| Next changeset 1:9bd94d9a1b2e (2021-05-17) |
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Commit message:
"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 1d3a1a449c7398c8fad07663224738265f77c0be" |
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added:
bionano_scaffold_edited.xml macros.xml test-data/assembly.fasta test-data/assembly.fasta.gz test-data/colormap_assembly.cmap test-data/configuration.xml test-data/test_01.agp test-data/test_01.gap test-data/test_01_report.txt test-data/test_02.agp test-data/test_02.gap test-data/test_02_report.txt test-data/test_03.agp test-data/test_03.gap test-data/test_03_report.txt test-data/test_04.agp test-data/test_04.gap test-data/test_04_report.txt |
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| diff -r 000000000000 -r fec6a0b53189 bionano_scaffold_edited.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bionano_scaffold_edited.xml Mon May 17 15:07:05 2021 +0000 |
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| b'@@ -0,0 +1,617 @@\n+<tool id="bionano_scaffold" name="Bionano Hybrid Scaffold" version="@TOOL_VERSION@+@GALAXY_TOOL_VERSION@" profile="20.01">\n+ <description>automates the scaffolding process</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="edam_ontology"/>\n+ <expand macro="requirements"/>\n+ <version_command>perl /HybridScaffold/hybridScaffold.pl --version</version_command>\n+ <command detect_errors="exit_code"><![CDATA[\n+ #set RefAligner = \'/usr/local/bin/RefAligner\'\n+ ## softlinks do not work\n+ cp \'${ngs_fasta}\' ./ngs.fasta\n+ && cp \'${bionano_cmap}\' ./bionano.cmap\n+ #if $configuration_options.configuration == \'vgp\'\n+ && cp \'${vgp_mode}\' ./config.xml\n+ #else\n+ #import os\n+ #set cores = os.environ.get(\'GALAXY_SLOTS\', 2)\n+ #set memory = os.environ.get(\'GALAXY_MEMORY_MB\', 4000) / 1000\n+ && cp \'${configuration_file}\' ./config.xml\n+ && sed -i \'s|attr="maxmem" val0=.* display|attr="maxmem" val0="$memory" display|\' ./config.xml\n+ && sed -i \'s|attr="maxthreads" val0=.* display|attr="maxthreads" val0="$cores" display|\' ./config.xml\n+ && sed -i \'s|attr="maxvirtmem" val0=.*/>|attr="maxvirtmem" val0="$cores"/>|\' ./config.xml\n+ && sed -i \'s|attr="insertThreads" val0=.*/>|attr="insertThreads" val0="$cores"/>|\' ./config.xml\n+ #end if\n+ ## output the configuration file on stdout\n+ && cat ./config.xml\n+ && perl \'/HybridScaffold/hybridScaffold.pl\'\n+ -n ./ngs.fasta\n+ -b ./bionano.cmap\n+ -c ./config.xml\n+ -r $RefAligner\n+ #if $conflict_resolution\n+ -M \'${conflict_resolution}\'\n+ #end if\n+ #if not $conflict_resolution\n+ -B $conflict_filter_genome\n+ -N $conflict_filter_sequence\n+ #end if\n+ ##$align_molecules_options.align_molecules\n+ ###if $align_molecules_options.align_molecules\n+ ## -m $align_molecules_options.bionano_molecules\n+ ## -q \'${align_molecules_options.optarguments_xml}\'\n+ ## -p ##/home/bionano/tools/pipeline/1.0/Pipeline/1.0/ \n+ ###end if\n+ ##$quimeric_quality_options.quimeric_quality\n+ ###if $quimeric_quality_options.quimeric_quality\n+ ## -m $align_molecules_options.bionano_molecules\n+ ## #if $quimeric_quality_conditional.noise_parameter\n+ ## -e \'${quimeric_quality_conditional.noise_parameter}\'\n+ ## #end if\n+ ###end if\n+ -f\n+ $zip_file\n+ -o ./\n+ ##;\n+ ##sleep 1000000\n+\n+ ]]> </command>\n+ <configfiles>\n+ <configfile name="vgp_mode"><![CDATA[\n+ #if $configuration_options.configuration == \'vgp\'\n+ #import os\n+ #set cores = os.environ.get(\'GALAXY_SLOTS\', 2)\n+ #set memory = os.environ.get(\'GALAXY_MEMORY_MB\', 4000) / 1000\n+ <hybridScaffold>\n+ <version>\n+ <flag attr="version" val0="\\$Id: hybridScaffold_DLE1_config.xml 7702 2018-06-25 20:53:51Z apang \\$"/>\n+ </version>\n+ <global>\n+ <flag attr="maxmem" val0="$memory" display="Maximum memory (GB)" group="Global options" description="Define the maximum amount of RAM in gigabytes to be used by each process."/>\n+ <flag attr="maxthreads" val0="$cores" display="Max threads" group="Global options" description="Define maximum number of threads to be used by each process."/>\n+ <flag attr="maxvirtmem" val0="$memory"/>\n+ <flag attr="RAmem" val0="3" val1="1"/>\n+ </global>\n+ <fasta2cmap>\n+ <flag attr="enzyme" val0="$configuration_options.enzyme" display="Enzyme" group="FASTA to CMAP digestion" description="Define single enzyme for '..b' </assert_stdout>\n+ <assert_stdout>\n+ <has_text text="hybridScaffold"/>\n+ </assert_stdout>\n+ </test>\n+ <test expect_num_outputs="5">\n+ <param name="ngs_fasta" value="assembly.fasta.gz"/>\n+ <param name="bionano_cmap" value="colormap_assembly.cmap"/>\n+ <param name="conflict_filter_genome" value="2"/>\n+ <param name="conflict_filter_sequence" value="3"/>\n+ <conditional name="configuration_options">\n+ <param name="configuration" value="vgp"/>\n+ <param name="enzyme" value="BspQI"/>\n+ </conditional>\n+ <param name="zip_file" value="true"/>\n+ <output name="ngs_contigs_scaffold_fasta" ftype="fasta">\n+ <assert_contents>\n+ <has_size value="4753369" delta="100" />\n+ <has_n_lines n="2"/>\n+ <has_line line=">Super-Scaffold_1"/>\n+ </assert_contents>\n+ </output>\n+ <output name="ngs_contigs_scaffold_agp" file="test_04.agp" ftype="txt"/>\n+ <output name="ngs_contigs_scaffold_gap" file="test_04.gap" ftype="txt"/>\n+ <output name="report" file="test_04_report.txt" ftype="txt"/>\n+ <output name="results" ftype="zip">\n+ <assert_contents>\n+ <has_archive_member path=".