAGATTGGACAAGGGGATCCGAAGATGTTTTG\n+>read17_contig0_position354_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n+AAACCGTGATGGCTGTCCTTGGAGTCATACGCAAGAAGGATGGTCTCCAGACACCGGCGCACCAGTTTTCACGCCGAAAGCATAAACGACGAGCACATAT\n+>read18_contig0_position326_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n+TTAAGCGTGACAGTCCCAGTGAACCCACAAACCGTGATGGCTGTCCTTGGAGTCATACGCAAGAAGGATGGTCTCCAGACACCGGCGCACCAGTTTTCAC\n+>read19_contig0_position323_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+AAAACTGGTGCGCCGGTGTCTGGAGACCATCCTTCTTGCGTATGACTCCAAGGACAGCCATCACGGTTTGTGGGTTCACTGGGACTGTCACGCTTAACCG\n+>read20_contig0_position700_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+GATTTGGTAGTCGTTATAGACAACTTTACTGGGGCGAACTAAAACGCTTGTGGACAGAATTTTGGCAGTGGCAATTAATCTCTAATGATGTGATATTAGG\n+>read21_contig0_position553_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+AAGATGTTTTGGCGCAGTTAGTCACAGGGGGAGCCCCTGCCTACAAAAAGCGCTTACTGTTGACTGTCTAGGGATACAGCGAAAGCGGCAGTCGTTGAAG\n+>read22_contig0_position553_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n+CTTCAACGACTGCCGCTTTCGCTGTATCCCTAGACAGTCAACAGTAAGCGCTTTTTGTAGGCAGGGGCTCCCCCTGTGACTAACTGCGCCA'..b'on323_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+AAAACTGGTGCGCCGGTGTCTGGAGACCATCCTTCTTGCGTATGACTCCAAGGACAGCCATCACGGTTTGTGGGTTCACTGGGACTGTCACGCTTAACCG\n+>read978_contig0_position876_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+ATCTTATAAGTAGACGCAATGCGGAATCTTATAGAATCGCCCGATAGCGTTGTGTTGGTGGACACGGCTGATTACCCTCTCACCCGCGCTATTAGCTTCC\n+>read979_contig0_position604_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+TAGGGTCTAAAATGTAAGAATTCGGTGAGTTAGATTGGACAAGGGGATCCGAAGATGTTTTGGCGCAGTTAGTCACAGGGGGAGCCCCTGCCTACAAAAA\n+>read980_contig0_position647_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+ACAGAATTTTGGCAGTGGCAATTAATCTCTAATGATGTGATATTAGGGTCTAAAATGTAAGAATTCGGTGAGTTAGATTGGACAAGGGGATCCGAAGATG\n+>read981_contig0_position495_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n+ACCTCGAGCTGTTGCGTTGTTGCGCTGCCTAGATGCAGTGTCGCACATATCACTTTTGCTTCAACGACTGCCGCTTTCGCTGTATCCCTAGACAGTCAAC\n+>read982_contig0_position68_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n+AATAGGTTATAGCCTTGTAGTTAACATGTAGCCCGGCCCTATTAGTACAGTAGTGCCTTCATCGGCATTCTGTTTATTAAGTTTTTTCTACAGCAAAACG\n+>read983_contig0_position567_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n+GCTTTCGCTGTATCCCTAGACAGTCAACAGTAAGCGCTTTTTGTAGGCAGGGGCTCCCCCTGTGACTAACTGCGCCAAAACATCTTCGGATCCCCTTGTC\n+>read984_contig0_position490_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n+AGAACACCTCGAGCTGTTGCGTTGTTGCGCTGCCTAGATGCAGTGTCGCACATATCACTTTTGCTTCAACGACTGCCGCTTTCGCTGTATCCCTAGACAG\n+>read985_contig0_position712_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+CCGTAACATGCGGATTTGGTAGTCGTTATAGACAACTTTACTGGGGCGAACTAAAACGCTTGTGGACAGAATTTTGGCAGTGGCAATTAATCTCTAATGA\n+>read986_contig0_position813_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n+ACTTCTTATTAATTCTTTTTTCGTGAGGAGCAGCGGATCTTAATGGATGGCCGCAGGTGGTATGGAAGCTAATAGCGCGGGTGAGAGGGTAATCAGCCGT\n+>read987_contig0_position269_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+CAGCCATCACGGTTTGTGGGTTCACTGGGACTGTCACGCTTAACCGGACGGAACTCGAGAAGGCATACGACTGGTCGTAAGACCGCTCTGATCCGACACC\n+>read988_contig0_position773_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n+AAAGTTGTCTATAACGACTACCAAATCCGCATGTTACGGGACTTCTTATTAATTCTTTTTTCGTGAGGAGCAGCGGATCTTAATGGATGGCCGCAGGTGG\n+>read989_contig0_position785_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+TTAGCTTCCATACCACCTGCGGCCATCCATTAAGATCCGCTGCTCCTCACGAAAAAAGAATTAATAAGAAGTCCCGTAACATGCGGATTTGGTAGTCGTT\n+>read990_contig0_position494_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n+CACCTCGAGCTGTTGCGTTGTTGCGCTGCCTAGATGCAGTGTCGCACATATCACTTTTGCTTCAACGACTGCCGCTTTCGCTGTATCCCTAGACAGTCAA\n+>read991_contig0_position711_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+CGTAACATGCGGATTTGGTAGTCGTTATAGACAACTTTACTGGGGCGAACTAAAACGCTTGTGGACAGAATTTTGGCAGTGGCAATTAATCTCTAATGAT\n+>read992_contig0_position870_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+TAAGTAGACGCAATGCGGAATCTTATAGAATCGCCCGATAGCGTTGTGTTGGTGGACACGGCTGATTACCCTCTCACCCGCGCTATTAGCTTCCATACCA\n+>read993_contig0_position217_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+ACTCGAGAAGGCATACGACTGGTCGTAAGACCGCTCTGATCCGACACCACCATAACGCGGCACTCATGATTATCATCACTTTTTTAGTCCCTATTACAGA\n+>read994_contig0_position442_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+TGTGCGACACTGCATCTAGGCAGCGCAACAACGCAACAGCTCGAGGTGTTCTTCGCAGAGAAACCGCACGTCCAGTTCTAACACTCTCATATGTGCTCGT\n+>read995_contig0_position627_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n+TGTGACTAACTGCGCCAAAACATCTTCGGATCCCCTTGTCCAATCTAACTCACCGAATTCTTACATTTTAGACCCTAATATCACATCATTAGAGATTAAT\n+>read996_contig0_position270_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+ACAGCCATCACGGTTTGTGGGTTCACTGGGACTGTCACGCTTAACCGGACGGAACTCGAGAAGGCATACGACTGGTCGTAAGACCGCTCTGATCCGACAC\n+>read997_contig0_position766_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n+CCCCAGTAAAGTTGTCTATAACGACTACCAAATCCGCATGTTACGGGACTTCTTATTAATTCTTTTTTCGTGAGGAGCAGCGGATCTTAATGGATGGCCG\n+>read998_contig0_position14_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+ACTAATAGGGCCGGGCTACATGTTAACTACAAGGCTATAACCTATTGATGACCCGGTCCATACATAACTTGGTATCGTGCATGTAGCGTTCAAGGGCTAT\n+>read999_contig0_position609_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n+GTAGGCAGGGGCTCCCCCTGTGACTAACTGCGCCAAAACATCTTCGGATCCCCTTGTCCAATCTAACTCACCGAATTCTTACATTTTAGACCCTAATATC\n'

diff -r 000000000000 -r dc70286127fe test-data/discosnp/reads2
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/discosnp/reads2 Fri Oct 20 03:15:43 2017 -0400

b'@@ -0,0 +1,2000 @@\n+>read0_contig0_position645_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n+AACATCTTCGGATCCCCTTGTCCAATCTAACTCACCGAATTCTTACATTTTAGACCCTAATATCACATCATTAGAGATTAATTGCCACTGCCAAAATTCT\n+>read1_contig0_position200_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+ACTGGTCGTAAGACCGCTCTGATCCGACACCACCATAACGCGGCACTCATGATTATCATCACTTTTTTAGTCCCTATTACAGAGCTGCCGGGTGGATGAC\n+>read2_contig0_position362_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n+ATGGCTGTCCTTGGAGTCATACGCAAGAAGGATGGTCTCCAGACACCGGCGCACCAGTTTTCACGCCGAAAGCATAAACGACGAGCACATATGAGAGTGT\n+>read3_contig0_position190_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+AGACCGCTCTGATCCGACACCACCATAACGCGGCACTCATGATTATCATCACTTTTTTAGTCCCTATTACAGAGCTGCCGGGTGGATGACTCTCTACCGC\n+>read4_contig0_position440_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n+CGACGAGCACATATGAGAGTGTTAGAACTGGACGTGCGGTTTCTCTGCGAAGTACACCTCGAGCTGTTGCGTTGTTGCGCTGCCTAGATGCAGTGTCGCA\n+>read5_contig0_position505_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n+GTTGCGTTGTTGCGCTGCCTAGATGCAGTGTCGCACATATCACTTTTGCTTCAACGACTGCCGCTTTCGCTGTATCCCTAGACAGTCAACAGTAAGCGCT\n+>read6_contig0_position161_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+GCGGCACTCATGATTATCATCACTTTTTTAGTCCCTATTACAGAGCTGCCGGGTGGATGACTCTCTACCGCGCTCTGTGGAAGTGCACTTGATCGTTTTG\n+>read7_contig0_position741_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+CCTCACGAAAAAAGAATTAATAAGAAGTCCCGTAACATGCGGATTTGGTAGTCGTTATAGACAACTTTACTGGGGCGAACTAAAACGCTTGTGGACAGAA\n+>read8_contig0_position160_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+CGGCACTCATGATTATCATCACTTTTTTAGTCCCTATTACAGAGCTGCCGGGTGGATGACTCTCTACCGCGCTCTGTGGAAGTGCACTTGATCGTTTTGC\n+>read9_contig0_position559_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n+CGACTGCCGCTTTCGCTGTATCCCTAGACAGTCAACAGTAAGCGCTTTTTGTAGGCAGGGGCTCCCCCTGTGACTAACTGCGCCAAAACATCTTCGGATC\n+>read10_contig0_position250_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+GTTCACTGGGACTGTCACGCTTAACCGGACGGAACTCGAGAAGGCATACGACTGGTCGTAAGACCGCTCTGATCCGACACCACCATAACGCGGCACTCAT\n+>read11_contig0_position71_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+GATCGTTTTGCTGTAGAAAAAACTTAATAAACAGAATGCCGATGAAGGCACTACTGTACTAATAGGGCCGGGCTACATGTTAACTACTAGGCTATAACCT\n+>read12_contig0_position471_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+AAGCGGCAGTCGTTGAAGCAAAAGTGATATGTGCGACACTGCATCTAGGCAGCGCAACAACGCAACAGCTCGAGGTGTACTTCGCAGAGAAACCGCACGT\n+>read13_contig0_position94_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+CCGCGCTCTGTGGAAGTGCACTTGATCGTTTTGCTGTAGAAAAAACTTAATAAACAGAATGCCGATGAAGGCACTACTGTACTAATAGGGCCGGGCTACA\n+>read14_contig0_position758_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+CATTAAGATCCGCTGCTCCTCACGAAAAAAGAATTAATAAGAAGTCCCGTAACATGCGGATTTGGTAGTCGTTATAGACAACTTTACTGGGGCGAACTAA\n+>read15_contig0_position242_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+GGACTGTCACGCTTAACCGGACGGAACTCGAGAAGGCATACGACTGGTCGTAAGACCGCTCTGATCCGACACCACCATAACGCGGCACTCATGATTATCA\n+>read16_contig0_position821_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n+TTAATTCTTTTTTCGTGAGGAGCAGCGGATCTTAATGGATGGCCGCAGGTGGTATGGAAGCTAATAGCGCGGGTGAGAGGGTAATCAGCCGTGTCCACCA\n+>read17_contig0_position284_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+GTATGACTCCAAGGACAGCCATCACGGTTTGTGGGTTCACTGGGACTGTCACGCTTAACCGGACGGAACTCGAGAAGGCATACGACTGGTCGTAAGACCG\n+>read18_contig0_position283_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n+GCGGTCTTACGACCAGTCGTATGCCTTCTCGAGTTCCGTCCGGTTAAGCGTGACAGTCCCAGTGAACCCACAAACCGTGATGGCTGTCCTTGGAGTCATA\n+>read19_contig0_position320_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+ACTGGTGCGCCGGTGTCTGGAGACCATCCTTCTTGCGTATGACTCCAAGGACAGCCATCACGGTTTGTGGGTTCACTGGGACTGTCACGCTTAACCGGAC\n+>read20_contig0_position232_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n+AAAAAAGTGATGATAATCATGAGTGCCGCGTTATGGTGGTGTCGGATCAGAGCGGTCTTACGACCAGTCGTATGCCTTCTCGAGTTCCGTCCGGTTAAGC\n+>read21_contig0_position118_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+AGCTGCCGGGTGGATGACTCTCTACCGCGCTCTGTGGAAGTGCACTTGATCGTTTTGCTGTAGAAAAAACTTAATAAACAGAATGCCGATGAAGGCACTA\n+>read22_contig0_position840_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+TCGCCCGATAGCGTTGTGTTGGTGGACACGGCTGATTACCCTCTCACCCGCGCTATTAGCTTCCATACCACCTGCGGCCATCCATTAAGAT'..b'on648_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+GACAGAATTTTGGCAGTGGCAATTAATCTCTAATGATGTGATATTAGGGTCTAAAATGTAAGAATTCGGTGAGTTAGATTGGACAAGGGGATCCGAAGAT\n+>read978_contig0_position284_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n+CGGTCTTACGACCAGTCGTATGCCTTCTCGAGTTCCGTCCGGTTAAGCGTGACAGTCCCAGTGAACCCACAAACCGTGATGGCTGTCCTTGGAGTCATAC\n+>read979_contig0_position23_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+CACTACTGTACTAATAGGGCCGGGCTACATGTTAACTACTAGGCTATAACCTATTGATGACCCGGTCCATACATAACTTGGTATCGTGCATGTAGCGTTC\n+>read980_contig0_position795_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n+AAATCCGCATGTTACGGGACTTCTTATTAATTCTTTTTTCGTGAGGAGCAGCGGATCTTAATGGATGGCCGCAGGTGGTATGGAAGCTAATAGCGCGGGT\n+>read981_contig0_position852_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n+TTAATGGATGGCCGCAGGTGGTATGGAAGCTAATAGCGCGGGTGAGAGGGTAATCAGCCGTGTCCACCAACACAACGCTATCGGGCGATTCTATAAGATT\n+>read982_contig0_position852_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+AATCTTATAGAATCGCCCGATAGCGTTGTGTTGGTGGACACGGCTGATTACCCTCTCACCCGCGCTATTAGCTTCCATACCACCTGCGGCCATCCATTAA\n+>read983_contig0_position700_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+GATTTGGTAGTCGTTATAGACAACTTTACTGGGGCGAACTAAAACGCTTGTGGACAGAATTTTGGCAGTGGCAATTAATCTCTAATGATGTGATATTAGG\n+>read984_contig0_position445_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n+AGCACATATGAGAGTGTTAGAACTGGACGTGCGGTTTCTCTGCGAAGTACACCTCGAGCTGTTGCGTTGTTGCGCTGCCTAGATGCAGTGTCGCACATAT\n+>read985_contig0_position631_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+GGCAATTAATCTCTAATGATGTGATATTAGGGTCTAAAATGTAAGAATTCGGTGAGTTAGATTGGACAAGGGGATCCGAAGATGTTTTGGCGCAGTTAGT\n+>read986_contig0_position655_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+GCTTGTGGACAGAATTTTGGCAGTGGCAATTAATCTCTAATGATGTGATATTAGGGTCTAAAATGTAAGAATTCGGTGAGTTAGATTGGACAAGGGGATC\n+>read987_contig0_position599_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n+AGCGCTTTTTGTAGGCAGGGGCTCCCCCTGTGACTAACTGCGCCAAAACATCTTCGGATCCCCTTGTCCAATCTAACTCACCGAATTCTTACATTTTAGA\n+>read988_contig0_position455_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+AGCAAAAGTGATATGTGCGACACTGCATCTAGGCAGCGCAACAACGCAACAGCTCGAGGTGTACTTCGCAGAGAAACCGCACGTCCAGTTCTAACACTCT\n+>read989_contig0_position371_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+CCAGTTCTAACACTCTCATATGTGCTCGTCGTTTATGCTTTCGGCGTGAAAACTGGTGCGCCGGTGTCTGGAGACCATCCTTCTTGCGTATGACTCCAAG\n+>read990_contig0_position489_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n+AAGTACACCTCGAGCTGTTGCGTTGTTGCGCTGCCTAGATGCAGTGTCGCACATATCACTTTTGCTTCAACGACTGCCGCTTTCGCTGTATCCCTAGACA\n+>read991_contig0_position353_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n+TATGTGCTCGTCGTTTATGCTTTCGGCGTGAAAACTGGTGCGCCGGTGTCTGGAGACCATCCTTCTTGCGTATGACTCCAAGGACAGCCATCACGGTTTG\n+>read992_contig0_position321_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n+TCCGGTTAAGCGTGACAGTCCCAGTGAACCCACAAACCGTGATGGCTGTCCTTGGAGTCATACGCAAGAAGGATGGTCTCCAGACACCGGCGCACCAGTT\n+>read993_contig0_position665_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n+TCCAATCTAACTCACCGAATTCTTACATTTTAGACCCTAATATCACATCATTAGAGATTAATTGCCACTGCCAAAATTCTGTCCACAAGCGTTTTAGTTC\n+>read994_contig0_position792_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n+ACCAAATCCGCATGTTACGGGACTTCTTATTAATTCTTTTTTCGTGAGGAGCAGCGGATCTTAATGGATGGCCGCAGGTGGTATGGAAGCTAATAGCGCG\n+>read995_contig0_position459_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n+TGTTAGAACTGGACGTGCGGTTTCTCTGCGAAGTACACCTCGAGCTGTTGCGTTGTTGCGCTGCCTAGATGCAGTGTCGCACATATCACTTTTGCTTCAA\n+>read996_contig0_position726_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n+TTGCCACTGCCAAAATTCTGTCCACAAGCGTTTTAGTTCGCCCCAGTAAAGTTGTCTATAACGACTACCAAATCCGCATGTTACGGGACTTCTTATTAAT\n+>read997_contig0_position81_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n+CTAGTAGTTAACATGTAGCCCGGCCCTATTAGTACAGTAGTGCCTTCATCGGCATTCTGTTTATTAAGTTTTTTCTACAGCAAAACGATCAAGTGCACTT\n+>read998_contig0_position143_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n+ATTAAGTTTTTTCTACAGCAAAACGATCAAGTGCACTTCCACAGAGCGCGGTAGAGAGTCATCCACCCGGCAGCTCTGTAATAGGGACTAAAAAAGTGAT\n+>read999_contig0_position438_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n+AACGACGAGCACATATGAGAGTGTTAGAACTGGACGTGCGGTTTCTCTGCGAAGTACACCTCGAGCTGTTGCGTTGTTGCGCTGCCTAGATGCAGTGTCG\n'

diff -r 000000000000 -r dc70286127fe test-data/discosnp/vcf_file.vcf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/discosnp/vcf_file.vcf Fri Oct 20 03:15:43 2017 -0400

@@ -0,0 +1,23 @@
+##fileformat=VCFv4.1
+##filedate=2017102
+##source=VCF_creator
+##SAMPLE=file://discoRes_k_25_c_auto_D_0_P_1_b_0_coherent.fa
+##REF=<ID=REF,Number=1,Type=String,Description="Allele of the path Disco aligned with the least mismatches">
+##FILTER=<ID=MULTIPLE,Description="Mapping type : PASS or MULTIPLE or .">
+##INFO=<ID=Ty,Number=1,Type=String,Description="SNP, INS, DEL or .">
+##INFO=<ID=Rk,Number=1,Type=Float,Description="SNP rank">
+##INFO=<ID=UL,Number=1,Type=Integer,Description="length of the unitig left">
+##INFO=<ID=UR,Number=1,Type=Integer,Description="length of the unitig right">
+##INFO=<ID=CL,Number=1,Type=Integer,Description="length of the contig left">
+##INFO=<ID=CR,Number=1,Type=Integer,Description="length of the contig right">
+##INFO=<ID=Genome,Number=1,Type=String,Description="Allele of the reference;for indel reference is . ">
+##INFO=<ID=Sd,Number=1,Type=Integer,Description="Reverse (-1) or Forward (1) Alignement">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Cumulated depth accross samples (sum)">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Phred-scaled Genotype Likelihoods">
+##FORMAT=<ID=AD,Number=2,Type=Integer,Description="Depth of each allele by sample">
+##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
+#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT G1 G2
+SNP_higher_path_3 24 3 A T . . Ty=SNP;Rk=1;UL=.;UR=.;CL=.;CR=.;Genome=.;Sd=. GT:DP:PL:AD:HQ 0/0:74:8,227,1484:74,0:0,0 1/1:86:1724,263,8:0,86:0,0
+SNP_higher_path_2 24 2 C G . . Ty=SNP;Rk=1;UL=.;UR=.;CL=.;CR=.;Genome=.;Sd=. GT:DP:PL:AD:HQ 1/1:124:2484,378,10:0,124:0,0 0/0:134:10,408,2684:134,0:0,0
+SNP_higher_path_1 24 1 A T . . Ty=SNP;Rk=1;UL=.;UR=.;CL=.;CR=.;Genome=.;Sd=. GT:DP:PL:AD:HQ 1/1:110:2204,335,9:0,110:0,0 0/0:114:9,347,2284:114,0:0,0

diff -r 000000000000 -r dc70286127fe test-data/discosnp/vcf_file_paired.vcf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/discosnp/vcf_file_paired.vcf Fri Oct 20 03:15:43 2017 -0400

@@ -0,0 +1,23 @@
+##fileformat=VCFv4.1
+##filedate=2017102
+##source=VCF_creator
+##SAMPLE=file://discoRes_k_31_c_auto_D_0_P_1_b_0_coherentBWA_MEM.sam
+##REF=<ID=REF,Number=1,Type=String,Description="Allele of the path Disco aligned with the least mismatches">
+##FILTER=<ID=MULTIPLE,Description="Mapping type : PASS or MULTIPLE or .">
+##INFO=<ID=Ty,Number=1,Type=String,Description="SNP, INS, DEL or .">
+##INFO=<ID=Rk,Number=1,Type=Float,Description="SNP rank">
+##INFO=<ID=UL,Number=1,Type=Integer,Description="length of the unitig left">
+##INFO=<ID=UR,Number=1,Type=Integer,Description="length of the unitig right">
+##INFO=<ID=CL,Number=1,Type=Integer,Description="length of the contig left">
+##INFO=<ID=CR,Number=1,Type=Integer,Description="length of the contig right">
+##INFO=<ID=Genome,Number=1,Type=String,Description="Allele of the reference;for indel reference is . ">
+##INFO=<ID=Sd,Number=1,Type=Integer,Description="Reverse (-1) or Forward (1) Alignement">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Cumulated depth accross samples (sum)">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Phred-scaled Genotype Likelihoods">
+##FORMAT=<ID=AD,Number=2,Type=Integer,Description="Depth of each allele by sample">
+##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
+#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT G1
+read661_contig0_position139_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0 62 3 C G . MULTIPLE Ty=SNP;Rk=0;UL=.;UR=.;CL=.;CR=.;Genome=C;Sd=1 GT:DP:PL:AD:HQ 0/1:258:1927,18,1727:124,134:0,0
+read780_contig0_position26_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1 43 2 A T . MULTIPLE Ty=SNP;Rk=0;UL=.;UR=.;CL=.;CR=.;Genome=A;Sd=1 GT:DP:PL:AD:HQ 0/1:160:1260,18,1020:74,86:0,0
+read656_contig0_position454_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1 62 1 T A . MULTIPLE Ty=SNP;Rk=0;UL=.;UR=.;CL=.;CR=.;Genome=T;Sd=1 GT:DP:PL:AD:HQ 0/1:224:1628,17,1548:110,114:0,0

diff -r 000000000000 -r dc70286127fe test-data/kissplice/alternative_splicing.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/kissplice/alternative_splicing.fa Fri Oct 20 03:15:43 2017 -0400

diff -r 000000000000 -r dc70286127fe test-data/kissplice/reads1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/kissplice/reads1 Fri Oct 20 03:15:43 2017 -0400

