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Changeset 0:1f9f2edc8cf4 (2022-10-19)

Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/minipolish commit 2772d922443f5838d84646282be6fbfad2df1c77

added:
macros.xml
minipolish.xml
test-data/miniasm.gfa
test-data/reads.fastq
test-data/reads.fastq.gz
test-data/test_01.gfa
test-data/test_02.gfa

diff -r 000000000000 -r 1f9f2edc8cf4 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Wed Oct 19 14:58:27 2022 +0000

@@ -0,0 +1,19 @@
+<macros>
+    <token name="@TOOL_VERSION@">0.1.3</token>
+    <token name="@SUFFIX_VERSION@">0</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">minipolish</requirement>
+        </requirements>
+    </xml>
+    <xml name="biotools">
+        <xrefs>
+            <xref type="bio.tools">minipolish</xref>
+        </xrefs>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.12688/f1000research.21782.4</citation>
+        </citations>
+    </xml>
+</macros>

diff -r 000000000000 -r 1f9f2edc8cf4 minipolish.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/minipolish.xml Wed Oct 19 14:58:27 2022 +0000

[

@@ -0,0 +1,87 @@
+<tool id="minipolish" name="minipolish" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="20.01">
+    <description>polishing miniasm assemblies</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="biotools"/>
+    <version_command>gfastats --version</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+        #if $reads.ext.startswith("fasta")
+            #set ext="fasta"
+        #else
+            #set ext="fastq"
+        #end if
+        #if $reads.ext.endswith(".gz")
+            #set ext=ext+".gz"
+        #end if
+        ln -s '$reads' reads.$ext &&
+        minipolish
+        -t \${GALAXY_SLOTS:-4}
+        --rounds $rounds
+        $pacbio
+        $skip_initial
+        reads.$ext
+        '${assembly}' > $polished_gfa
+    ]]></command>
+    <inputs>
+        <param name="reads" type="data" format="fasta,fastq,fastq.gz,fastqsanger.gz" label="Long reads for polishing"/>
+        <param name="assembly" type="data" format="gfa1" label="Miniasm assembly to be polished"/>
+        <param argument="--rounds" type="integer" min="0" value="2" label="Rounds" help="Number of full Racon polishing rounds. Default: 2" />
+        <param argument="--pacbio" type="boolean" truevalue="--pacbio" falsevalue="" checked="false" label="PacBio reads" help="Use this flag for PacBio reads to make Minipolish use the map-pb
+            Minimap2 preset. Default: assumes Nanopore reads and uses the map-ont preset" />
+        <param argument="--skip_initial" type="boolean" truevalue="--skip_initial" falsevalue="" checked="false" label="Skip the initial polishing round" help="Appropriate if the input GFA does
+            not have 'a' lines. Default: do the initial polishing round" />
+    </inputs>
+    <outputs>
+        <data name="polished_gfa" format="gfa1" label="${tool.name} on ${on_string}: polished GFA"/>
+    </outputs>
+    <tests>
+        
+        <test expect_num_outputs="1">
+            <param name="reads" value="reads.fastq"/>
+            <param name="assembly" value="miniasm.gfa"/>
+            <param name="rounds" value="2"/>
+            <output name="polished_gfa" file="test_01.gfa" ftype="gfa1"/>
+
+        </test>
+        
+        <test expect_num_outputs="1">
+            <param name="reads" value="reads.fastq.gz"/>
+            <param name="assembly" value="miniasm.gfa"/>
+            <param name="rounds" value="3"/>
+            <param name="pacbio" value="true"/>
+            <param name="skip_initial" value="true"/>
+            <output name="polished_gfa" file="test_02.gfa" ftype="gfa1"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+.. class:: infomark
+
+**Purpose**
+
+Miniasm is a great long-read assembly tool: straight-forward, effective and very fast. However, it does not include a polishing step, so its assemblies have a high error rate – they are essentially made of stitched-together pieces of long reads.
+
+Racon is a great polishing tool that can be used to clean up assembly errors. It's also very fast and well suited for long-read data. However, it operates on FASTA files, not the GFA graphs that miniasm makes.
+
+That's where Minipolish comes in. With a single command, it will use Racon to polish up a miniasm assembly, while keeping the assembly in graph form.
+
+It also takes care of some of the other nuances of polishing a miniasm assembly:
+
+- Adding read depth information to contigs
+- Fixing sequence truncation that can occur in Racon
+- Adding circularising links to circular contigs if not already present (so they display better in Bandage)
+- 'Rotating' circular contigs between polishing rounds to ensure clean circularisation
+
+.. class:: infomark
+
+**CIGARs**
+
+It is important to note here something that Minipolish does not do: change/fix the CIGAR strings indicating contig overlap. While circular contigs will be connected with an overlap-free link (i.e. a CIGAR of 0M), links between linear contigs will have overlap.
+
+So take CIGAR overlaps between polished contigs with a grain of salt. They will still indicate the approximate amount of overlap, not the exact amount.
+
+  ]]></help>
+    <expand macro="citations" />
+</tool>

diff -r 000000000000 -r 1f9f2edc8cf4 test-data/miniasm.gfa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/miniasm.gfa Wed Oct 19 14:58:27 2022 +0000

