Galaxy |

Changeset 0:aaa868913641 (2022-09-22)

Next changeset 1:bd2a15dbcea1 (2023-10-20)

Commit message:
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a

diff -r 000000000000 -r aaa868913641 macro.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macro.xml Thu Sep 22 07:51:48 2022 +0000

[

@@ -0,0 +1,43 @@
+
+<macros>
+  <token name="@TOOL_VERSION@">0.5.0</token>
+  <token name="@VERSION_SUFFIX@">0</token>
+  <token name="@PROFILE@">21.05</token>
+  <token name="@THREADS@">\${GALAXY_SLOTS:-7}</token>
+  <xml name="version_command">
+     <version_command><![CDATA[polypolish -V]]></version_command>
+  </xml>
+  <xml name="xrefs">
+    <xrefs>
+      <xref type='bio.tools'>Polypolish</xref>
+    </xrefs>
+  </xml>
+  <xml name="requirements">
+    <requirements>
+      <requirement type="package" version="@TOOL_VERSION@">polypolish</requirement>
+      <requirement type="package" version="1.13">samtools</requirement>
+    </requirements>
+  </xml>
+  <xml name="citations">
+      <citations>
+          <citation type="doi">10.1371/journal.pcbi.1009802</citation>
+      </citations>
+  </xml>
+  
+  <xml name="filter_option">
+      <conditional name="insert_filter">
+          <param name="filter_select" type="select" label="Filter by insert size ? [recommanded]"
+                 help="Exclude some alignments based on their insert size. It reduce the number of excessive alignments,
+                 particularly near the edges of repeat sequences">
+              <option value="filter" selected="true">Filter by insert size</option>
+              <option value="non_filter"> No filtering step</option>
+          </param>
+          <when value="filter">
+              <param name="low" argument="--low" type="float" min="0" value="0.1" label="Low percentile threshold" help="Select the lower value to remove [default: 0.1]"/>
+              <param name="high" argument="--high" type="float" min="0" value="99.9" label="High percentile threshold" help="Select the lower value to remove [default: 99.9]"/>
+          </when>
+          <when value="non_filter">
+          </when>
+      </conditional>
+  </xml>
+</macros>

diff -r 000000000000 -r aaa868913641 polypolish.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/polypolish.xml Thu Sep 22 07:51:48 2022 +0000

[

b'@@ -0,0 +1,422 @@\n+<tool id="polypolish" name="Polypolish" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">\n+ <description>\n+ Short-read polishing of long-read bacterial genome assemblies\n+ </description>\n+ <macros>\n+ <import>macro.xml</import>\n+ </macros>\n+ <expand macro=\'xrefs\'/>\n+ <expand macro="requirements" />\n+ <expand macro="version_command" />\n+ <command detect_errors="aggressive"><![CDATA[\n+ ln -s \'$input.fasta_file\' input_data &&\n+ #*======================================\n+ For single SAM\n+ ======================================*#\n+ #if $input.sam_data_type.sam_selector == \'single\'\n+ #if $input.sam_data_type.single_sam.ext == \'unsorted.bam\'\n+ samtools view -h $input.sam_data_type.single_sam > input_sam &&\n+ #elif $input.sam_data_type.single_sam.ext == \'sam\'\n+ ln -s $input.sam_data_type.single_sam input_sam &&\n+ #end if\n+ polypolish input_data input_sam > \'$polished_fasta\'\n+ #*======================================\n+ For paired SAM\n+ ======================================*#\n+ #elif $input.sam_data_type.sam_selector == \'paired\'\n+ #if $input.sam_data_type.R1_sam.ext == \'unsorted.bam\'\n+ samtools view -h $input.sam_data_type.R1_sam > sample_R1.sam &&\n+ #elif $input.sam_data_type.R1_sam.ext == \'sam\'\n+ ln -s \'$input.sam_data_type.R1_sam\' sample_R1.sam &&\n+ #end if\n+ #if $input.sam_data_type.R2_sam.ext == \'unsorted.bam\'\n+ samtools view -h $input.sam_data_type.R2_sam > sample_R2.sam &&\n+ #elif $input.sam_data_type.R2_sam.ext == \'sam\'\n+ ln -s \'$input.sam_data_type.R2_sam\' sample_R2.sam &&\n+ #end if\n+ #if $input.sam_data_type.insert_filter.filter_select == \'filter\'\n+ polypolish_insert_filter.py --low \'$input.sam_data_type.insert_filter.low\'\n+ --high \'$input.sam_data_type.insert_filter.high\'\n+ --in1 sample_R1.sam\n+ --in2 sample_R2.sam\n+ --out1 \'filtered_1.sam\'\n+ --out2 \'filtered_2.sam\' &&\n+ polypolish input_data \'filtered_1.sam\' \'filtered_2.sam\' > $polished_fasta\n+ #else\n+ polypolish input_data sample_R1.sam sample_R2.sam > $polished_fasta\n+ #end if\n+ #*======================================\n+ For multiple single-end SAM\n+ ======================================*#\n+ #elif $input.sam_data_type.sam_selector == \'multiple_single\'\n+ mkdir single_collection &&\n+ #for $value, $single_sam in enumerate($input.sam_data_type.single_collection):\n+ #if $single_sam.ext == \'unsorted.bam\'\n+ samtools view -h $single_sam > \'single_collection/$(single_sam.element_identifier).sam\' &&\n+ #elif $single_sam.ext == \'sam\'\n+ ln -s $single_sam \'single_collection/$(single_sam.element_identifier).$(single_sam.ext)\' &&\n+ #end if\n+ #end for\n+ polypolish input_data single_collection/*.sam > \'$polished_fasta\'\n+ #*======================================\n+ For multiple paired-end SAM\n+ ======================================*#\n+ #elif $input.sam_data_type.sam_selector == "multiple_paired"\n+ mkdir paired_collection &&\n+ #for $value, $paired_sam in enumerate($input.sam_data_type.paired_collection):\n+ #if $paired_sam.forward.ext == \'unsorted.bam\'\n+ samtools view -h $paired_sam.forward > \'paired_collection/forward_input$(value)$(paired_sam.forward.element_identifier).sam\' &&\n+ #else\n+'..b'onal>\n+ </section>\n+ <section name="options">\n+ <param name="debug" value="false"/>\n+ <param name="keep_logfile" value="false"/>\n+ </section>\n+ <output name="polished_fasta" value="polished.fasta"/>\n+ </test>\n+ \n+ <test expect_num_outputs="1">\n+ <section name="input">\n+ <param name="fasta_file" value="contigs.fa"/>\n+ <conditional name="sam_data_type">\n+ <param name="sam_selector" value="multiple_paired"/>\n+ <param name="paired_collection">\n+ <collection type="list:paired">\n+ <element name="paired_1">\n+ <collection type="paired">\n+ <element name="forward" value="aligned_test_file/alignement_R1.bam" ftype="unsorted.bam"/>\n+ <element name="reverse" value="aligned_test_file/alignement_R2.bam" ftype="unsorted.bam"/>\n+ </collection>\n+ </element>\n+ <element name="paired_2">\n+ <collection type="paired">\n+ <element name="forward" value="aligned_test_file/alignement_R1_bis.bam" ftype="unsorted.bam"/>\n+ <element name="reverse" value="aligned_test_file/alignement_R2_bis.bam" ftype="unsorted.bam"/>\n+ </collection>\n+ </element>\n+ <element name="paired_3">\n+ <collection type="paired">\n+ <element name="forward" value="aligned_test_file/alignement_R1_ter.bam" ftype="unsorted.bam"/>\n+ <element name="reverse" value="aligned_test_file/alignement_R2_ter.bam" ftype="unsorted.bam"/>\n+ </collection>\n+ </element>\n+ </collection>\n+ </param>\n+ </conditional>\n+ </section>\n+ <section name="options">\n+ <param name="debug" value="false"/>\n+ <param name="keep_logfile" value="false"/>\n+ </section>\n+ <output name="polished_fasta" value="polished.fasta"/>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+ **What it does**\n+ Polypolish is a tool for polishing genome assemblies with short reads.\n+ Polypolish uses SAM/BAM files where each read has been aligned to all possible locations (not just a single best location).\n+ This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix.\n+\n+ **Polypolish pipeline steps**\n+ 1. [Optional] Filter aligned reads\n+ - Exclude some alignments based on their insert size\n+ - This should reduce the number of excessive alignments, particularly near the edges of repeat sequences, improving Polypolish\'s ability to fix errors in those regions.\n+ 2. Clean assembly with filtered reads\n+\n+ **Inputs**\n+ Polypolish need SAM/BAM input format obtain from aligner with option to keep all possible location\n+ Polypolish take on or more assembly as input fasta.\n+ It need also raw data reads in single or paired-end SAM/BAM format.\n+ You can use multiple aligned data to polish the same assembly.\n+ **WARNING It can only work if multiple location information is available in sam/bam files**\n+ For example using bwa mem to align raw data before use, you need :\n+ 1. To align each read data independantly (also for paired data)\n+ 2. Set the option "Output all alignments for single-ends or unpaired paired-ends" in Select analysis mode>Set input/output options\n+ - This allow multiple ailgnemnt output need to use polypolish\n+\n+ \n+ ]]></help>\n+ <expand macro="citations"/>\n+</tool>\n'

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diff -r 000000000000 -r aaa868913641 test-data/aligned_test_file/alignement_R1.bam