b"@@ -0,0 +1,672 @@\n+>dm3_ct_UserTrack_3545_read range=chrX:3599037-3599111 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+ACTTTTGTATAACTGCATTCTGTATTGTAATATTTAAGCTATTATTATTATGATAATTATTATTATTATTAAATA\n+>dm3_ct_UserTrack_3545_read range=chrX:3599042-3599116 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+TGTTTACTTTTGTATAACTGCATTCTGTATTGTAATATTTAAGCTATTATTATTATGATAATTATTATTATTATT\n+>dm3_ct_UserTrack_3545_read range=chrX:3599051-3599125 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+TTGCTTCTTTGTTTACTTTTGTATAACTGCATTCTGTATTGTAATATTTAAGCTATTATTATTATGATAATTATT\n+>dm3_ct_UserTrack_3545_read range=chrX:3599066-3599140 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+TTACTCCCGATTGATTTGCTTCTTTGTTTACTTTTGTATAACTGCATTCTGTATTGTAATATTTAAGCTATTATT\n+>dm3_ct_UserTrack_3545_read range=chrX:3599081-3599155 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+ATGTATGTTTAGCAATTACTCCCGATTGATTTGCTTCTTTGTTTACTTTTGTATAACTGCATTCTGTATTGTAAT\n+>dm3_ct_UserTrack_3545_read range=chrX:3599087-3599161 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+GTATGTATGTATGTTTAGCAATTACTCCCGATTGATTTGCTTCTTTGTTTACTTTTGTATAACTGCATTCTGTAT\n+>dm3_ct_UserTrack_3545_read range=chrX:3599091-3599165 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+GTATGTATGTATGTATGTTTAGCAATTACTCCCGATTGATTTGCTTCTTTGTTTACTTTTGTATAACTGCATTCT\n+>dm3_ct_UserTrack_3545_read range=chrX:3599097-3599171 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+GTATATGTATGTATGTATGTATGTTTAGCAATTACTCCCGATTGATTTGCTTCTTTGTTTACTTTTGTATAACTG\n+>dm3_ct_UserTrack_3545_read range=chrX:3599102-3599176 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+TATATGTATATGTATGTATGTATGTATGTTTAGCAATTACTCCCGATTGATTTGCTTCTTTGTTTACTTTTGTAT\n+>dm3_ct_UserTrack_3545_read range=chrX:3599105-3599179 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+CAATATATGTATATGTATGTATGTATGTATGTTTAGCAATTACTCCCGATTGATTTGCTTCTTTGTTTACTTTTG\n+>dm3_ct_UserTrack_3545_read range=chrX:3599114-3599188 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+GAACACATCCAATATATGTATATGTATGTATGTATGTATGTTTAGCAATTACTCCCGATTGATTTGCTTCTTTGT\n+>dm3_ct_UserTrack_3545_read range=chrX:3599117-3599191 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+CTGGAACACATCCAATATATGTATATGTATGTATGTATGTATGTTTAGCAATTACTCCCGATTGATTTGCTTCTT\n+>dm3_ct_UserTrack_3545_read range=chrX:3599119-3599193 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+CCCTGGAACACATCCAATATATGTATATGTATGTATGTATGTATGTTTAGCAATTACTCCCGATTGATTTGCTTC\n+>dm3_ct_UserTrack_3545_read range=chrX:3599119-3599193 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+CCCTGGAACACATCCAATATATGTATATGTATGTATGTATGTATGTTTAGCAATTACTCCCGATTGATTTGCTTC\n+>dm3_ct_UserTrack_3545_read range=chrX:3599128-3599202 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+TTTTCTTTGCCCTGGAACACATCCAATATATGTATATGTATGTATGTATGTATGTTTAGCAATTACTCCCGATTG\n+>dm3_ct_UserTrack_3545_read range=chrX:3599130-3599204 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+TATTTTCTTTGCCCTGGAACACATCCAATATATGTATATGTATGTATGTATGTATGTTTAGCAATTACTCCCGAT\n+>dm3_ct_UserTrack_3545_read range=chrX:3599134-3599208 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+TAGTTATTTTCTTTGCCCTGGAACACATCCAATATATGTATATGTATGTATGTATGTATGTTTAGCAATTACTCC\n+>dm3_ct_UserTrack_3545_read range=chrX:3599137-3599211 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+AAATAGTTATTTTCTTTGCCCTGGAACACATCCAATATATGTATATGTATGTATGTATGTATGTTTAGCAATTAC\n+>dm3_ct_UserTrack_3545_read range=chrX:3599138-3599212 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+CAAATAGTTATTTTCTTTGCCCTGGAACACATCCAATATATGTATATGTATGTATGTATGTATGTTTAGCAATTA\n+>dm3_ct_UserTrack_3545_read range=chrX:3599142-3599216 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+GTTACAAATAGTTATTTTCTTTGCCCTGGAACACATCCAATATATGTATATGTATGTATGTATGTATGTTTAGCA\n+>dm3_ct_UserTrack_3545_read range=chrX:3599154-3599228 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+TGGAGACTTTCCGTTACAAATAGTTATTTTCTTTGCCCTGGAACACATCCAATATATGTATATGTATGTATGTAT\n+>dm3_ct_UserTrack_3545_read range=chrX:3599177-3599251 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+ACACTAATGTTTCTGACAAGCTTTGGAGACTTTCCGTTACAAATAGTTATTTTCTTTGCCCTGGAACACATCCAA\n+>dm3_ct_UserTrack_3545_read range=chrX:3599178-3599252 5'pad=0 3'pad=0 strand=- repeat"..b"strand=- repeatMasking=none\n+CGATCCTGTTAATTCATCAGTTGCCGATTCTCCGATCGCGCCTGTAACTTTTTTGTTTAGTTTAGTGCATCAAGT\n+>dm3_ct_UserTrack_3545_read range=chrX:3613489-3613563 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+CGTTCCGATCCTGTTAATTCATCAGTTGCCGATTCTCCGATCGCGCCTGTAACTTTTTTGTTTAGTTTAGTGCAT\n+>dm3_ct_UserTrack_3545_read range=chrX:3613494-3613568 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+TGTTGCGTTCCGATCCTGTTAATTCATCAGTTGCCGATTCTCCGATCGCGCCTGTAACTTTTTTGTTTAGTTTAG\n+>dm3_ct_UserTrack_3545_read range=chrX:3613499-3613573 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+TTTACTGTTGCGTTCCGATCCTGTTAATTCATCAGTTGCCGATTCTCCGATCGCGCCTGTAACTTTTTTGTTTAG\n+>dm3_ct_UserTrack_3545_read range=chrX:3613504-3613578 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+GCCAATTTACTGTTGCGTTCCGATCCTGTTAATTCATCAGTTGCCGATTCTCCGATCGCGCCTGTAACTTTTTTG\n+>dm3_ct_UserTrack_3545_read range=chrX:3613508-3613582 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+AGCAGCCAATTTACTGTTGCGTTCCGATCCTGTTAATTCATCAGTTGCCGATTCTCCGATCGCGCCTGTAACTTT\n+>dm3_ct_UserTrack_3545_read range=chrX:3613511-3613585 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+AAAAGCAGCCAATTTACTGTTGCGTTCCGATCCTGTTAATTCATCAGTTGCCGATTCTCCGATCGCGCCTGTAAC\n+>dm3_ct_UserTrack_3545_read range=chrX:3613516-3613590 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+AACCGAAAAGCAGCCAATTTACTGTTGCGTTCCGATCCTGTTAATTCATCAGTTGCCGATTCTCCGATCGCGCCT\n+>dm3_ct_UserTrack_3545_read range=chrX:3613517-3613591 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+AAACCGAAAAGCAGCCAATTTACTGTTGCGTTCCGATCCTGTTAATTCATCAGTTGCCGATTCTCCGATCGCGCC\n+>dm3_ct_UserTrack_3545_read range=chrX:3613517-3613591 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+AAACCGAAAAGCAGCCAATTTACTGTTGCGTTCCGATCCTGTTAATTCATCAGTTGCCGATTCTCCGATCGCGCC\n+>dm3_ct_UserTrack_3545_read range=chrX:3613519-3613593 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+AGAAACCGAAAAGCAGCCAATTTACTGTTGCGTTCCGATCCTGTTAATTCATCAGTTGCCGATTCTCCGATCGCG\n+>dm3_ct_UserTrack_3545_read range=chrX:3613524-3613598 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+AGAAGAGAAACCGAAAAGCAGCCAATTTACTGTTGCGTTCCGATCCTGTTAATTCATCAGTTGCCGATTCTCCGA\n+>dm3_ct_UserTrack_3545_read range=chrX:3613529-3613603 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+GAACGAGAAGAGAAACCGAAAAGCAGCCAATTTACTGTTGCGTTCCGATCCTGTTAATTCATCAGTTGCCGATTC\n+>dm3_ct_UserTrack_3545_read range=chrX:3613533-3613607 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+CGGCGAACGAGAAGAGAAACCGAAAAGCAGCCAATTTACTGTTGCGTTCCGATCCTGTTAATTCATCAGTTGCCG\n+>dm3_ct_UserTrack_3545_read range=chrX:3613536-3613610 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+GTGCGGCGAACGAGAAGAGAAACCGAAAAGCAGCCAATTTACTGTTGCGTTCCGATCCTGTTAATTCATCAGTTG\n+>dm3_ct_UserTrack_3545_read range=chrX:3613551-3613625 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+AACTTTAATTGCGGTGTGCGGCGAACGAGAAGAGAAACCGAAAAGCAGCCAATTTACTGTTGCGTTCCGATCCTG\n+>dm3_ct_UserTrack_3545_read range=chrX:3613552-3613626 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+GAACTTTAATTGCGGTGTGCGGCGAACGAGAAGAGAAACCGAAAAGCAGCCAATTTACTGTTGCGTTCCGATCCT\n+>dm3_ct_UserTrack_3545_read range=chrX:3613559-3613633 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+ACCAACGGAACTTTAATTGCGGTGTGCGGCGAACGAGAAGAGAAACCGAAAAGCAGCCAATTTACTGTTGCGTTC\n+>dm3_ct_UserTrack_3545_read range=chrX:3613570-3613644 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+AAGCAAGCAAAACCAACGGAACTTTAATTGCGGTGTGCGGCGAACGAGAAGAGAAACCGAAAAGCAGCCAATTTA\n+>dm3_ct_UserTrack_3545_read range=chrX:3613572-3613646 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+TCAAGCAAGCAAAACCAACGGAACTTTAATTGCGGTGTGCGGCGAACGAGAAGAGAAACCGAAAAGCAGCCAATT\n+>dm3_ct_UserTrack_3545_read range=chrX:3613576-3613650 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+TCTTTCAAGCAAGCAAAACCAACGGAACTTTAATTGCGGTGTGCGGCGAACGAGAAGAGAAACCGAAAAGCAGCC\n+>dm3_ct_UserTrack_3545_read range=chrX:3613590-3613664 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+CTTTCACACTAGTTTCTTTCAAGCAAGCAAAACCAACGGAACTTTAATTGCGGTGTGCGGCGAACGAGAAGAGAA\n+>dm3_ct_UserTrack_3545_read range=chrX:3613591-3613665 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+ACTTTCACACTAGTTTCTTTCAAGCAAGCAAAACCAACGGAACTTTAATTGCGGTGTGCGGCGAACGAGAAGAGA\n"

diff -r 000000000000 -r dc70286127fe test-data/kissplice/reads2
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/kissplice/reads2 Fri Oct 20 03:15:43 2017 -0400

b"@@ -0,0 +1,782 @@\n+>dm3_ct_UserTrack_3545_read range=chrX:3599019-3599093 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+TCTGTATTGTAATATTTAAGCTATTATTATTATGATAATTATTATTATTATTAAATATATAAGTTATATATGCAA\n+>dm3_ct_UserTrack_3545_read range=chrX:3599020-3599094 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+TTCTGTATTGTAATATTTAAGCTATTATTATTATGATAATTATTATTATTATTAAATATATAAGTTATATATGCA\n+>dm3_ct_UserTrack_3545_read range=chrX:3599028-3599102 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+TAACTGCATTCTGTATTGTAATATTTAAGCTATTATTATTATGATAATTATTATTATTATTAAATATATAAGTTA\n+>dm3_ct_UserTrack_3545_read range=chrX:3599029-3599103 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+ATAACTGCATTCTGTATTGTAATATTTAAGCTATTATTATTATGATAATTATTATTATTATTAAATATATAAGTT\n+>dm3_ct_UserTrack_3545_read range=chrX:3599042-3599116 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+TGTTTACTTTTGTATAACTGCATTCTGTATTGTAATATTTAAGCTATTATTATTATGATAATTATTATTATTATT\n+>dm3_ct_UserTrack_3545_read range=chrX:3599043-3599117 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+TTGTTTACTTTTGTATAACTGCATTCTGTATTGTAATATTTAAGCTATTATTATTATGATAATTATTATTATTAT\n+>dm3_ct_UserTrack_3545_read range=chrX:3599043-3599117 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+TTGTTTACTTTTGTATAACTGCATTCTGTATTGTAATATTTAAGCTATTATTATTATGATAATTATTATTATTAT\n+>dm3_ct_UserTrack_3545_read range=chrX:3599046-3599120 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+TCTTTGTTTACTTTTGTATAACTGCATTCTGTATTGTAATATTTAAGCTATTATTATTATGATAATTATTATTAT\n+>dm3_ct_UserTrack_3545_read range=chrX:3599046-3599120 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+TCTTTGTTTACTTTTGTATAACTGCATTCTGTATTGTAATATTTAAGCTATTATTATTATGATAATTATTATTAT\n+>dm3_ct_UserTrack_3545_read range=chrX:3599052-3599126 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+TTTGCTTCTTTGTTTACTTTTGTATAACTGCATTCTGTATTGTAATATTTAAGCTATTATTATTATGATAATTAT\n+>dm3_ct_UserTrack_3545_read range=chrX:3599052-3599126 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+TTTGCTTCTTTGTTTACTTTTGTATAACTGCATTCTGTATTGTAATATTTAAGCTATTATTATTATGATAATTAT\n+>dm3_ct_UserTrack_3545_read range=chrX:3599056-3599130 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+TTGATTTGCTTCTTTGTTTACTTTTGTATAACTGCATTCTGTATTGTAATATTTAAGCTATTATTATTATGATAA\n+>dm3_ct_UserTrack_3545_read range=chrX:3599060-3599134 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+CCGATTGATTTGCTTCTTTGTTTACTTTTGTATAACTGCATTCTGTATTGTAATATTTAAGCTATTATTATTATG\n+>dm3_ct_UserTrack_3545_read range=chrX:3599062-3599136 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+TCCCGATTGATTTGCTTCTTTGTTTACTTTTGTATAACTGCATTCTGTATTGTAATATTTAAGCTATTATTATTA\n+>dm3_ct_UserTrack_3545_read range=chrX:3599066-3599140 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+TTACTCCCGATTGATTTGCTTCTTTGTTTACTTTTGTATAACTGCATTCTGTATTGTAATATTTAAGCTATTATT\n+>dm3_ct_UserTrack_3545_read range=chrX:3599070-3599144 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+GCAATTACTCCCGATTGATTTGCTTCTTTGTTTACTTTTGTATAACTGCATTCTGTATTGTAATATTTAAGCTAT\n+>dm3_ct_UserTrack_3545_read range=chrX:3599074-3599148 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+TTTAGCAATTACTCCCGATTGATTTGCTTCTTTGTTTACTTTTGTATAACTGCATTCTGTATTGTAATATTTAAG\n+>dm3_ct_UserTrack_3545_read range=chrX:3599077-3599151 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+ATGTTTAGCAATTACTCCCGATTGATTTGCTTCTTTGTTTACTTTTGTATAACTGCATTCTGTATTGTAATATTT\n+>dm3_ct_UserTrack_3545_read range=chrX:3599081-3599155 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+ATGTATGTTTAGCAATTACTCCCGATTGATTTGCTTCTTTGTTTACTTTTGTATAACTGCATTCTGTATTGTAAT\n+>dm3_ct_UserTrack_3545_read range=chrX:3599091-3599165 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+GTATGTATGTATGTATGTTTAGCAATTACTCCCGATTGATTTGCTTCTTTGTTTACTTTTGTATAACTGCATTCT\n+>dm3_ct_UserTrack_3545_read range=chrX:3599102-3599176 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+TATATGTATATGTATGTATGTATGTATGTTTAGCAATTACTCCCGATTGATTTGCTTCTTTGTTTACTTTTGTAT\n+>dm3_ct_UserTrack_3545_read range=chrX:3599104-3599178 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+AATATATGTATATGTATGTATGTATGTATGTTTAGCAATTACTCCCGATTGATTTGCTTCTTTGTTTACTTTTGT\n+>dm3_ct_UserTrack_3545_read range=chrX:3599105-3599179 5'pad=0 3'pad=0 strand=- repeat"..b"strand=- repeatMasking=none\n+CGCCTGTAACTTTTTTGTTTAGTTTAGTGCATCAAGTGCGAGATAACACAGCAAAGCAACAACAAACGAAGCGAC\n+>dm3_ct_UserTrack_3545_read range=chrX:3613449-3613523 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+TCGCGCCTGTAACTTTTTTGTTTAGTTTAGTGCATCAAGTGCGAGATAACACAGCAAAGCAACAACAAACGAAGC\n+>dm3_ct_UserTrack_3545_read range=chrX:3613462-3613536 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+GCCGATTCTCCGATCGCGCCTGTAACTTTTTTGTTTAGTTTAGTGCATCAAGTGCGAGATAACACAGCAAAGCAA\n+>dm3_ct_UserTrack_3545_read range=chrX:3613475-3613549 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+TAATTCATCAGTTGCCGATTCTCCGATCGCGCCTGTAACTTTTTTGTTTAGTTTAGTGCATCAAGTGCGAGATAA\n+>dm3_ct_UserTrack_3545_read range=chrX:3613478-3613552 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+TGTTAATTCATCAGTTGCCGATTCTCCGATCGCGCCTGTAACTTTTTTGTTTAGTTTAGTGCATCAAGTGCGAGA\n+>dm3_ct_UserTrack_3545_read range=chrX:3613481-3613555 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+TCCTGTTAATTCATCAGTTGCCGATTCTCCGATCGCGCCTGTAACTTTTTTGTTTAGTTTAGTGCATCAAGTGCG\n+>dm3_ct_UserTrack_3545_read range=chrX:3613484-3613558 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+CGATCCTGTTAATTCATCAGTTGCCGATTCTCCGATCGCGCCTGTAACTTTTTTGTTTAGTTTAGTGCATCAAGT\n+>dm3_ct_UserTrack_3545_read range=chrX:3613489-3613563 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+CGTTCCGATCCTGTTAATTCATCAGTTGCCGATTCTCCGATCGCGCCTGTAACTTTTTTGTTTAGTTTAGTGCAT\n+>dm3_ct_UserTrack_3545_read range=chrX:3613489-3613563 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+CGTTCCGATCCTGTTAATTCATCAGTTGCCGATTCTCCGATCGCGCCTGTAACTTTTTTGTTTAGTTTAGTGCAT\n+>dm3_ct_UserTrack_3545_read range=chrX:3613494-3613568 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+TGTTGCGTTCCGATCCTGTTAATTCATCAGTTGCCGATTCTCCGATCGCGCCTGTAACTTTTTTGTTTAGTTTAG\n+>dm3_ct_UserTrack_3545_read range=chrX:3613496-3613570 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+ACTGTTGCGTTCCGATCCTGTTAATTCATCAGTTGCCGATTCTCCGATCGCGCCTGTAACTTTTTTGTTTAGTTT\n+>dm3_ct_UserTrack_3545_read range=chrX:3613505-3613579 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+AGCCAATTTACTGTTGCGTTCCGATCCTGTTAATTCATCAGTTGCCGATTCTCCGATCGCGCCTGTAACTTTTTT\n+>dm3_ct_UserTrack_3545_read range=chrX:3613505-3613579 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+AGCCAATTTACTGTTGCGTTCCGATCCTGTTAATTCATCAGTTGCCGATTCTCCGATCGCGCCTGTAACTTTTTT\n+>dm3_ct_UserTrack_3545_read range=chrX:3613507-3613581 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+GCAGCCAATTTACTGTTGCGTTCCGATCCTGTTAATTCATCAGTTGCCGATTCTCCGATCGCGCCTGTAACTTTT\n+>dm3_ct_UserTrack_3545_read range=chrX:3613512-3613586 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+GAAAAGCAGCCAATTTACTGTTGCGTTCCGATCCTGTTAATTCATCAGTTGCCGATTCTCCGATCGCGCCTGTAA\n+>dm3_ct_UserTrack_3545_read range=chrX:3613513-3613587 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+CGAAAAGCAGCCAATTTACTGTTGCGTTCCGATCCTGTTAATTCATCAGTTGCCGATTCTCCGATCGCGCCTGTA\n+>dm3_ct_UserTrack_3545_read range=chrX:3613520-3613594 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+GAGAAACCGAAAAGCAGCCAATTTACTGTTGCGTTCCGATCCTGTTAATTCATCAGTTGCCGATTCTCCGATCGC\n+>dm3_ct_UserTrack_3545_read range=chrX:3613525-3613599 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+GAGAAGAGAAACCGAAAAGCAGCCAATTTACTGTTGCGTTCCGATCCTGTTAATTCATCAGTTGCCGATTCTCCG\n+>dm3_ct_UserTrack_3545_read range=chrX:3613545-3613619 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+AATTGCGGTGTGCGGCGAACGAGAAGAGAAACCGAAAAGCAGCCAATTTACTGTTGCGTTCCGATCCTGTTAATT\n+>dm3_ct_UserTrack_3545_read range=chrX:3613548-3613622 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+TTTAATTGCGGTGTGCGGCGAACGAGAAGAGAAACCGAAAAGCAGCCAATTTACTGTTGCGTTCCGATCCTGTTA\n+>dm3_ct_UserTrack_3545_read range=chrX:3613550-3613624 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+ACTTTAATTGCGGTGTGCGGCGAACGAGAAGAGAAACCGAAAAGCAGCCAATTTACTGTTGCGTTCCGATCCTGT\n+>dm3_ct_UserTrack_3545_read range=chrX:3613558-3613632 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+CCAACGGAACTTTAATTGCGGTGTGCGGCGAACGAGAAGAGAAACCGAAAAGCAGCCAATTTACTGTTGCGTTCC\n+>dm3_ct_UserTrack_3545_read range=chrX:3613584-3613658 5'pad=0 3'pad=0 strand=- repeatMasking=none\n+CACTAGTTTCTTTCAAGCAAGCAAAACCAACGGAACTTTAATTGCGGTGTGCGGCGAACGAGAAGAGAAACCGAA\n"

diff -r 000000000000 -r dc70286127fe test-data/lordec/coli-pacbio-test-mini.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/lordec/coli-pacbio-test-mini.fa Fri Oct 20 03:15:43 2017 -0400

