| Next changeset 1:e76e813f615a (2017-12-18) |
|
Commit message:
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty |
|
added:
macros.xml snap_caller.xml test-data/a.bam test-data/a.bcf test-data/a.fa test-data/a.sam test-data/a.vcf test-data/a_part1.bam test-data/a_part2.bam test-data/a_part2.bcf test-data/ce11ToCe10.over.chain test-data/header_only.bam test-data/header_only.sam test-data/reads_1_w_header.bam test-data/reads_1and2_w_header.bam test-data/rebased.vcf test-data/so_coordinate.bam test-data/so_queryname.sam test-data/split_pair_reads_1.fastqsanger test-data/split_pair_reads_2.fastqsanger test-data/vaf_linkage.pdf tool-data/all_fasta.loc.sample tool_data_table_conf.xml.sample |
| b |
| diff -r 000000000000 -r d801b0675eb5 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Sat Nov 11 18:18:54 2017 -0500 |
| [ |
| @@ -0,0 +1,46 @@ +<macros> + <token name="@MIMODD_VERSION_REQUIRED@">0.1.8</token> + <token name="@MIMODD_REAL_VERSION@">0.1.8</token> + <token name="@MIMODD_WRAPPER_VERSION@">0.1.8_0</token> + <token name="@HELP_FOOTER@"><![CDATA[ +---- + +.. class:: infomark + + For **additional help** see these resources: + +- The complete `MiModD User Guide <http://mimodd.readthedocs.io/en/v0.1.8/usage_toc.html>`__ + +- The `MiModD help forum <https://groups.google.com/forum/#!forum/mimodd>`__ reachable also via `email <mailto:mimodd@googlegroups.com>`__ + + ]]></token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@MIMODD_VERSION_REQUIRED@">MiModD</requirement> + <yield /> + </requirements> + </xml> + <xml name="stdio"> + <stdio> + <exit_code range="1:" /> + </stdio> + </xml> + <xml name="version_command"> + <version_command><![CDATA[mimodd version -q]]></version_command> + </xml> + <xml name="citations"> + <citations> + <citation type="bibtex"> +@misc{ +maier_mimodd_2014, +title = {{MiModD} - {Mutation} {Identification} in {Model} {Organism} {Genomes}}, +shorttitle = {{MiModD}}, +url = {https://sourceforge.net/projects/mimodd/}, +author = {Maier, Wolfgang and Moos, Katharina and Seifert, Mark and Baumeister, Ralf}, +year = {2014}, publisher={SourceForge.net} } + </citation> + </citations> + </xml> +</macros> + + |
| b |
| diff -r 000000000000 -r d801b0675eb5 snap_caller.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snap_caller.xml Sat Nov 11 18:18:54 2017 -0500 |
| [ |
| b'@@ -0,0 +1,546 @@\n+<tool id="mimodd_align" name="MiModD Read Alignment" version="@MIMODD_WRAPPER_VERSION@">\n+ <description>maps sequence reads to a reference genome using SNAP</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ <macro name="require_metadata">\n+ <param name="header" type="data" format="sam" \n+ label="metadata source for this sample" />\n+ </macro>\n+ <macro name="sam_bam_selector" token_format="sam">\n+ <param name="ifile" type="data" format="@FORMAT@"\n+ label="input file"/>\n+ <param name="header" type="data" format="sam" optional="true" \n+ label="(optional) metadata source for this sample"\n+ help="a SAM format dataset providing information about the sequences in the input data in its header; do NOT provide this dataset if the information is already part of your input dataset unless you want to have the original metadata overwritten. If needed, a metadata source dataset can be generated with the MiModD Run Annotation tool." />\n+ </macro>\n+ </macros>\n+ <expand macro="requirements" />\n+ <expand macro="stdio" />\n+ <expand macro="version_command" />\n+ <command><![CDATA[\n+ ## Currently Galaxy does not autoconvert collections of fastq.gz files.\n+ ## This tool wrapper fixes that by allowing fastq and fastq.gz as input\n+ ## collection formats.\n+ ## gz_input is then used as flag to indicate a fastq.gz input file\n+ #set gz_input = False\n+\n+\tmimodd snap-batch -s\n+\t #if str($reference.source) == "cached":\n+ #set ref_genome = $reference.genome.fields.path\n+ #else:\n+ #set ref_genome = $reference.genome\n+ #end if\n+\t #for $i in $datasets\n+\t\t"snap ${i.mode_choose.mode} \'$ref_genome\'\n+\t\t#if $str($i.mode_choose.mode) == "paired" and $str($i.mode_choose.input.iformat) == "fastq":\n+\t\t #if $str($i.mode_choose.input.pe_source.type) == \'collection\':\n+ ## PE input provided as a paired collection - if the forward\n+ ## dataset is gzipped we assume the reverse dataset is too.\n+\t\t \'${i.mode_choose.input.pe_source.input_data.forward}\'\n+\t\t \'${i.mode_choose.input.pe_source.input_data.reverse}\'\n+\t\t #if $i.mode_choose.input.pe_source.input_data.forward.is_of_type(\'fastq.gz\'):\n+\t\t #set gz_input = True\n+\t\t #end if\n+\t\t #else\n+\t\t ## PE input provided as separate fastq datasets\n+ \'${i.mode_choose.input.pe_source.ifile1}\'\n+ \'${i.mode_choose.input.pe_source.ifile2}\'\n+ #end if\n+\t\t#else:\n+\t\t ## Input is either SE data or not in fastq format =>\n+\t\t ## only one input dataset\n+ \'${i.mode_choose.input.ifile}\'\n+\t\t#end if\n+\t\t#if $gz_input:\n+\t\t ## a gzipped fastq input dataset was encountered\n+\t\t --iformat gz\n+\t\t#else\n+\t\t --iformat ${i.mode_choose.input.iformat}\n+\t\t#end if\n+ --ofile \'$ofile\' --oformat ${output_options.oformat}\n+ ${output_options.sort} ${output_options.explicit_mmatch_notation}\n+ --idx-seedsize $indexing.seedsize\n+ --idx-slack $indexing.slack\n+ --idx-overflow $indexing.overflow\n+\t\t#set $aln_spec = $i.mode_choose.aln_options\n+\t\t#if $str($i.mode_choose.mode) == "paired":\n+\t\t #set $aln_global = $alignment.paired\n+\t\t #set $treat_overlaps = $aln_spec.discard_overlapping_mates or $aln_global.discard_overlapping_mates\n+ --spacing #if $aln_spec.sp_min then $aln_spec.sp_min else $aln_global.sp_min\n+ #if $aln_spec.sp_max then $aln_spec.sp_max else $aln_global.sp_max\n+ #else\n+ #set $aln_global = $alignment.single\n+ #set $treat_overlaps = ""\n+\t\t#end if\n+ --maxseeds #if $aln_spec.maxseeds then $aln_spec.maxseeds else $aln_global.maxseeds\n+ --maxhits #if $aln_spec.maxhits then $aln_spec.maxhits else $aln_global.maxhits \n+ --clipping #if $aln_spec.clipping then $aln_spec.clipping else $aln_global.clipping\n+ --maxdist #if $aln_spec.maxdist then $aln_spec.maxdist else $aln_global.maxdist \n+ '..b'n use\n+ the *MiModD Run Annotation* and *MiModD Convert* tools to convert data from\n+ fastq format to SAM/BAM format while attaching run metadata to it.\n+ \n+ While alignments **directly from fastq format** are supported, this **is less\n+ reliable** due to less strict specifications of this format. If you find\n+ the tool complaining about malformed fastq input, it is likely that you can\n+ fix this problem by converting the data to SAM/BAM format first.\n+\n+- If you wish to align paired-end data directly from fastq format, the mate\n+ sequence data has to be split over two datasets as is mostly standard today.\n+ If you have your paired-end data as a single dataset you may look into the\n+ *FASTQ splitter* and *FASTQ de-interlacer* tools for Galaxy, which are\n+ available from the `Fastq Manipulation category`_ of the Galaxy Tool Shed and\n+ may be able to convert your files to the expected format.\n+\n+*Run Metadata*\n+\n+- **Every input file requires accompanying Run Metadata!** Most importantly,\n+ this includes a *read-group ID* (an identifier of the sequencing run that\n+ produced the data) and a *sample name* (identifying the\n+ biological sample sequenced in the run).