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Changeset 19:284a1cb82b61 (2024-07-11)

Previous changeset 18:df25d4fb79b7 (2024-01-17) Next changeset 20:5161f204ba63 (2024-10-23)

Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766

modified:
hifiasm.xml
test-data/hifiasm-out-hifi-a.gfa
test-data/hifiasm-out-hifi-p.gfa
test-data/hifiasm-out11-primary.gfa

diff -r df25d4fb79b7 -r 284a1cb82b61 hifiasm.xml
--- a/hifiasm.xml Wed Jan 17 21:31:58 2024 +0000
+++ b/hifiasm.xml Thu Jul 11 14:44:22 2024 +0000

b'@@ -1,11 +1,11 @@\n <tool id="hifiasm" name="Hifiasm" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">\n <description>haplotype-resolved de novo assembler for PacBio Hifi reads</description>\n <macros>\n- <token name="@TOOL_VERSION@">0.19.8</token>\n- <token name="@VERSION_SUFFIX@">1</token>\n+ <token name="@TOOL_VERSION@">0.19.9</token>\n+ <token name="@VERSION_SUFFIX@">0</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+ <param name="reads" type="data" format="@FORMATS@" multiple="true" label="Input reads"/>\n </xml>\n </macros>\n <requirements>\n@@ -184,48 +184,48 @@\n <option value="trio">Trio mode</option>\n </param>\n <when value="standard">\n- <expand macro="reads" />\n+ <expand macro="reads"/>\n </when>\n <when value="trio">\n- <expand macro="reads" />\n+ <expand macro="reads"/>\n <conditional name="trioinput">\n <param name="trio_input_selector" type="select" label="What parental information are you using?">\n <option value="reads">Parental reads (FASTQ files, gzipped or otherwise)</option>\n <option value="lists">Lists of reads assigned by parent (text files)</option>\n </param>\n <when value="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="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 </when>\n <when value="lists">\n- <param name="hap1_list" type="data" format="txt,tabular" label="Haplotype 1 read list" />\n- <param name="hap2_list" type="data" format="txt,tabular" label="Haplotype 2 read list" />\n+ <param name="hap1_list" type="data" format="txt,tabular" label="Haplotype 1 read list"/>\n+ <param name="hap2_list" type="data" format="txt,tabular" label="Haplotype 2 read list"/>\n </when>\n </conditional>\n- <param name="max_kmers" argument="-c" type="integer" value="2" label="Lower bound of the binned k-mer\'s frequency" />\n- <param name="min_kmers" argument="-d" type="integer" value="5" label="Upper bound of the binned k-mer\'s