| Next changeset 1:88bcfaea2fb6 (2021-10-16) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419" |
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added:
bwa-mem2.xml macros.xml read_group_macros.xml test-data/bwa-aln-bam-input.bam test-data/bwa-aln-test1-fasta.bam test-data/bwa-aln-test1.bam test-data/bwa-aln-test2.bam test-data/bwa-aln-test3.bam test-data/bwa-mem-fasta1.fa test-data/bwa-mem-fastq1.fq test-data/bwa-mem-fastq1.fq.gz test-data/bwa-mem-fastq2.fq test-data/bwa-mem-mt-genome.fa test-data/bwa-mem-test1-fasta.bam test-data/bwa-mem-test1.bam test-data/bwa-mem-test2.bam test-data/bwa-mem-test3.bam test-data/bwa-mem-test4.bam test-data/bwa_mem2_index.loc test-data/test-cache/bwa-mem-mt-genome.fa.0123 test-data/test-cache/bwa-mem-mt-genome.fa.amb test-data/test-cache/bwa-mem-mt-genome.fa.ann test-data/test-cache/bwa-mem-mt-genome.fa.bwt.2bit.64 test-data/test-cache/bwa-mem-mt-genome.fa.pac tool-data/bwa_mem2_index.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
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| diff -r 000000000000 -r 82217dccdbcf bwa-mem2.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bwa-mem2.xml Fri Oct 08 10:19:48 2021 +0000 |
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| b'@@ -0,0 +1,399 @@\n+<tool id="bwa_mem2" name="BWA-MEM2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">\n+ <description>- map medium and long reads (> 100 bp) against reference genome</description>\n+ <macros>\n+ <import>read_group_macros.xml</import>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="requirements"/>\n+ <expand macro="stdio"/>\n+ <expand macro="xrefs"/>\n+ <command><![CDATA[\n+@pipefail@\n+@set_reference_fasta_filename@\n+\n+## Begin BWA-MEM command line\n+\n+bwa-mem2 mem\n+#if str( $output_sort ) == "unsorted":\n+ -t 1\n+#else\n+ -t "\\${GALAXY_SLOTS:-1}"\n+#end if\n+## Verbosity is set to 1 (errors only)\n+-v 1\n+\n+#if str( $fastq_input.fastq_input_selector ) == "paired_iv":\n+ ## For interleaved fastq files set -p option\n+ -p\n+ ## check that insert statistics is used\n+ #if str( $fastq_input.iset_stats ):\n+ -I \'${fastq_input.iset_stats}\'\n+ #end if\n+#end if\n+\n+#if str( $analysis_type.analysis_type_selector ) not in ["illumina", "full"]:\n+ -x \'$analysis_type.analysis_type_selector\'\n+#elif str( $analysis_type.analysis_type_selector ) == "full":\n+ ## Algorithmic options\n+ #if str( $analysis_type.algorithmic_options.algorithmic_options_selector ) == "set":\n+ -k \'${analysis_type.algorithmic_options.k}\'\n+ -w \'${analysis_type.algorithmic_options.w}\'\n+ -d \'${analysis_type.algorithmic_options.d}\'\n+ -r \'${analysis_type.algorithmic_options.r}\'\n+ -y \'${analysis_type.algorithmic_options.y}\'\n+ -c \'${analysis_type.algorithmic_options.c}\'\n+ -D \'${analysis_type.algorithmic_options.D}\'\n+ -W \'${analysis_type.algorithmic_options.W}\'\n+ -m \'${analysis_type.algorithmic_options.m}\'\n+ ${analysis_type.algorithmic_options.S}\n+ ${analysis_type.algorithmic_options.P}\n+ ${analysis_type.algorithmic_options.e}\n+ #end if\n+\n+ ## Scoring options\n+ #if str( $analysis_type.scoring_options.scoring_options_selector ) == "set":\n+ -A \'${analysis_type.scoring_options.A}\'\n+ -B \'${analysis_type.scoring_options.B}\'\n+ -O \'${analysis_type.scoring_options.O}\'\n+ -E \'${analysis_type.scoring_options.E}\'\n+ -L \'${analysis_type.scoring_options.L}\'\n+ -U \'${analysis_type.scoring_options.U}\'\n+ #end if\n+\n+ ## IO options\n+ #if str( $analysis_type.io_options.io_options_selector ) == "set":\n+ -T \'${analysis_type.io_options.T}\'\n+ -h \'${analysis_type.io_options.h}\'\n+ ${analysis_type.io_options.a}\n+ ${analysis_type.io_options.C}\n+ ${analysis_type.io_options.V}\n+ ${analysis_type.io_options.Y}\n+ ${analysis_type.io_options.M}\n+ ${analysis_type.io_options.five}\n+ ${analysis_type.io_options.q}\n+ #end if\n+\n+#end if\n+\n+## Handle read group options...\n+@define_read_group_helpers@\n+#if str( $fastq_input.fastq_input_selector ) == "paired":\n+ #set $rg_auto_name = $read_group_name_default($fastq_input.fastq_input1, $fastq_input.fastq_input2)\n+#else:\n+ #set $rg_auto_name = $read_group_name_default($fastq_input.fastq_input1)\n+#end if\n+@set_use_rg_var@\n+@set_read_group_vars@\n+#if $use_rg\n+ @set_rg_string@\n+ -R \'$rg_string\'\n+#end if\n+\n+#if str( $fastq_input.fastq_input_selector ) == "paired":\n+ ## check that insert statistics is used\n+ #if str( $fastq_input.iset_stats ):\n+ -I \'${fastq_input.iset_stats}\'\n+ #end if\n+\n+ \'${reference_fasta_filename}\'\n+ \'${fastq_input.fastq_input1}\' \'${fastq_input.fastq_input2}\'\n+#elif str( $fastq_input.fastq_input_selector ) == "paired_collection":\n+ ## check that insert statistics is used\n+ #if str( $fastq_input.iset_stats ):\n+ -I \'${fastq_input.iset_stats}\'\n+ #end if\n+\n+ \'${reference_fasta_filename}\'\n+ \'${fastq_input.fastq_input1.forward}\' \'${fastq_input.fastq_input1.reverse}\'\n+#else:\n+ \'${reference_fasta_filename}\'\n+ \'${fastq_input.fastq_input1}\'\n+#end if\n+\n+#if str( $output_sort ) == "coordinate":\n+ | sam'..b'est>\n+ <test>\n+ <param name="reference_source_selector" value="cached" />\n+ <param name="ref_file" value="mtgenome"/>\n+ <param name="fastq_input_selector" value="paired"/>\n+ <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>\n+ <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>\n+ <param name="analysis_type_selector" value="illumina"/>\n+ <output name="bam_output" ftype="bam" file="bwa-mem-test1.bam" lines_diff="4" />\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+**What is does**\n+BWA-MEM2 is the new version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case, dataset and the running machine.\n+The algorithm is robust to sequencing errors and applicable to a wide range of sequence lengths from 70bp to a few megabases.\n+\n+The Galaxy implementation takes fastq files as input and produces output in BAM format, which can be further processed using various BAM utilities exiting in Galaxy (BAMTools, SAMTools, Picard).\n+\n+-----\n+\n+**Indices: Selecting reference genomes for BWA**\n+\n+Galaxy wrapper for BWA allows you select between precomputed and user-defined indices for reference genomes using **Will you select a reference genome from your history or use a built-in index?