Galaxy |

Changeset 1:6505bd37670d (2021-03-03)

Previous changeset 0:bf0a4667e3ce (2021-03-02) Next changeset 2:f3c89da3af16 (2021-06-20)

Commit message:
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85"

modified:
hifiasm.xml

added:
test-data/hifiasm-in2-0.fa.gz
test-data/hifiasm-in2-1.fa.gz
test-data/hifiasm-in2-2.fa.gz
test-data/hifiasm-in2-3.fa.gz
test-data/hifiasm-in2-4.fa.gz
test-data/hifiasm-out2-alternate.gfa
test-data/hifiasm-out2-primary.gfa
test-data/hifiasm-out2-processed.gfa
test-data/hifiasm-out2-raw.gfa

diff -r bf0a4667e3ce -r 6505bd37670d hifiasm.xml
--- a/hifiasm.xml Tue Mar 02 20:23:49 2021 +0000
+++ b/hifiasm.xml Wed Mar 03 16:16:42 2021 +0000

[

b'@@ -1,10 +1,10 @@\n-<tool id="hifiasm" name="Hifiasm" version="@VERSION@">\n+<tool id="hifiasm" name="Hifiasm" version="@VERSION@+galaxy0">\n <description>de novo assembler</description>\n <macros>\n <token name="@VERSION@">0.14</token>\n <token name="@FORMATS@">fasta,fasta.gz,fastq,fastq.gz</token>\n <xml name="reads">\n- <param name="reads" type="data" format="@FORMATS@" label="Input reads" />\n+ <param name="reads" type="data" format="@FORMATS@" multiple="true" label="Input reads" />\n </xml>\n </macros>\n <requirements>\n@@ -14,15 +14,35 @@\n <version_command>hifiasm --version</version_command>\n <command detect_errors="exit_code">\n <![CDATA[\n- #if str($mode.mode_selector) == \'standard\':\n- ln -s \'$mode.reads\' input.${mode.reads.extension} &&\n- #else:\n- ln -s \'$mode.hap1_reads\' hap1_reads.${mode.hap1_reads.extension} &&\n- ln -s \'$mode.hap2_reads\' hap2_reads.${mode.hap2_reads.extension} &&\n- yak count -k31 -b37 -t\\${GALAXY_SLOTS:-1} -o hap1.yak hap1_reads.${mode.hap1_reads.extension} &&\n- yak count -k31 -b37 -t\\${GALAXY_SLOTS:-1} -o hap2.yak hap2_reads.${mode.hap2_reads.extension} &&\n+ #set $input_files = list()\n+ #set $hap1_inputs = list()\n+ #set $hap2_inputs = list()\n+ #for idx, read in enumerate($mode.reads):\n+ #set $inputfile = \'input_%d.%s\' % ($idx, $read.dataset.extension)\n+ ln -s \'$read\' $inputfile &&\n+ $input_files.append($inputfile)\n+ #end for\n+ #set $input_filenames = \' \'.join($input_files)\n+ #if str($mode.mode_selector) == \'trio\':\n+ #for idx, read in enumerate($mode.hap1_reads):\n+ #set $inputfile = \'hap1_input_%d.%s\' % ($idx, $read.dataset.extension)\n+ ln -s \'$read\' $inputfile &&\n+ $hap1_inputs.append($inputfile)\n+ #end for\n+ #for idx, read in enumerate($mode.hap2_reads):\n+ #set $inputfile = \'hap2_input_%d.%s\' % ($idx, $read.dataset.extension)\n+ ln -s \'$read\' $inputfile &&\n+ $hap2_inputs.append($inputfile)\n+ #end for\n+ #set $hap1_filenames = \' \'.join($hap1_inputs)\n+ #set $hap2_filenames = \' \'.join($hap2_inputs)\n+ yak count -k31 -b37 -t\\${GALAXY_SLOTS:-1} -o hap1.yak $hap1_filenames &&\n+ yak count -k31 -b37 -t\\${GALAXY_SLOTS:-1} -o hap2.yak $hap2_filenames &&\n #end if\n- hifiasm -i input.${mode.reads.extension} -t \\${GALAXY_SLOTS:-1} -o output -f $filter_bits\n+ hifiasm -i $input_filenames -t \\${GALAXY_SLOTS:-1} -o output -f $filter_bits\n+ #if str($mode.mode_selector) == \'trio\':\n+ -1 hap1.yak -2 hap2.yak\n+ #end if\n #if str($advanced_options.advanced_selector) == \'set\':\n -z $advanced_options.adapter_length\n -k $advanced_options.kmer_length\n@@ -39,7 +59,6 @@\n -x $assembly_options.max_overlap\n -y $assembly_options.min_overlap\n $assembly_options.disable_post_join\n- --pb-range $assembly_options.pb_range\n #end if\n #if str($mode.mode_selector) == \'trio\':\n -1 hap1.yak\n@@ -69,8 +88,8 @@\n </when>\n <when value="trio">\n <expand macro="reads" />\n- <param name="hap1_reads" type="data" format="fastq,fastq.gz" label="Haplotype 1 reads" />\n- <param name="hap2_reads" type="data" format="fastq,fastq.gz" label="Haplotype 2 reads" />\n+ <param name="hap1_reads" type="data" format="fastq,fastq.gz" multiple="true" label="Haplotype 1 reads" />\n+ <param name="hap2_reads" type="data" format="fastq,fastq.gz" multiple="true" label="Haplotype 2 reads" />\n <param name="max_kmers" argument="-c" type="integer" value="2" label="Lower bound of the binned k-mer\'s frequency" />\n '..b'a1" from_work_dir="output.r_utg.gfa" label="${tool.name} on ${on_string}, haplotype-resolved raw unitig graph">\n <filter>mode[\'mode_selector\'] == \'standard\'</filter>\n </data>\n- <data name="raw_unitigs" format="gfa1" from_work_dir="output.dip.r_utg.gfa" label="${tool.name} on ${on_string} Haplotype-resolved raw unitig graph">\n+ <data name="raw_unitigs" format="gfa1" from_work_dir="output.dip.r_utg.gfa" label="${tool.name} on ${on_string}, haplotype-resolved raw unitig graph">\n <filter>mode[\'mode_selector\'] == \'trio\'</filter>\n </data>\n- <data name="processed_unitigs" format="gfa1" from_work_dir="output.p_utg.gfa" label="${tool.name} on ${on_string} Processed unitig graph">\n+ <data name="processed_unitigs" format="gfa1" from_work_dir="output.p_utg.gfa" label="${tool.name} on ${on_string}, processed unitig graph">\n <filter>mode[\'mode_selector\'] == \'standard\'</filter>\n </data>\n- <data name="primary_contig_graph" format="gfa1" from_work_dir="output.p_ctg.gfa" label="${tool.name} on ${on_string} Primary assembly contig graph">\n+ <data name="primary_contig_graph" format="gfa1" from_work_dir="output.p_ctg.gfa" label="${tool.name} on ${on_string}, primary assembly contig graph">\n <filter>mode[\'mode_selector\'] == \'standard\'</filter>\n </data>\n- <data name="alternate_contig_graph" format="gfa1" from_work_dir="output.a_ctg.gfa" label="${tool.name} on ${on_string} Alternate assembly contig graph">\n+ <data name="alternate_contig_graph" format="gfa1" from_work_dir="output.a_ctg.gfa" label="${tool.name} on ${on_string}, alternate assembly contig graph">\n <filter>mode[\'mode_selector\'] == \'standard\'</filter>\n </data>\n- <data name="hap1_contigs" format="gfa1" from_work_dir="output.hap1.p_ctg.gfa" label="${tool.name} ${mode.hap1_reads.name} contig graph">\n+ <data name="hap1_contigs" format="gfa1" from_work_dir="output.hap1.p_ctg.gfa" label="${tool.name} ${mode.hap1_reads.name}, contig graph">\n <filter>mode[\'mode_selector\'] == \'trio\'</filter>\n </data>\n- <data name="hap2_contigs" format="gfa1" from_work_dir="output.hap2.p_ctg.gfa" label="${tool.name} ${mode.hap2_reads.name} contig graph">\n+ <data name="hap2_contigs" format="gfa1" from_work_dir="output.hap2.p_ctg.gfa" label="${tool.name} ${mode.hap2_reads.name}, contig graph">\n <filter>mode[\'mode_selector\'] == \'trio\'</filter>\n </data>\n </outputs>\n@@ -160,6 +178,15 @@\n <output name="primary_contig_graph" file="hifiasm-out1-primary.gfa" ftype="gfa1" />\n <output name="alternate_contig_graph" file="hifiasm-out1-alternate.gfa" ftype="gfa1" />\n </test>\n+ <test>\n+ <param name="reads" value="hifiasm-in2-0.fa.gz,hifiasm-in2-1.fa.gz,hifiasm-in2-2.fa.gz,hifiasm-in2-3.fa.gz,hifiasm-in2-4.fa.gz" ftype="fasta.gz" />\n+ <param name="filter_bits" value="0" />\n+ <param name="mode_selector" value="standard" />\n+ <output name="raw_unitigs" file="hifiasm-out2-raw.gfa" ftype="gfa1" />\n+ <output name="processed_unitigs" file="hifiasm-out2-processed.gfa" ftype="gfa1" />\n+ <output name="primary_contig_graph" file="hifiasm-out2-primary.gfa" ftype="gfa1" />\n+ <output name="alternate_contig_graph" file="hifiasm-out2-alternate.gfa" ftype="gfa1" />\n+ </test>\n </tests>\n <help><![CDATA[\n ***********************************\n@@ -196,7 +223,6 @@\n - *Maximum overlap drop ratio*\n - *Minimum overlap drop ratio*\n - *Skip post join contigs step* disable post join contigs step which may improve N50\n-- *Inconsistent contigs* If this option is set to a value greater than zero the tool generates an additional BED dataset containing regions that are >= x% inconsistent.\n \n #### Options for purging duplicates\n - *Purge level* 0: no purging; 1: light; 2: aggressive [0 for trio; 2 for unzip]\n'