\n+\n+- If an input dataset does not provide this information directly (fastq\n+ datasets never do; SAM/BAM datasets may provide it in their header), you need\n+ to specify a separate SAM/BAM dataset with an appropriate header as the\n+ source of the Run Metadata.\n+ \n+ You can use the *MiModD Run Annotation* tool to generate such a file.\n+ \n+- If a SAM/BAM input dataset already provides Run Metadata, you can still\n+ specify a different Run Metadata source, which will then overwrite the\n+ information already present in the input. This is useful, for example, to\n+ resolve read-group ID conflicts between multiple input datasets.\n+\n+- Every input dataset can only contain reads from a single read-group. If you\n+ would like, for example, to realign the reads in a multi-sample SAM/BAM\n+ dataset. You should first use the *MiModD Sort* tool to sort the data by read\n+ names (this step is only necessary for paired-end data), then split the reads\n+ into new per-read-group datasets using the *MiModD Convert* tool.\n+\n+- Several input datasets can declare identical read-group IDs and/or sample\n+ names.\n+ \n+ Identical read-group IDs mean that the datasets were produced in the\n+ same sequencing run, as is the case, for example, with partial fastq\n+ sequencing data. In the output dataset, the corresponding reads will be\n+ merged and it will not be possible to trace back their source.\n+ \n+ Identical sample names (but different read-group IDs) indicate that the same\n+ sample has been sequenced multiple times. In the output dataset, the\n+ corresponding reads will be tagged appropriately and tools like the\n+ *MiModD Variant Calling* tool will let you decide whether you want to treat\n+ them together or separately.\n+\n+----------\n+ \n+**Tool Options**\n+\n+The section *Alignment parameters* lets you configure global settings for the\n+alignment job that will be applied to all input datasets. For each input\n+dataset, however, you can overwrite some or all of these settings by specifying\n+new values in the section *Alignment options for this sample*. Some of the\n+alignment parameters may have **big** effects on the alignment quality, but\n+these effects are very dependent on the type of input sequences. You are\n+strongly encouraged to consult the in-depth `tool documentation`_ for detailed\n+explanations of the available options.\n+\n+.. _Fastq Manipulation category: https://toolshed.g2.bx.psu.edu/repository/browse_repositories_in_category?id=310ff67d4caf6531\n+.. _recipe for using gzipped fastq files in Galaxy: http://mimodd.readthedocs.org/en/latest/recipes.html#use-gzipped-fastq-files-in-galaxy\n+.. _tool documentation: http://mimodd.readthedocs.io/en/@MIMODD_REAL_VERSION@/tool_doc.html#snap\n+\n+@HELP_FOOTER@\n+ ]]></help>\n+ <expand macro="citations" />\n+</tool>\n+\n' |
| b |
| diff -r 000000000000 -r d801b0675eb5 test-data/a.bam |
| b |
| Binary file test-data/a.bam has changed |
| b |
| diff -r 000000000000 -r d801b0675eb5 test-data/a.bcf |
| b |
| Binary file test-data/a.bcf has changed |
| b |
| diff -r 000000000000 -r d801b0675eb5 test-data/a.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/a.fa Sat Nov 11 18:18:54 2017 -0500 |
| b |
| b'@@ -0,0 +1,3289 @@\n+>chrI\n+gcctaagcctaagcctaagcctaagcctaagcctaagcctaagcctaagc\n+ctaagcctaagcctaagcctaagcctaagcctaagcctaagcctaagcct\n+aagcctaagcctaagcctaagcctaagcctaagcctaagcctaagcctaa\n+gcctaagcctaagcctaagcctaagcctaagcctaagcctaagcctaagc\n+ctaagcctaagcctaagcctaagcctaagcctaagcctaagcctaagcct\n+aagcctaagcctaagcctaagcctaagcctaagcctaagcctaagcctaa\n+gcctaagcctaagcctaagcctaagcctaagcctaagcctaagcctaagc\n+ctaagcctaagcctaagcctaagcctaagcctaagcctaagcctaagcct\n+aagcctaagcctaagcctaagcctaagcctaaaaaattgagataagaaaa\n+cattttactttttcaaaattgttttcatgctaaattcaaaacgttttttt\n+tttagtgaagcttctagatatttggcgggtacctctaattttgcctgcct\n+gccaacctatatgctcctgtgtttaggcctaatactaagcctaagcctaa\n+gcctaatactaagcctaagcctaagactaagcctaatactaagcctaagc\n+ctaagactaagcctaagactaagcctaagactaagcctaatactaagcct\n+aagcctaagactaagcctaagcctaatactaagcctaagcctaagactaa\n+gcctaatactaagcctaagcctaagactaagcctaagactaagcctaaga\n+ctaagcctaatactaagcctaagcctaagactaagcctaagcctaaaaga\n+atatggtagctacagaaacggtagtacactcttctgaaaatacaaaaaat\n+ttgcaatttttatagctagggcactttttgtctgcccaaatataggcaac\n+caaaaataattgccaagtttttaatgatttgttgcatattgaaaaaaaca\n+tttttcgggttttttgaaatgaatatcgtagctacagaaacggttgtgca\n+ctcatctgaaagtttgtttttcttgttttcttgcactttgtgcagaattc\n+ttgattcttgattcttgcagaaatttgcaagaaaattcgcaagaaatttg\n+tattaaaaactgttcaaaatttttggaaattagtttaaaaatctcacatt\n+ttttttagaaaaattatttttaagaatttttcattttaggaatattgtta\n+tttcagaaaatagctaaatgtgatttctgtaattttgcctgccaaattcg\n+tgaaatgcaataaaaatctaatatccctcatcagtgcgatttccgaatca\n+gtatatttttacgtaatagcttctttgacatcaataagtatttgcctata\n+tgactttagacttgaaattggctattaatgccaatttcatgatatctagc\n+cactttagtataattgtttttagtttttggcaaaactattgtctaaacag\n+atattcgtgttttcaagaaatttttcatggtttttcttggtcttttcttg\n+gtatttttttgacaaaaatttttgtttcttgattcttgcaaaaatttttc\n+cgtttgacggccttgatgtgcactaccttcgcttaaatactacattttct\n+gaaaatgttataatagtgttcattgtttcatacaaatacttatttaatag\n+tatttctggttatataatttgtataaaaagtggttgacataacaaggctg\n+acgaaactttgtgatggctgaaaatattttcctagctttattgattttta\n+tttatacgtgtttgaataacttggccaaatcgccgagaaggaatagaata\n+ctggacgacattgtacatattttccaaaaaatcagaaagtagatgacggg\n+accaattctttctgtcaggttttacaaccgcccagtgcgtctacgtcaca\n+tgttgtataaatggttgtaaacaatatgcggaaacaatcaaatgcattcc\n+cataaggcataatatagaggctacaggcaatgagtatcgctctttgcttt\n+gtttaaagggggagtagagtttgtggggaaatatatgtttctgactctaa\n+ttttgcccctgataccgaatatcgatgtgaaaaaatttaaaaaaatttcc\n+ctgattttatattaatttttaaaatccgaaaatccattggatgcctatat\n+gtgagtttttaaacgcaaaattttcccggcagagacgccccgcccacgaa\n+accgtgccgcacgtgtgggtttacgagctgaatattttccttctattttt\n+atttgattttataccgattttcgtcgatttttctcattttttctcttttt\n+tttggtgttttttattgaaaattttgtgattttcgtaaatttattcctat\n+ttattaataaaaacaaaaacaattccattaaatatcccattttcagcgca\n+aaatcgactggagactaggaaaatcgtctggagatagaacggatcaacaa\n+gattattattatatcattaataatatttatcaattttcttctgagagtct\n+cattgagactcttatttacgccaagaaataaatttaacattaaaattgtt\n+catttttgaaaaaaaaataattaaaaaaacacattttttggaaaaaaaaa\n+taaataaaaaaaattgtcctcgaggatcctccggagcgcgtcgaatcaat\n+gtttccggaactctgaaaattaaatgtttgtatgattgtagaaccctttc\n+gctattgagatttgataacttttaagtaataaaattttcgcagtaagaca\n+ttaaaacatttcacaattaagctggttctgaactgtgtgaagtatattga\n+aaaaaactaactgatacaaaaatataattttatgatagttttctggatgt\n+cccaatataaacgatgtcaattctgcgacatgctacagtcatccacgaaa\n+gtaacccgaataccgacaaaagaagaggaacgccaactttggatagacgc\n+tctaggggctgattttggtcggaaaatagtcgggaaaaaatagaggacat\n+tacagatgaggatgaggatgaagatagaaatttgccgacaacttcgtcat\n+gccgctgatttttttgatgttctacgcttaaattttcagcgaacgaacta\n+ttttttatattttgattgtttttaaataatatttgccataagaaattctc\n+acttttccaggaaacgtcgtttcgccgcgattttcctcgtctccagtcga\n+ttttgcgctgaaaatgggatatttaatggaattgtttttgtttttattaa\n+taaataggaataaatttacgaaaatcacaaaattttcaataaaaaacacc\n+aaaaaaaaagagaaaaaatgagaaaaatcgacgaaaatcggtataaaatc\n+aaataaaaatagaaggaaaatattcagctcgtaaacccgcaagtgcggca\n+cggtttcgtgggcggggcgtctctggcgggaaaattttgcgtttgaaaac\n+tcacatataggcatccaatggattttcggattttcaaaattaatataaaa\n+tcagggaaatttttttaaattttgtcacatcgatattcggtatcaggggc\n+aaaattagagtcagaaacatatatttccccacaaactctactcccccttt\n+aacaaccacccgaggatatattcgacaaacgatctatctactaggaataa\n+ctcgattattgacatattatagacttcttttagtatttgtaaaatagagg\n+atcagacccaaaattcagcccgcgaaggcatgacgtcagcgcgaggcagt\n+agtttccagaagaactctgt'..b'\n+ggttacaggacatcagtgatattgaagatatgaatatagagatattcctg\n+ggttagaatttgactcttatataaaatcactagatcaattaagtttaggt\n+gaaccacgtttattagaagttgataatcgttgtgttattccttgtgatac\n+taacattcgtttttgtattacatctgctgatgttattcatgcttgggcat\n+taaattctttatctgtaaaattagatgctataagaggaattttaagaaca\n+tttagttacaggtttcctatagtgggagttttttatggtcaatgttcaga\n+gatttgtggagcaaatcatagttttataccaattgctttagaggtaacat\n+tattggataattttaaaagatgatgttttggtactatagaataatttagc\n+ttaatagtttatattaaaatgtttacttgtggtgtaagagaatatagagc\n+tttaaattttacttgtttaaatattggtattgcatactattacaataaaa\n+tttcatgttaatgaaaaatagaaacaaagggtagagtaaatattagtttt\n+attgtttcatactaaaaattatatttattagagttgatatgtcgaccttt\n+gtgataactgtttttatttttatattagaaaattatatattatataatta\n+ttttaggaaatttaaaatttgaagtgttttaaatttatgttttacaacat\n+tttcctaattttatttaagtttaatttttaatttaataaagttttattaa\n+ataaataatttgtaaattagtaaattttataaatttaatttattattaaa\n+atataattgaagaacttgaagtcttgatcaaatgttttttaaagacttag\n+gctttatattaaagctggcttctgccctatgatatttaaatggcagtctt\n+agcgtgaggacattaaggtagcaaaataatttgtgcttttattgagttcc\n+agtatgaatgaagttattggttagttctatttatgttttatgtttgaatt\n+taatttttatttaagaaaaaataaatatatttatacaaagataagtcttc\n+ggaaattctgttattacacaattaaataattgtgtaataaattttctagg\n+gcagaatattatataatagtatttcactatatttaatttaaagaattact\n+ccggagttaacagaaaatcatacctaatctagtacttatagtaaggtaag\n+ttttacatcgatgttgtattcagataatctaagagaggagaaggcttagt\n+agtttagactgttcttctattaattaatctgacgtgatattagtttaatt\n+cattgtgagatagaattgtttatcttgataaatatttatatttaatacat\n+ttagtacgaaaggaacattgtaaaagttttaaactttaaagattttgaaa\n+tctttattttagtgctattaatagttttagtgtttacgctagttttatta\n+tttgctttttatttgattaattttttattaagaattaaggatataggaaa\n+aaataaaattagagcgtttgaatgtggttttgtaagagttggaaaaattc\n+aaaattcttttagaattcatttttttattatgatattgatatttgttatt\n+tttgatttagaaattgttatgtttttaggtattttagtatcagatttaag\n+ttcgtatatcaggtttttaataatattcatcttcatcttgggaggatttt\n+acatagagtgatgatatggtaaattagtttgagtaatttaattaatattt\n+ctatttttttgattggatttgttttttttataggtggaattagtgtttgg\n+cttatacccacatttaaattaggaatcttttttttagaatgagatttttt\n+aaggttaaaatttaatttttattttaatagaatcttattttcgtttattc\n+tttttttggtaacgtttagagttttagtttttagtacttattatttaaat\n+agtgagttaaactttaattattattattttgtattgttaattttcgtagg\n+tagaatgtttaggctaaattttagaaacagtatttttacaatgttactaa\n+gatgagatttattgggtatttctaggttttttttagttttattttataat\n+aattgagatagatgtaggggtgcaataaatacagcattaactaatcgtct\n+aggtgattattttatatttgtcttttttggtttatcggtttttagaggtt\n+attattttttaagatttagaatatttagaagttatatatctttattatta\n+cttttaacagcttttactaaaagagcacaatttccatttagatcttggtt\n+acccaaagctataagagcccccacaccggtgaggtctttggttcatagta\n+gaactttagttacagcaggattaattctattaataaattttaataattta\n+gtaatacagaaagattttatcagttttgttctgattattggcctatttac\n+tatatttttttctagcttagcaagtttggtcgaagaagatttgaagaagg\n+tggtagccttgaggacactttcacaaataggtttttcaatagttactttg\n+ggcctagggcttaggtttatttcatttattcatttagttagacatgcttt\n+gttcaaaagatgtttatttatacaagtaggttacattattcattgttcat\n+ttggacaacaagatggacgtaattataggaataatggtaatttaccaaat\n+tttattcagttacaaatattagtaaccctattttgtttatgtggattaat\n+tttctcaaggggtgctgtaagaaaagattttattttagaattattttttt\n+ctaataactatataatgttttttagattaatattttttgtttcagtgttt\n+ttgacttttggttacagttttcgtctttgaaaaagattttttttaaggtt\n+taataaagtaataaatcattacagtagcacagtatttataaattttttaa\n+gtttagtattagttattttttctattagatttttatgatgaataaatttt\n+aatcttcttaacatcccaagacttttcttatacgtagatttttttggccc\n+tctagtatttttatttataataatttttttatcttttttaattttaaaaa\n+tattatttaaggagttaatatacaagtttttagttgattatttggctaaa\n+aatagtatttataaaataaagaatttaaaatttatagatttatttttaaa\n+taatattaattctaaggggtacaccttatttttaagcagtggtatattta\n+aaaattactatttaaaaaggttaaattttaatagtgtagtagttttaatt\n+tttattttttttataatttgttaagggattttagtttaataaaaatatat\n+gttttgcatacataagataataattctagatagttttacacgcgcgtata\n+cgcgcgttataaatatatatatatatatatatatatatatatatatataa\n+taataatattatatttatattataaatataatatttattataaattatat\n+attatatttatattataaatataatatttattataaattatatattatat\n+ttatattataaatataatatttattataaattatatattatatttatatt\n+ataaatataatatttattataaattatatattatatttatattataaata\n+taatatttattatatattatatatattatatttatattataaatataata\n+tttattattaataattcatcatatttatattataaatatgatgaagtact\n+aaaaaaaagatgaatattctataatatatttagatatattatagagtatt\n+tatcttattatttatagatatatactttgtatatatctatatta\n' |
| b |
| diff -r 000000000000 -r d801b0675eb5 test-data/a.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/a.sam Sat Nov 11 18:18:54 2017 -0500 |
| b |
| b'@@ -0,0 +1,824 @@\n+@HD\tVN:1.5\tSO:coordinate\n+@RG\tID:000\tSM:N2\n+@RG\tID:266-1\tSM:ot266\tDS:mutant strain carrying the vab-3 allele ot266\tCN:Columbia University\tPL:Illumina\n+@SQ\tSN:chrI\tLN:25050\tM5:7d9f340160ce45568f9bf48d8e16dcf4\n+@SQ\tSN:chrII\tLN:25050\tM5:ba5a89bf12f55a4bd88ddf14e6d27bd6\n+@SQ\tSN:chrIII\tLN:25050\tM5:ba78739f84b6c850448bec286bdd8798\n+@SQ\tSN:chrIV\tLN:25050\tM5:0807d4df5c3593363a5b015f19ef81c2\n+@SQ\tSN:chrV\tLN:25050\tM5:cf942c1556ef72fd9ba352e4a7d9cf9e\n+@SQ\tSN:chrX\tLN:25050\tM5:5ce1b12d74140cfc288b493c16fe280b\n+@SQ\tSN:MtDNA\tLN:13794\tM5:199e147d502d88e45047413dc83c039c\n+@PG\tID:SNAP\tPN:MiModD snap\tVN:0.1.8.0\tCL:paired /var/tmp/batch_dataset_548966_dataset_35_20_0.3 /var/tmp/batch_dataset_54896612531.sam -d 8 -S 200 -n 25 -a 7 -F s -o /var/tmp/batch_dataset_54896615435.tmp -h 250 -c 2 -C++ -M -s 100 10000 -t 2\n+BS-DSFCONTROL03:121:D0M8KACXX:5:1314:19049:65217\t99\tchrI\t556\t60\t100M\t=\t702\t246\tCCTATATGCTCCTGTGTTTAGGCCTAATACTAAGCCTAAGCCTAAGCCTAATACTAAGCCTAAGCCTAAGACTAAGCCTAATACTAAGCCTAAGCCTAAG\tCCCFFFFDHHHHHJJJJJJJIJJJJJJIIIIIJIJJJJJGIIJIIHIJIJJHIJIJJHIJJIIJJJIIIIGGGIJHHHHHFFEFFFEECEEDDCACDDC?\tPG:Z:SNAP\tRG:Z:000\tNM:i:0\n+EAGLE:1:56:17087:17617/1\t0\tchrI\t575\t60\t101M\t*\t0\t0\tAGGCCTAATACTAAGCCTAAGCCTAAGCCTAATACTAAGCCTAAGCCTAAGACTAAGCCTAATACTAAGCCTAAGCCTAAGACTAAGCCTAAGACTAAGCC\tGGFGGGDGFGEFBGFGFGGGGGGFGGEGGGGGGGGGGGGGGGGGEGGFFEFGGFFGEAFGFDEGGGGGGGEEFDDEEEEEGFGGEGEDBEEAEDEECFEBC\tPG:Z:SNAP\tRG:Z:266-1\tNM:i:0\n+BS-DSFCONTROL03:121:D0M8KACXX:5:1314:19049:65217\t147\tchrI\t702\t60\t100M\t=\t556\t-246\tAGCCTAAGACTAAGCCTAAGCCTAATACTAAGCCTAAGCCTAAGACTAAGCCTAATACTAAGCCTAAGCCTAAGACTAAGCCTAAGACTAAGCCTAAGAC\tCCC>AA>;(CCC;C@3HEEEGCIGED=EGGGJHGJIGGCIJIIDFGGIGDIHJIHEGIHJIIEGGIIGJJJIGIGJIJJJIGDIHGIHHFHGFFFFFCB@\tPG:Z:SNAP\tRG:Z:000\tNM:i:0\n+EAGLE:2:81:6795:13435/1\t16\tchrI\t842\t60\t101M\t*\t0\t0\tTTGAAATGAATATCGTAGCTACAGAAACGGTAGTACACTCTTCTGAAAATACAAAAAAGTTGCAATTTTTTTAGCTAGGACACTTTTTGTCTGCCCAAATA\tA:@EEEEEBEEEEEEEEEGEEEEGEEEEEEEED=BFEEEGEEGEGFGGGEEGGGGGGGGFGGGFDDAGG=GGEGGGFFFEFEECBFDGGEGDGDGGGFGEG\tPG:Z:SNAP\tRG:Z:266-1\tNM:i:8\n+EAGLE:1:46:9721:15037/1\t16\tchrI\t842\t60\t101M\t*\t0\t0\tTTGAAATGAATATCGTAGCTACAGAAACGGTAGTACACTCTTCTGAAAATACAAAAAATTTGCAATTTTTTTAGCTAGGACACTTTTTGTCTGCCCAAATA\tAEEBEBBEEEAAEFEFFFE?FCCCBC?DDBD5DD=D:DDC:CC?C>6EB@CEEEDDEECEEEEE8BFFEEFEEADDCCC@CBCCEEFDFFAEFGFDFGGGD\tPG:Z:SNAP\tRG:Z:266-1\tNM:i:7\n+EAGLE:2:77:15674:6412/1\t0\tchrI\t844\t60\t101M\t*\t0\t0\tGAAATGAATATCGTAGCTACAGAAACGGCAGTACACTCTTCTGAAAATACAAAAAATTTGCAATTTTTATAGCTAGGACACTTTTTGTCTGCCCAAACATA\tGFFGGGCGDFGEGDFEEFEGGFEGFEEEACC?BCCDDCDECBECDEFEECEEDEEEEEEEEBEEEEEEAEEEEE=AC:=CBBCCCC@::?CACC@BBBABE\tPG:Z:SNAP\tRG:Z:266-1\tNM:i:6\n+EAGLE:2:88:10221:3318/1\t16\tchrI\t845\t60\t101M\t*\t0\t0\tAAATGAATATCGTAGCTACAGAAACGGTAGTACACTCTTCTGAAAATACAAAAAATTTGCAATTTTTTTAGCTAGGACACTTTTTGTCTGCCCATATATAG\tAEBABBEEBGEGEBGGGEEEEGEEGGEEGGCEEEFEFEEBGGFDEGAEFGGEDFF=EEGEGGGGGG?DBDFGGFGGDFECCFDDCGEEEE:AG?GFFGDGG\tPG:Z:SNAP\tRG:Z:266-1\tNM:i:5\n+EAGLE:2:87:4119:14575/1\t16\tchrI\t845\t60\t101M\t*\t0\t0\tAAATGAATATCGTAGCTACAGAAACGGTAGTACACTCTTCTGAAAATACAAAAAATTTGCAATTTTTATAGCTAGGACACTTTTTGTCTGCCCAAATTTAA\tGEEGEDEEGEGGEAEFEB?DEEDBGGBGGFGEFBGFGGBGGGGGFGGEGFGGGGGGGGGGGGFEFAGGGGEGGDGGGGDFGGBFGGGGDFDGGDGGGGGEG\tPG:Z:SNAP\tRG:Z:266-1\tNM:i:5\n+EAGLE:2:95:9634:15406/1\t16\tchrI\t845\t60\t101M\t*\t0\t0\tAAATGAATATCGTAGCTACAGAAACGGTAGTACACTCTTCTGAAAATACAAAAAATTTGCAATTTTTTTAGCTAGGACACTTTTTGTCTGCCCAAATATAA\tFEEE?GEFEBE:ECE=BEGGGEGEGBFFFEFAFDFFGEBBGGGFGDGEGGGEEEEE5FFFFCFGAEGGEGGGGGGGFGDGGGFGGGGGGGFGDFFFGGGFD\tPG:Z:SNAP\tRG:Z:266-1\tNM:i:5\n+BS-DSFCONTROL03:121:D0M8KACXX:5:2113:3662:39793\t73\tchrI\t846\t60\t100M\t=\t846\t0\tAATGAATATCGTAGCTACAGAAACGGTAGTACACTCTTCTGAAAATACAAAAAATTTGCAATTTTTATAGCTAGGACACTTTTTGTCTGCCCAAATTTAA\tCCCFFFFFHHHHHJJJJIIIIJIJJJFGIGIIJJIGIJIJJGEHIHJHEHHHJIIJJJJJIJJIGIJIHHHHHHEFFFFECEEDBDDCCDDDDD?CDDDC\tPG:Z:SNAP\tRG:Z:000\tNM:i:5\n+BS-DSFCONTROL03:121:D0M8KACXX:5:2113:3662:39793\t133\tchrI\t846\t0\t*\t=\t846\t0\tGTGTACTACCGTTTCTGGAGCTACGATTTATTTTTCAAAACACGCAAAAAGTGTTTTTCACTATGTACAAAATCATCTCAAAATCGGAAATATTTTTTGT\t<<<@@@@@@@@@@???