| Previous changeset 10:2061fb3b81b4 (2023-01-24) Next changeset 12:da9d8bf98802 (2023-02-24) |
|
Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit c8948d0cc178c85b078e8789304831cee5b3fa9f |
|
modified:
hifiasm.xml |
|
added:
test-data/hifiasm-out11-primary.gfa test-data/hifiasm-out11-raw.gfa |
|
removed:
test-data/nanopore.first5.fasta.gz test-data/nanopore.first50.fasta.gz |
| b |
| diff -r 2061fb3b81b4 -r cd7936c5a9a5 hifiasm.xml --- a/hifiasm.xml Tue Jan 24 17:46:39 2023 +0000 +++ b/hifiasm.xml Thu Feb 23 22:34:21 2023 +0000 |
| [ |
| @@ -1,8 +1,8 @@ <tool id="hifiasm" name="Hifiasm" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>haplotype-resolved de novo assembler for PacBio Hifi reads</description> <macros> - <token name="@TOOL_VERSION@">0.18.5</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@TOOL_VERSION@">0.18.8</token> + <token name="@VERSION_SUFFIX@">0</token> <token name="@FORMATS@">fasta,fasta.gz,fastq,fastq.gz</token> <xml name="reads"> <param name="reads" type="data" format="@FORMATS@" multiple="true" label="Input reads" /> @@ -117,8 +117,8 @@ #end if #if str($hic_partition.hic_partition_selector) == 'set': - --h1 ${ ' '.join(["'%s'" % $x for $x in $hic1_inputs]) } - --h2 ${ ' '.join(["'%s'" % $x for $x in $hic2_inputs]) } + --h1 ${ ','.join(["'%s'" % $x for $x in $hic1_inputs]) } + --h2 ${ ','.join(["'%s'" % $x for $x in $hic2_inputs]) } #if $hic_partition.seed: --seed $hic_partition.seed #end if @@ -135,7 +135,7 @@ #end if #if str($ont_integration.ont_integration_selector) == 'set': - --ul ${ ' '.join(["'%s'" % $x for $x in $ultralong_inputs]) } + --ul ${ ','.join(["'%s'" % $x for $x in $ultralong_inputs]) } #if $ont_integration.ul_rate: --ul-rate $ont_integration.ul_rate #end if @@ -272,16 +272,16 @@ </inputs> <outputs> <!--Standard mode--> - <data name="raw_unitigs" format="gfa1" from_work_dir="output.r_utg.gfa" label="${tool.name} on ${on_string}: haplotype-resolved raw unitig graph"> + <data name="raw_unitigs" format="gfa1" from_work_dir="output.r_utg.gfa" label="${tool.name} on ${on_string}: haplotype-resolved raw unitig graph for pseudohaplotype assembly"> <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'blank'</filter> </data> - <data name="processed_unitigs" format="gfa1" from_work_dir="output.p_utg.gfa" label="${tool.name} on ${on_string}: processed unitig graph"> + <data name="processed_unitigs" format="gfa1" from_work_dir="output.p_utg.gfa" label="${tool.name} on ${on_string}: processed unitig graph for pseudohaplotype assembly"> <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'blank'</filter> </data> - <data name="primary_contig_graph" format="gfa1" from_work_dir="output.p_ctg.gfa" label="${tool.name} on ${on_string}: primary assembly contig graph"> + <data name="primary_contig_graph" format="gfa1" from_work_dir="output.p_ctg.gfa" label="${tool.name} on ${on_string}: primary assembly contig graph for pseudohaplotype assembly"> <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'blank'</filter> </data> - <data