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diff -r 000000000000 -r aaa868913641 test-data/aligned_test_file/alignement_R1.sam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/aligned_test_file/alignement_R1.sam Thu Sep 22 07:51:48 2022 +0000

b'@@ -0,0 +1,1417 @@\n+@SQ\tSN:contig00001\tLN:5513\n+@SQ\tSN:contig00002\tLN:3532\n+@SQ\tSN:contig00003\tLN:3227\n+@SQ\tSN:contig00004\tLN:3138\n+@PG\tID:bwa\tPN:bwa\tVN:0.7.17-r1188\tCL:bwa mem -t 6 -a contigs.fa R1.fastqred.gz\n+M00536:853:000000000-C843B:1:1101:13480:1462\t4\t*\t0\t0\t*\t*\t0\t0\tAAATAGATTGGTACCTTTATTTTTAGCCAATAAAGCACGCCTAGACAATTTGCGTTTTTCACGCTTTAGTTTCTTTTCCATTTTGGAGATCGGAAGTGCACACGTCTTAACTCCAGTCACTACATCTTTTCTCGTATGCCGTCTTCTTCTTTATAATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT\t--6CCCCFGDEFFFGGGGCFGGGGC,@C9,C,,,,;,C+69C,,,;,,;CE,6+@C+BD<,6,,BCF,,<CF@FFFF@@,CEEF,+,,,::,,,,+,,,,9,:+::B,,,:B99,,:9,9B,9,:9,,,9,:9,A+A,59+@6AC5A,9AA,,,,,,,,,,++++3++++3+3*11**1****1*1**1/**/////**/*//*/////*//////*/*/////))//)/////)/))/*00*.)0)).)).).),),.,0(.,,((,,,((,,,(-,(,-,,,,,,,(,-,,(,-((,(,\tAS:i:0\tXS:i:0\n+M00536:853:000000000-C843B:1:1101:13016:1699\t4\t*\t0\t0\t*\t*\t0\t0\tATGCGAACAGCAGAGGAGTAGATTCATTCGGTATGAATATCGGTGGAAAACATGCGTTTCCATTCGGCGTGGTAAAATTCGTACATGCACAGCATAGTTCAAGCTATGAAGTAGACGGTATCGTTCAGTATATATGATCGCACTGGTTTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTACATCGGATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAATTTTTTTTTATTTACTTTTTTTTTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTTTTCTTTTTTCTTTTTTTT\tCCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGDFFFFFFGFFGGGGFFAFGFFFEEGEGGGFCCGGGGGGGGGGGGGGGGGGGDGGF9AEFGFGAAAEFCAAFCCFCGGGGGGCFGDGGGFGGFGGGGGGGGFGGGEE8FGGGCCC@@DEFCFEGGGF99@FEE?FFGCFGFGGGGCC6EEGFGGCGCGEEGGGGGGFGGGF6,5,7*)847**+++)1))*+1++++*0**)).).))/**-/(),),)((,(,((,,((((((((-)).)(-))-)-(-))).,,(\tAS:i:0\tXS:i:0\n+M00536:853:000000000-C843B:1:1101:17713:1721\t4\t*\t0\t0\t*\t*\t0\t0\tATAATAAGCCCAAAAATAATGGGGTAAATACACCTTGTATTTGGGGTGATTACTATTATTTAGAAGCTTTAGTGAGAATGACTAGTAATTGGTCTTCTTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTACATCGGATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAATTTTTTTTTTCTTTTTTTTTTTTTTTTTTTTTCTTTTCTTCTTTACTTTTTTTTCTTCTTTTTTTATTTTTTTCTTCTTTCTATTTCTTTTTTTTTTCCTTTCTTTCTTTTTTTTTTTCTTTCTTT\t9CCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGDGD8FGDEGCGGAFGG9FC,CDGGGC<FACCA<FEFGGFGGGGFGFDGGGGGGGGA9FFEC7,+8<BEFFFCFGGC9@FGGFF8FGGGGGGGGGGGCCEFGGGDFDFFEGGGGGGCFFFC8,=9,+++++,3,,,3++**,,3,,,**/***///:3*/*1/+<?+0++0++2++22***9)))0**0**:0*)))*1*/*..)***1*/)*)*)*)*))).(-(,,(-)))))))..)).)(((((,(..6).))\tAS:i:0\tXS:i:0\n+M00536:853:000000000-C843B:1:1101:12539:1769\t4\t*\t0\t0\t*\t*\t0\t0\tATTACTTGCTCAATCAGCAGAATATCAGGAAATCGTCGCATCACAGGAGGAAGAATAGTTATGAAAGTAAAAAAATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTACATCGGATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAACAAATCTTTTCTTTTTTTTTTTTTTTTTTTTTCTTTTTTTTTTTTTATATTCTATTTTTTTTTTTTTTTTTTTTATTTTAAGTTATTCTCTTTTTTTTCTTCTGTATATTTCTTCTTATTTTTCATTTTTTCTTTACTTTTTTTTTAT\tCCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCGGDGGGGGFGGGGGGGFFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCFGGGGFGGGGGGGGGGGGGCFEGGGGGGGGGGGGGGGGGGGGGGFFDGDEEGD@+38,,8,,,,,,,,,,+****1******1***++2+++///*/2***++0++++03++2*/**2)*/)/1))/)*2**:****//*2/2**1***0.))***-*.*-*-*-))))))))))-)()))-)-425-))).2))),,,(,-\tAS:i:0\tXS:i:0\n+M00536:853:000000000-C843B:1:1101:15017:1781\t4\t*\t0\t0\t*\t*\t0\t0\tGTGGTAGTCCCTGCCCATGACTATGCAGATAAGATTCAAGCGCAAAGTCCTACAAAAGATCCTTCTGCTGTGATTGCAATCGAATTACCAGATGAAGTCATCATTACCGGGCGTACAAGTTCATTGATGGATGCGTCAGCGGCAGTTATCTTAAATGCAGTAAAACATTTAGCCCATATCGCAGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTACATCGGATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAACACCTTCGTATCTTCCACTGACTTAATCATTTTTTTTT\tCCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDGGFCGCFEF@CF8FGGGGGGGFFFG<DFFEFGGGFGGFFGGFFGGDFG9<9FGAFFGGGGGG@BECGGEGCGGGGEAFGFGGA<DEFGGGGGGGGGGDEFGCGGGGGGGGGGGGGGGGCFGGGGGG,3DFGFGGC>ECEGGGBFEGGGCCGGGGGGGGGGCFFAFFCFGGFGGGGGGGDGCDDFCCFCGGFFDGF<;FF6AFFFFFFFF05(81)-)(((-1)(((,.(-).6))).),).).)))-))).,,,,\tAS:i:0\tXS:i:0\n+M00536:853:000000000-C843B:1:1101:7894:1803\t4\t*\t0\t0\t*\t*\t0\t0\tGTCAGTACAAAGGACGCAGCACTGATAATGATCCAGATCAATAATACTGTATAGGAAAGAGAACCTGCCATATAGCCAAATAATTTGTCACCGACAAAATAAGAAAGAGCCACACCTAGATAAAGAACACTTGTACAAAACAGCACAGCACGTTGCGGTACTTGATGCTTGTTTTATACAGCTAGTTTTCTAGAGATCGGAAGAGCACACGTCTGAATTCCAGTCACTACATCGGACATCGTATGCCGTCTTCTGCTTGAAAATAAAAATTATGCCGTCTTTTGCTTGAATCTAATACAAT\t@ABCCFCC<9<,<,CCEGGGGGG8@'..b'GCCGCTGGCGGTATTCGTATGATGGAGGCGGCAATGCGAGGATTAGAAGAGGGGACTCCAGAAGGTGGAAAACGTCCGCTACTTCTAGCTATCACTCAGCTTACTTCTACAAGTGAAGAAGAAATGCATGCCGATCAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTACATCGGATCTCGTAT\tCCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGFGFGGFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFF44AAFFF0\tAS:i:0\tXS:i:0\n+M00536:853:000000000-C843B:1:1102:10666:11597\t4\t*\t0\t0\t*\t*\t0\t0\tCTAACGATACGGCTAAGCAGATTCAACCCTACGACTTTCCCTTTACCATCAGGTGTAGCAATTACTTTTCCAAAGTCAGGGAGTTCTTTTTTCGCTGTCTCGTATTCTTCGCTCTCATATTGCAGACAGCACATCAAGCGTCCGCATAAACCGGAAATTTTTGTTGGATTCAAAGATAAACTTTGATCTTTTGCCATTTTGATTGATACAGGCACGAAATCGCCTAAAAAAGAAGAACAGCATAATGGACGCCCACATGGACCAATTCCGCCTATTATCTTTGCTTCATCGCGGACACCAA\tCCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGFGFGGFEFAEFFFFFFFFFFFFFFFFFFFFFAFFFFFFFFFFFFFFFFFFFFFF2\tAS:i:0\tXS:i:0\n+M00536:853:000000000-C843B:1:1102:11833:11626\t4\t*\t0\t0\t*\t*\t0\t0\tAAAACTTGCAAGCCAATCTGTAACGTGTATTTTTCTTGATCTTGGATATATAACAGAGGACCTAAGAAATCATTCCAAGCTGCGTTGAAGGAATTGATCGCAATGGTAATCAAGGCAGGTTTCGTCAATGGAAGCATCAAATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTACATCGGATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAACTATGAAATACGACCCGATGCTCCCTACCCCCACCCCCCGCACCAACCAGACCTTCCCACAGCAAAGCACAGCACACTTA\tCCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG@EGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG1*4*,0,,+,,+42**)))))1**+2**2*;*1)))00))))))0))7()-8.)(.)1((()0-((((((,(.(,(,(((().\tAS:i:0\tXS:i:0\n+M00536:853:000000000-C843B:1:1102:23952:11634\t4\t*\t0\t0\t*\t*\t0\t0\tGCAGATGGAAGCGAAGCTTAATGATGCTGAACGTGAAAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTACATCGGATCTCGTATGCCGTCTTCTGCTTTAAAAAAAAAACACGTCTGAACTCCAGTCACAATCCAGCATCTCTTATCCCGTCTTCCTCTTGAAAACACACTTCCTCTCTTTTATTAATCTATTATTAGTAACATCATTATCCCCTCCTTCTTACAATTCTCCTTGTTACTTACCACTACCTGTCACTCTCTCTTATACTCTTACTCACACCCTTCTCACCACCTA\t@@CBCEGFGEG@@CB:@EDC@FC,E<FEECCDDDFFGEG<;8C@<;;F:8F@A6@6:FFGGEFGDE<<9EFCFGAF<@9,,8FF,<FGCGGD,+?:,C,<FEE9,9,<EFCF7:C?FB+:?=+B5A9FF8A<,,C,AFFF9AD,C,C<,CFA,78+,@,@@9>9>F,,8=93:,,+,,8,3,,4,,5,3,,7,733,55>3,,,3,,,,,4,>2,25,,:A*=79,4,,:,+1++++20++++++++++2+/))))0*1/3+1++))2)+)1)+)*))))1)/(./(((.(8).6.)-,.(\tAS:i:0\tXS:i:0\n+M00536:853:000000000-C843B:1:1102:20187:11655\t4\t*\t0\t0\t*\t*\t0\t0\tTGCAACTGCCGGTGGCACACCATCAGGCATTTTGATGATCAATTTTTCATTTCCGCTTAAACGTACAAAGATTTCTGTTGAAATAATCCCAACAATAATAGCAATAAACAAACCGTTTGAGCTCATACCTAATGCTCCGCCTAAAGCGAAGAAAGAGCCTAAAGAAATCACACCTGCGGAAACACCGTCTTTTCGGTAGCCGTTAGCTAAATGATAAGCAAGCAAGAAAGCAATCAAGACAGAAAGAATGGCAAATGTACCGTTCCAAGCAGCAGCCCCGAATCCTTTCCATGATTCACCC\tCCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGFF8?FGFCCFFFFFFFFFFFFFFFFFFFFFDF@FFFFFFFFFBAAAAFBA<AB<6)6<1\tAS:i:0\tXS:i:0\n+M00536:853:000000000-C843B:1:1102:14430:11676\t4\t*\t0\t0\t*\t*\t0\t0\tAACGACGATAGCTGCATGGTGATCATAGACCAAACCGGCAGGAGTTACCACATTTACTGTTAAATATTGATCCATGGGGCACCCCTTTCTAGTAGCCTAGTGTTTTCGCTTTTTCTACGACGTCTTCGATTCGGCCAACACTTCGGAAAGCTTCTTCAGGAAGATCATCGTATTTGCCTTCCAAGATTTCGCGGAATCCTTTCACTGTTTCTTCTACAGGGACATATGAACCTAGAAGACCAGTAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTACATCGGATCTCGTATGCCG\tCCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGFGGGFGFGGFFFFFFAFAFFFFFFFFFFFFFFFFFBDBFFFFFFFFF:>BF?3:?FFF1\tAS:i:0\tXS:i:0\n+M00536:853:000000000-C843B:1:1102:25570:11747\t4\t*\t0\t0\t*\t*\t0\t0\tCGAAATG\t*\tAS:i:0\tXS:i:0\n'