b'@@ -0,0 +1,50 @@\n+>m120131_103014_sidney_c100278822550000001523007907041295_s1_p0/10002\n+GACAATCACTAACACGCCAGCAAATAACGCCGGGAAAAGCGCAATTCGTTTACTCACGCTTTACCTCCGATGGCGTTATCCAGAAATGCGCACAAAGTGCATTGCCGGAGCGTCGCACCATAAATACCAGACTGCAGGTACGCGCTGGAAAGCGTCCCGGCGCGGACAATACGGCATGGCCTGCCACAGCGGCGTTGCCATTAGCGCATCCATTGTCTTTGGCTGTTGTCGTGATCAAACAGAGCACATCCAACGGTCCTTTATATCGCCGCCAGACGAATCGATACTGACGCGGTACTGCCCAGAAGTTGGTTTCCCCTTGCCCAGCATTTGGGATGCCGTACCATCAAGAATTTCTGGAACAAGCTGTTTGGACGAAGACCAGCATATGCGCGGATCGATAAGTCGGTCGTCAGCAAATTAACGGACGCGCACCACGCCTTCCAAGCGGGGTTTCAATGCTGCGGATAAAGTCTTCATATTTGCGCTAAATGCGTTTCCGCTGCGCTTTGCAGGTTTAAGTAAATCCTGCCAGTTTCCGTCAGCGAATTTACGCGCCATCGCCAACGGCTGTTTGTACGTCACTGAAGTTAAATCCGCGACCCGGCGCAATACGAGCCAGCATTTCTGGTTGAAGGCCATATCCTGCGACCAGACCATAAACGATGTTTCAGATTCGGTCAGCAGTTTCAAGGTTAGGTCTGTGCGCAAACCGACGTCGATCACTGAGGTCCCGGCCAATGGGGTTCGCTGACCCACAGCGATATTGTTGTGTATCCGCCACGCCGTAAGGCCACGATGCCGAGCGCCAGCAGTAATTTCCACCGGCAACCATCTCCAGCGCCACAATACATAATTGGGATTCAATAGCCGCCGCGTGGGCGGTAATTCATCTGCCATAACAATCGAGAAAGGCCATCGCCCGTTAACAGGTCGGACGGCGCGAATAAGAAGGATAAGCCGTCATCAATAAACAAAACTCACAGGTGCAGCACCACGCCCGGATGCGGTCAAAATACCCATGCGGGATGCATAAATCATTTCCGAGGGTTTTCGTGTCGCCGCGCATAATTTTCCGCAGGCCGGTTCCTGAGCATCATTTCAGCCGCGCAGGGCGACAGATAATCACAGTAGCGTGCCGCCATATTGATATCGTGCAACAGGCAATGACCGTCAGGCCACGCTCCTGACTTAAACGGTGCACCAGCGACAGCAACATCAACCTGTGGGCGATATCCAGCGCCGAGGTCGGTTCGTCGAGCAATCAGATCAACGGCTATTCCTGCGCCCACCAGCTGGCGAATCCCGCCCGCTGACGTTCGCCGCAGAGAGACTATGACCAGCCGATGCGCCAAGCGGTTTAGCCAAACCAGCGAGATAGCTACCTCGACTTTTTCGCCGATCTGCCGCCCCAAAGCGCCCCAGCGCGCCATGCCACGGGTAAGACGACCATCGCCACCAGTTCCACGCCACGGTCATCCCTTCGCCGGAGGAAGCTGCTGCGGCAATAAAGCCACTTTGCGGGCAAACGCTTGCGCTCCAGCTTTCCCAGCGGTTGGGCATCAAGAAGTAATCTTCCCCTCCGACGGCGGCTGATGACGGGCCAAGCATTTTGAGCAGAGTGGATTTACCAGAACCGTTGTGACCAAATCAGACCGGTCACTTTCCCGGCAGGAAAGGTTTAACTGACAGCGGATGCAAAGCGTGCGCCGGGCACACGAAAGGAGATATAGCGGCAGTGCAAAAGTGGTATCGAATGATTCGTGTATCTCCTGCATAACAGCCAAACTTGTGAAATGGGCAGGAAATCCGGCCCCAATAAGAGAAAATTAGAAACGGAAGGTTGCGGGTTGCAACAGACCTGACTTCTGCGCCCCAGAAGCAGCCATAAAGTGTTAAAGCAGGCTGCCGACGTATTCACGATCGATACGGTTTGTTAACATGCAGCGGCCAGCGTTGGAGCCAGCCATGCCGACTCGCGCCAGATCATATACGTACTAACCAGCATCCACGACCGTATATACTCCCCACTTTAAAGGAAGTTAGCCGATCACCGCATAACTGGAGCCAGTATACAACGACCACCGTGGCCCAGCCCGTCAGATCCTGAAGGCGAGCGGGCGTCAAAGAAGGTGTAGTCAGACCCACAACTGAAGCCATGTGTTTTGGCACCTGTGCATGGCGTATTGCCTTTATTACGGTGTATCGGTGGTGTATTCCGGATCGGTGTAAGTAATAAGAACCTGACTACGTTAACACTCGCCGACAGCGCCGCTTTCGGCTGCTGATTTCTACGCACGTGCGCGGATCTCGATCCACCTTTCAACGAGAAGTAAGTGGACCGCTCAGGGTCGCGCCATCAGGTTTGTTGGTTTTAGTGAGATTATACAACGGCCACGCAGTAACTACAATCGGACGATCTTCCGGTACTATATTTCACGCCGACTTCATACTGCTTACCTTTTAGACGGTGGCGAAAATATTAACCATCCCTCCCTGAACTTGCGAAAAGGTTCATAACGATTCGCTTATAGCTGAAGTAAGGGTTACACCTAATTATCAAACAGGTAGTTTAATCACCACCACCCAGGTAACTGTTTTGTCATCCACTGTTTATCGGTCGTCCCGGCAACGCGGTTTAAGAGATTCTTGATCTGCCCGTCTAAACGACGCGCCTAGGGTACCAGCACTTTATACCACTGCGCCTGATCCCTGAACATAAACGCCCGTTTTTTCTGTTTATTCAGATGCGGTAAGGGCGGAGTTTGCGGATCTTTGGCATTTGAGGTCGAAATCGGTATTCACCGGATTGTACAGATTGAGCAGTGGCACAGAGTCGTCGTAACCAAACCAGGCGTTTGATGTCATTACGCATACGCATAAAGTCGACCCGTCAGCAGGGTGTGGCCGATATCGCCAGTGGCAAACTTTGCTCTGCAACTGGGTATCCAACGGAGAAGTTTTTGGCAGCTCTCATCATCAACGACGTATTACGTGCCAGATATATGGCGCTTTATCCGCTGGCGCTAAATGCGGCACACTGTTGCTGTAAGCATTCGCCGACGGAGCAGACGCGCGTAACCATAAAACGCCTGTTTTGCGAGTTTTTGTTTCAGCAAGCGCAGGTCTGACCACAGTAAAGGTGGTCGTTTAAATTCGTGATCGAAAGCTGTAGCCGACCATCTTTCTCATTCGAGAATAGGTGTTGTTCGTCGCCCCTTCATTAAAGTCTGTCCGGCAGACGCTTACCGTCGGCCAGCGGCTCAACGTTCCCTTCTTTCGGCAACCATCCGGTAAACCGGTTTCCGGCTCGTTCTGGGAAGTTAAGAATGGACAGGTAACAATTGGTTTAAATCATCCGACGTCCAGGTGAACGCCGGTGCAATAGCATTAACGCTGCTCTCTTGACCCTTTCTGCGGGCATTGCAGAACTGCGCAAGACCGGTCAGGCGATAAGAGTAAACACCGTCATTCATTCCAACCGAATCGCTAAAGTCAATAACCACGTCTGGAACAGGCTGTCAGTACGGCTTTAAACTGAACTTCTTTCAGCGGTTCGGTGGTCGGACGCTTTGCTGTAGCCAATATTCAACAGGCGCCAGGACTGCTTTTAACCGTAAGCAGGAAACTCGGCCAGCGCATAATTTCAGCGCGTTCCAGCATATACGGGTCAACTGACCGCATCGTATAAGAAGTTGGCCCTGCAAACTTCAAGGCCATTCAGATAGTTATTCTGGCTTTGGCCCGCCTTCTGCCGCAAAAGCCGGTCGAATGATCAGGTGGTCATAGGTGTTGGATGCGCCAAGCGTACCAACAGAAGACACCCGGCGGTAGCTAAGCGCTTCTTACCGAGCTTCGGCTGATTGCAGCGCCATTCTCTTCGGCGGTCACAACAGAAATAGACTGTGGG'..b'CGGAGGCAGTACGATTATTTTCAGCGGGACCACTCCGGCA\n+>m120131_103014_sidney_c100278822550000001523007907041295_s1_p0/10620\n+GGTTTTTGGGGGGAAAAAAGGGAAATTTTCCTCTGGCGGGGTTCCCCCAATAGGCCCGAGCCCCAATTGTTCGGGCGACAGGGCGGGGTTGGGGAAGCACTTTTCACTAACAAGAACGTGGGTCGAGGGGCGCCCGACGCTGTTTAAGGGAGTTTTTCCAGCCGCGGATGTGCAGCCTAAATTTCCATGGGGCCTTTGGGAATCATTGCCCCGGTTCAGCTCAACTGTTTCAATGGTTCCCAAACGGCCTTTGGCCGGCTGGCGACCGCCGGTTGCGCCCCGGTGAGTAAGCCAGTCCGCCGGTGCAGAATGCTGTGCCGGGCCGAGGGTTTGGGTCCGGGAAGGATGGCCAACTCGCCATGCCCAGGGTATTCGTTGAAATCGGCCAGCGGAATTCATCGCGCGATGGTTAAATCGCTGGACCGGGGGTTCCGAGGGCTCTGGAACTGAGGTTCCCGGGGACCGCGGCACGCCGGTTGGGTCGGACGGGGGTGCCGGGAACAATTGGCCCCCCAAGCAGTTTTTTTTGACCAGGCCGGGTATTCGAGAGCTTCCAGACCGCAGCCGAGCGTGTCGAGCAGGCAGGTAATGTGGCGGGTCGTAGGCCACTTTAGAGCTGATTTCGTAGTTCATGACGTAATCGAGAATATCAACGATTTCACAGATCAAGATTCCGGGGCGGAATTTTGTGATTTTGAGCTGAACATATGGGTACGTTTCCTTATTGTTATTCGTAGGGTTTACTGGCGCTTATCCACGCGAACAAACGGGCGGGTCTTCCGGTCCATACATAGATTGGCGGAAGTACGGATAATTTTTGTTGTCCTGAACGCTTTTTCGTATAATGTGCGCCGCCCAGCCGGTGCGCGGGCGATTAACAAACAGTGGTGTGAACATCGTCGGTGGGAACGCCCATCATGGTGTAGGAATCAGCAAGAGAACCAGTCGAATTGGGGAACATCTTTTTGCTCTCCAACATCAACCGGTTTCCAGGCGATCGGCCGATGTGGACATCTTCAGCCGGAGCCGCCTTCTGCGAGAGCTGCCTTCGCCACAGCGTTTTAATCACCCTGGTGGCGCGGTCAGCGATGGTGTAAACCGGATGAACCAAGAACCAATGACCCACTTCTTTGTTCTCACGCGCTTTGCGGATATCTGCTCGGCTGTCGTCCGGCGTTCCGTAGCGTTGCATGATCTCCAGCGACACTTCATTCGCCCCCCGTGTTGGCCCCGCCGCAGTGCGCCAATCGCGGCCAATAATCGCGGAATACATATCATAGAGCCGGTGCCGTCGCAATCATCCCGACTGGTAAAGTGGAGCGTAAACTCGGTGTTTCGCGGCGAACAGCACCAGTCGAGATAATGCATCGCCTTTTTTGCCCAGCTTTGCGATGGCTTTCGCCGTGCAGCCAGAGGCAGGAAGTGACCGCCGATGGAGTCGTCCATCGTTTTCTCGGTTGGATGCGTTCGCACGTTGTGGCTGTAGTGAACCAATAGGAGAACGAGCTAAGCGACGCCACAGTTTGGTCGGGCCAATATCCCGCGCCGCCAGAGACGGTATGCCCCTCTTTGTTCTGGCAGCGTGCAGCCGAGCGCGAACACCGGTTGCGCATAACATCCATCGGGTGCGACGCCGCCGGTAAGGCTTCCAGCACGGTACGCACGTTAGGCCGGTAAAACGCGCAGGCTTTCCAGTTCGTTTTGTAAGCGGCGAGTTCGTCACGGGTCGGAGTTTGCCGTGGATCAGGCAGATGCGCCACTTCTTCAAATCGCAATGTTTCGCCAATCAAGAATATCGTAGTCCGCGGTAATGCAGGTCCATTGCGCCACTTAAACCCTCACGGTGCAGAGCGCCGTATTGCCCCGCCCGAACGCCAGAAAGTGCCAGCAGATTGTTTTCGGTTTTAATGGACATGGGTACTGTTGCAGGATCGTTGTGTCGCTCATGTTGGTCGTCATTGTTATCATTTGTAGGCGAGATTTTTGTCCGGATTGCGACGCATATGCGTCTATCCGACCTACCAGTTCAGTTCACCCCGTAGGCCTGAAAGTCGCGTCAGCGGCGCATCAGGCACGGTGTCGGATGCGACGCTTATGCGTCTATCCGACCTACAGTTTCAGTGCACCGCCGTAGGCCCTGATAAGTCGCTTCAGCGCGCATCAGGCATTCGGTTGTCGGATGCTACGCTTTGCCGTCTTATCCGAACCTATACAGTTCAGTGTGCACCCGTAGTGCCTGATATGTCACGTCAGCGGGCATCAGGCAATGCGGTTGTCCGGATGCGACGCGCCATCCGTCTTACTCGACCTACAGTTCAGTGCACCTCGTAGGCCTGATAAGTCGGCGTCAGCGACGCATCAGGCCATCGGCTGTCGAATACAATCAACGGGCGTTTTTTATTTCACCTGGCTTACGGGCCAAACAGGTTGTCGAGCTCTCATTCGTAACTGGTAGTAAGTTGATGCTTTCGTACAGCTCGTTGGCGGTCTGCAATGGTGTCGATGACGCTTTTCTGCGTGCCTCCTGGCCGGACGGTTGGTAGACATGTTCAGCGGCGCGGTTCATGGCGCAGGATACGGCTGAAAGTGGGTACAGCGCCATTGCGACATGGCGCTGCGGAATTGTCGTGGTAAACAAGCGGCGGTGGGGCACCAAATGTCGGTGAATTTGGCGGAGATCGCACTCACCGCATCGGCAAACTGGCGGTAACATGGCAGATGTTTCGGTAATCGCCTCCGGGAACAACACTCGGCACCCGCTCAACATAGGCCGCGTCACGCTCGATCGGCATCCAGCCCCTCTACCGCCAGAGCATCGGTGGCGCGCCATGATCACGAAATCAGGATTCGGTTTCCGCATCCACCGCCGCGCGGATCCGATCCACCATCTCGTTCTTTCGAGACGACGCTTTATTCGACCGATGACCCGCAGCGTTTCGCACCAACCTGATCCTTCAAGTATGCAGATCCTGCCGCACCGGCTTTTAATGCATCGATTTCACGGTGCGCGCCACGGTTAAAGGTCCGAAGAACGCAAAAAAACCGATATCCGCATCCAACCAGCAGCGGCGCGAACAAACGCGTGATACGGCGAATGTCGGTCAGCACATCATCAAGGGTAGAAATACCCGAGATCGGGCACCCCAGCGAACCTGCCGCCACGCCAGCCTTGTCCAGAAAGATAAATTTGCTGATATTCCGGCACGCTGCGCCAACAGTCGCATGATTAGCGTTGAGGTGCCAACAATCTGCAATGGATTTTCTTTAGTCAGTGCAGGCCGAAACGCTTTACCTGGAGAGTGAAGAGACATAGCTCCCAGTCCTTTGGTATCAACTTGTTATTTGCGTTGATAAAGACAAAGCAGGGGTGTGGCCACAATTGCCTTAATAAATTAAATGTTTAATTTAAATTTTGTTTAGAGATAAGTCATGGAACTAATCCGCAAAATATGCCGTTTACAGTAACGTTCAGCAAGTGTTCACCGCGTTTCAGTGTGCAACAATTAGGAAACAAGACTAAACCAATATTCGGTTTCTTACTTTGCGTGCGCTATGGCAACTCCACACGGCTTAATGACGACAACCGGTTATCTGGACGGTATCTGTAACGGCGCCTGTTCGAGCTGTTTCGCCGATATCAGCCTCGAGTTGATCACCTGGGCGAACATTACCCCTATTCAGCTTGGCTTTGAAAAGCATTTGTGACCTAACATCCGCAAGAAACTGGCCAAACGAACGCTGTGACGCCATCATCGCGGGCGTGGTCGAAACGGCGCTGTACCTGAAAGCCGCCTGCAAGTGCCAGTTATTTTGATTAAACTGTCGAGCGGCACGATGTGTTTACAGGCACGCCAAAGCCGGAAAACCACCTCTTCTAATCGGCGT\n'

diff -r 000000000000 -r dc70286127fe test-data/lordec/corrected_reads.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/lordec/corrected_reads.fa Fri Oct 20 03:15:43 2017 -0400

b'@@ -0,0 +1,2025 @@\n+>m120131_103014_sidney_c100278822550000001523007907041295_s1_p0/10002\n+gacaatcactaacacgccagcaaataacgccgggaaaagcgcaattcgtttactcacgctttacctccga\n+tggcgttatccagaaatgcgcacaaagtgcattgccggagcgtcgcaccataaataccagactgcaggta\n+cgcgctggaaagcgtcccggcgcggacaatacggcatggcctgccacagcggcgttgccattagcgcatc\n+cattgtctttggctgttgtcgtgatcaaacagagcacatccaacggtcctttatatcgccgccagacgaa\n+tcgatactgacgcggtactgcccagaagttggtttccccttgcccagcatttgggatgccgtaccatcaa\n+gaatttctggaacaagctgtttggacgaagaccagcatatgcgcggatcgataagtcggtcgtcagcaaa\n+ttaacggacgcgcaccacgccttccaagcggggtttcaatgctgcggataaagtcttcatatttgcgcta\n+aatgcgtttccgctgcgctttgcaggtttaagtaaatcctgccagtttccgtcagcgaatttacgcgcca\n+tcgccaacggctgtttgtacgtcactgaagttaaatccgcgacccggcgcaatacgagccagcatttctg\n+gttgaaggccatatcctgcgaccagaccataaacgatgtttcagattcggtcagcagtttcaaggttagg\n+tctgtgcgcaaaccgacgtcgatcactgaggtcccggccaatggggttcgctgacccacagcgatattgt\n+tgtgtatccgccacgccgtaaggccacgatgccgagcgccagcagtaatttccaccggcaaccatctcca\n+gcgccacaatacataattgggattcaatagccgccgcgtgggcggtaattcatctgccataacaatcgag\n+aaaggccatcgcccgttaacaggtcggacggcgcgaataagaaggataagccgtcatcaataaacaaaac\n+tcacaggtgcagcaccacgcccggatgcggtcaaaatacccatgcgggatgcataaatcatttccgaggg\n+ttttcgtgtcgccgcgcataattttccgcaggccggttcctgagcatcatttcagccgcgcagggcgaca\n+gataatcacagtagcgtgccgccatattgatatcgtgcaacaggcaatgaccgtcaggccacgctcctga\n+cttaaacggtgcaccagcgacagcaacatcaacctgtgggcgatatccagcgccgaggtcggttcgtcga\n+gcaatcagatcaacggctattcctgcgcccaccagctggcgaatcccgcccgctgacgttcgccgcagag\n+agactatgaccagccgatgcgccaagcggtttagccaaaccagcgagatagctacctcgactttttcgcc\n+gatctgccgccccaaagcgccccagcgcgccatgccacgggtaagacgaccatcgccaccagttccacgc\n+cacggtcatcccttcgccggaggaagctgctgcggcaataaagccactttgcgggcaaacgcttgcgctc\n+cagctttcccagcggttgggcatcaagaagtaatcttcccctccgacggcggctgatgacgggccaagca\n+ttttgagcagagtggatttaccagaaccgttgtgaccaaatcagaccggtcactttcccggcaggaaagg\n+tttaactgacagcggatgcaaagcgtgcgccgggcacacgaaaggagatatagcggcagtgcaaaagtgg\n+tatcgaatgattcgtgtatctcctgcataacagccaaacttgtgaaatgggcaggaaatccggccccaat\n+aagagaaaattagaaacggaaggttgcgggttgcaacagacctgacttctgcgccccagaagcagccata\n+aagtgttaaagcaggctgccgacgtattcacgatcgatacggtttgttaacatgcagcggccagcgttgg\n+agccagccatgccgactcgcgccagatcatatacgtactaaccagcatccacgaccgtatatactcccca\n+ctttaaaggaagttagccgatcaccgcataactggagccagtatacaacgaccaccgtggcccagcccgt\n+cagatcctgaaggcgagcgggcgtcaaagaaggtgtagtcagacccacaactgaagccatgtgttttggc\n+acctgtgcatggcgtattgcctttattacggtgtatcggtggtgtattccggatcggtgtaagtaataag\n+aacctgactacgttaacactcgccgacagcgccgctttcggctgctgatttctacgcacgtgcgcggatc\n+tcgatccacctttcaacgagaagtaagtggaccgctcagggtcgcgccatcaggtttgttggttttagtg\n+agattatacaacggccacgcagtaactacaatcggacgatcttccggtactatatttcacgccgacttca\n+tactgcttaccttttagacggtggcgaaaatattaaccatccctccctgaacttgcgaaaaggttcataa\n+cgattcgcttatagctgaagtaagggttacacctaattatcaaacaggtagtttaatcaccaccacccag\n+gtaactgttttgtcatccactgtttatcggtcgtcccggcaacgcggtttaagagattcttgatctgccc\n+gtctaaacgacgcgcctagggtaccagcactttataccactgcgcctgatccctgaacataaacgcccgt\n+tttttctgtttattcagatgcggtaagggcggagtttgcggatctttggcatttgaggtcgaaatcggta\n+ttcaccggattgtacagattgagcagtggcacagagtcgtcgtaaccaaaccaggcgtttgatgtcatta\n+cgcatacgcataaagtcgacccgtcagcagggtgtggccgatatcgccagtggcaaactttgctctgcaa\n+ctgggtatccaacggagaagtttttggcagctctcatcatcaacgacgtattacgtgccagatatatggc\n+gctttatccgctggcgctaaatgcggcacactgttgctgtaagcattcgccgacggagcagacgcgcgta\n+accataaaacgcctgttttgcgagtttttgtttcagcaagcgcaggtctgaccacagtaaaggtggtcgt\n+ttaaattcgtgatcgaaagctgtagccgaccatctttctcattcgagaataggtgttgttcgtcgcccct\n+tcattaaagtctgtccggcagacgcttaccgtcggccagcggctcaacgttcccttctttcggcaaccat\n+ccggtaaaccggtttccggctcgttctgggaagttaagaatggacaggtaacaattggtttaaatcatcc\n+gacgtccaggtgaacgccggtgcaatagcattaacgctgctctcttgaccctttctgcgggcattgcaga\n+actgcgcaagaccggtcaggcgataagagtaaacaccgtcattcattccaaccgaatcgctaaagtcaat\n+aaccacgtctggaacaggctgtcagtacggctttaaactgaacttctttcagcggttcggtggtcggacg\n+ctttgctgtagccaatattcaacaggcgccaggactgcttttaaccgtaagcaggaaactcggccagcgc\n+ataatttcagcgcgttccagcatatacgggtcaactgaccgcatcgtataagaagttggccctgcaaact\n+tcaaggccattcagatagttattctggctttggcccgccttctgccgcaaaagccggtcgaatgatcagg\n+tggtcataggtgttggatgc'..b'0\n+ggtttttggggggaaaaaagggaaattttcctctggcggggttcccccaataggcccgagccccaattgt\n+tcgggcgacagggcggggttggggaagcacttttcactaacaagaacgtgggtcgaggggcgcccgacgc\n+tgtttaagggagtttttccagccgcggatgtgcagcctaaatttccatggggcctttgggaatcattgcc\n+ccggttcagctcaactgtttcaatggttcccaaacggcctttggccggctggcgaccgccggttgcgccc\n+cggtgagtaagccagtccgccggtgcagaatgctgtgccgggccgagggtttgggtccgggaaggatggc\n+caactcgccatgcccagggtattcgttgaaatcggccagcggaattcatcgcgcgatggttaaatcgctg\n+gaccgggggttccgagggctctggaactgaggttcccggggaccgcggcacgccggttgggtcggacggg\n+ggtgccgggaacaattggccccccaagcagttttttttgaccaggccgggtattcgagagcttccagacc\n+gcagccgagcgtgtcgagcaggcaggtaatgtggcgggtcgtaggccactttagagctgatttcgtagtt\n+catgacgtaatcgagaatatcaacgatttcacagatcaagattccggggcggaattttgtgattttgagc\n+tgaacatatgggtacgtttccttattgttattcgtagggtttactggcgcttatccacgcgaacaaacgg\n+gcgggtcttccggtccatacatagattggcggaagtacggataatttttgttgtcctgaacgctttttcg\n+tataatgtgcgccgcccagccggtgcgcgggcgattaacaaacagtggtgtgaacatcgtcggtgggaac\n+gcccatcatggtgtaggaatcagcaagagaaccagtcgaattggggaacatctttttgctctccaacatc\n+aaccggtttccaggcgatcggccgatgtggacatcttcagccggagccgccttctgcgagagctgccttc\n+gccacagcgttttaatcaccctggtggcgcggtcagcgatggtgtaaaccggatgaaccaagaaccaatg\n+acccacttctttgttctcacgcgctttgcggatatctgctcggctgtcgtccggcgttccgtagcgttgc\n+atgatctccagcgacacttcattcgccccccgtgttggccccgccgcagtgcgccaatcgcggccaataa\n+tcgcggaatacatatcatagagccggtgccgtcgcaatcatcccgactggtaaagtggagcgtaaactcg\n+gtgtttcgcggcgaacagcaccagtcgagataatgcatcgccttttttgcccagctttgcgatggctttc\n+gccgtgcagccagaggcaggaagtgaccgccgatggagtcgtccatcgttttctcggttggatgcgttcg\n+cacgttgtggctgtagtgaaccaataggagaacgagctaagcgacgccacagtttggtcgggccaatatc\n+ccgcgccgccagagacggtatgcccctctttgttctggcagcgtgcagccgagcgcgaacaccggttgcg\n+cataacatccatcgggtgcgacgccgccggtaaggcttccagcacggtacgcacgttaggccggtaaaac\n+gcgcaggctttccagttcgttttgtaagcggcgagttcgtcacgggtcggagtttgccgtggatcaggca\n+gatgcgccacttcttcaaatcgcaatgtttcgccaatcaagaatatcgtagtccgcggtaatgcaggtcc\n+attgcgccacttaaaccctcacggtgcagagcgccgtattgccccgcccgaacgccagaaagtgccagca\n+gattgttttcggttttaatggacatgggtactgttgcaggatcgttgtgtcgctcatgttggtcgtcatt\n+gttatcatttgtaggcgagatttttgtccggattgcgacgcatatgcgtctatccgacctaccagttcag\n+ttcaccccgtaggcctgaaagtcgcgtcagcggcgcatcaggcacggtgtcggatgcgacgcttatgcgt\n+ctatccgacctacagtttcagtgcaccgccgtaggccctgataagtcgcttcagcgcgcatcaggcattc\n+ggttgtcggatgctacgctttgccgtcttatccgaacctatacagttcagtgtgcacccgtagtgcctga\n+tatgtcacgtcagcgggcatcaggcaatgcggttgtccggatgcgacgcgccatccgtcttactcgacct\n+acagttcagtgcacctcgtaggcctgataagtcggcgtcagcgacgcatcaggccatcggctgtcgaata\n+caatcaacgggcgttttttatttcacctggcttacgggccaaacaggttgtcgagctctcattcgtaact\n+ggtagtaagttgatgctttcgtacagctcgttggcggtctgcaatggtgtcgatgacgcttttctgcgtg\n+cctcctggccggacggttggtagacatgttcagcggcgcggttcatggcgcaggatacggctgaaagtgg\n+gtacagcgccattgcgacatggcgctgcggaattgtcgtggtaaacaagcggcggtggggcaccaaatgt\n+cggtgaatttggcggagatcgcactcaccgcatcggcaaactggcggtaacatggcagatgtttcggtaa\n+tcgcctccgggaacaacactcggcacccgctcaacataggccgcgtcacgctcgatcggcatccagcccc\n+tctaccgccagagcatcggtggcgcgccatgatcacgaaatcaggattcggtttccgcatccaccgccgc\n+gcggatccgatccaccatctcgttctttcgagacgacgctttattcgaccgatgacccgcagcgtttcgc\n+accaacctgatccttcaagtatgcagatcctgccgcaccggcttttaatgcatcgatttcacggtgcgcg\n+ccacggttaaaggtccgaagaacgcaaaaaaaccgatatccgcatccaaccagcagcggcgcgaacaaac\n+gcgtgatacggcgaatgtcggtcagcacatcatcaagggtagaaatacccgagatcgggcaccccagcga\n+acctgccgccacgccagccttgtccagaaagataaatttgctgatattccggcacgctgcgccaacagtc\n+gcatgattagcgttgaggtgccaacaatctgcaatggattttctttagtcagtgcaggccgaaacgcttt\n+acctggagagtgaagagacatagctcccagtcctttggtatcaacttgttatttgcgttgataaagacaa\n+agcaggggtgtggccacaattgccttaataaattaaatgtttaatttaaattttgtttagagataagtca\n+tggaactaatccgcaaaatatgccgtttacagtaacgttcagcaagtgttcaccgcgtttcagtgtgcaa\n+caattaggaaacaagactaaaccaatattcggtttcttactttgcgtgcgctatggcaactccacacggc\n+ttaatgacgacaaccggttatctggacggtatctgtaacggcgcctgttcgagctgtttcgccgatatca\n+gcctcgagttgatcacctgggcgaacattacccctattcagcttggctttgaaaagcatttgtgacctaa\n+catccgcaagaaactggccaaacgaacgctgtgacgccatcatcgcgggcgtggtcgaaacggcgctgta\n+cctgaaagccgcctgcaagtgccagttattttgattaaactgtcgagcggcacgatgtgtttacaggcac\n+gccaaagccggaaaaccacctcttctaatcggcgt\n'