name="alternate_contig_graph" format="gfa1" from_work_dir="output.a_ctg.gfa" label="${tool.name} on ${on_string}: alternate assembly contig graph"> + <data name="alternate_contig_graph" format="gfa1" from_work_dir="output.a_ctg.gfa" label="${tool.name} on ${on_string}: alternate assembly contig graph for pseudohaplotype assembly"> <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'blank'</filter> </data> <!--Trio outputs without Hi-c reads--> @@ -291,10 +291,10 @@ <data name="hap2_contigs" format="gfa1" from_work_dir="output.dip.hap2.p_ctg.gfa" label="${tool.name} on ${on_string}: hap2.p_ctg contig graph"> <filter>mode['mode_selector'] == 'trio' and hic_partition['hic_partition_selector'] == 'blank'</filter> </data> - <data name="raw_unitigs_trio" format="gfa1" from_work_dir="output.dip.r_utg.gfa" label="${tool.name} on ${on_string}: haplotype-resolved raw unitig graph"> + <data name="raw_unitigs_trio" format="gfa1" from_work_dir="output.dip.r_utg.gfa" label="${tool.name} on ${on_string}: haplotype-resolved raw unitig graph for HiC-phased assembly"> <filter>mode['mode_selector'] == 'trio' and hic_partition['hic_partition_selector'] == 'blank'</filter> </data> - <data name="processed_unitigs_trio" format="gfa1" from_work_dir="output.dip.p_utg.gfa" label="${tool.name} on ${on_string}: haplotype-resolved processed unitig graph"> + <data name="processed_unitigs_trio" format="gfa1" from_work_dir="output.dip.p_utg.gfa" label="${tool.name} on ${on_string}: haplotype-resolved processed unitig graph for HiC-phased assembly"> <filter>mode['mode_selector'] == 'trio' and hic_partition['hic_partition_selector'] == 'blank'</filter> </data> <!-- Stardand mode with Hi-C partition outputs --> @@ -314,10 +314,10 @@ <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'set'</filter> </data> <!--Trio outputs with Hi-c reads--> - <data name="hap1_contigs_hic" format="gfa1" from_work_dir="output.hic.bench.r_utg.gfa" label="${tool.name} on ${on_string}: raw initig graph"> + <data name="hap1_contigs_hic" format="gfa1" from_work_dir="output.hic.bench.r_utg.gfa" label="${tool.name} on ${on_string}: raw unitig graph"> <filter>mode['mode_selector'] == 'trio' and hic_partition['hic_partition_selector'] == 'set'</filter> </data> - <data name="hap2_contigs_hic" format="gfa1" from_work_dir="output.hic.bench.p_utg.gfa" label="${tool.name} on ${on_string}: processsed initig graph"> + <data name="hap2_contigs_hic" format="gfa1" from_work_dir="output.hic.bench.p_utg.gfa" label="${tool.name} on ${on_string}: processsed unitig graph"> <filter>mode['mode_selector'] == 'trio' and hic_partition['hic_partition_selector'] == 'set'</filter> </data> <!