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--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/aligned_test_file/alignement_R1_ter.sam Thu Sep 22 07:51:48 2022 +0000

diff -r 000000000000 -r aaa868913641 test-data/aligned_test_file/alignement_R2.bam

Binary file test-data/aligned_test_file/alignement_R2.bam has changed

diff -r 000000000000 -r aaa868913641 test-data/aligned_test_file/alignement_R2.sam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/aligned_test_file/alignement_R2.sam Thu Sep 22 07:51:48 2022 +0000

b'@@ -0,0 +1,1228 @@\n+@SQ\tSN:contig00001\tLN:5513\n+@SQ\tSN:contig00002\tLN:3532\n+@SQ\tSN:contig00003\tLN:3227\n+@SQ\tSN:contig00004\tLN:3138\n+@PG\tID:bwa\tPN:bwa\tVN:0.7.17-r1188\tCL:bwa mem -t 6 -a contigs.fa R2.fastqred.gz\n+M00536:853:000000000-C843B:1:1101:13480:1462\t4\t*\t0\t0\t*\t*\t0\t0\tCCAAAATGGAAAAGAAACTAATGCGTGTACAACTCATTTTGTCTAGGCGTGCTTTATTGTCTAATAATAAAGGTACCAATCTATTTAGATCGGTTGTGCGTCGTGTAGGGTTAGTGTGTCTTAGGTTGTGTAGATCTCGTTTGTCTCCGTTTCTTTTTTATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTC\t88,,,,=,,,,,,,,,,;C,,,,6+B,,,;,,;,6,,,<C,C<E,,,,+8+,CEE,CF,,;C,,,,,<,,,,,;,;;,,:6C,CEF,,,:5,,,,+,,,,87+8,A,,,,,,,,,,:,9A,9,,,9A,@+@,,,:9C;,+9++94,44+9,94,@@,,+,,,,,,++1+1111119/1*////)///)//1))/...).))...).0))..((-(-*)-)((,,,,(-((-,((,(,((,(-(,(,(,(((((-,((-(,(,,,(,,,(,,,((,((-,(,,,,(,(((((-((,(,(,,(\tAS:i:0\tXS:i:0\n+M00536:853:000000000-C843B:1:1101:13016:1699\t4\t*\t0\t0\t*\t*\t0\t0\tAAACCAGTGCGATCATATATACTGAACGATACCGTCTACTTCATAGCTTGAACTATGCTGTGCATGTACGAATTTTACCACGCCGAATGGAAACGCATGTTTTCCACCGATATTCATACCGAATGAATCTACTCCTCTGCTGTTCGCATAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTCGTAGGTTGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAACTCTTATTCTTTTTTTCTTTCTCTTTTTTTTTTTTCTTTTTTTTTTTTTTTTTCTTTTTTTCACTTTTTCTC\t-@CCCGGGFFGGGGGGGGFGFGGC9CEFCGDEEBFEGCFGGFCFDCDFGCDCFGDGCFG9F,C9FEFCFEC8FFGGGFE9E::F:C@F<@C9EECC7FFFGGGDEEFB:+C@FG<<FDEE+++C:,,FEGCEFDEEFG?BD8EFECC>E6,>DDDDC6=,8DEGG6E6DC=C>8,9=7+D+DC>F+CCFG>?9C>8+?9;B**:*3@64?>9@2@=+9@*48*0(((,(())))).).1..).(-()))).).))).,(-(((-()))).,((((((-((,((.)-)),,()))))-)())\tAS:i:0\tXS:i:0\n+M00536:853:000000000-C843B:1:1101:17713:1721\t4\t*\t0\t0\t*\t*\t0\t0\tCAGAAGACCAATTACTAGTCATTCTCACTAAAGCTTCTAAATAATAGTAATCACCCCAAATACAAGGTGTATTTACCCCATTATTTTTGGGCTTATTATAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTCGTAGGTTGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAATTTCTTTTTCTTTCATTTTTCTTTTTTTTTTCTTTTTTTCTCCTTCTTTACTTTTTTTTTTTTTTTTTTTCTTATCTTTCTTTCTTTATCTTCTTTTTTCTTCTTTTGTTTTTTCTCTTTCC\t-8A<CFGGGGFGGGFGCFGGGGGGGGCFGA8,@EFGGGGCCFC<F9CF<CFGAEEFFD@8F<FD9<AFGGGGGGGFEFF7FG9FGGGGG@CEGG?EFAFCB9FFEG7=C8<BCFG7CFGFAAD,,,=,9FDGGCG,>+EF?ECFAF9EACDDDB=+AF>E=CGCC==EG8@=,,68++9++2+58++5*==++++++3+*1+?13*/*)2)***/*).(/).).)/)))))/)))((,(-(42(4(((((.-)-).4.).)).44)).)--).-4))-().))).)).((,(((-)).)))\tAS:i:0\tXS:i:0\n+M00536:853:000000000-C843B:1:1101:12539:1769\t4\t*\t0\t0\t*\t*\t0\t0\tATTTTTTTACTTTCATAACTATTCTTCCTCCTGTGATGCGACGATTTCCTGATATTCTGCTGATTGAGCAAGTAATAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTCGTAGGTTGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAACTATTTTTATTTTTTTTTTTCTTCTTTTTTTTTTTCTTTTTATATTTTTTTTTCTTATTTTTTCTCTTTTTCTTGTTTTCTTTTTTTCTTTTTTCATTTTCTTCTTTACTTTTGTTGTCTTTTTTTTGTGCTTCTCTCCTTATTT\t9CCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFDGGGGDFGDFGGFFGGCFFGGGGGFGFGGGFGFEECFGFGGGGGGGGGCCGGGGGGGGGDGFFCEFFCF8FGFGGGGCFGGGGGGGGGFGGGGGGGGGGGGGGGGEGGFGGCFEFCCC=8>5,37,,,3,35,7<*1**4/*,+14+++*)2/))1)3+1+0)1+1+**1.))))*)).)./.-())6)-))(-).).(,))))).,(.-).))((-)).)))-))).)))-))-.((.).-).)(,,((()-.)))))().)).)\tAS:i:0\tXS:i:0\n+M00536:853:000000000-C843B:1:1101:15017:1781\t4\t*\t0\t0\t*\t*\t0\t0\tCTGCGATATGGGCTAAATGTTTTACTGCATTTAAGATAACTGCCGCTGACGCATCCATCAATGAACTTGTACGCCCGGTAATGATGACTTCATCTGGTAATTCGATTGCAATCACAGCAGAAGGATCTTTTGTAGGACTTTGCGCTTGAATCTTATCTGCATAGTCATGGGCAGGGACTACCACAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTCGTAGGTTGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAACATTTCACTTTGTTTTTTTCTTTCCTCTCCGTCCAC\tCCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGG9FE9FFGGGGGGDGGE@FGGEGEFFGGGGGGCDFGGCEFGGGGGGGGGGGEFGCGFCFGGGGGGCFC<EGFCCFGC9?AEGCEEF<EC@EFGDFFFGGFEFGG9>EFFGAFCEGGFGGGGGFFGGGFGGGGAEEEGCFFDF6+?FDFDFFFDC?8D?DGDBD5AAEFBEF*@9AFFF?>CFDEEFFFFF>=CA24)>5/??ECEBB@(5>B@>766;1=ECEFE<C<6(2(3(-,.))).).))))(((((,.6).)))))(((-((()\tAS:i:0\tXS:i:0\n+M00536:853:000000000-C843B:1:1101:7894:1803\t4\t*\t0\t0\t*\t*\t0\t0\tCTAGAAAACTAGCTGTTTTAAACAAGCATCTAGTACCGCAACTTGCTGTGCTTTTTTGTTCCAGTGTTCTTTATCTAGGTGTTGCTCTTTCTTTTTTTGTCGGTGACAAATTATTTTGCTATCTGGCAGGTTCTCTTTCCTATACAGTATTATTGATCTGGCTCATTATCAGTTCTGCGTCCTTTGTTCTTTCAGATCTGAATCGCGTCGTGTAGGGGAAGAGTATCGTATGTTGGGTGTATCTCGGTGGTCGCCGTAACATTAAATAAACAACGATGACCTCCGGTTCTGATACTCCAAT\t@<6BCC@,CFFDFFFGFFFA8,;@C'..b'GGGFFGGGGGEGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGFFGGDGFFGGGGGGGGGGGGGGGGGGGGGGGEGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGEGFFGGGCFGGCEFFFFFGGGGGFGFGGDGGGFFGFGFF?F>BFFFFFFFFFFCFFFFDFFFFFD@EEEFFFFFFFFFFF<@E4@EFCEEFF@E?CAF244<B<A<2<(4:9<:3:AFFFBFAF:?:0:?,\tAS:i:0\tXS:i:0\n+M00536:853:000000000-C843B:1:1102:3230:7738\t4\t*\t0\t0\t*\t*\t0\t0\tCAGAATTTGGGATTGAGGTTATCTGTTATAATTTTATGCCAGTATTTGATTGGGTAAAATCGGATTTGGATTATCGTTTAGATGATGGGTCTTCTACGTTAGCCTATATTTCAAAAAATATCCCTACTGATCCGGAGGAAATTATTAGAGAAGTAGAAAATTCTACTAATAATTTTGAATTGCCGGGTTGGGAACCTCATCGGTTATCACAAATTAAGCAATTATTAGAAGCCTATAAAGAAGTTGATGAAGAGAAATTACGAGAGAACTTTGCATATTTTCTCAAAGCAATTATCCCGAC\tCCCCCGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGFGGEGGGGGGGGGGGGGGGFGGGFGGEGGGGGGGGGGGGGGGGCGFGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGFEFGGCFGGFGGGGGFFGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGDEGGFGGGGGGGGGGGGFGFAFGF?AFF8<?FFFFFF@F=EAFFFEFFF<CCEFFFCFEFFEEFFF@EEFEEEFF@@FFFE4>E@CEC6CEEF<)6??AE;@@<EFCFC@(6(\tAS:i:0\tXS:i:0\n+M00536:853:000000000-C843B:1:1102:17581:7750\t4\t*\t0\t0\t*\t*\t0\t0\tATACGCCCTCGCCTAATATACGTCCGTCTTTTTGAATACGTTCAACTAATTCTTTCACTTTATTTGCTCCTTTATCATTTATTAATACCGAAATAACCGCTTTTGTGCAAAAACCTACTATGTTTCTGTTAAAGAAAAACACCCTCCACTTTATCATAAGAAAAGAAGGGTGAAATAGCCAATCTTTTACTTATAGTCCAGCATTTACGGTACTGGCTAGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTCGTAGGTTGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAA\tCCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGFFFGFFFFFFFFFFFFFFFFDDFFFFFFFFFFFFFFFFDFFFFFFFFFFFFFFFFFFFFFFF5<CFFFF>DF>>F>08<?FFBAAA<B07937-\tAS:i:0\tXS:i:0\n+M00536:853:000000000-C843B:1:1102:4716:7781\t4\t*\t0\t0\t*\t*\t0\t0\tTGCTTGGTCAAATGGAAAAATACAGTCTGGGAACCCCAGCTACGCGTGCAGAGATTATCGAGAAACTAATCAAATCTGAACTGATGGAACGTATCCCTCAAGGACTGCAAGTATCTCCTAAAGGTAAGCAATTATTAGTATTGGTAAATCCCTCTTTAGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTCGTAGGTTGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAACAAAGAAAACTGTACAGGAGCAAATGGTTGAGGAAGACAGTGAAAAATATAATAAGGATA\tCCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGFFFGFFFFFFFEFFF>=FFFFFFFFEFFF1>1(((((,,/(((.)).))))(((,-,())).)(((()((.((()).))-.3).)4))))).3.\tAS:i:0\tXS:i:0\n+M00536:853:000000000-C843B:1:1102:22993:7847\t4\t*\t0\t0\t*\t*\t0\t0\tCCGATTGATCACATAAAAGGTGTCGAGAATCGCAAAAAATCAGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTCGTAGGTTGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAGAATAATAGAGACATAAGATGAAATGTAACATAACACTATAAACATAAAACAAAACCAAGCCTATCATATAATACATCCAATTTCGTAACACAATCAACTCAAACAACTACATAAATGTACAGCAATACACGCTGTCTAGCATACATGACCTTCACGTACACACCACATACGA\tCCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG@3+8+++,,8,,3,@@,,,8,,3,,5;DA9,7>,,7,,7,,,,>,,,2,54;,,5,=,,/,4,/****0+*,+21,++++*++*))+2+1.))0)+))(*4).)1)/2))(((..))))..)).).)))(,)))).23(((.))))-)-)..)-)())(),(.((4))(,(((.))((\tAS:i:0\tXS:i:0\n+M00536:853:000000000-C843B:1:1102:13033:7850\t4\t*\t0\t0\t*\t*\t0\t0\tCTTCTTTTTGAGTGAGGCGTGAAACGATTCGATACCGGCATTATCGTAGGGACAGCCCTTACGACTGAAGGAGTGCCGAATGTTCAATTCATTCAGCTTTGCCTCATAGGCTTCGCTAGTGTACTGAGAACCCAAATCTGAGTGGATAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTCGTAGGTTGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAACATAACCCTCTATATCCTATTACTCTTCTTCTTTTTCAACCTACTGCTCCTCCCTCTCTTCATTCCATTCTCTC\tCCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFFGGGDEGGGGGGGGEEEGGGCGGGCEGGGGDGFGGGFFFGCEFGGGGGGGGGGDFFGFGGGCCDGFGFF;C>FFFFFFFAA3>BE6B((/+.5(,22()6)6))5)))))-64-)-).).-))()))(.(,,).6))5((,.4(..).)-)).)).))-).\tAS:i:0\tXS:i:0\n+M00536:853:000000000-C843B:1:1102:22126:7854\t4\t*\t0\t0\t*\t*\t0\t0\tATCACGGTAGTCGTATCAGAAAAATAAGGAGGGATAATCAGTGGGTCAAAAAGTACATCCAATTGGAATGCGTGTAGGCATCATCCGCGACTGGGATGCTAAATGGTATGCTGAAAAAGAGTATGCTGAGTTCTTACACGAAGATTTAAGAATCCGTAAATTTATTTCAACTAAACTTGCTGATGCTGCTGTATCAACAGTTGAAATCGAACGCGCAACAGGTCGCGTAAACATTTCAATTCACACAGCTAAA\t*\tAS:i:0\tXS:i:0\n'

