Galaxy |

Changeset 5:7d4435f9c77d (2021-05-06)

Previous changeset 4:ccc77612cbb9 (2020-08-17) Next changeset 6:7c02beb8ba3d (2024-10-05)

Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 8d37fef93da141323cc120b5fec737432e497dcf"

modified:
kissplice.xml
macros.xml

added:
test-data/commet/A.fa.gz
test-data/commet/B.fa.gz
test-data/commet/C.fa.gz
test-data/commet/D.fa.gz
test-data/discosnp/reads1.gz
test-data/discosnp/reads2.gz
test-data/discosnpRAD/loci_reads.gz
test-data/kissplice/reads1.gz
test-data/kissplice/reads2.gz
test-data/lordec/coli-pacbio-test-mini.fa.gz
test-data/lordec/ill-test-5K-1.fa.gz
test-data/lordec/ill-test-5K-2.fa.gz
test-data/mapsembler2/reads1.gz
test-data/mapsembler2/reads2.gz
test-data/mapsembler2/starter.fa.gz
test-data/takeabreak/toy_example_reads.fasta.gz
test-data/takeabreak/toy_example_with_inv_reads.fasta.gz

removed:
test-data/commet/A.fa
test-data/commet/B.fa
test-data/commet/C.fa
test-data/commet/D.fa
test-data/discosnp/reads1
test-data/discosnp/reads2
test-data/discosnpRAD/loci_reads
test-data/kissplice/reads1
test-data/kissplice/reads2
test-data/lordec/coli-pacbio-test-mini.fa
test-data/lordec/ill-test-5K-1.fa
test-data/lordec/ill-test-5K-2.fa
test-data/mapsembler2/reads1
test-data/mapsembler2/reads2
test-data/mapsembler2/starter.fa
test-data/takeabreak/toy_example_reads.fasta
test-data/takeabreak/toy_example_with_inv_reads.fasta

diff -r ccc77612cbb9 -r 7d4435f9c77d kissplice.xml
--- a/kissplice.xml Mon Aug 17 10:39:09 2020 -0400
+++ b/kissplice.xml Thu May 06 12:44:17 2021 +0000

[

@@ -1,5 +1,4 @@
-<?xml version='1.0' encoding='utf-8'?>
-<tool profile="16.04" id="kissplice" name="KisSplice" version="2.4.0">
+<tool id="kissplice" name="KisSplice" version="2.4.0+galaxy0" profile="@PROFILE@">
     <description>is a local transcriptome assembler for SNPs, indels and AS events</description>
     <macros>
         <import>macros.xml</import>
@@ -8,17 +7,12 @@
         <requirement type="package" version="2.4.0p1">kissplice</requirement>
     </requirements>
     <version_command>kissplice --version</version_command>
-    <command><![CDATA[
-
-        ## prepare symlinks
+    <command detect_errors="exit_code"><![CDATA[
         #set $samples = ""
-
-        #for x in $list_reads
-            #set $filename = os.path.basename(str($x)) + "." + $x.ext
-            ln -sf '${x}' '${filename}' &&
+        #for input in $list_reads
+            @single_reads@
             #set $samples += " -r '" + $filename + "'"
         #end for
-
         kissplice
         $samples
         -k ${k}
@@ -26,11 +20,9 @@
         -C ${C}
         ${output_context}
         --counts ${counts}
-
     ]]></command>
     <inputs>
-
-        <param name='list_reads' argument="-r" multiple="true" format="fasta,fastq" type="data" label="Reads file" />
+        <param name='list_reads' argument="-r" multiple="true" format="fasta,fasta.gz,fastq,fastq.gz" type="data" label="Reads file" />
         <param argument="-k" type="integer" value="41" label="K-mer length" />
         <param argument="-c" type="integer" value="2" label="K-mers present strictly less than this number of times in the dataset will be discarded (integer value required)" />
         <param argument="-C" type="float" value="0.05" label="Edges with relative coverage below this number are removed (value in [0,1) required)" />
@@ -63,16 +55,14 @@
             <filter>output_option == 'all_files'</filter>
         </data>
     </outputs>
-
     <tests>
         <test>
-            <param name="list_reads" value="kissplice/reads1,kissplice/reads2" ftype="fasta" />
+            <param name="list_reads" value="kissplice/reads1.gz,kissplice/reads2.gz" ftype="fasta.gz" />
             <param name="k" value="25"/>
             <param name="output_option" value="alternative_file" />
             <output name="type1" file="kissplice/alternative_splicing.fa"/>
         </test>
     </tests>
-
     <help><![CDATA[