diff -r 000000000000 -r dc70286127fe test-data/lordec/ill-test-5K-1.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/lordec/ill-test-5K-1.fa Fri Oct 20 03:15:43 2017 -0400

b'@@ -0,0 +1,10000 @@\n+>727:3:1:1215:17862/1\n+ATGCTCCCTCGCTGTGGTTGAACGTTGGAGTTCTTGTTTGAAATTTGTGTGAGCTCGGGAAGCGCCGCAACCGCGC\n+>727:3:1:1215:17862/2\n+TCGGTGTGTCGACAGAATAATTTACCGGTGAGCATGCGAGAGGTGGCGGAGGCGTGCTCGGTGAACGTGTTCACCC\n+>727:3:1:1215:4882/1\n+CGGTCGCGACGCCCGCGCGGACGCCCGCGCGCGATCTCGCACGGGACGGTGCTCGCGCGCGGCGGCGCGCGAGGCG\n+>727:3:1:1215:4882/2\n+GCGCGTCCTCGCCTCGAACCACCGTCGCGGACGCCTCGGTCGTCGACGTCGTCCGCACGCGCGTCCGCGCCGCCGC\n+>727:3:1:1215:16163/1\n+TTGCGCCATTGTATTTATAATTCTTTTCATTCAACGTTCAACACGAAACTATTTTTTTGCCGCACGCGTCTCGCGG\n+>727:3:1:1215:16163/2\n+GGCGTGCTCGACACATGTCGGTGCGTCTTTGGCTATCAATGGCTCCGTGTGAAGGCGAATCCGCAATCACTCGCCG\n+>727:3:1:1215:13615/1\n+CAAGGGCCACGAGCGCCCGCTGACGTTCATTCGGTACAACCGCGAGGGTGATCTCTTGTTCACGTGCGCGAAAGAT\n+>727:3:1:1215:13615/2\n+CAGCTTCGCCGTGGTGTCCGCGCTCCCCGTGAGCAGGGTCGAGCTATCATCGCTCACGTCGCACGTCCACACCGCG\n+>727:3:1:1215:8146/1\n+GTTTCCTTGATCATATACGCAATACTCGTGGTAAGACCGCGAGAAATCACGCTCACTGAAGCGTAACCTACGCTCA\n+>727:3:1:1215:8146/2\n+TCCATCGTTGTCTTTTACGTGTCGGAGTCTGCTATCACAGATGCGCTACCGCCTAGCTTGAGTGCCGCCGAGTTGC\n+>727:3:1:1216:13424/1\n+GGAGCGATGTCGGAAGCTCGGACCGTTCGACGCGGTGGTGTGGAACTTTCCGTGCGTCGCGCGGGAGGCGGATGGT\n+>727:3:1:1216:13424/2\n+GCCCTGCATCCCAACCTTGTGCGTGATGTGAATCTCCCCTCCGTCCTCGGCGAGCAACTCTGCGGCGCCGGCGACA\n+>727:3:1:1216:18066/1\n+CGTTACCGCCTTCGTCTACGCCCTCGCCGTGACCGTTTGGGACTACCTCAAATGGCTCAACCGCTTCACTCCGTGG\n+>727:3:1:1216:18066/2\n+CGTCGTGCGCAATGAGTGCGAATTACAAGCGTGCGGTGAACGAAGTGCGGTGAATGAACGTGTAATTTTACGGAAC\n+>727:3:1:1216:17478/1\n+TAATGATGCCCCTGTGTATGGTGCAAGGTATTGGAGCGTTGCTGGGAATCAGCCGTTTCCGGTAAGGAAATTTGTG\n+>727:3:1:1216:17478/2\n+TATCATTGGTGACCGTCAAACTGGAAAAACTGCAGTAGCAACAGATACAATCATTAACCAAAAAGGTGGTGACGTA\n+>727:3:1:1216:12383/1\n+AGGCACTCAAAAATGTTCCCCTTGTGCTCGGCGACGATTCTCGGATGCGAGTCCAACAAATACGTCAGCGCGTGCA\n+>727:3:1:1216:12383/2\n+GAAATCTTGGAGACGACATCCGCGAAATCGCTCATGTACGAGTGCGTGCGCACGGCGGTGATGGGAATGACGAGTC\n+>727:3:1:1216:9679/1\n+TGATGTGCCAAACATTTCTGGACTTTACGCCTGCTGTTGTGGCAACGGCAGGTATTTTTTTCGCGGGGTATAATAT\n+>727:3:1:1216:9679/2\n+CGCGCGCGGCAGGGGCGCGCGCGGGCGTGGGCGGCGGCGAGACGAACGACCGATCGGGAAATTCTTTGTTCATAGA\n+>727:3:1:1216:5432/1\n+TTGAGACAAGCATATGACTACTGGCAGGATCAACCAGGTATCTATCCTTTCGACACGACAACGACGAATATATCAA\n+>727:3:1:1216:5432/2\n+TCTGTAGGACCTACGTGAGGGCGTTTCAATCGCGTTCGCACATGAGGCGGGAGCCTTGTGTGGGTTCGGGAGACGT\n+>727:3:1:1216:13469/1\n+GCGATCGATCGCGATCGATCGGAAAAAGGGGTGAAGACGAATCGTCGCTCAGATCGGAAGAGCGGTTCAGCAGGAA\n+>727:3:1:1216:13469/2\n+GAGCGACGATTCGTCTTCACCCCTTTTTCCGATCGATCGCGATCGATCGCAGATCGGAAGAGCGTCGTGTAGGGAA\n+>727:3:1:1216:18215/1\n+TCAGAACGATGGCTTTCGAACACTCAAAGCACGCATGGAGTCGTGCACGTACCATGGATATCATGCATGTAGTATT\n+>727:3:1:1216:18215/2\n+ATATGCTGGGTACGCTTCCTTAATGGCTTGACACATTCTTTCTGACTTTCGGCGCGTTTAGAGAGATCATTAATCG\n+>727:3:1:1216:15138/1\n+GGCGTCGAAACGGTTTTTGAAATCGTGCGTGGGCATCTAGCAGCTATGTTTTACACGTCCATCGTCATGTTGGACT\n+>727:3:1:1216:15138/2\n+CGAAGGAAAATCTCATGGCCACGTTTCGCGGCGACGCGTTTCATCGCGTTAGGGCGTACCGCACGCGATCCAAGCG\n+>727:3:1:1217:8088/1\n+CGAACCGCTCACCGTGTCGCCTTCGCGCGACGTCGTACCACGCCAAGTACGCGCCCCAGCTCGCGGCGCTTCCCAC\n+>727:3:1:1217:8088/2\n+GAAGACGCGGCTGCAAGTGCGCACGGACGCGCGCCCGAGCGGTGGCGCGGTGTTTGCGAGCGCGTACGCGACGTTT\n+>727:3:1:1217:20730/1\n+CGAGATCTGAGAGCATCTTGTTTGGATAATTACGTAGTACGACGCGCGAGAGTCGTTCGTGACGCGATGCCATCAA\n+>727:3:1:1217:20730/2\n+CAATCCACGTCGCCGATCACGACGTTTTCGTTGTCGGCAAAAGCCTCGCCGAGCTGCTTCCACGCCGGCGCGAGCG\n+>727:3:1:1217:16303/1\n+ACGCGAGCGTGCGACGACGACGGAAGGGACCGTTCGTCTCAAGCGTAAGTTGAGAAAATCGAGAGTTCAGCGCTCC\n+>727:3:1:1217:16303/2\n+AACTTCTAGTCTTCTACACGGTAGCTATAATTGTGATTGATCCCGCTAGCAAAAGAAACGCCAGTACAGGTAGACG\n+>727:3:1:1217:9509/1\n+CGCAGTGGGTTCAACTCGACGCGCTACGCTACGAGCTCGCTCACGCTCAGAACCACTCGTTGTGCTCCTCTAAGTC\n+>727:3:1:1217:9509/2\n+CTGGATCCGTCGAGGCATGACCGCGCCGCACAATCGATATGGTATCAAGCCGGGGCGTCACTGGGACGGAGTCGAT\n+>727:3:1:1217:15479/1\n+TGAGAGCGCGCGTCATGTCCGACGCGCCCGTCGACGCATCGAGCGCTCGAGCGCGCGCGACGGTGGGGAACGGGGG\n+>727:3:1:1217:15479/2\n+ACCCATCCGTGCTACATGTGCTATCCGATCGCACGTGCGCGCTGATCCGCGTCTTCACCGGCGACGGGACCGCCTT\n+>727:3:1:1217:11276/1\n+CGGTCAAATTATTGTCGATCACTGCATCGTAATTCGGTTCATAGAAAAAGGCGATGGAGTATCTGGATTTTTTTGA\n+>727:3:1:1217:11276/2\n+ACGCGGGATTGCAGGTTAAGCACGAAGA'..b'99/1\n+CCACCGAAATCCTCGGCGACGCTCCCCACGGCGAGCATACGCTGAATAGCCTCCAGTCTAAACGCCTCGGCGACTT\n+>727:3:1:1505:4799/2\n+ATCTCGCCGGTCGCGGCGCGAACGCGCCCCGAGGGCCTCCACCGCCGCCGCCAATCTCCACCATGGTCACCGTGCC\n+>727:3:1:1505:16871/1\n+ACACCAGGATCGCCGAGTAACAACATGTTAATGTCGCCACGCAGACGAGTCTTTCCCTTGACGAATTTTTCCTGTC\n+>727:3:1:1505:16871/2\n+ATCAAGCGAAAGGGAGACTTGTTCTCATCGGATAATCTCACCGACGAGGATCGCGAAGACATTCGCAAATTGAGTC\n+>727:3:1:1506:15171/1\n+CCCCAAGAGTGTGAGAGCCCGGAGTTTTTCACCCCATGATGTTGCTGGTTCCCGCTCGGGCATGCGCTCTCGGTTC\n+>727:3:1:1506:15171/2\n+GGCCGGATCGGGCACATTTGGGTTTCTCATTCCGCCTTCTATCATCCTGATCGTCTATGGCGCTGCAACAGAACAA\n+>727:3:1:1506:4142/1\n+GAAAGAGTGATCGCACCTCCCATCACTGTCGATGGTGACGCGTCGTCACGCATCGTCTCCGGACGAAGAACTCGAG\n+>727:3:1:1506:4142/2\n+GCGAGCGTAGAGCACGAGTCATCGGACGACGACGAGACGCGCTCGCACGCCGCCGTGGAGTGTCGAAAGGCGTTGG\n+>727:3:1:1506:13936/1\n+CAACCGGAACGCCATCCTCAGGGACGTCGGTACCGGAGAACAAGAACGGGTGATTGCAGCACTTTCGGAGCTGCAT\n+>727:3:1:1506:13936/2\n+AGACGAAAATTATGTGCCCTCTCTCTGAGGCGCAGACCTTCTGGTATCGTCGTCTGCTGCTTCGCGAGGCGACCGC\n+>727:3:1:1507:6480/1\n+CCAAATAGATGTGTCCAATTCAAGTTCATCATAGTACACGTGTAATGGATCCTTCACGTTCGCGTACCAATAACGC\n+>727:3:1:1507:6480/2\n+ACCTCAGCAGGTCGACGGGTCGTCCTGTGGAGTACTTACAGTTTACAACATCACCTTAGCTGCCATGGGTATTGCC\n+>727:3:1:1507:8108/1\n+ATTAAGCGTCGTTACCACCACTTCGCCCACGTCGCCGGGGGCAACCGGATTGCCGGTGCCGGGCGTCACAATCTCG\n+>727:3:1:1507:8108/2\n+CTCAGGATCACCAAGGCTGCGGTCGGTGGTGGTGCACTTTTCCCGTCGCTGCGCGCGGAATATGCGGCGCGCGGTA\n+>727:3:1:1507:2739/1\n+TGATGTTTTGGACGTCGTGAACGACGTTCGAACATTGAAGAAGCCGTGTTTGTATGTATACGCTCAAATCACGTGG\n+>727:3:1:1507:2739/2\n+TGCCGGAGTCTCCACAGTCGTACAACATTTTTGATCCATCCCCTGCAACTCCGCCTTCGCGCACGACGGAGATCAG\n+>727:3:1:1507:2504/1\n+GTAAAGTTGCAGTCATACGTCAGACCCAACGCGTCTCTAACCGTGGTGAACAGCCTACCACCCACAACTTCAGCGA\n+>727:3:1:1507:2504/2\n+CGAAATCCCTAGCTTTATCAACGTGGAGTCGTACACGCCTGAACAGATTGCCGCTTTGAAGGATCCGGTGAACGAG\n+>727:3:1:1507:5290/1\n+CGAGCGCGAACGACCGAGCGCGACCGAGCGCTTCGCGCGCGTCGATGAGCGCCGCGAACGAGCTGTCGCAGCGCAT\n+>727:3:1:1507:5290/2\n+CTGTAATTATGCGAGTGCGCGCGCTGTCGCTTCGCCGTCCGTCGCTCGTTCGCCCCATTGTCGGTGATCGTCGACG\n+>727:3:1:1507:2235/1\n+CGTCACAAACGCGTGTCGACACTGCGCTATCATTTCAGAAAAACGTCAATATTTAGTTTGAGTCGACATCCGCAGT\n+>727:3:1:1507:2235/2\n+TAATTCTAGCTGCGCGAAAGATTAAGCAACGACTTCGAAACTAACTCAAGACGTACCGACATTCCACACAAAAAAA\n+>727:3:1:1508:17390/1\n+ACATCGAGCAGGCGCTCGAGCATGAGAACAACCATCGCGTTCTCTACGCCCAACTCTTGGGTATGGACGACGACGT\n+>727:3:1:1508:17390/2\n+AGCGCAGTTACATTTCACAGCCAGGCGCTCAGGCCGTGTCAGGACCAATGGAGACGTTCTAACAGACGTCGATACA\n+>727:3:1:1508:15577/1\n+GTACCGGGTGCAGTGGTACTACTCACTGTACGAGTCGTGTCGGGTCGGATTACGATCGGAATCGTCCGTGGAGGCC\n+>727:3:1:1508:15577/2\n+GAAAACGGCGAGCTTTGGAATCAACAACACGATGGTCCTTCGAATAATAGAAGCCTTACAGTCTTGAAGACGAAAA\n+>727:3:1:1508:3880/1\n+TCAAGGTTCTCGTCAACCGAGGCACGGCCAGCGCCTCGGAAGTTCTCAGTGGTGCTCTGAAGGACAACAAACGCGC\n+>727:3:1:1508:3880/2\n+GGTCGGTCCGGGGTAATTCCAATTTTGTTGATGTCCGTCCCCAAGGGTGTGCGGTATTGGGCGACGGTGACGCTCA\n+>727:3:1:1508:3976/1\n+AGAAAGACAAATTGAGAGAGGTGTGCGAAAATGAAGGCGAGTACGCGAGCATCATCTGTCGATTTGGACCGGGTGG\n+>727:3:1:1508:3976/2\n+GGGCTTGAGATGAGCAGCAAAGAGTCCACGTCTGACGGTACACTAGGAGCGTATTCATCTATAGGCTCCAAAGCCC\n+>727:3:1:1508:20180/1\n+AAGGAGTCGAAGATGGCCAAGGATTCGCTCAACATGGAGACGCGCGAGAAGACGGCGCTGCAAAAGCAGTTGGACG\n+>727:3:1:1508:20180/2\n+GAGACGCTGAATTTCTTCCTCGGCGCGCACGCGAAGCTCCTCCTTGGCGCTCACCGCTTGCTGCAAGCTCTGACGA\n+>727:3:1:1508:14183/1\n+CGTCTGGCGGAGCCCCGGTTGAGGTATCCATGCGGAATAGTCGCGGATGCATCCAAGTGTCGACGCTACGCTTGTC\n+>727:3:1:1508:14183/2\n+GCGAAGTATTCGGAAGACGTCTTGGACAAGGTCGACTGCGAGGGAGGCGACCTGTACGAGTCCACGCGATTTTGGT\n+>727:3:1:1508:6365/1\n+CGCTAACGTGGATCAGTGAGAAACGCGCGCAATCGCCGTCGAGGACGCCCGAGCACGCCCAACCCGCTCTCGCTCC\n+>727:3:1:1508:6365/2\n+TCGAAGCGCTTGTGTGGCTGACGCTGGGCCCGAGAGCGACGGGCGCGACCTCGTGCGCGATCGTTCCCGGGTTGAA\n+>727:3:1:1509:14390/1\n+GCAGCACTCTGGATTGAACTTTTGTCCTCCGAATCCCGGTTCCACCGTCATCACCAGCACCATGTCCACCGCACCT\n+>727:3:1:1509:14390/2\n+CATGTTCACGTATCACGCGGAGACGACGAAGACGGCGGGGGAGGCGGCGGAGCTGTGTCGAAAGATTCGAGCGAGG\n+>727:3:1:1509:5851/1\n+TTCGCCGATGAAGGCGAGCGATGGGGGAGAGAAGAAGACCATGTGCTCGCTCGACTTGGATAACAAGGACGGGAGC\n+>727:3:1:1509:5851/2\n+GTTCCTCGGGGGCAAACTTGTGACAGATGTCCGTCCAGAACGTGGGCGAACTCTCGTCCGAGCAGTCGGCTTCAGG\n'

diff -r 000000000000 -r dc70286127fe test-data/lordec/ill-test-5K-2.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/lordec/ill-test-5K-2.fa Fri Oct 20 03:15:43 2017 -0400