#################################################################################'..b"FCCE>FDEDEAAGAGCCEEGEEGGFEFEFEGD@EFADEFCC>E?E=BBBAEBF\tPG:Z:SNAP\tRG:Z:266-1\tNM:i:0\n+EAGLE:2:35:14999:3587/1\t0\tMtDNA\t12745\t60\t101M\t*\t0\t0\tTTTTTTCTAATAACTATATAATGTTTTTTAGATTAATATTTTTTGTTTCAGTGTTTTTGACTTTTGGTTACAGTTTTCGTCTTTGAAAAAGATTTTTTTTC\tDEFFFFFFFFBFD?FFFBFFFFFAFEEBECFDFFFFFDAFFFFFFCFFFBECECEFFEC?FBFFFDDEE??CDBEFFFFEEFFFFABFFFE8CFFFFFFE;\tPG:Z:SNAP\tRG:Z:266-1\tNM:i:1\n+BS-DSFCONTROL03:121:D0M8KACXX:5:1101:18737:28666\t99\tMtDNA\t12755\t60\t100M\t=\t12783\t128\tTAACTATATAATGTTTTTTAGATTAATATTTTTTGTTTCAGTGTTTTTGACTTTTGGTTACAGTTTTCGTCTTTGAAAAAGATTTTTTTTAAGGTTTAAT\tCCCFFFFEHHHHHJJJJJJGJGHJJJIGIIJJJJJHIJIIIGHIJJJJJHIIJJJJJIJJJJJIGHHHHFFFFEECECEDDBDDDDDDDDBCCDCCDDDA\tPG:Z:SNAP\tRG:Z:000\tNM:i:0\n+EAGLE:1:53:16100:4061/1\t0\tMtDNA\t12755\t60\t101M\t*\t0\t0\tTAACTATATAATGTTTTTTAGATTAATATTTTTTGTTTCAGTGTTTTTGACTTTTGGTTACAGTTTTCGTCTTTGAAAAAGATTTTTTTTAAGGTTTAATA\tFFDFFDEFDFAFE=FDFE@AFB?DFFF5FF?D@<@ACAEEE:ECEEEAA=FFDFDFADDFEEE@EEEEE@AABBB=AEEEDCCFDBEFE@@@DBADEDBBF\tPG:Z:SNAP\tRG:Z:266-1\tNM:i:0\n+BS-DSFCONTROL03:121:D0M8KACXX:5:1303:13602:38947\t147\tMtDNA\t12781\t60\t100M\t=\t12495\t-386\tTATTTTTTGTTTCAGTGTTTTTGACTTTTGGTTACAGTTTTCGTCTTTGAAAAAGATTTTTTTTAAGGTTTAATAAAGTAATAAATCATTACAGTAGCAC\t:?BBBB?CC@5CCCA9'=>>5(;>C;;A>>?;B@BFEFHEBG@=@>FB;BCGB?<GDEDC9<F<EEA<4D>HEGJHE<C<?<?A<2,,?B=2A4DDD8@?\tPG:Z:SNAP\tRG:Z:000\tNM:i:0\n+BS-DSFCONTROL03:121:D0M8KACXX:5:1101:18737:28666\t147\tMtDNA\t12783\t60\t100M\t=\t12755\t-128\tTTTTTTGTTTCAGTGTTTTTGACTTTTGGTTACAGTTTTCGTCTTTGAAAAAGATTTTTTTTAAGGTTTAATAAAGTAATAAATCATTACAGTAGCACAG\tBDBDDDDCCDDDDBBDDDDEDCDDDDEEEFFFFFFHHFIJJJJJJJJIIHJIIJJJJJJJHGJJJJIJIJJIJJJJIJJJJJJJJJJGHHHHFFFDFCCC\tPG:Z:SNAP\tRG:Z:000\tNM:i:0\n+EAGLE:2:109:6839:9395/1\t16\tMtDNA\t12786\t60\t101M\t*\t0\t0\tTTTGTTTCAGTGTTTTTGACTTTTGGTTACAGTTTTCGTCTTTGAAAAAGATTTTTTTTAAGGTTTAATAAAGTAATAAATCATTACAGTAGCACAGTATT\tGGGGGFEFFGGGGGGDGGDGFDGGGGGGFGGGGGGFFGGGFGGGGGGGGGGGGGGGGGGFBGGGGGDGGGGGGGGGGGGGGFGGGGGGGGEGGFGGGGGGG\tPG:Z:SNAP\tRG:Z:266-1\tNM:i:0\n+EAGLE:2:89:16184:15896/1\t16\tMtDNA\t12850\t60\t101M\t*\t0\t0\tTTAATAAAGTAATAAATCATTACAGTAGCACAGTATTTATAAATTTTTTAAGTTTAGTATTAGTTATTTTTTCTATTAGATTTTTATGATGAATAAATTTT\tEEEEFEEDFEEEGEBEEGEEBEGEEFGEGEGDGBFGFGGFGDFGEGGFEGGGFGEGGGGGFFGCEGGGGGGDGFFGDEGDGGGEGFDGGGGEGFGFGGGGG\tPG:Z:SNAP\tRG:Z:266-1\tNM:i:0\n+EAGLE:2:73:18789:5004/1\t0\tMtDNA\t12862\t60\t97M1I3M\t*\t0\t0\tTAAATCATTACAGTAGCACAGTATTTATAAATTTTTTAAGTTTAGTATTAGTTATTTTTTCTATTAGATTTTTATGATGAATAAATTTTAATCTAATAGAA\tGFEGFGGF=FEADEEEEEEDEEDEEFFFFFGGGGGGDGGGEGDFABE:EEBA=BBFFCCCGE@FF?BBBCACCB8>BEEEFFFGGFFGGE?EEEBD5?BBE\tPG:Z:SNAP\tRG:Z:266-1\tNM:i:4\n+BS-DSFCONTROL03:121:D0M8KACXX:5:1114:11635:22812\t99\tMtDNA\t12940\t60\t100M\t=\t13083\t243\tGAATAAATTTTAATCTTCTTAACATCCCAAGACTTTTCTTATACGTAGATTTTTTTGGTCCTCTAGTATTTTTATTTATAATAATTTTTTTATCTTTTTT\tCCCFFFFFHHHHHJJJJIJJJJJJJIJJJJJJJJJJJJJJJJIIJHIJIJGHJJJJJIHHIJJJFHEHHHHHFFFFFFFEEFEEEFEDDDDDDDDDDDD<\tPG:Z:SNAP\tRG:Z:000\tNM:i:1\n+EAGLE:1:50:13913:15312/1\t16\tMtDNA\t13005\t60\t101M\t*\t0\t0\tGTATTTTTATTTATAATAATTTTTTTATCTTTTTTAATTTTAAAAATATTATTTAAGGAGTTAATATACAAGTTTTTAGTTGATTATTTGGCTAAAAATAG\t?>:>;::BCBB::FFF@@8<96BABC=@DFFBF=EDFDEFCAE=?EE?FAFEEC?=EEEC=FDEEBEEDAFF?EFFEBEDDEEEEBCDDD?E@<DDDEECE\tPG:Z:SNAP\tRG:Z:266-1\tNM:i:0\n+BS-DSFCONTROL03:121:D0M8KACXX:5:1114:11635:22812\t147\tMtDNA\t13083\t60\t100M\t=\t12940\t-243\tGTTGATTATTTGGCTAAAAATAGTATTTATAAAATAAAGAATTTAAAATTTATAGATTTATTTTTAAATAATATTAATTCTAAGGGGTACACCTTATTTT\t@CFEDEFFFHGHGIJJJJJJJIHEGJJIHCJJJJJJJJJJJJJJJJJJJJJJJIJJIJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJHHHDHFFFFFCC@\tPG:Z:SNAP\tRG:Z:000\tNM:i:0\n+BS-DSFCONTROL03:121:D0M8KACXX:5:2115:12001:40456\t99\tMtDNA\t13159\t60\t100M\t=\t13242\t183\tATTCTAAGGGGTACACCTTATTTTTAAGCAGTGGTATATTTAAAAATTACTATTTAAAAAGGTTAAATTTTAATAGTGTAGTAGTTTTAATTTTTATTTT\t@@@FFFFDFFHDFGGEB;AB<EHGGGBH@FH?CC?F@GGIII>DGHGEDBDHHEDHGHIIGCHGI@@FGHIHGGIC==EC>)=A?CD>DDDEEECAACDD\tPG:Z:SNAP\tRG:Z:000\tNM:i:0\n+BS-DSFCONTROL03:121:D0M8KACXX:5:2115:12001:40456\t147\tMtDNA\t13242\t60\t100M\t=\t13159\t-183\tGTTTTAATTTTTATTTTTTTTATAATTTGTTAAGGGATTTTAGTTTAATAAAAATATATGTTTTGCATACATAAGATAATAATTCTAGATAGTTTTACAC\t@DDDDDDDCACDDDFGJIIJIJIIG@HIIJIHIHJJIIGJJIHGGIEIIGIIIIJIGIJJJJIGGCIIIGJIJJJIJJJIHIIJJJJHHFDGFFDDD@@@\tPG:Z:SNAP\tRG:Z:000\tNM:i:0\n" |
| b |
| diff -r 000000000000 -r d801b0675eb5 test-data/a.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/a.vcf Sat Nov 11 18:18:54 2017 -0500 |
| b |
| b'@@ -0,0 +1,192 @@\n+##fileformat=VCFv4.2\n+##FILTER=<ID=PASS,Description="All filters passed">\n+##reference=/home/wolma/galaxy_2017/database/files/000/dataset_35.dat\n+##contig=<ID=chrI,length=25050>\n+##contig=<ID=chrII,length=25050>\n+##contig=<ID=chrIII,length=25050>\n+##contig=<ID=chrIV,length=25050>\n+##contig=<ID=chrV,length=25050>\n+##contig=<ID=chrX,length=25050>\n+##contig=<ID=MtDNA,length=13794>\n+##ALT=<ID=X,Description="Represents allele(s) other than observed.">\n+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">\n+##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel">\n+##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel">\n+##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">\n+##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3">\n+##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)">\n+##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)">\n+##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)">\n+##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)">\n+##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">\n+##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">\n+##INFO=<ID=ICB,Number=1,Type=Float,Description="Inbreeding Coefficient Binomial test (bigger is better)">\n+##INFO=<ID=HOB,Number=1,Type=Float,Description="Bias in the number of HOMs number (smaller is better)">\n+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes for each ALT allele, in the same order as listed">\n+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">\n+##INFO=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases">\n+##INFO=<ID=MQ,Number=1,Type=Integer,Description="Average mapping quality">\n+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">\n+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Number of high-quality