** flag. This flag has two options:\n+\n+ 1. **Use a built-in genome index** - when selected (this is default), Galaxy provides the user with **Select reference genome index** dropdown. Genomes listed in this dropdown have been pre-indexed with bwa index utility and are ready to be mapped against.\n+ 2. **Use a genome from the history and build index** - when selected, Galaxy provides the user with **Select reference genome sequence** dropdown. This dropdown is populated by all FASTA formatted files listed in your current history. If your genome of interest is uploaded into history it will be shown there. Selecting a genome from this dropdown will cause Galaxy to first transparently index it using `bwa index` command, and then run mapping with `bwa mem`.\n+\n+If your genome of interest is not listed here you have two choices:\n+\n+ 1. Contact galaxy team using **Help->Support** link at the top of the interface and let us know that an index needs to be added\n+ 2. Upload your genome of interest as a FASTA file to Galaxy history and selected **Use a genome from the history and build index** option.\n+\n+-----\n+\n+**Galaxy-specific option**\n+\n+Galaxy allows four levels of control over bwa-mem options provided by **Select analysis mode** menu option. These are:\n+\n+ 1. *Simple Illumina mode*: The simplest possible bwa mem application in which it alignes single or paired-end data to reference using default parameters. It is equivalent to the following command: bwa mem <reference index> <fastq dataset1> [fastq dataset2]\n+ 2. *PacBio mode*: The mode adjusted specifically for mapping of long PacBio subreads. Equivalent to the following command: bwa mem -k17 -W40 -r10 -A1 -B1 -O1 -E1 -L0 <reference index> <PacBio dataset in fastq format>\n+ 3. *Full list of options*: Allows access to all options through Galaxy interface.\n+\n+-----\n+\n+**Bam sorting mode**\n+\n+The generated bam files can be sorted according to three criteria: coordinates, names and input order.\n+\n+In coordinate sorted mode the reads are sorted by coordinates. It means that the reads from the beginning of the first chromosome are first in the file. \n+\n+When sorted by read name, the file is sorted by the reference ID (i.e., the QNAME field). \n+\n+Finally, the *No sorted (sorted as input)* option yield a BAM file in which the records are sorted in an order corresponding to the order of the reads in the original input file. This option requires using a single thread to perform the conversion from SAM to BAM format, so the runtime is extended.\n+\n+\n+@RG@\n+\n+@info@\n+ ]]></help>\n+ <expand macro="citations" />\n+</tool>\n' |
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| diff -r 000000000000 -r 82217dccdbcf macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Oct 08 10:19:48 2021 +0000 |
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| b'@@ -0,0 +1,189 @@\n+<macros>\n+ <import>read_group_macros.xml</import>\n+\n+ <token name="@TOOL_VERSION@">2.2.1</token>\n+ <token name="@VERSION_SUFFIX@">0</token>\n+\n+ <xml name="xrefs">\n+ <xrefs>\n+ <xref type="bio.tools">bwa-mem2</xref>\n+ </xrefs>\n+ </xml>\n+\n+ <token name="@pipefail@"><![CDATA[set -o | grep -q pipefail && set -o pipefail;]]></token>\n+\n+ <token name="@set_rg_string@">\n+ #set $rg_string = "@RG\\\\tID:" + str($rg_id)\n+ #set $rg_string += $format_read_group("\\\\tSM:", $rg_sm)\n+ #set $rg_string += $format_read_group("\\\\tPL:", $rg_pl)\n+ #set $rg_string += $format_read_group("\\\\tLB:", $rg_lb)\n+ #set $rg_string += $format_read_group("\\\\tCN:", $rg_cn)\n+ #set $rg_string += $format_read_group("\\\\tDS:", $rg_ds)\n+ #set $rg_string += $format_read_group("\\\\tDT:", $rg_dt)\n+ #set $rg_string += $format_read_group("\\\\tFO:", $rg_fo)\n+ #set $rg_string += $format_read_group("\\\\tKS:", $rg_ks)\n+ #set $rg_string += $format_read_group("\\\\tPG:", $rg_pg)\n+ #set $rg_string += $format_read_group("\\\\tPI:", $rg_pi)\n+ #set $rg_string += $format_read_group("\\\\tPU:", $rg_pu)\n+ </token>\n+\n+ <token name="@set_reference_fasta_filename@"><![CDATA[\n+ #if str( $reference_source.reference_source_selector ) == "history":\n+ #set $reference_fasta_filename = "localref.fa"\n+ ln -s \'${reference_source.ref_file}\' \'${reference_fasta_filename}\' &&\n+ bwa-mem2 index\n+ \'${reference_fasta_filename}\' &&\n+ #else:\n+ #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )\n+ #end if\n+ ]]></token>\n+\n+ <xml name="requirements">\n+ <requirements>\n+ <requirement type="package" version="@TOOL_VERSION@">bwa-mem2</requirement>\n+ <requirement type="package" version="1.13">samtools</requirement>\n+ </requirements>\n+ </xml>\n+\n+ <xml name="stdio">\n+ <stdio>\n+ <exit_code range="1:" />\n+ <exit_code range=":-1" />\n+ <regex match="Error:" />\n+ <regex match="Exception:" />\n+ <regex match="\\[bns_restore_core\\] Parse error reading" />\n+ </stdio>\n+ </xml>\n+\n+ <macro name="reference_source_conditional">\n+ <conditional name="reference_source">\n+ <param name="reference_source_selector" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below">\n+ <option value="cached">Use a built-in genome index</option>\n+ <option value="history">Use a genome from history and build index</option>\n+ </param>\n+ <when value="cached">\n+ <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">\n+ <options from_data_table="bwa_mem2_indexes">\n+ <filter type="sort_by" column="2" />\n+ <validator type="no_options" message="No indexes are available" />\n+ </options>\n+ <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>\n+ </param>\n+ </when>\n+ <when value="history">\n+ <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" help="You can upload a FASTA sequence to the history and use it as reference" />\n+ </when>\n+ </conditional>\n+ </macro>\n+\n+ <macro name="dbKeyActionsBwaMem">\n+ <expand macro="dbKeyActions">\n+ <option type="from_data_table" name="bwa_mem_indexes" column="1" offset="0">\n+ <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>\n+ <filter type="param_va'..b'referenced by each read with the RG:Z field, allowing tools to determine the read group information associated with each read, including the sample from which the read came. Also, a read group is effectively treated as a separate run of the NGS instrument in tools like base quality score recalibration (a GATK component) -- all reads within a read group are assumed to come from the same instrument run and to therefore share the same error model."