b'@@ -0,0 +1,10 @@\n+S\tutg000001l\tTGAGCTCTTCCCGCTTCACTGCGCCGTTACTATGAGGAATCCTTGTTAGTTTCTTTCCTCCGCCCATTAATAACCCAAAATTCAGCGGGTGAATGCCACCCAATCGAGATCCATAGATGAAACATTCACTTGGCAGGCGACGGCAGCTGGCTGCCGCCTCCATTCCAACGGTCTGCATTCAGCTCGCCTCAAGCTTTCCCCTGCCACAGCAGACTACGGAACACACGGTAGAATTGCATCTACCAAATCTAATGTTGCGTTACCCGTTCGGGTGGCCTTCAGGCACCAGCCTCTGCATCAAAATCAATGAGTTTCAGCAGAGTTGTAAGGCAGACACTGTCAGGGGTCCAGCGATGCCACAAATGCAGCAGCGGCTGAGTGGGAGTTTTGAGGACTTTCAGATAAGCATGCTCTTGGGCATTACCAAAAAGCGCAATGATTCCAAAGTTTTGATGATTCACGAGGTCCTGTGCGTGGCATTATCGCATTTCACTGCGTTCTTCATCGTTGTGGGATCCAAGACATCCATTGCTGAAAGTTGTAATAAATTGAACGGTTAAGTGACAGAGGGCTTCTCTGTTAGGAGATGCACATTGTCCTGGTGTTTGGATTCCTGGTTACGTTTTCATTTTGGCAATGGGCAGGCCAGAAGGAGCCATCAGGCAACTCCAGCTCTAGTTTTGGCATGTTTGATAGGGCAGTGAAACGGCCACCAAGGCTCCAGTGTGTCGGGCTCAGTCTCCGCCATGTTGTTCTCCCGGGTATGTAAGGTTTGGATGGTGTGATAATGATCCTTCCCATAGGTTCTCCGGAAACCTTGTTGCGACTTCACCTTCCTCTAGATGATAAGGTTTGGAGAGTTCTAAATAGCCAAATCCCAATAAGGAGACAGGCCACAATCTCGACTCCTCACCGGACCATCCAATCGGTGGTGCGTGGTGATGCCAATACAAAGGGCAGGGACGTAATCATTGCAGATTGATGATACGTTACTAGAATTCCTCGTTCAAGATTAATAATTGCAATAATCTATCCCTATCACGATGCATGTTAACAAGATTTTAGCACTGCCGGCCAGGTTATCTTCGTTGAGTGCATCAGTGTGTGCAGCCTGCAGGACATCTAAAGGGCATCACAGACCTGTTATTGCCGCCATCTTCCTTCATCTTGTGAAATGAACGTCCCTCTAAGAAGCTCTTGCCAATGAAAAACCATTCGCAGAACTATTTAGCAGGCGGTCTCGTTCGTTAACGGAATTAACAGACAAATCACTCCACCAACCTAGAGCATTATGCACCCACCCTTATGGGTGAAAGAACTCTCCAATCTGTCAATCCCTCACTATGTCTGGACCTGGTAAGTTTTCCGTGTTGGGTGGAAAATTAAGCCACCAGGCTCCCTCCCCTAGTGGTACCCTTCCGTCAATTTCTTTAAGTTTCAGCCTTAAACCATACCTCCCCGGAACCCAAAGACTTTGATTTCTCACTCTGATTGCTGGCAGTCAAAACAACCGCCAATCAGTCGACATAGTTTATGGTTAAGACTACGATGGTATCTAATCATCTTTGATCCCCGCTTTCGTTCTTGTTCATGAAAACATCCTTACTAAATGCTTTCGCAATGTCGGTTAATCTTGCAAGAAATCCAAGAATTTCACCTCTGACAATACAACTGATAACCCCTGTCTCTTTTAATCATTACCGGTACCAAACCAACAAAAATGGCTCAAGGTCTATCTTATTATTCCATGCTAATATATTTCTGCACAGCCTACTTTGCCTCTAATTTTTTCCACAGTAACCAGTGGTATACACACCGACAACAATGCAAGCAGGATTATCCCCAGGATGGCCAGGAACAACAGAATTGCCGCACTGAGTGTGAGACCGGTCGCTCACCACCAGAAATCAACTGCTCGAGCTTTTTAACTGCAACAGCTTTAATATACGCTATTGGGCTAGTGCGCGGCTGCTGGCGCAGACTTGCCCTCAATTGATACTCGATAAGGGATTTAATTGTTCTCATTCCAATTGCCAGACCTGTAAAGGCCCGGCACATTGTTATTTATTGTCACACTACCTCACTGTTTCGTATTGGGTAATTTACGCCTGCTGCTTCGCCCAGATGTGTGCTTATCTCTCAGGCTCCCTCTCGAGAAATCTTCTGATTCGTTACCGGTCAAACCATGGCTGGTCAATACACTACCATCAAAGCTGACCAGGGCAGAAACTACAGATGATCCATCTTGACATGGAGCCATGCGATCGATAAGTTATTATGAATCACCAAAGCACGTCGAAGGCCGGTTTGGTCTATACCTAATAATACTACCCTTCGCGAACAGTCGGGTATTGATGCATGTATTAGCTCTAGGTACTACAGGTATCCAAGTAGTGGGACTATCCAAAGCAATAACTGATGCATAATGAGCCATTACGCGGTTTCCTGTATAATGGTTATACTAGGTATGCATGGCTTAATCTTGAGGCAGGCGTATGACTACTGGCAGAATCAACCAGGTTGCTTTCCGTACCCATGGCTTGGAATGTACAATCGGTCCTCCTAACAGCTTGCGAGCGGACCAGTAGCATACTAATGATAGTTCCTTCTTACCAGGGATGTATTATTATGTTGAGTTCCAAGAGAGTGGTGGCAGAAGTTAAGCAGCAAAAATTACTACCATCACTTGTAGGTGATAACAAAGTGAGCTGAGCAGTTTTACCACCACCTCTTCTGGTATAGATAGCGGTTCCTAGCGGAAGATGACGCGCCAATAATTTACACCTTTTTCTTTCCGAATCTCAGAGAGAGGTGACAACCGAAAAAAGGGCCCTACAGGACCTTGCTCGACATTTTCACCTCACCACCAACACTCAAAAAGTAGGAACATTTTAAAATTGGAGCTCCACTTGCAGTGCATGAAGTCAGTCAATTTCATCTCCACCAAGCTACAGGATCCAAAAAAGTGATGGACTCTTTTTCCATGGTACCACTTCTTGTGTGGTCAACAAACTGTTTCCCTAATAATGGTTGTGAGCCCATAACATTGAAAGATAATAAATAGAAAGGAAAAGAAATATTGCCTTTGTACCAATTTAGTACCCCCTTCTAAGCTGCTCCCCGCAACCACACAAATCCTCTCCCTACACCACACCAATTCCATGTCACCTCTGCCAGCCATTGAGTAGAGGCATCAGCGTTCACAAGTCTTATCTCTATGTGCATCTCTTCCTCCTACATTCATATTAACTCCCTCAAAGATCCCCAGCCACAGCTTCAAAACACAAACTCTCTTTCCCACTCACTCTAGCCACTCTCAACGCATCTCCCAAAACCAACATCTCTTTCATGCACACTTGTCATACTAGTCTCACCCCTTTTTGCGCTTTGATTCATCATCGGTTTGAAAATCCAAGTAAGACTGGTAGAACATTGAGGCAAAACTTCTGAAAGCTTTTGATATGTGCGTTTGATGTGTGAAACCAAGGTAACAAGACACTCTTAGAGCTGGCACTGAGGTCCCAGTCTTTTTTAAGCATTAGTTGCTTTTACCACTTGTAGAGATAATATATTGAATATGTAGTACCTCATCTTGAGTGCACACCTGCAGCACTTTGAGAGGAAGCAAATACAATAACTCTTTAGTGTACTCACACAGCACTGAGAGGAAGCAAATACAATAACAAGACACTCTTGAGTGTACTGAGGTCCCCCAGTCACACTTTTAAGCATTGGTTGCTTTTACTTGTACTTGTAGAGATAATATATTGAATATGGTACCTCACCATCTTGAGTGCACACACAGCACTTTGAGAAGCAAATACAACTCTTTAGTGTACTCACACAGCACTTTGAGAGGAAACCAATACAAATAACAAGACCTCTTGATGTACTGAAGGTCCCAGTCACCTTTTAACATTGGTTGCTTTTTACTTGTACTGTAGAGATAATATATTGAATATATGACA'..b'AAAATCATAATCCAGTCTGTGCTTCCTTATTGGTCGGGGTGTCAAACATCCATCCAACAGCATAATAACTCAGACAAGACGAGTAAACCAAAGCAGCACGATTGCACCGACAACCAAAGCAGATCAGCTCTCCTCAAACGCCGCCAACCTACGGCGACTGTCCCCGCCGTCACATTCCCCACGCCTGCACCGCCACATGACCTCTATTTGGCTCAAACTCGATATCCTACCTGCCTCGTCTCCTTTCCACCGGCATCCGAATCGGCGACGACTATGACTCACGCAAACTTTTCAGTTACGACCAGGTGTGGTGGTCCAGAACTCATTATCGGTGAAGACGGTGATTGGATGGAATGTTTCGAGGGCTGTGGTGGTGTTGGGAATCGATATGGATGCACTAATAGTTATTCGCTTGTTATGGTGGTGTGGGGGCGGGTATGAAATTGAAGCGAAGCAGAAACTGAGCGTTGGATGAAATACGACATCTCTTTGCCGTTCTTCTTCTAGTAGATTCTTAACTGTTCATGGTATGCATGTATCTCTGTATATCATGATGTACTATTCAATCTTCTTCCATGATACACATATCGTTAAGTAAACACAATACAATATATCGGATACACAGAACACAGCAATGCATCTCTGATGTTTCAGCCCGTAGGACCAAATAGAATGGATAAAATACCAAGACAGCCCTACCAGCACAGAGGAACATTCAACTCTTTGAACAATTCACCAACGTTTTGGATGGAAAGTATCAATACAGCACGAACGATATGTATGCTACTATTATCATGGGAGTTGATAGACGATGACTTGGGTCAACGACTACAATACGAATGTCCGATTTCTTGGGGGGAGACAGGCGTTGAACCGTTACCTGGTGATCTCATACCGTACTTGGCATAAAGTTGTCAGTCACAAGGAGTAAATTTTGATTAGGTAGTCAATACGAAGAGAGGAGAACAAGAAGAAACAATAACAATGCACAGTATTCGTTAGAAGGATGAAGAGACAGCCATTACACAGCAACTGGTTAGCAGAGATGCTGTCGTCTTTACCAGTTGCTGTTAAGTTTTCGGTATTGATGTGTTCGTTAGCGTCATCAGCTCATTACATAGAAAGCAGAATTTCATCTACTCTGTCGACATGAATAACACCGATTCAGTTGTATGATAAAGTAGAAGTAGTAGTTCAATGTTGCACCAGCTTTTCACATGGGTTTTAGCTCGAAGAAACAGAGGTATTCCACAAAATTTAGGCAGGCTGGTTCTCATCAAAAAGGTAATTACATGAGAAGAAACCGTGTCTTAGGACTCTTCGATAGAAGCTCTCTTCTCTATCTCCCTTGTCTATACGATTGATGGCCTCCCGTTCGCCTCTCTTCGGAGGATGTACATTGGCTAGTTATTAAAGTGACGGTTTCTTTCTCTATCTCTATCTCACATTTGATTATTGGCATTGAAATATGTAATGACTACAGGACATAGTTGCAGAGAATCTGAGTCATTGAGGAACAAATGGAGGTGCTCAGTAAAAGGGAGAGAGAAAGATGATAAGATAATACCAATGCGATACAGGGAAGCGAGCCCCAACATGTGGCCAACCGAAAATGCAATTTGATAACTCATGTGAGACGGAAGACACGAGCTAGTGGTGAGCAGTGAGATGAAGACAGAGGTTCCGTTTGAAGTTTTGATAGTCATCAAGCCCGTCGATATCATGTTTCAAACTGCAACCACCAACCCCTACCGCCGACCCACCACCGACAAGCAATCAATCTCAATCTGCCTCAGACATCTTGGCGTTATGGCTACTCGAACATCAGTTTGAATTTCCGACGTTGATTAATCGATTGCGACGTCTTGTGGCACTGTCTGTGCACGTACACCAATCTTGTGTGTTCTTGCACACCAGCCGATCTATATTCAGTGAAAGCTGTTTACGCGCCGCAACGGTGGTTAGTACCGCTCTGATTTCACTTTGTCATTGCGGTGGACATTAAGCTGCCATGGCTTCAATCTTTGAGCGGTTTGATACCCACAGCAAAGTGGAGCACTTCGATGACGAAGATGCCTGACAAATTTTGATTGCAGCCCGGCGGTGAAAATCTCTCGATTGGATATGATTGGATACCGAACCTTCTCTAAGTTAACGCTTTATTACAATACATGCAACACTGATCCTCATCTTTTTACCATGCCCTCCTCTCTTATCTCTTTAATTGGGGACGATGCATTTGACCACCTAACTATGCGACGCAACGCCACGCTTCGGCAGTACGCTCCACAAGAACAGTACACGGTAACTCTTTCTCCTTCAATGCACTTCTACGTTATATAAATGAGGAGATTTCTACTCAACTTCTCGGTGGAGAATGATGACGAGGATGGGCAAGTACAAGGACAGAGCCGACAATCTAATGTCTGGGGAAGTGATGATACCAACGACAAATCAGAAGAAGTCAAGCAATCAGCAGCCAACCCAACTACAAACACCAACACTTCAAACACTTCTGCCCGGCACTTTACAAAATTCACCTCTCCTCACTTTCCCTCATCAACCTCAAACGACAAATTCACCTCTTCACCAATGAGATCACATATTCACCCAAATCCCAAAGCCAGAAGTCATTTCATCCTTCACGAAAACGAGTATAGTGTGGTTTAGAAAGCCAGGATTATAAAAACTACGAGGGTTTAGGCATGAGGAAAACTTGCCGGGTCATGTGGTGTTAGTTTCTCAAGAGATGAGGAAGAAGATTTGATGGTAATAAGAACGTGATATTTCGCAGCCAAGGCATGGGCAGGGTTTGCATTCAAGCTTCAACCGTATCCACCTATTGCAAATTGATGATAGTTGCAACTGTAGATGGTACTGAGCCGACGGAGAGGATTGGTGGAATGATTTTTACCATATCTGTCCAAGGTGTTTATGCTCATCATCATTGTTCTCGACAATATCCTATCAACAACAACTACTGCTATAATGGAAATGTCGTTCTTCAAAGCAGGAGGAGCAACAATTGGTACAACAACTACAGAAATGCCATTTGTTGGATGCTATCATGGAATTGATGGGCGCTGTTTGCACTCTTCTGTGAGAATATTATTCTTCAGAGTAGATTTTAAGCGACGGTGATCTTATCAATGCAGTGCTCTATACTCTTCCCTTCTCATTATTGTCTCGAACCACGCTATTCGTGCCCCGACAAACCTTCATCTCTTGTGGAGAGAGAGTCTGGAAACTCTCGATACGATGTTATGGCAATTCAAACTGGACTCGGATGACTCTATGGAA\tLN:i:474411\n+a\tutg000001l\t0\t9e8531fe-c069-48a3-830d-389c8fecb193:13-45076\t+\t27862\n+a\tutg000001l\t27862\t9ccba80c-3cfc-4a84-ac82-be59adfba785:86-53227\t-\t15555\n+a\tutg000001l\t43417\t51de1f36-57f6-472c-a04a-392b2415c83a:18-41021\t+\t1629\n+a\tutg000001l\t45046\tee42dbb3-96d9-4f8f-895c-8d036630582a:4-59383\t+\t22613\n+a\tutg000001l\t67659\tbfa67498-aefe-4663-a559-c17dccc42ad6:26-47766\t+\t8069\n+a\tutg000001l\t75728\t7b0fa21f-e776-4397-af1e-b095fa69adc3:8-47559\t+\t19350\n+a\tutg000001l\t95078\teb46a980-8f00-4251-88ef-2e24235aeed4:49-44944\t-\t15292\n+a\tutg000001l\t110370\td37fa02f-0fef-46ee-9af7-98d611a0cb1d:11-40558\t-\t8070\n+a\tutg000001l\t118440\ta0d87e54-9887-4a2d-bd19-a2ca29e68c3a:13-34163\t+\t3421\n\\ No newline at end of file\n'