b'@@ -0,0 +1,10000 @@\n+>727:3:1:1509:4930/1\n+TGGACGGACGGGTGACGATTTTTGGAAGGGTGATCGATGGACACGGGACGCTGGATTCGTTGGAACGTCTCGTCGG\n+>727:3:1:1509:4930/2\n+GATCTCTCAGCGATCGATCGCGACGAACTCCTAGGCTCGACATCGCGCCGACACACCGTGTAACTCGACGTCAACT\n+>727:3:1:1509:4684/1\n+TTATAACAACAACAAACAGCGTTAGCTCACTTTTTCTTCGATGACTTTCCGGGAGAGTTGAAAAATCCGAAAAAAT\n+>727:3:1:1509:4684/2\n+CAAGCCGGTGAAGAAGAAGTACGACTCTCTGTCGCGTATGCTGACGAAGAAGGACCCACGCAAGACTGAGGTTCCC\n+>727:3:1:1509:9991/1\n+CGGCGTCCTCGCACGTCCACCAACACGTCGACATCTTCATCGAATTTCTCGAGTTATGTGTACGCGAAAGGTACGG\n+>727:3:1:1509:9991/2\n+TCTATTCGACATTGATTGATCGCACATTGTCACGGAAACACCAGGAATTACAATCGTTGCTTCAGGTTTGAATTCA\n+>727:3:1:1509:2858/1\n+TAGGCGAGCGAAAGAATGTACTGTCAGTATTAAAGACAGTGCTATCAATGTGTGTGTGTTCGACGCCAACGAGCGC\n+>727:3:1:1509:2858/2\n+ATTCTCAAGTACTTGTAAAGTGTGGGTTCTATGAGGGTAGAGCTTGTCATCGAACACGTTTGACGCGCGACGCGGG\n+>727:3:1:1509:10955/1\n+ATCGACATGGCGAAGATTAAAGCCAACGTCGGGGCGAGCGTGGACGAGAGTGAAATCCAAGCGGCTCCGGGGCGGA\n+>727:3:1:1509:10955/2\n+GTTGTGCTCGTGACTATGGACCAGTAGCATCCGTCCAAGAAGGTGATGTCCTCTATCATGTGCATCGCCACCGCGC\n+>727:3:1:1509:2917/1\n+CCCGATGCCTTTCCTGCTGACGTCTTCATTCAAGCAGAGCATCCTCTTCTTCCTCGATGAGATGTACGGCACCACC\n+>727:3:1:1509:2917/2\n+CGCCCCAGTTCGAGCGAGAGCTGTCTCGATCGTGGATTTCAATAACGCCGGATTTGGGATGTCCAGAAGGCGAAGA\n+>727:3:1:1509:9324/1\n+GCTATTCCACAGAGAGAAATCGTCCAAAGGTGGGTGGACGCGACGCCGGAAGGGTTTTCGTTCATTGTGAAGGCTT\n+>727:3:1:1509:9324/2\n+GGTGCCAACGCGACGTTAAATCGTTCCCAAAGTGCATCCTTCGCGTGCGGCGACATTGACGCGTACCGCACCCTCC\n+>727:3:1:1510:3933/1\n+TCGGGTCGCGCGCGAGGCGGCGGCGAGAGGCGGATGCGTCGTCGTGGACGCCAAGGGGGGGGGGGGGGAGAGGGGC\n+>727:3:1:1510:3933/2\n+TCTCGCCTCGCGTTCACCGCCTCGCGCTCGTTTGTTGAAATCCACTCTGGCAGCGTCACGCCTCTGTCATCGCCCT\n+>727:3:1:1510:16626/1\n+GCGATCTTCTTGCCCCACGCGCTCGCCGCCCACTTGCTCTCGACCTCGCCGGCCTTCCACGCCGCGTTGAGCGCAG\n+>727:3:1:1510:16626/2\n+TGTTTCGCGAACAAGAGACTGACCGGGCGATTTCGTTCGACGAATAGGTGCTTGTCGCCGCTCCGGGCGTGAAGCG\n+>727:3:1:1510:18102/1\n+GTGTGATGTCCTGGTTGTTACAAGCGGTTCGCGGTGAGACACGTATCCGTATATTCACGCGCCGTAGCCGAAGACC\n+>727:3:1:1510:18102/2\n+GACGATCACTATAGCACCGTGACTATAACCTTTCGAGAGCCCGATCCTGGAAACTGTTGGGTTGACCTCGTGCAGA\n+>727:3:1:1510:12840/1\n+GATGAATTCGTCGTCGACGCGGCGGGCTAATTCAGCGCACACGCTGAGCTCGACGAGCGTCGTCTCGCCATCCGCT\n+>727:3:1:1510:12840/2\n+GAAGAACGAGATCGAGCGCCGGAAGTCACCGATGTCTCTCCGAGCGCGCTCGTTCTCTCGATCGACGAATCATTCG\n+>727:3:1:1510:10780/1\n+ACGAAAGAGTGGACCGCGGCATTGTTAATGCGCTGTCACGCTCTGAATGCCATTTCAGCGCAGGTTCGCGCCGTCC\n+>727:3:1:1510:10780/2\n+CGACGATGATGGAACGTTATCATCCTCGTCTGATTCGCTCAGTCCTCTCGCCGCGCACAGTACATCGATGACGGCG\n+>727:3:1:1510:2715/1\n+GTTCCACGTCAGCTGCGGAGCATACGCTGAAGCCAGAGAAGTTGCCGAGCGCGCAATCGTAGCGATACCGGCCTCA\n+>727:3:1:1510:2715/2\n+TCGTACATTGATATGAGCGTCATATGCAAGTGCTTTGCATTGGAAAGCTGGACCGCGCGAGTGAAAAGCTTTTTCA\n+>727:3:1:1510:14260/1\n+AAGGGCACCTACCGAGTGCATGAGCGTTGCGAGCTGCAGACTCTGAGCCTGCGTCTCGACCGTGTTCTCTCGGCTA\n+>727:3:1:1510:14260/2\n+CCCGCCGGTTTGCCGCCTGTGATCGCTCACGCGAACGCCGATGATATGGATGAGAATAGAACAACACCAAGACAAG\n+>727:3:1:1510:8478/1\n+GACCTCGACAGCCTTGAAGTCATGCGTGTGGTGATCTCCCAACCCGCGTGGAGCGAGGAGATGGAAGTGTACTGGG\n+>727:3:1:1510:8478/2\n+TTCCCATCCCTCCATCATCATCTTCAAACTCTTCATCTGGCTCAGGTGTCGGATCATCAACAGGAGGTCCGTCACC\n+>727:3:1:1510:11902/1\n+GGAGCGCAACGTCGCGGACGAGGGTTTGAATTTGCTCTTAGAGATGATGAAGTATTTCCAGCTTTCGGAGTACTGC\n+>727:3:1:1510:11902/2\n+TCAGTTGATCGCTTTCGCTGATAGCAAAGAGATTTTGTAGGATGAGCGCGTGCAGTTTGAAACCCGGTTTGTGGAA\n+>727:3:1:1510:4735/1\n+AATTCATAAGGGCCATGCGGACTTGACGTCATCCTCCCCTTCCTCCTTTATCTCAAAGGCAGTTAGTTCAATGATT\n+>727:3:1:1510:4735/2\n+GACACAACGCGCAAAACCTTACCAATTTTTGACATAGAAAAGAATGCATTCGGTCTGAGTGTGTTTTATTTTCTAC\n+>727:3:1:1510:17184/1\n+CGCGACTCACGGTGTTTTGCTTGATATCTTCGTCCCTCGGTGATTGGACGAAAACCCGAACCACGCGTCCACACTT\n+>727:3:1:1510:17184/2\n+GGCCGCGACGGCTCCGAAGACTGAGACGAGCGATTATGCGAAGAAGGAAGAGACGCGTGCGGATGCGTCTACGGAG\n+>727:3:1:1511:12390/1\n+TTCGACGTGTTGTTCCTCTTGATACTCGTATTCACAGTCCGACGTCGCGGTGTCGTACGCGTCCGATCGCTCGTTT\n+>727:3:1:1511:12390/2\n+TTTGCGCACAGTACGGCGTTCGCGCGCGGCGCGGTGTCACGTGTCGATTCGCTCGGCGCGGCGTTACGTCGAGAAG\n+>727:3:1:1511:18993/1\n+TTTGAAATTATTATGGAAGAAAATTCGTGGAAATACGGCGTCTTCTCGCGTGATTCGTGATTGAAGCGCACGAGTA\n+>727:3:1:1511:18993/2\n+TTGGCGACTTGTTGAACTTGGGCGACGGCGGACATC'..b'7115/1\n+GTCGCTCAGTCGGAGCGCCAACGCGCGGTCGATCCGGCGAGCGAATCCACTCGCGAGCGCCTGCGTCGTCGTCGCG\n+>727:3:1:1800:7115/2\n+GCACGGTACCGATGAATGCACCGGCATTTTCAACATTCCATACATCTTTCACGATGTTGACGACCAGGACGACGAA\n+>727:3:1:1800:1978/1\n+ATTCTCATCCATAAAGCTCGGATCAGTCTCCAGAGTCTTCTCCAACGAGAACGAGTTCACCCCCAACACGACGTTG\n+>727:3:1:1800:1978/2\n+GCGGTGCAGCAGGTGGCGTTCGCGGATCGAATTTTGTTGAATAAGATCGATCTCGTGAGCGAGGAGGAGTTGGAGA\n+>727:3:1:1800:11933/1\n+GTGAACGGTAGGTTCGAGTGGGACCGTCTGCGTAATTTGATCGACATGGCGGGCATCGGAGCCAAGGGGGGCGGCC\n+>727:3:1:1800:11933/2\n+GAACGCGATGGCCAGAAGTACGCACCCGAGGGAGAAGGACTCCTTGATGTGCTCGGCAAGCGAGACCGAACGAAGA\n+>727:3:1:1800:10061/1\n+CATCACGCGCACCGTGCGCGTCCGCGCGCGCGTTCGAGGAGTGCGGCGTCGCGTCGCGAGCGTCGGGGTCGACCGA\n+>727:3:1:1800:10061/2\n+AGTTCCGAACGTCCTGGACGAACACGGTTAACCCCCGCATGCCGCCGAGGAAGGGCGCCATCGCGCGAGACGCGCG\n+>727:3:1:1801:7548/1\n+CGGTCGCGTGCCGGGCGGTGTCCTGGGCGTCCGCTTCGTCGATCGCGTATGTAAACGCGTCTCTGAGAGCGCACCA\n+>727:3:1:1801:7548/2\n+CTCACGGACGCGTGCGATGGTTCCGGGGATGACGCCGAAGACGACCCCGAGCGATCGTCGGCATCCGCGCAGGCAA\n+>727:3:1:1801:16717/1\n+AAAGGAGAAAAGTGCACATGCAGACGATTACAAAATGTCGGATGACGATTTCGATGAAGACGCGGACAGCGACGAA\n+>727:3:1:1801:16717/2\n+GAAATCGCCGATGAGGTATTGGAAGACGAGCGGGCGACCGAGGTCACGATTTGGTGGCCGGCGTCGTTTTGATTCT\n+>727:3:1:1801:8260/1\n+TAAGATCCCGCTAGGATGTGTTGTCATTCCGGAAGACGCGGAAATCCTACCGGCGGACTACAAGCCCGAAGGCCCG\n+>727:3:1:1801:8260/2\n+GCTCCGCTATAGATTTCTTACGTGGCAAACGATTACGAAGCATTTCTTCCATGTTCTTCGCTTCTTCCTCGGACAT\n+>727:3:1:1801:14691/1\n+TCAAAGCGATAAGCCACGCTTGAGTGGTCTTCCTGGCTCGCTCCACTGTGGTCAAGGAGAGATTGTGCCAAACCAC\n+>727:3:1:1801:14691/2\n+GCGTTCGATACGTTCATTAAGATTCGCGACGATTACATCAATAATCAAGCGCCAGCCAGCAGTGCAATCGTGGTTT\n+>727:3:1:1801:8089/1\n+GACGGGTCCAAGGTGGTGATCAGCGAGTTTGCGAGCACGGCGGACATAGAGCGAGCGACGGTGGAGATGTACGCGC\n+>727:3:1:1801:8089/2\n+GTCTAGAGAGGTCAACACGTTGGTCAATCCGCGATAACACGGCTCGAGCGGATGCGCTTTGGACGCGAGCCCGATA\n+>727:3:1:1802:7234/1\n+CGGCGCGCTCGCATAGCATGATTTTTCAATAAAGCAAATGTTTCTCTTCAACGCGCGCTTCGCGGTATCCGCGCCG\n+>727:3:1:1802:7234/2\n+GTGACTAAAAACTCATCGACGACAAAGGGCGGGCACGGGAGCGCGCCGCTCTTCGCTCGCTCGATCGCGGTGGCGA\n+>727:3:1:1802:16027/1\n+CGCCAAGGTTGCCAAGATATAATGTCTCGTGGCGCGGCTTCTGCATCCGCTTTCGACTTCGGGTTAGTGTCTCAGC\n+>727:3:1:1802:16027/2\n+TTCGGGCTTGAGTTCTTTGGAGCAGTCCCAGTATCGATGACCAGGTTCACCACAATTGTAGCACTTTGCTCCCCCT\n+>727:3:1:1802:2336/1\n+TTGTGGCGTACTGGGAAGATGCAGAGCGAACTGATTTACGAGTAAACATGAAGCGAGCGGTCGGCCTTCCGTCGTG\n+>727:3:1:1802:2336/2\n+GTCTCTTCATTGAGATTCCGACACTGCTGTCGACTTGTCGAGAGAAATGACATCCAATGTTCCCACTCTGGAGATG\n+>727:3:1:1802:2722/1\n+GCCACTCCAACGAGTGTCTTCACCGCCACTACGTTCTTTGAGCGCATCTTGTGCGGAATGTGCAAGCTCGTGAACT\n+>727:3:1:1802:2722/2\n+AGCCGATGCTCGAGCTGATTTGGAATCCGATTTTGTCCGTTCTCAGCGCGGCATTTGAAGATAGCGAGAGCGTTTC\n+>727:3:1:1802:1481/1\n+CCAAGGCCGCTGTCACGCGGCTCAGCTTTACAGAAAAGCACCGATTGGAGGAGCTGCCCGCCGTGATGGCCCGGCT\n+>727:3:1:1802:1481/2\n+TCAGCCCTCTGCGCGCTCCGCCAAGGCCAGCCATTCCTCTTCCGCCTCGGCCAGAGCGCTCTGCAGGGGGGCACGC\n+>727:3:1:1802:19981/1\n+AAGAGCGCGTTTAATGACGATAAAATACGTCTGAACATGCCAGCTAATTTCACAACTTACCGCTGACCCAACAACA\n+>727:3:1:1802:19981/2\n+GACCTATGCCACCATGGACGAACATGTGATAAATACAAGGCTTCGTTCGGTGCGTTCGTGTTCTTGAACGATGGCG\n+>727:3:1:1802:3178/1\n+CGCGTTGACTTGGTCACCCGTCATGCAGAACATCAAGTACTCTCTGTACATGGCTTGACGAGTAATGACGTCCATG\n+>727:3:1:1802:3178/2\n+AGCTTCCGCCGAGTCCGAAGAACTCCGATGGGCGGGTGAAACGTCCTCCGAGGCGCCCTCCGAGGAGAAGGAAGAG\n+>727:3:1:1802:4631/1\n+GAGCGGCACAACGCGGCCATTGATGCGACAAACGCTGCGAATGCGCTTTGTCTTACCGTTCGAGTCAACGTACTGC\n+>727:3:1:1802:4631/2\n+GAAGCTGGAGGCGACGTTTCACGTGGCGACAGAGTCGCTGGGTATGATTTATGACGTGGTGAACGATCAAATTACG\n+>727:3:1:1802:16411/1\n+CACCGACGCTGCGGTGTACGTCGGAGAGGGCGCGCCGGGGATCATCCCGGAGGACGATTTGGAGAGTTTAGGGAGC\n+>727:3:1:1802:16411/2\n+GCGTCTGGCGCTATGAATAAAGAGAACAGCGCCATCCGTTTCCATCCGTTCGCGACGCGTTCTGCGCGTTGACTTG\n+>727:3:1:1802:7981/1\n+CGAAGACGCGACATTATCATCTTCGGCCCAAGTGCCTCTGAAAATGACATCAATGTCGACGCGGCTCGGGATCCGA\n+>727:3:1:1802:7981/2\n+CATTGGACTTGCCTCTTTCCCAGGTTGGAGCGAAAGCAACTTTCAGGTGATGGATAAAATGTTTGAAACGTTGGAG\n+>727:3:1:1803:4152/1\n+GTTGCGCTCTCATCAACGCTGCTGCTTGCATCGCCAAACAACTCATCCTCAACCTCTTCCTCGACTTCTTCAACCG\n+>727:3:1:1803:4152/2\n+AGGCGCTCGCCGAGAGCGCCGGTGTCGAGTTGAAACCATTCCCGCAGGTGCGCGACCTCGAGGAGAGTGAGCCGAT\n'

diff -r 000000000000 -r dc70286127fe test-data/lordec/stat_file.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/lordec/stat_file.txt Fri Oct 20 03:15:43 2017 -0400

@@ -0,0 +1,25 @@
+0 6641 -1 6641
+0 2528 -1 2528
+0 1821 -1 1821
+0 11808 -1 11808
+0 6928 -1 6928
+79 6317 61 6134 58 21
+0 6872 -1 6872
+0 6308 -1 6308
+0 1314 -1 1314
+0 10203 -1 10203
+0 6956 -1 6956
+0 3431 -1 3431
+0 7301 -1 7301
+0 3449 -1 3449
+0 4101 -1 4101
+0 2415 -1 2415
+0 2712 -1 2712
+0 4631 -1 4631
+0 1822 -1 1822
+0 8738 -1 8738
+0 6917 -1 6917
+0 3188 -1 3188
+0 10824 -1 10824
+0 7183 -1 7183
+0 3855 -1 3855

diff -r 000000000000 -r dc70286127fe test-data/lordec/trimmed_reads.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/lordec/trimmed_reads.fa Fri Oct 20 03:15:43 2017 -0400

@@ -0,0 +1,4 @@
+>m120131_103014_sidney_c100278822550000001523007907041295_s1_p0/10155
+GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
+GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
+GGGGGGGGGG

diff -r 000000000000 -r dc70286127fe test-data/mapsembler2/assembly.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mapsembler2/assembly.fa Fri Oct 20 03:15:43 2017 -0400

b'@@ -0,0 +1,6 @@\n+>ligne\n+GCTTCCATTGACTCAATGTAGTCACGCGGATGATGACGGAACTGGTTATTCGGGGCATCACAAAATTGCC\n+>left_extension_0\n+TCCGGCCTACAAAATCGCAGCGTGTAGGCCAGATAAGACGCGTCAGCGTCGCATCAGGCGTTACATACCGGATGCGGCTACTTAGCGACGAAACCCGTAATACACTTCGTTCCAGCGCAGCGCGTCTTTAAACGCTGGCAGGCGTGTGTCGTTATCAATCACCGTGATTTCAATGTCGTGCATCTCGGCGAATTGGCGCATATCGTTGAGGTTCAGTGCATGGCTGAAGACGGTATGGTGCGCGCCACCAGCGAGGATCCACGCTTCGGAAGCAGTTGGCAGATCCGGTTGCGCTTTCCACAGCGCATTCGCCACCGGCAGTTTCGGCAGGGAGTGCGGTGTTTTCACCGTGTCGATGCAGTTAACCAGTAGACGGTAACGATCGCCGAGATCAATCAAGCTGGCGACAATCGCTGGGCCGGTTTGGGTATTGAAGATCAGGCGGGCAGGATCGTCCTTACCACCAATACCGAGATGCTGAACGTCGAGGATCGGTTTCTCTTCTGCGGCGATCGACGGGCAGACTTCCAGCATATGGGAGCCGAGCACCAGGTCATTACCTTTCTCGAAGTGATAGGTGTAGTCCTCCATAAAGGAGGTGCCGCCCTGCAGACCGGTTGACATCACCTTCATGATGCGAAGCAGGGCGGCAGTTTTCCAGTCGCCTTCGCCCGCAAAGCCGTAACCCTGCTGCATCAGACGCTGTACGGCCAGACCAGGAAGCTGTTTCAGACCGTGCAAATCTTCAAAGGTGGTGGTGAACGCGTGGAAGCCACCTTGTTCCAGGAAACGCTTCATCCCCAGCTCAATACGCGCCGCTTCCAGCACGTTCTGTCGTTTTTTGCCGTGGATTTGTGTGGCAGGCGTCATGGTGTAGCAGCTTTCGTACTCATCGACCAGCGCGTTAACATCGCCGTCGCTGATGGAGTTCACCACCTGCACCAGATCGCCAACCGCCCAGGTATTGACGGAGAAACCGAACTTGATCTGTGCGGCAACTTTATCGCCATCGGTGACCGCCACTTCACGCATGTTATCGCCAAATCGGCAGACTTTCAGATGACGGGTATCCTGTTTAGAGACCGCCTGACGCATCCAGGAGCCGATACGCTCATGGGCTTGTTTATCCTGCCAGTGACCGGTAACCACGGCATGTTGCTGACGCATACGCGCGCCAATGAAGCCGAACTCGCGACCGCCATGTGCAGTCTGGTTCAGGTTCATAAAGTCCATATCGATACTGTCCCACGGCAGCGCCGCGTTGAACTGGGTGTGGAATTGCAGCAACGGTTTGTTGAGCATGGTCAGGCCGTTGATCCACATTTTGGCCGGGGAGAAGGTGTGCAGCCACACCACCAGACCAGCGCAACGATCGTCGTAATTCGCGTCGCGGCAAATAGCGGTGATTTCATCCGGCGTGGTGCCCAGCGGTTTCAACACCAGTTTGCAGGGCAGTTTCGCTTCCGTATTCAGCGCATTAACGACGTGCTCGGCATGTTGGGTGACCTGACGCAGGGTTTCCGGGCCATACAGATGCTGGCTGCCAATGACAAACCACACTTCATAATTATCAAAAATCGTCATTATCGTGTCCTTATAGAGTCGCAACGGCCTGGGCAGCCTGTGCCGGGGCGGAAGTTGGAAGATAGTGTTGTTCGGCGCTCATCGCCCATTGCTGATAGCGGCGATAAAGCTGTTCAAAGCGTTGTGCCTGCTCGCTGCACGGTTGCAGGGTTTTCTCTACCGCACTGGCCATTTTTTGCTGAGCTGATGGGATGTCTGCGTGCACTTTCGCGGCGACGGCAGCAAAAATCGCCGCACCGAGCGCACAGCACTGGTCAGAGGCAACAATTTGCAGCGGGCGATTCAGCACGTCGCAGCAGGCCTGCATAATGACCTGGTTTTTCCGCGCGATGCCGCCCAGTGCCATCACGTTATTAACGGCGATCCCCTGATCGGTAAAGCACTCCATGATTGCGCGTGCGCCAAAGGCGGTGGCAGCAATCAAACCGCCGAACAGCAGCGGAGCGTCGGTAGCGAGGTTAAGATCGGTAATCACCCCTTTCAGGCGTTGGTTAGCGTTCGGTGTGCGGCGGCCGTTAAACCAGTCGAGCACCACCGGCAGGTGATCCAGAGACGGATTTTTGGCCCATGCTTCGGTCAGCGCCGGAAGCAGTTGTTTCTGGCTGGCGTTGATTTGCGTTTTCAGTTCCGGATGCTGGGCGGCAAGCTGTTCCAGCGGCCAGCCGAGTACGCGACCAAACCAGGCGTAGATATCACCAAACGCCGATTGGCCTGCTTCCAGACCGATAAATCCAGGCACCACGCTGCCATCAACCTGACCGCAAATACCTTTAACTGCCCGCTCGCCAACGCTCTGTTTGTCGGCAATCAGAATGTCGCAGGTGGAAGTACCGATAACTTTTACCAGTGCGTTAGGCTGTGCGCCTGCGCCAACTGCGCCCATATGGCAGTCAAACGCGCCGCCGGAAATCACCACGCTTTCAGGCAGGCCGAGACGCTGCGCCCATTCCGGGCATAAGGTGCCCACCGGAATATCGGCAGTCCAAGTGTCAGTGAACAGCGGGGAAGGCAAATGGCGATTGAGGATCGGGTCCAGCTCATCAAAGAAACTGGCTGGCGGCAGGCCGCCCCAGCTTTCGTGCCACAGAGATTTATGCCCGGCGCTGCAACGTCCGCGACGAATATCCTGCGGGCGGGTGGTACCGGAAAGCAGAGCTGGCACCCAGTCGCACAGCTCAATCCACGATGCGGCAGATTGCGCCACGGCGCTGTCCTGGCGAGTCACATGCAGGATTTTTGCCCAGAACCATTCGCTGGAATAAATACCACCAATGTAGCGGGAGTAGTCAACGTTGCCCGGCGCGTGGCACAAACGGGTAATCTCTTCCGCTTCTTCAACCGCAGTGTGGTCTTTCCACAATACGAACATCGCGTTCGGGTTTTCGGCAAACTCCGGGCGCAGCGCCAGCACGTTTCCGTCGGCATCAATCGGTGCGGGCGTCGAGCCGGTACTGTCAACGCCAATCCCGACCACAGCTGCGCGCTGTTCGACGCTAAGCTCTGCAAGCACGGTTTTCAGTGCCGCTTCCATTGACTCAATGTAGTCACGCGGA\n+>right_extension_0\n+ACTGGTTATTCGGGGCATCACAAAATTGCCCTTTCTGCCAACGGGGATACCACTCTACGCTGGTGGCGATCTCTTCACCGGTAGCGCAGTCCACCGCCAAAGCTCGCACAGAATCACTGCCAAAATCGAGGCCAATTGCAATCGCCATCGTTTCACTCCATCCAAAAAAACGGGTATGGAGAAACAGTAGAGAGTTGCGATAAAAAGCGTCAGGTAGGATCCGCTAATCTTATGGATAAAAATGCTATGGCATAGCAAAGTGTGACGCCGTGCAAATAATCAATGTGGACTTTTCTGCCGTGATTATAGACACTTTTGTTACGCGTTTTTGTCATGGCTTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCGGTTGGGTTAGCGAGAAGAGCCAGTAAAAGACGCAGTGACGGCAATGTCTGATGCAATATGGACAATTGGTTTCTTCTCTGAATGGTGGGAGTATGAAAAGTATGGCTGAAGCGCAAAATGATCCCCTGCTGCCGGGATACTCGTTTAACGCCCATCTGGTGGCGGGTTTAACGCCGATTGAGGCCAACGGTTATCTCGATTTTTTTATCGACCGACCGCTGGGAATGAAAGGTTATATTCTCAATCTCACCATTCGCGGTCAGGGGGTGGTGAAAAATCAGGGACGAGAATTTGTCTGCCGACCGGGTGATATTTTGCTGTTCCCGCCAGGAGAGATTC'..b'ATAGATTGCCAGCTCGATAGTGGTCGCCTGCGGACCGCCCCCCAGCGATAGCACGGTGGCGAAGCTGGCGAAACAGAGCATAAAGATAAGCGCAGCAACCGGCGGGATTTGTCGCCGTAACCACGGCCATTCGACGAAGCGGAAAAAATGCCAGCTACGCATCCCAAGCTGGGCGGCAAGTTGACGCTGTTCGCCGGGGATGTTTTCCAGTGCCTGGAGTAATAAGCGGCTCGCCATCGGCAGATTAAAAAACACATGGGCCAGCAAAATACCTTGCAGGCCGTAGGGCGAAAAGGTCCACTCCAGACCGAGCGATTGGCAGAGTGTTGCCAGCCAGCCCTGGCGACCATAGACGCTAAGAATGCCGAAAACAGCGACCAACACCGGGAGGATCAAGGTCATTGCACACAGACGCAACAGCGCCAGCCGACCCGGAAAGCGCCTGCGATAGAGCGCGCGGGCGAGGAATATCGCGGGTATGACAGAGAGCAGTGCCGAGAGAAACGCCTGCCAGAAGGAGAAGCGCACCACATGCCACAGATAGCTGTCCTGCCAGACTGCCACCCAGTCATCCTGCGGCGCGTTCCACCACAGGGCGAGAAACGCCGCCAGCGCAACCGCTACCACCAGCGTGGTGGCGCTTACACCTGGAATTAACCAGCCGGGAATTAACGGCTGACGGCGCGTTGCCATTCGCTAATCCATGCCTGACGTTGTGCCGCCACTTCGGCTGGCGTGAACTCCAACGTGGTTGCGGGTTTGGTCAATTTTTCAAAACCGGCAGGCAGCGTGACGTTTGCCACCGGATACATCCAGTTGCCGGTTGGGATCGCATTCTGGAAAGCCGGAGAAACCATAAACTGGAGGAATTTTTGCGCCAGCTCCGGCTGCTTGCTGGCAGCGGTGCGGGCGGCGACTTCCACTTGCAGATAGTGACCTTCGCTGAAGTTCGCGGCGGCGTAGTTATCTTTCTTCTCTTCGAGAATGTGATAAGCCGGAGAGGTGGTGTAACTCAGTACCAGATCGCTTTCACCTTTTAAAAACAGGCCGTAGGCTTCGCTCCAGCCTTTGGTGACCGTGACCGTTTTCTTCGCCAGTTTCTGCCAGGCTTGTGGGGCGTCATCGCCATAGACTTTTTGCATCCATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGTCATTATTCCAGCCGCCGGGAACGTTAACGGCATCCGCTGCCACACCGCTTTTGGCAAACAGTCCGGTTTTACTGGCGGCGTCTAACAGGTTGTTATCCAGCCCCAGCACCACATCGGCTTTACTGTTTTTGCCTTCCATCCGTAGACGGTTGAGAAGCGAAACGCCATCTTCCAGCGCCACCAGTTTCAGTTCGCAATTACAGTCGGCTTCAAAGGCTTTTTTAACCACCGGACCAGGCCCCCAGTCGGCGGCGAAGGAATCGTAGGTATAAACAGTCAGAACGGGTTTAGCGAAAACGGGCGCTGTGCACAGCAACAGCAGGGGCAGACATTTTTTTAACACTTTGCACCTCAAAAAAGAGTGGCAAAGGACTTGAGAAGGAGCCTCAAATCCCTTCGCCGGCGTTATCCGGATCAGGTTCGACGGGTATTTTCTCAGCGCACGCGTACGCGTGGCACCCCGTTGAGAACGGCGTTAGTGTAGTGATTTTGTTATCAACCAGCAATCATGGATCCGGTGGCGCAAACCACGCTGATTTAAAATCGAACCAGCCGAGGGTATTCATGCGCAGGCCGCGCATACTGCGTTGCCCCTGAATGATCAGCCAGTGGTGCAATAATGGCACCATCGCTTTGCTGGCGACCAGTTGCTGGCACCAGTTCGCCAGATTCATCTCGCCATTGCGCCAGCGAGCAGCGTCGGCTTGCCAGTCAATGGGAATGCAATGTTGTAGCAGTGGCACTTCGCATAAATGTGCGAAAACAGAGAAGTCCAGCGGCAGGGTAAAGTTGGCGCTGTTTAGCCAGATATCACTTTCGATCTCTCCTGTATGCCACTGATCGTAGTCGATCTCTTTGATTTTCAGCGTGACCTGGTGACTTGCCAGAATCTGCTGCATGATCCCGGCAATCACCCGATGCTCACTGTGATCCTGATAAAAGGTTAGGGTGAGGCTTTCCAGGCCAGCCGGTTTTTCGCTCTTTATGGTGCGGGCATGGTGCCAACGGGGGAGCAGTCCATAAGCCGGGAACCACAGTTGCTGGTACTGTTCCTCAGCGAAATAGACCAGATTAGTTGGAGAAAGCACATAGCTTACCCAGTCCCTGACTTGCTGATTCGCCCCGCGATGGGTGCGGCTGTCGAACAGTAAATAGTAGCAACCTTCCTCCAGGCGGCTTTCAATCTCTTTTTCCTCGCCCTGTGGACCTTTTAGCATCAGCCCTCCGGCTGGCTCGTCGGCAATTTCCGGCAGAACCCAGACGTTAACTTCGTCGATTAATGCCCGGTAACCGAAGAAGTCATCGAATGCCTGAATTTTCAGTTGATTGGTGCTGTTGCGAATCACCGCATACGGACCGGTGCCGATGGGATGGCTGGCAAAGTTACTGAGGGTTTCCCATTCGCGCGGCAGGATCATCGCCGGAACTTGCCCCAGCAGTAACGGTAACCAGCGGTCCGGTTGCGTGAGATGGATATCCAGCGTCCAGGGCGTCGGCGACACAATGTCAGCAATATGCGAATAGAGCGGCAGCGTATTGATTCGTTTTAAAGAGGCGATCACATCGTCCATTTCCAGTTCACGACCATGGTGAAAATGGACTCCTGGACGCAAAAAGAAACGCCAGTGAAGCGGTGAAATTTGCTGCCAGTGGTGGGCGATGTCTGCTTCCAGTTCCCCATTTTCCTCATTTATGCGCGTTAGCGAACTGAAGATTTGCCGGGCGATATGGGTTTCGGAACGGCGCAATGCGCTGCCAGGTAGCAGATTACGCAACGGACGATAGTAGAGCACGCGCAGGATGTGCCGCCCCTGGCGGAAGCTGCGGCCCAGATGAGAAACCAGCATTTGCCGCACAGTCGCTTTGTCGCCAACCAACTGCACCAGTTGATCGATACGATCCTGCTCCAGCAGGTCTTCCGCCCGCTGTTGCTGAAGCGCCAGCCCGGTATAGAGGAATGTCAGACGCGAGCGTTTACCGCGCCCGACTTCCGCTTCCCACGTCAGCCAGCCGCGATCCTGCATGGTGTTGAGCAGGGTGCGCATATGACGACGCGAGCAGCTCAATAACGCTGCCAGTTCGTTGAGCGTTGTGTCCTGCGATTTACCCTCGCAGCATTGCCACAGGCGGATGAACTGTTGTTGCAGACGAGCAGATGGCATAAAAGGGGAACTCCTGTGCAAAAGACAGCAATTTTATTTTCCCTATATTAAGTCAATAATTCCTAACGATGAAGCAAGGGGGTGCCCCATGCGTCAGTTTTATCAGCACTATTTTACCGCGACAGCGAAGTTGTGCTGGTTGCGTTGGTTAAGCGTCCCACAACGATTAACCATGCTTGAAGGACTGATGCAGTGGGATGACCGCAATTCTGAAAGTTGACTTGCCTGCATCATGTGTGACTGAGTATTGGTGTAAAATCACCCGCCAGCAGATTATACCTGCTGGTTTTTTTTATTCTCGCCGCGCTAAAAAGGGAACGTATGATCTGGATAATGACGATGGCTCGCCGTATGAACGGTGTTTACGCGGCATTTATGCTGGTCGCTTTTATGATGGGGGTGGCCGGGGCGCTACAGGCTCCTACATTGAGCTTATTTCTGAGTCGTGAGGTTGGCGCGCAACCTTTCTGGATCGGCCTCTTTTATACGGTGAATGCTATTGCTGGGATCGGCGTAAGCCTCTGGTT\n'

diff -r 000000000000 -r dc70286127fe test-data/mapsembler2/assembly_2.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mapsembler2/assembly_2.fa Fri Oct 20 03:15:43 2017 -0400