diff -r bf0a4667e3ce -r 6505bd37670d test-data/hifiasm-in2-0.fa.gz

Binary file test-data/hifiasm-in2-0.fa.gz has changed

diff -r bf0a4667e3ce -r 6505bd37670d test-data/hifiasm-in2-1.fa.gz

Binary file test-data/hifiasm-in2-1.fa.gz has changed

diff -r bf0a4667e3ce -r 6505bd37670d test-data/hifiasm-in2-2.fa.gz

Binary file test-data/hifiasm-in2-2.fa.gz has changed

diff -r bf0a4667e3ce -r 6505bd37670d test-data/hifiasm-in2-3.fa.gz

Binary file test-data/hifiasm-in2-3.fa.gz has changed

diff -r bf0a4667e3ce -r 6505bd37670d test-data/hifiasm-in2-4.fa.gz

Binary file test-data/hifiasm-in2-4.fa.gz has changed

diff -r bf0a4667e3ce -r 6505bd37670d test-data/hifiasm-out2-primary.gfa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hifiasm-out2-primary.gfa Wed Mar 03 16:16:42 2021 +0000

b'@@ -0,0 +1,7 @@\n+S\tptg000001l\tGAAGTTTTGTCTGAGAGGAGTACCAGGCCGTGTGAGGTGTCAGTCTGCCCCTACTTGGGGGTGCCTCCCAGTTAGGCTACTCGGGTGTCAGAGACCCACTTGAGGAGGCAGTCTGTCCATTCTCAGATGTCCAGCTGCGTGCTGGGAGAACCACTACTCTCTTCAAGGCTGTCAGACAGGGACATTTAAGTCTGCAGAGGATTCTGCTGACTTTTCTTTGGCTGTGCCTTGCCCCTAGAGGTGGAGTCTACAGAGGCAGGCAGGCCTCCTTGAGCTGCGGTGGGCTCCACCCAGTTCGAGCTTCCCAGCTGCTTTGTTTATCTACTCAAGCCTTGGCAATGGCAGGCGCCCCCTCCCCCGGCCTCACTGCTGCCTTGCAGTTTGATCTCAGACTGCTGTGCTAGCAATGAGTGAGACTCCATGGGCGTAGGGCCCTCCGAGCCAGGGGTGGGATATAATCTCCTGGTGTGCCATTTGCTAAGACTGTTGGAAAAGTGCAGTATTAGGGTGGGAGTGACCTGATTTTCCAGGTGCTGTCTGTCACCCCTTTCTTTGACTAGGAAAGGGAATTCCCTGACCCCTTGCGCTTCCTGGGTGAGGCGATGCCTTGCCCTGCTTCGGCTCATGCTCGGTGCACTGCACCCACTGTCCTGCACCCACTTTCCGACACTCCCCAGTGAGATGAACCCAGTACCTCAGTTGGAAATGCAGAAATCACCCATCTTCTGCATCGCTCATGCTGGGAACTGTGGACTGGAGCTGTTCCTATTCAGCCATCTTGGCTCCACACTGTCAAATGCTTTTTCTGCATCTATTGTTATGATCATGTGATTTTTCTTCTTTAGCCTTTTGATGTGCTGAACACATCAATTCAAATGATTTTCAAATGTTGAACCAGTCTTGCCTTACCTGGGATAATATACACCGCCTGGTTATGGTGTATTTTTTTAAATAACTGTCGGAGTCAATTCACTAATATTTTGTTGAGAATTTTTGCATCTATGTTCATGAGAAATACCGGGCTATAGTTTTCTTTTCTTGTGATGTTTTTGTCTGGTTTTAGTATTAGAGTAATGTTGGCCTCACAAAGAATTTGGAAGTATTCCCAATGCTTCTGTATTCTGGAAGAGATTGTGGAGAATTTGTATAATTTCTTTCATAAATGTTTGGTAGAATTCACCAGTGAACCCATCTGGGCCTGGTGCTTCTGTTTGAAACTGTTATTAATTATTGGTTCAATTTCTGTAATAGATATAGGCCTATTCAGATAATCTATGTCTTCTTCTGTGAGAATTATCTTTCAAGAAATTGGTTCATTTTACATAGGTTATCAAATTTTGGGCATAGAGAGTTGTTCATAATATTGCTGTATAACCTTTTAATGTCCATGAGACTACAGTGATATCCTCTTTTTCATTACTGATATTAGTGATTTGTCTTCCTTCTTTTTTGTCTTAGCCTGACTGGAGGTTCATCAATTTTGTTGATCTTTTCAAAGAACTAGGTTTTATTTTTGTTAATTTTCTCTATTGATTTCCTGTTTTCAGTTTCATTGATTTTGGCACTAATTTTTATTATATGTTTTCTCCTGCTTATTTTGGATCTAATTTTTTTCTAGTTTCCTAAGGTGGAAGCTTGGATCATTACTCTCCAATCTTTCTTTTGTTCTAATATGTGCATTCAATGCTAAGCACAGCCTTCCCTGCAAATTTTGAAAAATTTTATCTTATTTTTATTTAGTTTAAAATATTTTTAATTTCTTTTGAGATTTCTGTTTTGACCCATAGGTTACTTAAAAGTGTGCTGTTTAATCCCCAATAATTTTGGAGTTCTCCAGCTGTTATTGATTTCCATTTTAATTCTATTGTGGCATGAATGCAGATATTGTATGATAATTTCTGTTCTTTTAAATGTGCTAAGGTCTGCTTTATGACCCAGAACATGGTTTATTTTGATGAATGTTCCATGTGAGCTTGAGAAGAATGTGTGTTGTGCTGTCACTGAATGATGTAGTTCATAGATGTCAATTATATCCAGTTGATTAATGTGGTATTATTGCTATGTCCTTAAGAATTTTCTGCCAGCAGACTCTGTTTATTTCAGAAAGAGGAGTGTCTAATTGTCAAACTATATTAGTGAATTCATCTGTTTCTCTTTCTAGTTTGGTCAGTTTTTACTCATGTATTTTGAGGTTCTCATGTTAGGCACATACACAAAAAGATTGTGTATATCTTTTTGGAGAATTAACCCTTTTAAAATTATGTAATGCCCATTTATCCCTGATAATTTTTCTTGCTTTGAAGTCTGTTGTGTCAGAAATTAATATAGCTATTCTGATTTCATTTTAGTATTAGCATGATATATATTTCTTCTTCCATTTGCTTTTAATCTGTATATTTTTTAATAAAGTGAGTATTTTGTAGACAGCACGTAGTTGGGTCTTGTCTTTTGATCCACTCTGATATTCTGTATCTTTTAATTGGTATATTTAGACCACTGATTGTTGACACAAGTGACACTACTATATTTATTACTGCTTTCTTTTCACTACCTGTGTCCTTGCTTCTATTTTAGTCTTCCAATCTTTGTCTTCTTTTTGAGGTTTTCATTAATCATTTTATGATATTCTATTTTTCTTTTTTCTTAGCATAGCAATATACTTTTTTTTAAACAAAAAGCGATTGCCACAGAGTTTTCAATATACATTTATAATTAATCCCAGCATACCCTTAGATAATACTATACTACTTCATAGAGAGTACAAGAACCTTATGATAACAAAAGAAGCCTAATTCTCTCTCCCATCACTGTATCATTGCTGTCATTCATTTCACTTTTGTATAAGAGTATATAATCGAATACATTGTTGCTATGATTTTGAACAAACTGTTATCTGTTAGATCAATTAATGATAAGGGAAAAGTTTTAATTTTAATTTTGCTAATTCTTTCGCTGATGCTCTTTCTTTCTTTATGTAGATCCATGATTTGAACTATATGATTTTCCTCTTCTATGAAGACCTTCAACATTTCTTGTAAGGTAGGTCTGCTTGGCACAAAACCCTCAATTTTTGTTGTCTGAAAATGGCTTTATGTCTCCTCTACTTTTGAAGGATAATTTCACTGGGTGCAGCATTCTAAGTTGCTTTTTTTCCCTCAACACTTACATATTTCATACCTTTCTCTTCTTGTTTGCATGATTTCTAAGAAATCAGTGGTAATTCTCTTTGGTCTTCTAGGTAAGAATTTTTTTTTCTCCTGAATTTCTTCAAGAATTTTTATCTTTGGTTTTCTGCAGTTCGAATAGGATATGCCTCTGTGTGTGTGTGTGTGTGAGAGAGAGAGAGAGAGAGAGAGAGGGATTTGGCAATTTGGCATTTATCCTGCTTGGTTTTCTCTGAGCTTCCTGAATACATGGTTTGTTGTCTGACATTAATGTTAGAAAATTCTCAGTCATTATTGTTTCCCATATTCCTATTGTTTCTTTTTGTTTTCTTCTTCTGATATTCCCACTATATGCATTTACACATTCTATGGTGGTCCCACAGTTCTTTGGCTTTTTGTTTTGTTTTGTTTTTTTCTCAGTTTTCTTTTTCTTTGTTTTTCCATTTTAGAAGTTTCCATTAATATATCTTCAAGCTCAGAGATTTTTTTTCCTCAGCCATGTAAAGTTTACTAATTAGCACAAAAAAGGCATTTTTCATGTCTGCTACAGATTTTTTCTTCTGTAGCATTTCTTTTCAATCCTTTCTTAGAATTTCCATCTCTCTGATTACATTGACCATCTGTTCTTACATTCTGTCTACTTTATCCATTAGAATCCTTTTCATGTTAACCATACCTGTTTTAAATTCCAGGTCTACTCCCAATATTCCTGCCACATCTGAGTCTGGTTTTTATACTTGCTCTATGTTTTAAAACTGTGCTTTCTCCTTTTAGTATCCCTTGCCATTTTTTCTTGATAACCAGA'..b'CCTTTCCCTTACCTGGACATCACTGTCTCCTCTAACAGCTGAGGTGTCACTGGGAAGTGAAATTGATTACAACTTTTTAAAAATTCCACAGCTGTCGTTTTTACCTCAGCTGCTTCCCATAATTCCACAGATGGTAAACATATGTTTATAGGCACATTGAAAAAGAAGCTATATTGGATGCCTCCCATCTTTAATTCTTATTTTTCCTTTCATGCAGAAAGTCAAAGTCATAGAACTGGGGAATCTTACACATTTGAAGATTAATATTTCTGTGCATTAAGACTTTGGAAACAGCAGGACAGCTAATGATATGCTAATGAGCTGACAGTTTTTATTGATCATAATGAAAGTCGACAAGTGTCTTTCTTGGCGGTTTTGCATGCTGGAATATTTTATTAACGTCTTCAGGGCAGAAGTACATGATTGGTTGCATTTTGAAAACCCTCCCTGTGAGTTTACAGGTCCTACTTTTTGTTAGCCTGTTTCCAAAGCTTGAGTCCCTGCCAGTTTATAAACAGAACACATCTTCATCCATATATTTACATGCCCAGCAGGAAACTCTCCCACCCCTTTTTCCTCTCTCTTTCAAAGCAATTTGTTTCAGTATTTTAGCATACAAAAAAATAGAACCATTTTCTTCAATGTAAACAGAGATCTGCAGGGAAATAAGAGCGTTAAAAAAGAATTAGCATTTGTTTGGTGGTGAAGCTGCTTTTGTTTGTATCAGAAAGCTCTGCATGTTTAGAAGAGCTTGCTTAATCTTAGTTATTCCATACACAAGAGGGACCTAATTGGATAATTTTCTAATTTTTTAATTGCATCTTTCTATATTTCTTAATGCAAAATGAGAAACGTTCTAGGAATAATAGAAATAATGGGCATTAGTTCCCTAAACATTAAAAATCCATAATATACAATGTACCTGGTGCAAATTTATTTTTCAGTGCATGGTGAGCTGACAGCAGGAGGTACAGGGTGGCAACAGGTGGATTAAACAAAAGGAAAAAAAATCCATTTTTCTGCCGTCCATCCGTACTAAATAGTAAGCTTATTAATTTTGGGCTCTGCACCTTAGGGATTTATTTAGGGCCTCAGATCAGCTGAGGTTCATCATTACACTAACAATAAGAAAATGGATTGTTTAGCAAATTAATAGTGTAAATAAGATTACGGGGGGCGGGGGGATGGGGGGAAGAATATTAGGCTACCTAAAAAGACTTCTGTTTTCTAGCACTGAAAAACTGTCTTAGCAAATTATTATTATCTAATACAAATAGTTTTGCATGTTTGATTGGTATCTATCTATTAAGGCAATCAAGATAAAATCTCATTTTGATAACAAGACCTCTTTGTAGCAACAAGTTGTTGGTTCATGTTAAGGGGATCCCTTAAATTATATATTTTTACCTACAGCATATTGTAGTGACCCAGCACTGGTTTTGGAGTGTTAATCGAAAAGTGTCTGGATCTGTCTCTAGCTAATGATAAACAAGTCTCAATCAATTTAGAAAAGTTTATTTTGCCAAGGTTAAGGATGCACCCATGACACAACTTCAGGAGGTCCTGAGGACATGTGCCCAAGGTGGTCCTCATGTATACCTTGCTTTATACATCTTAGGGAGACATAATACCTCCATCAGTACATGTAAGATTTACATTGGTTTGATCTGGAAGGGTAGGACAACCAGAAGGGTGGCAGCTTCCAGGTCATAGGTAGATTTAAAATTTTTCTGATCGGCTATTGGTTGAAAGCGTTATCAGTAGTAAAGAATGTCTGGGTTCTGATAAGGGGTTGTGGAGAAGAAGCTTTTATCATGCAGATGAAGCCTCTAAATAGCAGGCTTCAGGGAGAATATATTGTAAATGTGTATCATTAGACTTAAGGTCTGTGTTGATGTAAATGCTGGAGAGGTTTAATGAAGCATGTTCAACTCCTTTTCCATCATGGTCTGAACTAGATTTCCGGGTTAACTCTGGAATGCCCTTGGCGGAGAGAAGGGGGTTCATTCAGATGGTTGGGGGCTTAGAACTTTATTTTTGGTTTTCAAGAGTTAGTAGCCCTGTAGTATATAGCCTAGGATTAAGGTATCCTTTAGAAAAGCTACTTAGAGTATCAAAGCCTTAAATTTCTCATAGGTCATATGACCAGGTAATCTGGTCCTAGATAAGTAGTTCTTATGGAAAGTATCAAAATGACCTCAGACAGTTTTCAAAATAGTCATGACTGTTCTTTCAACCTCTTCCAAAATTCTGATATATACCCTAAATTAAAAACTATTGCCCCACATGATCTTCACAGATCCTAACTGTGCTCAAAATTATGTGGTTCAGTATTGTATAATTCATAGTTTTCAATAATTTGATGCTTTAGAATATTTATTGTGTTTACTATGTGAAATCTACTACAATAGGAACTTCAGGGGATACTAAGATGAAAATCTATTATCTTTGGTGTTTATAATACAGTCTAGTAATTCTGTTGGGTTTTATTCAGTTCCAAATCAGTAAGATTTTACTCTATTTATATATGAGTTGGATGCAATAATTTTAACCATTGTGAACTTTTAATGAGTAAATGCTCTTGCTCCAAAAGAAGCAAATGGTTGACAATAAAGCAGAATTTTTCAAAGTGAGGTCCTTTTACCATTCATCAGAATCATCTGGAAGAGGTTTTGTTTAAAAAATGAATATTCCTGGGCCCACTCCAATCCTACTGAAACAGGATCCTTTGGGTTGACACAAGAATCTGAATGTTAAGCAGACACTCAAGGTGATTCTCAGGAACTTGAAGTTTGAGAAACACTGCCAAAATGAATAATATGAAATAAAGCATATGTCTGAAAAAAGGAGATCAAATGAGGTCAGCTAATACAGGCCCAGATAGAGTTGCATTTTTCAGTTAAATGTAGATACATTTAGAGTTAAATGAGGAGAAATAATAAAAATTTTGTCTTTTTATCCCTTATCTCCCTTGGGAGAAGTTGTAGTGCTGAAAGGCACATTTTCATCTGTGGAAATCCTCATAGATGATATATATATATATATATATATATATATATATATATATATATATTTTTTTTTTTTTTTTTTGAGAGGAATAAGGCTGATTGAGCTCCTTTGTAGTTTTATGCATTATAAAATCCCTTTTGTAGTTTTATGAAGGAAACTACATGCTTAGCAAATGCTTCTTTTATCAGCAAATGTCCTGGCAGTAAATTGTCCATATAGCAATTTAATGCCAGACCTTCTGATTCTTATTCTGGGGAAGGTGCTGGGATATACATAAATGTGTGTAGTCACATGCATACACACACATGCACTCAGACATCTTTAGATTATAAGTGGTATCTGTAGGGTATCACCACTTTTCTTTTAATCCAGCATTGACTTACAACCATTCAAATAAATTAACATTCCCATCTTGATTCATTTGGTAAGAACACATTTTCATGCCAGTATGTGGGCTCACCTCTATGACCTTTCCTTATAAAAAATACCAAGTGCTTTGGGTTTTTGTGTTAATGAGCATTGGGAAGCTGTCAGCTTTTATTTCTGTTTTTTGTTCAAGTCAACATCATTGACCTTCACCTAATGATCTATGTAACATACACACGCAGGTACCACAGATTAAAAGTGGAAAGACAGGGAAGTAAGGAGAGATGCACATAGAGGAAAGGTGTGAGAGCAGGTGATTTGTAAATCATAATGTCACTAAAATGAGTAAGATCACTTGAAAAGGAAAGGAAAACTGCTGTGTGCTGTATTTTCTTGCTTTAGGATTAGCGGGATGGGGTATTATTTTAAAATGAGTTTTCAGTTTGGTTTTG\tLN:i:25000\trd:i:0\n+A\tptg000002l\t0\t-\tm64012_190920_173625/16714108/ccs\t0\t12049\tid:i:17\tHG:A:a\n+A\tptg000002l\t8768\t+\tm64011_190901_095311/27789106/ccs\t0\t16232\tid:i:60\tHG:A:a\n'

