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Changeset 10:2061fb3b81b4 (2023-01-24)

Previous changeset 9:c388a21dcbf1 (2023-01-20) Next changeset 11:cd7936c5a9a5 (2023-02-23)

Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 0fb623fa67741a34587f9e5b110f22f68f0b59fa

modified:
hifiasm.xml

added:
test-data/hifiasm-out-hifiul.bp.p_ctg.gfa
test-data/hifiasm-out-hifiul.bp.r_utg.gfa
test-data/nanopore.fasta.gz
test-data/nanopore.first5.fasta.gz
test-data/nanopore.first50.fasta.gz

diff -r c388a21dcbf1 -r 2061fb3b81b4 hifiasm.xml
--- a/hifiasm.xml Fri Jan 20 22:27:43 2023 +0000
+++ b/hifiasm.xml Tue Jan 24 17:46:39 2023 +0000

[

b'@@ -2,7 +2,7 @@\n <description>haplotype-resolved de novo assembler for PacBio Hifi reads</description>\n <macros>\n <token name="@TOOL_VERSION@">0.18.5</token>\n- <token name="@VERSION_SUFFIX@">0</token>\n+ <token name="@VERSION_SUFFIX@">1</token>\n <token name="@FORMATS@">fasta,fasta.gz,fastq,fastq.gz</token>\n <xml name="reads">\n <param name="reads" type="data" format="@FORMATS@" multiple="true" label="Input reads" />\n@@ -21,6 +21,7 @@\n #set $hap2_inputs = list()\n #set $hic1_inputs = list()\n #set $hic2_inputs = list()\n+ #set $ultralong_inputs = list()\n #for idx, read in enumerate($mode.reads):\n #set $inputfile = \'input_%d.%s\' % ($idx, $read.dataset.extension)\n ln -s \'$read\' $inputfile &&\n@@ -40,6 +41,14 @@\n $hic2_inputs.append($inputfile)\n #end for\n #end if\n+ #if str($ont_integration.ont_integration_selector) == \'set\'\n+ mkdir ultralong &&\n+ #for idx, read in enumerate($ont_integration.ul):\n+ #set $inputfile = \'./ultralong/input_%d.%s\' % ($idx, $read.dataset.extension)\n+ ln -s \'$read\' $inputfile &&\n+ $ultralong_inputs.append($inputfile)\n+ #end for\n+ #end if\n #if str($mode.mode_selector) == \'trio\':\n #for idx, read in enumerate($mode.hap1_reads):\n #set $inputfile = \'hap1_input_%d.%s\' % ($idx, $read.dataset.extension)\n@@ -108,8 +117,8 @@\n #end if\n \n #if str($hic_partition.hic_partition_selector) == \'set\':\n- --h1 \'${ \' \'.join(["%s" % $x for $x in $hic1_inputs]) }\'\n- --h2 \'${ \' \'.join(["%s" % $x for $x in $hic2_inputs]) }\'\n+ --h1 ${ \' \'.join(["\'%s\'" % $x for $x in $hic1_inputs]) }\n+ --h2 ${ \' \'.join(["\'%s\'" % $x for $x in $hic2_inputs]) }\n #if $hic_partition.seed:\n --seed $hic_partition.seed\n #end if\n@@ -125,6 +134,16 @@\n --l-msjoin $hic_partition.l_msjoin\n #end if\n \n+ #if str($ont_integration.ont_integration_selector) == \'set\':\n+ --ul ${ \' \'.join(["\'%s\'" % $x for $x in $ultralong_inputs]) }\n+ #if $ont_integration.ul_rate:\n+ --ul-rate $ont_integration.ul_rate\n+ #end if\n+ #if $ont_integration.ul_tip:\n+ --ul-tip $ont_integration.ul_tip\n+ #end if\n+ #end if\n+\n ## Changed the default outputs of hifiasm. Hifiasm outputs a primary assembly and two balanced haplotypes in default. Incorporated the option \'--primary\' to output primary assembly and alternate assembly.