@@ -0,0 +1,6 @@
+>ligne
+GCTTCCATTGACTCAATGTAGTCACGCGGATGATGACGGAACTGGTTATTCGGGGCATCACAAAATTGCC
+>left_extension_0
+TCCGGCCTACAAAATCGCAGCGTGTAGGCCAGATAAGACGCGTCAGCGTCGCATCAGGCGTTACATACCGGATGCGGCTACTTAGCGACGAAACCCGTAATACACTTCGTTCCAGCGCAGCGCGTCTTTAAACGCTGGCAGGCGTGTGTCGTTATCAATCACCGTGATTTCAATGTCGTGCATCTCGGCGAATTGGCGCATATCGTTGAGGTTCAGTGCATGGCTGAAGACGGTATGGTGCGCGCCACCAGCGAGGATCCACGCTTCGGAAGCAGTTGGCAGATCCGGTTGCGCTTTCCACAGCGCATTCGCCACCGGCAGTTTCGGCAGGGAGTGCGGTGTTTTCACCGTGTCGATGCAGTTAACCAGTAGACGGTAACGATCGCCGAGATCAATCAAGCTGGCGACAATCGCTGGGCCGGTTTGGGTATTGAAGATCAGGCGGGCAGGATCGTCCTTACCACCAATACCGAGATGCTGAACGTCGAGGATCGGTTTCTCTTCTGCGGCGATCGACGGGCAGACTTCCAGCATATGGGAGCCGAGCACCAGGTCATTACCTTTCTCGAAGTGATAGGTGTAGTCCTCCATAAAGGAGGTGCCGCCCTGCAGACCGGTTGACATCACCTTCATGATGCGAAGCAGGGCGGCAGTTTTCCAGTCGCCTTCGCCCGCAAAGCCGTAACCCTGCTGCATCAGACGCTGTACGGCCAGACCAGGAAGCTGTTTCAGACCGTGCAAATCTTCAAAGGTGGTGGTGAACGCGTGGAAGCCACCTTGTTCCAGGAAACGCTTCATCCCCAGCTCAATACGCGCCGCTTCCAGCACGTTCTGTCGTTTTTTGCCGTGGATTTGTGTGGCAGGCGTCATGGTGTAGCAGCTTTCGTACTCATCGACCAGCGCGTTAACATCGCCGTCGCTGATGGAGTTCACCACCTGCACCAGATCGCCAACCGCCCAGGTATTGACGGAGAAACCGAACTTGATCTGTGCGGCAACTTTATCGCCATCGGTGACCGCCACTTCACGCATGTTATCGCCAAATCGGCAGACTTTCAGATGACGGGTATCCTGTTTAGAGACCGCCTGACGCATCCAGGAGCCGATACGCTCATGGGCTTGTTTATCCTGCCAGTGACCGGTAACCACGGCATGTTGCTGACGCATACGCGCGCCAATGAAGCCGAACTCGCGACCGCCATGTGCAGTCTGGTTCAGGTTCATAAAGTCCATATCGATACTGTCCCACGGCAGCGCCGCGTTGAACTGGGTGTGGAATTGCAGCAACGGTTTGTTGAGCATGGTCAGGCCGTTGATCCACATTTTGGCCGGGGAGAAGGTGTGCAGCCACACCACCAGACCAGCGCAACGATCGTCGTAATTCGCGTCGCGGCAAATAGCGGTGATTTCATCCGGCGTGGTGCCCAGCGGTTTCAACACCAGTTTGCAGGGCAGTTTCGCTTCCGTATTCAGCGCATTAACGACGTGCTCGGCATGTTGGGTGACCTGACGCAGGGTTTCCGGGCCATACAGATGCTGGCTGCCAATGACAAACCACACTTCATAATTATCAAAAATCGTCATTATCGTGTCCTTATAGAGTCGCAACGGCCTGGGCAGCCTGTGCCGGGGCGGAAGTTGGAAGATAGTGTTGTTCGGCGCTCATCGCCCATTGCTGATAGCGGCGATAAAGCTGTTCAAAGCGTTGTGCCTGCTCGCTGCACGGTTGCAGGGTTTTCTCTACCGCACTGGCCATTTTTTGCTGAGCTGATGGGATGTCTGCGTGCACTTTCGCGGCGACGGCAGCAAAAATCGCCGCACCGAGCGCACAGCACTGGTCAGAGGCAACAATTTGCAGCGGGCGATTCAGCACGTCGCAGCAGGCCTGCATAATGACCTGGTTTTTCCGCGCGATGCCGCCCAGTGCCATCACGTTATTAACGGCGATCCCCTGATCGGTAAAGCACTCCATGATTGCGCGTGCGCCAAAGGCGGTGGCAGCAATCAAACCGCCGAACAGCAGCGGAGCGTCGGTAGCGAGGTTAAGATCGGTAATCACCCCTTTCAGGCGTTGGTTAGCGTTCGGTGTGCGGCGGCCGTTAAACCAGTCGAGCACCACCGGCAGGTGATCCAGAGACGGATTTTTGGCCCATGCTTCGGTCAGCGCCGGAAGCAGTTGTTTCTGGCTGGCGTTGATTTGCGTTTTCAGTTCCGGATGCTGGGCGGCAAGCTGTTCCAGCGGCCAGCCGAGTACGCGACCAAACCAGGCGTAGATATCACCAAACGCCGATTGGCCTGCTTCCAGACCGATAAATCCAGGCACCACGCTGCCATCAACCTGACCGCAAATACCTTTAACTGCCCGCTCGCCAACGCTCTGTTTGTCGGCAATCAGAATGTCGCAGGTGGAAGTACCGATAACTTTTACCAGTGCGTTAGGCTGTGCGCCTGCGCCAACTGCGCCCATATGGCAGTCAAACGCGCCGCCGGAAATCACCACGCTTTCAGGCAGGCCGAGACGCTGCGCCCATTCCGGGCATAAGGTGCCCACCGGAATATCGGCAGTCCAAGTGTCAGTGAACAGCGGGGAAGGCAAATGGCGATTGAGGATCGGGTCCAGCTCATCAAAGAAACTGGCTGGCGGCAGGCCGCCCCAGCTTTCGTGCCACAGAGATTTATGCCCGGCGCTGCAACGTCCGCGACGAATATCCTGCGGGCGGGTGGTACCGGAAAGCAGAGCTGGCACCCAGTCGCACAGCTCAATCCACGATGCGGCAGATTGCGCCACGGCGCTGTCCTGGCGAGTCACATGCAGGATTTTTGCCCAGAACCATTCGCTGGAATAAATACCACCAATGTAGCGGGAGTAGTCAACGTTGCCCGGCGCGTGGCACAAACGGGTAATCTCTTCCGCTTCTTCAACCGCAGTGTGGTCTTTCCACAATACGAACATCGCGTTCGGGTTTTCGGCAAACTCCGGGCGCAGCGCCAGCACGTTTCCGTCGGCATCAATCGGTGCGGGCGTCGAGCCGGTACTGTCAACGCCAATCCCGACCACAGCTGCGCGCTGTTCGACGCTAAGCTCTGCAAGCACGGTTTTCAGTGCCGCTTCCATTGACTCAATGTAGTCACGCGGA
+>right_extension_0
+ACTGGTTATTCGGGGCATCACAAAATTGCCCTTTCTGCCAACGGGGATACCACTCTACGCTGGTGGCGATCTCTTCACCGGTAGCGCAGTCCACCGCCAAAGCTCGCACAGAATCACTGCCAAAATCGAGGCCAATTGCAATCGCCATCGTTTCACTCCATCCAAAAAAACGGGTATGGAGAAACAGTAGAGAGTTGCGATAAAAAGCGTCAGGTAGGATCCGCTAATCTTATGGATAAA

diff -r 000000000000 -r dc70286127fe test-data/mapsembler2/coherent.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mapsembler2/coherent.fa Fri Oct 20 03:15:43 2017 -0400

@@ -0,0 +1,6 @@
+>ligne|C1_40|C2_38|
+GCTTCCATTGACTCAATGTAGTCACGCGGATGATGACGGAACTGGTTATTCGGGGCATCACAAAATTGCC
+>left_extension_0|C1_950|C2_969|
+TCCGGCCTACAAAATCGCAGCGTGTAGGCCAGATAAGACGCGTCAGCGTCGCATCAGGCGTTACATACCGGATGCGGCTACTTAGCGACGAAACCCGTAATACACTTCGTTCCAGCGCAGCGCGTCTTTAAACGCTGGCAGGCGTGTGTCGTTATCAATCACCGTGATTTCAATGTCGTGCATCTCGGCGAATTGGCGCATATCGTTGAGGTTCAGTGCATGGCTGAAGACGGTATGGTGCGCGCCACCAGCGAGGATCCACGCTTCGGAAGCAGTTGGCAGATCCGGTTGCGCTTTCCACAGCGCATTCGCCACCGGCAGTTTCGGCAGGGAGTGCGGTGTTTTCACCGTGTCGATGCAGTTAACCAGTAGACGGTAACGATCGCCGAGATCAATCAAGCTGGCGACAATCGCTGGGCCGGTTTGGGTATTGAAGATCAGGCGGGCAGGATCGTCCTTACCACCAATACCGAGATGCTGAACGTCGAGGATCGGTTTCTCTTCTGCGGCGATCGACGGGCAGACTTCCAGCATATGGGAGCCGAGCACCAGGTCATTACCTTTCTCGAAGTGATAGGTGTAGTCCTCCATAAAGGAGGTGCCGCCCTGCAGACCGGTTGACATCACCTTCATGATGCGAAGCAGGGCGGCAGTTTTCCAGTCGCCTTCGCCCGCAAAGCCGTAACCCTGCTGCATCAGACGCTGTACGGCCAGACCAGGAAGCTGTTTCAGACCGTGCAAATCTTCAAAGGTGGTGGTGAACGCGTGGAAGCCACCTTGTTCCAGGAAACGCTTCATCCCCAGCTCAATACGCGCCGCTTCCAGCACGTTCTGTCGTTTTTTGCCGTGGATTTGTGTGGCAGGCGTCATGGTGTAGCAGCTTTCGTACTCATCGACCAGCGCGTTAACATCGCCGTCGCTGATGGAGTTCACCACCTGCACCAGATCGCCAACCGCCCAGGTATTGACGGAGAAACCGAACTTGATCTGTGCGGCAACTTTATCGCCATCGGTGACCGCCACTTCACGCATGTTATCGCCAAATCGGCAGACTTTCAGATGACGGGTATCCTGTTTAGAGACCGCCTGACGCATCCAGGAGCCGATACGCTCATGGGCTTGTTTATCCTGCCAGTGACCGGTAACCACGGCATGTTGCTGACGCATACGCGCGCCAATGAAGCCGAACTCGCGACCGCCATGTGCAGTCTGGTTCAGGTTCATAAAGTCCATATCGATACTGTCCCACGGCAGCGCCGCGTTGAACTGGGTGTGGAATTGCAGCAACGGTTTGTTGAGCATGGTCAGGCCGTTGATCCACATTTTGGCCGGGGAGAAGGTGTGCAGCCACACCACCAGACCAGCGCAACGATCGTCGTAATTCGCGTCGCGGCAAATAGCGGTGATTTCATCCGGCGTGGTGCCCAGCGGTTTCAACACCAGTTTGCAGGGCAGTTTCGCTTCCGTATTCAGCGCATTAACGACGTGCTCGGCATGTTGGGTGACCTGACGCAGGGTTTCCGGGCCATACAGATGCTGGCTGCCAATGACAAACCACACTTCATAATTATCAAAAATCGTCATTATCGTGTCCTTATAGAGTCGCAACGGCCTGGGCAGCCTGTGCCGGGGCGGAAGTTGGAAGATAGTGTTGTTCGGCGCTCATCGCCCATTGCTGATAGCGGCGATAAAGCTGTTCAAAGCGTTGTGCCTGCTCGCTGCACGGTTGCAGGGTTTTCTCTACCGCACTGGCCATTTTTTGCTGAGCTGATGGGATGTCTGCGTGCACTTTCGCGGCGACGGCAGCAAAAATCGCCGCACCGAGCGCACAGCACTGGTCAGAGGCAACAATTTGCAGCGGGCGATTCAGCACGTCGCAGCAGGCCTGCATAATGACCTGGTTTTTCCGCGCGATGCCGCCCAGTGCCATCACGTTATTAACGGCGATCCCCTGATCGGTAAAGCACTCCATGATTGCGCGTGCGCCAAAGGCGGTGGCAGCAATCAAACCGCCGAACAGCAGCGGAGCGTCGGTAGCGAGGTTAAGATCGGTAATCACCCCTTTCAGGCGTTGGTTAGCGTTCGGTGTGCGGCGGCCGTTAAACCAGTCGAGCACCACCGGCAGGTGATCCAGAGACGGATTTTTGGCCCATGCTTCGGTCAGCGCCGGAAGCAGTTGTTTCTGGCTGGCGTTGATTTGCGTTTTCAGTTCCGGATGCTGGGCGGCAAGCTGTTCCAGCGGCCAGCCGAGTACGCGACCAAACCAGGCGTAGATATCACCAAACGCCGATTGGCCTGCTTCCAGACCGATAAATCCAGGCACCACGCTGCCATCAACCTGACCGCAAATACCTTTAACTGCCCGCTCGCCAACGCTCTGTTTGTCGGCAATCAGAATGTCGCAGGTGGAAGTACCGATAACTTTTACCAGTGCGTTAGGCTGTGCGCCTGCGCCAACTGCGCCCATATGGCAGTCAAACGCGCCGCCGGAAATCACCACGCTTTCAGGCAGGCCGAGACGCTGCGCCCATTCCGGGCATAAGGTGCCCACCGGAATATCGGCAGTCCAAGTGTCAGTGAACAGCGGGGAAGGCAAATGGCGATTGAGGATCGGGTCCAGCTCATCAAAGAAACTGGCTGGCGGCAGGCCGCCCCAGCTTTCGTGCCACAGAGATTTATGCCCGGCGCTGCAACGTCCGCGACGAATATCCTGCGGGCGGGTGGTACCGGAAAGCAGAGCTGGCACCCAGTCGCACAGCTCAATCCACGATGCGGCAGATTGCGCCACGGCGCTGTCCTGGCGAGTCACATGCAGGATTTTTGCCCAGAACCATTCGCTGGAATAAATACCACCAATGTAGCGGGAGTAGTCAACGTTGCCCGGCGCGTGGCACAAACGGGTAATCTCTTCCGCTTCTTCAACCGCAGTGTGGTCTTTCCACAATACGAACATCGCGTTCGGGTTTTCGGCAAACTCCGGGCGCAGCGCCAGCACGTTTCCGTCGGCATCAATCGGTGCGGGCGTCGAGCCGGTACTGTCAACGCCAATCCCGACCACAGCTGCGCGCTGTTCGACGCTAAGCTCTGCAAGCACGGTTTTCAGTGCCGCTTCCATTGACTCAATGTAGTCACGCGGA
+>right_extension_0|C1_100|C2_104|
+ACTGGTTATTCGGGGCATCACAAAATTGCCCTTTCTGCCAACGGGGATACCACTCTACGCTGGTGGCGATCTCTTCACCGGTAGCGCAGTCCACCGCCAAAGCTCGCACAGAATCACTGCCAAAATCGAGGCCAATTGCAATCGCCATCGTTTCACTCCATCCAAAAAAACGGGTATGGAGAAACAGTAGAGAGTTGCGATAAAAAGCGTCAGGTAGGATCCGCTAATCTTATGGATAAA

diff -r 000000000000 -r dc70286127fe test-data/mapsembler2/reads1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mapsembler2/reads1 Fri Oct 20 03:15:43 2017 -0400

b'@@ -0,0 +1,12884 @@\n+>read0_contig1_position14664_M0_I0_D0_NG0______er0.01__indel0__rgeom0_rev0\n+CTTCGTCGATTAATGCCCGGTAACCGAAGAAGTCATCGAATGCCTGAATTTTCAGTTGATTGGTGCTGTTGCGAATCACCGCATACGGACCGGTGCCGAT\n+>read1_contig0_position10342_M2_I0_D0_NG0______er0.01__indel0__rgeom0_rev0\n+ATCGATATTTTGGGTAAAGTGGTTGGGGTTTAGGAGATAGTCTTGTGCGGGTGGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACAAAACGCACT\n+>read2_contig0_position8799_M1_I0_D0_NG0______er0.01__indel0__rgeom0_rev1\n+GACGACCGTAGTGATGAATCTCTCCTGGCGGGAACAGCAAAATATCACCCGGTCGGCAGACAAATTCTCGTCCCTGATTATTCACCACCCCCTGACCGCG\n+>read3_contig0_position10136_M1_I0_D0_NG0______er0.01__indel0__rgeom0_rev1\n+CTCAAACGGTCAGTCGCTTTACCGCTGCGCCAAAACCGCCAGCACAGCCAGCCACCAACCCACAAAAACACCGCTGTTGCCAGCAGCAACCATTTAAACT\n+>read4_contig0_position8407_M1_I0_D0_NG0______er0.01__indel0__rgeom0_rev0\n+TGGCATAGCAAAGTGTGACGCCGTTCAAATAATCAATGTGGACTTTTCTGCCGTGATTATAGACACTTTTGTTACGCGTTTTTGTCATGGCTTTGGTCCC\n+>read5_contig0_position12476_M2_I0_D0_NG0______er0.01__indel0__rgeom0_rev1\n+TCTCTGTCATACCCGCGATATTCCTCGCCCGCGCGCTCTATCGCAGGCGCTTTCCGGGTCGGCTGGCGCTGTTGCGTCTGTGTGCAATGACCATGATCGT\n+>read6_contig1_position3130_M2_I0_D0_NG0______er0.01__indel0__rgeom0_rev0\n+CTTCGCCTAATAGCTCCTGAGCGGCAGTTTCCAGCGAGAATGAAGAGAAATTCCAGAACGCGGATTTCAGCGCCTCTATACCGTCGATAATTAGCCGACC\n+>read7_contig1_position6683_M0_I0_D0_NG0______er0.01__indel0__rgeom0_rev1\n+CAGCTCAGCAAAAAATGGCCAGTGCGGTAGAGAAAACCCTGCAACCGTGCAGCGAGCAGGCACAACGCTTTGAACAGCTTTATCGCCGCTATCAGCAATG\n+>read8_contig1_position11390_M0_I0_D0_NG0______er0.01__indel0__rgeom0_rev0\n+TGCGCCAGTGGACGTTTCAGGGCGCGCAGCTCCACCACTTTTAAGCGTGACCAGCCTTCAATCCCCAGCGACTGACATAACATGCTGTAGCGGGCGGTGA\n+>read9_contig1_position7205_M1_I0_D0_NG0______er0.01__indel0__rgeom0_rev1\n+AATCGGCGTTTGGTGATATCTACGCCTGGTTTGGTCGCGTACTCGGCTGGCCGCTGGAACAGCTTGCCGCCCAGTATCCGGAACTGAAAACGCAAATCAA\n+>read10_contig1_position110_M1_I0_D0_NG0______er0.01__indel0__rgeom0_rev0\n+GCTCCGGGTAGAGCATATCGCGAGCACGATCTTCCGCACTTTTACGTGCGCCCATAATGCCGGAGACTTTAATAGCCGTCTCATACTGCGTCGGTAGCGG\n+>read11_contig1_position9406_M1_I0_D0_NG0______er0.01__indel0__rgeom0_rev0\n+GTTTTGACGATCAACTCTATTTCTCGCGATTATTTAAAAAATGCACCGGGGCCAGCCCGAGCGAGTTTCGTGCCGGTTGTGAAGAAAAAGTGAATGATGT\n+>read12_contig1_position1158_M1_I0_D0_NG0______er0.01__indel0__rgeom0_rev1\n+TACTGAAGAGTCCGGCGTAGCCCTGCGTGAGGTTTTCCTTGATAGCAAACTGGTGTTCAGCAAACCGCAGGACCGTCTGTTTGCCGGGCAGATTGACCGT\n+>read13_contig0_position10684_M1_I0_D0_NG0______er0.01__indel0__rgeom0_rev0\n+ATCTCCTGACGTAACGCCGGATCGAGCGCAGAGAACGGTTCATCGAGAAATAAAATCGGCTGTTCGCGTACCAGACAACGCGCTAACGCCACTCGCTGTC\n+>read14_contig0_position12413_M2_I0_D0_NG0______er0.01__indel0__rgeom0_rev1\n+TGGCGCTGTTGCGTCTGTGTGCAATGACCTTGATCCTCCCGGTGTTGGTCGCTGTTTTCGGCAATCTTAGCGTCTATGGTCGCCAGGGCTGGGTGGCAAC\n+>read15_contig1_position15972_M0_I0_D0_NG0______er0.01__indel0__rgeom0_rev0\n+ACAGGCTCCTACATTGAGCTTATTTCTGAGTCGTGAGGTTGGCGCGCAACCTTTCTGGATCGGCCTCTTTTATACGGTGAATGCTATTGCTGGGATCGGC\n+>read16_contig0_position7126_M1_I0_D0_NG0______er0.01__indel0__rgeom0_rev1\n+GGAACTGAAAACGCAAATCAACGCCAGCCAGAAACAACTGCCTCCGGCGCTGACCGAAGCATGGGCCAAAAATCCGTCTCTGGATCACCTGCCGGTGGTG\n+>read17_contig1_position5666_M1_I0_D0_NG0______er0.01__indel0__rgeom0_rev0\n+TTTTCCAGTCGCCTTCGCCCGCAAAGCCGTAACCTTGCTGCATCAGACGCTGTACGGCCAGACCAGGAAGCTGTTTCAGACCGTGCAAATCTTCAAAGGT\n+>read18_contig0_position12826_M1_I0_D0_NG0______er0.01__indel0__rgeom0_rev0\n+AACTCCAACGTGGTTGCGGGTTTGGTCAATTTTTCAAAACCGGCAGGCAGCGTGAAGTTTGCCACCGGATACATCCAGTTGCCGGTTGGGATCGCATTCT\n+>read19_contig0_position4126_M2_I0_D0_NG0______er0.01__indel0__rgeom0_rev1\n+TATGGGGATATTCTGCCGTCAGTTAGCGCTGCAGTTACCGGATATGTAGCAAACGCTGCTGGATAAACACTATCTGCGTAAGCATGGCGCGAAGGCATAT\n+>read20_contig0_position102_M1_I0_D0_NG0______er0.01__indel0__rgeom0_rev0\n+ATAAATACGCTCCGGGTAGAGCATATCGCGAGCACGATCTTCCGCACTTTTACGTGCGCCCATAATGCCGGAGACTTTAATACCCGTCTGATACTGCGTC\n+>read21_contig1_position3958_M1_I0_D0_NG0______er0.01__indel0__rgeom0_rev1\n+TTTTGATGGATTTTCAGCGTGGCGCAGGCAGGTTTTATCTTAACCCGACACTGGCAGGACACCCCGCAAGGGACAGAAGTCTCCTTCTGGCTGGCGACGG\n+>read22_contig0_position15934_M1_I0_D0_NG0______er0.01__indel0__r'..b'GGCGATTGCAATTGGCCTCGATTTTGGCAGT\n+>read6420_contig1_position13892_M1_I0_D0_NG0______er0.01__indel0__rgeom0_rev1\n+AGGAGCAACGCAGTATGCGCGGCCTGCGCATGAATACCCTCGGCTGGTTCGATTTTAAATCAGCGTGGTTTGCGCCACCGGATCCATGATTGCTGGTTGA\n+>read6421_contig0_position7764_M3_I0_D0_NG0______er0.01__indel0__rgeom0_rev0\n+CGCACAGCTCAATCCACGATGCGGCAGATTGCGCCAGGGCGCTGTCCTGGCGAGTCACATGCAGGATTTTTGCCCAGAACCTTTCGCTGGGATAAATACC\n+>read6422_contig1_position9921_M0_I0_D0_NG0______er0.01__indel0__rgeom0_rev0\n+GTTGCATCAACACAGCATGTTCACCATTCTGGTCGGTCGTTTTGTTGGCCCGACGCGTCCGCTGGTGCCAATGGTGGCGGGAATGCTGGATCTGCCGGTG\n+>read6423_contig1_position9241_M4_I0_D0_NG0______er0.01__indel0__rgeom0_rev1\n+ATGCGTTGGTCCTCGCGCCAGCTTAAGGCGCTAATCCCTCACTGCTGGCGGAAAAAATGTGACAGACGCGACCGCGACAAGCAAACATGCTGTGCGACGC\n+>read6424_contig0_position1714_M1_I0_D0_NG0______er0.01__indel0__rgeom0_rev1\n+CAACGTTCACCACTGGATTACGAACACTATCTGACCCGCCAGCTACAACCCGTGGCGGAGGGAATACTCCCTTTTATTGAGGATAATCTTGCTACACTTA\n+>read6425_contig0_position739_M1_I0_D0_NG0______er0.01__indel0__rgeom0_rev1\n+TATTTGATGATGAGCGTTAAGCCGAAGCTCAGCACGATGCTTACAACCCGTTTGACACCGAACAGCTGGTGATTTGCTCGCTGGATTTTGCCCGTCGTAG\n+>read6426_contig0_position12819_M0_I0_D0_NG0______er0.01__indel0__rgeom0_rev1\n+GATCCCAACCGGCAACTGGATGTATCCGGTGGCAAACGTCACGCTGCCTGCCGGTTTTGAAAAATTGACCAAACCCGCAACCACGTTGGAGTTCACGCCA\n+>read6427_contig0_position11597_M1_I0_D0_NG0______er0.01__indel0__rgeom0_rev0\n+TTGAGCAGTAAAAAGAAGCCGGTAGCCACCACAATCCCCGGCATGGCGAGGATCAACATGCCGCTCATCTCCAGCACCTGACCCGCCAGCATTTTCTGCC\n+>read6428_contig0_position11251_M3_I0_D0_NG0______er0.01__indel0__rgeom0_rev0\n+GGTGACCGCACCGTCCTGGCTGCGATAGGAGCCAATGTGCTGGTTGACATAAAACGGCAGGGTGCGGAAATCATCGTTACCGAACAACGCCACCACGCCA\n+>read6429_contig0_position15510_M2_I0_D0_NG0______er0.01__indel0__rgeom0_rev0\n+ACCATTGCCACGGGCGGATGAACTGTTGTTGCAGACGAGCAGATGGCATAAAAGGGGAACTCCTGTGCAAAAGACAGCAATTTTATTTTCCCTATATTAA\n+>read6430_contig1_position1369_M1_I0_D0_NG0______er0.01__indel0__rgeom0_rev1\n+TTGGAACCGTTGTCGCGGTGGATGCGCGAGCTGTCACTTTACTTTTCCCATCTACTGGTGAAAACCGTCTGTACGCACGCAGTGATTCCCCCGTGACCCG\n+>read6431_contig1_position15805_M0_I0_D0_NG0______er0.01__indel0__rgeom0_rev0\n+ATTGGTGTAAAATCACCCGCCAGCAGATTATACCTGCTGGTTTTTTTTATTCTCGCCGCGCTAAAAAGGGAACGTATGATCTGGATAATGACGATGGCTC\n+>read6432_contig1_position7392_M1_I0_D0_NG0______er0.01__indel0__rgeom0_rev0\n+GTTTGTCGGCAATCAGAATGTCGCAGGTGGAAGTACCTATAACTTTTACCAGTGCGTTAGGCTGTGCGCCTGCGCCAACTGCGCCCATATGGCAGTCAAA\n+>read6433_contig0_position8629_M2_I0_D0_NG0______er0.01__indel0__rgeom0_rev0\n+GTGGGAGTATGAAAAGAATGGCTGAAGCGCAAAATGATCCCCTGCTGCCGGGATACTAGTTTAACGCCCATCTGGTGGCGGGTTTAACGCCGATTGAGGC\n+>read6434_contig1_position4112_M0_I0_D0_NG0______er0.01__indel0__rgeom0_rev1\n+GCCGTCAGTTAGCGCCGCAGTTACCGGATATGCAGCAAACGCTGCTGGATAAACACTATCTGCGTAAGCATGGCGCGAAGGCATATTACGGGCAGTAATG\n+>read6435_contig1_position14366_M2_I0_D0_NG0______er0.01__indel0__rgeom0_rev1\n+TGGTCTATTTCGCTGAGGAACAGTACCAGCGACTGTGGCTCCCGGCTTATGGACTGCTCCCCCGTTGGCACCATGCCCGCACCATAAAGAGCGAAAAACC\n+>read6436_contig1_position3225_M1_I0_D0_NG0______er0.01__indel0__rgeom0_rev0\n+CGACCTTTAGCCTGGGCGAAAAAGACGCCGTTTTTAAAGCCGTGCTCGCGCCACTCCAGCTCGCTATTATCGCGCCCAAGACGCAGCGGAAGACGGTAAC\n+>read6437_contig1_position4776_M1_I0_D0_NG0______er0.01__indel0__rgeom0_rev0\n+CTTCTATTACCTGGCGTTTGAGATCTTCTAACATGTTGACTCCTTCGTGCCGGATGCGCTTTGCTTATCCGGCCTACAAAATCGCAGCGTGTAGGCCTGA\n+>read6438_contig0_position2276_M1_I0_D0_NG0______er0.01__indel0__rgeom0_rev1\n+CGCACATTCGGAAGAAGAAGCGGCGAAAATCGGTCGTGCAGTGGTGCAGCACGTTAACGCCTGGTGGGCGGAAACGCTGCAAAAACAACGGCTGACCAGC\n+>read6439_contig0_position14744_M3_I0_D0_NG0______er0.01__indel0__rgeom0_rev1\n+TACCGTTACAGCTGGGGCAAGTTCCGGCGATGATCCTGGCGCGCGAATGGGAAACCCTCAGGAACTTTGCCAGCCATCCCATCGGCACCGGTCCGTATGC\n+>read6440_contig1_position1375_M3_I0_D0_NG0______er0.01__indel0__rgeom0_rev0\n+ACCGGGGAATCACTGCGTGCGTACAGACGGTTCTCACCAGTAGATGGGAAACGTAAAGTGACAGTTCGCGCATCCACCGCGACAACGGTTCCAAGTCCCA\n+>read6441_contig0_position4359_M0_I0_D0_NG0______er0.01__indel0__rgeom0_rev1\n+CACGCCGACTATTTCTACGGCACCATTCCCTGCACCCGCAAAATGACCGACGCAGAAATCAACGGCGAATATGAGTGGGAAACCGGTAACGTCATCGTAG\n'