\n+ "SM","Sample. Use pool name where a pool is being sequenced.","Required. As important as ID.","The name of the sample sequenced in this read group. GATK tools treat all read groups with the same SM value as containing sequencing data for the same sample. Therefore it\'s critical that the SM field be correctly specified, especially when using multi-sample tools like the Unified Genotyper (a GATK component)."\n+ "PL","Platform/technology used to produce the read. Valid values: ILLUMINA, SOLID, LS454, HELICOS and PACBIO.","Important. Not currently used in the GATK, but was in the past, and may return. The only way to known the sequencing technology used to generate the sequencing data","It\'s a good idea to use this field."\n+ "LB","DNA preparation library identify","Essential for MarkDuplicates","MarkDuplicates uses the LB field to determine which read groups might contain molecular duplicates, in case the same DNA library was sequenced on multiple lanes."\n+\n+\n+**Example of Read Group usage**\n+\n+Suppose we have a trio of samples: MOM, DAD, and KID. Each has two DNA libraries prepared, one with 400 bp inserts and another with 200 bp inserts. Each of these libraries is run on two lanes of an illumina hiseq, requiring 3 x 2 x 2 = 12 lanes of data. When the data come off the sequencer, we would create 12 BAM files, with the following @RG fields in the header::\n+\n+ Dad\'s data:\n+ @RG ID:FLOWCELL1.LANE1 PL:illumina LB:LIB-DAD-1 SM:DAD PI:200\n+ @RG ID:FLOWCELL1.LANE2 PL:illumina LB:LIB-DAD-1 SM:DAD PI:200\n+ @RG ID:FLOWCELL1.LANE3 PL:illumina LB:LIB-DAD-2 SM:DAD PI:400\n+ @RG ID:FLOWCELL1.LANE4 PL:illumina LB:LIB-DAD-2 SM:DAD PI:400\n+ \n+ Mom\'s data:\n+ @RG ID:FLOWCELL1.LANE5 PL:illumina LB:LIB-MOM-1 SM:MOM PI:200\n+ @RG ID:FLOWCELL1.LANE6 PL:illumina LB:LIB-MOM-1 SM:MOM PI:200\n+ @RG ID:FLOWCELL1.LANE7 PL:illumina LB:LIB-MOM-2 SM:MOM PI:400\n+ @RG ID:FLOWCELL1.LANE8 PL:illumina LB:LIB-MOM-2 SM:MOM PI:400\n+ \n+ Kid\'s data:\n+ @RG ID:FLOWCELL2.LANE1 PL:illumina LB:LIB-KID-1 SM:KID PI:200\n+ @RG ID:FLOWCELL2.LANE2 PL:illumina LB:LIB-KID-1 SM:KID PI:200\n+ @RG ID:FLOWCELL2.LANE3 PL:illumina LB:LIB-KID-2 SM:KID PI:400\n+ @RG ID:FLOWCELL2.LANE4 PL:illumina LB:LIB-KID-2 SM:KID PI:400\n+\n+Note the hierarchical relationship between read groups (unique for each lane) to libraries (sequenced on two lanes) and samples (across four lanes, two lanes for each library).\n+ </token>\n+ <token name="@info@">\n+-----\n+\n+.. class:: infomark\n+\n+**More info**\n+\n+To obtain more information about BWA and ask questions use these resources:\n+\n+ 1. https://biostar.usegalaxy.org/\n+ 2. https://www.biostars.org/\n+ 3. https://github.com/bwa-mem2/bwa-mem2\n+ 4. http://bio-bwa.sourceforge.net/\n+\n+ </token>\n+\n+ <xml name="citations">\n+ <citations>\n+ <citation type="doi">10.1093/bioinformatics/btp324</citation>\n+ <citation type="doi">10.1093/bioinformatics/btp698</citation>\n+ <citation type="bibtex">@misc{1303.3997,\n+ Author = {Heng Li},\n+ Title = {Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM},\n+ Year = {2013},\n+ Eprint = {arXiv:1303.3997},\n+ url = {http://arxiv.org/abs/1303.3997},\n+ }</citation>\n+ </citations>\n+ </xml>\n+\n+</macros>\n' |
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| diff -r 000000000000 -r 82217dccdbcf read_group_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/read_group_macros.xml Fri Oct 08 10:19:48 2021 +0000 |
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| b'@@ -0,0 +1,294 @@\n+<macros>\n+ <!-- Import this at the top of your command block and then\n+ define rg_auto_name. -->\n+ <token name="@define_read_group_helpers@">\n+#def identifier_or_name($input1)\n+ #if hasattr($input1, \'element_identifier\')\n+ #return $input1.element_identifier\n+ #else\n+ #return $input1.name.rstrip(\'.gz\').rstrip(\'.fastq\').rstrip(\'.fq\')\n+ #end if\n+#end def\n+\n+#def clean(name)\n+ #import re\n+ #set $name_clean = re.sub(\'[^\\w\\-_\\.]\', \'_\', $name)\n+ #return $name_clean\n+#end def\n+\n+#def read_group_name_default($input1, $input2=None)\n+ #if $input2 is None\n+ #return $clean($identifier_or_name($input1))\n+ #else\n+ #import itertools\n+ #set $input_name1 = $clean($identifier_or_name($input1))\n+ #set $input_name2 = $clean($identifier_or_name($input2))\n+ #set $common_prefix = \'\'.join([c[0] for c in itertools.takewhile(lambda x: all(x[0] == y for y in x), zip(*[$input_name1, $input_name2]))])\n+ #if len($common_prefix) > 3\n+ #return $common_prefix\n+ #else\n+ #return $input_name1\n+ #end if\n+ #end if\n+#end def\n+\n+#def format_read_group(prefix, value, quote=\'\', arg=\'\')\n+ #if $value\n+ #return $arg + $quote + $prefix + $value + $quote\n+ #else\n+ #return \'\'\n+ #end if\n+#end def\n+\n+#def rg_param(name)\n+ #if $varExists("rg")\n+ #return $rg.get($name, None)\n+ #else\n+ #return $getVar($name, None)\n+ #end if\n+#end def\n+\n+#set $use_rg = True\n+ </token>\n+ <!-- preconditions use_rg and rg_auto_name have been\n+ defined.\n+ -->\n+ <token name="@set_read_group_vars@">\n+#if $use_rg\n+ #if $rg_param(\'read_group_id_conditional\') is None\n+ #set $rg_id = $rg_auto_name\n+ #elif $rg_param(\'read_group_id_conditional\').do_auto_name\n+ #set $rg_id = $rg_auto_name\n+ #else\n+ #set $rg_id = str($rg_param(\'read_group_id_conditional\').ID)\n+ #end if\n+\n+ #if $rg_param(\'read_group_sm_conditional\') is None\n+ #set $rg_sm = \'\'\n+ #elif $rg_param(\'read_group_sm_conditional\').do_auto_name\n+ #set $rg_sm = $rg_auto_name\n+ #else\n+ #set $rg_sm = str($rg_param(\'read_group_sm_conditional\').SM)\n+ #end if\n+\n+ #if $rg_param(\'PL\')\n+ #set $rg_pl = str($rg_param(\'PL\'))\n+ #else\n+ #set $rg_pl = \'\'\n+ #end if\n+\n+ #if $rg_param(\'read_group_lb_conditional\') is None\n+ #set $rg_lb = \'\'\n+ #elif $rg_param(\'read_group_lb_conditional\').do_auto_name\n+ #set $rg_lb = $rg_auto_name\n+ #else\n+ #set $rg_lb = str($rg_param(\'read_group_lb_conditional\').LB)\n+ #end if\n+\n+ #if $rg_param(\'CN\')\n+ #set $rg_cn = str($rg_param(\'CN\'))\n+ #else\n+ #set $rg_cn = \'\'\n+ #end if\n+\n+ #if $rg_param("DS")\n+ #set $rg_ds = str($rg_param("DS"))\n+ #else\n+ #set $rg_ds = \'\'\n+ #end if\n+\n+ #if $rg_param("DT")\n+ #set $rg_dt = str($rg_param("DT"))\n+ #else\n+ #set $rg_dt = \'\'\n+ #end if\n+\n+ #if $rg_param("FO")\n+ #set $rg_fo = str($rg_param("FO"))\n+ #else\n+ #set $rg_fo = \'\'\n+ #end if\n+\n+ #if $rg_param("KS")\n+ #set $rg_ks = str($rg_param("KS"))\n+ #else\n+ #set $rg_ks = \'\'\n+ #end if\n+\n+ #if $rg_param("PG")\n+ #set $rg_pg = str($rg_param("PG"))\n+ #else\n+ #set $rg_pg = \'\'\n+ #end if\n+\n+ #if $rg_param("PI") != None\n+ #set $rg_pi = str($rg_param("PI"))\n+ #else\n+ #set $rg_pi = \'\'\n+ #end if\n+\n+ #if $rg_param("PU")\n+ #set $rg_pu = str($rg_param("PU"))\n+ #else\n+ #set $rg_pu = \'\'\n+ #end if\n+#end if\n+ </token>\n+ <token name="@set_use_rg_var@">\n+#set $use_rg = str($rg.rg_selector) != "do_not_set"\n+ </token>\n+ <xml name="read_group_auto_name_conditional">\n+ <param name="do_auto_name" type="boolean" label="Auto-assign" help="Use dataset name or collection information to automatically assign this value" checked="no" />\n+ <when value="true">\n+ '..b'ription (DS)" />\n+ </xml>\n+ <xml name="read_group_dt_param">\n+ <param name="DT" type="text" label="Date that run was produced (DT)" help="ISO8601 format date or date/time, like YYYY-MM-DD" />\n+ </xml>\n+ <xml name="read_group_fo_param">\n+ <param name="FO" type="text" optional="true" label="Flow order (FO)" help="The array of nucleotide bases that correspond to the nucleotides used for each flow of each read. Multi-base flows are encoded in IUPAC format, and non-nucleotide flows by various other characters. Format: /\\*|[ACMGRSVTWYHKDBN]+/">\n+ <validator type="regex" message="Invalid flow order">\\*|[ACMGRSVTWYHKDBN]+$</validator>\n+ </param>\n+ </xml>\n+ <xml name="read_group_ks_param">\n+ <param name="KS" type="text" label="The array of nucleotide bases that correspond to the key sequence of each read (KS)" />\n+ </xml>\n+ <xml name="read_group_pg_param">\n+ <param name="PG" type="text" label="Programs used for processing the read group (PG)" />\n+ </xml>\n+ <xml name="read_group_pi_param">\n+ <param name="PI" type="integer" optional="true" label="Predicted median insert size (PI)" />\n+ </xml>\n+ <xml name="read_group_pu_param">\n+ <param name="PU" type="text" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" optional="True" />\n+ </xml>\n+ <xml name="read_group_pu_required_param">\n+ <param name="PU" type="text" value="run" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" optional="False" />\n+ </xml>\n+ <!-- Only ID is required - all groups available -->\n+ <xml name="read_group_inputs_spec">\n+ <expand macro="read_group_id_conditional" />\n+ <expand macro="read_group_sm_conditional" />\n+ <expand macro="read_group_pl_param" />\n+ <expand macro="read_group_lb_conditional" />\n+ <expand macro="read_group_cn_param" />\n+ <expand macro="read_group_ds_param" />\n+ <expand macro="read_group_dt_param" />\n+ <expand macro="read_group_fo_param" />\n+ <expand macro="read_group_ks_param" />\n+ <expand macro="read_group_pg_param" />\n+ <expand macro="read_group_pi_param" />\n+ <expand macro="read_group_pu_param" />\n+ </xml>\n+ <!-- ID, SM, LB, PU, PL all required - not ks, pg, or fo params. -->\n+ <xml name="read_group_inputs_picard">\n+ <expand macro="read_group_id_conditional" />\n+ <expand macro="read_group_sm_required_conditional" />\n+ <expand macro="read_group_lb_required_conditional" />\n+ <expand macro="read_group_pl_param" />\n+ <expand macro="read_group_pu_required_param" />\n+ <expand macro="read_group_cn_param" />\n+ <expand macro="read_group_ds_param" />\n+ <expand macro="read_group_pi_param" />\n+ <expand macro="read_group_dt_param" />\n+ </xml>\n+ <xml name="read_group_conditional">\n+ <conditional name="rg">\n+ <param name="rg_selector" type="select" label="Set read groups information?" help="Specifying read group information can greatly simplify your downstream analyses by allowing combining multiple datasets.">\n+ <option value="set">Set read groups (SAM/BAM specification)</option>\n+ <option value="set_picard">Set read groups (Picard style)</option>\n+ <option value="set_id_auto">Automatically assign ID</option>\n+ <option value="do_not_set" selected="True">Do not set</option>\n+ </param>\n+ <when value="set_picard">\n+ <expand macro="read_group_inputs_picard" />\n+ </when>\n+ <when value="set">\n+ <expand macro="read_group_inputs_spec" />\n+ </when>\n+ <when value="set_id_auto">\n+ </when>\n+ <when value="do_not_set">\n+ </when>\n+ </conditional>\n+ </xml>\n+</macros>\n' |
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| diff -r 000000000000 -r 82217dccdbcf test-data/bwa-mem-fasta1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa-mem-fasta1.fa Fri Oct 08 10:19:48 2021 +0000 |
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| b'@@ -0,0 +1,200 @@\n+>M01368:8:000000000-A3GHV:1:1101:6911:8255/1\n+ATCTGGTTCCTACTTCAGGGCCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATT\n+>M01368:8:000000000-A3GHV:1:1101:14518:9998/1\n+GTTATTATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGGGATAGACCTGTGATCCATCGTGAT\n+>M01368:8:000000000-A3GHV:1:1101:18422:19051/1\n+GTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACG\n+>M01368:8:000000000-A3GHV:1:1101:25545:21098/1\n+ATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATAAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGGCTTATTTAAGGGGAACGGGTGGGG\n+>M01368:8:000000000-A3GHV:1:1101:5446:12248/1\n+AATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTAT\n+>M01368:8:000000000-A3GHV:1:1101:5861:6452/1\n+ATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTT\n+>M01368:8:000000000-A3GHV:1:1102:10403:6021/1\n+CGCTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTG\n+>M01368:8:000000000-A3GHV:1:1102:10677:23253/1\n+CCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTAATTCTGTCTCTTATACACA\n+>M01368:8:000000000-A3GHV:1:1102:13809:1733/1\n+ATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGAGGGCTATTTAGGTTTTATGCTGTCTCTTATACACATCTCCG\n+>M01368:8:000000000-A3GHV:1:1102:17584:10050/1\n+ATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATCTCGTATGCCGTCTTCT\n+>M01368:8:000000000-A3GHV:1:1102:18842:24844/1\n+CACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCT\n+>M01368:8:000000000-A3GHV:1:1102:21788:11027/1\n+GCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTAATTCTG\n+>M01368:8:000000000-A3GHV:1:1102:5728:8777/1\n+ATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACCAGATG\n+>M01368:8:000000000-A3GHV:1:1102:5983:21093/1\n+GTATCCGACATCTGGTTCCTACTTCAGGGT'..b'CCATGCATTTGGTATTTTCGTCTGGGCGGTGTCCACGCAATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGA\n+>M01368:8:000000000-A3GHV:1:1112:10272:7828/1\n+GTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATCTCGTATGCCGTCTT\n+>M01368:8:000000000-A3GHV:1:1112:9832:16531/1\n+CTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGGGCTGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCTTGAAGTAGGAACC\n+>M01368:8:000000000-A3GHV:1:1112:9832:6701/1\n+CGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGA\n+>M01368:8:000000000-A3GHV:1:1113:13532:8618/1\n+GGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACCAGATGTCGGCTACAGTTCACTTTAGCTACCTCCAAGTGTTATG\n+>M01368:8:000000000-A3GHV:1:1113:21679:18011/1\n+GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGAGGGTGTGCACGCGATAGCATTGCGAGACGCTTGAGCCGGAGCACCCTATGTCGCAGTATATGTCTTTGATTCCTGCCTCTTCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAACTGTCTCTTATACACATATCCACGCCCACGAGACTAAGGCGAAGTTCATT\n+>M01368:8:000000000-A3GHV:1:1113:25528:14016/1\n+CCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGG\n+>M01368:8:000000000-A3GHV:1:1113:5741:16959/1\n+TAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGA\n+>M01368:8:000000000-A3GHV:1:1114:10130:11959/1\n+CGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTCTGATCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATCTCGTATGCCGTCTTCTGCTTGCAACAAACACACATCCAGA\n+>M01368:8:000000000-A3GHV:1:1114:14540:5315/1\n+CTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGGGGGCTATTTAGGTTTTT\n+>M01368:8:000000000-A3GHV:1:1114:15066:16302/1\n+TAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAACGGTTGTTAATTAATTATTGCTTGTAGGACA\n+>M01368:8:000000000-A3GHV:1:1114:16639:15258/1\n+CCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGCGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTCCAATATTACAGGCGAACATACTTACTAAATTGTGT\n+>M01368:8:000000000-A3GHV:1:1114:2404:13066/1\n+TCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCTGTCTATTATACACATC\n+>M01368:8:000000000-A3GHV:1:1114:9184:6959/1\n+GGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACCAGATGTCGGATACAGTTCACTTTCTGTCTCTTA\n' |
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| diff -r 000000000000 -r 82217dccdbcf test-data/bwa-mem-fastq1.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa-mem-fastq1.fq Fri Oct 08 10:19:48 2021 +0000 |
| b |
| b'@@ -0,0 +1,400 @@\n+@M01368:8:000000000-A3GHV:1:1101:6911:8255/1\n+ATCTGGTTCCTACTTCAGGGCCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATT\n++\n+BCCCCFFFFFFFGGGGGGGGGGGHHHHGHGHHHHHHHHHGGGGGGHHHHGHHHHHHHHHHGHHHHHHGGHGGHHHGHHHHFHHGHHHHHHHHHGHEHEFFGHHEGGCEFGGFHHHBGHHGHHHHGHFHHHGHGHGHGGCDFDDACGGGGGGGAAFFFFFFFFFBAFFFFFB;FFFFFFADDFFFFFFFFFFEFFFFFFFFFFBFFFFFFFFFFFFFFEFFFFFFFFBFEFFFFEFE;DFFFDFBFF/9BFB\n+@M01368:8:000000000-A3GHV:1:1101:14518:9998/1\n+GTTATTATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGGGATAGACCTGTGATCCATCGTGAT\n++\n+AAAAAFFFFFFFGGGGGGGGGGHGGHHHHGHHHHHHHGCGHHHHHHHHHHHHHHHGGGGGHHHHHHHHHGHHGFHFE5BGEEHFGGGHHHHHHHHFBHHGGGGFHGHHFGHHHHGHHHHHHGEGGGGFHFHGEGHHGGCDGDGHGGGDGGHGGCGGGHGHHH/ACDG?.1FGCDCCGCA.CC@CDCHFHGFFGGGEBFGAB//CEFBFGG.:;D;;A0AFFFFFB..:@ABFF//;BFFFFFBF/9D:A//\n+@M01368:8:000000000-A3GHV:1:1101:18422:19051/1\n+GTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACG\n++\n+CCCCCFDDDDDFGGGGGGGGGGHHHHHHHHHHHHHHHHGHHHHHHFHHHHGGGGHHHHHHHHHGHHHHHHHHHHHHGGHGGHHHHHHHHHHHHHHHHHHHHHHHHHHHGHHHHHGCGGGHHHHHHHHHHHHHHHHHHHHHHGFDHGFHCFGGGGFGGFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF;FFFFFFFFFFFFFFFFFFFFFFFFFFFFEFBFFFFFFFFFF:FFF.\n+@M01368:8:000000000-A3GHV:1:1101:25545:21098/1\n+ATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATAAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGGCTTATTTAAGGGGAACGGGTGGGG\n++\n+33AA?DFD5BDFGGGFEBDGEGHEGHGEGHCEGGHHCHGHHFFHHGFGAGE53FF2FAFFGDE5FFFE5GFBFGAEE1GHHHGHHHEHE3FGHF@GEGEGGHHGG3FAGFFDE?EEE3GFEGFGFGGCG?GHHHFHGGGC@DHFFHD/A<C@EGFDCGGGHFHHHEGFGHBFHG0:CEHFCHGGED.;0CEF.F99B0CFFEEFGGG0FBFBBF0F/FFBDE?/9//9B.FFBFFFFFFBF..A..;@B--\n+@M01368:8:000000000-A3GHV:1:1101:5446:12248/1\n+AATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTAT\n++\n+CCCCDFFFFCCFGGGGGGGGFGHHHHHGGGGHHHHHHHHHHHHHHHHGBGHGGHGGHHHHHHHHHHGHGHGGGGGHHHHHHHHGHHHHHHHHHGGGGGHHHHFFGHHHGGGGGGHHHGFGGHHGGGGHHHHHHGGGGGGHGHHGGGGGGGHGGGGGGHHHHHHHHHHHHHFHGGGHHHHGGGGGG:FE;EGEGGGGG/;?FGGGGGGGFFFFGGFFFFFFFFFBFFFFFFFFFFBFFFFFFEFFFFFEFFF\n+@M01368:8:000000000-A3GHV:1:1101:5861:6452/1\n+ATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTT\n++\n+ABCCCFFFFFFFGGGGGGGGGGHHHHHHHHHHHGHHHHGHHHHHHHHHHHGGGGHHHHHHHHFHHHHHHGGHGHGGHGGHHHHHHHGGHFHHHGGGGGHHHHHHHHHHHHHHHHHHGGGGGHHHHHEGGHHGGGGGGHHHGGGGHGGGGGHHHHHHGGGDCGHHHHGGGGGGGHEFGGGGHGHHHGHGGGFGGGGGGGEGGGGGGG?E0CEFGGGGGFEE9EEFFFFFBFFFFFFFBFFBD.AFFFFFFF0\n+@M01368:8:000000000-A3GHV:1:1102:10403:6021/1\n+CGCTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTG\n++\n+>A@AAAAD2ADDFFGGGGGFGGHA?EAEFBEAGHFABFGG5FDF5DB1EEGAFDFB53FF5FH@G5FFEHGHEFHFFHBE333GF43GCGGGGE@0?BFGGB0B?FHGFDGGHHHBFFDEGGHGFFFDFE@<1>@FFFGHHHHFHEFGDABFFGG/@DCE<CG1<GF0/DD000=<DHGBDFDCECE/:AC?-;-;9B/ABBB-AD9BFB99AB?BDFBAD-.9..@;=;;..9..9/9;BEF;A:9/BFF\n+@M01368:8:000000000-A3GHV:1:1102:10677:23253/1\n+CCTTAAATAAGACATCACGATGGATCACAGGTCTATCACC'..b'FHGDF@@?CGFHCEGGGFD.CCC?EGHBHHHFHHFBCFFGEB/CEGGGGDAA.90C9CEBFGGBBF/9.9FBFFFBBFF//99FFFFEABF//99FFEFFFBFF\n+@M01368:8:000000000-A3GHV:1:1113:5741:16959/1\n+TAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGA\n++\n+ABBBBFFFFFFFGGGFGGGGGGHHHGHHGGHBGHGAGFFCAFGHGFFGHHGFHHHHHGGGGGHGHHHHHHHHE3BFFHHHGG0EDF@GHFFGGGHGGGGGGGGGGGGGHHGGEEFHGFHHDDG@DGGGHHGDGGGGGHGG?CF?HHGHHHGHGHHHFFHGGGHHHHGGCD.;0<C;CGGGGEFF/.;0;FFFBF/0;0CFGFFB..9B/;0CBFFBBFFFFBAC?DED9;B9AD;.FFFB/B/;FBA/B//\n+@M01368:8:000000000-A3GHV:1:1114:10130:11959/1\n+CGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTCTGATCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATCTCGTATGCCGTCTTCTGCTTGCAACAAACACACATCCAGA\n++\n+>A33>FFFFFF@FFFGGGGFGGD4EGGGGGHHGFFGHFGGHHHFEFHECFHHHEHGAGBCCGCCEGGHGHEGFBFHFHHHHGGGHFHGHEGGGFEGEGG??@DBGHGGC-@FFGHFHFHB-??DA-DD@9:BEBG@B?E?A.ABBFBFA??F.FF/BFFB/B9B/9;BF9FF9FFFFFFFFFFFFFF?BB?;9EE;-;DDB9//;B-B@;ABFFEFFFF/-.9A.;//9/BF./B/..9.9:...//////\n+@M01368:8:000000000-A3GHV:1:1114:14540:5315/1\n+CTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGGGGGCTATTTAGGTTTTT\n++\n+AABCCFFFFFFFGGGGGGGGGGHHHHHHHFHHHHGHHGHHGGGHGGHHHHHHHGHHHHHHGGGGGHHFHHHFGHHGGFHHHHHGGGGGHHHGHGGHHHGGGGGGHGHGGGGHHGGGGHHHHHEGDDFGFFFHHGGGGGCDAFCFGFDHHHHGGHGHHHHHHBCGEHHHHGGHG.ACGEHGG0CBFFF:A;BB0;09CGF00CFFFE0AA?