**Description**

diff -r ccc77612cbb9 -r 7d4435f9c77d macros.xml
--- a/macros.xml Mon Aug 17 10:39:09 2020 -0400
+++ b/macros.xml Thu May 06 12:44:17 2021 +0000

[

@@ -1,34 +1,73 @@
<macros>
     <token name="@DISCOSNP_VERSION@">2.5.4</token>

+    <token name="@PROFILE@">20.01</token>
+
     <xml name="discosnp_requirements">
         <requirements>
             <requirement type="package" version="@DISCOSNP_VERSION@">discosnp</requirement>
         </requirements>
     </xml>

-    <token name="@discosnp_single_reads@"><![CDATA[
-        #for $input in $input_type_options.list_reads
-            #set $filename = os.path.basename(str($input)) + "." + $input.ext
-            ln -sf '${input}' '${filename}' &&
+    <token name="@discosnp_single_for@"><![CDATA[
+        #for $input in $input_type_options.list_reads:
+    ]]></token>
+
+    <token name="@discosnp_single_end_for@"><![CDATA[
             echo '${filename}' >> input.lst &&
         #end for
     ]]></token>

-    <token name="@discosnp_paired_reads@"><![CDATA[
-        #for $i, $paired in enumerate( $input_type_options.list_paired_reads )
+    <token name="@single_reads@"><![CDATA[
+        #import re
+        #set $base_filename = re.sub('[^\w_]', '_', $input.element_identifier)
+        #if $input.ext.startswith('fasta'):
+            #set filename = $base_filename + ".fasta"
+        #else:
+            #set filename = $base_filename + ".fastq"
+        #end if
+        #if $input.ext.endswith('.gz'):
+            gunzip -c '${input}' > '${filename}' &&
+        #else:
+            ln -sf '${input}' '${filename}' &&
+        #end if
+    ]]></token>

-            #set $filenameFWD = os.path.basename(str($paired.forward)) + "." + $paired.forward.ext
-            ln -sf '${paired.forward}' '${filenameFWD}' &&
+    <token name="@discosnp_paired_for@"><![CDATA[
+        #for $i, $paired in enumerate($input_type_options.list_paired_reads):
+    ]]></token>

-            #set $filenameREV = os.path.basename(str($paired.reverse)) + "." + $paired.reverse.ext
-            ln -sf '${paired.reverse}' '${filenameREV}' &&
+    <token name="@discosnp_paired_end_for@"><![CDATA[
+            echo '${forward}' > "paired_${i}.lst" &&
+            echo '${reverse}' >> "paired_${i}.lst" &&
+            echo "paired_${i}.lst" >> input.lst &&
+        #end for
+    ]]></token>

-            echo '${filenameFWD}' > "paired_${i}.lst" &&
-            echo '${filenameREV}' >> "paired_${i}.lst" &&
-            echo "paired_${i}.lst" >> input.lst &&
+    <token name="@paired_reads@"><![CDATA[
+        #set $base_forward = re.sub('[^\w_]', '_', $paired.forward.element_identifier)
+        #if $paired.forward.ext.startswith('fasta'):
+            #set forward = $base_forward + ".fasta"
+        #else:
+            #set forward = $base_forward + ".fastq"
+        #end if
+        #if $paired.forward.ext.endswith('.gz'):
+            gunzip -c '$paired.forward' > '$forward' &&
+        #else:
+            ln -sf '${paired.forward}' '$forward' &&
+        #end if

-        #end for
+        #set $base_reverse = re.sub('[^\w_]', '_', $paired.reverse.element_identifier)
+        #if $paired.reverse.ext.startswith('fasta'):
+            #set reverse = $base_reverse + ".fasta"
+        #else:
+            #set reverse = $base_reverse + ".fastq"
+        #end if
+        #if $paired.reverse.ext.endswith('.gz'):
+            gunzip -c '$paired.reverse' > '$reverse' &&
+        #else:
+            ln -sf '${paired.reverse}' '$reverse' &&
+        #end if
     ]]></token>