*/status.txt"/>\n+ </assert_contents>\n+ </output>\n+ <assert_stdout>\n+ <has_text text=\'attr="maxmem" val0="4.0"\'/>\n+ </assert_stdout>\n+ <assert_stdout>\n+ <has_text text=\'attr="maxthreads" val0="2"\'/>\n+ </assert_stdout>\n+ <assert_stdout>\n+ <has_text text=\'attr="insertThreads" val0="2"\'/>\n+ </assert_stdout>\n+ <assert_stdout>\n+ <has_text text=\'attr="maxvirtmem" val0="4.0"\'/>\n+ </assert_stdout>\n+ <assert_stdout>\n+ <has_text text="hybridScaffold"/>\n+ </assert_stdout>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+.. class:: infomark\n+\n+**Purpose**\n+\n+The Hybrid Scaffold pipeline automates the comprehensive scaffolding process and is consisted of five major steps: 1) generate in silico maps for sequence assembly; 2) align in silico sequence maps against Bionano genome maps to identify and resolve potential conflicts in either data set; 3) merge the non-conflicting maps into hybrid scaffolds; 4) align sequence maps to the hybrid scaffolds; and 5) generate AGP and FASTA files for the scaffolds. \n+\n+----\n+ \n+.. class:: infomark\n+ \n+**Coverage**\n+\n+For Hybrid Scaffold, we recommend using as input a minimum of 80X effective molecule coverage in order to build an accurate and contiguous consensus genome map assembly for each enzyme. When using nickases, using more coverage does not significantly improve map contiguity. When using a DLS enzyme such as DLE-1, effective coverage up to and beyond 100X has shown improved map contiguities for some plants and animals.\n+\n+----\n+ \n+.. class:: infomark\n+ \n+**Input Bionano assembly**\n+\n+When running the de novo assembly pipeline for hybrid scaffolding applications, users are recommended to use assembly parameters for non-haplotype-aware assembly. The current Hybrid Scaffold pipeline does not explicitly handle haplotype information and assumes there is only one genome map or NGS sequence contig covering a given genomic region. If multiple haplotypes are present, the pipeline may make false positive conflict cuts and incorrectly mix haplotypes in the final scaffolds. We understand that haplotype information is important in many applications, and a fully haplotype-aware Hybrid Scaffold pipeline is in our roadmap for a future release.\n+\n+\n+ ]]> </help>\n+ <expand macro="citations"/>\n+</tool>\n' |
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| diff -r 000000000000 -r fec6a0b53189 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon May 17 15:07:05 2021 +0000 |
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| @@ -0,0 +1,28 @@ +<macros> + <token name="@TOOL_VERSION@">3.6.1</token> + <token name="@GALAXY_TOOL_VERSION@">galaxy0</token> + <xml name="edam_ontology"> + <edam_topics> + <edam_topic>topic_0196</edam_topic> + </edam_topics> + <edam_operations> + <edam_operation>operation_0525</edam_operation> + </edam_operations> + </xml> + <xml name="requirements"> + <requirements> + <container type="docker">bionanodocker/bionano-docker-scaffold:latest</container> + </requirements> + </xml> + <macro name="sanitize_string" > + <sanitizer invalid_char=""> + <valid initial="string.letters,string.digits"> + </valid> + </sanitizer> + </macro> + <xml name="citations"> + <citations> + <citation type="doi">10.1186/s12864-015-1911-8</citation> + </citations> + </xml> +</macros> |
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| diff -r 000000000000 -r fec6a0b53189 test-data/assembly.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/assembly.fasta Mon May 17 15:07:05 2021 +0000 |
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| b'@@ -0,0 +1,79224 @@\n+>Super_scaffold_3\n+TTCATCGGTTAAATCATCGCCCAGAAATACGGGCGTTCGCCCGATAAAGGGAGCTTCCTG\n+CATAAAAGCTGCAATTGCCTCACCTTTACTGGTACCTCTCGGTTTGATCTCGACAACACA\n+CTTTCCCTGCTGTAACGCCATTTGTGGCCAGATCTGAGTAATACGTTGCGCTAATGTCAT\n+TAATGCGTCTTCATGCTGCGGAGCCTGACGATAATGCAGCGCAAAAGCCATCCCTTTCGC\n+CTCCAGCTCCGCGCCGGGATACTGAGCGATGACTGTATGCAGTTGCACGCTAATATCACG\n+CGCAATCGCATCCGGCAGATGAACGATATGTGTTTTACCATTGATGTCACGGCGCTCCGC\n+CCCATGCACGCCCGCTAACGGGAAGCGATAAGGTTTTGCCAGTGCGTCAAGCTCCACCAT\n+TGAGCGCCCTGATATCAATGCCAATGCACCATCACTTGCGGTTGCCAGTAGCTGTAGTCC\n+TTGCAGAATATTGTCAGGCACGACGACCTGATCGGGATGCGGTTTGATTTCCGCCAGCGT\n+TCCATCAAGATCAAAAAACCAGGCATATTTCGCGGATAGTTCAGGGGTTTCGGTTAACGG\n+TTCTGTCACCCGGTTCTCCTCCTTCTCTTTTCTTATTGTGTTGCGCAGAACGCGCTTTAC\n+AGACATGTAAGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACC\n+GTTATGGCGGTTGGCTATGGTGGGAAAAAACGCTAAATTGTTGCAGAAAAAAGCATCAGA\n+CAGTGCGTTTCGCTTTTTGCTTGTAACGGTCGAAGATCACCGCTGCCAGCAGGATTAAGC\n+CGCGAACCACGTACTGCGCGAAAGGAGAAATATTAAGCAGGTTCATGGCGTTTTCCACGG\n+TGCCTAAAATTAAGATACCCGCCACCACATATGAGATTTTTCCGATGCCACCTTTCAGAG\n+AAACGCCACCTAAAACGCAGGCGGAGATAACAATCAGCTCATAACCAATCGACGTCATTG\n+GCTGCCCACTGGTCATACGTGAAGCCAGAATAATTCCGGCTATCGCTGATACCAGGCCTG\n+AGAGAACAAAGATAATAATTTTGGTGCGAACAACCGGTACACCCGCCAGACGCGCGGCCT\n+CTTCGTTCCCGCCAATCGCCAGGGTGTTACGACCAAAGGTGGTTTTATTCAGCAGCAAAC\n+CAAAGATAATCAGACACGCGACGGTGAGCCAGATTGGCGCAGGCAGACCGAACCAGTTGG\n+CGTAACCAAGGGCAAAGAAGCTTTCATCTTCGATACCGACCGCTTTACCGTCTGAAATGA\n+TGTACGCCAGACCTCGAACAATCTGCATCGTTGCCAATGTCGTGATCAGAGCATTTATTT\n+TCAGTTTGGCGATAACAAAGCCATTGACCAGGCCACAGAGAACGCCCAGCAACAACCCCG\n+CTGCCACGCCAATCCACAGGCTTTCAGTCAGGTTAATAACCACCGCCGTGGTGACACCCG\n+CACAGGCAATTACGGAGGCGACAGAAAGGTCAAAGTCACCGGAAGCGAGGCAGAACAACA\n+TGCCACAAGCCACCATCCCCGACATGGAAATTGCCAGGCCCAACCCTTTCATATTAATGA\n+AGGTGGCAAAATTTGGGACAAAAATGGCACAGGCGATAAAGAGCACCGCAAACACCACCA\n+GCATGCCGTACTGATCCCAGATACGCCCGAAGCTGAATGACGACTTAGGTGCGCCAGACC\n+CCGATGTAGAAACAGAAGACATCATACTCTCCTTACTCAGGCAACAGCCTGGCTGACTTT\n+AGGCATCGCAAGGCTCAGTGCCTGACGCTCATCTGCCTGCTCGTGTAACAATTCACCGGC\n+GATTTCACCTTCCCGCATCACCACAATCCGGTCGGCAACGCCGAGGACTTCAGGTAAGTC\n+GCTGGAGGCAAACAGCACCGCCACGCCCTGCGCCGCCAGCGCATAAATTACGTTATATAT\n+TTCGTGCTTAGCGCCAACATCAATGCCGCGCGTAGGTTCATCCAGCAAAATGACCTTCAT\n+CTCTTCCGATAACCAGCGGCCCAGAATGGCTTTTTGCTGATTTCCGCCTGAGAGATTCAT\n+GATCAGTTGCTCCGCGCCCGGCGTTTTGATGTTGAGCGAACGAATGTGGTGATCGGCATT\n+GTTTTCTTCCCAACCGTTGTTGATTACACAACCGCCGAGCACATGTTTACGTCTGGCACT\n+GATGTTGATATTGTCGCGAACGGAGTGCACGGGAATAATGCCTTCCGCTTTGCGATCTTC\n+CGGGCAGAGCATCATGCCTGCGGCAATGGCGTGGCTCGGTTTACGAATATCGATCGGCTG\n+TTGGTCGATATAAACCTGACCGGCGGTGATTTGCGTCCCGCCAAACATGCCTTTCATTAA\n+TTCGCTACGCCCCGCCCCTACCAGACCAAACAGCCCAACAATTTCACCACTGCGAACCGC\n+CAGACTTATTGGCGTACGCACGCCTGGTGCTTTCACAGCATCAAGACGTAGGCGCTCCTC\n+GCCATAACTACGCGGTTGCCAGCCGTAGATATCGCCAATGTCGCGCCCGACCATCGCCTG\n+CACCAGCGCGTCGTGGTCAACCTGCTGCATATCGGTAAAGGTTTTGACATAACGTCCATC\n+TTTAAAGACAGTAATGGCATCGCTGAGGGCAAATATTTCTTCCATACGGTGAGAAACGTA\n+TAAGATTACCCGCCCCTCTTTTCGCAGTTCACGAATAACGCGGAAAAGATTGTCGATTTC\n+ACGGGCAGAGAGGGAGCTGGTTGGCTCATCAAAGGCGATAATTTTGGCGTTACGCGCCAG\n+CGCTTTGGCGATTTCAACCATCTGCCACTGACCAATGGAGAGATATTTCAGCGGCGTGTC\n+CGGGTCAATATCCATACCAAGATGTTTAAGTTGTAAACCCGCCTCATAATTCAGCAATGA\n+GCGATTCACAATGCCGCCTTTATGCGGCAGCTGGCCGAGATAGATGTTTTCCGCGACGGT\n+CATTTCCGGCACGAGATGCAGTTCCTGGTAAATAATCGCCACGCCCGCGTTAAGTGCTGC\n+GGTCGTGTCGGAAAAGGACATTTCCTGCCCATTAATCACTACAGAACCCGTGGTTGGCGC\n+ATAGTTGCCGCTGAGGATTTTTAAGAGAGTTGATTTTCCTGCGCCATTTTCACCCATCAA\n+CGCATGAACCTGACCGGCATAGCAGTCAAAACTAATATCCGTCAGCGCCTTAACGCCGGG\n+AAACGTTTTACCGATGCCGCGAAATGAGAGATACGGGGTAGACTGTTGCATAACGTCTCC\n+GTGAATCACTGGTCGTTCACACCCCCTCTGCATCATGCAGAGGGGAATTTTTCCGGCAAA\n+TTACTTACCGCCTAAACCTTTTTTCTCCAGTTCTTCTTTAAAGTTGTCACGCGTGATCAG\n+TACCACGTCGGTAACTTCGGTAAATTTTGGCGGTTCAACGTCTTTTGCTACCCAGTTGTA\n+AAGCATTTCGCTGGATTTATAGCCATGTACGTCCGGGCTTGGCAGCAGGGAACCGTAGAA\n+GCCGGTTGCCTGTGCTTTAGACAGTTCGCTCACCGCATCCACACCGTTAATGCCAATGCC\n+GATGATATCGGCCGCTTTAAAGCCCTGACCTTCCGTCGCGCGTACGCCGCCCAGCACGGT\n+GCTGTCGTTCATACCGACGATCAGCCAATGTTTAACTTCCGGATGTTGAACCAGCATTGA\n+GTTGGCAGCGTCAAATGCCCCCGGGATGTCGTTAGATTTGGTAGGTACCTGATAAATTTG\n+TTTTTCCGGGAATCCGGCCGCTTTCAGCGCATCCATAGATCCCGTAGTACGGC'..b'TGGTTTAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTA\n+AATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTC\n+AATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAGGAAGGTGCGAATAAGC\n+GGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTT\n+CTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGTTAT\n+CCCCAGTTTTTAGTGAGATCTCTCCCACTGACGTATCATTTGGTCCGCCCGAAACAGGTT\n+GGCCAGCGTGAATAACATCGCCAGTTGGTTATCGTTTTTCAGCAACCCCTTGTATCTGGC\n+TTTCACGAAGCCGAACTGTCGCTTGATGATGCGAAATGGGTGCTCCACCCTGGCCCGGAT\n+GCTGGCTTTCATGTATTCGATGTTGATGGCCGTTTTGTTCTTGCGTGGATGCTGTTTCAA\n+GGTTCTTACCTTGCCGGGGCGCTCGGCGATCAGCCAGTCCACATCCACCTCGGCCAGCTC\n+CTCGCGCTGTGGCGCCCCTTGGTAGCCGGCATCGGCTGAGACAAATTGCTCCTCTCCATG\n+CAGCAGATTACCCAGCTGATTGAGGTCATGCTCGTTGGCCGCGGTGGTGACCAGGCTGTG\n+GGTCAGGCCACTCTTGGCATCGACACCAATGTGGGCCTTCATGCCAAAGTGCCACTGATT\n+GCCTTTCTTGGTCTGATGCATCTCCGGATCGCGTTGCTGCTCTTTGTTCTTGGTCGAGCT\n+GGGTGCCTCAATGATGGTGGCATCGACCAAGGTGCCTTGAGTCATCATGACGCCTGCTTC\n+GGCCAGCCAGCGATTGATGGTCTTGAACAATTGGCGGGCCAGTTGATGCTGCTCCAGCAG\n+GTGGCGGAAATTCATGATGGTGGTGCGGTCCGGCAAGGCGCTATCCAGGGATAACCGGGC\n+AAACAGACGCATGGAGGCGATTTCGTACAGAGCATCTTCCATCGCGCCATCGCTCAGGTT\n+GTACCAATGCTGCATGCAGTGAATGCGTAGCATGGTTTCCAGCGGATAAGGTCGCCGGCC\n+ATTACCAGCCTTGGGGTAAAACGGCTCGATGACTTCCACCATGTTTTGCCATGGCAGAAT\n+CTGCTCCATGCGGGACAAGAAAATCTCTTTTCTGGTCTGACGGCGCTTACTGCTGAATTC\n+ACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAATCCTGTTCTATGGCTCCAGATGAC\n+AAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAACATAAATGTATAAGTCAT\n+ACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAA\n+AATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAAT\n+AATCATCTGCTATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAACAGAC\n+ACTTACCGCACAACAAACTAATTAAATACAAAGAAAGGCAACAATCAACTTAATGTTAAT\n+GAAATGTTTTACATATATTAACCACTTGTTTAATGCGGAGAATCAGTACACTATTTTCTT\n+ATAATTACATTTGAAATTATATGATCACCGGGAGTGATTGATTAATTATCTTTACTAATA\n+ATCAGACTAATATTTACCTGTTTGACCGAGTTGGGATTGCGTCGTTTCTCCATTAGGAGT\n+AAAGCTTTAATGTCACCTGAAGTTCACAGAATAAGGAACAGGTTATGAGCTATAGCAATA\n+TTCTTGTCGCTGTTGCGGTTACACCGGAAAGTCAGCAACTGCTGGCAAAAGCGGTATCTA\n+TCGCCAGGCCAGTAAAGGGACACATCAGTTTAATTACTCTCGCTTCCGACCCGGAAATGT\n+ACAATCAATTAGCTGCGCCGATGCTTGAAGATTTACGCAGCGTGATGCATGAAGAAACGC\n+AAAGCTTTCTTGATAAGTTAATTCAGGATGCGGGGTATCCCGTTGACAAGACGTTTATTG\n+CCTACGGTGAGTTAAGCGAACATATTCTGGAAGTATGTCACAAGCATCATTTCGATTTGG\n+TGATTTGCGGTAATCACAATCACAGTTTCTTTTCGCGAGCATCCTGCTCGGCGAAAAGAG\n+TTATTGCCTCAAGTGAGGTCGATGTGCTGTTAGTTCCACTTACGGGAGATTAACCGCTCC\n+TACGCAAGCTTTGGAAAGGTAGCAACTTTATCGCGCTGCTGGCTTTCCGCGCTTCGCGGA\n+ACTATCTGCTTTAGGTCGCTAATGAAGCACTCCTGCCAGTGGTTAATATCGTTTTTCACG\n+ATAACGTCCAGCATTTCTGCATGACGGGAAATACGTTCCGCCAGCGACATAGTCAATGCA\n+CGATCCAGCGCAGCTGCAACTTCGTCACGATCGTAGGGGTTAACAATTAACGCCGACGTT\n+AACTCGTTTGCCGCTCCCGCAAATTGCGAAAGAACAAGAACGCCCGGATTGGCTGGGTCC\n+TGAGCAGCAACATACTCTTTTGCTACCAGGTTCATCCCGTCACGCAGTGGCGTCACTAAG\n+CCCACGTCAGAGTAGCGGAATATTTTCATCAGTAATTTACGGTCAAAATGCTGATTCAAA\n+TAATAAAGCGGCGTCCAGCCTAATTGCCCGTATTTACCATTAATTCGTCCAGCTTCATTT\n+TCGAGCTGATGACGAATATCCTGATAGGCTTGCACATCACCACGCGACGTTGGTGCAATC\n+TGGGTATAACGAATTTTACCATGATGCTGCGGATATTTTTCCAGCAACGCTTCATAGGCG\n+AGAAAACGCTCTGGCAAACCTTTGGAATAATCCAGCCGTTCGACAGAAAAGATATTTTGT\n+ACGTTTTTCAGTTCCGCTTTAAGTTGCGCCAGTTTTGGCGGCAGTGGCCCGGCAGCCTGT\n+TTGGCTATTTCTTTCGGTTCAATGCCGATCGGGTAGACTTCTGTTCGAAATGCTTTGCCC\n+CAGGCTGTATGGCTTTTTGCGCTACGTGTCGTGACGCGGGTCAGGTTAGAAAGACAATCC\n+AGGAACGCCAGACGATCGTTTTCTGTCTGGAAACCCAGCAAATCATAATCACAAAGCTGT\n+TCAAGCAAGGTGTCATATGTCGGCAGCGCGTTGAAGATTTCCGGTGTCGGGAAAGGAATA\n+TGCAGAAAGAAACCAATGCGATTATTCACTCCCCGTTTGCGTAATTCATGCGCAAATGGC\n+AACAGGTGATAATCGTGGATCCAGATAATGTCATCGTCTTGCAACAGCGGCAGTAATTTA\n+TCTGCCAGCAACGCATTTACGCGTAGATAGCCGTCCCAGGCAGGACGCTGAAATTGCACC\n+AGATCGAGCCGATAATGAAAAGCGGGCCAGAGAACGGCATTGGAGAATTGGTTGTAGTAT\n+TCGTCAAGGTCCTGTTCGCTGAGGTTAAAAGAGGCCCACGTAATGTTACCTTTTTTCACC\n+TTTTTTAGCGGCTGATCCTCATTCCCTGTTTCACCACTCCAGCCAAACCACAGTCCGCCT\n+GCGGCTTTCAGTGCCCCCAGTATGCCAACGGCAAGGCCACCGGCACTGGCGGCGTGCTCG\n+TCTGGTGGTGCAATCCGGTTAGATACTACGACTAAACGACTCATAGTCATCACTCCTGTT\n+ATTTTCTCTTTTTTGTTGTAATGCGGTGGTTATCATTTCAAGCCAGCTCCAGACATCCGG\n+CACACCCGCCAGTCGCCATGATGCCTGAGTTGCACCTGTGCCAATTTTTACTGACATTCC\n+GCCCAGTCGGTTAACGACTGCGAAGCCAGA\n' 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| diff -r 000000000000 -r fec6a0b53189 test-data/assembly.fasta.gz |
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| Binary file test-data/assembly.fasta.gz has changed |
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| diff -r 000000000000 -r fec6a0b53189 test-data/colormap_assembly.cmap --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/colormap_assembly.cmap Mon May 17 15:07:05 2021 +0000 |
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| b'@@ -0,0 +1,544 @@\n+# hostname=phihost-mic5.local.net\n+# $ cd /home/bionano; /home/bionano/dev-tools/RefAligner.mic -i /home/bionano/sample_assembly_working_directory/strict_t_150/ref/NC_010473_mock_scaffolds_BspQI_res29.cmap -maxthreads 180 -i /home/bionano/sample_assembly_working_directory/strict_t_150/contigs/Esch_coli_1_2015_000_strict_t_150_refineFinal1_sv/Esch_coli_1_2015_000_strict_t_150_refineFinal1_contig1.cmap -o /home/bionano/sample_assembly_working_directory/strict_t_150/contigs/Esch_coli_1_2015_000_strict_t_150_refineFinal1_sv/Esch_coli_1_2015_000_strict_t_150_refineFinal1_contig1 -f -stdout -stderr -output-veto-filter .align$ -sv 3 -FP 0.6 -FN 0.06 -sf 0.20 -sd 0.10 -mres 1e-3 -T 1e-10 -A 8 -biaswt 0 -f -maxmem 4 -FP 0.015432 -readparameters /home/bionano/sample_assembly_working_directory/strict_t_150/contigs/Esch_coli_1_2015_000_strict_t_150_refineFinal1/alignref/ESCH_COLI_1_2015_000_STRICT_T_150_REFINEFINAL1.errbin -sr 0.009624 -bpp 496.62 -sf 0.167667 -FN 0.025773 -sd 0.053921\n+# CompileDir= /home/users2/vdergachev/tools/tools.3625.3827/3625 SVNversion=3827 $Header: http://svn.bnm.local:81/svn/Informatics/RefAligner/branches/3625/RefAligner.cpp 3617 2015-03-06 23:19:53Z tanantharaman $\n+# FLAGS: USE_SSE=0 USE_AVX=0 USE_MIC=1 USE_PFLOAT=1 USE_RFLOAT=1 DEBUG=1 VERB=1\n+# CMAP File Version:\t0.1\n+# Label Channels:\t1\n+# Nickase Recognition Site 1:\tGCTCTTC\n+# Number of Consensus Maps:\t1\n+#h CMapId\tContigLength\tNumSites\tSiteID\tLabelChannel\tPosition\tStdDev\tCoverage\tOccurrence\tGmeanSNR\tlnSNRsd\tSNR count\tSNR ...\n+#f int\tfloat\tint\tint\tint\tfloat\tfloat\tfloat\tfloat\tfloat\tfloat\tint\tfloat ...\n+1\t3905510.6\t449\t1\t1\t19.9\t112.1\t106.0\t106.0\t25.0977\t0.4630\t0\n+1\t3905510.6\t449\t2\t1\t1690.5\t290.0\t108.0\t106.0\t9.9068\t0.5258\t0\n+1\t3905510.6\t449\t3\t1\t45912.6\t126.1\t114.0\t92.0\t9.1663\t0.4374\t0\n+1\t3905510.6\t449\t4\t1\t49569.5\t205.8\t116.0\t100.0\t9.3623\t0.3865\t0\n+1\t3905510.6\t449\t5\t1\t68965.9\t123.8\t120.0\t116.0\t22.9988\t0.5240\t0\n+1\t3905510.6\t449\t6\t1\t72280.3\t139.9\t126.0\t118.0\t12.9415\t0.3856\t0\n+1\t3905510.6\t449\t7\t1\t78126.2\t168.6\t126.0\t116.0\t34.2842\t0.3893\t0\n+1\t3905510.6\t449\t8\t1\t89229.5\t147.4\t126.0\t104.0\t30.3351\t0.4853\t0\n+1\t3905510.6\t449\t9\t1\t96345.7\t140.5\t130.0\t110.0\t13.0156\t0.4289\t0\n+1\t3905510.6\t449\t10\t1\t102282.2\t182.6\t132.0\t118.0\t39.1442\t0.4546\t0\n+1\t3905510.6\t449\t11\t1\t116313.4\t136.8\t134.0\t108.0\t34.7224\t0.2964\t0\n+1\t3905510.6\t449\t12\t1\t121639.0\t155.7\t136.0\t128.0\t9.0093\t0.4622\t0\n+1\t3905510.6\t449\t13\t1\t130258.2\t134.2\t138.0\t136.0\t17.9499\t0.4729\t0\n+1\t3905510.6\t449\t14\t1\t135174.6\t133.8\t138.0\t136.0\t30.0908\t0.4298\t0\n+1\t3905510.6\t449\t15\t1\t140019.2\t128.1\t136.0\t120.0\t8.4286\t0.4418\t0\n+1\t3905510.6\t449\t16\t1\t143974.9\t216.3\t134.0\t130.0\t31.5553\t0.4515\t0\n+1\t3905510.6\t449\t17\t1\t165999.9\t114.5\t134.0\t128.0\t13.6637\t0.4622\t0\n+1\t3905510.6\t449\t18\t1\t167998.9\t109.4\t126.0\t72.0\t7.3318\t0.4200\t0\n+1\t3905510.6\t449\t19\t1\t169318.0\t138.5\t122.0\t102.0\t9.0981\t0.4185\t0\n+1\t3905510.6\t449\t20\t1\t174930.2\t151.9\t124.0\t114.0\t16.2596\t0.5397\t0\n+1\t3905510.6\t449\t21\t1\t182850.7\t133.6\t122.0\t114.0\t20.9485\t0.3784\t0\n+1\t3905510.6\t449\t22\t1\t187664.0\t175.5\t122.0\t108.0\t30.8344\t0.5198\t0\n+1\t3905510.6\t449\t23\t1\t200187.0\t135.2\t114.0\t106.0\t29.8861\t0.4160\t0\n+1\t3905510.6\t449\t24\t1\t205249.2\t116.1\t114.0\t108.0\t18.7684\t0.3999\t0\n+1\t3905510.6\t449\t25\t1\t207456.7\t233.2\t110.0\t106.0\t12.8564\t0.4385\t0\n+1\t3905510.6\t449\t26\t1\t234004.5\t127.9\t102.0\t100.0\t17.4401\t0.4374\t0\n+1\t3905510.6\t449\t27\t1\t237934.3\t140.3\t100.0\t88.0\t11.9504\t0.4838\t0\n+1\t3905510.6\t449\t28\t1\t243845.2\t141.5\t100.0\t98.0\t10.6039\t0.4281\t0\n+1\t3905510.6\t449\t29\t1