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Changeset 0:bf0a4667e3ce (2021-03-02)

Next changeset 1:6505bd37670d (2021-03-03)

Commit message:
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"

added:
hifiasm.xml
test-data/hifiasm-in1.fa.gz
test-data/hifiasm-out1-alternate.gfa
test-data/hifiasm-out1-primary.gfa
test-data/hifiasm-out1-processed.gfa
test-data/hifiasm-out1-raw.gfa

diff -r 000000000000 -r bf0a4667e3ce hifiasm.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/hifiasm.xml Tue Mar 02 20:23:49 2021 +0000

[

b'@@ -0,0 +1,229 @@\n+<tool id="hifiasm" name="Hifiasm" version="@VERSION@">\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+ </xml>\n+ </macros>\n+ <requirements>\n+ <requirement type="package" version="@VERSION@">hifiasm</requirement>\n+ <requirement type="package" version="0.1">yak</requirement>\n+ </requirements>\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.${mode.hap2_reads.extension} &&\n+ #end if\n+ hifiasm -i input.${mode.reads.extension} -t \\${GALAXY_SLOTS:-1} -o output -f $filter_bits\n+ #if str($advanced_options.advanced_selector) == \'set\':\n+ -z $advanced_options.adapter_length\n+ -k $advanced_options.kmer_length\n+ -w $advanced_options.window_size\n+ -D $advanced_options.drop_kmers\n+ -N $advanced_options.max_overlaps\n+ -r $advanced_options.correction_rounds\n+ #end if\n+ #if str($assembly_options.assembly_selector) == \'set\':\n+ -a $assembly_options.cleaning_rounds\n+ -m $assembly_options.pop_contigs\n+ -p $assembly_options.pop_unitigs\n+ -n $assembly_options.remove_tips\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+ -2 hap2.yak\n+ -c $mode.max_kmers\n+ -d $mode.min_kmers\n+ #end if\n+ #if str($purge_options.purge_selector) == \'set\':\n+ -l $purge_options.purge_level\n+ -s $purge_options.similarity_threshold\n+ -O $purge_options.minimum_overlap\n+ #if $purge_options.purge_cov:\n+ --purge-cov $purge_options.purge_cov\n+ #end if\n+ $purge_options.high_het\n+ #end if\n+ ]]>\n+ </command>\n+ <inputs>\n+ <conditional name="mode">\n+ <param name="mode_selector" type="select" label="Assembly mode">\n+ <option value="standard">Standard</option>\n+ <option value="trio">Trio mode</option>\n+ </param>\n+ <when value="standard">\n+ <expand macro="reads" />\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="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+ </when>\n+ </conditional>\n+ <param name="filter_bits" argument="-f" type="integer" min="0" value="37" label="Bits for bloom filter" help="A value of 0 disables the bloom filter" />\n+ <conditional name="advanced_options">\n+ <param name="advanced_selector" type="select" label="Advan'..b' <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+ </tests>\n+ <help><![CDATA[\n+***********************************\n+HiFiASM - a fast de novo assembler\n+***********************************\n+\n+Hifiasm is a fast haplotype-resolved de novo assembler for PacBio Hifi reads. It can assemble a human genome in several hours and works with the California redwood genome, one of the most complex genomes sequenced so far. Hifiasm can produce primary/alternate assemblies of quality competitive with the best assemblers. It also introduces a new graph binning algorithm and achieves the best haplotype-resolved assembly given trio data.\n+\n+#### Assembly mode\n+- *Standard*\n+- *Trio* When parental short reads are available, hifiasm can generate a pair of haplotype-resolved assemblies with trio binning.\n+\n+#### Trio Options\n+- *Haplotype 1 reads* : list of hap1/paternal read names\n+- *Haplotype 2 reads* : list of hap2/maternal read names\n+- *Lower bound of the binned k-mer\'s frequency*\n+- *Upper bound of the binned k-mer\'s frequency*\n+\n+*Bits for bloom filter* (-f) - A value of 0 disables the bloom filter for small genomes. For genomes much larger than human, applying -f 38 or even - f39 is preferred to save memory on k-mer counting.\n+\n+#### Advanced options\n+- *Length of adapters to be removed* Old HiFi reads may contain short adapter sequences at the ends of reads. You can specify 20 to trim both ends of reads by 20bp.\n+- *K-mer length* (must be <64)\n+- *Minimizer window size*\n+- *Drop K-mers* K-mers that occur more than this value multiplied by the coverage will be discarded\n+- *Maximum overlaps to consider* consider up to max(-D*coverage,-N) overlaps for each oriented read\n+- *Correction rounds* round of correction\n+\n+#### Assembly options\n+- *Cleaning rounds* round of assembly cleaning\n+- *Minimum contig bubble* size Pop contig graph bubbles smaller than this value\n+- *Minimum unitig bubble* size Pop unitig graph bubbles smaller than this value\n+- *Tip unitigs* Keep only tip unitigs with a number of reads greater than or equal to this value\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+- *Similarity threshold for duplicate haplotigs*\n+- *Minimum overlapped reads for duplicate haplotigs*\n+- *Coverage upper bound* If not set, this will be determined automatically\n+- *Experimental high-heterozygosity mode* enable this mode for high heterozygosity sample NB: May be unstable\n+\n+\n+### Outputs\n+\n+Non Trio assembly\n+- Haplotype-resolved raw unitig graph in GFA format. This graph keeps all haplotype information, including somatic mutations and recurrent sequencing errors.\n+- Haplotype-resolved processed unitig graph without small bubbles : Small bubbles might be caused by somatic mutations or noise in data, which are not the real haplotype information.\n+- Primary assembly contig graph : This graph collapses different haplotypes.\n+- Alternate assembly contig graph : This graph consists of all assemblies that are discarded in primary contig graph.\n+\n+\n+Trio assembly\n+- Haplotype-resolved raw unitig graph in GFA format . This graph keeps all haplotype information.\n+- Phased paternal/haplotype1 contig graph. This graph keeps the phased paternal/haplotype1 assembly.\n+- Phased maternal/haplotype2 contig graph. This graph keeps the phased maternal/haplotype2 assembly.\n+\n+\n+\n+]]></help>\n+ <citations>\n+ <citation type="doi">10.1038/s41592-020-01056-5</citation>\n+ </citations>\n+</tool>\n'

diff -r 000000000000 -r bf0a4667e3ce test-data/hifiasm-in1.fa.gz

Binary file test-data/hifiasm-in1.fa.gz has changed

diff -r 000000000000 -r bf0a4667e3ce test-data/hifiasm-out1-primary.gfa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hifiasm-out1-primary.gfa Tue Mar 02 20:23:49 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 000000000000 -r bf0a4667e3ce test-data/hifiasm-out1-processed.gfa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hifiasm-out1-processed.gfa Tue Mar 02 20:23:49 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 000000000000 -r bf0a4667e3ce test-data/hifiasm-out1-raw.gfa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hifiasm-out1-raw.gfa Tue Mar 02 20:23:49 2021 +0000