| Previous changeset 4:3f7be05a1597 (2021-09-22) Next changeset 6:5bec28269d95 (2022-02-12) |
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Commit message:
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" |
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modified:
hifiasm.xml |
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added:
test-data/hic_1.fastq.gz test-data/hic_2.fastq.gz test-data/hifiasm-out-hifi-a.gfa test-data/hifiasm-out-hifi-p.gfa |
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| diff -r 3f7be05a1597 -r 045c7c3d8e59 hifiasm.xml --- a/hifiasm.xml Wed Sep 22 21:13:59 2021 +0000 +++ b/hifiasm.xml Wed Oct 06 20:11:11 2021 +0000 |
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| b'@@ -2,7 +2,7 @@\n <description>haplotype-resolved de novo assembler for PacBio Hifi reads</description>\n <macros>\n <token name="@TOOL_VERSION@">0.16.1</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@@ -19,12 +19,27 @@\n #set $input_files = list()\n #set $hap1_inputs = list()\n #set $hap2_inputs = list()\n+ #set $hic1_inputs = list()\n+ #set $hic2_inputs = list()\n #for idx, read in enumerate($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($hic_partition.hic_partition_selector) == \'set\'\n+ mkdir HiCF HiCR &&\n+ #for idx, read in enumerate($hic_partition.h1):\n+ #set $inputfile = \'./HiCF/input_%d.%s\' % ($idx, $read.dataset.extension)\n+ ln -s \'$read\' $inputfile &&\n+ $hic1_inputs.append($inputfile)\n+ #end for\n+ #for idx, read in enumerate($hic_partition.h2):\n+ #set $inputfile = \'./HiCR/input_%d.%s\' % ($idx, $read.dataset.extension)\n+ ln -s \'$read\' $inputfile &&\n+ $hic2_inputs.append($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, $read.dataset.extension)\n@@ -93,8 +108,8 @@\n #end if\n \n #if str($hic_partition.hic_partition_selector) == \'set\':\n- --h1 \'${ \' \'.join(["%s" % $x for $x in $hic_partition.h1]) }\'\n- --h2 \'${ \' \'.join(["%s" % $x for $x in $hic_partition.h2]) }\'\n+ --h1 \'${ \' \'.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@@ -136,7 +151,61 @@\n <param name="yak_kmer_length" type="integer" min="0" max="64" value="31" label="Yak counter k-mer length" />\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+ <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="assembly_options">\n+ <param name="assembly_selector" type="select" label="Assembly options">\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 name="cleaning_rounds" argument="-a" type="integer" value="4" label="Cleaning rounds" />\n+ <param name="adapter_length" argument="-z" type="integer" min="0" value="0" label="Length of adapters