\t249943.4\t161.0\t96.0\t42.0\t10.2061\t0.4148\t0\n+1\t3905510.6\t449\t30\t1\t259563.9\t137.2\t98.0\t84.0\t19.6946\t0.3725\t0\n+1\t3905510.6\t449\t31\t1\t264964.2\t147.9\t100.0\t94.0\t10.7442\t0.4218\t0\n+1\t3905510.6\t449\t32\t1\t272168.7\t122.3\t100.0\t76.0\t8.6743\t0.4994\t0\n+1\t3905510.6\t449\t33\t1\t275257.2\t195.0\t98.0\t90.0\t10.4615\t0.4600\t0\n+1\t3905510.6\t449\t34\t1\t292066.2\t167.9\t100.0\t90.0\t16.1133\t0.4646\t0\n+1\t3905510.6\t449\t35\t1\t303025.6\t163.3\t100.0\t80.0\t23.2789\t0.4701\t0\n+1\t3905510.6\t449\t36\t1\t313075.8\t143.1\t104.0\t90.0\t11.3080\t0.5283\t0\n+1\t3905510.6\t449\t37\t1\t319450.0\t124.2\t104.0\t102.0\t'..b'444.6\t236.7\t86.0\t68.0\t10.2286\t0.5476\t0\n+4\t719804.4\t83\t22\t1\t291958.4\t155.9\t82.0\t78.0\t27.4763\t0.5987\t0\n+4\t719804.4\t83\t23\t1\t300602.8\t107.0\t84.0\t48.0\t14.3380\t0.6151\t0\n+4\t719804.4\t83\t24\t1\t301612.6\t129.2\t86.0\t78.0\t19.1460\t0.4525\t0\n+4\t719804.4\t83\t25\t1\t305741.2\t132.2\t80.0\t76.0\t26.7020\t0.6081\t0\n+4\t719804.4\t83\t26\t1\t310332.8\t128.9\t86.0\t66.0\t9.4743\t0.4779\t0\n+4\t719804.4\t83\t27\t1\t314418.0\t211.5\t88.0\t84.0\t18.2800\t0.4354\t0\n+4\t719804.4\t83\t28\t1\t335213.4\t114.7\t94.0\t80.0\t9.1841\t0.4937\t0\n+4\t719804.4\t83\t29\t1\t337238.1\t109.4\t94.0\t84.0\t14.8201\t0.4119\t0\n+4\t719804.4\t83\t30\t1\t338546.9\t145.5\t98.0\t80.0\t13.8746\t0.4870\t0\n+4\t719804.4\t83\t31\t1\t345335.9\t121.8\t100.0\t94.0\t11.7842\t0.3469\t0\n+4\t719804.4\t83\t32\t1\t348359.7\t192.6\t100.0\t96.0\t16.0489\t0.5073\t0\n+4\t719804.4\t83\t33\t1\t364622.7\t162.5\t98.0\t84.0\t16.3767\t0.4206\t0\n+4\t719804.4\t83\t34\t1\t374520.5\t131.4\t98.0\t98.0\t16.6360\t0.4377\t0\n+4\t719804.4\t83\t35\t1\t378992.5\t127.5\t100.0\t98.0\t34.6125\t0.5349\t0\n+4\t719804.4\t83\t36\t1\t382859.2\t131.3\t98.0\t86.0\t9.7771\t0.4539\t0\n+4\t719804.4\t83\t37\t1\t387311.7\t130.7\t96.0\t88.0\t15.2950\t0.5321\t0\n+4\t719804.4\t83\t38\t1\t391661.7\t124.6\t94.0\t90.0\t21.0815\t0.5674\t0\n+4\t719804.4\t83\t39\t1\t395086.8\t145.1\t94.0\t88.0\t32.2448\t0.3353\t0\n+4\t719804.4\t83\t40\t1\t401803.7\t119.0\t96.0\t70.0\t8.2248\t0.4834\t0\n+4\t719804.4\t83\t41\t1\t404419.8\t127.7\t98.0\t94.0\t22.4450\t0.3724\t0\n+4\t719804.4\t83\t42\t1\t408319.6\t168.2\t98.0\t74.0\t10.3620\t0.4033\t0\n+4\t719804.4\t83\t43\t1\t419342.9\t210.9\t96.0\t86.0\t24.2311\t0.3232\t0\n+4\t719804.4\t83\t44\t1\t439991.8\t167.9\t96.0\t84.0\t42.7850\t0.3401\t0\n+4\t719804.4\t83\t45\t1\t450966.1\t197.9\t98.0\t70.0\t34.9331\t0.3950\t0\n+4\t719804.4\t83\t46\t1\t468461.5\t217.2\t104.0\t82.0\t11.6821\t0.4707\t0\n+4\t719804.4\t83\t47\t1\t490714.9\t115.6\t118.0\t108.0\t26.0961\t0.4486\t0\n+4\t719804.4\t83\t48\t1\t492861.4\t165.6\t118.0\t74.0\t8.5159\t0.3845\t0\n+4\t719804.4\t83\t49\t1\t503376.6\t162.4\t122.0\t92.0\t24.8831\t0.4608\t0\n+4\t719804.4\t83\t50\t1\t513265.5\t144.3\t126.0\t110.0\t13.6303\t0.5979\t0\n+4\t719804.4\t83\t51\t1\t519839.1\t110.3\t126.0\t72.0\t9.5494\t0.4807\t0\n+4\t719804.4\t83\t52\t1\t521266.6\t144.0\t126.0\t120.0\t21.9932\t0.4142\t0\n+4\t719804.4\t83\t53\t1\t527802.0\t137.7\t130.0\t122.0\t35.3081\t0.4052\t0\n+4\t719804.4\t83\t54\t1\t533280.9\t132.4\t134.0\t128.0\t27.7468\t0.4857\t0\n+4\t719804.4\t83\t55\t1\t537910.5\t146.4\t134.0\t124.0\t25.0369\t0.5257\t0\n+4\t719804.4\t83\t56\t1\t544853.2\t133.3\t134.0\t126.0\t17.3667\t0.4075\t0\n+4\t719804.4\t83\t57\t1\t549620.8\t106.9\t136.0\t116.0\t17.6608\t0.4368\t0\n+4\t719804.4\t83\t58\t1\t550618.7\t176.2\t136.0\t88.0\t17.9613\t0.4285\t0\n+4\t719804.4\t83\t59\t1\t563277.2\t158.0\t146.0\t126.0\t25.4715\t0.4676\t0\n+4\t719804.4\t83\t60\t1\t572313.7\t117.5\t148.0\t126.0\t15.7217\t0.5495\t0\n+4\t719804.4\t83\t61\t1\t574722.4\t108.1\t148.0\t112.0\t10.8791\t0.3850\t0\n+4\t719804.4\t83\t62\t1\t575866.4\t118.1\t150.0\t112.0\t10.7377\t0.4117\t0\n+4\t719804.4\t83\t63\t1\t578352.6\t135.8\t148.0\t144.0\t16.4218\t0.4133\t0\n+4\t719804.4\t83\t64\t1\t583512.4\t225.6\t148.0\t142.0\t18.2632\t0.4908\t0\n+4\t719804.4\t83\t65\t1\t607978.5\t131.9\t144.3\t142.3\t13.8434\t0.4098\t0\n+4\t719804.4\t83\t66\t1\t612520.3\t114.4\t140.3\t130.3\t15.2611\t0.3763\t0\n+4\t719804.4\t83\t67\t1\t614494.9\t150.2\t140.3\t136.3\t17.5217\t0.3722\t0\n+4\t719804.4\t83\t68\t1\t622116.5\t122.8\t136.3\t128.3\t11.6120\t0.4696\t0\n+4\t719804.4\t83\t69\t1\t625275.5\t132.7\t136.3\t134.3\t23.6405\t0.3317\t0\n+4\t719804.4\t83\t70\t1\t629942.1\t121.1\t138.3\t102.0\t6.6359\t0.3459\t0\n+4\t719804.4\t83\t71\t1\t632862.1\t123.4\t138.3\t138.3\t17.8257\t0.4504\t0\n+4\t719804.4\t83\t72\t1\t636122.4\t133.7\t136.3\t134.3\t19.4468\t0.4325\t0\n+4\t719804.4\t83\t73\t1\t640945.3\t178.6\t136.3\t130.3\t23.2584\t0.3911\t0\n+4\t719804.4\t83\t74\t1\t654125.7\t132.1\t126.3\t116.0\t19.6411\t0.4760\t0\n+4\t719804.4\t83\t75\t1\t658704.1\t170.4\t124.3\t114.3\t35.6432\t0.4120\t0\n+4\t719804.4\t83\t76\t1\t670173.7\t184.0\t120.3\t84.3\t13.4079\t0.3875\t0\n+4\t719804.4\t83\t77\t1\t684518.7\t129.4\t116.3\t110.3\t24.6816\t0.3978\t0\n+4\t719804.4\t83\t78\t1\t688676.4\t131.3\t116.3\t112.3\t29.3456\t0.4526\t0\n+4\t719804.4\t83\t79\t1\t693134.3\t151.3\t116.3\t110.3\t20.8188\t0.4594\t0\n+4\t719804.4\t83\t80\t1\t700955.4\t152.2\t110.3\t106.3\t25.8896\t0.4854\t0\n+4\t719804.4\t83\t81\t1\t708922.2\t132.8\t104.3\t104.3\t38.4145\t0.2978\t0\n+4\t719804.4\t83\t82\t1\t713614.2\t141.9\t98.3\t98.3\t15.5525\t0.5768\t0\n+4\t719804.4\t83\t83\t1\t719784.4\t0.0\t72.0\t72.0\t7.5225\t0.3328\t0\n+4\t719804.4\t83\t84\t0\t719804.4\t0.0\t1.0\t1.0\t0.0000\t0.0000\t0\n' |