     <xml name="discosnp_inputs">
@@ -39,14 +78,14 @@
                 <option value="mix">Both single and paired reads</option>
             </param>
             <when value="single">
-                <param name='list_reads' argument="-r" format="fasta,fastq" type="data" multiple="true" label="Single read files" />
+                <param name='list_reads' argument="-r" format="fasta,fasta.gz,fastq,fastq.gz" type="data" multiple="true" label="Single read files" />
             </when>
             <when value="paired">
-                <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" />
+                <param name='list_paired_reads' argument="-r" format="fasta,fasta.gz,fastq,fastq.gz" type="data_collection" collection_type="list:paired" multiple='true' label="List of paired read files" />
             </when>
             <when value="mix">
-                <param name='list_reads' argument="-r" format="fasta,fastq" type="data" multiple="true" label="Single read files" />
-                <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"/>
+                <param name='list_reads' argument="-r" format="fasta,fasta.gz,fastq,fastq.gz" type="data" multiple="true" label="Single read files" />
+                <param name='list_paired_reads' argument="-r" format="fasta,fasta.gz,fastq,fastq.gz" type="data_collection" collection_type="list:paired" multiple='true' label="List of paired read files"/>
             </when>
         </conditional>
     </xml>
@@ -97,8 +136,8 @@
     ]]></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 name="inputs" argument="-2" type="data" format="fasta,fastq.gz,fastq,fastq.gz" multiple="true" label="Short read FASTA/Q files" />
+        <param argument="-i" type="data" format="fasta,fastq.gz,fastq,fastq.gz" 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>

diff -r ccc77612cbb9 -r 7d4435f9c77d test-data/commet/A.fa
--- a/test-data/commet/A.fa Mon Aug 17 10:39:09 2020 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,24000 +0,0 @@\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 ccc77612cbb9 -r 7d4435f9c77d test-data/commet/A.fa.gz

Binary file test-data/commet/A.fa.gz has changed

diff -r ccc77612cbb9 -r 7d4435f9c77d test-data/commet/B.fa
--- a/test-data/commet/B.fa Mon Aug 17 10:39:09 2020 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,24000 +0,0 @@\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 ccc77612cbb9 -r 7d4435f9c77d test-data/commet/B.fa.gz

Binary file test-data/commet/B.fa.gz has changed

diff -r ccc77612cbb9 -r 7d4435f9c77d test-data/commet/C.fa
--- a/test-data/commet/C.fa Mon Aug 17 10:39:09 2020 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,20000 +0,0 @@\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 ccc77612cbb9 -r 7d4435f9c77d test-data/commet/C.fa.gz

Binary file test-data/commet/C.fa.gz has changed

diff -r ccc77612cbb9 -r 7d4435f9c77d test-data/commet/D.fa
--- a/test-data/commet/D.fa Mon Aug 17 10:39:09 2020 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

diff -r ccc77612cbb9 -r 7d4435f9c77d test-data/commet/D.fa.gz

Binary file test-data/commet/D.fa.gz has changed

diff -r ccc77612cbb9 -r 7d4435f9c77d test-data/discosnp/reads1
--- a/test-data/discosnp/reads1 Mon Aug 17 10:39:09 2020 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,2000 +0,0 @@\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 ccc77612cbb9 -r 7d4435f9c77d test-data/discosnp/reads1.gz

Binary file test-data/discosnp/reads1.gz has changed

diff -r ccc77612cbb9 -r 7d4435f9c77d test-data/discosnp/reads2
--- a/test-data/discosnp/reads2 Mon Aug 17 10:39:09 2020 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,2000 +0,0 @@\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 ccc77612cbb9 -r 7d4435f9c77d test-data/discosnp/reads2.gz