\n --primary\n $input_filenames\n@@ -207,6 +226,18 @@\n <param argument="--l-msjoin" type="integer" min="0" value="500000" label="Detect misjoined unitigs of greater than or equal to specified size" help="A value of 0 disables this filter"/>\n </when>\n </conditional>\n+ <conditional name="ont_integration">\n+ <param name="ont_integration_selector" type="select" label="Options for ONT integration">\n+ <option value="blank">Leave default</option>\n+ <option value="set">Specify</option>\n+ </param>\n+ <when value="blank" />\n+ <when value="set">\n+ <param argument="--ul" type="data" format="fastq,fastq.gz,fasta,fasta.gz" multiple="true" label="Ultra-long (>10kb) reads" />\n+ <param argument="--ul-rate" type="float" value="0.2" optional="true" label="error rate of ultra-long reads (default 0.2)" />\n+ <param argument="--ul-tip" type="integer" value="6" optional="true" label="remove tip unitigs composed of less than (INT) reads for the UL assembly (default 6)" />\n+ </when>\n+ </conditional>\n <conditional name="advanced_options">\n <param name="advanced_selector" type="select" label="Advanced'..b'="filter_bits" value="0"/>\n <conditional name="mode">\n@@ -381,7 +414,7 @@\n <has_text text="--primary" />\n </assert_command>\n </test>\n- \n+ \n <test expect_num_outputs="5">\n <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" />\n <param name="filter_bits" value="0" />\n@@ -394,7 +427,7 @@\n <output name="processed_unitigs" file="hifiasm-out3-processed.gfa" ftype="gfa1" />\n <output name="primary_contig_graph" file="hifiasm-out3-primary.gfa" ftype="gfa1" />\n </test>\n- \n+ \n <test expect_num_outputs="5">\n <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" />\n <param name="filter_bits" value="0" />\n@@ -407,7 +440,7 @@\n <output name="processed_unitigs" file="hifiasm-out4-processed.gfa" ftype="gfa1" />\n <output name="primary_contig_graph" file="hifiasm-out4-primary.gfa" ftype="gfa1" />\n </test>\n- \n+ \n <test expect_num_outputs="5">\n <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" />\n <param name="filter_bits" value="0" />\n@@ -420,7 +453,7 @@\n <output name="processed_unitigs" file="hifiasm-out5-processed.gfa" ftype="gfa1" />\n <output name="primary_contig_graph" file="hifiasm-out5-primary.gfa" ftype="gfa1" />\n </test>\n- \n+ \n <test expect_num_outputs="5">\n <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" />\n <param name="filter_bits" value="0" />\n@@ -433,7 +466,7 @@\n <output name="processed_unitigs" file="hifiasm-out6-processed.gfa" ftype="gfa1" />\n <output name="primary_contig_graph" file="hifiasm-out6-primary.gfa" ftype="gfa1" />\n </test>\n- \n+ \n <test expect_num_outputs="5">\n <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" />\n <param name="filter_bits" value="0" />\n@@ -446,7 +479,7 @@\n <output name="processed_unitigs" file="hifiasm-out7-processed.gfa" ftype="gfa1" />\n <output name="primary_contig_graph" file="hifiasm-out7-primary.gfa" ftype="gfa1" />\n </test>\n- \n+ \n <test expect_num_outputs="5">\n <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" />\n <param name="filter_bits" value="0" />\n@@ -459,6 +492,19 @@\n <output name="processed_unitigs" file="hifiasm-out8-processed.gfa" ftype="gfa1" />\n <output name="primary_contig_graph" file="hifiasm-out8-primary.gfa" ftype="gfa1" />\n </test>\n+ \n+ <test expect_num_outputs="5">\n+ <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" />\n+ <param name="mode_selector" value="standard" />\n+\t <param name="filter_bits" value="0" />\n+ <conditional name="ont_integration">\n+ <param name="ont_integration_selector" value="set" />\n+ <param name="ul" value="nanopore.first5.fasta.gz" />\n+ <param name="ul_tip" value="1" />\n+ </conditional>\n+ <output name="primary_contig_graph" file="hifiasm-out-hifiul.bp.p_ctg.gfa" ftype="gfa1" />\n+ <output name="raw_unitigs" file="hifiasm-out-hifiul.bp.r_utg.gfa" ftype="gfa1" />\n+ </test>\n </tests>\n <help><![CDATA[\n .. class:: infomark\n'