bases">\n+##FORMAT=<ID=DPR,Number=R,Type=Integer,Description="Number of high-quality bases observed for each allele">\n+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Phred-scaled Genotype Quality">\n+##source=MiModD varcall (version 0.1.8.0)\n+##MiModDCommand=mimodd varcall /home/wolma/galaxy_2017/database/files/000/dataset_35.dat /home/wolma/galaxy_2017/database/files/000/dataset_54.dat --index-files /home/wolma/galaxy_2017/database/files/_metadata_files/000/metadata_14.dat --ofile /home/wolma/galaxy_2017/database/files/000/dataset_58.dat --depth 250 --verbose --quiet\n+##samtoolsCommand=n.a. (wrapped by MiModD)\n+##bcftools_callCommand=n.a. (wrapped by MiModD)\n+##rginfo=<ID=0,Rgid="000",Name="N2">\n+##rginfo=<ID=1,Rgid="266-1",Name="ot266",Description="mutant strain carrying the vab-3 allele ot266">\n+##samtoolsVersion=1.2+htslib-1.2.1\n+##bcftools_callVersion=1.2+htslib-1.2.1\n+##bcftools_concatVersion=1.2+htslib-1.2.1\n+##bcftools_viewVersion=1.2+htslib-1.2.1\n+##bcftools_viewCommand=view /home/wolma/galaxy_2017/database/files/000/dataset_58.dat\n+#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tN2\tot266\n+chrI\t855\t.\tG\tC\t231.0\t.\tDP=27;VDB=2.48853e-13;SGB=13.8822;MQSB=1;MQ0F=0;AC=2;AN=2;DP4=0,0,11,13;MQ=60\tGT:PL:DP:DPR:GQ\t./.:0,0,0:0:0,0:0\t1/1:255,72,0:24:0,24:86\n+chrI\t885\t.\tt\ttTCT\t69.0\t.\tINDEL;IDV=4;IMF=0.0769231;DP=56;VDB=2.27029e-09;SGB=1.27626;MQSB=1;MQ0F=0;ICB=0.3;HOB=0.125;AC=1;AN=4;DP4=16,17,3,1;MQ=60\tGT:PL:DP:DPR:GQ\t0/0:0,3,60:1:1,0:11\t0/1:105,0,255:36:32,4:96\n+chrI\t912\t.\tA\tT\t195.0\t'..b',0,0:0:0,0:0\t1/1:38,3,0:1:0,1:4\n+chrX\t1622\t.\tG\tT\t13.4669\t.\tDP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60\tGT:PL:DP:DPR:GQ\t./.:0,0,0:0:0,0:0\t1/1:38,3,0:1:0,1:4\n+chrX\t1648\t.\tA\tC\t12.5173\t.\tDP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60\tGT:PL:DP:DPR:GQ\t./.:0,0,0:0:0,0:0\t1/1:37,3,0:1:0,1:4\n+chrX\t1650\t.\tT\tA\t10.6576\t.\tDP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60\tGT:PL:DP:DPR:GQ\t./.:0,0,0:0:0,0:0\t1/1:35,3,0:1:0,1:4\n+chrX\t6015\t.\tA\tT\t13.4669\t.\tDP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60\tGT:PL:DP:DPR:GQ\t1/1:38,3,0:1:0,1:4\t./.:0,0,0:0:0,0:0\n+chrX\t6032\t.\tG\tA\t8.01478\t.\tDP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60\tGT:PL:DP:DPR:GQ\t1/1:32,3,0:1:0,1:4\t./.:0,0,0:0:0,0:0\n+chrX\t6058\t.\tta\tt\t15.3937\t.\tINDEL;IDV=1;IMF=1;DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,0,1;MQ=60\tGT:PL:DP:DPR:GQ\t1/1:40,3,0:1:0,1:4\t./.:0,0,0:0:0,0:0\n+chrX\t6118\t.\tA\tG\t15.394\t.\tDP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,0,1;MQ=60\tGT:PL:DP:DPR:GQ\t1/1:40,3,0:1:0,1:4\t./.:0,0,0:0:0,0:0\n+chrX\t6143\t.\tG\tA\t12.5173\t.\tDP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,0,1;MQ=60\tGT:PL:DP:DPR:GQ\t1/1:37,3,0:1:0,1:4\t./.:0,0,0:0:0,0:0\n+chrX\t6984\t.\tT\tA\t13.4669\t.\tDP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60\tGT:PL:DP:DPR:GQ\t./.:0,0,0:0:0,0:0\t1/1:38,3,0:1:0,1:4\n+chrX\t7025\t.\tA\tG\t12.5173\t.\tDP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60\tGT:PL:DP:DPR:GQ\t./.:0,0,0:0:0,0:0\t1/1:37,3,0:1:0,1:4\n+chrX\t10527\t.\tc\tcC\t8.86989\t.\tINDEL;IDV=1;IMF=1;DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60\tGT:PL:DP:DPR:GQ\t./.:0,0,0:0:0,0:0\t1/1:33,3,0:1:0,1:4\n+chrX\t10535\t.\tT\tC\t11.8912\t.\tDP=2;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60\tGT:PL:DP:DPR:GQ\t./.:0,0,0:0:0,0:0\t1/1:36,3,0:1:0,1:6\n+chrX\t10562\t.\tC\tG\t18.2649\t.\tDP=7;VDB=0.18;SGB=0.00473136;RPB=0.8;MQB=1;MQSB=1;BQB=0.9;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=4,1,2,0;MQ=60\tGT:PL:DP:DPR:GQ\t./.:0,0,0:0:0,0:0\t0/1:49,0,131:7:5,2:48\n+chrX\t10595\t.\tT\tG\t148.0\t.\tDP=7;VDB=0.00429645;SGB=2.55596;MQSB=1;MQ0F=0;AC=2;AN=2;DP4=0,0,6,1;MQ=60\tGT:PL:DP:DPR:GQ\t./.:0,0,0:0:0,0:0\t1/1:172,21,0:7:0,7:29\n+chrX\t10629\t.\tgt\tg\t45.8065\t.\tINDEL;IDV=4;IMF=0.666667;DP=6;VDB=0.14;SGB=0.0985265;MQ0F=0;AC=2;AN=2;DP4=0,0,2,0;MQ=60\tGT:PL:DP:DPR:GQ\t./.:0,0,0:0:0,0:0\t1/1:70,6,0:2:0,2:13\n+chrX\t10630\t.\tT\tC,G\t10.4616\t.\tDP=2;VDB=0.32;SGB=0.0985265;MQSB=1;MQ0F=0;AC=1,1;AN=2;DP4=0,0,1,1;MQ=60\tGT:PL:DP:DPR:GQ\t./.:0,0,0,0,0,0:0:0,0,0:0\t1/2:58,29,26,32,0,29:2:0,1,1:25\n+chrX\t10643\t.\tG\tT\t34.5919\t.\tDP=3;VDB=0.02;SGB=0.0985265;MQSB=1;MQ0F=0;AC=2;AN=2;DP4=0,0,1,1;MQ=60\tGT:PL:DP:DPR:GQ\t./.:0,0,0:0:0,0:0\t1/1:59,6,0:2:0,2:11\n+chrX\t15480\t.\tT\tC\t13.4669\t.\tDP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60\tGT:PL:DP:DPR:GQ\t./.:0,0,0:0:0,0:0\t1/1:38,3,0:1:0,1:4\n+chrX\t15495\t.\tG\tC\t13.4669\t.\tDP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60\tGT:PL:DP:DPR:GQ\t./.:0,0,0:0:0,0:0\t1/1:38,3,0:1:0,1:4\n+chrX\t24890\t.\tC\tG\t13.4669\t.\tDP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60\tGT:PL:DP:DPR:GQ\t./.:0,0,0:0:0,0:0\t1/1:38,3,0:1:0,1:4\n+chrX\t24935\t.\tA\tC\t11.5799\t.\tDP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60\tGT:PL:DP:DPR:GQ\t./.:0,0,0:0:0,0:0\t1/1:36,3,0:1:0,1:4\n+MtDNA\t954\t.\tG\tT\t4.79534\t.\tDP=2;SGB=-0.516033;RPB=1;MQB=1;BQB=1;MQ0F=0;ICB=0.5;HOB=0.5;AC=2;AN=4;DP4=0,1,0,1;MQ=60\tGT:PL:DP:DPR:GQ\t0/1:36,3,0:1:0,1:3\t0/1:0,3,33:1:1,0:3\n+MtDNA\t5979\t.\tC\tA\t7.18923\t.\tDP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,0,1;MQ=60\tGT:PL:DP:DPR:GQ\t./.:0,0,0:0:0,0:0\t1/1:31,3,0:1:0,1:4\n+MtDNA\t8429\t.\tA\tG\t38.5774\t.\tDP=2;VDB=0.36;SGB=-0.759771;MQSB=1;MQ0F=0;AC=4;AN=4;DP4=0,0,1,1;MQ=60\tGT:PL:DP:DPR:GQ\t1/1:26,3,0:1:0,1:9\t1/1:37,3,0:1:0,1:9\n+MtDNA\t12134\t.\tA\tG\t6.22224\t.\tDP=2;SGB=-0.516033;RPB=1;MQB=1;BQB=1;MQ0F=0;ICB=0.5;HOB=0.5;AC=2;AN=4;DP4=0,1,0,1;MQ=60\tGT:PL:DP:DPR:GQ\t0/1:0,3,41:1:1,0:3\t0/1:38,3,0:1:0,1:3\n+MtDNA\t12637\t.\tG\tT\t8.72328\t.\tDP=2;SGB=-0.516033;RPB=1;MQB=1;BQB=1;MQ0F=0;ICB=0.5;HOB=0.5;AC=2;AN=4;DP4=1,0,1,0;MQ=60\tGT:PL:DP:DPR:GQ\t0/1:41,3,0:1:0,1:3\t0/1:0,3,25:1:1,0:3\n+MtDNA\t12998\t.\tC\tT\t14.4264\t.\tDP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60\tGT:PL:DP:DPR:GQ\t1/1:39,3,0:1:0,1:4\t./.:0,0,0:0:0,0:0\n' |
| b |
| diff -r 000000000000 -r d801b0675eb5 test-data/a_part1.bam |
| b |
| Binary file test-data/a_part1.bam has changed |
| b |
| diff -r 000000000000 -r d801b0675eb5 test-data/a_part2.bam |
| b |
| Binary file test-data/a_part2.bam has changed |
| b |
| diff -r 000000000000 -r d801b0675eb5 test-data/a_part2.bcf |
| b |
| Binary file test-data/a_part2.bcf has changed |
| b |
| diff -r 000000000000 -r d801b0675eb5 test-data/ce11ToCe10.over.chain --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ce11ToCe10.over.chain Sat Nov 11 18:18:54 2017 -0500 |
| b |