Binary file test-data/discosnp/reads2.gz has changed

diff -r ccc77612cbb9 -r 7d4435f9c77d test-data/discosnpRAD/loci_reads
--- a/test-data/discosnpRAD/loci_reads Mon Aug 17 10:39:09 2020 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,1000 +0,0 @@\n->read0_contig1_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n-TCTAGCGATTAACGTCAACGGACTTAACGGGGGATAATTTTTCGGGAGAATACAGTTACCGGGTGACTCCAACGCAGGGGACAACGAAAGCGGTTTAGGGGGGAATGCACGCTACGTCGCATTTTGAGTGAAAACCGGATCCACACTCAG\n->read1_contig3_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n-ACTACTTTGTTGTCCGCTCCAGGCAGGAATTAGGGCCCTAACGACACCTAATCCCTTCGCTGGACATATGATCGGGTAAAGAAGCTCGCATCCAATCGCTATTGACTAAGTAGGACACTAATTATCGGACGCTCCCCGGGGGAGGTCAAC\n->read2_contig4_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n-AAGAAGAGCTATGTTTTCGTCTCCTATATTTCTGACGGACCACGCCTAATTCCCACCTGGAGCCCTATTACAGAGGTCGCGTGCGTTTTTGGGTCACCCATCTGGTTTCCCCGCTCCGCATAGGTCATCATACGAACAGCCGCGATAGGA\n->read3_contig4_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n-TCCTATCGCGGCTGTTCGTATGATGACCTATGCGGAGCGGGGAAACCAGATGGGTGACCCAAAAACGCACGCGACCTCTGTAATAGGGCTCCAGGTGGGAATTAGGCGTGGTCCGTCAGAAATATAGGAGACGAAAACATAGCTCTTCTT\n->read4_contig0_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n-AAGCAGATTAGGACGACTCGGTGCTTTCGTGGATATGCTGTGGCCCGAGTGATGGGCGTCGTGTATGCAGAGGCCGTCGATGACTAAAGTTCCCTTGGCTTCGGTCAAGCCGTTTACATTATACCCGTATTTGGGACTGAGACCGTGTTG\n->read5_contig3_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n-GTTGACCTCCCCCGGGGAGCGTCCGATAATTAGTGTCCTACTTAGTCAATAGCGATTGGATGCGAGCTTCTTTACCCGATCATATGTCCAGCGAAGGGATTAGGTGTCGTTAGGGCCCTAATTCCTGCCTGGAGCGGACAACAAAGTAGT\n->read6_contig3_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n-ACTACTTTGTTGTCCGCTCCAGGCAGGAATTAGGGCCCTAACGACACCTAATCCCTTCGCTGGACATATGATCGGGTAAAGAAGCTCGCATCCAATCGCTATTGACTAAGTAGGACACTAATTATCGGACGCTCCCCGGGGGAGGTCAAC\n->read7_contig3_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n-GTTGACCTCCCCCGGGGAGCGTCCGATAATTAGTGTCCTACTTAGTCAATAGCGATTGGATGCGAGCTTCTTTACCCGATCATATGTCCAGCGAAGGGATTAGGTGTCGTTAGGGCCCTAATTCCTGCCTGGAGCGGACAACAAAGTAGT\n->read8_contig2_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n-TCCCTCCTTCACTCCCTGTATCATACGGTGCCGCTCCTCAGGGGTTATTGAAAACTAGACCGTCTAGCCAATATAAAGGGAACTTGTAAGATCGCCTCTCCTGTCCAGGGCGAGTGAGCTGGTCGTTGGCTTATGAGCTGACTCAACGAC\n->read9_contig4_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n-AAGAAGAGCTATGTTTTCGTCTCCTATATTTCTGACGGACCACGCCTAATTCCCACCTGGAGCCCTATTACAGAGGTCGCGTGCGTTTTTGGGTCACCCATCTGGTTTCCCCGCTCCGCATAGGTCATCATACGAACAGCCGCGATAGGA\n->read10_contig4_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n-TCCTATCGCGGCTGTTCGTATGATGACCTATGCGGAGCGGGGAAACCAGATGGGTGACCCAAAAACGCACGCGACCTCTGTAATAGGGCTCCAGGTGGGAATTAGGCGTGGTCCGTCAGAAATATAGGAGACGAAAACATAGCTCTTCTT\n->read11_contig2_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