diff -r 000000000000 -r aaa868913641 test-data/aligned_test_file/alignement_R2_bis.bam

Binary file test-data/aligned_test_file/alignement_R2_bis.bam has changed

diff -r 000000000000 -r aaa868913641 test-data/aligned_test_file/alignement_R2_bis.sam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/aligned_test_file/alignement_R2_bis.sam Thu Sep 22 07:51:48 2022 +0000

diff -r 000000000000 -r aaa868913641 test-data/aligned_test_file/alignement_R2_ter.bam

Binary file test-data/aligned_test_file/alignement_R2_ter.bam has changed

diff -r 000000000000 -r aaa868913641 test-data/aligned_test_file/alignement_R2_ter.sam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/aligned_test_file/alignement_R2_ter.sam Thu Sep 22 07:51:48 2022 +0000

diff -r 000000000000 -r aaa868913641 test-data/contigs.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/contigs.fa Thu Sep 22 07:51:48 2022 +0000

b'@@ -0,0 +1,262 @@\n+>contig00001 len=5513 cov=11.7 corr=0 origname=NODE_1_length_5513_cov_11.741181_pilon sw=shovill-spades/1.1.0 date=20220302\n+CAGCATCGGACTCAGATAGTAATCCACGCTCTTTTAAAATGTCAACAAGAGAATCTCTAC\n+CATGAACAAAATGTGACTCATATCTAAACCAGTCCTTGACGAACGTGCCAAGCATATTAA\n+GCCACTTCTCCTCATCCAACGCGTCAGTTTTTGACAGAATCGTTAGTTGATGGCGAAAGG\n+TCGCAAAGTAAGAGCTTCTCGAGCTGCGCAAGGATAGGTCGAATTTTCTCATTTTCCGCC\n+AGCAGTCCACTTCGATTTAATTCGTAAACAAGCAGTAGTAATTCCTGCTTTATCAAGATA\n+ATTTTTCGACTCATCAGAAATATCCGAAAGTGTTAACTTCTGCGTCATGGAAGCGATAAA\n+ACTCTGCAGGTTGGATACGCCAATCATTTTTATCGAAGCGCGCATAAATTTGAGCAGATT\n+TGTCGTCACAGGTTGCGCCGCCAAAACGTCGGCTACAGTAACTTTTCCCAGCCTCAATCT\n+CATCTCTCTTTTTGCGTTCTGCTTCAATATCTGGTTGAACGGCGTCGCGTCGTAACCCAG\n+CTTGGTAAGTTGGATTAAGCACTCCGTGGACAGATTTGTCATTGTGAGCATTTTCATCCC\n+GAAGTTGCGGCTCATTCTGATTCTGAACAGCTTCTTGGGAAGTAGCGACAGCTTGGTTTT\n+TAGTGAGTTGTTCCATTCTTTAGCTCCTAGACCTTTAGCAGCAAGGTCCATATCTGACTT\n+TTTGTTAACGTATTTAGCCACATAGAAACCAACAGCCATATAACTGGTAGCTTTAAGCGG\n+CTCACCTTTAGCATCAACAGGCCACAACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTA\n+GCGAACTGCGATGGGCATACTGTAACCATAAGGCCACGTATTTTGCAAGCTATTTAACTG\n+GCGGCGATTGCGTACCCGACGACCAAAATTAGGGTCAACGCTACCTGTAGGAAGTGTCCG\n+CATAAAGTGCACCGCATGGAAATGAAGACGGCCATTAGCTGTACCATACTCAGGCACACA\n+AAAATACTGATAGCAGTCGGCGTGTGAATCATTAGCCTTGCGACCCTCGGCAGCAAGAAC\n+CATACGACCAATATCACGAAAATAGTCACGCAAAGCATTGGGATTATCATAAAACGCCTC\n+TAATCGGTCGTCAGCCAACGTGAGAGTGTCAAAAACGATAAACCAACCATCAGCATGAGC\n+CTGTCGCATTGCATTCATCAAACGCTGAATAGCAAAGCCTCTACGCGATTTCATAGTGGA\n+GGCCTCCAGCAATCTTGAACACTCATCCTTAATACCTTTCTTTTTGGGGTAATTATACTC\n+ATCGCGAATATCCTTAAGAGGGCGTTCAGCAGCCAGCTTGCGGCAAAACTGCGTAACCGT\n+CTTCTCGTTCTCTAAAAACCATTTTTCGTCCCCTTCGGGGCGGTGGTCTATAGTGTTATT\n+AATATCAAGTTGGGGGAGCACATTGTAGCATTGTGCCAATTCATCCATTAACTTCTCAGT\n+AACAGATACAAACTCATCACGAACGTCAGAAGCAGCCTTATGGCCGTCAACATACATATC\n+ACCATTATCGAACTCAACGCCCTGCATACGAAAAGACAGAATCTCTTCCAAGAGCTTGAT\n+GCGGTTATCCATCTGCTTATGGAAGCCAAGCATTGGGGATTGAGAAAGAGTAGAAATGCC\n+ACAAGCCTCAATAGCAGGTTTAAGAGCCTCGATACGCTCAAAGTCAAAATAATCAGCGTG\n+ACATTCAGAAGGGTAATAAGAACGAACCATAAAAAAGCCTCCAAGATTTGGAGGCATGAA\n+AACATACAATTGGGAGGGTGTCAATCCTGACGGTTATTTCCTAGACAAATTAGAGCCAAT\n+ACCATCAGCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCAACAGCTTTATCAAT\n+ACCATGAAAAATATCAACCACACCAGAAGCAGCATCAGTGACGACATTAGAAATATCCTT\n+TGCAGTAGCGCCAATATGAGAAGAGCCATACCGCTGATTCTGCGTTTGCTGATGAACTAA\n+GTCAACCTCAGCACTAACCTTGCGAGTCATTTCTTTGATTTGGTCATTGGTAAAATACTG\n+ACCAGCCGTTTGAGCTTGAGTAAGCATTTGGCGCATAATCTCGGAAACCTGCTGTTGCTT\n+GGAAAGATTGGTGTTTTCCATAATAGACGCAACGCGAGCAGTAGACTCCTTCTGTTGATA\n+AGCAAGCATCTCATTTTGTGCATATACCTGGTCTTTCGTATTCTGGCGTGAAGTCGCCGA\n+CTGAATGCCAGCAATCTCTTTTTGAGTCTCATTTTGCATCTCGGCAATCTCTTTCTGATT\n+GTCCAGTTGCATTTTAGTAAGCTCTTTTTGATTCTCAAATCCGGCGTCAACCATACCAGC\n+AGAGGAAGCATCAGCACCAGCACGCTCCCAAGCATTAAGCTCAGGAAATGCAGCAGCAAG\n+ATAATCACGAGTATCCTTTCCTTTATCAGCGGCAGACTTGCCACCAAGTCCAACCAAATC\n+AAGCAACTTATCAGAAACGGCAGAAGTGCCAGCCTGCAACGTACCTTCAAGAAGTCCTTT\n+ACCAGCTTTAGCCATAGCACCAGAAACAAAACTAGGGACGGCCTCATCAGGGTTAGGAAC\n+ATTAGAGCCTTGAATGGCAGATTTAATACCAGCATCACCCATGCCTACAGTATTGTTATC\n+GGTAGCAAGCACATCACCTTGAATGCCACCGGAGGCGGCTTTTTGACCGCCTCCAAACAA\n+TTTAGACATGGCGCCACCAGCAAGAGCAGAAGCAATACCGCCAGCAATAGCACCAAACAT\n+AAATCACCTCACTTAAGTGGCTGGAGACAAATAATCTCTTTAATAACCTGATTCAGCGAA\n+ACCAATCCGCGGCATTTAGTAGCGGTAAAGTTAGACCAAACCATGAAACCAACATAAACA\n+TTATTGCCCGGCGTACGGGGAAGGACGTCAATAGTCACACAGTCCTTGACGGTATAATAA\n+CCACCATCATGGCGACCATCCAAAGGATAAACATCATAGGCAGTCGGGAGGGTAGTCGGA\n+ACCGAAGAAGACTCAAAGCGAACCAAACAGGCAAAAAATTTAGGGTCGGCATCAAAAGCA\n+ATATCAGCACCAACAGAAACAACCTGATTAGCGGCGTTGACAGATGTATCCATCTGAATG\n+CAATGAAGAAAACCACCATTACCAGCATTAACCGTCAAACTATCAAAATATAACGTTGAC\n+GATGTAGCTTTAGGTGTCTGTAAAACAGGTGCCGAAGAAGCTGGAGTAACAGAAGTGAGA\n+ACCAGCTTATCAGAAAAAAAGTTTGAATTATGGCGAGAAATAAAAGTCTGAAACATGATT\n+AAACTCCTAAGCAGAAAACCTACCGCGCTTCGCTTGGTCAACCCCTCAGCGGCAAAAATT\n+AAAATTTTTACCGCTTCGGCGTTATAACCTCACACTCAATCTTTTATCACGAAGTCATGA\n+TTGAATCGCGAGTGGTCGGCAGATTGCGATAAACGGTCACATTAAATTTAACCTGACTAT\n+TCCACTGCAACAACTGAACGGACTGGAAACACTGGTCATAATCATGGTGGCGAATAAGTA\n+CGCGTTCTTGCAAATCACCAGAAGGCGGTTCCTGAATGAATGGGAAGCCTTCAAGAAGGT\n+GATAAGCAGGAGAAACATACGAAGGCGCATAACGATACCACTGACCCTCAGCAATCTTAA\n+ACTTCTTAGAC'..b'AAAATTATTGTTAATGGTTGGGTT\n+AATCATGGTCCATGGGCACCTAGAAGGTAGTGGTAGGGAGGTTATTATAATGGATTTTAC\n+TAAAGAAGAAAAACTTTTAAATGCAATTAGTAAAGTATACAATGAAGCAACTATAGATGA\n+CTATCCTGACTTAAAAGAAAAGCTCTTTCTTTATTCTAAAGAAATCAGTGAGGGAAAAAG\n+TGTTGGTGAAGTTAGTATGAAATTAAGTAGTTTTCTTGGAAGATATATTTTAAAACATAA\n+ATTTGGATTACCTAAATCTTTAATAGAATTACAAGAAATTGTTAGTAAGGAATCTCAAGT\n+ATATAGAGGATGGGCTTCTATTGGTATTTGGAGTTAATTCTTTGGAATAAAATGAAAATG\n+GGACTGAAGAATCAATTCTGATTCATCAGTCCCATAAATTATAGAGCCGAAAAATTATCA\n+TATTTATAGATTTATTAATAGTAAATGGCATAAGAATCTTTGAACAACGAAAAAAATGTA\n+GCTCTACCTAATTATTGATTTGCAACAATTTCACCGAAGGTGAAACAAGCGAAACTTTAC\n+AAAAAGTGGCTAGCATTTGCTAGTCTTTTTTGTATTGTGGAGAGTGG\n+>contig00004 len=3138 cov=2.3 corr=1 origname=NODE_4_length_3138_cov_2.261375_pilon sw=shovill-spades/1.1.0 date=20220302\n+TTTTTTTCCGATATAATTTGCTGGTAAATCTATCACAGCCAATGAGAGTCCGGGATTGCT\n+TTCTTCCTGATAATCTTTCCGTTGGTATAAAATCTTTTCGCCTAGATATACAGTAATCCA\n+TTGATGGTTTCCTTTGATTAGTAAATTTGCTTCGTCCAACGGTTTTTCAAGTGTCGTTTC\n+CATAATGAATGTTTCGTCTTTATCCACGGTAGGAATCGTACGAGTGTACTTGCTGTCAAA\n+CTTAAAATCAGGATCATCTTTTGTATAGAAAACCCACGAATCTTTTATTTCTTTCATTTG\n+ATTGCTGTCCGCAGGAGAAAAAATAAAATAAAAGAAATAAGCAATTCCTGTTAAAAATAA\n+CAATGATAATATAATGATTATGCTCCACTTTATACGTAAATAAAAAGATTCTTTTTTATT\n+ATATATGTTATTAAAAAAAGACATAAAGGTATTCCTTTGAGAGTATAAAATATTTTGTGT\n+AAATGAAAAAATCCATACAAAAAAGGAAGTCCCTTCTGTAGAATAAAGTTAACGACAACC\n+AATTCACAGAAAAGAGGACTTCCCTATGAATGATTTTACTACAGAAATTGTGCAAACTCT\n+AGTCACTAAAGGCGATTTAAATGAATTATTCCGTTCGCACTTAGAAAAAGCGATAAACAC\n+ACTCCTACGGACTGAATTAACGGCTTTTTTAGATTACGAAAAATATGATCGCACTGGTTT\n+TAATTCAGGTAATTCGAGAAACGGTTCTTACTTTCGATCAATCAAAACCGAATATGGTGA\n+ATTAACATTGGAAATACCTAGAGATCGTAATGGTGAGTTTAAACAACAAACTTTACCAGC\n+CTACAAAAGAACAAACGATACATTGGAAACCACTATTATCCATTTATTCGAAAAAGGTGT\n+TACGATGTCTGAAATTGCTGATTTGATCGAAAAAATGTACGGTCATCACTATACTCCACA\n+AACCATGTCCAACATGACTAAAGTTCTGACTGAAGAAGTAAATGCCTTTAAATCCAGAGC\n+CTTAAATGATAAGTATGTCGCTATTTTTATGGACGTTACTTACATTCCACTAAAACGTCA\n+AACTGTATCCAAAGAAGCGATTTATATTGCCATTGGTATACGAGAAGACGGCACTAAAGA\n+AGTACTGAGTTATGCGATTGCTCCAACTGAATCAACATACGTTTGGAATGAGCTGCTACA\n+GGATATTAACTCCAGAGGAGTTCAAGAAGTCTTGCTTTTTATTACGGACGGCTTAAAAGG\n+CATGAAAGATACTATCCATCAAATTTATCCTAAAGCAAAATATCAGCATTGTTGTATCCA\n+TGTATCTCGTAACATCGCTCATAAAGTACGTGTCAAAGACCGAAAAGAAATCTGTGATGA\n+CTTTAAGGCTGTTTATCAAGCTAACTCAAAAGAAGAAGCGAATACCTTCTTATCCGGCAT\n+GATTGAGAAATGGAAGAAAAACTATCCTAAAGTGACGCAGTCACTCATAGAAAACCAAGA\n+CTTATTAACTTTTTATGATTTTCCACCTAGCATTCGTAGAACCATTTACTCAACCAATCT\n+AATCGAGTCTTTCAATAAGCAAATTAAAAGATACAGCCGTAGAAAAGAGCAGTTTCAAAA\n+TGAAGAATCACTAGAACGCTTTCTAGTCAGCATTTTTGATACATACAATCAAAAATTTCT\n+AAACAGAAGCCATAAAGGTTTTCAACAGGTAACCGATACATTAGTTTCAATGTTTACTGA\n+GTAACTAATTATTTTGCAGGAGGACAATTTATTTACACAAAATTATTGACGCTCCCTAAC\n+AAAATCCCACCTACTTTATCTTATAACTTGTTTTTTTGCATAAAAACTAAATAAAGAGTG\n+CGGCATTTCGCACTTTTTTATTATATATTATTTGTCAAATTAAGCGAGACAAAACTTTCC\n+ATTTACGTAACTCAAAAAAACTTCTAATGGTGTTTGGTAATTTAGTGATTTTCTAGGGAT\n+ATGGTTTCTTTTGGACGCAACGGATGAGATGAATCCTTGATTGACTTGGTGGAAGTCCAT\n+TTCTTTTGGTAGTCCATCTTTTCGGAGGAGTCCGTTTGAATGTTCATTTAATCCCCGTTG\n+GGAAGGCGTTCCTGGGTCTGCGAAATAAATATCAATATCATTCGTATTACTAATACTTTT\n+CCAATTAGAGAATTCTTTTCCACAATCAAAGGTAATTGATTTGAAAAGATTTTTGGGTAC\n+GGATTGAAGCCATTCATTAATCGAATTTTCAATATCAACTGCCTTACGGCCTTCTGGTTT\n+CAAGGCGATAATGGCTTTTGAAAGTCGCTCAACGAGTGTGATGACGGCACTTTTATGGTG\n+GATGCCGACAATCGTATCACCCTCTAAATGTCCAAATTCTTCTTCGAAAACGACATAATC\n+TTTTTTACGTTCAGAAATATTTCTTTTGAATGCCTGTTTTCCACGTTTTTCCTTATAACC\n+ATTTGGTTTTCGTTTTCCTTGCATCGGTAAATGTAAAACATTGAATTCTCCCGTCTTAAA\n+CCGGCGATAGAGGGTACTTACTGAACAAGAGAAGGTTCGCTCTGCACGGCCAATAATGAC\n+GTCTGGGGTCCAACCTTCAGTTGATCTTTTTGCAATGTATTCTTTTTCCTCAGCAGGAAA\n+AATGATTTCGGTTCTCCCACAACGTCGCTTATTTTCTTTGTATTGTTCAAAGTATTCAAG\n+TGCTGTTCCACCACATTTGAGAAAGTTATAGACATTGTAAATTGTTTGGCGTCCACGTTT\n+AAGCTGCTTCGCAACGATAGCAACCGGAGTTTCTTGATGAAAATATGCTTCTATCATTAC\n+AAGCTCGTTTGGTGTAAGATGGGTATAAGTCATTTATGTTCACTCTCCTTGTATGCTTTA\n+GCGGGTATTACAATTGGAGTGTAACATAAATGGCTTTTTTATTTGTCTCGCTTAATTATA\n+CAAACGGCGTTGTTAAATAAATAGGAACAAAAAAATTAAATTATTTAATACACACATTAG\n+GGATCATTCATTGAAGGATTAGAAGACAACGAGGATGGCGAAAAATATGATTACAATAGA\n+AAAGTCGTTCTAAACCAATCAGTTCCTAGTATCACACAACGCAAGCCAGTCGATTTGGTG\n+AGATTAGAGGAGTGAAAG\n'