frequency" />\n- <param name="yak_kmer_length" type="integer" min="0" max="64" value="31" label="Yak counter k-mer length" />\n- <param name="trio_dual" argument="--trio-dual" type="boolean" truevalue="--trio-dual" falsevalue="" label="Utilize homology information to correct trio-phasing errors" />\n+ <param name="max_kmers" argument="-c" type="integer" value="2" label="Lower bound of the binned k-mer\'s frequency"/>\n+ <param name="min_kmers" argument="-d" type="integer" value="5" label="Upper bound of the binned k-mer\'s frequency"/>\n+ <param name="yak_kmer_length" type="integer" min="0" max="64" value="31" label="Yak counter k-mer length"/>\n+ <param argument="--trio-dual" type="boolean" truevalue="--trio-dual" falsevalue="" label="Utilize homology information to correct trio-phasing errors"/>\n </when>\n </conditional>\n- <param name="filter_bits" argument="-f" type="integer" min="0" value="37" label="Bits for bloom filter" help="A'..b' name="assembly_options">\n <param name="assembly_selector" value="set"/>\n <param name="hom-cov" value="1000"/>\n </conditional>\n- <output name="raw_unitigs" file="hifiasm-out8-raw.gfa" ftype="gfa1" />\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+ <output name="raw_unitigs" file="hifiasm-out8-raw.gfa" ftype="gfa1"/>\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+ <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.fasta.gz" />\n- <param name="ul_tip" value="1" />\n+ <param name="ont_integration_selector" value="set"/>\n+ <param name="ul" value="nanopore.fasta.gz"/>\n+ <param name="ul_tip" value="1"/>\n </conditional>\n- <output name="primary_contig_graph" file="hifiasm-out11-primary.gfa" ftype="gfa1" />\n- <output name="raw_unitigs" file="hifiasm-out11-raw.gfa" ftype="gfa1" />\n+ <output name="primary_contig_graph" file="hifiasm-out11-primary.gfa" ftype="gfa1"/>\n+ <output name="raw_unitigs" file="hifiasm-out11-raw.gfa" ftype="gfa1"/>\n </test>\n \n <test expect_num_outputs="6">\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- <param name="log_out" value="yes" />\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+ <param name="log_out" value="yes"/>\n <conditional name="ont_integration">\n- <param name="ont_integration_selector" value="set" />\n- <param name="ul" value="nanopore.fasta.gz,nanopore.fasta.gz" />\n- <param name="ul_tip" value="1" />\n+ <param name="ont_integration_selector" value="set"/>\n+ <param name="ul" value="nanopore.fasta.gz,nanopore.fasta.gz"/>\n+ <param name="ul_tip" value="1"/>\n </conditional>\n <output name="log_file" ftype="txt">\n <assert_contents>\n@@ -579,11 +579,11 @@\n </test>\n \n <test expect_num_outputs="6">\n- <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" />\n- <param name="filter_bits" value="0" />\n- <param name="mode_selector" value="standard" />\n- <param name="bins_out" value="yes" />\n- <output_collection name="bin_files" type="list" count="3" />\n+ <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz"/>\n+ <param name="filter_bits" value="0"/>\n+ <param name="mode_selector" value="standard"/>\n+ <param name="bins_out" value="yes"/>\n+ <output_collection name="bin_files" type="list" count="3"/>\n </test>\n \n <test expect_num_outputs="6">\n'

diff -r df25d4fb79b7 -r 284a1cb82b61 test-data/hifiasm-out-hifi-a.gfa
--- a/test-data/hifiasm-out-hifi-a.gfa Wed Jan 17 21:31:58 2024 +0000
+++ b/test-data/hifiasm-out-hifi-a.gfa Thu Jul 11 14:44:22 2024 +0000

b'@@ -1,9 +1,40 @@\n-S\tatg000001l\tAAAAAAAAAAAAGAAAAGAAAAGAAAAGAAACAACATAACAAGACAAAACAAAGCAGGAGAGAGGAAGTGCAGTATCTGATTGTAAGTTTGAATTGAGGGTGGATATAGGGATGGACTGCATTTTGGGTGATGGCAAGAAATCAGAGGTTTGTGGCCACTGTTTAGATTAGTCTCAGCCTTCAAATGGTGGTTCCTGAGGTAGAGTCTGGGGAATGATAGCTGTAGAAACTGGATTACAGAGAATTGAGGAGAAAGTAGGTGGTGAGGAAACAAGGACAGCTCAAGTGGATGAATAGGACATCTGTTACTTTTGCCACCCAGCGTTCTTTTACCCTGCTGCTAAATGTTTCTCGATTTCCTTCTGGGACCCACCCGTGCTCGCTTTCAGTCCATATGGATTTAGCATTGGAACTCATAACTTTTCTTTAAGACCATTATAACAGTGCATTTTCCTGGCCACAAGGACTGGTTCAGGATTTGTCCTGTTACACAAGCCAATCAAAGTAGGTTTGTTTTTGTTTTTTATCCTGGTAATATTGGACAATGAGTCTCATTTTTCTACTGCGGGAGGGAATCTGGAAGAACATGATGACAGGGAAGAGGCTGTCTGAGGAGGAAGCCAACAGAGAGAACTGAATAAAGGGATAAGGTTGAACCAGATCCTGATGATACTGTTGCTGGGGGGCCTCTATACCCAGCCCTGCCTGAAGTCAGGACCACCCCCTAGTTTTGCTTAACCCCATTTAATCAGTTTCTGTCATTTTTTAACAAAGCACTAACTGCTTGTAGGGTAACTCAGCTTCTATGTGAAGAAAAGCAGTAAGAATCCTTCATATCCTAATGGGAAAATCATTGTATTTTTATGAGGGTGAGATATATTTGGTGTAGAGATTATGCAAATCTGGTGATCAAGGTTCTTATTATTAAGCCAAAGGGAAGACAGTGTTTTAGATGGAAGAATAATTAGTAGGTTTGACTACAAAACCTATGCATTTTTCCCTCAGGCATGACCACATTATTATCAATTTCAACAGATATATTCTTGAAAGAAGGTTTTTTTTTCTTATTCACTAAAACAGTTACTTATTTTTTTTTTCATATTTGATAGCAGCTTTTTTTATTGGTTACAAAACCTAAGCCCATATACAAAATTAGGAACACATTTAGATGCCTCTTTTGAAAGAACATTTTGTCTTTTTAAACTGAGTTTAAAAAAAATAAAAACAATGCAATTTTTAAACACTATTTGAAAACTTAAAAGTGCAGCAATATACTTAGTTTCCTTTATCTACGAAATGGTGCAATTCCAATTCAAAACTGGTAAGGTCACAAATTGAATCAAGGAAATGCATACAAATGTCTGCATTACTTGATGCTAATGTTCACTTGAATGTTAGTTTGCACTTTAAAAACATGAGAGGAAATAGGAATCATCACAGTAGAGGCCCAATTTTAATCATAATGTGTGCAAATTTTAAAAGGTAACTGTCAGTTAAGTAAGGAAAGTCCAGAAGAAACTAAACTGGAAGGGGTACAGTTCACAATATCAAGAAGATTTGGGACAAAAAACTGCAAAAGTCTAAAATACCCATTGGTGATGTTTTTTAAAAAATCTTGCTTTCAGCTTTCAGGAGTTAATATTCTTTGTTTTAACTTGATAATTGGATATGGTTGATTTATATTGGGTTTAAACTGTGGAGCTTTCATGTTTACTGTAATTTAGTCTTAAAATATTTTTTACTTAGTAACCAGTACTTTTGCTAATGTGGTTGGCAACAAACCAGCAACTATTTAAAAGTGTCATAAGGGTTCATTCTTTGAGTACTGGGAAAGTTAATTCAGATCCTACTCAAAAAGCATCTTCACATATTAAAAGATTCAGACAGGGATCTGTGTAGAGGAGTAATTTGCAGTTATTTAACATAAACCTGATTTGCAGTGATCTCTAAGTAACAGTTACTTATTGTATGAATGCATATGTGGGCTTTTTAGGTACTTTTCTCCTCTCCACTCCACTCGGGGGCCTTTCAGTTTAGGGCTATGACACAGCCACCACTTTGCATCATTTACACCATCCTGAAAACCTGCAGGGCTCTTCCTTGCTCCTGGCTGTTGGAATTGAAATATCTTTTTTCCTCTTCTTCAGAATGGTGTTTTGATTTCTTATCAGCTGCCAGCTGGATTTGAAGGCCTATAGCCTAATCACCTAGATAGATAAGGAAAGTTGTCATATTTTGTCTTTGGCTGATAGGAATTTAGAACACAAACAAACTCAAAAGAGTCAACCTTTGGGTAAGATTAAACCAGTGACTCTAATTCAGATCATTCCATAAATTGTATTATCTTGAGCAAAACACTCTATTCCTTGACATTGCAGATTATAAATGTTGGGAATAAAGAGAAATAAGTGAATCCCAAACCTTTTTATATTATGATACACATATAAATTATAATGTTTGATAGGTACATGGAAATAAATAGATGAGGCTTCTCACTGCTAAAGGTGGCCAGGCTGGTTTGAGGGGATCAGTAGCTCAGCATACCTTACCCTATTCTTGACACTCTGGTTGGGAAGCTCTTGAATTTGTAAACCATATGGACTGGGTTTTCGTCCTGGCTCAGTCACTAAGCCCCACTACGTTCTTGTGGCATTCTCTTTTCCTTTTGAGTCCTCGGTTCTGAATGCTTAAATGAGGAATCTGAGGTCTAGTTCAAATGTAAATGCCATTTATCAGGCATATATAAAAAAGCATTATCAGATATAAAAATGGAGGTTTTTGAGATATACTGAGACTTTAAGCATGAAAGCATCTATAAGAGTTTACCACTTAGATCTGTTTAATTACTGCTAAGGACACTTACTTTTTAAAAAACAGCATGCCTACATTATCTAGATACCTGTATGACAGTATGTGATGGACAGTGTCAGGGTCTGACTTAAGCACCCAGAGATTAGTCACAGAATTTCTGAGGTGAGGGCATTCAGATCCTCTATTCCCCCAATATAAAAGGAGACTCTTTAAAAATCATCATTGTATAGTTGCATAGAACATCATGCAAATATGCAATTGAAGATCCAAGCATATAAATCCATAATCTTATACATTATTAACTAGCCTAACCCTCCTTAGTCAAATATAATCACATGAAGTTAGAGACAATTTAGTTCCAGTAACATACTACACTCTCTCCCAGCCCCCCACCTCCACCCGCCATCAACAGCAAGTGCAGACCACTTTCATGGGACAGGGCAGCACTAGATCCACCAGGTAGGAATATTTAGGGACAAATGATCAGGATGTAAGGAAGCTGAAGTTACCACCAGGCAGTGCTCATTCTGGTGGGCAAATCCAGGGTCCAAGGGAATCAATAATTAATGATCATAGTCCAGGTAAACTTTGGCAATGACATGAGGAGGTTCAAGGCGATGGAATGGATCACCATGAAGAAGACTTTGGAGTTGAAATATTCAATGAACCAAGCAGATTTTGGCTTTAAGATGGTCTGTAAGTGAGTAGTTATGTTACATACACTAAGATGAAGTTCTGGAACAACTTCAATGATAGAGCTTCAGACTACCGGAAAATCAAGGGCAAGAACAAGATTAATGTTCATGAAAGACAGGGTTGTGTTCATTGAATGCACACAGGCACACACAGAAATTAATGGACACATATGGAGTGTTTACACGCAAGACTGTGTCACATGTTTACACACACTGCTCCATTTAATTCTTGCTAAATCTCCAAAGGACATTCATTATTCTATTTATAGATGAGACAACAGAGACTTAGTAGCTACCAATAGTCACACAGTTAGTAAATGGCAGAAACAAGATTCGAACTCAGGTCTGACTTCAAAGTTCATTTTCTTTTCACTGGTATGTTACAGAGGCTAGGTAACTAGGATCTTGAGAATAGGGACCAAGGAAGAAACACTGAGTAAAATGGGTAGATCCAATTGGTTT'..b'CACTACTGGGTATCTACCAAGAAGAAAAGAAGTCATTATATGAAAAAGACATACACACGGTTATAGCAGCACAATTCTCAATTGCAAAGACACGGAACCAGCCTAAATGTCCATCAACCAATGAATGGATAAAGAAATTGTGGCATGTATATATAAATACTACTCAGCCATAAAAGGAAATGAAATAATGGCATTCACAGCAACCTGAATGAAACTGGAGACCATTATTCTAAGTGAAGCAACTCAGGAATGGAAAACCAAATATTGTATGTTCTCACTTATAAGTGGGAGCTAAGCTATGAGGGCACAAAGGTATAAGAATGACAGAAGGGATCCTGGGGACTTAGGTGAAAGGGTGAGAGAGGGTGAGGGATAAAAGACTACATGTTGGGTACTGTGTACACCACTCGGGTGATGAGTGCACCAAAAATCTCACAAATCACCACTAAAGAATTTATCTATGTAACAAAAAACCACCTGTGCCCCAAAAACTAGTGAAATTTTTTTAAAAATATAAAAAATAAACACCAAATCATAGAATTTAAAAAAAAGAAAATGTGGCCTATATACACAATGAAATACTATTCAGCCAAAAAAAGAAAATGAACTCATGTCATTTGCAGCAACACGGATGGAACTGGAGGTCATTATCTTAAGTGAAATAAGCCAGGCATAAAAAAGGCAAGTATCTGGCCAGGCGCAGTGGCTCAGGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGTGGGTGGATCACGAGGTCAGGAGTTCAAGACCAGCCTGGCCAAGACAGTGAAACCCCGTCTCTACTAAAAATACAAAAAAATTAGCCGGGCATGGTGGCACACACCTGTAATCCCAGCTCCTCCAGAGGCTGAGGCAGAGAAATGCTTAAACCTGGAGGGGCGGAGGTTGCAGTGAGCCAAGATCGCGCCACTGCACTCCAGCCTGGGCAACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAAAGGCAAATATCACATGTTCTCACTTATATGTGGGAGCTAAAAAATTTGAATACACAGCTAGAGAGTGGAAAGATAGAGAGCGGAAAGACAGATAACAGAGACTGGGAAGGGTGAATGGGGTACATGGAGCAAGGATGAAGAGAAGCTGGTTAAAGGGTACATATACACAGTAGGACAGAAGGAATAATTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGGGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGGACTACAGGCGCCCGCCACTACGCCCGGCTAATTTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTTTTAGCCGGGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCCAGAGGGAATAATTTCAATGTTTGATAGCAGAGTAGGTTGACTATACTTAACAAAAATGTATTATACTCAGGCAATGGACACCCTAAATACGTTGACTTGATCACTATACGTTATATACATATAACAACATTTACATGTACCCCACAAATTTATGCAAATCTTAAAAATTCTGTGCATGCCTTTTAGTGTATACAAATGCATATCTCTATTAGACATTAGGTACCTAGAGTATTCTTTCTTGGTCATAGGACATATATATGTCCATTTTATTAACCATACTAACAAACAGCTTTCCTTAGTACTTAAATCAATTTCATTCCCACCAGCAGTGAATGAAGGCTCCAGTTGTTCCACATCCTTGCAAATACATGGTATGGTCTGTGTTTTTAATTTGACCCATTCTGATGGATATTCAGTAGCATCTCAGTATGGCTTTACTTTCCCTGATGACTAATCATATTGATACCATCCCCTTTGTTTACTGGCCTTTTGGACATTCCCTTTTGTGAAGTGCCTGGTAGCATTTTTCTCAAATGTTTTTATTGGATAGACTTTTCATTATTGATGTAAAGGGGTCCTTTATACAGCTTGGATAAAAGGCCTTTGTGGGACACAACTACTTTGAATAGCTCCTCCTATTCCTTGACATGCCTTTTTACTCTCTTAGTCATCTATTTTGATGAGAAAAGTTCCAAATTTTAATATATTCCAATGGATCAGTCTTTTCCTTTATAGTTATTATTTCTTACATCTTATTTAAAAAGTATTTTTCCTACATCGAGGTCATAAAGTATTCTCCTACATTATCTTTTATAAGCTTTGTCAGTTTAACTTTTTGATCTATAGCCCACTTGGAATTGATTTTGCATTATCAGTTGTGTGAAACAGGGTCAAGATTAGTGCTTTCCCCATGGGGATATTCAGTTGACCCAGCACACTGTAGTGAGTAGGCCATCCATGCCTGCTATTCTGCCAGGCTACAACATACAGTTTGAGATTATGTTATTCAGTACATACATCTTTAAAATAGCTTATTATTATGTGGTGACCTTTTTGGCCTTGCAGTTTGAAATCAGCAGTTTCTCCAGCCTTCTCATGTTTAGTTTGGCCTATTTTTCTTTTTTTTTTTTTTTTTTAACTACCTCACTATCAACATTTATGAGTCCTTATTTTTTATTGTTTCACTGTAAGCAATATACAACAGGCTTTGGGTTTTATGAATTCAATATAATACTCTTATTTTTCATTCTAAGTGTAAATCACTTAAATTGATAATAACAATTGTGAAATGGAATTATATATGGTATCTTATATTAAATATTTCTCTTCTTACCTTATTTTGGGTTGATGAGGCTTAAAAAAAATCCCCTTTTCT\tLN:i:17946\trd:i:0\n+A\tatg000009l\t0\t-\tm64012_190921_234837/159975018/ccs\t0\t12767\tid:i:79\tHG:A:a\n+A\tatg000009l\t1618\t+\tm64011_190901_095311/29166179/ccs\t0\t16328\tid:i:75\tHG:A:a\n+L\tatg000001l\t+\tatg000002l\t-\t8258M\tL1:i:8162\tL2:i:0\n+L\tatg000001l\t+\tatg000005l\t-\t706M\tL1:i:15714\tL2:i:0\n+L\tatg000002l\t+\tatg000001l\t-\t8257M\tL1:i:7962\tL2:i:0\n+L\tatg000002l\t-\tatg000005l\t-\t8671M\tL1:i:7548\tL2:i:0\n+L\tatg000003l\t+\tatg000007l\t-\t11799M\tL1:i:506\tL2:i:0\n+L\tatg000003l\t+\tatg000008l\t-\t7855M\tL1:i:4450\tL2:i:0\n+L\tatg000004l\t+\tatg000009l\t-\t9949M\tL1:i:2100\tL2:i:0\n+L\tatg000004l\t+\tatg000006l\t-\t3281M\tL1:i:8768\tL2:i:0\n+L\tatg000005l\t+\tatg000002l\t+\t8667M\tL1:i:9694\tL2:i:0\n+L\tatg000005l\t+\tatg000001l\t-\t706M\tL1:i:17655\tL2:i:0\n+L\tatg000006l\t+\tatg000009l\t+\t11285M\tL1:i:4947\tL2:i:0\n+L\tatg000006l\t+\tatg000004l\t-\t3281M\tL1:i:12951\tL2:i:0\n+L\tatg000007l\t+\tatg000003l\t-\t11802M\tL1:i:1878\tL2:i:0\n+L\tatg000007l\t-\tatg000008l\t-\t9733M\tL1:i:3947\tL2:i:0\n+L\tatg000008l\t+\tatg000007l\t+\t9736M\tL1:i:10012\tL2:i:0\n+L\tatg000008l\t+\tatg000003l\t-\t7855M\tL1:i:11893\tL2:i:0\n+L\tatg000009l\t+\tatg000004l\t-\t9945M\tL1:i:8001\tL2:i:0\n+L\tatg000009l\t-\tatg000006l\t-\t11284M\tL1:i:6662\tL2:i:0\n'

diff -r df25d4fb79b7 -r 284a1cb82b61 test-data/hifiasm-out-hifi-p.gfa
--- a/test-data/hifiasm-out-hifi-p.gfa Wed Jan 17 21:31:58 2024 +0000
+++ b/test-data/hifiasm-out-hifi-p.gfa Thu Jul 11 14:44:22 2024 +0000

b'@@ -1,10 +0,0 @@\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 df25d4fb79b7 -r 284a1cb82b61 test-data/hifiasm-out11-primary.gfa
--- a/test-data/hifiasm-out11-primary.gfa Wed Jan 17 21:31:58 2024 +0000
+++ b/test-data/hifiasm-out11-primary.gfa Thu Jul 11 14:44:22 2024 +0000