n-TCCCTCCTTCACTCCCTGTATCATACGGTGCCGCTCCTCAGGGGTTATTGAAAACTAGACCGTCTAGCCAATATAAAGGGAACTTGTAAGATCGCCTCTCCTGTCCAGGGCGAGTGAGCTGGTCGTTGGCTTATGAGCTGACTCAACGAC\n->read12_contig2_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n-TCCCTCCTTCACTCCCTGTATCATACGGTGCCGCTCCTCAGGGGTTATTGAAAACTAGACCGTCTAGCCAATATAAAGGGAACTTGTAAGATCGCCTCTCCTGTCCAGGGCGAGTGAGCTGGTCGTTGGCTTATGAGCTGACTCAACGAC\n->read13_contig1_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n-TCTAGCGATTAACGTCAACGGACTTAACGGGGGATAATTTTTCGGGAGAATACAGTTACCGGGTGACTCCAACGCAGGGGACAACGAAAGCGGTTTAGGGGGGAATGCACGCTACGTCGCATTTTGAGTGAAAACCGGATCCACACTCAG\n->read14_contig1_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n-CTGAGTGTGGATCCGGTTTTCACTCAAAATGCGACGTAGCGTGCATTCCCCCCTAAACCGCTTTCGTTGTCCCCTGCGTTGGAGTCACCCGGTAACTGTATTCTCCCGAAAAATTATCCCCCGTTAAGTCCGTTGACGTTAATCGCTAGA\n->read15_contig3_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n-ACTACTTTGTTGTCCGCTCCAGGCAGGAATTAGGGCCCTAACGACACCTAATCCCTTCGCTGGACATATGATCGGGTAAAGAAGCTCGCATCCAATCGCTATTGACTAAGTAGGACACTAATTATCGGACGCTCCCCGGGGGAGGTCAAC\n->read16_contig2_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n-TCCCTCCTTCACTCCCTGTATCATACGGTGCCGCTCCTCAGGGGTTATTGAAAACTAGACCGTCTAGCCAATATAAAGGGAACTTGTAAGATCGCCTCTCCTGTCCAGGGCGAGTGAGCTGGTCGTTGGCTTATGAGCTGACTCAACGAC\n->read17_contig4_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n-AAGAAGAGCTATGTTTTCGTCTCCTATATTTCTGACGGACCACGCCTAATTCCCACCTGGAGCCCTATTACAGAGGTCGCGTGCGTTTTTGGGTCACCCATCTGGTTTCCCCGCTCCGCATAGGTCATCATACGAACAGCCGCGA'..b'g2_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n-GTCGTTGAGTCAGCTCATAAGCCAACGACCAGCTCACTCGCCCTGGACAGGAGAGGCGATCTTACAAGTACCCTTTATATTGGCTAGACGGTCTAGTTTTCAATAACCCCTGAGGAGCGGCACAGTATGATACAGGGAGTGAAGGAGGGA\n->read233_contig0_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n-CAACACGGTCTCAGTCCCAAATACGGGTATAATGTAAACGGCTTGACCGAAGCCAAGGGAACTTTAGTCATCGACGGCCTCTGCATACACGACGCCCATCACTCGGGCCACAGCATATCCACGAAAGCACCGAGTCGTCCTAATCTGCTT\n->read234_contig2_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n-GTCGTTGAGTCAGCTCATAAGCCAACGACCAGCTCACTCGCCCTGGACAGGAGAGGCGATCTTACAAGTACCCTTTATATTGGCTAGACGGTCTAGTTTTCAATAACCCCTGAGGAGCGGCACAGTATGATACAGGGAGTGAAGGAGGGA\n->read235_contig4_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n-TTCTATCGCGGCTGTTCGTATGATGACCTATGCGGAGAGGGGAAACCAGATGGGTGACCCAAAAACGCACGCGACCTCTGTAATAGGGCTCCAGGTGGGAATTAGGCGTGGTCCGTCAGGAATATAGGAGACGAAAACATAGCTCTTCTT\n->read236_contig2_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n-TCCCTCCTTCACTCCCTGTATCATACTGTGCCGCTCCTCAGGGGTTATTGAAAACTAGACCGTCTAGCCAATATAAAGGGTACTTGTAAGATCGCCTCTCCTGTCCAGGGCGAGTGAGCTGGTCGTTGGCTTATGAGCTGACTCAACGAC\n->read237_contig1_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n-TCTAGCGATTAACGTCAACGGACTTAACGGGGGATAATTTTTCGGGAGAATACAGTTACCGGGTGACTCCAACGCAGGGGACAACGAAAGCGGTTTAGGGGGGAATGCACGCTACGTCGCATTTTGAGTGAAAACCGGATCCACACTCAG\n->read238_contig0_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n-CAACACGGTCTCAGTCCCAAATACGGGTATAATGTAAACGGCTTGACCGAAGCCAAGGGAACTTTAGTCATCGACGGCCTCTGCATACACGACGCCCATCACTCGGGCCACAGCATATCCACGAAAGCACCGAGTCGTCCTAATCTGCTT\n->read239_contig3_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n-GTTGACCTCCCCCAGGGAGCGTCCGATAATTAGTGTCCTACTTAGTCAATAGGGATTGGATGCGAGCTTCTTTACCCGATCATACGTCCAGCGAAGGGATTAGCTGTCGTTAGGGCCCTAATTCCTGCCTGGAGCGGACAACAAAGTAGT\n->read240_contig2_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n-GTCGTTGAGTCAGCTCATAAGCCAACGACCAGCTCACTCGCCCTGGACAGGAGAGGCGATCTTACAAGTACCCTTTATATTGGCTAGACGGTCTAGTTTTCAATAACCCCTGAGGAGCGGCACAGTATGATACAGGGAGTGAAGGAGGGA\n->read241_contig3_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n-GTTGACCTCCCCCAGGGAGCGTCCGATAATTAGTGTCCTACTTAGTCAATAGGGATTGGATGCGAGCTTCTTTACCCGATCATACGTCCAGCGAAGGGATTAGCTGTCGTTAGGGCCCTAATTCCTGCCTGGAGCGGACAACAAAGTAGT\n->read242_contig1_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n-TCTAGCGATTAACGTCAACGGACTTAACGGGGGATAATTTTTCGGGAGAATACAGTTACCGGGTGACTCCAACGCAGGGGACAACGAAAGCGGTTTAGGGGGGAATGCACGCTACGTCGCATTTTGAGTGAAAACCGGATCCACACTCAG\n->read243_contig0_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n-AAGCAGATTAGGACGACTCGGTGCTTTCGTGGATATGCTGTGGCCCGAGTGATGGGCGTCGTGTATGCAGAGGCCGTCGATGACTAAAGTTCCCTTGGCTTCGGTCAAGCCGTTTACATTATACCCGTATTTGGGACTGAGACCGTGTTG\n->read244_contig1_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n-TCTAGCGATTAACGTCAACGGACTTAACGGGGGATAATTTTTCGGGAGAATACAGTTACCGGGTGACTCCAACGCAGGGGACAACGAAAGCGGTTTAGGGGGGAATGCACGCTACGTCGCATTTTGAGTGAAAACCGGATCCACACTCAG\n->read245_contig0_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n-CAACACGGTCTCAGTCCCAAATACGGGTATAATGTAAACGGCTTGACCGAAGCCAAGGGAACTTTAGTCATCGACGGCCTCTGCATACACGACGCCCATCACTCGGGCCACAGCATATCCACGAAAGCACCGAGTCGTCCTAATCTGCTT\n->read246_contig1_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n-CTGAGTGTGGATCCGGTTTTCACTCAAAATGCGACGTAGCGTGCATTCCCCCCTAAACCGCTTTCGTTGTCCCCTGCGTTGGAGTCACCCGGTAACTGTATTCTCCCGAAAAATTATCCCCCGTTAAGTCCGTTGACGTTAATCGCTAGA\n->read247_contig0_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0\n-AAGCAGATTAGGACGACTCGGTGCTTTCGTGGATATGCTGTGGCCCGAGTGATGGGCGTCGTGTATGCAGAGGCCGTCGATGACTAAAGTTCCCTTGGCTTCGGTCAAGCCGTTTACATTATACCCGTATTTGGGACTGAGACCGTGTTG\n->read248_contig3_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n-GTTGACCTCCCCCAGGGAGCGTCCGATAATTAGTGTCCTACTTAGTCAATAGGGATTGGATGCGAGCTTCTTTACCCGATCATACGTCCAGCGAAGGGATTAGCTGTCGTTAGGGCCCTAATTCCTGCCTGGAGCGGACAACAAAGTAGT\n->read249_contig4_position0_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1\n-AAGAAGAGCTATGTTTTCGTCTCCTATATTCCTGACGGACCACGCCTAATTCCCACCTGGAGCCCTATTACAGAGGTCGCGTGCGTTTTTGGGTCACCCATCTGGTTTCCCCTCTCCGCATAGGTCATCATACGAACAGCCGCGATAGAA\n'