diff -r bf0a4667e3ce -r 6505bd37670d test-data/hifiasm-out2-processed.gfa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hifiasm-out2-processed.gfa Wed Mar 03 16:16:42 2021 +0000

b'@@ -0,0 +1,7 @@\n+S\tutg000001l\tGAAGTTTTGTCTGAGAGGAGTACCAGGCCGTGTGAGGTGTCAGTCTGCCCCTACTTGGGGGTGCCTCCCAGTTAGGCTACTCGGGTGTCAGAGACCCACTTGAGGAGGCAGTCTGTCCATTCTCAGATGTCCAGCTGCGTGCTGGGAGAACCACTACTCTCTTCAAGGCTGTCAGACAGGGACATTTAAGTCTGCAGAGGATTCTGCTGACTTTTCTTTGGCTGTGCCTTGCCCCTAGAGGTGGAGTCTACAGAGGCAGGCAGGCCTCCTTGAGCTGCGGTGGGCTCCACCCAGTTCGAGCTTCCCAGCTGCTTTGTTTATCTACTCAAGCCTTGGCAATGGCAGGCGCCCCCTCCCCCGGCCTCACTGCTGCCTTGCAGTTTGATCTCAGACTGCTGTGCTAGCAATGAGTGAGACTCCATGGGCGTAGGGCCCTCCGAGCCAGGGGTGGGATATAATCTCCTGGTGTGCCATTTGCTAAGACTGTTGGAAAAGTGCAGTATTAGGGTGGGAGTGACCTGATTTTCCAGGTGCTGTCTGTCACCCCTTTCTTTGACTAGGAAAGGGAATTCCCTGACCCCTTGCGCTTCCTGGGTGAGGCGATGCCTTGCCCTGCTTCGGCTCATGCTCGGTGCACTGCACCCACTGTCCTGCACCCACTTTCCGACACTCCCCAGTGAGATGAACCCAGTACCTCAGTTGGAAATGCAGAAATCACCCATCTTCTGCATCGCTCATGCTGGGAACTGTGGACTGGAGCTGTTCCTATTCAGCCATCTTGGCTCCACACTGTCAAATGCTTTTTCTGCATCTATTGTTATGATCATGTGATTTTTCTTCTTTAGCCTTTTGATGTGCTGAACACATCAATTCAAATGATTTTCAAATGTTGAACCAGTCTTGCCTTACCTGGGATAATATACACCGCCTGGTTATGGTGTATTTTTTTAAATAACTGTCGGAGTCAATTCACTAATATTTTGTTGAGAATTTTTGCATCTATGTTCATGAGAAATACCGGGCTATAGTTTTCTTTTCTTGTGATGTTTTTGTCTGGTTTTAGTATTAGAGTAATGTTGGCCTCACAAAGAATTTGGAAGTATTCCCAATGCTTCTGTATTCTGGAAGAGATTGTGGAGAATTTGTATAATTTCTTTCATAAATGTTTGGTAGAATTCACCAGTGAACCCATCTGGGCCTGGTGCTTCTGTTTGAAACTGTTATTAATTATTGGTTCAATTTCTGTAATAGATATAGGCCTATTCAGATAATCTATGTCTTCTTCTGTGAGAATTATCTTTCAAGAAATTGGTTCATTTTACATAGGTTATCAAATTTTGGGCATAGAGAGTTGTTCATAATATTGCTGTATAACCTTTTAATGTCCATGAGACTACAGTGATATCCTCTTTTTCATTACTGATATTAGTGATTTGTCTTCCTTCTTTTTTGTCTTAGCCTGACTGGAGGTTCATCAATTTTGTTGATCTTTTCAAAGAACTAGGTTTTATTTTTGTTAATTTTCTCTATTGATTTCCTGTTTTCAGTTTCATTGATTTTGGCACTAATTTTTATTATATGTTTTCTCCTGCTTATTTTGGATCTAATTTTTTTCTAGTTTCCTAAGGTGGAAGCTTGGATCATTACTCTCCAATCTTTCTTTTGTTCTAATATGTGCATTCAATGCTAAGCACAGCCTTCCCTGCAAATTTTGAAAAATTTTATCTTATTTTTATTTAGTTTAAAATATTTTTAATTTCTTTTGAGATTTCTGTTTTGACCCATAGGTTACTTAAAAGTGTGCTGTTTAATCCCCAATAATTTTGGAGTTCTCCAGCTGTTATTGATTTCCATTTTAATTCTATTGTGGCATGAATGCAGATATTGTATGATAATTTCTGTTCTTTTAAATGTGCTAAGGTCTGCTTTATGACCCAGAACATGGTTTATTTTGATGAATGTTCCATGTGAGCTTGAGAAGAATGTGTGTTGTGCTGTCACTGAATGATGTAGTTCATAGATGTCAATTATATCCAGTTGATTAATGTGGTATTATTGCTATGTCCTTAAGAATTTTCTGCCAGCAGACTCTGTTTATTTCAGAAAGAGGAGTGTCTAATTGTCAAACTATATTAGTGAATTCATCTGTTTCTCTTTCTAGTTTGGTCAGTTTTTACTCATGTATTTTGAGGTTCTCATGTTAGGCACATACACAAAAAGATTGTGTATATCTTTTTGGAGAATTAACCCTTTTAAAATTATGTAATGCCCATTTATCCCTGATAATTTTTCTTGCTTTGAAGTCTGTTGTGTCAGAAATTAATATAGCTATTCTGATTTCATTTTAGTATTAGCATGATATATATTTCTTCTTCCATTTGCTTTTAATCTGTATATTTTTTAATAAAGTGAGTATTTTGTAGACAGCACGTAGTTGGGTCTTGTCTTTTGATCCACTCTGATATTCTGTATCTTTTAATTGGTATATTTAGACCACTGATTGTTGACACAAGTGACACTACTATATTTATTACTGCTTTCTTTTCACTACCTGTGTCCTTGCTTCTATTTTAGTCTTCCAATCTTTGTCTTCTTTTTGAGGTTTTCATTAATCATTTTATGATATTCTATTTTTCTTTTTTCTTAGCATAGCAATATACTTTTTTTTAAACAAAAAGCGATTGCCACAGAGTTTTCAATATACATTTATAATTAATCCCAGCATACCCTTAGATAATACTATACTACTTCATAGAGAGTACAAGAACCTTATGATAACAAAAGAAGCCTAATTCTCTCTCCCATCACTGTATCATTGCTGTCATTCATTTCACTTTTGTATAAGAGTATATAATCGAATACATTGTTGCTATGATTTTGAACAAACTGTTATCTGTTAGATCAATTAATGATAAGGGAAAAGTTTTAATTTTAATTTTGCTAATTCTTTCGCTGATGCTCTTTCTTTCTTTATGTAGATCCATGATTTGAACTATATGATTTTCCTCTTCTATGAAGACCTTCAACATTTCTTGTAAGGTAGGTCTGCTTGGCACAAAACCCTCAATTTTTGTTGTCTGAAAATGGCTTTATGTCTCCTCTACTTTTGAAGGATAATTTCACTGGGTGCAGCATTCTAAGTTGCTTTTTTTCCCTCAACACTTACATATTTCATACCTTTCTCTTCTTGTTTGCATGATTTCTAAGAAATCAGTGGTAATTCTCTTTGGTCTTCTAGGTAAGAATTTTTTTTTCTCCTGAATTTCTTCAAGAATTTTTATCTTTGGTTTTCTGCAGTTCGAATAGGATATGCCTCTGTGTGTGTGTGTGTGTGAGAGAGAGAGAGAGAGAGAGAGAGGGATTTGGCAATTTGGCATTTATCCTGCTTGGTTTTCTCTGAGCTTCCTGAATACATGGTTTGTTGTCTGACATTAATGTTAGAAAATTCTCAGTCATTATTGTTTCCCATATTCCTATTGTTTCTTTTTGTTTTCTTCTTCTGATATTCCCACTATATGCATTTACACATTCTATGGTGGTCCCACAGTTCTTTGGCTTTTTGTTTTGTTTTGTTTTTTTCTCAGTTTTCTTTTTCTTTGTTTTTCCATTTTAGAAGTTTCCATTAATATATCTTCAAGCTCAGAGATTTTTTTTCCTCAGCCATGTAAAGTTTACTAATTAGCACAAAAAAGGCATTTTTCATGTCTGCTACAGATTTTTTCTTCTGTAGCATTTCTTTTCAATCCTTTCTTAGAATTTCCATCTCTCTGATTACATTGACCATCTGTTCTTACATTCTGTCTACTTTATCCATTAGAATCCTTTTCATGTTAACCATACCTGTTTTAAATTCCAGGTCTACTCCCAATATTCCTGCCACATCTGAGTCTGGTTTTTATACTTGCTCTATGTTTTAAAACTGTGCTTTCTCCTTTTAGTATCCCTTGCCATTTTTTCTTGATAACCAGA'..b'CCTTTCCCTTACCTGGACATCACTGTCTCCTCTAACAGCTGAGGTGTCACTGGGAAGTGAAATTGATTACAACTTTTTAAAAATTCCACAGCTGTCGTTTTTACCTCAGCTGCTTCCCATAATTCCACAGATGGTAAACATATGTTTATAGGCACATTGAAAAAGAAGCTATATTGGATGCCTCCCATCTTTAATTCTTATTTTTCCTTTCATGCAGAAAGTCAAAGTCATAGAACTGGGGAATCTTACACATTTGAAGATTAATATTTCTGTGCATTAAGACTTTGGAAACAGCAGGACAGCTAATGATATGCTAATGAGCTGACAGTTTTTATTGATCATAATGAAAGTCGACAAGTGTCTTTCTTGGCGGTTTTGCATGCTGGAATATTTTATTAACGTCTTCAGGGCAGAAGTACATGATTGGTTGCATTTTGAAAACCCTCCCTGTGAGTTTACAGGTCCTACTTTTTGTTAGCCTGTTTCCAAAGCTTGAGTCCCTGCCAGTTTATAAACAGAACACATCTTCATCCATATATTTACATGCCCAGCAGGAAACTCTCCCACCCCTTTTTCCTCTCTCTTTCAAAGCAATTTGTTTCAGTATTTTAGCATACAAAAAAATAGAACCATTTTCTTCAATGTAAACAGAGATCTGCAGGGAAATAAGAGCGTTAAAAAAGAATTAGCATTTGTTTGGTGGTGAAGCTGCTTTTGTTTGTATCAGAAAGCTCTGCATGTTTAGAAGAGCTTGCTTAATCTTAGTTATTCCATACACAAGAGGGACCTAATTGGATAATTTTCTAATTTTTTAATTGCATCTTTCTATATTTCTTAATGCAAAATGAGAAACGTTCTAGGAATAATAGAAATAATGGGCATTAGTTCCCTAAACATTAAAAATCCATAATATACAATGTACCTGGTGCAAATTTATTTTTCAGTGCATGGTGAGCTGACAGCAGGAGGTACAGGGTGGCAACAGGTGGATTAAACAAAAGGAAAAAAAATCCATTTTTCTGCCGTCCATCCGTACTAAATAGTAAGCTTATTAATTTTGGGCTCTGCACCTTAGGGATTTATTTAGGGCCTCAGATCAGCTGAGGTTCATCATTACACTAACAATAAGAAAATGGATTGTTTAGCAAATTAATAGTGTAAATAAGATTACGGGGGGCGGGGGGATGGGGGGAAGAATATTAGGCTACCTAAAAAGACTTCTGTTTTCTAGCACTGAAAAACTGTCTTAGCAAATTATTATTATCTAATACAAATAGTTTTGCATGTTTGATTGGTATCTATCTATTAAGGCAATCAAGATAAAATCTCATTTTGATAACAAGACCTCTTTGTAGCAACAAGTTGTTGGTTCATGTTAAGGGGATCCCTTAAATTATATATTTTTACCTACAGCATATTGTAGTGACCCAGCACTGGTTTTGGAGTGTTAATCGAAAAGTGTCTGGATCTGTCTCTAGCTAATGATAAACAAGTCTCAATCAATTTAGAAAAGTTTATTTTGCCAAGGTTAAGGATGCACCCATGACACAACTTCAGGAGGTCCTGAGGACATGTGCCCAAGGTGGTCCTCATGTATACCTTGCTTTATACATCTTAGGGAGACATAATACCTCCATCAGTACATGTAAGATTTACATTGGTTTGATCTGGAAGGGTAGGACAACCAGAAGGGTGGCAGCTTCCAGGTCATAGGTAGATTTAAAATTTTTCTGATCGGCTATTGGTTGAAAGCGTTATCAGTAGTAAAGAATGTCTGGGTTCTGATAAGGGGTTGTGGAGAAGAAGCTTTTATCATGCAGATGAAGCCTCTAAATAGCAGGCTTCAGGGAGAATATATTGTAAATGTGTATCATTAGACTTAAGGTCTGTGTTGATGTAAATGCTGGAGAGGTTTAATGAAGCATGTTCAACTCCTTTTCCATCATGGTCTGAACTAGATTTCCGGGTTAACTCTGGAATGCCCTTGGCGGAGAGAAGGGGGTTCATTCAGATGGTTGGGGGCTTAGAACTTTATTTTTGGTTTTCAAGAGTTAGTAGCCCTGTAGTATATAGCCTAGGATTAAGGTATCCTTTAGAAAAGCTACTTAGAGTATCAAAGCCTTAAATTTCTCATAGGTCATATGACCAGGTAATCTGGTCCTAGATAAGTAGTTCTTATGGAAAGTATCAAAATGACCTCAGACAGTTTTCAAAATAGTCATGACTGTTCTTTCAACCTCTTCCAAAATTCTGATATATACCCTAAATTAAAAACTATTGCCCCACATGATCTTCACAGATCCTAACTGTGCTCAAAATTATGTGGTTCAGTATTGTATAATTCATAGTTTTCAATAATTTGATGCTTTAGAATATTTATTGTGTTTACTATGTGAAATCTACTACAATAGGAACTTCAGGGGATACTAAGATGAAAATCTATTATCTTTGGTGTTTATAATACAGTCTAGTAATTCTGTTGGGTTTTATTCAGTTCCAAATCAGTAAGATTTTACTCTATTTATATATGAGTTGGATGCAATAATTTTAACCATTGTGAACTTTTAATGAGTAAATGCTCTTGCTCCAAAAGAAGCAAATGGTTGACAATAAAGCAGAATTTTTCAAAGTGAGGTCCTTTTACCATTCATCAGAATCATCTGGAAGAGGTTTTGTTTAAAAAATGAATATTCCTGGGCCCACTCCAATCCTACTGAAACAGGATCCTTTGGGTTGACACAAGAATCTGAATGTTAAGCAGACACTCAAGGTGATTCTCAGGAACTTGAAGTTTGAGAAACACTGCCAAAATGAATAATATGAAATAAAGCATATGTCTGAAAAAAGGAGATCAAATGAGGTCAGCTAATACAGGCCCAGATAGAGTTGCATTTTTCAGTTAAATGTAGATACATTTAGAGTTAAATGAGGAGAAATAATAAAAATTTTGTCTTTTTATCCCTTATCTCCCTTGGGAGAAGTTGTAGTGCTGAAAGGCACATTTTCATCTGTGGAAATCCTCATAGATGATATATATATATATATATATATATATATATATATATATATATATTTTTTTTTTTTTTTTTTGAGAGGAATAAGGCTGATTGAGCTCCTTTGTAGTTTTATGCATTATAAAATCCCTTTTGTAGTTTTATGAAGGAAACTACATGCTTAGCAAATGCTTCTTTTATCAGCAAATGTCCTGGCAGTAAATTGTCCATATAGCAATTTAATGCCAGACCTTCTGATTCTTATTCTGGGGAAGGTGCTGGGATATACATAAATGTGTGTAGTCACATGCATACACACACATGCACTCAGACATCTTTAGATTATAAGTGGTATCTGTAGGGTATCACCACTTTTCTTTTAATCCAGCATTGACTTACAACCATTCAAATAAATTAACATTCCCATCTTGATTCATTTGGTAAGAACACATTTTCATGCCAGTATGTGGGCTCACCTCTATGACCTTTCCTTATAAAAAATACCAAGTGCTTTGGGTTTTTGTGTTAATGAGCATTGGGAAGCTGTCAGCTTTTATTTCTGTTTTTTGTTCAAGTCAACATCATTGACCTTCACCTAATGATCTATGTAACATACACACGCAGGTACCACAGATTAAAAGTGGAAAGACAGGGAAGTAAGGAGAGATGCACATAGAGGAAAGGTGTGAGAGCAGGTGATTTGTAAATCATAATGTCACTAAAATGAGTAAGATCACTTGAAAAGGAAAGGAAAACTGCTGTGTGCTGTATTTTCTTGCTTTAGGATTAGCGGGATGGGGTATTATTTTAAAATGAGTTTTCAGTTTGGTTTTG\tLN:i:25000\trd:i:0\n+A\tutg000002l\t0\t-\tm64012_190920_173625/16714108/ccs\t0\t12049\tid:i:17\tHG:A:a\n+A\tutg000002l\t8768\t+\tm64011_190901_095311/27789106/ccs\t0\t16232\tid:i:60\tHG:A:a\n'

diff -r bf0a4667e3ce -r 6505bd37670d test-data/hifiasm-out2-raw.gfa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hifiasm-out2-raw.gfa Wed Mar 03 16:16:42 2021 +0000