diff -r 000000000000 -r 1f9f2edc8cf4 test-data/reads.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/reads.fastq Wed Oct 19 14:58:27 2022 +0000

b'@@ -0,0 +1,36 @@\n+@51de1f36-57f6-472c-a04a-392b2415c83a runid=2fdae66b28c95c27857e236709f82e78094d4aac sampleid= read=25670 ch=406 start_time=2018-01-30T09:43:53Z\n+ATCCCCTGACTCTCCTAAATGCCACATACTCCTCAATCCAAGCCGATATTCGACAATACAACTACAACACATGATCACATACCTTCACACTTCCCTCGACGACGGGCAACTCGTTTCCGAATGAAAATCTGATATACAGTCAAGCGTATTCTACCACATTGATGGAGAGATGGGACTTCTTTCTTAGTTAGCCTGTATTCTTCTACAGGTTTGTTTCTGTAGTTTGTCGTTGTGTCTTTTTTGGTGGTTGTTGCATCGTCGTATAGAATACCATCGAAACATCATTATTGCTTGGTGCACACAGCGACTTTTCCTTCATAGCAACAAGATCAATGTACTCCTTTGAAAAGCGTATAATGGACTTGGATCTCTTGTTCATCAATCCAAGCGGAAAATGATCTCTCGATCTCCTCCCAATCAGCCGCCCTGCATTGAGTGTACACGGGCCAACGTTGCAGTAGACTAAAGTGCAATGTCGCAATTCCGTTGCGTTTTGTTTAGGATGGTGGAGAGGTAGTTTCCATGGATTGTCGATGAATAACTCTTCGAGGAGGCCGAGGGTGGTAAAGTGGATGGAGGAGGTTACGCGATGAACGAGTGGAGTTGGTTGCGATGGTACTGCTGCAATTGTTGCCATTTGTTGTTGACGAAAGTGAATTATCATCATCAAGTGTGTGCTGATGTGTTTCAATACAGCAGCTTTGGGAGTCTTTAACTCGTCACCTGAGGAGAGATGTAGATGCTCGTTATGATTGATGGCTCCCTTCTCTTCCTCGTACTTTTGGCTTTGCTGGTACAGAAGTAATGGTGTTGGTTGCTGGAGATTGTCGTTAGCTCTTCTTTTGCACATTGTTGGTGGTATCAAATGACAAGATCACCCATTCAACAGTTGAGCTTTGGAAGGCAGGGATTTGTTCGTGTTGTGACTTCAATATTTCCTTGTTACCTTAACGACGAAACTCTACTCTCAAACCAGTCACCACTGTTCGCACATTCCTTTAAGATCATGCCCCGTCTCTAGTCGATTGTTGTTATCACTGCCTGCTTTGCATCCTCGCCTCCCTCAACATCATCCCTCATTGCCATCTTTATAAATCCCTCCACAAGAAGCAATACTCTCTTATAGGACCGTATGCCCGAAGGAAACAAGCCCATATCCCGTATGTCTTACTGCTTTATGAAAAGCTCGTTCAATAGTAGATGCTGACTTTGACTTGTTGCTATTCGAGTGAAAAGTAGGAGACGAGTGTTTGGATTAGTCCCGTCTTTGTCGTTACGACTGATGTGTCCGAGGTGTGAGTATGAAGATACAGTGCTAGCCAGATCGTGATACTGCTCCATAAAGATCTGTGCAATGACCAAAGTGTAGACGAATCAACGAGCACATACCGTTGCTGTAACTTTGGTTGCATTCACATCAGAGGTATTAGAGCATCTCTTATGGAAGTGTATTGGCAAACAGCTGCGTAGATGGAAGATGACGTTGCCATGAACTTGGTACTCTTGATTGGTATTCGTTGTAGGATGAGACGTATTCGTTTGTTGCTTCGATTGGAAGATATTTGCGTTTGTAGATTTGTAACTTCTTCCGTTTCTTTACTGTCGTTGTTGTTGGTAGCTCAGTTGTTTGTTCAGTTCCTTCCCTTCCGATTGTTGCGTCAGAAAAAATTGACGTCTCTGGTGATACCGACGTTTGCCACTTTAGATTTGAAGGAGTCCAGCTTTAGCCATCATTTCTACTCAGCTGATAGTATCATTTGCAAAAGAGAAGAAGATCTCGTCGGATGGATCGGTCGATGAAGGTTGTTACACTGCATTCGTCATAATCAGCGTGTTTTGCGTCTCAACGCCAGATGTAAATCGATGTGCCGACGTAGACGATCCGACTCATCATAACCTCCACGGTGGCAATCAGTGCGCACTTTGGTACGTTTGAAGAATGGGTACAGCGTACGCTGCAATCCGTCTCCCGCTCTGAAGAACAAGCCGAGCGAGATAGTGGTGAATGTGGTGATACGTGTAGCCAGTACTTTGTGTGGTCGGTGGTCAAGGCTTCAAAGCAGAGAATAAGCCACATCCAACCCAGAATGGCTCCTCTGTTCCTTCCTCGTAGATAGCCGTCGAACGTAGGGTTATCGAACCACGAGAGTAGTCGGGTGGTGAAGCTGGCAGATTGTGTATTGTCCAGTTCATTATAAAACGCAGGAGGAAAGAAACTCTTTTTTGGCCCTTTCTGGCCAAAAGTAACTTTCCCCTTTTAGTGACAGCACCAGGGGACAAATTAAGTAACTTTTTGTCCGGTACTTCCAAATAAACGGCCATCTATTTTCTCCTTATTATAATAAGTAAAAACTATAACTAGGGGACAATGAACAAGAAAATAAGTGGACACGATCTTCGAACCCTGCGAGAACGTGCAAATCGGACCTCAGACCACATCCAATCCCAATCATCACCAGCCAATCATCTGATCTGGCCAACAGCAACACACGGCAACTCTGACACAGGATAAAGCTGCTATTGGGCTGTAGCGTAAATGGTAGATAGCAGAAGAATTTTCGTCGTCCACGACCAATGTCTCGTATTGGTGCATTTCCTCGTCGAAATTCACGTCGTCAGTCGTCTCCCGAGCATCGTTGCATAGTTGATGAAAGTCATGTTGGACATATGGTTGACTTGCAAATTGTACATCGCTTTTGTATATGTCACCAATCGACTCTTACAATCATCTCGTATGCCCTCTCCTCTCTTTGCATAGACATCAATGCAGACATCACAGCGCTTACAACACGTCATCGCTTTCTCCGGAAGAGCCCAACACAAACAACTGTCTTCATACTATGATGGCATCAGCAGCAGCGAAGAGTATGGCGATCACCTCCAAGACAATCCTGCTTAATAACAACATCGTCGTCATCACCATCCATTGCAGAATAAATCCTCCACGTCAATACCCAATGTATCATCACCAACTTTGTCTCCAATACGGATTTACGGTGGAGGTCACTCTAGAGCTCGGGGAGGCAGTGGTGCTCCACGTCGCCAGGAAGGACAACAGGTGGAGATAGCATTAGTGGTCACTGCATCGTTTAGGCTATTCTTGAGGAAACGCCTGTTCAATGAAAGTTATCAATGAACTGCCCTGATCGTTCATTCACCACCTTCTAAATCAACAACCAACCCACCGTCGTCCTCTCGTCAACAGCAACAGCAGCAACGTCTCAGCCTCTCACCAACACGTCTGGCTAAAGCTGCCACAAACACTAAACCGTATACAAAGCAGGATATCATCATCCTGTCCTGTCAATGGAATTGCAAATCCTTCCTTTGGGACGTATAAGTGCATGTGTGAGGTGAGGAGTTGGTGATGGAGGTTCAAAGAGGTAGTTGTCAAGTGAAGGGGTCATTTGTATGCAGTGGCAGTGGAAAATGCAGTTTGTTGGAGGGACTATTGGAAGAGTATAGATGGAGAGGATGAGGGCAGGGTGATCCGGGAAATGCTAATGAGACAAATGATGGAGAGGTGGTGCAGCGTTAGAGAAGGAACAACAAGCAGCAAACCGCGAGAAGGTCAGATTCAAGCTGTAGCAATGAGGAGGATGATGTTGCTTCCAATGCAGCACAATCCAGCCCGAGGCAACGTCCTCCTCCCAACCCACCAGAGCCACTGCTGCTGCAAATTCTTCTCCCACCCCAATCCACAATATGACCACCTATAGCCTTAGAGCAACAACAGCAACCGCCACCTCCCCCAGCTGCAGAGCAACAACCTCCTCCTCCTCTAGCTCAGCAAGTGCAACCTGAAGTGCCTAGGCAGCGAAGTCTGGACCCAGAG'..b'/..5(&%$+%$&+,57877<F@?::;/0/3=139:5++)))*,0285789;9<=@?HBE<>>;789:6$&(1/2.+)**((.58;;;1(3(,*12%7010$((\',,,,219:874,*0(&\',&%&%$\'+(\'%&\'%&+..5./))-%%/*1$$$\'77+1610,03868-\'&**-,/2&&&%%12%(\'$%(&\',+---**+/1-21+9;=7BA@8+)+\'3/;410-/$(3&&&&67:521$#\'&&%$(&*-/0&&,*.+./100++3350.+\'\';0009,)\'\'+***(*$(($$#&#&&)$%%#&%&%%(),0))*)()20,\'*&&69<:%%54;:%%72)\'%%\'(&-***./=<89<:/.13307/=?@64+&\',4\'(%%(&4:5:.133.\'((5<98=:%%&,/\'\'+\'17<=<==>;45:77<99/+&(++&%&%%&,9;?A?:=..3-0())*%*389<:6@>>:+/59221==::7:6522302-\'((5;::;>?;<;2+&$$\'*&%%66666:=8387011&#\'&*8;*3756&\'3.--$&-/2*)++)(.$$#$$&#$+$$$,+568<89*.529(.%\'\'*&\'&+<=5-B<93?*-48261/6::7:8**&&$",57232-,0:&*/%%(+)0:;112;:91),5:+00,-0544,+%$%&&%()&&%&,&3.&)0/;<>07+2&10-+,)*,((*/&%(/0/2++,6.:/,<=<9A35<?@BD<=B?6768633A?B5,)(\'()\'0167<;??=+++2?AD?56877756.2*-4&&+,+\'134<1./-*.+09;@A*.***),,/)-./.+-/--=,?1+++/.--002%157<>9655/1699+,+-74=<B=9;--,)-4;577++**($$\'#)%\',*318=@AAA?A,(4,9:98510115)$$%)$$%*2.&&%%%%*++&,,)$3$\'*\'\'(&))%*/1014643997DB@?;=0;>@CD6:4*&./3,5,...(3&%),**%-(//1:;56<<7-,%%$$%-5=B@45579;:-+0+./2\'--A58&\'((*:6733:8:<<</&*&3:899>@C>>K=?EB?A3)-/()%%.3.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diff -r 000000000000 -r 1f9f2edc8cf4 test-data/reads.fastq.gz