to be removed" />\n+ <param name="pop_contigs" argument="-m" type="integer" value="10000000" label="Minimum contig bubble size" help="Pop contig graph bubbles smaller than this value" />\n+ <param name="pop_unitigs" argument="-p" type="integer" value="100000" label="Minimum unitig bubble size" help="Pop unitig graph bubbles smaller than this value" />\n+ <param name="remove_tips" argument="-n" type="integer" value="3" label="Tip unitigs" help="Keep only tip unitigs with a number of reads greater than or equal to this value" />\n+ <param'..b'*\n+.. class:: infomark\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+----\n+\n+.. class:: infomark\n+\n+**Assembly mode**\n+\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 \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+.. class:: infomark\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+**Outputs**\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-#### Hi-C-partition options\n+Non Trio assembly:\n \n-- *RNG seed* \n-- *Rounds of reweighting Hi-C links* : increasing this may improves phasing results but takes longer time.\n-- *Rounds of perturbation* : increasing this may improves phasing results but takes longer time.\n-- *Fraction to flip for perturbation* : increasing this may improves phasing results but takes longer time.\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+Trio assembly:\n+\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' |
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| diff -r 3f7be05a1597 -r 045c7c3d8e59 test-data/hic_1.fastq.gz |
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| Binary file test-data/hic_1.fastq.gz has changed |
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| diff -r 3f7be05a1597 -r 045c7c3d8e59 test-data/hic_2.fastq.gz |
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| Binary file test-data/hic_2.fastq.gz has changed |
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| diff -r 3f7be05a1597 -r 045c7c3d8e59 test-data/hifiasm-out-hifi-a.gfa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hifiasm-out-hifi-a.gfa Wed Oct 06 20:11:11 2021 +0000 |
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@@\n+S\tatg000001l\tAAAAAAAAAAAAGAAAAGAAAAGAAAAGAAACAACATAACAAGACAAAACAAAGCAGGAGAGAGGAAGTGCAGTATCTGATTGTAAGTTTGAATTGAGGGTGGATATAGGGATGGACTGCATTTTGGGTGATGGCAAGAAATCAGAGGTTTGTGGCCACTGTTTAGATTAGTCTCAGCCTTCAAATGGTGGTTCCTGAGGTAGAGTCTGGGGAATGATAGCTGTAGAAACTGGATTACAGAGAATTGAGGAGAAAGTAGGTGGTGAGGAAACAAGGACAGCTCAAGTGGATGAATAGGACATCTGTTACTTTTGCCACCCAGCGTTCTTTTACCCTGCTGCTAAATGTTTCTCGATTTCCTTCTGGGACCCACCCGTGCTCGCTTTCAGTCCATATGGATTTAGCATTGGAACTCATAACTTTTCTTTAAGACCATTATAACAGTGCATTTTCCTGGCCACAAGGACTGGTTCAGGATTTGTCCTGTTACACAAGCCAATCAAAGTAGGTTTGTTTTTGTTTTTTATCCTGGTAATATTGGACAATGAGTCTCATTTTTCTACTGCGGGAGGGAATCTGGAAGAACATGATGACAGGGAAGAGGCTGTCTGAGGAGGAAGCCAACAGAGAGAACTGAATAAAGGGATAAGGTTGAACCAGATCCTGATGATACTGTTGCTGGGGGGCCTCTATACCCAGCCCTGCCTGAAGTCAGGACCACCCCCTAGTTTTGCTTAACCCCATTTAATCAGTTTCTGTCATTTTTTAACAAAGCACTAACTGCTTGTAGGGTAACTCAGCTTCTATGTGAAGAAAAGCAGTAAGAATCCTTCATATCCTAATGGGAAAATCATTGTATTTTTATGAGGGTGAGATATATTTGGTGTAGAGATTATGCAAATCTGGTGATCAAGGTTCTTATTATTAAGCCAAAGGGAAGACAGTGTTTTAGATGGAAGAATAATTAGTAGGTTTGACTACAAAACCTATGCATTTTTCCCTCAGGCATGACCACATTATTATCAATTTCAACAGATATATTCTTGAAAGAAGGTTTTTTTTTCTTATTCACTAAAACAGTTACTTATTTTTTTTTTCATATTTGATAGCAGCTTTTTTTATTGGTTACAAAACCTAAGCCCATATACAAAATTAGGAACACATTTAGATGCCTCTTTTGAAAGAACATTTTGTCTTTTTAAACTGAGTTTAAAAAAAATAAAAACAATGCAATTTTTAAACACTATTTGAAAACTTAAAAGTGCAGCAATATACTTAGTTTCCTTTATCTACGAAATGGTGCAATTCCAATTCAAAACTGGTAAGGTCACAAATTGAATCAAGGAAATGCATACAAATGTCTGCATTACTTGATGCTAATGTTCACTTGAATGTTAGTTTGCACTTTAAAAACATGAGAGGAAATAGGAATCATCACAGTAGAGGCCCAATTTTAATCATAATGTGTGCAAATTTTAAAAGGTAACTGTCAGTTAAGTAAGGAAAGTCCAGAAGAAACTAAACTGGAAGGGGTACAGTTCACAATATCAAGAAGATTTGGGACAAAAAACTGCAAAAGTCTAAAATACCCATTGGTGATGTTTTTTAAAAAATCTTGCTTTCAGCTTTCAGGAGTTAATATTCTTTGTTTTAACTTGATAATTGGATATGGTTGATTTATATTGGGTTTAAACTGTGGAGCTTTCATGTTTACTGTAATTTAGTCTTAAAATATTTTTTACTTAGTAACCAGTACTTTTGCTAATGTGGTTGGCAACAAACCAGCAACTATTTAAAAGTGTCATAAGGGTTCATTCTTTGAGTACTGGGAAAGTTAATTCAGATCCTACTCAAAAAGCATCTTCACATATTAAAAGATTCAGACAGGGATCTGTGTAGAGGAGTAATTTGCAGTTATTTAACATAAACCTGATTTGCAGTGATCTCTAAGTAACAGTTACTTATTGTATGAATGCATATGTGGGCTTTTTAGGTACTTTTCTCCTCTCCACTCCACTCGGGGGCCTTTCAGTTTAGGGCTATGACACAGCCACCACTTTGCATCATTTACACCATCCTGAAAACCTGCAGGGCTCTTCCTTGCTCCTGGCTGTTGGAATTGAAATATCTTTTTTCCTCTTCTTCAGAATGGTGTTTTGATTTCTTATCAGCTGCCAGCTGGATTTGAAGGCCTATAGCCTAATCACCTAGATAGATAAGGAAAGTTGTCATATTTTGTCTTTGGCTGATAGGAATTTAGAACACAAACAAACTCAAAAGAGTCAACCTTTGGGTAAGATTAAACCAGTGACTCTAATTCAGATCATTCCATAAATTGTATTATCTTGAGCAAAACACTCTATTCCTTGACATTGCAGATTATAAATGTTGGGAATAAAGAGAAATAAGTGAATCCCAAACCTTTTTATATTATGATACACATATAAATTATAATGTTTGATAGGTACATGGAAATAAATAGATGAGGCTTCTCACTGCTAAAGGTGGCCAGGCTGGTTTGAGGGGATCAGTAGCTCAGCATACCTTACCCTATTCTTGACACTCTGGTTGGGAAGCTCTTGAATTTGTAAACCATATGGACTGGGTTTTCGTCCTGGCTCAGTCACTAAGCCCCACTACGTTCTTGTGGCATTCTCTTTTCCTTTTGAGTCCTCGGTTCTGAATGCTTAAATGAGGAATCTGAGGTCTAGTTCAAATGTAAATGCCATTTATCAGGCATATATAAAAAAGCATTATCAGATATAAAAATGGAGGTTTTTGAGATATACTGAGACTTTAAGCATGAAAGCATCTATAAGAGTTTACCACTTAGATCTGTTTAATTACTGCTAAGGACACTTACTTTTTAAAAAACAGCATGCCTACATTATCTAGATACCTGTATGACAGTATGTGATGGACAGTGTCAGGGTCTGACTTAAGCACCCAGAGATTAGTCACAGAATTTCTGAGGTGAGGGCATTCAGATCCTCTATTCCCCCAATATAAAAGGAGACTCTTTAAAAATCATCATTGTATAGTTGCATAGAACATCATGCAAATATGCAATTGAAGATCCAAGCATATAAATCCATAATCTTATACATTATTAACTAGCCTAACCCTCCTTAGTCAAATATAATCACATGAAGTTAGAGACAATTTAGTTCCAGTAACATACTACACTCTCTCCCAGCCCCCCACCTCCACCCGCCATCAACAGCAAGTGCAGACCACTTTCATGGGACAGGGCAGCACTAGATCCACCAGGTAGGAATATTTAGGGACAAATGATCAGGATGTAAGGAAGCTGAAGTTACCACCAGGCAGTGCTCATTCTGGTGGGCAAATCCAGGGTCCAAGGGAATCAATAATTAATGATCATAGTCCAGGTAAACTTTGGCAATGACATGAGGAGGTTCAAGGCGATGGAATGGATCACCATGAAGAAGACTTTGGAGTTGAAATATTCAATGAACCAAGCAGATTTTGGCTTTAAGATGGTCTGTAAGTGAGTAGTTATGTTACATACACTAAGATGAAGTTCTGGAACAACTTCAATGATAGAGCTTCAGACTACCGGAAAATCAAGGGCAAGAACAAGATTAATGTTCATGAAAGACAGGGTTGTGTTCATTGAATGCACACAGGCACACACAGAAATTAATGGACACATATGGAGTGTTTACACGCAAGACTGTGTCACATGTTTACACACACTGCTCCATTTAATTCTTGCTAAATCTCCAAAGGACATTCATTATTCTATTTATAGATGAGACAACAGAGACTTAGTAGCTACCAATAGTCACACAGTTAGTAAATGGCAGAAACAAGATTCGAACTCAGGTCTGACTTCAAAGTTCATTTTCTTTTCACTGGTATGTTACAGAGGCTAGGTAACTAGGATCTTGAGAATAGGGACCAAGGAAGAAACACTGAGTAAAATGGGTAGATCCAATTGGTTTT'..b'TAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAACAGGCATCCAACAGAGTGGGAGAAAATTTTTGCAGTCTACTTACTGACAAAAGTCTAATATCCAGAATTTACAAGGAACTTAAACATATTTATGAGAAAAACTTCATCACAAAGTGGGCAAAAGAGATGAACAGACACTTCTCAAAGGAAGACATTTACACGGCCAAAAAACGTATGAAAAAGAGTTAAACATCACTGATCATCAGAGAAATGCAAATCAAAATGATAATGAGATACCATCTTACGCCAGTCAGAATGGCGATTATTAAAAAGGCAAGAAACAATAGATCCTGGTGAGGCTGTGGAGAAATACGAACATTTTTATGCTATTGGTGGGAATGTAAATTAGTTCAACCATTGTGGAAGACAGTATGGCAATTCTTCAAAGATATAAAACCAGAAATACCATTTGACCCAGGAATCCCATTGCTGGGTATATAGCCAAAGGAATATAAGTCAATCTGCTGAAAAGACACATGCACACGTATGTTTATTACAGCACTATTCACAATAGCAAAGACATGGAACTAACCCAAATTCTCAACAATGATAGACTATTTGATAAAGAAAATGTGGTACATATACACCAGGGAGTACTACACAGCCATAAAAAGGGACACGATCATGTTCTTTGCAGGGACATGGATGAAGCTGGAAGCCATCATCTTCAGCAAACTAACACAGAAGGAGAAAACCAAACACCACATGTTCTCACTCATAAGTGGGAGTTGAACAATGAGAACACATGGGCACAGAGAGGGGAACATCACACACTGGGGCCTGTTGCGGGATGGGGGAAAGGGGAGGGAATTTAGAGGACAGGTCAATAATACATCAAGCCCCCATGGCACACGTATACCTATGTAACAAACCTGCACATTCTGCACATGTATCCTGGAACTTAAAGTAAAATTTAAAAATAAAATTTAAAGTAAAAATAAAATTTTGATTAAAAAAGTTAAAAAATAAAATCACGCAGCTGCTGTGGAAAACAGTTTGTTGGTTCCTCAAAAATTTAAACACAGAATTACATGTAATCCAGCAATTCCTCTCCTAGGTTTATAGGTAAGAGAATTGAAAACAGGGACTCAAACAGACACTTGTATGTCAGTGTTCACTGCAGCCTTATTCAAAATACACAAAAGATGGAATGAAGCCAAATGTCTACCCATGTATGAATGGATAAAGAAAACTTGGTATATGTATCCAGTGGGATATTATTCATCCATAAGAAAGGAATGAAGTTCTGATACGTACTACAGTGTGGATAAGCCCTAAAAACTATGCTATGTGAAGGAACCATGCACAAAAGGACAACTATTCTTTAATTCCACTTATATGAAATATCAAAAATAGGCAAATTTATTGAGACAGAAAGTAAATTAATGGTTAACAGGGGATGGTGGCGGGAGTCATGGGAGTTATTGCTTAATGGTTACAGAGTTTTTGTTGAGGCAATAGAAAAGTTTGATTAATAGTGGTGATGGTTGCATAACACTGTGAATGTATTTAATGCCACTGAATTGTGCACTTAAAATGTTTATAATGGAAAATTTTAAAAAAACAAAACAAAACAGGTAGCTTGGTCCTATTTCCAAAGTCTGATTCAGTGGACCTAGGTTGGGACCCAAATCTTTTCATTTCTAACAAGCTGCCAGGTGATGGTGATGCTGCTGGTTCTGGGACATGCTTTAGACAGAAACATAACAAGAACTCCAGGGCCGGGAAGAAGAATCTTGGTTTCAAGGGATGGAGATCTGAGTTTGAATCCTGAACATACCTCTTTATTATAGCTGTTGAACTTGTGTTGCTTTGCTTTTTGAAGCCAATGAAGTTAACTCTCTTGCTTAAATTCTTTTAGTGACTCTCTATTGCATGTCAAACCAGCGTAAGATCTGGTCCTTGCTGTCCTCTGCAACCTTCTCTCATGCCATTTTCTCTTCTGCCCACCATGCCTCAGCCACACTACTCTTTTATAGTTCCTTGAACATAACAGGGCCTTTTCACCTGCTTGTGCCCAGGACAGTTTTCATTCGGTTGTTTGAAATGTTGTCTTCTTTATTTTTCTAAATTAATTATAATTTGTATTTTAAGTGCTAGGGTACATGTGCAGGATATTTTCCTGGAGCACCCTCTCTTTGCAGGTCCGTCACCATTACTGCATATATCGGTTAGCTATTGCTGCACAACAAACCCCCAAAACTCAGGGGCTTATGTCAGTAACCTCACAGGTCTGCTCAAAAATTGTGTTGATAAGGATCGGTCTTGGTTGATCCCCTCTAGATTTACTCATATGCCTGTAGCTGGCTGGTGGAGTTGGCCAAAGGCTGACTTAACTGGGATAGTCTCAGTGCCATGGTGATTAACTCCTGGCTGGGGCAATGTTGACGACTGGACCATGTGTCTTTCATTATCTAACAGGCCAGCCTGGGCTTGTTCCCGTGGTGCTCGGCAATGTTTCAAGGTAGAGTAGATGTTCACAAGACCCTTGAGGCCTAGGCTGGGAACTGGCACACCATCACTTCCACAGTGCTTTACTGATCAAAGCAAGTCACAAGACTAGCCCCAGACTTAAGGGATGGGGAAACAGACTCCCCCTCTTGAAGTGAGGGTGTACAAAGTCACTGTTCAAAATGTGTGAGTACAAATGGGGAATCAATTTGCAATCATTCTATCACATACTTTCCAACTGAAACATCTCCATTTCCGGCCCCGCACTCACCACAGTTTGAGAGTGTAGGCAGGGCTGGCTTCATGGGCCATCAACCTGAGCAGTCCCAGGGGGGCCGTGCTTAGAAAGGTCCTGTGATTAGATTACTGCCCTGCTGTTGCCCTCTTCAATTGTTTAGTAAATTTTGAACAAGGGACTCTGCAAATTATGTAGCAGGTTCTAAGTATAGTTTATGTGGGTGTTTATTTGTTCATCATTGGTCTTTCTAGATTGTAGGCTTCACCAGGGTCAGAACTAGCTCTCATTCAGCAAGTGCTTAGAAGTACCAGGTACATAACTGGCAGACAATATACTGTTAATGAATGAATGTACCAGTTATGAATTTATCTTCTTATTTGTAAAGTTCCAGAGATGTCTTTCCTGAAGGTAATGCAGATTATATAAGAATATGTATTAAAAGCAACTTGCACATAGTACATTTGTAACACATGTCTCCATCCCTTTTTAGTATTTAAGCACATAAAAATGCATTTCTTGGCATTTAATGCTCCCTGTATGTTTAACTGTATACTGTAGAAATGAAGGCACTCTTCCTGTCTTTTAGGAATTTCTGTTTTAGTTATGAGGATATGATTAAGAGAGAGAGAACAGTTCTTCCTATTATCTATTCCAGCTTGATGAGTGTATGATTCTCTGTAGATATAAAGAACTTTGTGCTTGAGCTCAAATACCTGGTACAGACAGATAACACAAAGAACATTCAGAGACTTGGACAATCATTTTGCTGCAGAGGTGGGTTATGGGAATGTAGAGGACAGAACCAACAGTTATTGAATACTTCCTATGTTACAGACTTTGGCCCTGCATATAGTATCTCAGTTAATTACATTTCACCTTCAGAGAAATCCTACTAAGTTAGTGATTTTTATCCCCATTGTGTAGGTCAGGCAATTGGACTCAGATTAAGTAAGTTGCCAACCTTATATAGCCCAGAAGTGATGGAAATGGGATTTAGACCCAGGTCTTTATGATTTCAAAGTCTTTGCTCCTTCATTCAACAAATATTTATTAAGGGCTTACCCTGTGTTTCCACAGTTACCACTGTGTTGATT\tLN:i:17948\trd:i:0\n+A\tatg000002l\t0\t-\tm64011_190901_095311/29166179/ccs\t0\t16328\tid:i:75\tHG:A:a\n+A\tatg000002l\t5181\t+\tm64012_190921_234837/159975018/ccs\t0\t12767\tid:i:79\tHG:A:a\n' 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| diff -r 3f7be05a1597 -r 045c7c3d8e59 test-data/hifiasm-out-hifi-p.gfa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hifiasm-out-hifi-p.gfa Wed Oct 06 20:11:11 2021 +0000 |
| b |
| 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' |