diff -r c388a21dcbf1 -r 2061fb3b81b4 test-data/hifiasm-out-hifiul.bp.p_ctg.gfa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hifiasm-out-hifiul.bp.p_ctg.gfa Tue Jan 24 17:46:39 2023 +0000

b'@@ -0,0 +1,10 @@\n+S\tptg000001l\tGAAGTTTTGTCTGAGAGGAGTACCAGGCCGTGTGAGGTGTCAGTCTGCCCCTACTTGGGGGTGCCTCCCAGTTAGGCTACTCGGGTGTCAGAGACCCACTTGAGGAGGCAGTCTGTCCATTCTCAGATGTCCAGCTGCGTGCTGGGAGAACCACTACTCTCTTCAAGGCTGTCAGACAGGGACATTTAAGTCTGCAGAGGATTCTGCTGACTTTTCTTTGGCTGTGCCTTGCCCCTAGAGGTGGAGTCTACAGAGGCAGGCAGGCCTCCTTGAGCTGCGGTGGGCTCCACCCAGTTCGAGCTTCCCAGCTGCTTTGTTTATCTACTCAAGCCTTGGCAATGGCAGGCGCCCCCTCCCCCGGCCTCACTGCTGCCTTGCAGTTTGATCTCAGACTGCTGTGCTAGCAATGAGTGAGACTCCATGGGCGTAGGGCCCTCCGAGCCAGGGGTGGGATATAATCTCCTGGTGTGCCATTTGCTAAGACTGTTGGAAAAGTGCAGTATTAGGGTGGGAGTGACCTGATTTTCCAGGTGCTGTCTGTCACCCCTTTCTTTGACTAGGAAAGGGAATTCCCTGACCCCTTGCGCTTCCTGGGTGAGGCGATGCCTTGCCCTGCTTCGGCTCATGCTCGGTGCACTGCACCCACTGTCCTGCACCCACTTTCCGACACTCCCCAGTGAGATGAACCCAGTACCTCAGTTGGAAATGCAGAAATCACCCATCTTCTGCATCGCTCATGCTGGGAACTGTGGACTGGAGCTGTTCCTATTCAGCCATCTTGGCTCCACACTGTCAAATGCTTTTTCTGCATCTATTGTTATGATCATGTGATTTTTCTTCTTTAGCCTTTTGATGTGCTGAACACATCAATTCAAATGATTTTCAAATGTTGAACCAGTCTTGCCTTACCTGGGATAATATACACCGCCTGGTTATGGTGTATTTTTTTAAATAACTGTCGGAGTCAATTCACTAATATTTTGTTGAGAATTTTTGCATCTATGTTCATGAGAAATACCGGGCTATAGTTTTCTTTTCTTGTGATGTTTTTGTCTGGTTTTAGTATTAGAGTAATGTTGGCCTCACAAAGAATTTGGAAGTATTCCCAATGCTTCTGTATTCTGGAAGAGATTGTGGAGAATTTGTATAATTTCTTTCATAAATGTTTGGTAGAATTCACCAGTGAACCCATCTGGGCCTGGTGCTTCTGTTTGAAACTGTTATTAATTATTGGTTCAATTTCTGTAATAGATATAGGCCTATTCAGATAATCTATGTCTTCTTCTGTGAGAATTATCTTTCAAGAAATTGGTTCATTTTACATAGGTTATCAAATTTTGGGCATAGAGAGTTGTTCATAATATTGCTGTATAACCTTTTAATGTCCATGAGACTACAGTGATATCCTCTTTTTCATTACTGATATTAGTGATTTGTCTTCCTTCTTTTTTGTCTTAGCCTGACTGGAGGTTCATCAATTTTGTTGATCTTTTCAAAGAACTAGGTTTTATTTTTGTTAATTTTCTCTATTGATTTCCTGTTTTCAGTTTCATTGATTTTGGCACTAATTTTTATTATATGTTTTCTCCTGCTTATTTTGGATCTAATTTTTTTCTAGTTTCCTAAGGTGGAAGCTTGGATCATTACTCTCCAATCTTTCTTTTGTTCTAATATGTGCATTCAATGCTAAGCACAGCCTTCCCTGCAAATTTTGAAAAATTTTATCTTATTTTTATTTAGTTTAAAATATTTTTAATTTCTTTTGAGATTTCTGTTTTGACCCATAGGTTACTTAAAAGTGTGCTGTTTAATCCCCAATAATTTTGGAGTTCTCCAGCTGTTATTGATTTCCATTTTAATTCTATTGTGGCATGAATGCAGATATTGTATGATAATTTCTGTTCTTTTAAATGTGCTAAGGTCTGCTTTATGACCCAGAACATGGTTTATTTTGATGAATGTTCCATGTGAGCTTGAGAAGAATGTGTGTTGTGCTGTCACTGAATGATGTAGTTCATAGATGTCAATTATATCCAGTTGATTAATGTGGTATTATTGCTATGTCCTTAAGAATTTTCTGCCAGCAGACTCTGTTTATTTCAGAAAGAGGAGTGTCTAATTGTCAAACTATATTAGTGAATTCATCTGTTTCTCTTTCTAGTTTGGTCAGTTTTTACTCATGTATTTTGAGGTTCTCATGTTAGGCACATACACAAAAAGATTGTGTATATCTTTTTGGAGAATTAACCCTTTTAAAATTATGTAATGCCCATTTATCCCTGATAATTTTTCTTGCTTTGAAGTCTGTTGTGTCAGAAATTAATATAGCTATTCTGATTTCATTTTAGTATTAGCATGATATATATTTCTTCTTCCATTTGCTTTTAATCTGTATATTTTTTAATAAAGTGAGTATTTTGTAGACAGCACGTAGTTGGGTCTTGTCTTTTGATCCACTCTGATATTCTGTATCTTTTAATTGGTATATTTAGACCACTGATTGTTGACACAAGTGACACTACTATATTTATTACTGCTTTCTTTTCACTACCTGTGTCCTTGCTTCTATTTTAGTCTTCCAATCTTTGTCTTCTTTTTGAGGTTTTCATTAATCATTTTATGATATTCTATTTTTCTTTTTTCTTAGCATAGCAATATACTTTTTTTTAAACAAAAAGCGATTGCCACAGAGTTTTCAATATACATTTATAATTAATCCCAGCATACCCTTAGATAATACTATACTACTTCATAGAGAGTACAAGAACCTTATGATAACAAAAGAAGCCTAATTCTCTCTCCCATCACTGTATCATTGCTGTCATTCATTTCACTTTTGTATAAGAGTATATAATCGAATACATTGTTGCTATGATTTTGAACAAACTGTTATCTGTTAGATCAATTAATGATAAGGGAAAAGTTTTAATTTTAATTTTGCTAATTCTTTCGCTGATGCTCTTTCTTTCTTTATGTAGATCCATGATTTGAACTATATGATTTTCCTCTTCTATGAAGACCTTCAACATTTCTTGTAAGGTAGGTCTGCTTGGCACAAAACCCTCAATTTTTGTTGTCTGAAAATGGCTTTATGTCTCCTCTACTTTTGAAGGATAATTTCACTGGGTGCAGCATTCTAAGTTGCTTTTTTTCCCTCAACACTTACATATTTCATACCTTTCTCTTCTTGTTTGCATGATTTCTAAGAAATCAGTGGTAATTCTCTTTGGTCTTCTAGGTAAGAATTTTTTTTTCTCCTGAATTTCTTCAAGAATTTTTATCTTTGGTTTTCTGCAGTTCGAATAGGATATGCCTCTGTGTGTGTGTGTGTGTGAGAGAGAGAGAGAGAGAGAGAGAGGGATTTGGCAATTTGGCATTTATCCTGCTTGGTTTTCTCTGAGCTTCCTGAATACATGGTTTGTTGTCTGACATTAATGTTAGAAAATTCTCAGTCATTATTGTTTCCCATATTCCTATTGTTTCTTTTTGTTTTCTTCTTCTGATATTCCCACTATATGCATTTACACATTCTATGGTGGTCCCACAGTTCTTTGGCTTTTTGTTTTGTTTTGTTTTTTTCTCAGTTTTCTTTTTCTTTGTTTTTCCATTTTAGAAGTTTCCATTAATATATCTTCAAGCTCAGAGATTTTTTTTCCTCAGCCATGTAAAGTTTACTAATTAGCACAAAAAAGGCATTTTTCATGTCTGCTACAGATTTTTTCTTCTGTAGCATTTCTTTTCAATCCTTTCTTAGAATTTCCATCTCTCTGATTACATTGACCATCTGTTCTTACATTCTGTCTACTTTATCCATTAGAATCCTTTTCATGTTAACCATACCTGTTTTAAATTCCAGGTCTACTCCCAATATTCCTGCCACATCTGAGTCTGGTTTTTATACTTGCTCTATGTTTTAAAACTGTGCTTTCTCCTTTTAGTATCCCTTGCCATTTTTTCTTGATAACCAG'..b'CCTTTCCCTTACCTGGACATCACTGTCTCCTCTAACAGCTGAGGTGTCACTGGGAAGTGAAATTGATTACAACTTTTTAAAAATTCCACAGCTGTCGTTTTTACCTCAGCTGCTTCCCATAATTCCACAGATGGTAAACATATGTTTATAGGCACATTGAAAAAGAAGCTATATTGGATGCCTCCCATCTTTAATTCTTATTTTTCCTTTCATGCAGAAAGTCAAAGTCATAGAACTGGGGAATCTTACACATTTGAAGATTAATATTTCTGTGCATTAAGACTTTGGAAACAGCAGGACAGCTAATGATATGCTAATGAGCTGACAGTTTTTATTGATCATAATGAAAGTCGACAAGTGTCTTTCTTGGCGGTTTTGCATGCTGGAATATTTTATTAACGTCTTCAGGGCAGAAGTACATGATTGGTTGCATTTTGAAAACCCTCCCTGTGAGTTTACAGGTCCTACTTTTTGTTAGCCTGTTTCCAAAGCTTGAGTCCCTGCCAGTTTATAAACAGAACACATCTTCATCCATATATTTACATGCCCAGCAGGAAACTCTCCCACCCCTTTTTCCTCTCTCTTTCAAAGCAATTTGTTTCAGTATTTTAGCATACAAAAAAATAGAACCATTTTCTTCAATGTAAACAGAGATCTGCAGGGAAATAAGAGCGTTAAAAAAGAATTAGCATTTGTTTGGTGGTGAAGCTGCTTTTGTTTGTATCAGAAAGCTCTGCATGTTTAGAAGAGCTTGCTTAATCTTAGTTATTCCATACACAAGAGGGACCTAATTGGATAATTTTCTAATTTTTTAATTGCATCTTTCTATATTTCTTAATGCAAAATGAGAAACGTTCTAGGAATAATAGAAATAATGGGCATTAGTTCCCTAAACATTAAAAATCCATAATATACAATGTACCTGGTGCAAATTTATTTTTCAGTGCATGGTGAGCTGACAGCAGGAGGTACAGGGTGGCAACAGGTGGATTAAACAAAAGGAAAAAAAATCCATTTTTCTGCCGTCCATCCGTACTAAATAGTAAGCTTATTAATTTTGGGCTCTGCACCTTAGGGATTTATTTAGGGCCTCAGATCAGCTGAGGTTCATCATTACACTAACAATAAGAAAATGGATTGTTTAGCAAATTAATAGTGTAAATAAGATTACGGGGGGCGGGGGGATGGGGGGAAGAATATTAGGCTACCTAAAAAGACTTCTGTTTTCTAGCACTGAAAAACTGTCTTAGCAAATTATTATTATCTAATACAAATAGTTTTGCATGTTTGATTGGTATCTATCTATTAAGGCAATCAAGATAAAATCTCATTTTGATAACAAGACCTCTTTGTAGCAACAAGTTGTTGGTTCATGTTAAGGGGATCCCTTAAATTATATATTTTTACCTACAGCATATTGTAGTGACCCAGCACTGGTTTTGGAGTGTTAATCGAAAAGTGTCTGGATCTGTCTCTAGCTAATGATAAACAAGTCTCAATCAATTTAGAAAAGTTTATTTTGCCAAGGTTAAGGATGCACCCATGACACAACTTCAGGAGGTCCTGAGGACATGTGCCCAAGGTGGTCCTCATGTATACCTTGCTTTATACATCTTAGGGAGACATAATACCTCCATCAGTACATGTAAGATTTACATTGGTTTGATCTGGAAGGGTAGGACAACCAGAAGGGTGGCAGCTTCCAGGTCATAGGTAGATTTAAAATTTTTCTGATCGGCTATTGGTTGAAAGCGTTATCAGTAGTAAAGAATGTCTGGGTTCTGATAAGGGGTTGTGGAGAAGAAGCTTTTATCATGCAGATGAAGCCTCTAAATAGCAGGCTTCAGGGAGAATATATTGTAAATGTGTATCATTAGACTTAAGGTCTGTGTTGATGTAAATGCTGGAGAGGTTTAATGAAGCATGTTCAACTCCTTTTCCATCATGGTCTGAACTAGATTTCCGGGTTAACTCTGGAATGCCCTTGGCGGAGAGAAGGGGGTTCATTCAGATGGTTGGGGGCTTAGAACTTTATTTTTGGTTTTCAAGAGTTAGTAGCCCTGTAGTATATAGCCTAGGATTAAGGTATCCTTTAGAAAAGCTACTTAGAGTATCAAAGCCTTAAATTTCTCATAGGTCATATGACCAGGTAATCTGGTCCTAGATAAGTAGTTCTTATGGAAAGTATCAAAATGACCTCAGACAGTTTTCAAAATAGTCATGACTGTTCTTTCAACCTCTTCCAAAATTCTGATATATACCCTAAATTAAAAACTATTGCCCCACATGATCTTCACAGATCCTAACTGTGCTCAAAATTATGTGGTTCAGTATTGTATAATTCATAGTTTTCAATAATTTGATGCTTTAGAATATTTATTGTGTTTACTATGTGAAATCTACTACAATAGGAACTTCAGGGGATACTAAGATGAAAATCTATTATCTTTGGTGTTTATAATACAGTCTAGTAATTCTGTTGGGTTTTATTCAGTTCCAAATCAGTAAGATTTTACTCTATTTATATATGAGTTGGATGCAATAATTTTAACCATTGTGAACTTTTAATGAGTAAATGCTCTTGCTCCAAAAGAAGCAAATGGTTGACAATAAAGCAGAATTTTTCAAAGTGAGGTCCTTTTACCATTCATCAGAATCATCTGGAAGAGGTTTTGTTTAAAAAATGAATATTCCTGGGCCCACTCCAATCCTACTGAAACAGGATCCTTTGGGTTGACACAAGAATCTGAATGTTAAGCAGACACTCAAGGTGATTCTCAGGAACTTGAAGTTTGAGAAACACTGCCAAAATGAATAATATGAAATAAAGCATATGTCTGAAAAAAGGAGATCAAATGAGGTCAGCTAATACAGGCCCAGATAGAGTTGCATTTTTCAGTTAAATGTAGATACATTTAGAGTTAAATGAGGAGAAATAATAAAAATTTTGTCTTTTTATCCCTTATCTCCCTTGGGAGAAGTTGTAGTGCTGAAAGGCACATTTTCATCTGTGGAAATCCTCATAGATGATATATATATATATATATATATATATATATATATATATATATATTTTTTTTTTTTTTTTTTGAGAGGAATAAGGCTGATTGAGCTCCTTTGTAGTTTTATGCATTATAAAATCCCTTTTGTAGTTTTATGAAGGAAACTACATGCTTAGCAAATGCTTCTTTTATCAGCAAATGTCCTGGCAGTAAATTGTCCATATAGCAATTTAATGCCAGACCTTCTGATTCTTATTCTGGGGAAGGTGCTGGGATATACATAAATGTGTGTAGTCACATGCATACACACACATGCACTCAGACATCTTTAGATTATAAGTGGTATCTGTAGGGTATCACCACTTTTCTTTTAATCCAGCATTGACTTACAACCATTCAAATAAATTAACATTCCCATCTTGATTCATTTGGTAAGAACACATTTTCATGCCAGTATGTGGGCTCACCTCTATGACCTTTCCTTATAAAAAATACCAAGTGCTTTGGGTTTTTGTGTTAATGAGCATTGGGAAGCTGTCAGCTTTTATTTCTGTTTTTTGTTCAAGTCAACATCATTGACCTTCACCTAATGATCTATGTAACATACACACGCAGGTACCACAGATTAAAAGTGGAAAGACAGGGAAGTAAGGAGAGATGCACATAGAGGAAAGGTGTGAGAGCAGGTGATTTGTAAATCATAATGTCACTAAAATGAGTAAGATCACTTGAAAAGGAAAGGAAAACTGCTGTGTGCTGTATTTTCTTGCTTTAGGATTAGCGGGATGGGGTATTATTTTAAAATGAGTTTTCAGTTTGGTTTTG\tLN:i:25000\trd:i:0\n+A\tptg000003l\t0\t-\tm64012_190920_173625/16714108/ccs\t0\t12049\tid:i:17\tHG:A:a\n+A\tptg000003l\t8768\t+\tm64011_190901_095311/27789106/ccs\t0\t16232\tid:i:60\tHG:A:a\n'