diff -r 000000000000 -r dc70286127fe test-data/mapsembler2/reads2
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mapsembler2/reads2 Fri Oct 20 03:15:43 2017 -0400

b'@@ -0,0 +1,12884 @@\n+>read0_contig0_position15997_M1_I0_D0_NG0______er0.01__indel0__rgeom0_rev1\n+AACGTTTTGCCAACCAGAGGCTTACGCCGATCCCAGCAATAGCATTCACCGTATAAAAGAGGCCGATCCAGAAAGGTTCCGCGCCAACCTCACGACTCAG\n+>read1_contig1_position3126_M0_I0_D0_NG0______er0.01__indel0__rgeom0_rev0\n+TTTCCTTCGCCTAATAGCTCCTGAGCGACAGTTTCCAGCGAGAATGAAGAGAAATTCCAGAACGCGGATTTCAGCGCCTCGATACCGTCGATAATTAGCC\n+>read2_contig1_position8531_M2_I0_D0_NG0______er0.01__indel0__rgeom0_rev0\n+AAGGGGGGTTACCGGTTGGGTTAGCGTGAAGAGCCAGTAAAAGACGCAGTGACGGCAATGTCTGATGCAATATGGACAATTGGTTTCTTCTCTGAATGGT\n+>read3_contig1_position4288_M1_I0_D0_NG0______er0.01__indel0__rgeom0_rev0\n+AAACGGGCCGTGGGAATGGACCAGAACGCCGGGCATTTGCGCTGTATCGATACCCTGTTTTTCAAAGGTTTCTACGATGACGTTACCGGTTTCCCACTCA\n+>read4_contig1_position14292_M2_I0_D0_NG0______er0.01__indel0__rgeom0_rev0\n+GCATGATCCCGGCAATCACCCGATGCTCACTGTGATCCTGATAAAAGGTTAGGGTGAGGCTTTCCAGGCCAGCCTGTCTTTCGCTCTTTATGGTGCGGGC\n+>read5_contig0_position1466_M0_I0_D0_NG0______er0.01__indel0__rgeom0_rev0\n+CAAGTCCCAATTCGCTTTCTGTATCGCTGATCCAGCGTTGACCAAGTGTAAAAGGCATATGTGTTCGGCTCTATATCTTTAATTGCAGGCAATAACCACC\n+>read6_contig0_position4257_M0_I0_D0_NG0______er0.01__indel0__rgeom0_rev0\n+GCACCGCATCTTCGGCATTTTTGCCCCATGCAAACGGGCCGTGGGAATGGACCAGAACGCCGGGCATTTGCGCTGCATCGATACCCTGTTTTTCAAAGGT\n+>read7_contig0_position7067_M1_I0_D0_NG0______er0.01__indel0__rgeom0_rev1\n+CATGGGCCAAAAATCCGTCTCTGGATCACCTGCCGGTGGTGCTCGACTGGTTTAACGGCCGCCGCACACCGAACGCTAACTAACGCCTGAAAGGGGTGAT\n+>read8_contig1_position15076_M1_I0_D0_NG0______er0.01__indel0__rgeom0_rev1\n+TCCGTTGCGTAATCTGCTACCTGGCAGCGCATTGCGCCGTTCCGAATCCCATATCGCCCGGCAAATCTTCAGTTCGCTAACGCGCATAAATGAGGAAAAT\n+>read9_contig0_position650_M1_I0_D0_NG0______er0.01__indel0__rgeom0_rev0\n+GCGCATCTTCGCTCCACACCAGGTGATGCGCTTCATCGACCACCAGCAGGTCCCATTCGGCTTCACAGAGATGTTCCAGGCGCTGTTTGCTACGACAGGC\n+>read10_contig1_position11_M0_I0_D0_NG0______er0.01__indel0__rgeom0_rev1\n+CGTATTTATCAGGAATTTGAAGGTGATAACGCCACCTGGTGGAACTTCGATCCGCGCGTTGAGTGGCTGATGGGCTACCTGACCAGCCATCGCTCTCAGA\n+>read11_contig0_position8953_M1_I0_D0_NG0______er0.01__indel0__rgeom0_rev1\n+TGCCCAAACAGTTCGCTGAAATCCGGCTGGTGCGCTTCATCCGGGCGAAAGAAACCCGTATTGGCAAATATTGACGGCCAGTTAAGCCATTCATGCCAGT\n+>read12_contig1_position15488_M1_I0_D0_NG0______er0.01__indel0__rgeom0_rev0\n+GTGTCCTGCGATTTACCCTCGCAGCATTGCCACAGGCGGATGAACTGTTGTTGCAGACGAGCAGATGGCATAAAAGGGGAACTCATGTGCAAAAGACAGC\n+>read13_contig0_position4220_M2_I0_D0_NG0______er0.01__indel0__rgeom0_rev0\n+CCCATATAAGCGACCTGTTCCAGCACGATGGCGTTATGCACCGCTTCTTCGGCATTTTTGCCCCATGCAAACGGGCCGTGGGAATGGACCAGAACGCCGG\n+>read14_contig1_position4839_M0_I0_D0_NG0______er0.01__indel0__rgeom0_rev0\n+CTTATCCGGCCTACAAAATCGCAGCGTGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAGGCGTTGAATGCCGGATGCGCTTTGCTTATCCGGCCTACA\n+>read15_contig1_position14938_M1_I0_D0_NG0______er0.01__indel0__rgeom0_rev1\n+AATTTCACTGCTTCACTGGCGTTTCTTTTTGCGTCCAGGAGTCCATTTTCACCATGGTCGTGAACTGGAAATGGACGATGTGATCGCCTCTTTAAAACGA\n+>read16_contig0_position6916_M1_I0_D0_NG0______er0.01__indel0__rgeom0_rev1\n+GGCTGCCACCGCCTTTGGCGCACGCGCAATCATGGAGTGCTTTACCGATCAGGGGATCGCCGTTAATAACGTGATGGCACTGGGCGGCATCGCGCGGAAA\n+>read17_contig1_position13008_M1_I0_D0_NG0______er0.01__indel0__rgeom0_rev0\n+CACTTGCAGATAGTGACCTTCGCTGAAGTTCGCGGCGGCGTAGTTATCTTTCTTCTCTTCGAGAATGTGAGAAGCCGGAGAGGTGGTGTAACTCAGTACC\n+>read18_contig0_position1998_M0_I0_D0_NG0______er0.01__indel0__rgeom0_rev0\n+CGCGCATCCAGTTCACCCGCCATCAGTTTGTCGATGGTTTCGCGTACATATTCCTGATATGGCTCGTTGCGGAAGATGCGCAGGTATAGCTCCTGCTGAA\n+>read19_contig1_position4875_M0_I0_D0_NG0______er0.01__indel0__rgeom0_rev0\n+ATAAGACGCGCCAGCGTCGCATCAGGCGTTGAATGCCGGATGCGCTTTGCTTATCCGGCCTACAAAATCGCAGCGCGTAGGCCTGATAAGACGCGCCAGC\n+>read20_contig1_position13706_M0_I0_D0_NG0______er0.01__indel0__rgeom0_rev1\n+ATAACGCCGGCGAAGGGATTTGAGGCTCCTTCTCAAGTCCTTTGCCACTCTTTTTTGAGGTGCAAAGTGTTAAAAAAATGTCTGCCCCTGCTGTTGCTGT\n+>read21_contig0_position13800_M1_I0_D0_NG0______er0.01__indel0__rgeom0_rev1\n+CTGGTTGATAACAAAATCACTACACTAACGCCGTTCTCAACGGGGTGCCACGCGTACGCGTGCGCTGGGAAAATACCCGTCGAACCTGATCCGGATAACG\n+>read22_contig0_position8312_M0_I0_D0_NG0______er0.01__indel0__rgeo'..b'GAGAAGCGCACCACATGCCACAGATAGC\n+>read6420_contig0_position8754_M1_I0_D0_NG0______er0.01__indel0__rgeom0_rev0\n+GACCGACCGCTGGGAATTAAAGGTTATATTCTCAATCTCACCATTCGCGGTCAGGGGGTGGTGAAAAATCAGGGACGAGAATTTGTCTGCCGACCGGGTG\n+>read6421_contig0_position11275_M1_I0_D0_NG0______er0.01__indel0__rgeom0_rev0\n+ATAGGAGCCAATTTGCTGGTAGAGATAAAACGGCGGGGTGCGGAAATCATCGTTACCGAACAACGCCACCACGCCAAAATCACCAATCGACAGCACGCAT\n+>read6422_contig1_position821_M2_I0_D0_NG0______er0.01__indel0__rgeom0_rev1\n+CGTGTGCTAACTATCGTCCCGGAAACCTTACAGCATCAGTGGCTGGTAGAAATGCTGCGCCGTTTCAACGTGCGCTTTGCGCTATTTGATGATGAGCGTT\n+>read6423_contig1_position11731_M2_I0_D0_NG0______er0.01__indel0__rgeom0_rev0\n+CATGGTCAGCACTACGCACAATATACCTGCCGCCAGCGCAATACGCAACGAGGTCCACAGCGCCTGCCACAGCACCGGTTGTGCCAGCCCTTCCGGCAAC\n+>read6424_contig1_position3678_M2_I0_D0_NG0______er0.01__indel0__rgeom0_rev0\n+GTGATAAACCGCTCCATCACATAGCGTTCTGGCGGACGCACATCGGCGTCGTAGACGGTAACGCCACCTTCACGCAGGCGCTTTTCGTAATTCATCAATT\n+>read6425_contig0_position5114_M0_I0_D0_NG0______er0.01__indel0__rgeom0_rev1\n+ATGCGCCAATTCGCCGAGATGCACGACATTGAAATCACGGTGATTGATAACGACACACGCCTGCCAGCGTTTAAAGACGCGCTGCGCTGGAACGAAGTGT\n+>read6426_contig1_position14935_M0_I0_D0_NG0______er0.01__indel0__rgeom0_rev0\n+GATTCGTTTTAAAGAGGCGATCACATCGTCCATTTCCAGTTCACGACCATGGTGAAAATGGACTCCTGGACGCAAAAAGAAACGCCAGTGAAGCGGTGAA\n+>read6427_contig0_position12343_M1_I0_D0_NG0______er0.01__indel0__rgeom0_rev0\n+ATGGGTCAGCAAAATACCTTGCAGGCCGTAGGGCGAAAAGGTCCACTCCAGACCGAGCGATTGGCAGAGTGTTGCCAGCCAGCCCTGGCGACCATAGACG\n+>read6428_contig0_position6321_M0_I0_D0_NG0______er0.01__indel0__rgeom0_rev1\n+AATCACCGCTATTTGCCGCGACGCGAATTACGACGATCGTTGCGCTGGTCTGGTGGTGTGGCTGCACACCTTCTCCCCGGCCAAAATGTGGATCAACGGC\n+>read6429_contig0_position10682_M1_I0_D0_NG0______er0.01__indel0__rgeom0_rev1\n+CAGCGAGTGGCGTTAGCGCGTTGTCTGGTACGCGAAGAGCCGATTTTATTGCTCGATGAACCGTTCTCTGCGCTCGATCCGGCGTTACGTCAGGAGATGT\n+>read6430_contig0_position11517_M2_I0_D0_NG0______er0.01__indel0__rgeom0_rev0\n+TCAGCGCATAAGGTATCGCCATTAACGCATTGGTGAAAATCACAATGCCGTCAGCAGATTGTGGCAGGCCGATAGTGTTGTTGAGCAGTCAAAAGAAGCC\n+>read6431_contig0_position4832_M1_I0_D0_NG0______er0.01__indel0__rgeom0_rev0\n+CGCTTTGCTTATCCGGCCTACAAAATCGCAGCGTGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAGGAGTTGAATGCCGGATGCGCTTTGCTTATCCG\n+>read6432_contig0_position7509_M2_I0_D0_NG0______er0.01__indel0__rgeom0_rev1\n+TTGCCTTCCCCGCTGTTACCTGACACTTGGACTGCCGATATTCCGGTGGGCACCTTATGCCCGGAATGGGCGCAGCGTCTCGGCCTGCCTGAAAGCGTGG\n+>read6433_contig0_position14812_M2_I0_D0_NG0______er0.01__indel0__rgeom0_rev1\n+TATTGCTGTCATTGTGTCGCCGACGCCCTGGACGCTGGATATCCATCGCACGCAACCGGACCGCTGGTTACCGTTACTGCTGGGGCAAGTTCCGGCGATG\n+>read6434_contig1_position15620_M1_I0_D0_NG0______er0.01__indel0__rgeom0_rev0\n+CCTAACGATGAGGCAAGGGGGTGCCCCATGCGTCAGTTTTATCAGCACTATTTTACCGCGACAGCGAAGTTGTGCTGGTTGCGTTGGTTAAGCGTCCCAC\n+>read6435_contig1_position8927_M0_I0_D0_NG0______er0.01__indel0__rgeom0_rev0\n+GTGGGTTTACTTTCGTCCGCGCGCCTACTGGCATGAATGGCTTAACTGGCCGTCAATATTTGCCAATACGGGTTTCTTTCGCCCGGATGAAGCGCACCAG\n+>read6436_contig0_position7076_M2_I0_D0_NG0______er0.01__indel0__rgeom0_rev0\n+TTCAGGCGTTGGTTAGCGTTCGGTGTGCGGTGGCCGTTAAACCAGTCGAGCACCACCGGCAGGTGATCCAGAGACGGATTTTTGGCCCATGCTGCGGTCA\n+>read6437_contig1_position11640_M0_I0_D0_NG0______er0.01__indel0__rgeom0_rev1\n+CTGACCATGATGCTGCTATGGAGCAGTCGCGAACTGCGGGCGCGGCAGAAAATGCTGGCGGGTCAGGTGCTGGAGATGAGCGGCATGTTGATCCTCGCCA\n+>read6438_contig1_position4196_M1_I0_D0_NG0______er0.01__indel0__rgeom0_rev1\n+GCCCGTTTGCATGGGGCAAAAATGCCGAAGATGCGGTGCATGACGCCATCGTGCTGGAAGAGGTCGCTTATATGGGGATATTCTGCCGTCAGTTAGCGCC\n+>read6439_contig0_position9510_M2_I0_D0_NG0______er0.01__indel0__rgeom0_rev1\n+AATGTGCCTGTCAAATGGACGAAGCAGGGATTCTGCAAACCCTATGCTACTCCGTCGAGCCGTCAATTGTCTGATTCGTTACCGATTATGACAACTTGAC\n+>read6440_contig1_position14156_M0_I0_D0_NG0______er0.01__indel0__rgeom0_rev0\n+AAAACAGAGAAGTCCAGCGGCAGGGTAAAGTTGGCGCTGTTTAGCCAGATATCACTTTCGATCTCTCCTGTATGCCACTGATCGTAGTCGATCTCTTTGA\n+>read6441_contig0_position15427_M0_I0_D0_NG0______er0.01__indel0__rgeom0_rev0\n+GAGCAGGGTGCGCATATGACGACGCGAGCAGCTCAATAACGCTGCCAGTTCGTTGAGCGTTGTGTCCTGCGATTTACCCTCGCAGCATTGCCACAGGCGG\n'

diff -r 000000000000 -r dc70286127fe test-data/mapsembler2/starter.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mapsembler2/starter.fa Fri Oct 20 03:15:43 2017 -0400

@@ -0,0 +1,2 @@
+>ligne 1000
+GCTTCCATTGACTCAATGTAGTCACGCGGATGATGACGGAACTGGTTATTCGGGGCATCACAAAATTGCC

diff -r 000000000000 -r dc70286127fe test-data/mapsembler2/starter_extremities.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mapsembler2/starter_extremities.fa Fri Oct 20 03:15:43 2017 -0400

@@ -0,0 +1,6 @@
+>ligne 1000
+GCTTCCATTGACTCAATGTAGTCACGCGGATGATGACGGAACTGGTTATTCGGGGCATCACAAAATTGCC
+>extrem_left|id_0|abundance_45
+GCTTCCATTGACTCAATGTAGTCACGCGGAT
+>extrem_right|id_0|abundance_49
+AACTGGTTATTCGGGGCATCACAAAATTGCC

diff -r 000000000000 -r dc70286127fe test-data/takeabreak/inversion.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/takeabreak/inversion.fasta Fri Oct 20 03:15:43 2017 -0400