--Log output--> @@ -499,11 +499,28 @@ <param name="filter_bits" value="0" /> <conditional name="ont_integration"> <param name="ont_integration_selector" value="set" /> - <param name="ul" value="nanopore.first5.fasta.gz" /> + <param name="ul" value="nanopore.fasta.gz" /> <param name="ul_tip" value="1" /> </conditional> - <output name="primary_contig_graph" file="hifiasm-out-hifiul.bp.p_ctg.gfa" ftype="gfa1" /> - <output name="raw_unitigs" file="hifiasm-out-hifiul.bp.r_utg.gfa" ftype="gfa1" /> + <output name="primary_contig_graph" file="hifiasm-out11-primary.gfa" ftype="gfa1" /> + <output name="raw_unitigs" file="hifiasm-out11-raw.gfa" ftype="gfa1" /> + </test> + <!-- TEST 13: test multi-file nanopore input --> + <test expect_num_outputs="6"> + <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" /> + <param name="mode_selector" value="standard" /> + <param name="filter_bits" value="0" /> + <param name="log_out" value="yes" /> + <conditional name="ont_integration"> + <param name="ont_integration_selector" value="set" /> + <param name="ul" value="nanopore.fasta.gz,nanopore.fasta.gz" /> + <param name="ul_tip" value="1" /> + </conditional> + <output name="log_file" ftype="txt"> + <assert_contents> + <has_text text="--ul ./ultralong/input_0.fasta.gz,./ultralong/input_1.fasta.gz"/> + </assert_contents> + </output> </test> </tests> <help><![CDATA[ |
| b |
| diff -r 2061fb3b81b4 -r cd7936c5a9a5 test-data/hifiasm-out11-primary.gfa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hifiasm-out11-primary.gfa Thu Feb 23 22:34:21 2023 +0000 |
| b |
| b'@@ -0,0 +1,10 @@\n+S\tptg000001l\tGAAGTTTTGTCTGAGAGGAGTACCAGGCCGTGTGAGGTGTCAGTCTGCCCCTACTTGGGGGTGCCTCCCAGTTAGGCTACTCGGGTGTCAGAGACCCACTTGAGGAGGCAGTCTGTCCATTCTCAGATGTCCAGCTGCGTGCTGGGAGAACCACTACTCTCTTCAAGGCTGTCAGACAGGGACATTTAAGTCTGCAGAGGATTCTGCTGACTTTTCTTTGGCTGTGCCTTGCCCCTAGAGGTGGAGTCTACAGAGGCAGGCAGGCCTCCTTGAGCTGCGGTGGGCTCCACCCAGTTCGAGCTTCCCAGCTGCTTTGTTTATCTACTCAAGCCTTGGCAATGGCAGGCGCCCCCTCCCCCGGCCTCACTGCTGCCTTGCAGTTTGATCTCAGACTGCTGTGCTAGCAATGAGTGAGACTCCATGGGCGTAGGGCCCTCCGAGCCAGGGGTGGGATATAATCTCCTGGTGTGCCATTTGCTAAGACTGTTGGAAAAGTGCAGTATTAGGGTGGGAGTGACCTGATTTTCCAGGTGCTGTCTGTCACCCCTTTCTTTGACTAGGAAAGGGAATTCCCTGACCCCTTGCGCTTCCTGGGTGAGGCGATGCCTTGCCCTGCTTCGGCTCATGCTCGGTGCACTGCACCCACTGTCCTGCACCCACTTTCCGACACTCCCCAGTGAGATGAACCCAGTACCTCAGTTGGAAATGCAGAAATCACCCATCTTCTGCATCGCTCATGCTGGGAACTGTGGACTGGAGCTGTTCCTATTCAGCCATCTTGGCTCCACACTGTCAAATGCTTTTTCTGCATCTATTGTTATGATCATGTGATTTTTCTTCTTTAGCCTTTTGATGTGCTGAACACATCAATTCAAATGATTTTCAAATGTTGAACCAGTCTTGCCTTACCTGGGATAATATACACCGCCTGGTTATGGTGTATTTTTTTAAATAACTGTCGGAGTCAATTCACTAATATTTTGTTGAGAATTTTTGCATCTATGTTCATGAGAAATACCGGGCTATAGTTTTCTTTTCTTGTGATGTTTTTGTCTGGTTTTAGTATTAGAGTAATGTTGGCCTCACAAAGAATTTGGAAGTATTCCCAATGCTTCTGTATTCTGGAAGAGATTGTGGAGAATTTGTATAATTTCTTTCATAAATGTTTGGTAGAATTCACCAGTGAACCCATCTGGGCCTGGTGCTTCTGTTTGAAACTGTTATTAATTATTGGTTCAATTTCTGTAATAGATATAGGCCTATTCAGATAATCTATGTCTTCTTCTGTGAGAATTATCTTTCAAGAAATTGGTTCATTTTACATAGGTTATCAAATTTTGGGCATAGAGAGTTGTTCATAATATTGCTGTATAACCTTTTAATGTCCATGAGACTACAGTGATATCCTCTTTTTCATTACTGATATTAGTGATTTGTCTTCCTTCTTTTTTGTCTTAGCCTGACTGGAGGTTCATCAATTTTGTTGATCTTTTCAAAGAACTAGGTTTTATTTTTGTTAATTTTCTCTATTGATTTCCTGTTTTCAGTTTCATTGATTTTGGCACTAATTTTTATTATATGTTTTCTCCTGCTTATTTTGGATCTAATTTTTTTCTAGTTTCCTAAGGTGGAAGCTTGGATCATTACTCTCCAATCTTTCTTTTGTTCTAATATGTGCATTCAATGCTAAGCACAGCCTTCCCTGCAAATTTTGAAAAATTTTATCTTATTTTTATTTAGTTTAAAATATTTTTAATTTCTTTTGAGATTTCTGTTTTGACCCATAGGTTACTTAAAAGTGTGCTGTTTAATCCCCAATAATTTTGGAGTTCTCCAGCTGTTATTGATTTCCATTTTAATTCTATTGTGGCATGAATGCAGATATTGTATGATAATTTCTGTTCTTTTAAATGTGCTAAGGTCTGCTTTATGACCCAGAACATGGTTTATTTTGATGAATGTTCCATGTGAGCTTGAGAAGAATGTGTGTTGTGCTGTCACTGAATGATGTAGTTCATAGATGTCAATTATATCCAGTTGATTAATGTGGTATTATTGCTATGTCCTTAAGAATTTTCTGCCAGCAGACTCTGTTTATTTCAGAAAGAGGAGTGTCTAATTGTCAAACTATATTAGTGAATTCATCTGTTTCTCTTTCTAGTTTGGTCAGTTTTTACTCATGTATTTTGAGGTTCTCATGTTAGGCACATACACAAAAAGATTGTGTATATCTTTTTGGAGAATTAACCCTTTTAAAATTATGTAATGCCCATTTATCCCTGATAATTTTTCTTGCTTTGAAGTCTGTTGTGTCAGAAATTAATATAGCTATTCTGATTTCATTTTAGTATTAGCATGATATATATTTCTTCTTCCATTTGCTTTTAATCTGTATATTTTTTAATAAAGTGAGTATTTTGTAGACAGCACGTAGTTGGGTCTTGTCTTTTGATCCACTCTGATATTCTGTATCTTTTAATTGGTATATTTAGACCACTGATTGTTGACACAAGTGACACTACTATATTTATTACTGCTTTCTTTTCACTACCTGTGTCCTTGCTTCTATTTTAGTCTTCCAATCTTTGTCTTCTTTTTGAGGTTTTCATTAATCATTTTATGATATTCTATTTTTCTTTTTTCTTAGCATAGCAATATACTTTTTTTTAAACAAAAAGCGATTGCCACAGAGTTTTCAATATACATTTATAATTAATCCCAGCATACCCTTAGATAATACTATACTACTTCATAGAGAGTACAAGAACCTTATGATAACAAAAGAAGCCTAATTCTCTCTCCCATCACTGTATCATTGCTGTCATTCATTTCACTTTTGTATAAGAGTATATAATCGAATACATTGTTGCTATGATTTTGAACAAACTGTTATCTGTTAGATCAATTAATGATAAGGGAAAAGTTTTAATTTTAATTTTGCTAATTCTTTCGCTGATGCTCTTTCTTTCTTTATGTAGATCCATGATTTGAACTATATGATTTTCCTCTTCTATGAAGACCTTCAACATTTCTTGTAAGGTAGGTCTGCTTGGCACAAAACCCTCAATTTTTGTTGTCTGAAAATGGCTTTATGTCTCCTCTACTTTTGAAGGATAATTTCACTGGGTGCAGCATTCTAAGTTGCTTTTTTTCCCTCAACACTTACATATTTCATACCTTTCTCTTCTTGTTTGCATGATTTCTAAGAAATCAGTGGTAATTCTCTTTGGTCTTCTAGGTAAGAATTTTTTTTTCTCCTGAATTTCTTCAAGAATTTTTATCTTTGGTTTTCTGCAGTTCGAATAGGATATGCCTCTGTGTGTGTGTGTGTGTGAGAGAGAGAGAGAGAGAGAGAGAGGGATTTGGCAATTTGGCATTTATCCTGCTTGGTTTTCTCTGAGCTTCCTGAATACATGGTTTGTTGTCTGACATTAATGTTAGAAAATTCTCAGTCATTATTGTTTCCCATATTCCTATTGTTTCTTTTTGTTTTCTTCTTCTGATATTCCCACTATATGCATTTACACATTCTATGGTGGTCCCACAGTTCTTTGGCTTTTTGTTTTGTTTTGTTTTTTTCTCAGTTTTCTTTTTCTTTGTTTTTCCATTTTAGAAGTTTCCATTAATATATCTTCAAGCTCAGAGATTTTTTTTCCTCAGCCATGTAAAGTTTACTAATTAGCACAAAAAAGGCATTTTTCATGTCTGCTACAGATTTTTTCTTCTGTAGCATTTCTTTTCAATCCTTTCTTAGAATTTCCATCTCTCTGATTACATTGACCATCTGTTCTTACATTCTGTCTACTTTATCCATTAGAATCCTTTTCATGTTAACCATACCTGTTTTAAATTCCAGGTCTACTCCCAATATTCCTGCCACATCTGAGTCTGGTTTTTATACTTGCTCTATGTTTTAAAACTGTGCTTTCTCCTTTTAGTATCCCTTGCCATTTTTTCTTGATAACCAG'..b'CCTTTCCCTTACCTGGACATCACTGTCTCCTCTAACAGCTGAGGTGTCACTGGGAAGTGAAATTGATTACAACTTTTTAAAAATTCCACAGCTGTCGTTTTTACCTCAGCTGCTTCCCATAATTCCACAGATGGTAAACATATGTTTATAGGCACATTGAAAAAGAAGCTATATTGGATGCCTCCCATCTTTAATTCTTATTTTTCCTTTCATGCAGAAAGTCAAAGTCATAGAACTGGGGAATCTTACACATTTGAAGATTAATATTTCTGTGCATTAAGACTTTGGAAACAGCAGGACAGCTAATGATATGCTAATGAGCTGACAGTTTTTATTGATCATAATGAAAGTCGACAAGTGTCTTTCTTGGCGGTTTTGCATGCTGGAATATTTTATTAACGTCTTCAGGGCAGAAGTACATGATTGGTTGCATTTTGAAAACCCTCCCTGTGAGTTTACAGGTCCTACTTTTTGTTAGCCTGTTTCCAAAGCTTGAGTCCCTGCCAGTTTATAAACAGAACACATCTTCATCCATATATTTACATGCCCAGCAGGAAACTCTCCCACCCCTTTTTCCTCTCTCTTTCAAAGCAATTTGTTTCAGTATTTTAGCATACAAAAAAATAGAACCATTTTCTTCAATGTAAACAGAGATCTGCAGGGAAATAAGAGCGTTAAAAAAGAATTAGCATTTGTTTGGTGGTGAAGCTGCTTTTGTTTGTATCAGAAAGCTCTGCATGTTTAGAAGAGCTTGCTTAATCTTAGTTATTCCATACACAAGAGGGACCTAATTGGATAATTTTCTAATTTTTTAATTGCATCTTTCTATATTTCTTAATGCAAAATGAGAAACGTTCTAGGAATAATAGAAATAATGGGCATTAGTTCCCTAAACATTAAAAATCCATAATATACAATGTACCTGGTGCAAATTTATTTTTCAGTGCATGGTGAGCTGACAGCAGGAGGTACAGGGTGGCAACAGGTGGATTAAACAAAAGGAAAAAAAATCCATTTTTCTGCCGTCCATCCGTACTAAATAGTAAGCTTATTAATTTTGGGCTCTGCACCTTAGGGATTTATTTAGGGCCTCAGATCAGCTGAGGTTCATCATTACACTAACAATAAGAAAATGGATTGTTTAGCAAATTAATAGTGTAAATAAGATTACGGGGGGCGGGGGGATGGGGGGAAGAATATTAGGCTACCTAAAAAGACTTCTGTTTTCTAGCACTGAAAAACTGTCTTAGCAAATTATTATTATCTAATACAAATAGTTTTGCATGTTTGATTGGTATCTATCTATTAAGGCAATCAAGATAAAATCTCATTTTGATAACAAGACCTCTTTGTAGCAACAAGTTGTTGGTTCATGTTAAGGGGATCCCTTAAATTATATATTTTTACCTACAGCATATTGTAGTGACCCAGCACTGGTTTTGGAGTGTTAATCGAAAAGTGTCTGGATCTGTCTCTAGCTAATGATAAACAAGTCTCAATCAATTTAGAAAAGTTTATTTTGCCAAGGTTAAGGATGCACCCATGACACAACTTCAGGAGGTCCTGAGGACATGTGCCCAAGGTGGTCCTCATGTATACCTTGCTTTATACATCTTAGGGAGACATAATACCTCCATCAGTACATGTAAGATTTACATTGGTTTGATCTGGAAGGGTAGGACAACCAGAAGGGTGGCAGCTTCCAGGTCATAGGTAGATTTAAAATTTTTCTGATCGGCTATTGGTTGAAAGCGTTATCAGTAGTAAAGAATGTCTGGGTTCTGATAAGGGGTTGTGGAGAAGAAGCTTTTATCATGCAGATGAAGCCTCTAAATAGCAGGCTTCAGGGAGAATATATTGTAAATGTGTATCATTAGACTTAAGGTCTGTGTTGATGTAAATGCTGGAGAGGTTTAATGAAGCATGTTCAACTCCTTTTCCATCATGGTCTGAACTAGATTTCCGGGTTAACTCTGGAATGCCCTTGGCGGAGAGAAGGGGGTTCATTCAGATGGTTGGGGGCTTAGAACTTTATTTTTGGTTTTCAAGAGTTAGTAGCCCTGTAGTATATAGCCTAGGATTAAGGTATCCTTTAGAAAAGCTACTTAGAGTATCAAAGCCTTAAATTTCTCATAGGTCATATGACCAGGTAATCTGGTCCTAGATAAGTAGTTCTTATGGAAAGTATCAAAATGACCTCAGACAGTTTTCAAAATAGTCATGACTGTTCTTTCAACCTCTTCCAAAATTCTGATATATACCCTAAATTAAAAACTATTGCCCCACATGATCTTCACAGATCCTAACTGTGCTCAAAATTATGTGGTTCAGTATTGTATAATTCATAGTTTTCAATAATTTGATGCTTTAGAATATTTATTGTGTTTACTATGTGAAATCTACTACAATAGGAACTTCAGGGGATACTAAGATGAAAATCTATTATCTTTGGTGTTTATAATACAGTCTAGTAATTCTGTTGGGTTTTATTCAGTTCCAAATCAGTAAGATTTTACTCTATTTATATATGAGTTGGATGCAATAATTTTAACCATTGTGAACTTTTAATGAGTAAATGCTCTTGCTCCAAAAGAAGCAAATGGTTGACAATAAAGCAGAATTTTTCAAAGTGAGGTCCTTTTACCATTCATCAGAATCATCTGGAAGAGGTTTTGTTTAAAAAATGAATATTCCTGGGCCCACTCCAATCCTACTGAAACAGGATCCTTTGGGTTGACACAAGAATCTGAATGTTAAGCAGACACTCAAGGTGATTCTCAGGAACTTGAAGTTTGAGAAACACTGCCAAAATGAATAATATGAAATAAAGCATATGTCTGAAAAAAGGAGATCAAATGAGGTCAGCTAATACAGGCCCAGATAGAGTTGCATTTTTCAGTTAAATGTAGATACATTTAGAGTTAAATGAGGAGAAATAATAAAAATTTTGTCTTTTTATCCCTTATCTCCCTTGGGAGAAGTTGTAGTGCTGAAAGGCACATTTTCATCTGTGGAAATCCTCATAGATGATATATATATATATATATATATATATATATATATATATATATATTTTTTTTTTTTTTTTTTGAGAGGAATAAGGCTGATTGAGCTCCTTTGTAGTTTTATGCATTATAAAATCCCTTTTGTAGTTTTATGAAGGAAACTACATGCTTAGCAAATGCTTCTTTTATCAGCAAATGTCCTGGCAGTAAATTGTCCATATAGCAATTTAATGCCAGACCTTCTGATTCTTATTCTGGGGAAGGTGCTGGGATATACATAAATGTGTGTAGTCACATGCATACACACACATGCACTCAGACATCTTTAGATTATAAGTGGTATCTGTAGGGTATCACCACTTTTCTTTTAATCCAGCATTGACTTACAACCATTCAAATAAATTAACATTCCCATCTTGATTCATTTGGTAAGAACACATTTTCATGCCAGTATGTGGGCTCACCTCTATGACCTTTCCTTATAAAAAATACCAAGTGCTTTGGGTTTTTGTGTTAATGAGCATTGGGAAGCTGTCAGCTTTTATTTCTGTTTTTTGTTCAAGTCAACATCATTGACCTTCACCTAATGATCTATGTAACATACACACGCAGGTACCACAGATTAAAAGTGGAAAGACAGGGAAGTAAGGAGAGATGCACATAGAGGAAAGGTGTGAGAGCAGGTGATTTGTAAATCATAATGTCACTAAAATGAGTAAGATCACTTGAAAAGGAAAGGAAAACTGCTGTGTGCTGTATTTTCTTGCTTTAGGATTAGCGGGATGGGGTATTATTTTAAAATGAGTTTTCAGTTTGGTTTTG\tLN:i:25000\trd:i:0\n+A\tptg000003l\t0\t-\tm64012_190920_173625/16714108/ccs\t0\t12049\tid:i:17\tHG:A:a\n+A\tptg000003l\t8768\t+\tm64011_190901_095311/27789106/ccs\t0\t16232\tid:i:60\tHG:A:a\n' |