diff -r 000000000000 -r aaa868913641 test-data/contigs.fa.amb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/contigs.fa.amb Thu Sep 22 07:51:48 2022 +0000

@@ -0,0 +1,1 @@
+15410 4 0

diff -r 000000000000 -r aaa868913641 test-data/contigs.fa.ann
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/contigs.fa.ann Thu Sep 22 07:51:48 2022 +0000

@@ -0,0 +1,9 @@
+15410 4 11
+0 contig00001 len=5513 cov=11.7 corr=0 origname=NODE_1_length_5513_cov_11.741181_pilon sw=shovill-spades/1.1.0 date=20220302
+0 5513 0
+0 contig00002 len=3532 cov=5.1 corr=0 origname=NODE_2_length_3532_cov_5.072834_pilon sw=shovill-spades/1.1.0 date=20220302
+5513 3532 0
+0 contig00003 len=3227 cov=2.2 corr=0 origname=NODE_3_length_3227_cov_2.232903_pilon sw=shovill-spades/1.1.0 date=20220302
+9045 3227 0
+0 contig00004 len=3138 cov=2.3 corr=1 origname=NODE_4_length_3138_cov_2.261375_pilon sw=shovill-spades/1.1.0 date=20220302
+12272 3138 0

diff -r 000000000000 -r aaa868913641 test-data/contigs.fa.bwt

Binary file test-data/contigs.fa.bwt has changed

diff -r 000000000000 -r aaa868913641 test-data/contigs.fa.pac

Binary file test-data/contigs.fa.pac has changed

diff -r 000000000000 -r aaa868913641 test-data/contigs.fa.sa

Binary file test-data/contigs.fa.sa has changed

diff -r 000000000000 -r aaa868913641 test-data/debug_file_test_1.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/debug_file_test_1.tsv Thu Sep 22 07:51:48 2022 +0000

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diff -r 000000000000 -r aaa868913641 test-data/debug_file_test_2.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/debug_file_test_2.tsv Thu Sep 22 07:51:48 2022 +0000

b'@@ -0,0 +1,15411 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diff -r 000000000000 -r aaa868913641 test-data/logfile_test_1.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/logfile_test_1.log Thu Sep 22 07:51:48 2022 +0000

[

@@ -0,0 +1,80 @@
+
+[1;4;93mStarting Polypolish[0m [2m(2022-09-14 14:05:31)[0m
+[2m    Polypolish is a tool for polishing genome assemblies with short reads.
+Unlike other tools in this category, Polypolish uses SAM files where each read
+has been aligned to all possible locations (not just a single best location).
+This allows it to repair errors in repeat regions that other alignment-based
+polishers cannot fix.[0m
+
+Polypolish version: 0.5.0
+
+Input assembly:
+  input_data
+
+Input short-read alignments:
+  /tmp/tmpacfaqf7s/files/0/e/6/dataset_0e63b923-512f-4f9b-b6fa-8c6ead4a29db.dat
+
+Settings:
+  --fraction_invalid 0.2
+  --fraction_valid 0.5
+  --max_errors 10
+  --min_depth 5
+  --debug /tmp/tmpacfaqf7s/job_working_directory/000/3/outputs/galaxy_dataset_0fff3b6a-ddab-4999-b6a2-78a6dff1a4bc.dat
+
+
+[1;4;93mLoading assembly[0m [2m(2022-09-14 14:05:31)[0m
+contig00001 (5,513 bp)
+contig00002 (3,532 bp)
+contig00003 (3,227 bp)
+contig00004 (3,138 bp)
+
+
+[1;4;93mLoading alignments[0m [2m(2022-09-14 14:05:31)[0m
+/tmp/tmpacfaqf7s/files/0/e/6/dataset_0e63b923-512f-4f9b-b6fa-8c6ead4a29db.dat: 75 alignments from 72 reads
+
+Filtering for high-quality end-to-end alignments:
+  25 alignments kept
+  50 alignments discarded
+
+
+[1;4;93mPolishing assembly sequences[0m [2m(2022-09-14 14:05:31)[0m
+[2m    For each position in the assembly, Polypolish determines the read depth
+at that position and collects all aligned bases. It then polishes the assembly
+by looking for positions where the pileup unambiguously supports a different
+sequence than the assembly.[0m
+
+Polishing contig00001 (5,513 bp):
+  mean read depth: 1.0x
+  2,496 bp have a depth of zero (54.7252% coverage)
+  0 positions changed (0.0000% of total positions)
+  estimated pre-polishing sequence accuracy: 100.0000%
+
+Polishing contig00002 (3,532 bp):
+  mean read depth: 0.3x
+  2,629 bp have a depth of zero (25.5663% coverage)
+  0 positions changed (0.0000% of total positions)
+  estimated pre-polishing sequence accuracy: 100.0000%
+
+Polishing contig00003 (3,227 bp):
+  mean read depth: 0.2x
+  2,818 bp have a depth of zero (12.6743% coverage)
+  0 positions changed (0.0000% of total positions)
+  estimated pre-polishing sequence accuracy: 100.0000%
+
+Polishing contig00004 (3,138 bp):
+  mean read depth: 0.1x
+  2,842 bp have a depth of zero (9.4328% coverage)
+  0 positions changed (0.0000% of total positions)
+  estimated pre-polishing sequence accuracy: 100.0000%
+
+
+[1;4;93mFinished![0m [2m(2022-09-14 14:05:31)[0m
+Polished sequence (to stdout):
+  contig00001_polypolish (5,513 bp)
+  contig00002_polypolish (3,532 bp)
+  contig00003_polypolish (3,227 bp)
+  contig00004_polypolish (3,138 bp)
+
+Per-base debugging info written to /tmp/tmpacfaqf7s/job_working_directory/000/3/outputs/galaxy_dataset_0fff3b6a-ddab-4999-b6a2-78a6dff1a4bc.dat
+Time to run: 0:00:00.029839
+

diff -r 000000000000 -r aaa868913641 test-data/logfile_test_4.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/logfile_test_4.log Thu Sep 22 07:51:48 2022 +0000