| b |
| diff -r 000000000000 -r fec6a0b53189 test-data/configuration.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/configuration.xml Mon May 17 15:07:05 2021 +0000 |
| b |
| b'@@ -0,0 +1,293 @@\n+<hybridScaffold>\n+ <version>\n+ <flag attr="version" val0="$Id: hybridScaffold_DLE1_config.xml 7702 2018-06-25 20:53:51Z apang $"/>\n+ </version>\n+ <global>\n+ <flag attr="maxmem" val0="960" display="Maximum memory (GB)" group="Global options" description="Define the maximum amount of RAM in gigabytes to be used by each process."/>\n+ <flag attr="maxthreads" val0="54" display="Max threads" group="Global options" description="Define maximum number of threads to be used by each process."/>\n+ <flag attr="maxvirtmem" val0="960"/>\n+ <flag attr="RAmem" val0="3" val1="1"/>\n+ </global>\n+ <fasta2cmap>\n+ <flag attr="enzyme" val0="BspQI" display="Enzyme" group="FASTA to CMAP digestion" description="Define single enzyme for in-silico FASTA to CMAP digestion. Avalible enzymes: BspQI, BbvCI, BsmI, BsrDI, BssSI, DLE1."/>\n+ <flag attr="channelNum" val0="1" display="Channel number" group="FASTA to CMAP digestion" description="Specify the channel the enzyme was used."/>\n+ <flag attr="minLabels" val0="0" display="Minimum label sites" group="FASTA to CMAP digestion" description="Specify minimum number of label sites per digested contig."/>\n+ <flag attr="minLength" val0="0" display="Minimum length (Kb)" group="FASTA to CMAP digestion" description="Specify minimum length in Kb of each digested contig."/>\n+ </fasta2cmap>\n+ <align0>\n+ <flag attr="M" val0="1" val1="3"/>\n+ <flag attr="ScaleDelta" val0="0.02" val1="15"/>\n+ <flag attr="ScaleDeltaBPP"/>\n+ <flag attr="hashScaleDelta" val0="2"/>\n+ <flag attr="res" val0="2.9"/>\n+ <flag attr="FP" val0="0.6"/>\n+ <flag attr="FN" val0="0.06"/>\n+ <flag attr="sf" val0="0.20"/>\n+ <flag attr="sd" val0="0.0"/>\n+ <flag attr="sr" val0="0.01"/>\n+ <flag attr="extend" val0="1"/>\n+ <flag attr="outlier" val0="0.0001"/>\n+ <flag attr="endoutlier" val0="0.001"/>\n+ <flag attr="PVendoutlier"/>\n+ <flag attr="deltaX" val0="12"/>\n+ <flag attr="deltaY" val0="12"/>\n+ <flag attr="xmapchim" val0="12"/>\n+ <flag attr="hashgen" val0="5" val1="7" val2="2.4" val3="1.5" val4="0.05" val5="5.0" val6="1" val7="1" val8="4"/>\n+ <flag attr="hash" val0="-hashdelta" val1="26" val2="10" val3="46"/>\n+ <flag attr="hashMultiMatch" val0="30" val1="10"/>\n+ <flag attr="insertThreads" val0="54"/>\n+ <flag attr="nosplit" val0="2"/>\n+ <flag attr="biaswt" val0="0"/>\n+ <flag attr="T" val0="1e-10" display="P-value" group="Initial alignment" description="Minimum confidence value to output initial alignments. Recommended starting value of 1e-5/genome size in Mb."/>\n+ <flag attr="S" val0="-1000"/>\n+ <flag attr="indel"/>\n+ <flag attr="PVres" val0="2"/>\n+ <flag attr="rres" val0="0.9"/>\n+ <flag attr="MaxSE" val0="0.5"/>\n+ <flag attr="HSDrange" val0="1.0"/>\n+ <flag attr="outlierBC"/>\n+ <flag attr="xmapUnique" val0="12"/>\n+ <flag attr="AlignRes" val0="2."/>\n+ <flag attr="outlierExtend" val0="12" val1="24"/>\n+ <flag attr="Kmax" val0="12"/>\n+ <flag attr="resEstimate"/>\n+ <flag attr="f"/>\n+ <flag attr="mres" val0="0.9"/>\n+ </align0>\n+ <align1>\n+ <flag attr="res" val0="2.9"/>\n+ <flag attr="FP" val0="0.6"/>\n+ <flag attr="FN" val0="0.06"/>\n+ <flag attr="sf" val0="0.20"/>\n+ <flag attr="sd" val0="0.0"/>\n+ <flag attr="sr" val0="0.01"/>\n+ <flag attr="extend" val0="1"/>\n+ <flag attr="outlier" val0="0.0001"/>\n+ <flag attr="endoutlier" val0="0.001"/>\n+ <flag attr="PVendoutlier"/>\n+ <flag attr="deltaX" val0="12"/>\n+ <flag attr="deltaY" val0="12"/>\n+ <flag attr="xmapchim" val0="12"/>\n+ <flag attr="hashgen" val0="5" val1="7" val2="2.4" val3="1.5" val4="0.05" val5="5.0" val6="1" val7="1" val8="4"/>\n+ <flag attr="hash" val0="-hashdelta" val1="26" val2="10" val3="46"/>\n+ <flag attr="hashMultiMatch" val0="30" val1="10"/>\n+ <flag attr="insertThreads" val0="54"/>\n+ <flag attr="nosplit" val0="2"/>\n+ <flag attr="biaswt" val0="0"/>\n+ <flag attr="T" val0="1e-10" display="P-v'..b'r="HSDrange" val0="1.0"/>\n+ <flag attr="outlierBC"/>\n+ <flag attr="xmapUnique" val0="14"/>\n+ <flag attr="AlignRes" val0="2."/>\n+ <flag attr="outlierExtend" val0="6" val1="24"/>\n+ <flag attr="Kmax" val0="6"/>\n+ <flag attr="resEstimate"/>\n+ <flag attr="BestRef" val0="1"/>\n+ <flag attr="f"/>\n+ <flag attr="mres" val0="0.9"/>\n+ </align_final_BNG>\n+ <refineFinal1>\n+ <flag attr="refine" val0="1" display="Refine Map" group="Final Refinement" default0="3"/>\n+ <flag attr="usecolor" val0="1" default0="1" display="Color Channel" group="Final Refinement"/>\n+ <flag attr="A" val0="5" display="Aligned Sites Threshold" group="Final Refinement" default0="5"/>\n+ <flat attr="S" val0="-9"/>\n+ <flag attr="L" val0="130"/>\n+ <flag attr="maptype" val0="0"/>\n+ <flag attr="extend" val0="1" display="Allow Extended Molecule" group="Final Refinement" default0="1"/>\n+ <flag attr="MaxCov" val0="100" display="Max Coverage" group="Final Refinement" default0="100"/>\n+ <flag attr="Mprobeval" display="Fast Mode" group="Final Refinement"/>\n+ <flag attr="splitcnt"/>\n+ <flag attr="splitrev" val0="2"/>\n+ <flag attr="CmapSNR"/>\n+ <flag attr="splitsite"/>\n+ <flag attr="MinSplitLen" val0="50.0"/>\n+ <flag attr="MaxSE" val0="0.5"/>\n+ <flag attr="outlier" val0="2e-2" display="Min Outliers P-value" group="Second Refinement" default0="1e-5"/>\n+ <flag attr="outlierMax" val0="80."