| b'@@ -0,0 +1,871 @@\n+chain 1420037770 chrI 15072434 + 0 15072434 chrI 15072423 + 0 15072423 5\n+288367\t0\t1\n+49582\t0\t1\n+3348\t0\t1\n+884584\t1\t0\n+731267\t0\t1\n+203378\t1\t0\n+1324625\t0\t1\n+399852\t13\t13\n+122370\t1\t0\n+213502\t1\t0\n+782497\t1\t0\n+39234\t0\t3\n+867656\t1\t0\n+595979\t1\t0\n+295566\t2\t0\n+147478\t1\t1\n+23\t1\t1\n+191487\t13\t13\n+8983\t1\t0\n+213892\t1\t0\n+58238\t1\t0\n+125173\t11\t11\n+206247\t1\t0\n+126100\t1\t1\n+46\t1\t1\n+281857\t1\t0\n+118832\t1\t0\n+67661\t0\t1\n+470697\t1\t0\n+457535\t1\t0\n+70047\t4\t4\n+38252\t0\t1\n+84452\t1\t0\n+164033\t1\t0\n+319488\t1\t0\n+78543\t1\t0\n+82353\t0\t1\n+129773\t0\t1\n+246657\t1\t0\n+5362\t1\t0\n+354010\t0\t4\n+296600\t1\t0\n+240963\t1\t0\n+37688\t1\t0\n+81200\t0\t1\n+883251\t1\t0\n+528183\t1\t0\n+98784\t1\t1\n+39\t1\t1\n+65027\t1\t0\n+20874\t0\t1\n+542549\t1\t0\n+216555\t1\t1\n+30\t1\t1\n+489109\t1\t0\n+27002\t0\t1\n+222382\t0\t1\n+473092\n+\n+chain 1440101603 chrII 15279421 + 0 15279421 chrII 15279345 + 0 15279345 4\n+523340\t1\t0\n+72281\t0\t8\n+1033090\t1\t0\n+219329\t1\t0\n+1025107\t1\t0\n+69649\t1\t0\n+298884\t0\t1\n+80283\t1\t0\n+210227\t6\t6\n+264469\t1\t0\n+150004\t0\t1\n+195807\t4\t4\n+19\t1\t1\n+130806\t1\t0\n+48603\t0\t1\n+10950\t0\t1\n+40978\t1\t0\n+8097\t1\t0\n+8850\t1\t0\n+8123\t1\t0\n+69125\t11\t11\n+10907\t1\t0\n+5353\t1\t0\n+8256\t1\t0\n+17809\t0\t1\n+114\t1\t0\n+227028\t1\t0\n+45383\t1\t0\n+58370\t0\t1\n+20457\t1\t0\n+58010\t1\t0\n+87001\t1\t0\n+14949\t1\t0\n+74773\t1\t0\n+28654\t0\t1\n+10953\t1\t0\n+15259\t1\t0\n+40597\t1\t0\n+27717\t1\t0\n+6740\t1\t0\n+4824\t1\t1\n+45\t1\t1\n+17113\t1\t0\n+10452\t1\t0\n+10008\t1\t0\n+40\t1\t0\n+325484\t1\t0\n+101544\t1\t0\n+37009\t1\t0\n+81375\t1\t0\n+31951\t0\t1\n+15484\t1\t0\n+2002\t1\t0\n+18194\t1\t0\n+49533\t1\t0\n+10227\t1\t0\n+24688\t1\t0\n+679\t0\t1\n+16673\t0\t1\n+7053\t1\t0\n+1411\t1\t0\n+47812\t1\t0\n+17219\t1\t0\n+61795\t1\t0\n+86135\t1\t0\n+946\t1\t0\n+111201\t1\t0\n+218005\t0\t1\n+11971\t1\t0\n+73658\t1\t0\n+19417\t1\t0\n+72871\t1\t0\n+283\t1\t0\n+2842\t1\t0\n+3514\t0\t1\n+840\t1\t0\n+3474\t1\t0\n+955\t1\t0\n+2287\t1\t0\n+2361\t1\t0\n+1089\t0\t1\n+14383\t1\t0\n+5488\t1\t0\n+4796\t0\t1\n+4398\t16\t15\n+5031\t1\t0\n+113079\t1\t0\n+23\t1\t1\n+66852\t0\t1\n+5830\t0\t1\n+190601\t0\t1\n+198305\t1\t0\n+4222\t1\t0\n+53719\t1\t0\n+756\t0\t1\n+4814\t0\t1\n+30348\t1\t0\n+24557\t1\t0\n+20774\t1\t0\n+27794\t1\t0\n+5248\t1\t0\n+16975\t1\t0\n+88212\t0\t1\n+8139\t1\t0\n+9120\t1\t0\n+5934\t1\t0\n+299\t1\t0\n+3783\t0\t1\n+29302\t1\t0\n+22820\t1\t0\n+2328\t1\t0\n+55710\t0\t1\n+45380\t0\t1\n+3738\t0\t1\n+6318\t1\t0\n+15813\t1\t0\n+53875\t0\t1\n+153420\t1\t0\n+153960\t0\t1\n+23506\t0\t1\n+150079\t1\t0\n+261706\t0\t1\n+119773\t1\t0\n+980\t1\t0\n+5188\t1\t0\n+7342\t1\t0\n+3721\t1\t0\n+38949\t1\t0\n+15594\t1\t0\n+7944\t1\t0\n+2944\t1\t0\n+8840\t1\t0\n+63008\t1\t0\n+20236\t1\t0\n+117305\t0\t1\n+56817\t1\t0\n+60924\t0\t1\n+29445\t0\t1\n+118537\t0\t1\n+119230\t1\t0\n+8658\t1\t0\n+63097\t0\t1\n+2875\t0\t1\n+33991\t1\t0\n+20186\t0\t1\n+28450\t1\t0\n+33646\t0\t1\n+347416\t0\t1\n+7259\t1\t0\n+241675\t1\t0\n+220929\t0\t1\n+3002\t1\t0\n+136217\t0\t1\n+262982\t1\t0\n+147119\t0\t1\n+54695\t0\t1\n+131126\t1\t0\n+32574\t1\t0\n+1218\t1\t0\n+716\t1\t0\n+3556\t1\t0\n+2353\t1\t0\n+348169\t1\t0\n+3214\t1\t0\n+57644\t0\t1\n+81\t0\t1\n+90130\t0\t1\n+2762\t0\t1\n+14905\t1\t0\n+171057\t1\t0\n+7929\t0\t1\n+62035\t1\t0\n+269321\t1\t0\n+42811\t0\t1\n+289174\t1\t0\n+45545\t1\t0\n+61150\t1\t0\n+6930\t1\t0\n+1603\t1\t0\n+11627\t1\t0\n+75337\t0\t1\n+20219\t1\t1\n+38\t1\t0\n+11375\t0\t1\n+4399\t0\t1\n+17225\t1\t0\n+205976\t1\t0\n+8055\t1\t0\n+2824\t0\t1\n+701191\t0\t1\n+99519\t3\t0\n+48815\t1\t0\n+21995\t1\t0\n+138638\t1\t0\n+223081\t1\t0\n+196633\t0\t1\n+274626\t1\t0\n+540443\n+\n+chain 1298422871 chrIII 13783801 + 0 13783801 chrIII 13783700 + 0 13783700 6\n+38559\t1\t0\n+441671\t1\t0\n+63422\t1\t0\n+121743\t1\t0\n+6719\t1\t0\n+86754\t0\t1\n+32684\t1\t0\n+12353\t0\t1\n+1849\t1\t0\n+5970\t1\t0\n+10118\t1\t0\n+25395\t3\t0\n+24340\t1\t0\n+157191\t0\t1\n+124351\t0\t1\n+24720\t0\t1\n+422326\t1\t0\n+36527\t1\t1\n+85\t1\t1\n+324735\t1\t0\n+292394\t1\t0\n+73267\t0\t1\n+214327\t0\t1\n+111579\t0\t1\n+508663\t1\t0\n+882\t6\t6\n+92472\t21\t21\n+16578\t1\t1\n+27\t1\t1\n+68156\t0\t1\n+7040\t1\t0\n+8771\t0\t1\n+22246\t1\t0\n+331\t1\t0\n+12248\t1\t0\n+35539\t0\t1\n+4829\t1\t0\n+5824\t1\t0\n+37908\t1\t0\n+120270\t1\t0\n+5051\t1\t0\n+13804\t1\t0\n+11789\t1\t0\n+15400\t1\t0\n+74896\t0\t1\n+719\t1\t0\n+113657\t1\t0\n+6963\t0\t1\n+30063\t1\t0\n+18197\t1\t0\n+105520\t0\t1\n+4628\t1\t0\n+19202\t1\t0\n+4259\t1\t0\n+104\t1\t0\n+13678\t1\t0\n+15727\t1\t0\n+43284\t1\t0\n+117374\t1\t1\n+21\t1\t1\n+1574\t1\t0\n+129530\t1\t0\n+104666\t1\t0\n+2053\t1\t0\n+573\t1\t0\n+55164\t1\t0\n+102195\t0\t1\n+7782\t1\t0\n+15760\t1\t0\n+11953\t1\t0\n+43896\t0\t1\n+3280\t1\t0\n+1883\t1\t0\n+119248\t1\t0\n+130004\t1\t0\n+9095\t1\t0\n+14169\t0\t1\n+11083\t0\t1\n+10070\t0\t1\n+34120\t1\t0\n+12857\t0\t1\n+2225\t1\t0\n+16098\t1\t0\n+18356\t1\t0\n+39055\t1\t0\n+362323\t0\t1\n+3676\t1\t0\n+40883\t1\t0\n+'..b'820\t1\t0\n+512830\t0\t1\n+500725\t1\t0\n+176265\t1\t0\n+515683\t1\t0\n+67080\t0\t1\n+19249\t1\t0\n+380483\t1\t0\n+46682\t1\t0\n+260457\t1\t0\n+209117\t1\t0\n+552612\t1\t0\n+816610\t1\t0\n+106895\t1\t0\n+12606\t0\t1\n+53468\t1\t0\n+26564\t1\t0\n+275666\t1\t0\n+217083\t0\t1\n+1009889\t1\t0\n+114897\t0\t1\n+500861\t1\t0\n+279757\t1\t0\n+54691\t1\t0\n+209554\t0\t1\n+331356\t1\t1\n+31\t1\t1\n+349157\t1\t0\n+14536\t1\t0\n+82179\t6\t6\n+66027\t0\t1\n+40176\t1\t0\n+32467\t1\t0\n+64194\t1\t0\n+464096\t1\t0\n+1609\t1\t0\n+37905\t1\t0\n+113455\t1\t0\n+243754\t1\t0\n+217119\t0\t1\n+79872\t0\t1\n+15789\t0\t1\n+95\t1\t0\n+423256\t1\t0\n+337914\t1\t0\n+365409\t1\t0\n+469901\t0\t1\n+313459\t1\t0\n+1617\t0\t1\n+4139\t1\t0\n+84\t1\t0\n+75194\t0\t1\n+98987\t0\t1\n+23655\t1\t0\n+32932\t1\t0\n+25720\t0\t1\n+173956\t1\t0\n+1012065\t1\t0\n+484749\t1\t0\n+14808\t1\t0\n+15495\t0\t1\n+14960\t1\t0\n+233789\t1\t0\n+93485\t1\t0\n+21643\t1\t0\n+7923\t1\t0\n+36842\t1\t0\n+1761795\t1\t0\n+465931\t1\t0\n+26392\t1\t0\n+141077\t1\t0\n+126208\t1\t0\n+250326\t0\t1\n+12211\t1\t1\n+18\t1\t1\n+2465\n+\n+chain 1284774 chrM 13794 + 0 13794 chrM 13794 + 0 13794 21\n+13794\n+\n+chain 1970778631 chrV 20924180 + 0 20924180 chrV 20924149 + 0 20924149 1\n+46067\t12\t12\n+120476\t0\t1\n+1109151\t1\t0\n+501367\t1\t0\n+809514\t1\t0\n+689715\t1\t0\n+310727\t10\t0\n+163621\t1\t0\n+61321\t1\t0\n+327298\t0\t1\n+849676\t1\t0\n+173352\t1\t0\n+594036\t1\t0\n+1109131\t1\t0\n+91244\t1\t1\n+31\t2\t2\n+152235\t1\t0\n+96646\t0\t1\n+181165\t1\t0\n+505137\t1\t0\n+533871\t1\t0\n+107988\t1\t0\n+436036\t1\t0\n+38066\t0\t1\n+147968\t1\t0\n+134182\t1\t0\n+408407\t1\t0\n+52531\t0\t1\n+316822\t1\t0\n+96262\t1\t0\n+71747\t0\t1\n+100380\t0\t1\n+119\t0\t1\n+177955\t1\t0\n+34488\t0\t1\n+47765\t0\t1\n+2476\t0\t1\n+97350\t0\t1\n+166629\t0\t1\n+162898\t0\t1\n+756298\t1\t0\n+808254\t0\t1\n+57008\t0\t1\n+220276\t0\t1\n+117644\t0\t1\n+164846\t0\t1\n+128420\t0\t1\n+139963\t1\t0\n+87896\t0\t1\n+33363\t0\t1\n+166892\t1\t0\n+68228\t1\t0\n+183704\t1\t0\n+971868\t1\t0\n+8203\t1\t0\n+501310\t1\t0\n+87822\t1\t0\n+407506\t1\t0\n+524751\t1\t0\n+230024\t1\t0\n+184578\t1\t0\n+30419\t1\t0\n+284334\t1\t0\n+279971\t1\t0\n+506490\t1\t0\n+13210\t1\t0\n+544744\t0\t1\n+23456\t1\t0\n+228549\t1\t0\n+699556\t1\t0\n+308085\t1\t0\n+1130593\n+\n+chain 1668452079 chrX 17718942 + 0 17718942 chrX 17718866 + 0 17718866 