@@ -0,0 +1,48 @@
+>INV_a-u_0|rep_1
+AGATAACTACAGTGCCGCTTACAGCCCCTCATAGACCAGTTCATTCCAGATCTCCTTCC
+>INV_v-b_0|rep_1
+AGGCTATATTACAGACGTCGGCGACGACAGTGACAGAAACTGTGCAAGTACCTAATCTC
+>INV_a-vbar_0|rep_1
+AGATAACTACAGTGCCGCTTACAGCCCCTCTGTCGTCGCCGACGTCTGTAATATAGCCT
+>INV_ubar-b_0|rep_1
+GGAAGGAGATCTGGAATGAACTGGTCTATGTGACAGAAACTGTGCAAGTACCTAATCTC
+>INV_a-u_1|rep_1
+AGCATAGCCATTTATCGGAGCGCCTCGGTACACGGTATGACCAGACGCCTCGTGAGACC
+>INV_v-b_1|rep_1
+GTTGCGTTCCTAGCGCCTATATTTGTCTCTTTGCCGGCTTATGTGGACAAGCATAGCAT
+>INV_a-vbar_1|rep_1
+AGCATAGCCATTTATCGGAGCGCCTCGGTAGAGACAAATATAGGCGCTAGGAACGCAAC
+>INV_ubar-b_1|rep_1
+GGTCTCACGAGGCGTCTGGTCATACCGTGTTTGCCGGCTTATGTGGACAAGCATAGCAT
+>INV_a-u_2|rep_0
+AGTGTAGGTTCTGACCGATACGTGCTTCGTGGCGTAGGGCTTATGTCCCCAGTTGTAAAA
+>INV_v-b_2|rep_0
+TGTCCCCAGTTGTAAAATTGTGAGTTCTCACATCATCTACTGACGTCCCTGAGGCTGCAG
+>INV_a-vbar_2|rep_0
+AGTGTAGGTTCTGACCGATACGTGCTTCGTTGAGAACTCACAATTTTACAACTGGGGACA
+>INV_ubar-b_2|rep_0
+TTTTACAACTGGGGACATAAGCCCTACGCCCATCATCTACTGACGTCCCTGAGGCTGCAG
+>INV_a-u_3|rep_0
+ATGGGACAGTATCCGCCGCAAGTTCTAGTGCAATGGCGGTATAGTACGCTCGTACTGTAG
+>INV_v-b_3|rep_0
+GTGGGATCATCACTAATAAGGATACTGGGAAGACTCACAGGCCTCCGCCTATAGGCGGTG
+>INV_a-vbar_3|rep_0
+ATGGGACAGTATCCGCCGCAAGTTCTAGTGTCCCAGTATCCTTATTAGTGATGATCCCAC
+>INV_ubar-b_3|rep_0
+CTACAGTACGAGCGTACTATACCGCCATTGAGACTCACAGGCCTCCGCCTATAGGCGGTG
+>INV_a-u_4|rep_0
+CAAAGCCGCGTGACGACGGCTGTCGGCCCGCACCAGGGCTGTTCAATCGAGGCTCACGGG
+>INV_v-b_4|rep_0
+TCACGGGAGCTTATTGCGGGGATTCTGTTAGGCCCCATCAGTAGCCCGCTCGGCCCAGGA
+>INV_a-vbar_4|rep_0
+CAAAGCCGCGTGACGACGGCTGTCGGCCCGTAACAGAATCCCCGCAATAAGCTCCCGTGA
+>INV_ubar-b_4|rep_0
+CCCGTGAGCCTCGATTGAACAGCCCTGGTGGGCCCCATCAGTAGCCCGCTCGGCCCAGGA
+>INV_a-u_5|rep_0
+CAGAAATCCGCGTGATTACGAGTCGTGGTAAATTTAATCTGGCTGTGGTCTAGACATTCC
+>INV_v-b_5|rep_0
+GTCCTGTGAGCAGCGAAGGCCCATACGCGAGATACACTGCCAGAAATCCGCGTGATTACG
+>INV_a-vbar_5|rep_0
+CAGAAATCCGCGTGATTACGAGTCGTGGTATCGCGTATGGGCCTTCGCTGCTCACAGGAC
+>INV_ubar-b_5|rep_0
+GGAATGTCTAGACCACAGCCAGATTAAATTGATACACTGCCAGAAATCCGCGTGATTACG

diff -r 000000000000 -r dc70286127fe test-data/takeabreak/inversion_list.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/takeabreak/inversion_list.fasta Fri Oct 20 03:15:43 2017 -0400

diff -r 000000000000 -r dc70286127fe test-data/takeabreak/toy_example_reads.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/takeabreak/toy_example_reads.fasta Fri Oct 20 03:15:43 2017 -0400

b'@@ -0,0 +1,800 @@\n+>read0_contig0_position412_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev0\n+ATACTGGGAAGACTCACAGGCCTCCGCCTATAGGCGGTGCTTACTCTTACATAAAGCGGCTGTTAGTATTACCCCGCGAGGATTCGAAAAGGTGAACCAA\n+>read1_contig0_position457_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev1\n+CCGTCGTCACGCGGCTTTGAGGCCCGTCCCTCCGGATCGACCGGGTTGGTTCACCTTTTCGAATCCTCGCGGGGTAATACTAACAGCCGCTTTATGTAAG\n+>read2_contig0_position476_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev0\n+AGTATTACCCCGCGAGGATTCGAAAAGGTGAACCAACCCGGTCGATCCGGAGGGACGGGCCTCAAAGCCGCGTGACGACGGCTGTCGGCCCGTAACAGAA\n+>read3_contig0_position750_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev1\n+GCTCACAGGACACCTGGTATACGTAATGGTCTCACGAGGCGTCTGGTCATACCGTGTACCGAGGCGCTCCGATAAATGGCTATGCTATGCTTGTCCACAT\n+>read4_contig0_position467_M1_I0_D0_NG0______er0.001__indel0__rgeom0_rev1\n+GGGCCGACAGCCGTCGTCGCGCGGCTTTGAGGCCCGTCCCTCCGGATCGACCGGGTTGGTTCACCTTTTCGAATCCTCGCGGGGTAATACTAACAGCCGC\n+>read5_contig0_position401_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev1\n+TTTCGAATCCTCGCGGGGTAATACTAACAGCCGCTTTATGTAAGAGTAAGCACCGCCTATAGGCGGAGGCCTGTGAGTCTTCCCAGTATCCTTATTAGTG\n+>read6_contig0_position311_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev0\n+CATGTAATGGGACAGTATCCGCCGCAAGTTCTAGTGCAATGGCGGTATAGTACGCTCGTACTGTAGTAGAGGCGACACGGGTGGGATCATCACTAATAAG\n+>read7_contig0_position521_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev1\n+CACCAGGGCTGTTCAATCGAGGCTCACGGGAGCTTATTGCGGGGATTCTGTTACGGGCCGACAGCCGTCGTCACGCGGCTTTGAGGCCCGTCCCTCCGGA\n+>read8_contig0_position759_M1_I0_D0_NG0______er0.001__indel0__rgeom0_rev0\n+AGCATAGCATAGCCATTTATCGGAGCGCCTCGGTACACGGTATGACCAGATGCCTCGTGAGACCATTACGTATACCAGGTGTCCTGTGAGCAGCGAAGGC\n+>read9_contig0_position855_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev1\n+AGCAGACGCACCGCCTGGAATGTCTAGACCACAGCCAGATTAAATTTACCACGACTCGTAATCACGCGGATTTCTGGCAGTGTATCTCGCGTATGGGCCT\n+>read10_contig0_position774_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev1\n+GTATCTCGCGTATGGGCCTTCGCTGCTCACAGGACACCTGGTATACGTAATGGTCTCACGAGGCGTCTGGTCATACCGTGTACCGAGGCGCTCCGATAAA\n+>read11_contig0_position830_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev1\n+AGACCACAGCCAGATTAAATTTACCACGACTCGTAATCACGCGGATTTCTGGCAGTGTATCTCGCGTATGGGCCTTCGCTGCTCACAGGACACCTGGTAT\n+>read12_contig0_position92_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev1\n+CTTGCACAGTTTCTGTCACATAGACCAGTTCATTCCAGATCTCCTTCCGCATCAGTCAATGCCTCAATAGGGTGGAATCACAACAAGGCTATATTACAGA\n+>read13_contig0_position286_M1_I0_D0_NG0______er0.001__indel0__rgeom0_rev0\n+TACTGACGTCCCTGAGGCTGCAGTTCATGTAATGGGACAGTACCCGCCGCAAGTTCTAGTGCAATGGCGGTATAGTACGCTCGTACTGTAGTAGAGGCGA\n+>read14_contig0_position215_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev1\n+CATGAACTGCAGCCTCAGGGACGTCAGTAGATGATGGGCGTAGGGCTTATGTCCCCAGTTGTAAAATTGTGAGTTCTCAACGAAGCACGTATCGGTCAGA\n+>read15_contig0_position608_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev1\n+GAATTAACGAACGGCCTCGATTACTGGAAGGTATCGCTCAATATGTCGCTTTTCGGGTCCTGGGCCGAGCGGGCTACTGATGGGGCCCACCAGGGCTGTT\n+>read16_contig0_position805_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev1\n+ACGACTCGTAATCACGCGGATTTCTGGCAGTGTATCTCGCGTATGGGCCTTCGCTGCTCACAGGACACCTGGTATACGTAATGGTCTCACGAGGCGTCTG\n+>read17_contig0_position317_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev0\n+ATGGGACAGTATCCGCCGCAAGTTCTAGTGCAATGGCGGTATAGTACGCTCGTACTGTAGTAGAGGCGACACGGGTGGGATCATCACTAATAAGGATACT\n+>read18_contig0_position14_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev1\n+CACAACAAGGCTATATTACAGACGTCGGCGACGACAGAGGGGCTGTAAGCGGCACTGTAGTTATCTCTCCGTCCGAGAACGATATAGAAAGTTCCCGTAC\n+>read19_contig0_position824_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev1\n+CAGCCAGATTAAATTTACCACGACTCGTAATCACGCGGATTTCTGGCAGTGTATCTCGCGTATGGGCCTTCGCTGCTCACAGGACACCTGGTATACGTAA\n+>read20_contig0_position765_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev1\n+GTATGGGCCTTCGCTGCTCACAGGACACCTGGTATACGTAATGGTCTCACGAGGCGTCTGGTCATACCGTGTACCGAGGCGCTCCGATAAATGGCTATGC\n+>read21_contig0_position293_M1_I0_D0_NG0______er0.001__indel0__rgeom0_rev0\n+GTCCCTGAGGCTGCAGTTCATGTAATGGGACAGTATCCGCCGCAAGTTCTAGTGCAATGGCGGTATAGTACGCTCGTACAGTAGTAGAGGCGACACGGGT\n+>read22_contig0_position450_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev0\n+'..b'ACGCCTCGTGAGACCATTACGTATACCAGGTGTCCAGTGAGCAGCGAAGGCCCATACGCGAGATA\n+>read378_contig0_position327_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev0\n+ATCCGCCGCAAGTTCTAGTGCAATGGCGGTATAGTACGCTCGTACTGTAGTAGAGGCGACACGGGTGGGATCATCACTAATAAGGATACTGGGAAGACTC\n+>read379_contig0_position301_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev1\n+ATGATCCCACCCGTGTCGCCTCTACTACAGTACGAGCGTACTATACCGCCATTGCACTAGAACTTGCGGCGGATACTGTCCCATTACATGAACTGCAGCC\n+>read380_contig0_position630_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev1\n+ATAGGCGCTAGGAACGCAACAAGAATTAACGAACGGCCTCGATTACTGGAAGGTATCGCTCAATATGTCGCTTTTCGGGTCCTGGGCCGAGCGGGCTACT\n+>read381_contig0_position325_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev1\n+GTCTTCCCAGTATCCTTATTAGTGATGATCCCACCCGTGTCGCCTCTACTACAGTACGAGCGTACTATACCGCCATTGCACTAGAACTTGCGGCGGATAC\n+>read382_contig0_position554_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev1\n+GGGTCCTGGGCCGAGCGGGCTACTGATGGGGCCCACCAGGGCTGTTCAATCGAGGCTCACGGGAGCTTATTGCGGGGATTCTGTTACGGGCCGACAGCCG\n+>read383_contig0_position804_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev1\n+CGACTCGTAATCACGCGGATTTCTGGCAGTGTATCTCGCGTATGGGCCTTCGCTGCTCACAGGACACCTGGTATACGTAATGGTCTCACGAGGCGTCTGG\n+>read384_contig0_position872_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev0\n+ACACTGCCAGAAATCCGCGTGATTACGAGTCGTGGTAAATTTAATCTGGCTGTGGTCTAGACATTCCAGGCGGTGCGTCTGCTGTCGGGTGCCTCTGGTG\n+>read385_contig0_position34_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev0\n+GTTCTCGGACGGAGAGATAACTACAGTGCCGCTTACAGCCCCTCTGTCGTCGCCGACGTCTGTAATATAGCCTTGTTGTGATTCCACCCTATTGAGGCAT\n+>read386_contig0_position665_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev0\n+TATTGAGCGATACCTTCCAGTAATCGAGGCCGTTCGTTAATTCTTGTTGCGTTCCTAGCGCCTATATTTGTCTCTTTGCCGGCTTATGTGGACAAGCATA\n+>read387_contig0_position827_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev0\n+CGTATACCAGGTGTCCTGTGAGCAGCGAAGGCCCATACGCGAGATACACTGCCAGAAATCCGCGTGATTACGAGTCGTGGTAAATTTAATCTGGCTGTGG\n+>read388_contig0_position124_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev1\n+TCGGTCAGAACCTACACTAACGAGATTAGGTACTTGCACAGTTTCTGTCACATAGACCAGTTCATTCCAGATCTCCTTCCGCATCAGTCAATGCCTCAAT\n+>read389_contig0_position74_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev0\n+CCTCTGTCGTCGCCGACGTCTGTAATATAGCCTTGTTGTGATTCCACCCTATTGAGGCATTGACTGATGCGGAAGGAGATCTGGAATGAACTGGTCTATG\n+>read390_contig0_position527_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev1\n+GGGGCCCACCAGGGCTGTTCAATCGAGGCTCACGGGAGCTTATTGCGGGGATTCTGTTACGGGCCGACAGCCGTCGTCACGCGGCTTTGAGGCCCGTCCC\n+>read391_contig0_position46_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev1\n+CCGCATCAGTCAATGCCTCAATAGGGTGGAATCACAACAAGGCTATATTACAGACGTCGGCGACGACAGAGGGGCTGTAAGCGGCACTGTAGTTATCTCT\n+>read392_contig0_position801_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev0\n+TGACCAGACGCCTCGTGAGACCATTACGTATACCAGGTGTCCTGTGAGCAGCGAAGGCCCATACGCGAGATACACTGCCAGAAATCCGCGTGATTACGAG\n+>read393_contig0_position335_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev1\n+AGGCCTGTGAGTCTTCCCAGTATCCTTATTAGTGATGATCCCACCCGTGTCGCCTCTACTACAGTACGAGCGTACTATACCGCCATTGCACTAGAACTTG\n+>read394_contig0_position85_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev1\n+AGTTTCTGTCACATAGACCAGTTCATTCCAGATCTCCTTCCGCATCAGTCAATGCCTCAATAGGGTGGAATCACAACAAGGCTATATTACAGACGTCGGC\n+>read395_contig0_position281_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev1\n+TCTACTACAGTACGAGCGTACTATACCGCCATTGCACTAGAACTTGCGGCGGATACTGTCCCATTACATGAACTGCAGCCTCAGGGACGTCAGTAGATGA\n+>read396_contig0_position84_M1_I0_D0_NG0______er0.001__indel0__rgeom0_rev1\n+GTTTCTGTCACATAGACCAGATCATTCCAGATCTCCTTCCGCATCAGTCAATGCCTCAATAGGGTGGAATCACAACAAGGCTATATTACAGACGTCGGCG\n+>read397_contig0_position130_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev0\n+GCATTGACTGATGCGGAAGGAGATCTGGAATGAACTGGTCTATGTGACAGAAACTGTGCAAGTACCTAATCTCGTTAGTGTAGGTTCTGACCGATACGTG\n+>read398_contig0_position119_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev0\n+ACCCTATTGAGGCATTGACTGATGCGGAAGGAGATCTGGAATGAACTGGTCTATGTGACAGAAACTGTGCAAGTACCTAATCTCGTTAGTGTAGGTTCTG\n+>read399_contig0_position324_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev1\n+TCTTCCCAGTATCCTTATTAGTGATGATCCCACCCGTGTCGCCTCTACTACAGTACGAGCGTACTATACCGCCATTGCACTAGAACTTGCGGCGGATACT\n'

diff -r 000000000000 -r dc70286127fe test-data/takeabreak/toy_example_with_inv_reads.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/takeabreak/toy_example_with_inv_reads.fasta Fri Oct 20 03:15:43 2017 -0400

b'@@ -0,0 +1,800 @@\n+>read0_contig0_position49_M1_I0_D0_NG0______er0.001__indel0__rgeom0_rev1\n+AGCCTTGTTGTGATTCCACCCTATTGAGGCATTGACTGATGCGGAAGGAGATCTGGAATGAAGTGGTCTATGAGGGGCTGTAAGCGGCACTGTAGTTATC\n+>read1_contig0_position514_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev0\n+CGGTCGATCCGGAGGGACGGGCCTCAAAGCCGCGTGACGACGGCTGTCGGCCCGCACCAGGGCTGTTCAATCGAGGCTCACGGGAGCTTATTGCGGGGAT\n+>read2_contig0_position289_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev1\n+GAGGCGACACGGGTGGGATCATCACTAATAAGGATACTGGGACACTAGAACTTGCGGCGGATACTGTCCCATTACATGAACTGCAGCCTCAGGGACGTCA\n+>read3_contig0_position43_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev0\n+CGGAGAGATAACTACAGTGCCGCTTACAGCCCCTCATAGACCAGTTCATTCCAGATCTCCTTCCGCATCAGTCAATGCCTCAATAGGGTGGAATCACAAC\n+>read4_contig0_position15_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev1\n+ACTGATGCGGAAGGAGATCTGGAATGAACTGGTCTATGAGGGGCTGTAAGCGGCACTGTAGTTATCTCTCCGTCCGAGAACGATATAGAAAGTTCCCGTA\n+>read5_contig0_position694_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev1\n+TTTGCCGGCTTATGTGGACAAGCATAGCATAGCCATTTATCGGAGCGCCTCGGTAGAGACAAATATAGGCGCTAGGAACGCAACAAGAATTAACGAACGG\n+>read6_contig0_position799_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev0\n+TATGACCAGACGCCTCGTGAGACCATTACGTATACCAGGTGTCCTGTGAGCAGCGAAGGCCCATACGCGATACCACGACTCGTAATCACGCGGATTTCTG\n+>read7_contig0_position519_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev0\n+GATCCGGAGGGACGGGCCTCAAAGCCGCGTGACGACGGCTGTCGGCCCGCACCAGGGCTGTTCAATCGAGGCTCACGGGAGCTTATTGCGGGGATTCTGT\n+>read8_contig0_position892_M1_I0_D0_NG0______er0.001__indel0__rgeom0_rev1\n+GGCAAGTCCATCTAGCCAGTCACCAGAGGCACCCAACAGCAGACGCACCGCCTGGAATGTCTAGACCACAGCCAGATTAAATTGATACACTGCCAGAAAT\n+>read9_contig0_position409_M1_I0_D0_NG0______er0.001__indel0__rgeom0_rev1\n+GTTCACCTTTTCGAATCCTCGCGGGGTAATACTAACAGCCGCTTTATGTAAGAGTAAGCACCGCCTATAGGCGGAGGCCTGTGAGGCTCAATGGCGGTAT\n+>read10_contig0_position631_M1_I0_D0_NG0______er0.001__indel0__rgeom0_rev1\n+TATAGGCGCTAGGAACGCAACAAGAATTAACGAACGGCCTCGATTACTGGAAGGTATCGCTCAATATGTCGCTTATCGGGTCCTGGGCCGAGCGGGCTAC\n+>read11_contig0_position817_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev1\n+ATTAAATTGATACACTGCCAGAAATCCGCGTGATTACGAGTCGTGGTATCGCGTATGGGCCTTCGCTGCTCACAGGACACCTGGTATACGTAATGGTCTC\n+>read12_contig0_position555_M2_I0_D0_NG0______er0.001__indel0__rgeom0_rev0\n+GGCTGTCGGCCCGCACCAGGGCTGTTCAATCGAGGCTCACGGGAGATTATTGCGGGGATTCTGTTAGGCCCCATCAGTATCCCGCTCGGCCCAGGACCCG\n+>read13_contig0_position709_M2_I0_D0_NG0______er0.001__indel0__rgeom0_rev0\n+TGTTGCGTGCCTAGCGCCTATATTTGTCTCTACCGAGGCGCTCCGATAAATGGCTATGCTATGCTTGTCCACATAAGCCGGCAAGCACGGTATGACCAGA\n+>read14_contig0_position731_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev1\n+TACGTAATGGTCTCACGAGGCGTCTGGTCATACCGTGTTTGCCGGCTTATGTGGACAAGCATAGCATAGCCATTTATCGGAGCGCCTCGGTAGAGACAAA\n+>read15_contig0_position680_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev0\n+TCCAGTAATCGAGGCCGTTCGTTAATTCTTGTTGCGTTCCTAGCGCCTATATTTGTCTCTACCGAGGCGCTCCGATAAATGGCTATGCTATGCTTGTCCA\n+>read16_contig0_position751_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev1\n+TGCTCACAGGACACCTGGTATACGTAATGGTCTCACGAGGCGTCTGGTCATACCGTGTTTGCCGGCTTATGTGGACAAGCATAGCATAGCCATTTATCGG\n+>read17_contig0_position525_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev0\n+GAGGGACGGGCCTCAAAGCCGCGTGACGACGGCTGTCGGCCCGCACCAGGGCTGTTCAATCGAGGCTCACGGGAGCTTATTGCGGGGATTCTGTTAGGCC\n+>read18_contig0_position689_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev1\n+CGGCTTATGTGGACAAGCATAGCATAGCCATTTATCGGAGCGCCTCGGTAGAGACAAATATAGGCGCTAGGAACGCAACAAGAATTAACGAACGGCCTCG\n+>read19_contig0_position259_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev0\n+TGTAAAATTGTGAGTTCTCACATCATCTACTGACGTCCCTGAGGCTGCAGTTCATGTAATGGGACAGTATCCGCCGCAAGTTCTAGTGTCCCAGTATCCT\n+>read20_contig0_position95_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev1\n+GTACTTGCACAGTTTCTGTCACTGTCGTCGCCGACGTCTGTAATATAGCCTTGTTGTGATTCCACCCTATTGAGGCATTGACTGATGCGGAAGGAGATCT\n+>read21_contig0_position277_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev1\n+GTGGGATCATCACTAATAAGGATACTGGGACACTAGAACTTGCGGCGGATACTGTCCCATTACATGAACTGCAGCCTCAGGGACGTCAGTAGATGATGTG\n+>read22_contig0_position517_M1_I0_D0_NG0______er0.001__indel0__rgeom0_rev0\n+TC'..b'AGGCATTGACTGATGCGGAAGGAGATCTGGAATGAACTGGTCTATGAGGGGCTGTAAGCGGCA\n+>read378_contig0_position723_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev0\n+CGCCTATATTTGTCTCTACCGAGGCGCTCCGATAAATGGCTATGCTATGCTTGTCCACATAAGCCGGCAAACACGGTATGACCAGACGCCTCGTGAGACC\n+>read379_contig0_position823_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev0\n+ATTACGTATACCAGGTGTCCTGTGAGCAGCGAAGGCCCATACGCGATACCACGACTCGTAATCACGCGGATTTCTGGCAGTGTATCAATTTAATCTGGCT\n+>read380_contig0_position576_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev1\n+ATCGCTCAATATGTCGCTTTTCGGGTCCTGGGCCGAGCGGGCTACTGATGGGGCCTAACAGAATCCCCGCAATAAGCTCCCGTGAGCCTCGATTGAACAG\n+>read381_contig0_position365_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev1\n+TATGTAAGAGTAAGCACCGCCTATAGGCGGAGGCCTGTGAGTCTCAATGGCGGTATAGTACGCTCGTACTGTAGTAGAGGCGACACGGGTGGGATCATCA\n+>read382_contig0_position609_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev1\n+AGAATTAACGAACGGCCTCGATTACTGGAAGGTATCGCTCAATATGTCGCTTTTCGGGTCCTGGGCCGAGCGGGCTACTGATGGGGCCTAACAGAATCCC\n+>read383_contig0_position5_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev1\n+AAGGAGATCTGGAATGAACTGGTCTATGAGGGGCTGTAAGCGGCACTGTAGTTATCTCTCCGTCCGAGAACGATATAGAAAGTTCCCGTACAGGTTGATG\n+>read384_contig0_position197_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev1\n+GGACGTCAGTAGATGATGTGAGAACTCACAATTTTACAACTGGGGACATAAGCCCTACGCCACGAAGCACGTATCGGTCAGAACCTACACTAACGAGATT\n+>read385_contig0_position703_M1_I0_D0_NG0______er0.001__indel0__rgeom0_rev1\n+CATACCGTGTTTGCCGGCTTATGTGGACAAGCATAGCATAGCCATTTATCGGAGCGCCTCGGTGGAGACAAATATAGGCGCTAGGAACGCAACAAGAATT\n+>read386_contig0_position203_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev0\n+GTTAGTGTAGGTTCTGACCGATACGTGCTTCGTGGCGTAGGGCTTATGTCCCCAGTTGTAAAATTGTGAGTTCTCACATCATCTACTGACGTCCCTGAGG\n+>read387_contig0_position243_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev1\n+AGAACTTGCGGCGGATACTGTCCCATTACATGAACTGCAGCCTCAGGGACGTCAGTAGATGATGTGAGAACTCACAATTTTACAACTGGGGACATAAGCC\n+>read388_contig0_position894_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev1\n+GCGGCAAGTCCATCTAGCCAGTCACCAGAGGCACCCGACAGCAGACGCACCGCCTGGAATGTCTAGACCACAGCCAGATTAAATTGATACACTGCCAGAA\n+>read389_contig0_position43_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev1\n+GTTGTGATTCCACCCTATTGAGGCATTGACTGATGCGGAAGGAGATCTGGAATGAACTGGTCTATGAGGGGCTGTAAGCGGCACTGTAGTTATCTCTCCG\n+>read390_contig0_position694_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev0\n+CCGTTCGTTAATTCTTGTTGCGTTCCTAGCGCCTATATTTGTCTCTACCGAGGCGCTCCGATAAATGGCTATGCTATGCTTGTCCACATAAGCCGGCAAA\n+>read391_contig0_position877_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev1\n+CCAGTCACCAGAGGCACCCGACAGCAGACGCACCGCCTGGAATGTCTAGACCACAGCCAGATTAAATTGATACACTGCCAGAAATCCGCGTGATTACGAG\n+>read392_contig0_position192_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev1\n+TCAGTAGATGATGTGAGAACTCACAATTTTACAACTGGGGACATAAGCCCTACGCCACGAAGCACGTATCGGTCAGAACCTACACTAACGAGATTAGGTA\n+>read393_contig0_position164_M1_I0_D0_NG0______er0.001__indel0__rgeom0_rev1\n+TTACAACTGGGGACATAAGCCCTACGCCACGAAGCACGTATCGGTCAGAACCTACACTTACGAGATTAGGTACTTGCACAGTTTCTGTCACTGTCGTCGC\n+>read394_contig0_position694_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev1\n+TTTGCCGGCTTATGTGGACAAGCATAGCATAGCCATTTATCGGAGCGCCTCGGTAGAGACAAATATAGGCGCTAGGAACGCAACAAGAATTAACGAACGG\n+>read395_contig0_position647_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev1\n+CCTCGGTAGAGACAAATATAGGCGCTAGGAACGCAACAAGAATTAACGAACGGCCTCGATTACTGGAAGGTATCGCTCAATATGTCGCTTTTCGGGTCCT\n+>read396_contig0_position618_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev1\n+AACGCAACAAGAATTAACGAACGGCCTCGATTACTGGAAGGTATCGCTCAATATGTCGCTTTTCGGGTCCTGGGCCGAGCGGGCTACTGATGGGGCCTAA\n+>read397_contig0_position846_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev0\n+GAGCAGCGAAGGCCCATACGCGATACCACGACTCGTAATCACGCGGATTTCTGGCAGTGTATCAATTTAATCTGGCTGTGGTCTAGACATTCCAGGCGGT\n+>read398_contig0_position535_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev1\n+CTACTGATGGGGCCTAACAGAATCCCCGCAATAAGCTCCCGTGAGCCTCGATTGAACAGCCCTGGTGCGGGCCGACAGCCGTCGTCACGCGGCTTTGAGG\n+>read399_contig0_position584_M0_I0_D0_NG0______er0.001__indel0__rgeom0_rev1\n+TGGAAGGTATCGCTCAATATGTCGCTTTTCGGGTCCTGGGCCGAGCGGGCTACTGATGGGGCCTAACAGAATCCCCGCAATAAGCTCCCGTGAGCCTCGA\n'