/>\n+ <flag attr="outlierLambda" val0="20."/>\n+ <flag attr="endoutlier" val0="1e-3" display="Molecule Ends P-value Cutoff" group="Second Refinement" default0="1e-4"/>\n+ <flag attr="endoutlierRef" val0="1e-4" val1="1e-3"/>\n+ <flag attr="skip_dist" val0="0.0" val2="0.0"/>\n+ <flag attr="endoutlierFinal" val0="1"/>\n+ <flag attr="maxEnd" val0="90."/>\n+ <flag attr="RTHETA_FIX" val0="0"/>\n+ <flag attr="TB" val0="1e-6" val1="1e-6" val2="-TBmult" val3="0.1"/>\n+ <flag attr="nosplit" val0="2" display="Allow Chimeric Split" group="Final Refinement" default0="2"/>\n+ <flag attr="EndTrim" val0="0.0" display="Min End Trim Coverage" group="Final Refinement" default0="4.99"/>\n+ <flag attr="biaswt" val0="0.7" display="Bias" group="Final Refinement" default0="0"/>\n+ <flag attr="biaswtEnd" val0="0.0"/>\n+ <flag attr="biaswtRefine" val0="0.7" val2="1"/>\n+ <flag attr="biaswtOutlier" val0="0.0"/>\n+ <flag attr="LRbias" val0="1e0" display="Soft Threshold" group="Final Refinement" default0="1e2"/>\n+ <flag attr="deltaX" val0="6" display="Molecule Labels Metric" group="Final Refinement" default0="4"/>\n+ <flag attr="deltaY" val0="7" display="Mapped Labels Metric" group="Final Refinement" default0="6"/>\n+ <flag attr="RepeatMask" val0="5" val1="0.01" display="Repeat Mask P-values" group="Final Refinement" default0="2" default1="0.01"/>\n+ <flag attr="RepeatRec" val0="0.7" val1="0.6" val2="1.4"/>\n+ <flag attr="CovTrim" val0="2"/>\n+ <flag attr="CovTrimLen" val0="55"/>\n+ <flag attr="TrimNorm" val0="0"/>\n+ <flag attr="TrimNormMed" val0="100"/>\n+ <flag attr="TrimNormChim" val0="2"/>\n+ <flag attr="TrimNormMin" val0="2"/>\n+ <flag attr="PVres" val0="2"/>\n+ <flag attr="PVendoutlier"/>\n+ <flag attr="AlignRes" val0="1.5"/>\n+ <flag attr="rres" val0="1.2"/>\n+ <flag attr="cres" val0="5.6" val1="3" val2="0.1"/>\n+ <flag attr="hashgen" val00="5" val01="3" val02="2.4" val03="1.5" val04="0.05" val05="5.0" val06="1" val07="1" val08="3"/>\n+ <flag attr="hash" val00="-hashdelta" val01="10" val02="10" val03="-mres" val04="0.9"/>\n+ <flag attr="HSDrange" val0="1.0"/>\n+ <flag attr="hashoffset" val0="1"/>\n+ <flag attr="hashMultiMatch" val0="15"/>\n+ <flag attr="insertThreads" val0="54"/>\n+ <flag attr="BestRef" val0="1"/>\n+ <flag attr="BestRefPV" val0="1"/>\n+ <flag attr="ChimQuality"/>\n+ <flag attr="f" display="Overwrite Output Files" group="Final Refinement"/>\n+ <flag attr="T" val0="1e-11" display="P Value Cutoff Threshold"/>\n+ </refineFinal1>\n+</hybridScaffold>\n' |
| b |
| diff -r 000000000000 -r fec6a0b53189 test-data/test_01.agp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_01.agp Mon May 17 15:07:05 2021 +0000 |
| b |
| @@ -0,0 +1,9 @@ +##agp-version 2.0 +# Organism: +# Platform: +# Model: +# Enzyme(s): +# BioSample: +# BioProject: +# Obj_Name Obj_Start Obj_End PartNum Compnt_Type CompntId_GapLength CompntStart_GapType CompntEnd_Linkage Orientation_LinkageEvidence +Super-Scaffold_1 1 4753350 1 W Super_scaffold_3 1 4753350 + |
| b |
| diff -r 000000000000 -r fec6a0b53189 test-data/test_01.gap --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_01.gap Mon May 17 15:07:05 2021 +0000 |
| b |
| @@ -0,0 +1,1 @@ +#NGSId1 NGSId2 SuperScaffoldId XmapGapLength AdjustedGapLength NGSLength1 NGSLength2 |
| b |
| diff -r 000000000000 -r fec6a0b53189 test-data/test_01_report.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_01_report.txt Mon May 17 15:07:05 2021 +0000 |
| b |
| @@ -0,0 +1,45 @@ +Original BioNano Genome Map statistics: +Count = 2 +Min length (Mbp) = 0.720 +Median length (Mbp) = 2.313 +Mean length (Mbp) = 2.313 +N50 length (Mbp) = 3.906 +Max length (Mbp) = 3.906 +Total length (Mbp) = 4.625 + +Original NGS sequences statistics: +Count = 1 +Min length (Mbp) = 4.753 +Median length (Mbp) = 4.753 +Mean length (Mbp) = 4.753 +N50 length (Mbp) = 4.753 +Max length (Mbp) = 4.753 +Total length (Mbp) = 4.753 + +NGS FASTA sequence in hybrid scaffold statistics: +Count = 1 +Min length (Mbp) = 4.753 +Median length (Mbp) = 4.753 +Mean length (Mbp) = 4.753 +N50 length (Mbp) = 4.753 +Max length (Mbp) = 4.753 +Total length (Mbp) = 4.753 + +Hybrid scaffold FASTA statistics: +Count = 1 +Min length (Mbp) = 4.753 +Median length (Mbp) = 4.753 +Mean length (Mbp) = 4.753 +N50 length (Mbp) = 4.753 +Max length (Mbp) = 4.753 +Total length (Mbp) = 4.753 + +Hybrid scaffold FASTA plus not scaffolded NGS FASTA statistics: +Count = 1 +Min length (Mbp) = 4.753 +Median length (Mbp) = 4.753 +Mean length (Mbp) = 4.753 +N50 length (Mbp) = 4.753 +Max length (Mbp) = 4.753 +Total length (Mbp) = 4.753 + |
| b |
| diff -r 000000000000 -r fec6a0b53189 test-data/test_02.agp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_02.agp Mon May 17 15:07:05 2021 +0000 |
| b |
| @@ -0,0 +1,9 @@ +##agp-version 2.0 +# Organism: +# Platform: +# Model: +# Enzyme(s): +# BioSample: +# BioProject: +# Obj_Name Obj_Start Obj_End PartNum Compnt_Type CompntId_GapLength CompntStart_GapType CompntEnd_Linkage Orientation_LinkageEvidence +Super-Scaffold_1 1 4753350 1 W Super_scaffold_3 1 4753350 + |
| b |
| diff -r 000000000000 -r fec6a0b53189 test-data/test_02.gap --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_02.gap Mon May 17 15:07:05 2021 +0000 |
| b |
| @@ -0,0 +1,1 @@ +#NGSId1 NGSId2 SuperScaffoldId XmapGapLength AdjustedGapLength NGSLength1 NGSLength2 |
| b |