diff -r c388a21dcbf1 -r 2061fb3b81b4 test-data/hifiasm-out-hifiul.bp.r_utg.gfa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hifiasm-out-hifiul.bp.r_utg.gfa Tue Jan 24 17:46:39 2023 +0000

b'@@ -0,0 +1,10 @@\n+S\tutg000001l\tGAAGTTTTGTCTGAGAGGAGTACCAGGCCGTGTGAGGTGTCAGTCTGCCCCTACTTGGGGGTGCCTCCCAGTTAGGCTACTCGGGTGTCAGAGACCCACTTGAGGAGGCAGTCTGTCCATTCTCAGATGTCCAGCTGCGTGCTGGGAGAACCACTACTCTCTTCAAGGCTGTCAGACAGGGACATTTAAGTCTGCAGAGGATTCTGCTGACTTTTCTTTGGCTGTGCCTTGCCCCTAGAGGTGGAGTCTACAGAGGCAGGCAGGCCTCCTTGAGCTGCGGTGGGCTCCACCCAGTTCGAGCTTCCCAGCTGCTTTGTTTATCTACTCAAGCCTTGGCAATGGCAGGCGCCCCCTCCCCCGGCCTCACTGCTGCCTTGCAGTTTGATCTCAGACTGCTGTGCTAGCAATGAGTGAGACTCCATGGGCGTAGGGCCCTCCGAGCCAGGGGTGGGATATAATCTCCTGGTGTGCCATTTGCTAAGACTGTTGGAAAAGTGCAGTATTAGGGTGGGAGTGACCTGATTTTCCAGGTGCTGTCTGTCACCCCTTTCTTTGACTAGGAAAGGGAATTCCCTGACCCCTTGCGCTTCCTGGGTGAGGCGATGCCTTGCCCTGCTTCGGCTCATGCTCGGTGCACTGCACCCACTGTCCTGCACCCACTTTCCGACACTCCCCAGTGAGATGAACCCAGTACCTCAGTTGGAAATGCAGAAATCACCCATCTTCTGCATCGCTCATGCTGGGAACTGTGGACTGGAGCTGTTCCTATTCAGCCATCTTGGCTCCACACTGTCAAATGCTTTTTCTGCATCTATTGTTATGATCATGTGATTTTTCTTCTTTAGCCTTTTGATGTGCTGAACACATCAATTCAAATGATTTTCAAATGTTGAACCAGTCTTGCCTTACCTGGGATAATATACACCGCCTGGTTATGGTGTATTTTTTTAAATAACTGTCGGAGTCAATTCACTAATATTTTGTTGAGAATTTTTGCATCTATGTTCATGAGAAATACCGGGCTATAGTTTTCTTTTCTTGTGATGTTTTTGTCTGGTTTTAGTATTAGAGTAATGTTGGCCTCACAAAGAATTTGGAAGTATTCCCAATGCTTCTGTATTCTGGAAGAGATTGTGGAGAATTTGTATAATTTCTTTCATAAATGTTTGGTAGAATTCACCAGTGAACCCATCTGGGCCTGGTGCTTCTGTTTGAAACTGTTATTAATTATTGGTTCAATTTCTGTAATAGATATAGGCCTATTCAGATAATCTATGTCTTCTTCTGTGAGAATTATCTTTCAAGAAATTGGTTCATTTTACATAGGTTATCAAATTTTGGGCATAGAGAGTTGTTCATAATATTGCTGTATAACCTTTTAATGTCCATGAGACTACAGTGATATCCTCTTTTTCATTACTGATATTAGTGATTTGTCTTCCTTCTTTTTTGTCTTAGCCTGACTGGAGGTTCATCAATTTTGTTGATCTTTTCAAAGAACTAGGTTTTATTTTTGTTAATTTTCTCTATTGATTTCCTGTTTTCAGTTTCATTGATTTTGGCACTAATTTTTATTATATGTTTTCTCCTGCTTATTTTGGATCTAATTTTTTTCTAGTTTCCTAAGGTGGAAGCTTGGATCATTACTCTCCAATCTTTCTTTTGTTCTAATATGTGCATTCAATGCTAAGCACAGCCTTCCCTGCAAATTTTGAAAAATTTTATCTTATTTTTATTTAGTTTAAAATATTTTTAATTTCTTTTGAGATTTCTGTTTTGACCCATAGGTTACTTAAAAGTGTGCTGTTTAATCCCCAATAATTTTGGAGTTCTCCAGCTGTTATTGATTTCCATTTTAATTCTATTGTGGCATGAATGCAGATATTGTATGATAATTTCTGTTCTTTTAAATGTGCTAAGGTCTGCTTTATGACCCAGAACATGGTTTATTTTGATGAATGTTCCATGTGAGCTTGAGAAGAATGTGTGTTGTGCTGTCACTGAATGATGTAGTTCATAGATGTCAATTATATCCAGTTGATTAATGTGGTATTATTGCTATGTCCTTAAGAATTTTCTGCCAGCAGACTCTGTTTATTTCAGAAAGAGGAGTGTCTAATTGTCAAACTATATTAGTGAATTCATCTGTTTCTCTTTCTAGTTTGGTCAGTTTTTACTCATGTATTTTGAGGTTCTCATGTTAGGCACATACACAAAAAGATTGTGTATATCTTTTTGGAGAATTAACCCTTTTAAAATTATGTAATGCCCATTTATCCCTGATAATTTTTCTTGCTTTGAAGTCTGTTGTGTCAGAAATTAATATAGCTATTCTGATTTCATTTTAGTATTAGCATGATATATATTTCTTCTTCCATTTGCTTTTAATCTGTATATTTTTTAATAAAGTGAGTATTTTGTAGACAGCACGTAGTTGGGTCTTGTCTTTTGATCCACTCTGATATTCTGTATCTTTTAATTGGTATATTTAGACCACTGATTGTTGACACAAGTGACACTACTATATTTATTACTGCTTTCTTTTCACTACCTGTGTCCTTGCTTCTATTTTAGTCTTCCAATCTTTGTCTTCTTTTTGAGGTTTTCATTAATCATTTTATGATATTCTATTTTTCTTTTTTCTTAGCATAGCAATATACTTTTTTTTAAACAAAAAGCGATTGCCACAGAGTTTTCAATATACATTTATAATTAATCCCAGCATACCCTTAGATAATACTATACTACTTCATAGAGAGTACAAGAACCTTATGATAACAAAAGAAGCCTAATTCTCTCTCCCATCACTGTATCATTGCTGTCATTCATTTCACTTTTGTATAAGAGTATATAATCGAATACATTGTTGCTATGATTTTGAACAAACTGTTATCTGTTAGATCAATTAATGATAAGGGAAAAGTTTTAATTTTAATTTTGCTAATTCTTTCGCTGATGCTCTTTCTTTCTTTATGTAGATCCATGATTTGAACTATATGATTTTCCTCTTCTATGAAGACCTTCAACATTTCTTGTAAGGTAGGTCTGCTTGGCACAAAACCCTCAATTTTTGTTGTCTGAAAATGGCTTTATGTCTCCTCTACTTTTGAAGGATAATTTCACTGGGTGCAGCATTCTAAGTTGCTTTTTTTCCCTCAACACTTACATATTTCATACCTTTCTCTTCTTGTTTGCATGATTTCTAAGAAATCAGTGGTAATTCTCTTTGGTCTTCTAGGTAAGAATTTTTTTTTCTCCTGAATTTCTTCAAGAATTTTTATCTTTGGTTTTCTGCAGTTCGAATAGGATATGCCTCTGTGTGTGTGTGTGTGTGAGAGAGAGAGAGAGAGAGAGAGAGGGATTTGGCAATTTGGCATTTATCCTGCTTGGTTTTCTCTGAGCTTCCTGAATACATGGTTTGTTGTCTGACATTAATGTTAGAAAATTCTCAGTCATTATTGTTTCCCATATTCCTATTGTTTCTTTTTGTTTTCTTCTTCTGATATTCCCACTATATGCATTTACACATTCTATGGTGGTCCCACAGTTCTTTGGCTTTTTGTTTTGTTTTGTTTTTTTCTCAGTTTTCTTTTTCTTTGTTTTTCCATTTTAGAAGTTTCCATTAATATATCTTCAAGCTCAGAGATTTTTTTTCCTCAGCCATGTAAAGTTTACTAATTAGCACAAAAAAGGCATTTTTCATGTCTGCTACAGATTTTTTCTTCTGTAGCATTTCTTTTCAATCCTTTCTTAGAATTTCCATCTCTCTGATTACATTGACCATCTGTTCTTACATTCTGTCTACTTTATCCATTAGAATCCTTTTCATGTTAACCATACCTGTTTTAAATTCCAGGTCTACTCCCAATATTCCTGCCACATCTGAGTCTGGTTTTTATACTTGCTCTATGTTTTAAAACTGTGCTTTCTCCTTTTAGTATCCCTTGCCATTTTTTCTTGATAACCAG'..b'CCTTTCCCTTACCTGGACATCACTGTCTCCTCTAACAGCTGAGGTGTCACTGGGAAGTGAAATTGATTACAACTTTTTAAAAATTCCACAGCTGTCGTTTTTACCTCAGCTGCTTCCCATAATTCCACAGATGGTAAACATATGTTTATAGGCACATTGAAAAAGAAGCTATATTGGATGCCTCCCATCTTTAATTCTTATTTTTCCTTTCATGCAGAAAGTCAAAGTCATAGAACTGGGGAATCTTACACATTTGAAGATTAATATTTCTGTGCATTAAGACTTTGGAAACAGCAGGACAGCTAATGATATGCTAATGAGCTGACAGTTTTTATTGATCATAATGAAAGTCGACAAGTGTCTTTCTTGGCGGTTTTGCATGCTGGAATATTTTATTAACGTCTTCAGGGCAGAAGTACATGATTGGTTGCATTTTGAAAACCCTCCCTGTGAGTTTACAGGTCCTACTTTTTGTTAGCCTGTTTCCAAAGCTTGAGTCCCTGCCAGTTTATAAACAGAACACATCTTCATCCATATATTTACATGCCCAGCAGGAAACTCTCCCACCCCTTTTTCCTCTCTCTTTCAAAGCAATTTGTTTCAGTATTTTAGCATACAAAAAAATAGAACCATTTTCTTCAATGTAAACAGAGATCTGCAGGGAAATAAGAGCGTTAAAAAAGAATTAGCATTTGTTTGGTGGTGAAGCTGCTTTTGTTTGTATCAGAAAGCTCTGCATGTTTAGAAGAGCTTGCTTAATCTTAGTTATTCCATACACAAGAGGGACCTAATTGGATAATTTTCTAATTTTTTAATTGCATCTTTCTATATTTCTTAATGCAAAATGAGAAACGTTCTAGGAATAATAGAAATAATGGGCATTAGTTCCCTAAACATTAAAAATCCATAATATACAATGTACCTGGTGCAAATTTATTTTTCAGTGCATGGTGAGCTGACAGCAGGAGGTACAGGGTGGCAACAGGTGGATTAAACAAAAGGAAAAAAAATCCATTTTTCTGCCGTCCATCCGTACTAAATAGTAAGCTTATTAATTTTGGGCTCTGCACCTTAGGGATTTATTTAGGGCCTCAGATCAGCTGAGGTTCATCATTACACTAACAATAAGAAAATGGATTGTTTAGCAAATTAATAGTGTAAATAAGATTACGGGGGGCGGGGGGATGGGGGGAAGAATATTAGGCTACCTAAAAAGACTTCTGTTTTCTAGCACTGAAAAACTGTCTTAGCAAATTATTATTATCTAATACAAATAGTTTTGCATGTTTGATTGGTATCTATCTATTAAGGCAATCAAGATAAAATCTCATTTTGATAACAAGACCTCTTTGTAGCAACAAGTTGTTGGTTCATGTTAAGGGGATCCCTTAAATTATATATTTTTACCTACAGCATATTGTAGTGACCCAGCACTGGTTTTGGAGTGTTAATCGAAAAGTGTCTGGATCTGTCTCTAGCTAATGATAAACAAGTCTCAATCAATTTAGAAAAGTTTATTTTGCCAAGGTTAAGGATGCACCCATGACACAACTTCAGGAGGTCCTGAGGACATGTGCCCAAGGTGGTCCTCATGTATACCTTGCTTTATACATCTTAGGGAGACATAATACCTCCATCAGTACATGTAAGATTTACATTGGTTTGATCTGGAAGGGTAGGACAACCAGAAGGGTGGCAGCTTCCAGGTCATAGGTAGATTTAAAATTTTTCTGATCGGCTATTGGTTGAAAGCGTTATCAGTAGTAAAGAATGTCTGGGTTCTGATAAGGGGTTGTGGAGAAGAAGCTTTTATCATGCAGATGAAGCCTCTAAATAGCAGGCTTCAGGGAGAATATATTGTAAATGTGTATCATTAGACTTAAGGTCTGTGTTGATGTAAATGCTGGAGAGGTTTAATGAAGCATGTTCAACTCCTTTTCCATCATGGTCTGAACTAGATTTCCGGGTTAACTCTGGAATGCCCTTGGCGGAGAGAAGGGGGTTCATTCAGATGGTTGGGGGCTTAGAACTTTATTTTTGGTTTTCAAGAGTTAGTAGCCCTGTAGTATATAGCCTAGGATTAAGGTATCCTTTAGAAAAGCTACTTAGAGTATCAAAGCCTTAAATTTCTCATAGGTCATATGACCAGGTAATCTGGTCCTAGATAAGTAGTTCTTATGGAAAGTATCAAAATGACCTCAGACAGTTTTCAAAATAGTCATGACTGTTCTTTCAACCTCTTCCAAAATTCTGATATATACCCTAAATTAAAAACTATTGCCCCACATGATCTTCACAGATCCTAACTGTGCTCAAAATTATGTGGTTCAGTATTGTATAATTCATAGTTTTCAATAATTTGATGCTTTAGAATATTTATTGTGTTTACTATGTGAAATCTACTACAATAGGAACTTCAGGGGATACTAAGATGAAAATCTATTATCTTTGGTGTTTATAATACAGTCTAGTAATTCTGTTGGGTTTTATTCAGTTCCAAATCAGTAAGATTTTACTCTATTTATATATGAGTTGGATGCAATAATTTTAACCATTGTGAACTTTTAATGAGTAAATGCTCTTGCTCCAAAAGAAGCAAATGGTTGACAATAAAGCAGAATTTTTCAAAGTGAGGTCCTTTTACCATTCATCAGAATCATCTGGAAGAGGTTTTGTTTAAAAAATGAATATTCCTGGGCCCACTCCAATCCTACTGAAACAGGATCCTTTGGGTTGACACAAGAATCTGAATGTTAAGCAGACACTCAAGGTGATTCTCAGGAACTTGAAGTTTGAGAAACACTGCCAAAATGAATAATATGAAATAAAGCATATGTCTGAAAAAAGGAGATCAAATGAGGTCAGCTAATACAGGCCCAGATAGAGTTGCATTTTTCAGTTAAATGTAGATACATTTAGAGTTAAATGAGGAGAAATAATAAAAATTTTGTCTTTTTATCCCTTATCTCCCTTGGGAGAAGTTGTAGTGCTGAAAGGCACATTTTCATCTGTGGAAATCCTCATAGATGATATATATATATATATATATATATATATATATATATATATATATTTTTTTTTTTTTTTTTTGAGAGGAATAAGGCTGATTGAGCTCCTTTGTAGTTTTATGCATTATAAAATCCCTTTTGTAGTTTTATGAAGGAAACTACATGCTTAGCAAATGCTTCTTTTATCAGCAAATGTCCTGGCAGTAAATTGTCCATATAGCAATTTAATGCCAGACCTTCTGATTCTTATTCTGGGGAAGGTGCTGGGATATACATAAATGTGTGTAGTCACATGCATACACACACATGCACTCAGACATCTTTAGATTATAAGTGGTATCTGTAGGGTATCACCACTTTTCTTTTAATCCAGCATTGACTTACAACCATTCAAATAAATTAACATTCCCATCTTGATTCATTTGGTAAGAACACATTTTCATGCCAGTATGTGGGCTCACCTCTATGACCTTTCCTTATAAAAAATACCAAGTGCTTTGGGTTTTTGTGTTAATGAGCATTGGGAAGCTGTCAGCTTTTATTTCTGTTTTTTGTTCAAGTCAACATCATTGACCTTCACCTAATGATCTATGTAACATACACACGCAGGTACCACAGATTAAAAGTGGAAAGACAGGGAAGTAAGGAGAGATGCACATAGAGGAAAGGTGTGAGAGCAGGTGATTTGTAAATCATAATGTCACTAAAATGAGTAAGATCACTTGAAAAGGAAAGGAAAACTGCTGTGTGCTGTATTTTCTTGCTTTAGGATTAGCGGGATGGGGTATTATTTTAAAATGAGTTTTCAGTTTGGTTTTG\tLN:i:25000\trd:i:0\n+A\tutg000003l\t0\t-\tm64012_190920_173625/16714108/ccs\t0\t12049\tid:i:17\tHG:A:a\n+A\tutg000003l\t8768\t+\tm64011_190901_095311/27789106/ccs\t0\t16232\tid:i:60\tHG:A:a\n'

diff -r c388a21dcbf1 -r 2061fb3b81b4 test-data/nanopore.fasta.gz

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diff -r c388a21dcbf1 -r 2061fb3b81b4 test-data/nanopore.first5.fasta.gz

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diff -r c388a21dcbf1 -r 2061fb3b81b4 test-data/nanopore.first50.fasta.gz

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