diff -r ccc77612cbb9 -r 7d4435f9c77d test-data/discosnpRAD/loci_reads.gz

Binary file test-data/discosnpRAD/loci_reads.gz has changed

diff -r ccc77612cbb9 -r 7d4435f9c77d test-data/kissplice/reads1
--- a/test-data/kissplice/reads1 Mon Aug 17 10:39:09 2020 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b"@@ -1,672 +0,0 @@\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 ccc77612cbb9 -r 7d4435f9c77d test-data/kissplice/reads1.gz

Binary file test-data/kissplice/reads1.gz has changed

diff -r ccc77612cbb9 -r 7d4435f9c77d test-data/kissplice/reads2
--- a/test-data/kissplice/reads2 Mon Aug 17 10:39:09 2020 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b"@@ -1,782 +0,0 @@\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 ccc77612cbb9 -r 7d4435f9c77d test-data/kissplice/reads2.gz

Binary file test-data/kissplice/reads2.gz has changed

diff -r ccc77612cbb9 -r 7d4435f9c77d test-data/lordec/coli-pacbio-test-mini.fa
--- a/test-data/lordec/coli-pacbio-test-mini.fa Mon Aug 17 10:39:09 2020 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,50 +0,0 @@\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 ccc77612cbb9 -r 7d4435f9c77d test-data/lordec/coli-pacbio-test-mini.fa.gz

Binary file test-data/lordec/coli-pacbio-test-mini.fa.gz has changed

diff -r ccc77612cbb9 -r 7d4435f9c77d test-data/lordec/ill-test-5K-1.fa
--- a/test-data/lordec/ill-test-5K-1.fa Mon Aug 17 10:39:09 2020 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,10000 +0,0 @@\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 ccc77612cbb9 -r 7d4435f9c77d test-data/lordec/ill-test-5K-1.fa.gz

Binary file test-data/lordec/ill-test-5K-1.fa.gz has changed

diff -r ccc77612cbb9 -r 7d4435f9c77d test-data/lordec/ill-test-5K-2.fa
--- a/test-data/lordec/ill-test-5K-2.fa Mon Aug 17 10:39:09 2020 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,10000 +0,0 @@\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 ccc77612cbb9 -r 7d4435f9c77d test-data/lordec/ill-test-5K-2.fa.gz

Binary file test-data/lordec/ill-test-5K-2.fa.gz has changed

diff -r ccc77612cbb9 -r 7d4435f9c77d test-data/mapsembler2/reads1
--- a/test-data/mapsembler2/reads1 Mon Aug 17 10:39:09 2020 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,12884 +0,0 @@\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 ccc77612cbb9 -r 7d4435f9c77d test-data/mapsembler2/reads1.gz

Binary file test-data/mapsembler2/reads1.gz has changed

diff -r ccc77612cbb9 -r 7d4435f9c77d test-data/mapsembler2/reads2
--- a/test-data/mapsembler2/reads2 Mon Aug 17 10:39:09 2020 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,12884 +0,0 @@\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 ccc77612cbb9 -r 7d4435f9c77d test-data/mapsembler2/reads2.gz

Binary file test-data/mapsembler2/reads2.gz has changed

diff -r ccc77612cbb9 -r 7d4435f9c77d test-data/mapsembler2/starter.fa
--- a/test-data/mapsembler2/starter.fa Mon Aug 17 10:39:09 2020 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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

diff -r ccc77612cbb9 -r 7d4435f9c77d test-data/mapsembler2/starter.fa.gz

Binary file test-data/mapsembler2/starter.fa.gz has changed

diff -r ccc77612cbb9 -r 7d4435f9c77d test-data/takeabreak/toy_example_reads.fasta
--- a/test-data/takeabreak/toy_example_reads.fasta Mon Aug 17 10:39:09 2020 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,800 +0,0 @@\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 ccc77612cbb9 -r 7d4435f9c77d test-data/takeabreak/toy_example_reads.fasta.gz

Binary file test-data/takeabreak/toy_example_reads.fasta.gz has changed

diff -r ccc77612cbb9 -r 7d4435f9c77d test-data/takeabreak/toy_example_with_inv_reads.fasta
--- a/test-data/takeabreak/toy_example_with_inv_reads.fasta Mon Aug 17 10:39:09 2020 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,800 +0,0 @@\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'

diff -r ccc77612cbb9 -r 7d4435f9c77d test-data/takeabreak/toy_example_with_inv_reads.fasta.gz

Binary file test-data/takeabreak/toy_example_with_inv_reads.fasta.gz has changed