2\n+365023\t0\t1\n+59520\t1\t1\n+83\t1\t1\n+64150\t1\t1\n+24\t1\t1\n+93332\t1\t0\n+50100\t1\t0\n+239882\t1\t0\n+56187\t1\t0\n+205216\t1\t1\n+31\t1\t1\n+58960\t1\t0\n+6010\t1\t0\n+2980\t0\t1\n+1468\t1\t0\n+599940\t1\t0\n+362963\t1\t0\n+53132\t1\t0\n+151385\t0\t1\n+65081\t1\t0\n+86753\t0\t1\n+76638\t1\t0\n+92856\t0\t1\n+102821\t1\t0\n+99213\t1\t0\n+5814\t1\t0\n+318947\t1\t0\n+373\t1\t0\n+74234\t1\t0\n+788\t0\t1\n+29243\t1\t0\n+53254\t1\t0\n+35608\t0\t1\n+309218\t1\t0\n+21126\t1\t0\n+8877\t1\t0\n+51664\t1\t0\n+8450\t1\t0\n+667\t1\t0\n+88862\t1\t0\n+73166\t1\t0\n+43899\t1\t0\n+7206\t1\t0\n+61617\t1\t0\n+259376\t1\t0\n+144538\t1\t0\n+14187\t1\t0\n+8035\t1\t0\n+35410\t0\t1\n+1696\t0\t1\n+27102\t1\t0\n+109466\t1\t0\n+15952\t1\t0\n+18537\t1\t0\n+193640\t1\t0\n+280834\t1\t0\n+311195\t1\t0\n+1312\t1\t0\n+1534\t1\t0\n+713059\t1\t0\n+2203\t0\t1\n+2892\t1\t0\n+147098\t1\t0\n+286378\t1\t0\n+26340\t1\t0\n+145722\t1\t0\n+84317\t1\t0\n+32118\t1\t0\n+38351\t1\t0\n+4806\t0\t1\n+6350\t1\t0\n+38251\t1\t0\n+48873\t0\t1\n+148664\t1\t0\n+8155\t1\t0\n+66967\t1\t0\n+101375\t0\t1\n+96243\t1\t0\n+52201\t1\t0\n+18554\t1\t0\n+59690\t1\t0\n+5989\t1\t0\n+5241\t1\t0\n+191703\t0\t1\n+17466\t0\t1\n+7649\t0\t1\n+117783\t0\t1\n+42759\t1\t0\n+7022\t1\t0\n+10\t1\t1\n+19190\t1\t0\n+23579\t0\t1\n+87055\t1\t0\n+43801\t1\t0\n+67035\t1\t0\n+99540\t1\t0\n+176603\t0\t1\n+74325\t1\t0\n+5510\t0\t1\n+149444\t1\t0\n+148509\t1\t0\n+56325\t1\t0\n+93537\t1\t0\n+59304\t1\t0\n+60888\t1\t0\n+65\t1\t0\n+6876\t0\t1\n+7468\t1\t0\n+276908\t0\t1\n+8530\t0\t1\n+170578\t1\t0\n+403043\t1\t0\n+107346\t1\t0\n+88001\t0\t1\n+23258\t1\t0\n+173118\t1\t0\n+30465\t1\t0\n+100620\t1\t0\n+62280\t0\t1\n+4126\t1\t0\n+20159\t1\t0\n+48967\t1\t0\n+205739\t1\t0\n+230925\t0\t1\n+102121\t0\t1\n+159162\t1\t0\n+64642\t1\t0\n+71164\t1\t0\n+90786\t0\t1\n+34364\t1\t0\n+835\t1\t0\n+11432\t0\t1\n+94422\t1\t0\n+620787\t0\t1\n+23610\t1\t0\n+52377\t1\t0\n+107672\t0\t1\n+42438\t1\t0\n+235\t1\t0\n+10781\t1\t0\n+13289\t1\t0\n+34685\t0\t1\n+23366\t0\t1\n+267663\t0\t1\n+126899\t1\t0\n+47857\t0\t1\n+212992\t0\t1\n+15516\t0\t1\n+8186\t1\t0\n+76902\t1\t0\n+3098\t1\t0\n+223975\t0\t1\n+30765\t0\t1\n+197912\t1\t0\n+330005\t1\t0\n+108070\t0\t1\n+254\t1\t0\n+198485\t0\t1\n+22006\t0\t1\n+19263\t1\t0\n+78226\t1\t0\n+39665\t0\t1\n+184579\t1\t0\n+4456\t9\t9\n+270328\t0\t1\n+269016\t0\t1\n+355613\t1\t0\n+87979\t1\t0\n+40892\t13\t13\n+7866\t1\t0\n+57294\t4\t4\n+18253\t1\t0\n+53857\t1\t0\n+4785\t0\t1\n+32952\t0\t1\n+59549\t1\t0\n+40816\t1\t0\n+29424\t1\t0\n+5468\t0\t1\n+36229\t0\t1\n+167876\t1\t1\n+46\t1\t1\n+1224\t1\t0\n+585897\t1\t1\n+20\t1\t1\n+7231\t1\t0\n+323928\t0\t1\n+64761\t1\t0\n+42818\t1\t0\n+105115\t1\t0\n+127679\n+\n' |
| b |
| diff -r 000000000000 -r d801b0675eb5 test-data/header_only.bam |
| b |
| Binary file test-data/header_only.bam has changed |
| b |
| diff -r 000000000000 -r d801b0675eb5 test-data/header_only.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/header_only.sam Sat Nov 11 18:18:54 2017 -0500 |
| b |
| @@ -0,0 +1,2 @@ +@HD VN:1.5 +@RG ID:000 SM:N2 DS:C. elegans wt CN:ABC DT:2017-06-27 LB:XYZ PI:400 PL:ILLUMINA PU:SEQ123 |
| b |
| diff -r 000000000000 -r d801b0675eb5 test-data/reads_1_w_header.bam |
| b |
| Binary file test-data/reads_1_w_header.bam has changed |
| b |
| diff -r 000000000000 -r d801b0675eb5 test-data/reads_1and2_w_header.bam |
| b |
| Binary file test-data/reads_1and2_w_header.bam has changed |
| b |
| diff -r 000000000000 -r d801b0675eb5 test-data/rebased.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rebased.vcf Sat Nov 11 18:18:54 2017 -0500 |
| b |
| b'@@ -0,0 +1,186 @@\n+##fileformat=VCFv4.2\n+##FILTER=<ID=PASS,Description="All filters passed">\n+##reference=/home/wolma/galaxy_2017/database/files/000/dataset_35.dat\n+##contig=<ID=chrI,length=15072423>\n+##contig=<ID=chrII,length=15279345>\n+##contig=<ID=chrIII,length=13783700>\n+##contig=<ID=chrIV,length=17493793>\n+##contig=<ID=chrM,length=13794>\n+##contig=<ID=chrV,length=20924149>\n+##contig=<ID=chrX,length=17718866>\n+##ALT=<ID=X,Description="Represents allele(s) other than observed.">\n+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">\n+##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel">\n+##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel">\n+##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">\n+##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3">\n+##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)">\n+##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)">\n+##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)">\n+##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)">\n+##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">\n+##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">\n+##INFO=<ID=ICB,Number=1,Type=Float,Description="Inbreeding Coefficient Binomial test (bigger is better)">\n+##INFO=<ID=HOB,Number=1,Type=Float,Description="Bias in the number of HOMs number (smaller is better)">\n+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes for each ALT allele, in the same order as listed">\n+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">\n+##INFO=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases">\n+##INFO=<ID=MQ,Number=1,Type=Integer,Description="Average mapping quality">\n+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">\n+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Number of high-quality bases">\n+##FORMAT=<ID=DPR,Number=R,Type=Integer,Description="Number of high-quality bases observed for each allele">\n+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Phred-scaled Genotype Quality">\n+##source=MiModD varcall (version 0.1.8.0)\n+##MiModDCommand=mimodd varcall /home/wolma/galaxy_2017/database/files/000/dataset_35.dat /home/wolma/galaxy_2017/database/files/000/dataset_54.dat --index-files /home/wolma/galaxy_2017/database/files/_metadata_files/000/metadata_14.dat --ofile /home/wolma/galaxy_2017/database/files/000/dataset_58.dat --depth 250 --verbose --quiet\n+##samtoolsCommand=n.a. (wrapped by MiModD)\n+##bcftools_callCommand=n.a. (wrapped by MiModD)\n+##rginfo=<ID=0,Rgid="000",Name="N2">\n+##rginfo=<ID=1,Rgid="266-1",Name="ot266",Description="mutant strain carrying the vab-3 allele ot266">\n+##samtoolsVersion=1.2+htslib-1.2.1\n+##bcftools_callVersion=1.2+htslib-1.2.1\n+##bcftools_concatVersion=1.2+htslib-1.2.1\n+##bcftools_viewVersion=1.2+htslib-1.2.1\n+##bcftools_viewCommand=view /home/wolma/galaxy_2017/database/files/000/dataset_58.dat\n+#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tN2\tot266\n+chrI\t855\t.\tG\tC\t231.0\t.\tDP=27;VDB=2.48853e-13;SGB=13.8822;MQSB=1;MQ0F=0;AC=2;AN=2;DP4=0,0,11,13;MQ=60\tGT:PL:DP:DPR:GQ\t./.:0,0,0:0:0,0:0\t1/1:255,72,0:24:0,24:86\n+chrI\t885\t.\tt\ttTCT\t69.0\t.\tINDEL;IDV=4;IMF=0.0769231;DP=56;VDB=2.27029e-09;SGB=1.27626;MQSB=1;MQ0F=0;ICB=0.3;HOB=0.125;AC=1;AN=4;DP4=16,17,3,1;MQ=60\tGT:PL:DP:DPR:GQ\t0/0:0,3,60:1:1,0:11\t0/1:105,0,255:36:32,4:96\n+chrI'..b'6,0:2:0,2:9\n+chrV\t14481\t.\tG\tA\t4.15167\t.\tDP=2;SGB=-0.516033;RPB=1;MQB=1;BQB=1;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=0,1,0,1;MQ=60\tGT:PL:DP:DPR:GQ\t./.:0,0,0:0:0,0:0\t0/1:32,0,32:2:1,1:32\n+chrV\t14488\t.\tG\tT\t4.15167\t.\tDP=2;SGB=-0.516033;RPB=1;MQB=1;BQB=1;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=0,1,0,1;MQ=60\tGT:PL:DP:DPR:GQ\t./.:0,0,0:0:0,0:0\t0/1:32,0,32:2:1,1:32\n+chrV\t14528\t.\tG\tA\t3.56356\t.\tDP=2;SGB=-0.516033;RPB=1;MQB=1;BQB=1;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=0,1,0,1;MQ=60\tGT:PL:DP:DPR:GQ\t./.:0,0,0:0:0,0:0\t0/1:31,0,32:2:1,1:31\n+chrV\t14530\t.\tA\tG\t4.13076\t.\tDP=2;SGB=-0.516033;RPB=1;MQB=1;BQB=1;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=0,1,0,1;MQ=60\tGT:PL:DP:DPR:GQ\t./.:0,0,0:0:0,0:0\t0/1:32,0,22:2:1,1:23\n+chrV\t14538\t.\tT\tC\t32.4055\t.\tDP=2;VDB=0.06;SGB=0.0985265;MQ0F=0;AC=2;AN=2;DP4=0,0,0,2;MQ=60\tGT:PL:DP:DPR:GQ\t./.:0,0,0:0:0,0:0\t1/1:57,6,0:2:0,2:9\n+chrX\t1592\t.\tT\tC\t13.4669\t.