| diff -r 000000000000 -r fec6a0b53189 test-data/test_02_report.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_02_report.txt Mon May 17 15:07:05 2021 +0000 |
| b |
| @@ -0,0 +1,45 @@ +Original BioNano Genome Map statistics: +Count = 2 +Min length (Mbp) = 0.720 +Median length (Mbp) = 2.313 +Mean length (Mbp) = 2.313 +N50 length (Mbp) = 3.906 +Max length (Mbp) = 3.906 +Total length (Mbp) = 4.625 + +Original NGS sequences statistics: +Count = 1 +Min length (Mbp) = 4.753 +Median length (Mbp) = 4.753 +Mean length (Mbp) = 4.753 +N50 length (Mbp) = 4.753 +Max length (Mbp) = 4.753 +Total length (Mbp) = 4.753 + +NGS FASTA sequence in hybrid scaffold statistics: +Count = 1 +Min length (Mbp) = 4.753 +Median length (Mbp) = 4.753 +Mean length (Mbp) = 4.753 +N50 length (Mbp) = 4.753 +Max length (Mbp) = 4.753 +Total length (Mbp) = 4.753 + +Hybrid scaffold FASTA statistics: +Count = 1 +Min length (Mbp) = 4.753 +Median length (Mbp) = 4.753 +Mean length (Mbp) = 4.753 +N50 length (Mbp) = 4.753 +Max length (Mbp) = 4.753 +Total length (Mbp) = 4.753 + +Hybrid scaffold FASTA plus not scaffolded NGS FASTA statistics: +Count = 1 +Min length (Mbp) = 4.753 +Median length (Mbp) = 4.753 +Mean length (Mbp) = 4.753 +N50 length (Mbp) = 4.753 +Max length (Mbp) = 4.753 +Total length (Mbp) = 4.753 + |
| b |
| diff -r 000000000000 -r fec6a0b53189 test-data/test_03.agp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_03.agp Mon May 17 15:07:05 2021 +0000 |
| b |
| @@ -0,0 +1,9 @@ +##agp-version 2.0 +# Organism: +# Platform: +# Model: +# Enzyme(s): +# BioSample: +# BioProject: +# Obj_Name Obj_Start Obj_End PartNum Compnt_Type CompntId_GapLength CompntStart_GapType CompntEnd_Linkage Orientation_LinkageEvidence +Super-Scaffold_1 1 4753350 1 W Super_scaffold_3 1 4753350 + |
| b |
| diff -r 000000000000 -r fec6a0b53189 test-data/test_03.gap --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_03.gap Mon May 17 15:07:05 2021 +0000 |
| b |
| @@ -0,0 +1,1 @@ +#NGSId1 NGSId2 SuperScaffoldId XmapGapLength AdjustedGapLength NGSLength1 NGSLength2 |
| b |
| diff -r 000000000000 -r fec6a0b53189 test-data/test_03_report.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_03_report.txt Mon May 17 15:07:05 2021 +0000 |
| b |
| @@ -0,0 +1,45 @@ +Original BioNano Genome Map statistics: +Count = 2 +Min length (Mbp) = 0.720 +Median length (Mbp) = 2.313 +Mean length (Mbp) = 2.313 +N50 length (Mbp) = 3.906 +Max length (Mbp) = 3.906 +Total length (Mbp) = 4.625 + +Original NGS sequences statistics: +Count = 1 +Min length (Mbp) = 4.753 +Median length (Mbp) = 4.753 +Mean length (Mbp) = 4.753 +N50 length (Mbp) = 4.753 +Max length (Mbp) = 4.753 +Total length (Mbp) = 4.753 + +NGS FASTA sequence in hybrid scaffold statistics: +Count = 1 +Min length (Mbp) = 4.753 +Median length (Mbp) = 4.753 +Mean length (Mbp) = 4.753 +N50 length (Mbp) = 4.753 +Max length (Mbp) = 4.753 +Total length (Mbp) = 4.753 + +Hybrid scaffold FASTA statistics: +Count = 1 +Min length (Mbp) = 4.753 +Median length (Mbp) = 4.753 +Mean length (Mbp) = 4.753 +N50 length (Mbp) = 4.753 +Max length (Mbp) = 4.753 +Total length (Mbp) = 4.753 + +Hybrid scaffold FASTA plus not scaffolded NGS FASTA statistics: +Count = 1 +Min length (Mbp) = 4.753 +Median length (Mbp) = 4.753 +Mean length (Mbp) = 4.753 +N50 length (Mbp) = 4.753 +Max length (Mbp) = 4.753 +Total length (Mbp) = 4.753 + |
| b |
| diff -r 000000000000 -r fec6a0b53189 test-data/test_04.agp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_04.agp Mon May 17 15:07:05 2021 +0000 |
| b |
| @@ -0,0 +1,9 @@ +##agp-version 2.0 +# Organism: +# Platform: +# Model: +# Enzyme(s): +# BioSample: +# BioProject: +# Obj_Name Obj_Start Obj_End PartNum Compnt_Type CompntId_GapLength CompntStart_GapType CompntEnd_Linkage Orientation_LinkageEvidence +Super-Scaffold_1 1 4753350 1 W Super_scaffold_3 1 4753350 + |
| b |
| diff -r 000000000000 -r fec6a0b53189 test-data/test_04.gap --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_04.gap Mon May 17 15:07:05 2021 +0000 |
| b |
| @@ -0,0 +1,1 @@ +#NGSId1 NGSId2 SuperScaffoldId XmapGapLength AdjustedGapLength NGSLength1 NGSLength2 |
| b |
| diff -r 000000000000 -r fec6a0b53189 test-data/test_04_report.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_04_report.txt Mon May 17 15:07:05 2021 +0000 |
| b |
| @@ -0,0 +1,45 @@ +Original BioNano Genome Map statistics: +Count = 2 +Min length (Mbp) = 0.720 +Median length (Mbp) = 2.313 +Mean length (Mbp) = 2.313 +N50 length (Mbp) = 3.906 +Max length (Mbp) = 3.906 +Total length (Mbp) = 4.625 + +Original NGS sequences statistics: +Count = 1 +Min length (Mbp) = 4.753 +Median length (Mbp) = 4.753 +Mean length (Mbp) = 4.753 +N50 length (Mbp) = 4.753 +Max length (Mbp) = 4.753 +Total length (Mbp) = 4.753 + +NGS FASTA sequence in hybrid scaffold statistics: +Count = 1 +Min length (Mbp) = 4.753 +Median length (Mbp) = 4.753 +Mean length (Mbp) = 4.753 +N50 length (Mbp) = 4.753 +Max length (Mbp) = 4.753 +Total length (Mbp) = 4.753 + +Hybrid scaffold FASTA statistics: +Count = 1 +Min length (Mbp) = 4.753 +Median length (Mbp) = 4.753 +Mean length (Mbp) = 4.753 +N50 length (Mbp) = 4.753 +Max length (Mbp) = 4.753 +Total length (Mbp) = 4.753 + +Hybrid scaffold FASTA plus not scaffolded NGS FASTA statistics: +Count = 1 +Min length (Mbp) = 4.753 +Median length (Mbp) = 4.753 +Mean length (Mbp) = 4.753 +N50 length (Mbp) = 4.753 +Max length (Mbp) = 4.753 +Total length (Mbp) = 4.753 + |