[

@@ -0,0 +1,90 @@
+
+[1;4;93mStarting Polypolish[0m [2m(2022-09-14 14:06:52)[0m
+[2m    Polypolish is a tool for polishing genome assemblies with short reads.
+Unlike other tools in this category, Polypolish uses SAM files where each read
+has been aligned to all possible locations (not just a single best location).
+This allows it to repair errors in repeat regions that other alignment-based
+polishers cannot fix.[0m
+
+Polypolish version: 0.5.0
+
+Input assembly:
+  input_data
+
+Input short-read alignments:
+  paired_collection/forward_input0forward_filtered.sam
+  paired_collection/forward_input1forward_filtered.sam
+  paired_collection/forward_input2forward_filtered.sam
+  paired_collection/reverse_input0reverse_filtered.sam
+  paired_collection/reverse_input1reverse_filtered.sam
+  paired_collection/reverse_input2reverse_filtered.sam
+
+Settings:
+  --fraction_invalid 0.2
+  --fraction_valid 0.5
+  --max_errors 10
+  --min_depth 5
+  --debug /tmp/tmpacfaqf7s/job_working_directory/000/20/outputs/galaxy_dataset_a267d150-242f-43e2-b91d-3a230d92a70f.dat
+
+
+[1;4;93mLoading assembly[0m [2m(2022-09-14 14:06:52)[0m
+contig00001 (5,513 bp)
+contig00002 (3,532 bp)
+contig00003 (3,227 bp)
+contig00004 (3,138 bp)
+
+
+[1;4;93mLoading alignments[0m [2m(2022-09-14 14:06:52)[0m
+paired_collection/forward_input0forward_filtered.sam: 75 alignments from 72 reads
+paired_collection/forward_input1forward_filtered.sam: 75 alignments from 72 reads
+paired_collection/forward_input2forward_filtered.sam: 75 alignments from 72 reads
+paired_collection/reverse_input0reverse_filtered.sam: 64 alignments from 62 reads
+paired_collection/reverse_input1reverse_filtered.sam: 64 alignments from 62 reads
+paired_collection/reverse_input2reverse_filtered.sam: 64 alignments from 62 reads
+
+Filtering for high-quality end-to-end alignments:
+  144 alignments kept
+  273 alignments discarded
+
+
+[1;4;93mPolishing assembly sequences[0m [2m(2022-09-14 14:06:52)[0m
+[2m    For each position in the assembly, Polypolish determines the read depth
+at that position and collects all aligned bases. It then polishes the assembly
+by looking for positions where the pileup unambiguously supports a different
+sequence than the assembly.[0m
+
+Polishing contig00001 (5,513 bp):
+  mean read depth: 5.7x
+  1,751 bp have a depth of zero (68.2387% coverage)
+  0 positions changed (0.0000% of total positions)
+  estimated pre-polishing sequence accuracy: 100.0000%
+
+Polishing contig00002 (3,532 bp):
+  mean read depth: 2.0x
+  2,280 bp have a depth of zero (35.4473% coverage)
+  0 positions changed (0.0000% of total positions)
+  estimated pre-polishing sequence accuracy: 100.0000%
+
+Polishing contig00003 (3,227 bp):
+  mean read depth: 0.8x
+  2,652 bp have a depth of zero (17.8184% coverage)
+  0 positions changed (0.0000% of total positions)
+  estimated pre-polishing sequence accuracy: 100.0000%
+
+Polishing contig00004 (3,138 bp):
+  mean read depth: 0.6x
+  2,699 bp have a depth of zero (13.9898% coverage)
+  0 positions changed (0.0000% of total positions)
+  estimated pre-polishing sequence accuracy: 100.0000%
+
+
+[1;4;93mFinished![0m [2m(2022-09-14 14:06:52)[0m
+Polished sequence (to stdout):
+  contig00001_polypolish (5,513 bp)
+  contig00002_polypolish (3,532 bp)
+  contig00003_polypolish (3,227 bp)
+  contig00004_polypolish (3,138 bp)
+
+Per-base debugging info written to /tmp/tmpacfaqf7s/job_working_directory/000/20/outputs/galaxy_dataset_a267d150-242f-43e2-b91d-3a230d92a70f.dat
+Time to run: 0:00:00.024238
+

diff -r 000000000000 -r aaa868913641 test-data/polished.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/polished.fasta Thu Sep 22 07:51:48 2022 +0000