\tDP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60\tGT:PL:DP:DPR:GQ\t./.:0,0,0:0:0,0:0\t1/1:38,3,0:1:0,1:4\n+chrX\t1622\t.\tG\tT\t13.4669\t.\tDP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60\tGT:PL:DP:DPR:GQ\t./.:0,0,0:0:0,0:0\t1/1:38,3,0:1:0,1:4\n+chrX\t1648\t.\tA\tC\t12.5173\t.\tDP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60\tGT:PL:DP:DPR:GQ\t./.:0,0,0:0:0,0:0\t1/1:37,3,0:1:0,1:4\n+chrX\t1650\t.\tT\tA\t10.6576\t.\tDP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60\tGT:PL:DP:DPR:GQ\t./.:0,0,0:0:0,0:0\t1/1:35,3,0:1:0,1:4\n+chrX\t6015\t.\tA\tT\t13.4669\t.\tDP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60\tGT:PL:DP:DPR:GQ\t1/1:38,3,0:1:0,1:4\t./.:0,0,0:0:0,0:0\n+chrX\t6032\t.\tG\tA\t8.01478\t.\tDP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60\tGT:PL:DP:DPR:GQ\t1/1:32,3,0:1:0,1:4\t./.:0,0,0:0:0,0:0\n+chrX\t6058\t.\tta\tt\t15.3937\t.\tINDEL;IDV=1;IMF=1;DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,0,1;MQ=60\tGT:PL:DP:DPR:GQ\t1/1:40,3,0:1:0,1:4\t./.:0,0,0:0:0,0:0\n+chrX\t6118\t.\tA\tG\t15.394\t.\tDP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,0,1;MQ=60\tGT:PL:DP:DPR:GQ\t1/1:40,3,0:1:0,1:4\t./.:0,0,0:0:0,0:0\n+chrX\t6143\t.\tG\tA\t12.5173\t.\tDP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,0,1;MQ=60\tGT:PL:DP:DPR:GQ\t1/1:37,3,0:1:0,1:4\t./.:0,0,0:0:0,0:0\n+chrX\t6984\t.\tT\tA\t13.4669\t.\tDP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60\tGT:PL:DP:DPR:GQ\t./.:0,0,0:0:0,0:0\t1/1:38,3,0:1:0,1:4\n+chrX\t7025\t.\tA\tG\t12.5173\t.\tDP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60\tGT:PL:DP:DPR:GQ\t./.:0,0,0:0:0,0:0\t1/1:37,3,0:1:0,1:4\n+chrX\t10527\t.\tc\tcC\t8.86989\t.\tINDEL;IDV=1;IMF=1;DP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60\tGT:PL:DP:DPR:GQ\t./.:0,0,0:0:0,0:0\t1/1:33,3,0:1:0,1:4\n+chrX\t10535\t.\tT\tC\t11.8912\t.\tDP=2;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60\tGT:PL:DP:DPR:GQ\t./.:0,0,0:0:0,0:0\t1/1:36,3,0:1:0,1:6\n+chrX\t10562\t.\tC\tG\t18.2649\t.\tDP=7;VDB=0.18;SGB=0.00473136;RPB=0.8;MQB=1;MQSB=1;BQB=0.9;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=4,1,2,0;MQ=60\tGT:PL:DP:DPR:GQ\t./.:0,0,0:0:0,0:0\t0/1:49,0,131:7:5,2:48\n+chrX\t10595\t.\tT\tG\t148.0\t.\tDP=7;VDB=0.00429645;SGB=2.55596;MQSB=1;MQ0F=0;AC=2;AN=2;DP4=0,0,6,1;MQ=60\tGT:PL:DP:DPR:GQ\t./.:0,0,0:0:0,0:0\t1/1:172,21,0:7:0,7:29\n+chrX\t10629\t.\tgt\tg\t45.8065\t.\tINDEL;IDV=4;IMF=0.666667;DP=6;VDB=0.14;SGB=0.0985265;MQ0F=0;AC=2;AN=2;DP4=0,0,2,0;MQ=60\tGT:PL:DP:DPR:GQ\t./.:0,0,0:0:0,0:0\t1/1:70,6,0:2:0,2:13\n+chrX\t10630\t.\tT\tC,G\t10.4616\t.\tDP=2;VDB=0.32;SGB=0.0985265;MQSB=1;MQ0F=0;AC=1,1;AN=2;DP4=0,0,1,1;MQ=60\tGT:PL:DP:DPR:GQ\t./.:0,0,0,0,0,0:0:0,0,0:0\t1/2:58,29,26,32,0,29:2:0,1,1:25\n+chrX\t10643\t.\tG\tT\t34.5919\t.\tDP=3;VDB=0.02;SGB=0.0985265;MQSB=1;MQ0F=0;AC=2;AN=2;DP4=0,0,1,1;MQ=60\tGT:PL:DP:DPR:GQ\t./.:0,0,0:0:0,0:0\t1/1:59,6,0:2:0,2:11\n+chrX\t15480\t.\tT\tC\t13.4669\t.\tDP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60\tGT:PL:DP:DPR:GQ\t./.:0,0,0:0:0,0:0\t1/1:38,3,0:1:0,1:4\n+chrX\t15495\t.\tG\tC\t13.4669\t.\tDP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60\tGT:PL:DP:DPR:GQ\t./.:0,0,0:0:0,0:0\t1/1:38,3,0:1:0,1:4\n+chrX\t24890\t.\tC\tG\t13.4669\t.\tDP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60\tGT:PL:DP:DPR:GQ\t./.:0,0,0:0:0,0:0\t1/1:38,3,0:1:0,1:4\n+chrX\t24935\t.\tA\tC\t11.5799\t.\tDP=1;SGB=-0.157211;MQ0F=0;AC=2;AN=2;DP4=0,0,1,0;MQ=60\tGT:PL:DP:DPR:GQ\t./.:0,0,0:0:0,0:0\t1/1:36,3,0:1:0,1:4\n' |
| b |
| diff -r 000000000000 -r d801b0675eb5 test-data/so_coordinate.bam |
| b |
| Binary file test-data/so_coordinate.bam has changed |
| b |
| diff -r 000000000000 -r d801b0675eb5 test-data/so_queryname.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/so_queryname.sam Sat Nov 11 18:18:54 2017 -0500 |
| b |
| @@ -0,0 +1,2 @@ +@HD VN:1.5 SO:queryname +@RG ID:000 SM:N2 DS:C. elegans wt CN:ABC DT:2017-06-27 LB:XYZ PI:400 PL:ILLUMINA PU:SEQ123 |
| b |
| diff -r 000000000000 -r d801b0675eb5 test-data/split_pair_reads_1.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/split_pair_reads_1.fastqsanger Sat Nov 11 18:18:54 2017 -0500 |
| b |
| @@ -0,0 +1,20 @@ +@HWI-EAS91_1_30788AAXX:7:21:1542:1758/1 +GTCAATTGTACTGGTCAATACTAAAAGAATAGGATC ++HWI-EAS91_1_30788AAXX:7:21:1542:1758/1 +hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh +@HWI-EAS91_1_30788AAXX:7:22:1621:462/1 +ATAATGGCTATTATTGTGGGGGGGATGATGCTGGAA ++HWI-EAS91_1_30788AAXX:7:22:1621:462/1 +hhhhhhhhhhhhQAhh@hhhhNhhhfhMbCIScC?h +@HWI-EAS91_1_30788AAXX:7:45:408:807/1 +TACCCGATTTTTTGCTTTCCACTTTATCCTACCCTT ++HWI-EAS91_1_30788AAXX:7:45:408:807/1 +hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh +@HWI-EAS91_1_30788AAXX:7:49:654:1439/1 +CTAACTCTATTTATTGTATTTCAACTAAAAATCTCA ++HWI-EAS91_1_30788AAXX:7:49:654:1439/1 +hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh +@HWI-EAS91_1_30788AAXX:7:64:947:234/1 +TATCAAAAAAGAATATAATCTGAATCAACACTACAA ++HWI-EAS91_1_30788AAXX:7:64:947:234/1 +hhhhhhhhhhhhhhhhhhhhhhhRhhehhahhhhhJ |
| b |
| diff -r 000000000000 -r d801b0675eb5 test-data/split_pair_reads_2.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/split_pair_reads_2.fastqsanger Sat Nov 11 18:18:54 2017 -0500 |
| b |
| @@ -0,0 +1,20 @@ +@HWI-EAS91_1_30788AAXX:7:21:1542:1758/2 +GCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA ++HWI-EAS91_1_30788AAXX:7:21:1542:1758/2 +hhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR +@HWI-EAS91_1_30788AAXX:7:22:1621:462/2 +ACTAGCCCCAATATCAATCCTATATCAAATCTCACC ++HWI-EAS91_1_30788AAXX:7:22:1621:462/2 +hJhhhhChhhJhhhRhhKhePhc\KhhV\KhXhJhh +@HWI-EAS91_1_30788AAXX:7:45:408:807/2 +ATGAGTGCTAGGATCAGGATGGAGAGGATTAGGGCT ++HWI-EAS91_1_30788AAXX:7:45:408:807/2 +hhhhhhhhhhhhhhhhhh`hhhZh`hhhhhRXhhYh +@HWI-EAS91_1_30788AAXX:7:49:654:1439/2 +TAGGTTTATTGATAGTTGTGTTGTTGGTGTAAATGG ++HWI-EAS91_1_30788AAXX:7:49:654:1439/2 +hhhhhhhhhhhhhhhhhhhhhhhhhdhh_hG\XhU@ +@HWI-EAS91_1_30788AAXX:7:64:947:234/2 +CCTATTAGTGTGTAGAATAGGAAGTAGAGGCCTGCG ++HWI-EAS91_1_30788AAXX:7:64:947:234/2 +hhhhhhhh^hPhWfhhhhThWUhhfhh_hhNIVPUd |
| b |
| diff -r 000000000000 -r d801b0675eb5 test-data/vaf_linkage.pdf |
| b |
| Binary file test-data/vaf_linkage.pdf has changed |
| b |
| diff -r 000000000000 -r d801b0675eb5 tool-data/all_fasta.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/all_fasta.loc.sample Sat Nov 11 18:18:54 2017 -0500 |
| b |
| @@ -0,0 +1,18 @@ +#This file lists the locations and dbkeys of all the fasta files +#under the "genome" directory (a directory that contains a directory +#for each build). The script extract_fasta.py will generate the file +#all_fasta.loc. This file has the format (white space characters are +#TAB characters): +# +#<unique_build_id> <dbkey> <display_name> <file_path> +# +#So, all_fasta.loc could look something like this: +# +#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa +# +#Your all_fasta.loc file should contain an entry for each individual +#fasta file. So there will be multiple fasta files for each build, +#such as with hg19 above. +# |
| b |
| diff -r 000000000000 -r d801b0675eb5 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Sat Nov 11 18:18:54 2017 -0500 |
| b |
| @@ -0,0 +1,7 @@ +<tables> + <!-- Locations of all fasta files under genome directory --> + <table name="all_fasta" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/all_fasta.loc" /> + </table> +</tables> |