| b |
| diff -r 2061fb3b81b4 -r cd7936c5a9a5 test-data/hifiasm-out11-raw.gfa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hifiasm-out11-raw.gfa Thu Feb 23 22:34:21 2023 +0000 |
| b |
| b'@@ -0,0 +1,10 @@\n+S\tutg000001l\tGAAGTTTTGTCTGAGAGGAGTACCAGGCCGTGTGAGGTGTCAGTCTGCCCCTACTTGGGGGTGCCTCCCAGTTAGGCTACTCGGGTGTCAGAGACCCACTTGAGGAGGCAGTCTGTCCATTCTCAGATGTCCAGCTGCGTGCTGGGAGAACCACTACTCTCTTCAAGGCTGTCAGACAGGGACATTTAAGTCTGCAGAGGATTCTGCTGACTTTTCTTTGGCTGTGCCTTGCCCCTAGAGGTGGAGTCTACAGAGGCAGGCAGGCCTCCTTGAGCTGCGGTGGGCTCCACCCAGTTCGAGCTTCCCAGCTGCTTTGTTTATCTACTCAAGCCTTGGCAATGGCAGGCGCCCCCTCCCCCGGCCTCACTGCTGCCTTGCAGTTTGATCTCAGACTGCTGTGCTAGCAATGAGTGAGACTCCATGGGCGTAGGGCCCTCCGAGCCAGGGGTGGGATATAATCTCCTGGTGTGCCATTTGCTAAGACTGTTGGAAAAGTGCAGTATTAGGGTGGGAGTGACCTGATTTTCCAGGTGCTGTCTGTCACCCCTTTCTTTGACTAGGAAAGGGAATTCCCTGACCCCTTGCGCTTCCTGGGTGAGGCGATGCCTTGCCCTGCTTCGGCTCATGCTCGGTGCACTGCACCCACTGTCCTGCACCCACTTTCCGACACTCCCCAGTGAGATGAACCCAGTACCTCAGTTGGAAATGCAGAAATCACCCATCTTCTGCATCGCTCATGCTGGGAACTGTGGACTGGAGCTGTTCCTATTCAGCCATCTTGGCTCCACACTGTCAAATGCTTTTTCTGCATCTATTGTTATGATCATGTGATTTTTCTTCTTTAGCCTTTTGATGTGCTGAACACATCAATTCAAATGATTTTCAAATGTTGAACCAGTCTTGCCTTACCTGGGATAATATACACCGCCTGGTTATGGTGTATTTTTTTAAATAACTGTCGGAGTCAATTCACTAATATTTTGTTGAGAATTTTTGCATCTATGTTCATGAGAAATACCGGGCTATAGTTTTCTTTTCTTGTGATGTTTTTGTCTGGTTTTAGTATTAGAGTAATGTTGGCCTCACAAAGAATTTGGAAGTATTCCCAATGCTTCTGTATTCTGGAAGAGATTGTGGAGAATTTGTATAATTTCTTTCATAAATGTTTGGTAGAATTCACCAGTGAACCCATCTGGGCCTGGTGCTTCTGTTTGAAACTGTTATTAATTATTGGTTCAATTTCTGTAATAGATATAGGCCTATTCAGATAATCTATGTCTTCTTCTGTGAGAATTATCTTTCAAGAAATTGGTTCATTTTACATAGGTTATCAAATTTTGGGCATAGAGAGTTGTTCATAATATTGCTGTATAACCTTTTAATGTCCATGAGACTACAGTGATATCCTCTTTTTCATTACTGATATTAGTGATTTGTCTTCCTTCTTTTTTGTCTTAGCCTGACTGGAGGTTCATCAATTTTGTTGATCTTTTCAAAGAACTAGGTTTTATTTTTGTTAATTTTCTCTATTGATTTCCTGTTTTCAGTTTCATTGATTTTGGCACTAATTTTTATTATATGTTTTCTCCTGCTTATTTTGGATCTAATTTTTTTCTAGTTTCCTAAGGTGGAAGCTTGGATCATTACTCTCCAATCTTTCTTTTGTTCTAATATGTGCATTCAATGCTAAGCACAGCCTTCCCTGCAAATTTTGAAAAATTTTATCTTATTTTTATTTAGTTTAAAATATTTTTAATTTCTTTTGAGATTTCTGTTTTGACCCATAGGTTACTTAAAAGTGTGCTGTTTAATCCCCAATAATTTTGGAGTTCTCCAGCTGTTATTGATTTCCATTTTAATTCTATTGTGGCATGAATGCAGATATTGTATGATAATTTCTGTTCTTTTAAATGTGCTAAGGTCTGCTTTATGACCCAGAACATGGTTTATTTTGATGAATGTTCCATGTGAGCTTGAGAAGAATGTGTGTTGTGCTGTCACTGAATGATGTAGTTCATAGATGTCAATTATATCCAGTTGATTAATGTGGTATTATTGCTATGTCCTTAAGAATTTTCTGCCAGCAGACTCTGTTTATTTCAGAAAGAGGAGTGTCTAATTGTCAAACTATATTAGTGAATTCATCTGTTTCTCTTTCTAGTTTGGTCAGTTTTTACTCATGTATTTTGAGGTTCTCATGTTAGGCACATACACAAAAAGATTGTGTATATCTTTTTGGAGAATTAACCCTTTTAAAATTATGTAATGCCCATTTATCCCTGATAATTTTTCTTGCTTTGAAGTCTGTTGTGTCAGAAATTAATATAGCTATTCTGATTTCATTTTAGTATTAGCATGATATATATTTCTTCTTCCATTTGCTTTTAATCTGTATATTTTTTAATAAAGTGAGTATTTTGTAGACAGCACGTAGTTGGGTCTTGTCTTTTGATCCACTCTGATATTCTGTATCTTTTAATTGGTATATTTAGACCACTGATTGTTGACACAAGTGACACTACTATATTTATTACTGCTTTCTTTTCACTACCTGTGTCCTTGCTTCTATTTTAGTCTTCCAATCTTTGTCTTCTTTTTGAGGTTTTCATTAATCATTTTATGATATTCTATTTTTCTTTTTTCTTAGCATAGCAATATACTTTTTTTTAAACAAAAAGCGATTGCCACAGAGTTTTCAATATACATTTATAATTAATCCCAGCATACCCTTAGATAATACTATACTACTTCATAGAGAGTACAAGAACCTTATGATAACAAAAGAAGCCTAATTCTCTCTCCCATCACTGTATCATTGCTGTCATTCATTTCACTTTTGTATAAGAGTATATAATCGAATACATTGTTGCTATGATTTTGAACAAACTGTTATCTGTTAGATCAATTAATGATAAGGGAAAAGTTTTAATTTTAATTTTGCTAATTCTTTCGCTGATGCTCTTTCTTTCTTTATGTAGATCCATGATTTGAACTATATGATTTTCCTCTTCTATGAAGACCTTCAACATTTCTTGTAAGGTAGGTCTGCTTGGCACAAAACCCTCAATTTTTGTTGTCTGAAAATGGCTTTATGTCTCCTCTACTTTTGAAGGATAATTTCACTGGGTGCAGCATTCTAAGTTGCTTTTTTTCCCTCAACACTTACATATTTCATACCTTTCTCTTCTTGTTTGCATGATTTCTAAGAAATCAGTGGTAATTCTCTTTGGTCTTCTAGGTAAGAATTTTTTTTTCTCCTGAATTTCTTCAAGAATTTTTATCTTTGGTTTTCTGCAGTTCGAATAGGATATGCCTCTGTGTGTGTGTGTGTGTGAGAGAGAGAGAGAGAGAGAGAGAGGGATTTGGCAATTTGGCATTTATCCTGCTTGGTTTTCTCTGAGCTTCCTGAATACATGGTTTGTTGTCTGACATTAATGTTAGAAAATTCTCAGTCATTATTGTTTCCCATATTCCTATTGTTTCTTTTTGTTTTCTTCTTCTGATATTCCCACTATATGCATTTACACATTCTATGGTGGTCCCACAGTTCTTTGGCTTTTTGTTTTGTTTTGTTTTTTTCTCAGTTTTCTTTTTCTTTGTTTTTCCATTTTAGAAGTTTCCATTAATATATCTTCAAGCTCAGAGATTTTTTTTCCTCAGCCATGTAAAGTTTACTAATTAGCACAAAAAAGGCATTTTTCATGTCTGCTACAGATTTTTTCTTCTGTAGCATTTCTTTTCAATCCTTTCTTAGAATTTCCATCTCTCTGATTACATTGACCATCTGTTCTTACATTCTGTCTACTTTATCCATTAGAATCCTTTTCATGTTAACCATACCTGTTTTAAATTCCAGGTCTACTCCCAATATTCCTGCCACATCTGAGTCTGGTTTTTATACTTGCTCTATGTTTTAAAACTGTGCTTTCTCCTTTTAGTATCCCTTGCCATTTTTTCTTGATAACCAG'..b'CCTTTCCCTTACCTGGACATCACTGTCTCCTCTAACAGCTGAGGTGTCACTGGGAAGTGAAATTGATTACAACTTTTTAAAAATTCCACAGCTGTCGTTTTTACCTCAGCTGCTTCCCATAATTCCACAGATGGTAAACATATGTTTATAGGCACATTGAAAAAGAAGCTATATTGGATGCCTCCCATCTTTAATTCTTATTTTTCCTTTCATGCAGAAAGTCAAAGTCATAGAACTGGGGAATCTTACACATTTGAAGATTAATATTTCTGTGCATTAAGACTTTGGAAACAGCAGGACAGCTAATGATATGCTAATGAGCTGACAGTTTTTATTGATCATAATGAAAGTCGACAAGTGTCTTTCTTGGCGGTTTTGCATGCTGGAATATTTTATTAACGTCTTCAGGGCAGAAGTACATGATTGGTTGCATTTTGAAAACCCTCCCTGTGAGTTTACAGGTCCTACTTTTTGTTAGCCTGTTTCCAAAGCTTGAGTCCCTGCCAGTTTATAAACAGAACACATCTTCATCCATATATTTACATGCCCAGCAGGAAACTCTCCCACCCCTTTTTCCTCTCTCTTTCAAAGCAATTTGTTTCAGTATTTTAGCATACAAAAAAATAGAACCATTTTCTTCAATGTAAACAGAGATCTGCAGGGAAATAAGAGCGTTAAAAAAGAATTAGCATTTGTTTGGTGGTGAAGCTGCTTTTGTTTGTATCAGAAAGCTCTGCATGTTTAGAAGAGCTTGCTTAATCTTAGTTATTCCATACACAAGAGGGACCTAATTGGATAATTTTCTAATTTTTTAATTGCATCTTTCTATATTTCTTAATGCAAAATGAGAAACGTTCTAGGAATAATAGAAATAATGGGCATTAGTTCCCTAAACATTAAAAATCCATAATATACAATGTACCTGGTGCAAATTTATTTTTCAGTGCATGGTGAGCTGACAGCAGGAGGTACAGGGTGGCAACAGGTGGATTAAACAAAAGGAAAAAAAATCCATTTTTCTGCCGTCCATCCGTACTAAATAGTAAGCTTATTAATTTTGGGCTCTGCACCTTAGGGATTTATTTAGGGCCTCAGATCAGCTGAGGTTCATCATTACACTAACAATAAGAAAATGGATTGTTTAGCAAATTAATAGTGTAAATAAGATTACGGGGGGCGGGGGGATGGGGGGAAGAATATTAGGCTACCTAAAAAGACTTCTGTTTTCTAGCACTGAAAAACTGTCTTAGCAAATTATTATTATCTAATACAAATAGTTTTGCATGTTTGATTGGTATCTATCTATTAAGGCAATCAAGATAAAATCTCATTTTGATAACAAGACCTCTTTGTAGCAACAAGTTGTTGGTTCATGTTAAGGGGATCCCTTAAATTATATATTTTTACCTACAGCATATTGTAGTGACCCAGCACTGGTTTTGGAGTGTTAATCGAAAAGTGTCTGGATCTGTCTCTAGCTAATGATAAACAAGTCTCAATCAATTTAGAAAAGTTTATTTTGCCAAGGTTAAGGATGCACCCATGACACAACTTCAGGAGGTCCTGAGGACATGTGCCCAAGGTGGTCCTCATGTATACCTTGCTTTATACATCTTAGGGAGACATAATACCTCCATCAGTACATGTAAGATTTACATTGGTTTGATCTGGAAGGGTAGGACAACCAGAAGGGTGGCAGCTTCCAGGTCATAGGTAGATTTAAAATTTTTCTGATCGGCTATTGGTTGAAAGCGTTATCAGTAGTAAAGAATGTCTGGGTTCTGATAAGGGGTTGTGGAGAAGAAGCTTTTATCATGCAGATGAAGCCTCTAAATAGCAGGCTTCAGGGAGAATATATTGTAAATGTGTATCATTAGACTTAAGGTCTGTGTTGATGTAAATGCTGGAGAGGTTTAATGAAGCATGTTCAACTCCTTTTCCATCATGGTCTGAACTAGATTTCCGGGTTAACTCTGGAATGCCCTTGGCGGAGAGAAGGGGGTTCATTCAGATGGTTGGGGGCTTAGAACTTTATTTTTGGTTTTCAAGAGTTAGTAGCCCTGTAGTATATAGCCTAGGATTAAGGTATCCTTTAGAAAAGCTACTTAGAGTATCAAAGCCTTAAATTTCTCATAGGTCATATGACCAGGTAATCTGGTCCTAGATAAGTAGTTCTTATGGAAAGTATCAAAATGACCTCAGACAGTTTTCAAAATAGTCATGACTGTTCTTTCAACCTCTTCCAAAATTCTGATATATACCCTAAATTAAAAACTATTGCCCCACATGATCTTCACAGATCCTAACTGTGCTCAAAATTATGTGGTTCAGTATTGTATAATTCATAGTTTTCAATAATTTGATGCTTTAGAATATTTATTGTGTTTACTATGTGAAATCTACTACAATAGGAACTTCAGGGGATACTAAGATGAAAATCTATTATCTTTGGTGTTTATAATACAGTCTAGTAATTCTGTTGGGTTTTATTCAGTTCCAAATCAGTAAGATTTTACTCTATTTATATATGAGTTGGATGCAATAATTTTAACCATTGTGAACTTTTAATGAGTAAATGCTCTTGCTCCAAAAGAAGCAAATGGTTGACAATAAAGCAGAATTTTTCAAAGTGAGGTCCTTTTACCATTCATCAGAATCATCTGGAAGAGGTTTTGTTTAAAAAATGAATATTCCTGGGCCCACTCCAATCCTACTGAAACAGGATCCTTTGGGTTGACACAAGAATCTGAATGTTAAGCAGACACTCAAGGTGATTCTCAGGAACTTGAAGTTTGAGAAACACTGCCAAAATGAATAATATGAAATAAAGCATATGTCTGAAAAAAGGAGATCAAATGAGGTCAGCTAATACAGGCCCAGATAGAGTTGCATTTTTCAGTTAAATGTAGATACATTTAGAGTTAAATGAGGAGAAATAATAAAAATTTTGTCTTTTTATCCCTTATCTCCCTTGGGAGAAGTTGTAGTGCTGAAAGGCACATTTTCATCTGTGGAAATCCTCATAGATGATATATATATATATATATATATATATATATATATATATATATATTTTTTTTTTTTTTTTTTGAGAGGAATAAGGCTGATTGAGCTCCTTTGTAGTTTTATGCATTATAAAATCCCTTTTGTAGTTTTATGAAGGAAACTACATGCTTAGCAAATGCTTCTTTTATCAGCAAATGTCCTGGCAGTAAATTGTCCATATAGCAATTTAATGCCAGACCTTCTGATTCTTATTCTGGGGAAGGTGCTGGGATATACATAAATGTGTGTAGTCACATGCATACACACACATGCACTCAGACATCTTTAGATTATAAGTGGTATCTGTAGGGTATCACCACTTTTCTTTTAATCCAGCATTGACTTACAACCATTCAAATAAATTAACATTCCCATCTTGATTCATTTGGTAAGAACACATTTTCATGCCAGTATGTGGGCTCACCTCTATGACCTTTCCTTATAAAAAATACCAAGTGCTTTGGGTTTTTGTGTTAATGAGCATTGGGAAGCTGTCAGCTTTTATTTCTGTTTTTTGTTCAAGTCAACATCATTGACCTTCACCTAATGATCTATGTAACATACACACGCAGGTACCACAGATTAAAAGTGGAAAGACAGGGAAGTAAGGAGAGATGCACATAGAGGAAAGGTGTGAGAGCAGGTGATTTGTAAATCATAATGTCACTAAAATGAGTAAGATCACTTGAAAAGGAAAGGAAAACTGCTGTGTGCTGTATTTTCTTGCTTTAGGATTAGCGGGATGGGGTATTATTTTAAAATGAGTTTTCAGTTTGGTTTTG\tLN:i:25000\trd:i:0\n+A\tutg000003l\t0\t-\tm64012_190920_173625/16714108/ccs\t0\t12049\tid:i:17\tHG:A:a\n+A\tutg000003l\t8768\t+\tm64011_190901_095311/27789106/ccs\t0\t16232\tid:i:60\tHG:A:a\n' |
| b |
| diff -r 2061fb3b81b4 -r cd7936c5a9a5 test-data/nanopore.first5.fasta.gz |
| b |
| Binary file test-data/nanopore.first5.fasta.gz has changed |
| b |
| diff -r 2061fb3b81b4 -r cd7936c5a9a5 test-data/nanopore.first50.fasta.gz |
| b |
| Binary file test-data/nanopore.first50.fasta.gz has changed |