Binary file test-data/reads.fastq.gz has changed

diff -r 000000000000 -r 1f9f2edc8cf4 test-data/test_01.gfa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_01.gfa Wed Oct 19 14:58:27 2022 +0000

b'@@ -0,0 +1,1 @@\n+S\tutg000001l\tTGAGCTCTTCCCGCTTCACTGCGCCGTTACTATGAGGAATCCTTGTTAGTTTCTTTCCTCCGCCCATTAATAACCCAAAATTCAGCGGGTGAATGCCACCCAATCGAGATCCATAGATGAAACATTCACTTGGCAGGCGACGGCAGCTGGCTGCCGCCTCCATTCCAACGGTCTGCATTCAGCTCGCCTCAAGCTTTCCCCTGCCACAGCAGACTACGGAACACACGGTAGAATTGCATCTACCAAATCTAATGTTGCGTTACCCGTTCGGGTGGCCTTCAGGCACCAGCCTCTGCATCAAAATCAATGAGTTTCAGCAGAGTTGTAAGGCAGACACTGTCAGGGGTCCAGCGATGCCACAAATGCAGCAGCGGCTGAGTGGGAGTTTTGAGGACTTTCAGATAAGCATGCTCTTGGGCATTACCAAAAAGCGCAATGATTCCAAAGTTTTGATGATTCACGAGGTCCTGTGCGTGGCATTATCGCATTTCACTGCGTTCTTCATCGTTGTGGGATCCAAGACATCCATTGCTGAAAGTTGTAATAAATTGAACGGTTAAGTGACAGAGGGCTTCTCTGTTAGGAGATGCACATTGTCCTGGTGTTTGGATTCCTGGTTACGTTTTCATTTTGGCAATGGGCAGGCCAGAAGGAGCCATCAGGCAACTCCAGCTCTAGTTTTGGCATGTTTGATAGGGCAGTGAAACGGCCACCAAGGCTCCAGTGTGTCGGGCTCAGTCTCCGCCATGTTGTTCTCCCGGGTATGTAAGGTTTGGATGGTGTGATAATGATCCTTCCCATAGGTTCTCCGGAAACCTTGTTGCGACTTCACCTTCCTCTAGATGATAAGGTTTGGAGAGTTCTAAATAGCCAAATCCCAATAAGGAGACAGGCCACAATCTCGACTCCTCACCGGACCATCCAATCGGTGGTGCGTGGTGATGCCAATACAAAGGGCAGGGACGTAATCATTGCAGATTGATGATACGTTACTAGAATTCCTCGTTCAAGATTAATAATTGCAATAATCTATCCCTATCACGATGCATGTTAACAAGATTTTAGCACTGCCGGCCAGGTTATCTTCGTTGAGTGCATCAGTGTGTGCAGCCTGCAGGACATCTAAAGGGCATCACAGACCTGTTATTGCCGCCATCTTCCTTCATCTTGTGAAATGAACGTCCCTCTAAGAAGCTCTTGCCAATGAAAAACCATTCGCAGAACTATTTAGCAGGCGGTCTCGTTCGTTAACGGAATTAACAGACAAATCACTCCACCAACCTAGAGCATTATGCACCCACCCTTATGGGTGAAAGAACTCTCCAATCTGTCAATCCCTCACTATGTCTGGACCTGGTAAGTTTTCCGTGTTGGGTGGAAAATTAAGCCACCAGGCTCCCTCCCCTAGTGGTACCCTTCCGTCAATTTCTTTAAGTTTCAGCCTTAAACCATACCTCCCCGGAACCCAAAGACTTTGATTTCTCACTCTGATTGCTGGCAGTCAAAACAACCGCCAATCAGTCGACATAGTTTATGGTTAAGACTACGATGGTATCTAATCATCTTTGATCCCCGCTTTCGTTCTTGTTCATGAAAACATCCTTACTAAATGCTTTCGCAATGTCGGTTAATCTTGCAAGAAATCCAAGAATTTCACCTCTGACAATACAACTGATAACCCCTGTCTCTTTTAATCATTACCGGTACCAAACCAACAAAAATGGCTCAAGGTCTATCTTATTATTCCATGCTAATATATTTCTGCACAGCCTACTTTGCCTCTAATTTTTTCCACAGTAACCAGTGGTATACACACCGACAACAATGCAAGCAGGATTATCCCCAGGATGGCCAGGAACAACAGAATTGCCGCACTGAGTGTGAGACCGGTCGCTCACCACCAGAAATCAACTGCTCGAGCTTTTTAACTGCAACAGCTTTAATATACGCTATTGGGCTAGTGCGCGGCTGCTGGCGCAGACTTGCCCTCAATTGATACTCGATAAGGGATTTAATTGTTCTCATTCCAATTGCCAGACCTGTAAAGGCCCGGCACATTGTTATTTATTGTCACACTACCTCACTGTTTCGTATTGGGTAATTTACGCCTGCTGCTTCGCCCAGATGTGTGCTTATCTCTCAGGCTCCCTCTCGAGAAATCTTCTGATTCGTTACCGGTCAAACCATGGCTGGTCAATACACTACCATCAAAGCTGACCAGGGCAGAAACTACAGATGATCCATCTTGACATGGAGCCATGCGATCGATAAGTTATTATGAATCACCAAAGCACGTCGAAGGCCGGTTTGGTCTATACCTAATAATACTACCCTTCGCGAACAGTCGGGTATTGATGCATGTATTAGCTCTAGGTACTACAGGTATCCAAGTAGTGGGACTATCCAAAGCAATAACTGATGCATAATGAGCCATTACGCGGTTTCCTGTATAATGGTTATACTAGGTATGCATGGCTTAATCTTGAGGCAGGCGTATGACTACTGGCAGAATCAACCAGGTTGCTTTCCGTACCCATGGCTTGGAATGTACAATCGGTCCTCCTAACAGCTTGCGAGCGGACCAGTAGCATACTAATGATAGTTCCTTCTTACCAGGGATGTATTATTATGTTGAGTTCCAAGAGAGTGGTGGCAGAAGTTAAGCAGCAAAAATTACTACCATCACTTGTAGGTGATAACAAAGTGAGCTGAGCAGTTTTACCACCACCTCTTCTGGTATAGATAGCGGTTCCTAGCGGAAGATGACGCGCCAATAATTTACACCTTTTTCTTTCCGAATCTCAGAGAGAGGTGACAACCGAAAAAAGGGCCCTACAGGACCTTGCTCGACATTTTCACCTCACCACCAACACTCAAAAAGTAGGAACATTTTAAAATTGGAGCTCCACTTGCAGTGCATGAAGTCAGTCAATTTCATCTCCACCAAGCTACAGGATCCAAAAAAGTGATGGACTCTTTTTCCATGGTACCACTTCTTGTGTGGTCAACAAACTGTTTCCCTAATAATGGTTGTGAGCCCATAACATTGAAAGATAATAAATAGAAAGGAAAAGAAATATTGCCTTTGTACCAATTTAGTACCCCCTTCTAAGCTGCTCCCCGCAACCACACAAATCCTCTCCCTACACCACACCAATTCCATGTCACCTCTGCCAGCCATTGAGTAGAGGCATCAGCGTTCACAAGTCTTATCTCTATGTGCATCTCTTCCTCCTACATTCATATTAACTCCCTCAAAGATCCCCAGCCACAGCTTCAAAACACAAACTCTCTTTCCCACTCACTCTAGCCACTCTCAACGCATCTCCCAAAACCAACATCTCTTTCATGCACACTTGTCATACTAGTCTCACCCCTTTTTGCGCTTTGATTCATCATCGGTTTGAAAATCCAAGTAAGACTGGTAGAACATTGAGGCAAAACTTCTGAAAGCTTTTGATATGTGCGTTTGATGTGTGAAACCAAGGTAACAAGACACTCTTAGAGCTGGCACTGAGGTCCCAGTCTTTTTTAAGCATTAGTTGCTTTTACCACTTGTAGAGATAATATATTGAATATGTAGTACCTCATCTTGAGTGCACACCTGCAGCACTTTGAGAGGAAGCAAATACAATAACTCTTTAGTGTACTCACACAGCACTGAGAGGAAGCAAATACAATAACAAGACACTCTTGAGTGTACTGAGGTCCCCCAGTCACACTTTTAAGCATTGGTTGCTTTTACTTGTACTTGTAGAGATAATATATTGAATATGGTACCTCACCATCTTGAGTGCACACACAGCACTTTGAGAAGCAAATACAACTCTTTAGTGTACTCACACAGCACTTTGAGAGGAAACCAATACAAATAACAAGACCTCTTGATGTACTGAAGGTCCCAGTCACCTTTTAACATTGGTTGCTTTTTACTTGTACTGTAGAGATAATATATTGAATATATGACAC'..b'ACCAGAGAGGGAATAATGAGGAATCAATACATTCTGTTCCCTTATGATCAGAGGCAGAGAGTCCTCCAGGCTCGGCACCGGGCGGTACGGTGAGTGAGATGATCTCCATCATCACCATGGTCGATGCATCCTTCTTTTATCGAATTCTGCTCGGTCTATTTCCTTTGTTTGATTTGGTATTGGATTTTGCCCTTGTGGTTGTTGTCTTTCCAGGTCTACGGTACTAAATGTGCGCGTTCATGATGAATCCCCGTCCATCTCGTCCCAAACGGGGAATACAAACTAACTGTATGTCCCTGAGATACGGCTATATGCAAAATCTGTCTTTATTTAAACAAGGTAGATGAAGATAGACAAATCAGTCAGACATGATCAGTCGACTCCCTGAGCACGAACCAAAACTGGTCACCCGTCCCTCAGATCAAGGCCTCTGTCTTCGATATATGGGGTATAAGCGAGCAACCCAACCTCAATACTGACATTCGACATACAGTATCTCTTCGACCATATAATATTATCAATTCCCTAATCAGCAGCGTTTCCAAATCAACAGGTTTTGACGGCCACCAACGGCGTCACTCCAGCGCTCTGATGCACCGTCAAGTTGAGTCTACGGGAAGAACAGGAATCTACACCTTCTTGCGCGTCAAACAAGCAGCAATTCAGAGATATTTCATGTAGGCTACTAAAATCATAATCCAGTCTGTGCTTCCTTATTGGTCGGGGTGTCAAACATCCATCCAACAGCATAATAACTCAGACAAGACGAGTAAACCAAAGCAGCACGATTGCACCGACAACCAAAGCAGATCAGCTCTCCTCAAACGCCGCCAACCTACGGCGACTGTCCCCGCCGTCACATTCCCCACGCCTGCACCGCCACATGACCTCTATTTGGCTCAAACTCGATATCCTACCTGCCTCGTCTCCTTTCCACCGGCATCCGAATCGGCGACGACTATGACTCACGCAAACTTTTCAGTTACGACCAGGTGTGGTGGTCCAGAACTCATTATCGGTGAAGACGGTGATTGGATGGAATGTTTCGAGGGCTGTGGTGGTGTTGGGAATCGATATGGATGCACTAATAGTTATTCGCTTGTTATGGTGGTGTGGGGGCGGGTATGAAATTGAAGCGAAGCAGAAACTGAGCGTTGGATGAAATACGACATCTCTTTGCCGTTCTTCTTCTAGTAGATTCTTAACTGTTCATGGTATGCATGTATCTCTGTATATCATGATGTACTATTCAATCTTCTTCCATGATACACATATCGTTAAGTAAACACAATACAATATATCGGATACACAGAACACAGCAATGCATCTCTGATGTTTCAGCCCGTAGGACCAAATAGAATGGATAAAATACCAAGACAGCCCTACCAGCACAGAGGAACATTCAACTCTTTGAACAATTCACCAACGTTTTGGATGGAAAGTATCAATACAGCACGAACGATATGTATGCTACTATTATCATGGGAGTTGATAGACGATGACTTGGGTCAACGACTACAATACGAATGTCCGATTTCTTGGGGGGAGACAGGCGTTGAACCGTTACCTGGTGATCTCATACCGTACTTGGCATAAAGTTGTCAGTCACAAGGAGTAAATTTTGATTAGGTAGTCAATACGAAGAGAGGAGAACAAGAAGAAACAATAACAATGCACAGTATTCGTTAGAAGGATGAAGAGACAGCCATTACACAGCAACTGGTTAGCAGAGATGCTGTCGTCTTTACCAGTTGCTGTTAAGTTTTCGGTATTGATGTGTTCGTTAGCGTCATCAGCTCATTACATAGAAAGCAGAATTTCATCTACTCTGTCGACATGAATAACACCGATTCAGTTGTATGATAAAGTAGAAGTAGTAGTTCAATGTTGCACCAGCTTTTCACATGGGTTTTAGCTCGAAGAAACAGAGGTATTCCACAAAATTTAGGCAGGCTGGTTCTCATCAAAAAGGTAATTACATGAGAAGAAACCGTGTCTTAGGACTCTTCGATAGAAGCTCTCTTCTCTATCTCCCTTGTCTATACGATTGATGGCCTCCCGTTCGCCTCTCTTCGGAGGATGTACATTGGCTAGTTATTAAAGTGACGGTTTCTTTCTCTATCTCTATCTCACATTTGATTATTGGCATTGAAATATGTAATGACTACAGGACATAGTTGCAGAGAATCTGAGTCATTGAGGAACAAATGGAGGTGCTCAGTAAAAGGGAGAGAGAAAGATGATAAGATAATACCAATGCGATACAGGGAAGCGAGCCCCAACATGTGGCCAACCGAAAATGCAATTTGATAACTCATGTGAGACGGAAGACACGAGCTAGTGGTGAGCAGTGAGATGAAGACAGAGGTTCCGTTTGAAGTTTTGATAGTCATCAAGCCCGTCGATATCATGTTTCAAACTGCAACCACCAACCCCTACCGCCGACCCACCACCGACAAGCAATCAATCTCAATCTGCCTCAGACATCTTGGCGTTATGGCTACTCGAACATCAGTTTGAATTTCCGACGTTGATTAATCGATTGCGACGTCTTGTGGCACTGTCTGTGCACGTACACCAATCTTGTGTGTTCTTGCACACCAGCCGATCTATATTCAGTGAAAGCTGTTTACGCGCCGCAACGGTGGTTAGTACCGCTCTGATTTCACTTTGTCATTGCGGTGGACATTAAGCTGCCATGGCTTCAATCTTTGAGCGGTTTGATACCCACAGCAAAGTGGAGCACTTCGATGACGAAGATGCCTGACAAATTTTGATTGCAGCCCGGCGGTGAAAATCTCTCGATTGGATATGATTGGATACCGAACCTTCTCTAAGTTAACGCTTTATTACAATACATGCAACACTGATCCTCATCTTTTTACCATGCCCTCCTCTCTTATCTCTTTAATTGGGGACGATGCATTTGACCACCTAACTATGCGACGCAACGCCACGCTTCGGCAGTACGCTCCACAAGAACAGTACACGGTAACTCTTTCTCCTTCAATGCACTTCTACGTTATATAAATGAGGAGATTTCTACTCAACTTCTCGGTGGAGAATGATGACGAGGATGGGCAAGTACAAGGACAGAGCCGACAATCTAATGTCTGGGGAAGTGATGATACCAACGACAAATCAGAAGAAGTCAAGCAATCAGCAGCCAACCCAACTACAAACACCAACACTTCAAACACTTCTGCCCGGCACTTTACAAAATTCACCTCTCCTCACTTTCCCTCATCAACCTCAAACGACAAATTCACCTCTTCACCAATGAGATCACATATTCACCCAAATCCCAAAGCCAGAAGTCATTTCATCCTTCACGAAAACGAGTATAGTGTGGTTTAGAAAGCCAGGATTATAAAAACTACGAGGGTTTAGGCATGAGGAAAACTTGCCGGGTCATGTGGTGTTAGTTTCTCAAGAGATGAGGAAGAAGATTTGATGGTAATAAGAACGTGATATTTCGCAGCCAAGGCATGGGCAGGGTTTGCATTCAAGCTTCAACCGTATCCACCTATTGCAAATTGATGATAGTTGCAACTGTAGATGGTACTGAGCCGACGGAGAGGATTGGTGGAATGATTTTTACCATATCTGTCCAAGGTGTTTATGCTCATCATCATTGTTCTCGACAATATCCTATCAACAACAACTACTGCTATAATGGAAATGTCGTTCTTCAAAGCAGGAGGAGCAACAATTGGTACAACAACTACAGAAATGCCATTTGTTGGATGCTATCATGGAATTGATGGGCGCTGTTTGCACTCTTCTGTGAGAATATTATTCTTCAGAGTAGATTTTAAGCGACGGTGATCTTATCAATGCAGTGCTCTATACTCTTCCCTTCTCATTATTGTCTCGAACCACGCTATTCGTGCCCCGACAAACCTTCATCTCTTGTGGAGAGAGAGTCTGGAAACTCTCGATACGATGTTATGGCAATTCAAACTGGACTCGGATGACTCTATGGAA\tdp:f:0.893\n'

diff -r 000000000000 -r 1f9f2edc8cf4 test-data/test_02.gfa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_02.gfa Wed Oct 19 14:58:27 2022 +0000