b'@@ -0,0 +1,8 @@\n+>contig00001_polypolish\n+CAGCATCGGACTCAGATAGTAATCCACGCTCTTTTAAAATGTCAACAAGAGAATCTCTACCATGAACAAAATGTGACTCATATCTAAACCAGTCCTTGACGAACGTGCCAAGCATATTAAGCCACTTCTCCTCATCCAACGCGTCAGTTTTTGACAGAATCGTTAGTTGATGGCGAAAGGTCGCAAAGTAAGAGCTTCTCGAGCTGCGCAAGGATAGGTCGAATTTTCTCATTTTCCGCCAGCAGTCCACTTCGATTTAATTCGTAAACAAGCAGTAGTAATTCCTGCTTTATCAAGATAATTTTTCGACTCATCAGAAATATCCGAAAGTGTTAACTTCTGCGTCATGGAAGCGATAAAACTCTGCAGGTTGGATACGCCAATCATTTTTATCGAAGCGCGCATAAATTTGAGCAGATTTGTCGTCACAGGTTGCGCCGCCAAAACGTCGGCTACAGTAACTTTTCCCAGCCTCAATCTCATCTCTCTTTTTGCGTTCTGCTTCAATATCTGGTTGAACGGCGTCGCGTCGTAACCCAGCTTGGTAAGTTGGATTAAGCACTCCGTGGACAGATTTGTCATTGTGAGCATTTTCATCCCGAAGTTGCGGCTCATTCTGATTCTGAACAGCTTCTTGGGAAGTAGCGACAGCTTGGTTTTTAGTGAGTTGTTCCATTCTTTAGCTCCTAGACCTTTAGCAGCAAGGTCCATATCTGACTTTTTGTTAACGTATTTAGCCACATAGAAACCAACAGCCATATAACTGGTAGCTTTAAGCGGCTCACCTTTAGCATCAACAGGCCACAACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGCGAACTGCGATGGGCATACTGTAACCATAAGGCCACGTATTTTGCAAGCTATTTAACTGGCGGCGATTGCGTACCCGACGACCAAAATTAGGGTCAACGCTACCTGTAGGAAGTGTCCGCATAAAGTGCACCGCATGGAAATGAAGACGGCCATTAGCTGTACCATACTCAGGCACACAAAAATACTGATAGCAGTCGGCGTGTGAATCATTAGCCTTGCGACCCTCGGCAGCAAGAACCATACGACCAATATCACGAAAATAGTCACGCAAAGCATTGGGATTATCATAAAACGCCTCTAATCGGTCGTCAGCCAACGTGAGAGTGTCAAAAACGATAAACCAACCATCAGCATGAGCCTGTCGCATTGCATTCATCAAACGCTGAATAGCAAAGCCTCTACGCGATTTCATAGTGGAGGCCTCCAGCAATCTTGAACACTCATCCTTAATACCTTTCTTTTTGGGGTAATTATACTCATCGCGAATATCCTTAAGAGGGCGTTCAGCAGCCAGCTTGCGGCAAAACTGCGTAACCGTCTTCTCGTTCTCTAAAAACCATTTTTCGTCCCCTTCGGGGCGGTGGTCTATAGTGTTATTAATATCAAGTTGGGGGAGCACATTGTAGCATTGTGCCAATTCATCCATTAACTTCTCAGTAACAGATACAAACTCATCACGAACGTCAGAAGCAGCCTTATGGCCGTCAACATACATATCACCATTATCGAACTCAACGCCCTGCATACGAAAAGACAGAATCTCTTCCAAGAGCTTGATGCGGTTATCCATCTGCTTATGGAAGCCAAGCATTGGGGATTGAGAAAGAGTAGAAATGCCACAAGCCTCAATAGCAGGTTTAAGAGCCTCGATACGCTCAAAGTCAAAATAATCAGCGTGACATTCAGAAGGGTAATAAGAACGAACCATAAAAAAGCCTCCAAGATTTGGAGGCATGAAAACATACAATTGGGAGGGTGTCAATCCTGACGGTTATTTCCTAGACAAATTAGAGCCAATACCATCAGCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCAACAGCTTTATCAATACCATGAAAAATATCAACCACACCAGAAGCAGCATCAGTGACGACATTAGAAATATCCTTTGCAGTAGCGCCAATATGAGAAGAGCCATACCGCTGATTCTGCGTTTGCTGATGAACTAAGTCAACCTCAGCACTAACCTTGCGAGTCATTTCTTTGATTTGGTCATTGGTAAAATACTGACCAGCCGTTTGAGCTTGAGTAAGCATTTGGCGCATAATCTCGGAAACCTGCTGTTGCTTGGAAAGATTGGTGTTTTCCATAATAGACGCAACGCGAGCAGTAGACTCCTTCTGTTGATAAGCAAGCATCTCATTTTGTGCATATACCTGGTCTTTCGTATTCTGGCGTGAAGTCGCCGACTGAATGCCAGCAATCTCTTTTTGAGTCTCATTTTGCATCTCGGCAATCTCTTTCTGATTGTCCAGTTGCATTTTAGTAAGCTCTTTTTGATTCTCAAATCCGGCGTCAACCATACCAGCAGAGGAAGCATCAGCACCAGCACGCTCCCAAGCATTAAGCTCAGGAAATGCAGCAGCAAGATAATCACGAGTATCCTTTCCTTTATCAGCGGCAGACTTGCCACCAAGTCCAACCAAATCAAGCAACTTATCAGAAACGGCAGAAGTGCCAGCCTGCAACGTACCTTCAAGAAGTCCTTTACCAGCTTTAGCCATAGCACCAGAAACAAAACTAGGGACGGCCTCATCAGGGTTAGGAACATTAGAGCCTTGAATGGCAGATTTAATACCAGCATCACCCATGCCTACAGTATTGTTATCGGTAGCAAGCACATCACCTTGAATGCCACCGGAGGCGGCTTTTTGACCGCCTCCAAACAATTTAGACATGGCGCCACCAGCAAGAGCAGAAGCAATACCGCCAGCAATAGCACCAAACATAAATCACCTCACTTAAGTGGCTGGAGACAAATAATCTCTTTAATAACCTGATTCAGCGAAACCAATCCGCGGCATTTAGTAGCGGTAAAGTTAGACCAAACCATGAAACCAACATAAACATTATTGCCCGGCGTACGGGGAAGGACGTCAATAGTCACACAGTCCTTGACGGTATAATAACCACCATCATGGCGACCATCCAAAGGATAAACATCATAGGCAGTCGGGAGGGTAGTCGGAACCGAAGAAGACTCAAAGCGAACCAAACAGGCAAAAAATTTAGGGTCGGCATCAAAAGCAATATCAGCACCAACAGAAACAACCTGATTAGCGGCGTTGACAGATGTATCCATCTGAATGCAATGAAGAAAACCACCATTACCAGCATTAACCGTCAAACTATCAAAATATAACGTTGACGATGTAGCTTTAGGTGTCTGTAAAACAGGTGCCGAAGAAGCTGGAGTAACAGAAGTGAGAACCAGCTTATCAGAAAAAAAGTTTGAATTATGGCGAGAAATAAAAGTCTGAAACATGATTAAACTCCTAAGCAGAAAACCTACCGCGCTTCGCTTGGTCAACCCCTCAGCGGCAAAAATTAAAATTTTTACCGCTTCGGCGTTATAACCTCACACTCAATCTTTTATCACGAAGTCATGATTGAATCGCGAGTGGTCGGCAGATTGCGATAAACGGTCACATTAAATTTAACCTGACTATTCCACTGCAACAACTGAACGGACTGGAAACACTGGTCATAATCATGGTGGCGAATAAGTACGCGTTCTTGCAAATCACCAGAAGGCGGTTCCTGAATGAATGGGAAGCCTTCAAGAAGGTGATAAGCAGGAGAAACATACGAAGGCGCATAACGATACCACTGACCCTCAGCAATCTTAAACTTCTTAGACGAATCACCAGAACGGAAAACATCCTTCATAGAAATTTCACGCGGCGGCAAGTTGCCATACAAAACAGGGTCGCCAGCAATATCGGTATAAGTCAAAGCACCTTTAGCGTTAAGGTACTGAATCTCTTTAGTCGCAGTAGGCGGAAAACGAACAAGCGCAAGAGTAAACATAGTGCCATGCTCAGGAACAAAGAAACGCGGCACAGAATGTTTATAGGTCTGTTGAA'..b'GATTATTTAATATAACAAGCAATTTTAAAAAAACGAAAAGGAAAAACAATCATGAAAAAGAAAGTATTAAAACATTGTGTTATTCTAGGAATATTAGGAACTTGTCTAGCTGGCATCGGTACAGGAATAAAAGTTGATGCAGCTACTTACTATGGAAATGGTCTTTATTGTAACAAAGAAAAATGTTGGGTAGATTGGAATCAAGCTAAAGGAGAAATTGGAAAAATTATTGTTAATGGTTGGGTTAATCATGGTCCATGGGCACCTAGAAGGTAGTGGTAGGGAGGTTATTATAATGGATTTTACTAAAGAAGAAAAACTTTTAAATGCAATTAGTAAAGTATACAATGAAGCAACTATAGATGACTATCCTGACTTAAAAGAAAAGCTCTTTCTTTATTCTAAAGAAATCAGTGAGGGAAAAAGTGTTGGTGAAGTTAGTATGAAATTAAGTAGTTTTCTTGGAAGATATATTTTAAAACATAAATTTGGATTACCTAAATCTTTAATAGAATTACAAGAAATTGTTAGTAAGGAATCTCAAGTATATAGAGGATGGGCTTCTATTGGTATTTGGAGTTAATTCTTTGGAATAAAATGAAAATGGGACTGAAGAATCAATTCTGATTCATCAGTCCCATAAATTATAGAGCCGAAAAATTATCATATTTATAGATTTATTAATAGTAAATGGCATAAGAATCTTTGAACAACGAAAAAAATGTAGCTCTACCTAATTATTGATTTGCAACAATTTCACCGAAGGTGAAACAAGCGAAACTTTACAAAAAGTGGCTAGCATTTGCTAGTCTTTTTTGTATTGTGGAGAGTGG\n+>contig00004_polypolish\n+TTTTTTTCCGATATAATTTGCTGGTAAATCTATCACAGCCAATGAGAGTCCGGGATTGCTTTCTTCCTGATAATCTTTCCGTTGGTATAAAATCTTTTCGCCTAGATATACAGTAATCCATTGATGGTTTCCTTTGATTAGTAAATTTGCTTCGTCCAACGGTTTTTCAAGTGTCGTTTCCATAATGAATGTTTCGTCTTTATCCACGGTAGGAATCGTACGAGTGTACTTGCTGTCAAACTTAAAATCAGGATCATCTTTTGTATAGAAAACCCACGAATCTTTTATTTCTTTCATTTGATTGCTGTCCGCAGGAGAAAAAATAAAATAAAAGAAATAAGCAATTCCTGTTAAAAATAACAATGATAATATAATGATTATGCTCCACTTTATACGTAAATAAAAAGATTCTTTTTTATTATATATGTTATTAAAAAAAGACATAAAGGTATTCCTTTGAGAGTATAAAATATTTTGTGTAAATGAAAAAATCCATACAAAAAAGGAAGTCCCTTCTGTAGAATAAAGTTAACGACAACCAATTCACAGAAAAGAGGACTTCCCTATGAATGATTTTACTACAGAAATTGTGCAAACTCTAGTCACTAAAGGCGATTTAAATGAATTATTCCGTTCGCACTTAGAAAAAGCGATAAACACACTCCTACGGACTGAATTAACGGCTTTTTTAGATTACGAAAAATATGATCGCACTGGTTTTAATTCAGGTAATTCGAGAAACGGTTCTTACTTTCGATCAATCAAAACCGAATATGGTGAATTAACATTGGAAATACCTAGAGATCGTAATGGTGAGTTTAAACAACAAACTTTACCAGCCTACAAAAGAACAAACGATACATTGGAAACCACTATTATCCATTTATTCGAAAAAGGTGTTACGATGTCTGAAATTGCTGATTTGATCGAAAAAATGTACGGTCATCACTATACTCCACAAACCATGTCCAACATGACTAAAGTTCTGACTGAAGAAGTAAATGCCTTTAAATCCAGAGCCTTAAATGATAAGTATGTCGCTATTTTTATGGACGTTACTTACATTCCACTAAAACGTCAAACTGTATCCAAAGAAGCGATTTATATTGCCATTGGTATACGAGAAGACGGCACTAAAGAAGTACTGAGTTATGCGATTGCTCCAACTGAATCAACATACGTTTGGAATGAGCTGCTACAGGATATTAACTCCAGAGGAGTTCAAGAAGTCTTGCTTTTTATTACGGACGGCTTAAAAGGCATGAAAGATACTATCCATCAAATTTATCCTAAAGCAAAATATCAGCATTGTTGTATCCATGTATCTCGTAACATCGCTCATAAAGTACGTGTCAAAGACCGAAAAGAAATCTGTGATGACTTTAAGGCTGTTTATCAAGCTAACTCAAAAGAAGAAGCGAATACCTTCTTATCCGGCATGATTGAGAAATGGAAGAAAAACTATCCTAAAGTGACGCAGTCACTCATAGAAAACCAAGACTTATTAACTTTTTATGATTTTCCACCTAGCATTCGTAGAACCATTTACTCAACCAATCTAATCGAGTCTTTCAATAAGCAAATTAAAAGATACAGCCGTAGAAAAGAGCAGTTTCAAAATGAAGAATCACTAGAACGCTTTCTAGTCAGCATTTTTGATACATACAATCAAAAATTTCTAAACAGAAGCCATAAAGGTTTTCAACAGGTAACCGATACATTAGTTTCAATGTTTACTGAGTAACTAATTATTTTGCAGGAGGACAATTTATTTACACAAAATTATTGACGCTCCCTAACAAAATCCCACCTACTTTATCTTATAACTTGTTTTTTTGCATAAAAACTAAATAAAGAGTGCGGCATTTCGCACTTTTTTATTATATATTATTTGTCAAATTAAGCGAGACAAAACTTTCCATTTACGTAACTCAAAAAAACTTCTAATGGTGTTTGGTAATTTAGTGATTTTCTAGGGATATGGTTTCTTTTGGACGCAACGGATGAGATGAATCCTTGATTGACTTGGTGGAAGTCCATTTCTTTTGGTAGTCCATCTTTTCGGAGGAGTCCGTTTGAATGTTCATTTAATCCCCGTTGGGAAGGCGTTCCTGGGTCTGCGAAATAAATATCAATATCATTCGTATTACTAATACTTTTCCAATTAGAGAATTCTTTTCCACAATCAAAGGTAATTGATTTGAAAAGATTTTTGGGTACGGATTGAAGCCATTCATTAATCGAATTTTCAATATCAACTGCCTTACGGCCTTCTGGTTTCAAGGCGATAATGGCTTTTGAAAGTCGCTCAACGAGTGTGATGACGGCACTTTTATGGTGGATGCCGACAATCGTATCACCCTCTAAATGTCCAAATTCTTCTTCGAAAACGACATAATCTTTTTTACGTTCAGAAATATTTCTTTTGAATGCCTGTTTTCCACGTTTTTCCTTATAACCATTTGGTTTTCGTTTTCCTTGCATCGGTAAATGTAAAACATTGAATTCTCCCGTCTTAAACCGGCGATAGAGGGTACTTACTGAACAAGAGAAGGTTCGCTCTGCACGGCCAATAATGACGTCTGGGGTCCAACCTTCAGTTGATCTTTTTGCAATGTATTCTTTTTCCTCAGCAGGAAAAATGATTTCGGTTCTCCCACAACGTCGCTTATTTTCTTTGTATTGTTCAAAGTATTCAAGTGCTGTTCCACCACATTTGAGAAAGTTATAGACATTGTAAATTGTTTGGCGTCCACGTTTAAGCTGCTTCGCAACGATAGCAACCGGAGTTTCTTGATGAAAATATGCTTCTATCATTACAAGCTCGTTTGGTGTAAGATGGGTATAAGTCATTTATGTTCACTCTCCTTGTATGCTTTAGCGGGTATTACAATTGGAGTGTAACATAAATGGCTTTTTTATTTGTCTCGCTTAATTATACAAACGGCGTTGTTAAATAAATAGGAACAAAAAAATTAAATTATTTAATACACACATTAGGGATCATTCATTGAAGGATTAGAAGACAACGAGGATGGCGAAAAATATGATTACAATAGAAAAGTCGTTCTAAACCAATCAGTTCCTAGTATCACACAACGCAAGCCAGTCGATTTGGTGAGATTAGAGGAGTGAAAG\n'

diff -r 000000000000 -r aaa868913641 test-data/polished_test_1.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/polished_test_1.fasta Thu Sep 22 07:51:48 2022 +0000

diff -r 000000000000 -r aaa868913641 test-data/polished_test_2.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/polished_test_2.fasta Thu Sep 22 07:51:48 2022 +0000

diff -r 000000000000 -r aaa868913641 test-data/polished_test_3.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/polished_test_3.fasta Thu Sep 22 07:51:48 2022 +0000

diff -r 000000000000 -r aaa868913641 test-data/polished_test_4.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/polished_test_4.fasta Thu Sep 22 07:51:48 2022 +0000

diff -r 000000000000 -r aaa868913641 test-data/polished_test_5.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/polished_test_5.fasta Thu Sep 22 07:51:48 2022 +0000

diff -r 000000000000 -r aaa868913641 test-data/polished_test_6.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/polished_test_6.fasta Thu Sep 22 07:51:48 2022 +0000

diff -r 000000000000 -r aaa868913641 test-data/polished_test_7.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/polished_test_7.fasta Thu Sep 22 07:51:48 2022 +0000