//CFFFFFFFFFFFFFFFBEF;A.-=A--:BBFB90;;FE.\n+@M01368:8:000000000-A3GHV:1:1114:15066:16302/1\n+TAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAACGGTTGTTAATTAATTATTGCTTGTAGGACA\n++\n+BBBBAFFBDFBFBGGGGGFGGGBGFFFHGFHHGFFFHGHHHGHHHHFFHHHGHGC?AEFFHEFBFFFGHHHHH1FDGFFHGHGHFEGCGC-<<AHHHGGGGGGGFHH0GHFCCCADGGG?.9/A-???DGGFFF.9F9/EE-;;BBBFFBFFFFFFFFFEFFFFBFFBBFFFFF/BFFBFFFFF-DBFFF;/BFF//BB//9/BEA---9:BFFFFFF/F/.;.:@9.BBFF/;BFF/;/////9/////.\n+@M01368:8:000000000-A3GHV:1:1114:16639:15258/1\n+CCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGCGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTCCAATATTACAGGCGAACATACTTACTAAATTGTGT\n++\n+11>>ABFFFFFFGGCGC1BBF1GHHHBHHHHGFHGH1A100AA/GGEHGFBAA1FFD2FHHHHECG2F1BB/E0FC/A>EE/FGGFGEF1EGBBEHHCGGGHBGEHFHE0B?E--;C?CCGGG@A@GBFBBBB09?@??A-AB--ABE@=-=-9AE9A;FFFFFE=9-//;//;9FF/////;;///9B///;/B////9FFBB;--A@-;/9;9-:-/;;FFFE9BF?@;-9-99/B9F/://///99/;\n+@M01368:8:000000000-A3GHV:1:1114:2404:13066/1\n+TCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCTGTCTATTATACACATC\n++\n+CCCCCFFFFCFFGGGGGGGGGGHHHHHGHHHHHHHHHFFHHHHHGGGGHHHHHHHHFHHHHHHFGGHHGGHGGHHHHHHGHHFHHHHGGGGGGHHHHHHGHHHHHHHHHHGGGGGGGHH?FGHHHGGGGGGHHGGFGGHHGGGGHHHHHFGGGGFGHGHHGGGGGGGHGGGEGGHHGHHHHHHHHHGFBFFDA0FGGGFFGG0:EFGGGGGGGG;AEBF0B0BFFBFFFFFFFFFFFFFFFFFFFFFEFF0\n+@M01368:8:000000000-A3GHV:1:1114:9184:6959/1\n+GGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACCAGATGTCGGATACAGTTCACTTTCTGTCTCTTA\n++\n+AABBBFFFCCCBFGGGGGGGGGHHHHHHHHGGGGGGHHHG3FFHHHFGFGGGHHHGGGEHHGGGGHHHHHHGGGGGGHGHGGGGGGGDEGGGGEGGFHHHHHHHHHHHHGGGFGEHHGGFDGGGDFFGFHHHHGFCFHHHHHEFHFHGGFFGHHGGGHHHHDGHHHFHHHFFFFGFGGG.EFGGGGFGEBFGGGFGFGGGGFFBFGGBBFFFFFB/FEFF?///;A::AABBFFFBFFFFFFFFFBFFFF/\n' |
| b |
| diff -r 000000000000 -r 82217dccdbcf test-data/bwa-mem-fastq1.fq.gz |
| b |
| Binary file test-data/bwa-mem-fastq1.fq.gz has changed |
| b |
| diff -r 000000000000 -r 82217dccdbcf test-data/bwa-mem-fastq2.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa-mem-fastq2.fq Fri Oct 08 10:19:48 2021 +0000 |
| b |
| b'@@ -0,0 +1,400 @@\n+@M01368:8:000000000-A3GHV:1:1101:6911:8255/2\n+TCGCCTTACCGCTACTCACCCACGGCGGCCATCAGCCGATACTAAGTTTGGGGTATGGTGGGGGGGATAATGAATTAGGTTGTGGGGGAGGGTTTGTGGTTGAGAGAAACACAAAAAACAATCTTATATATGGGTAGTCGTTTTGTATTGGTTTTTTGTTTTGTTTGTGTTTTGAGTGTCGGTTTAGTTCGGTGTACTAGGGGGGGTGGATGGGGTCGGCTGGTGAGGGGGTCTTAGTGTATTGAGTGTGG\n++\n+1>11111@11111A111A100000000////011110//>>/12@1@22B/////1@>21/>>/-----9/;////9////--;-;-;-----;--------9/-/-///9-;-------9//////9/////-//-/9-;-;9--/////99-;--9-:-;----/---/-----////---9-/////--;A-//////---------9/-----;-----/-/-----;--;//////////9;///-\n+@M01368:8:000000000-A3GHV:1:1101:14518:9998/2\n+CATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATAA\n++\n+CCCCCFCCCCCFGGGGGGGGGGHHHHHHHHHHHHHHHHGFHHHHGGGGGHGFHHHHHHHHHHHHHHHHHHHGHGGEHGGGGCGGGHHGGCGGGGGHHGHHHGGGGGGGG.BFFFGAGADFGAFDGFGGCFFF;DDFFFFFFFFFFFFFFFFFFEFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFF09FFFE00;BE@;DABBFFFFFBBFB00;F:9;FFBFFF9BFFFFFFFFFFFFF90/::BFFFBF0\n+@M01368:8:000000000-A3GHV:1:1101:18422:19051/2\n+CTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGGGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGG\n++\n+BCCCCFFCFFFFGGGGGGGGGGHHHGHHHHHHHHHHHHHHHHGGGGHHHHHHHHEHHHHHHHGGHHGGHGGHHHHHHHGHGGHHHGGGGGHGHHHHGGGHFHFHHHHHGGGGGHBFFCGDHHHGGGGGGHGGGGGGHHGCGGGFGHHBGGGGGFFFHEGGGGGCDCCE@EFGHHHHFHEGHGFFHHGB;ECBFGGGEFEFFGF0AFGFGFFG.;;DFFFFFFFFFF090BFFFE?FEFBBFBFFFB990BF\n+@M01368:8:000000000-A3GHV:1:1101:25545:21098/2\n+GCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTTCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCAACCTATGTCGCAGTATCTGTCTTTGAT\n++\n+3AAA34BFFFFFGCGGCGGGCGHHHGHHHHCGHFGHFHGFGGCDGGBD5FGFFFHFHGGGHAEBFGHHHEHGGFHBGGFHHHGGGEEFHHHFHFFHDHGHGHHHHFFHHGGFAEGFFFFFBGHHHFFHHHHHHHFHFHHFHGFHGHGA/<@EFHEHH1GGHFFFHG1>=FGHFHGF.GE//-<BB?9.9BFFFB==AA/FFFFFA-@BA.;;D?F9FAB;---./99BFFFBBAE-.9B/BFB9F/9BFBB\n+@M01368:8:000000000-A3GHV:1:1101:5446:12248/2\n+ATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTT\n++\n+CCDDDCCCCFFFGGGGGGGGGGHHHHHGHHHHHHHHGHHHHHHGHHHHGGGGHHHHHHHHHHHHHHHHHHHHHHGGGGGHHHHHHHGFGHHHHHHHHHHHHHHHHHGHHHHHGGGGGHHHHHHHHHHHHHHHGHHHHHHGHGHGHHGGGGGGGGGGGFFFFFFFFFFFFFFAFFFFFFFFFFFFFBFC?.EAFFFFFFFFAFFFFFFFFFFFFFFFEFFFF0FFFFFFF0BFFFFFFFFF?.BDCFFEDA/\n+@M01368:8:000000000-A3GHV:1:1101:5861:6452/2\n+TTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACG\n++\n+BCCCCFBBCCCFGGGGGGGGGGHHHHHHHHHHHHHHHHGHHHHHHHHHHHGGGGHHHHHHHHGHHHHHHHHHHHHHGGHGGHHHHHHHGHHHHHHHHHHHHHHHHHHHGGHHHHGGGGGGEHGHHHHHHHHHHHGHHHHHHGHGHGHGGGGCGGGGGFFFFFFFFFFFFFFFFFFFFFFFF?FFEAF:DAEF9DEFFFFFFF-A.BFFFFFEFFFFEFFFFFFFF0FFEB0FFFFBFFFFFFADEFCF0/.\n+@M01368:8:000000000-A3GHV:1:1102:10403:6021/2\n+GGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGGGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGGGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGAGGTTAATAGGGGGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACGCTGAAGTAGGAACCAGATGTCGGATACAGTTGACTTTAGGTAACCCA\n++\n+AA?A34BF>AADEBGGGGFFCGGHHA5DFGAE?AAEDFHG2AEE1FBE00A1BGE0?E1FFGEEEGB4F43?EE/>///F??//@BCBAC<<BAGHB?11F/FGFGGBFBGBD.11><.<<<C0<A</<<=0GFHC@-.;FF09BFFGB00B0;FE.C/:CCF0;0C0;BBBFF@.9AF.:9EFF.;.BFF/FF/;/./BFB/..;;ABF/9FF//.;AAF9BBBA;-A.B/9///9/BF////;///:9.\n+@M01368:8:000000000-A3GHV:1:1102:10677:23253/2\n+AATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTG'..b'HGGGGGGGGGFEACFFFFFFFFFFFFFFFDFFFAFFFFBFAB@EFAAEFFFFF.ACF.BBFFEBFFFEB;FFFFFFFA/BFBFBBBFFFBFFFFFED.>DFFF.\n+@M01368:8:000000000-A3GHV:1:1113:5741:16959/2\n+GTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACG\n++\n+BBBBCFCCCCCFGGGGGGGGGGHHHHHHHGHHHHHHHHGHHHHGHDGHHHGGGGHHHHHHHHHHHHHHHGHHHHHGGGEGGHHHHFHHHHHHHHHHHHHHHHHHHHHHGHHGHHGGGGGHHHHHHHHHHHGHHHFHHHHHHGHGHGHGGGGCGGFGGFFFFFFFFFFFFFBFFFFFFFFFFFFFFAFFFFEAEFFFFFFFFFFF9BFFBFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFADAB-/BF.\n+@M01368:8:000000000-A3GHV:1:1114:10130:11959/2\n+ATCAGAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGATCTAGTGGAGAGTTCTGTGGGGCCGGGGATCCTTATAAAAAAAATAGA\n++\n+BCCDDFFFFFFFGGGGGGGGGGGHHHHHGGHHHGGGCGGHGHGGGGHHGGGGHHHHHHGGGEGGHHHFGGGGG?E1FE?/EEHHHHHGHHGHHHHGHFHGHGHHGDGGFG2FF2?GHHHHHGCCCFHGHGHHHHGHHFEHHFGHHGHH<1=DGHHHGHHGHGAGAEEDG.CGCGHC0CGBFHGFBBF0ABDDEFF@?--:BB@.;:BF;0.0:0.0:000:BF.-.------.9/;000::0;0:--.000\n+@M01368:8:000000000-A3GHV:1:1114:14540:5315/2\n+CACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCC\n++\n+CCCCCFFCCDCCGGGGGGGGGGHHHHHHHHHGGGGGHHHHHHHHHHHHHHHHHHHGHHHHHHHGHHHHFHFHHHGGGGGHHHHHHHHHHHHHGHHHHHHHHGGGGGGHHHFHHHGHHHHHHHHHHHHHHHHHHGHGHHHGGGFGHHHHHHHHFHHHHHF?1FHHGHGHGHGHHGGFFFFDBFBE;BCC.:BFFFFFFFFFFFFFF;AFFFFF-=-.AEDEFFFFF..9A;9FFFF0FFFFE00FFF0:BA.\n+@M01368:8:000000000-A3GHV:1:1114:15066:16302/2\n+TTATTATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGGGATAGACCTGTGATCCATCGTGTGG\n++\n+CCCCCFFFFFFFGGGGGGGGGGHHHHHHHHHHHHHHHDGHHHHFHHGHHGHHHHHGGGGEHHHHFHHFF5FHHFEGHHHGDHGGHGHGFGGGEHFGHHGGGGGHGHHHGHHFHHB3FGHHFGGGG?GFFHCCEBGFFECCDFEGFCFGCHHGFDDHHHGHHCFGGGGGFBFDGFG?-:..AFG.-C0C009;:00;00:9/:CEFFF?AE::9;9?0:FEF0;0..--./00::B/090000000;A....\n+@M01368:8:000000000-A3GHV:1:1114:16639:15258/2\n+TTATTATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCGCACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGGGATAGACCTGTGATCCATCGTGATG\n++\n+CDCCCFFFFFFFGGGGGGGGGGHHHHHHHHHHHHHHHHGHHHHHHHHGHHHHHHGGGGGHGIHHHIH5DEGHHHF?FGHGGHGGHEGGHFHHGHGEHHGGGGGFFFGHFBG2GHEBGHHGHGGEG/GFGABEDFGHEED?GGHHFFGGGCFEGD/GFHFFGEFGCGG?CC??D-EF@EEEFGCDDBBFGGGEBBFFF09090A.BFGA.9CCA0;EBAB00BBFF.@-./;BB;BFFF0:00099AAFFF0\n+@M01368:8:000000000-A3GHV:1:1114:2404:13066/2\n+ATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGACCATACTTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGACTGTCTCTTATACACATT\n++\n+CCCCCFFFFFFCGGGGGGGGGGHHHHHHHHHFFHHHHGGGGGHFFFHHFHHHHHHHHHHHHHHHGFEGGGHGEDFCDFHGHFG@@DGGHHHHHHGGGGCGGGGGEHGGCGBB?CF99EGFGGFGG?D9CFFFF/BBFFFFFEF9BFFAFFFFEFFFFFFFFFFFFFFFFFFFFF.FFBBFFFFFFFFFFFF-9;;;BFFFFFB9BFBFBFABFFEFFFFFFFFFF::BFFBFFFF.9//;FFFFF/BFFB/\n+@M01368:8:000000000-A3GHV:1:1114:9184:6959/2\n+AAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCCTGTCTCTTA\n++\n+CCCCBFFFFFFFGGGGGGGGGGHHHHHHHHHHHHHHHHHHHHHHHHHHGHHHHHHEHIHHGGGGHHHHHHHHHHHHHGHHHHHHHHGGGGGHHFHHHHHBGHHHHHHHHHHHHHHHHHGHHHHHGGGGGHHHHGHHHHHHHHHHHHHHHHHGHGHGHHGGGGCFFFFFFFFFFFFFFFFFFFFFFFFFF.CFFFFAF=D=EAEFFF0B:0AF-DAFBFFFFFFFFFBFFFFFFFFFFBFFFEFF9B900B0\n' |
| b |
| diff -r 000000000000 -r 82217dccdbcf test-data/bwa-mem-mt-genome.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa-mem-mt-genome.fa Fri Oct 08 10:19:48 2021 +0000 |
| b |
| b'@@ -0,0 +1,238 @@\n+>gi|251831106|ref|NC_012920.1|\n+GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGG\n+GTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTC\n+CTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTA\n+ATTAATTAATGCTTGTAGGACATAATAATAACAATTGAATGTCTGCACAGCCACTTTCCACACAGACATC\n+ATAACAAAAAATTTCCACCAAACCCCCCCTCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGCCA\n+AACCCCAAAAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAATTTTATCTTTTGGCGGTATGCAC\n+TTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCCATACTACTAATCTCATCAATA\n+CAACCCCCGCCCATCCTACCCAGCACACACACACCGCTGCTAACCCCATACCCCGAACCAACCAAACCCC\n+AAAGACACCCCCCACAGTTTATGTAGCTTACCTCCTCAAAGCAATACACTGAAAATGTTTAGACGGGCTC\n+ACATCACCCCATAAACAAATAGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAA\n+GCATCCCCGTTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAGGAACAAGCATCAAGCACGCAGC\n+AATGCAGCTCAAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAA\n+ACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACCGCGGTCACACGA\n+TTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTAGATCACCCCCTCCCCAATAAAGCTAAAACT\n+CACCTGAGTTGTAAAAAACTCCAGTTGACACAAAATAGACTACGAAAGTGGCTTTAACATATCTGAACAC\n+ACAATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCCTAAACCTCAACAGTTAAATC\n+AACAAAACTGCTCGCCAGAACACTACGAGCCACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATC\n+CCTCTAGAGGAGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTGCTCAGCCTATATA\n+CCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGTAAGCGCAAGTACCCACGTAAAGACGTTAGGTC\n+AAGGTGTAGCCCATGAGGTGGCAAGAAATGGGCTACATTTTCTACCCCAGAAAACTACGATAGCCCTTAT\n+GAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTAAGAGTAGAGTGCTTAGTTGAACAGGGCCCTGA\n+AGCGCGTACACACCGCCCGTCACCCTCCTCAAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCA\n+TTTATATAGAGGAGACAAGTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACGAACCAGAGTGTA\n+GCTTAACACAAAGCACCCAACTTACACTTAGGAGATTTCAACTTAACTTGACCGCTCTGAGCTAAACCTA\n+GCCCCAAACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTACCCAAATAAAGTATAGGCG\n+ATAGAAATTGAAACCTGGCGCAATAGATATAGTACCGCAAGGGAAAGATGAAAAATTATAACCAAGCATA\n+ATATAGCAAGGACTAACCCCTATACCTTCTGCATAATGAATTAACTAGAAATAACTTTGCAAGGAGAGCC\n+AAAGCTAAGACCCCCGAAACCAGACGAGCTACCTAAGAACAGCTAAAAGAGCACACCCGTCTATGTAGCA\n+AAATAGTGGGAAGATTTATAGGTAGAGGCGACAAACCTACCGAGCCTGGTGATAGCTGGTTGTCCAAGAT\n+AGAATCTTAGTTCAACTTTAAATTTGCCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAGTC\n+CAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGAGTAAAAAATTTAACACCCATAG\n+TAGGCCTAAAAGCAGCCACCAATTAAGAAAGCGTTCAAGCTCAACACCCACTACCTAAAAAATCCCAAAC\n+ATATAACTGAACTCCTCACACCCAATTGGACCAATCTATCACCCTATAGAAGAACTAATGTTAGTATAAG\n+TAACATGAAAACATTCTCCTCCGCATAAGCCTGCGTCAGATTAAAACACTGAACTGACAATTAACAGCCC\n+AATATCTACAATCAACCAACAAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAGGA\n+AAGGTTAAAAAAAGTAAAAGGAACTCGGCAAATCTTACCCCGCCTGTTTACCAAAAACATCACCTCTAGC\n+ATCACCAGTATTAGAGGCACCGCCTGCCCAGTGACACATGTTTAACGGCCGCGGTACCCTAACCGTGCAA\n+AGGTAGCATAATCACTTGTTCCTTAAATAGGGACCTGTATGAATGGCTCCACGAGGGTTCAGCTGTCTCT\n+TACTTTTAACCAGTGAAATTGACCTGCCCGTGAAGAGGCGGGCATAACACAGCAAGACGAGAAGACCCTA\n+TGGAGCTTTAATTTATTAATGCAAACAGTACCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCATT\n+AAAAATTTCGGTTGGGGCGACCTCGGAGCAGAACCCAACCTCCGAGCAGTACATGCTAAGACTTCACCAG\n+TCAAAGCGAACTACTATACTCAATTGATCCAATAACTTGACCAACGGAACAAGTTACCCTAGGGATAACA\n+GCGCAATCCTATTCTAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCG\n+ATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTACGTGATCTGAGTTCAGACCGG\n+AGTAATCCAGGTCGGTTTCTATCTACNTTCAAATTCCTCCCTGTACGAAAGGACAAGAGAAATAAGGCCT\n+ACTTCACAAAGCGCCTTCCCCCGTAAATGATATCATCTCAACTTAGTATTATACCCACACCCACCCAAGA\n+ACAGGGTTTGTTAAGATGGCAGAGCCCGGTAATCGCATAAAACTTAAAACTTTACAGTCAGAGGTTCAAT\n+TCCTCTTCTTAACAACATACCCATGGCCAACCTCCTACTCCTCATTGTACCCATTCTAATCGCAATGGCA\n+TTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATACAACTACGCAAAGGCCCCAACGTTGTAGGCC\n+CCTACGGGCTACTACAACCCTTCGCTGACGCCATAAAACTCTTCACCAAAGAGCCCCTAAAACCCGCCAC\n+ATCTACCATCACCCTCTACATCACCGCCCCGACCTTAGCTCTCACCATCGCTCTTCTACTATGAACCCCC\n+CTCCCCATACCCAACCCCCTGGTCAACCTCAACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAG\n+CCGTTTACTCAATCCTCTGATCAGGGTGAGCATCAAACTCAAACTACGCCCTGATCGGCGCACTGCGAGC\n+AGTAGCCCAAACAATCTCATATGAAGTCACCCTAGCCATCATTCTACTATCAACATTACTAATAAGTGGC\n+TCCTTTAACCTCTCCACCCTTATCACAACACAAGAACACCTCTGATTACTCCTGCCATCA'..b'CAGTTCTTCAAATATCTACTCATCTTCCTAATTACCATACTAATCTTAGTTACCGCTAA\n+CAACCTATTCCAACTGTTCATCGGCTGAGAGGGCGTAGGAATTATATCCTTCTTGCTCATCAGTTGATGA\n+TACGCCCGAGCAGATGCCAACACAGCAGCCATTCAAGCAATCCTATACAACCGTATCGGCGATATCGGTT\n+TCATCCTCGCCTTAGCATGATTTATCCTACACTCCAACTCATGAGACCCACAACAAATAGCCCTTCTAAA\n+CGCTAATCCAAGCCTCACCCCACTACTAGGCCTCCTCCTAGCAGCAGCAGGCAAATCAGCCCAATTAGGT\n+CTCCACCCCTGACTCCCCTCAGCCATAGAAGGCCCCACCCCAGTCTCAGCCCTACTCCACTCAAGCACTA\n+TAGTTGTAGCAGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAGAAAATAGCCCACTAATCCAAAC\n+TCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCGCAGCAGTCTGCGCCCTTACACAAAATGACATC\n+AAAAAAATCGTAGCCTTCTCCACTTCAAGTCAACTAGGACTCATAATAGTTACAATCGGCATCAACCAAC\n+CACACCTAGCATTCCTGCACATCTGTACCCACGCCTTCTTCAAAGCCATACTATTTATGTGCTCCGGGTC\n+CATCATCCACAACCTTAACAATGAACAAGATATTCGAAAAATAGGAGGACTACTCAAAACCATACCTCTC\n+ACTTCAACCTCCCTCACCATTGGCAGCCTAGCATTAGCAGGAATACCTTTCCTCACAGGTTTCTACTCCA\n+AAGACCACATCATCGAAACCGCAAACATATCATACACAAACGCCTGAGCCCTATCTATTACTCTCATCGC\n+TACCTCCCTGACAAGCGCCTATAGCACTCGAATAATTCTTCTCACCCTAACAGGTCAACCTCGCTTCCCC\n+ACCCTTACTAACATTAACGAAAATAACCCCACCCTACTAAACCCCATTAAACGCCTGGCAGCCGGAAGCC\n+TATTCGCAGGATTTCTCATTACTAACAACATTTCCCCCGCATCCCCCTTCCAAACAACAATCCCCCTCTA\n+CCTAAAACTCACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCCTAGACCTCAACTACCTAACC\n+AACAAACTTAAAATAAAATCCCCACTATGCACATTTTATTTCTCCAACATACTCGGATTCTACCCTAGCA\n+TCACACACCGCACAATCCCCTATCTAGGCCTTCTTACGAGCCAAAACCTGCCCCTACTCCTCCTAGACCT\n+AACCTGACTAGAAAAGCTATTACCTAAAACAATTTCACAGCACCAAATCTCCACCTCCATCATCACCTCA\n+ACCCAAAAAGGCATAATTAAACTTTACTTCCTCTCTTTCTTCTTCCCACTCATCCTAACCCTACTCCTAA\n+TCACATAACCTATTCCCCCGAGCAATCTCAATTACAATATATACACCAACAAACAATGTTCAACCAGTAA\n+CTACTACTAATCAACGCCCATAATCATACAAAGCCCCCGCACCAATAGGATCCTCCCGAATCAACCCTGA\n+CCCCTCTCCTTCATAAATTATTCAGCTTCCTACACTATTAAAGTTTACCACAACCACCACCCCATCATAC\n+TCTTTCACCCACAGCACCAATCCTACCTCCATCGCTAACCCCACTAAAACACTCACCAAGACCTCAACCC\n+CTGACCCCCATGCCTCAGGATACTCCTCAATAGCCATCGCTGTAGTATATCCAAAGACAACCATCATTCC\n+CCCTAAATAAATTAAAAAAACTATTAAACCCATATAACCTCCCCCAAAATTCAGAATAATAACACACCCG\n+ACCACACCGCTAACAATCAATACTAAACCCCCATAAATAGGAGAAGGCTTAGAAGAAAACCCCACAAACC\n+CCATTACTAAACCCACACTCAACAGAAACAAAGCATACATCATTATTCTCGCACGGACTACAACCACGAC\n+CAATGATATGAAAAACCATCGTTGTATTTCAACTACAAGAACACCAATGACCCCAATACGCAAAACTAAC\n+CCCCTAATAAAATTAATTAACCACTCATTCATCGACCTCCCCACCCCATCCAACATCTCCGCATGATGAA\n+ACTTCGGCTCACTCCTTGGCGCCTGCCTGATCCTCCAAATCACCACAGGACTATTCCTAGCCATGCACTA\n+CTCACCAGACGCCTCAACCGCCTTTTCATCAATCGCCCACATCACTCGAGACGTAAATTATGGCTGAATC\n+ATCCGCTACCTTCACGCCAATGGCGCCTCAATATTCTTTATCTGCCTCTTCCTACACATCGGGCGAGGCC\n+TATATTACGGATCATTTCTCTACTCAGAAACCTGAAACATCGGCATTATCCTCCTGCTTGCAACTATAGC\n+AACAGCCTTCATAGGCTATGTCCTCCCGTGAGGCCAAATATCATTCTGAGGGGCCACAGTAATTACAAAC\n+TTACTATCCGCCATCCCATACATTGGGACAGACCTAGTTCAATGAATCTGAGGAGGCTACTCAGTAGACA\n+GTCCCACCCTCACACGATTCTTTACCTTTCACTTCATCTTGCCCTTCATTATTGCAGCCCTAGCAACACT\n+CCACCTCCTATTCTTGCACGAAACGGGATCAAACAACCCCCTAGGAATCACCTCCCATTCCGATAAAATC\n+ACCTTCCACCCTTACTACACAATCAAAGACGCCCTCGGCTTACTTCTCTTCCTTCTCTCCTTAATGACAT\n+TAACACTATTCTCACCAGACCTCCTAGGCGACCCAGACAATTATACCCTAGCCAACCCCTTAAACACCCC\n+TCCCCACATCAAGCCCGAATGATATTTCCTATTCGCCTACACAATTCTCCGATCCGTCCCTAACAAACTA\n+GGAGGCGTCCTTGCCCTATTACTATCCATCCTCATCCTAGCAATAATCCCCATCCTCCATATATCCAAAC\n+AACAAAGCATAATATTTCGCCCACTAAGCCAATCACTTTATTGACTCCTAGCCGCAGACCTCCTCATTCT\n+AACCTGAATCGGAGGACAACCAGTAAGCTACCCTTTTACCATCATTGGACAAGTAGCATCCGTACTATAC\n+TTCACAACAATCCTAATCCTAATACCAACTATCTCCCTAATTGAAAACAAAATACTCAAATGGGCCTGTC\n+CTTGTAGTATAAACTAATACACCAGTCTTGTAAACCGGAGATGAAAACCTTTTTCCAAGGACAAATCAGA\n+GAAAAAGTCTTTAACTCCACCATTAGCACCCAAAGCTAAGATTCTAATTTAAACTATTCTCTGTTCTTTC\n+ATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACA\n+TTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCA\n+ATCCACATCAAAACCCCCTCCCCATGCTTACAAGCAAGTACAGCAATCAACCCTCAACTATCACACATCA\n+ACTGCAACTCCAAAGCCACCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAACAGTACATAG\n+TACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCCC\n+TCAGATAGGGGTCCCTTGACCACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTGCTACTCTCCTCG\n+CTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTC\n+ATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATG\n' |
| b |
| diff -r 000000000000 -r 82217dccdbcf test-data/bwa-mem-test1-fasta.bam |
| b |
| Binary file test-data/bwa-mem-test1-fasta.bam has changed |
| b |
| diff -r 000000000000 -r 82217dccdbcf test-data/bwa-mem-test1.bam |
| b |
| Binary file test-data/bwa-mem-test1.bam has changed |
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| diff -r 000000000000 -r 82217dccdbcf test-data/bwa-mem-test2.bam |
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| Binary file test-data/bwa-mem-test2.bam has changed |
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| diff -r 000000000000 -r 82217dccdbcf test-data/bwa-mem-test3.bam |
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| diff -r 000000000000 -r 82217dccdbcf test-data/bwa-mem-test4.bam |
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| diff -r 000000000000 -r 82217dccdbcf test-data/bwa_mem2_index.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa_mem2_index.loc Fri Oct 08 10:19:48 2021 +0000 |
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| @@ -0,0 +1,1 @@ +mtgenome mtGenome Mitochondiral genome ${__HERE__}/test-cache/bwa-mem-mt-genome.fa \ No newline at end of file |
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| diff -r 000000000000 -r 82217dccdbcf test-data/test-cache/bwa-mem-mt-genome.fa.0123 |
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| Binary file test-data/test-cache/bwa-mem-mt-genome.fa.0123 has changed |
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| diff -r 000000000000 -r 82217dccdbcf test-data/test-cache/bwa-mem-mt-genome.fa.amb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-cache/bwa-mem-mt-genome.fa.amb Fri Oct 08 10:19:48 2021 +0000 |
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| @@ -0,0 +1,2 @@ +16569 1 1 +3106 1 N |
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| diff -r 000000000000 -r 82217dccdbcf test-data/test-cache/bwa-mem-mt-genome.fa.ann --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-cache/bwa-mem-mt-genome.fa.ann Fri Oct 08 10:19:48 2021 +0000 |
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| @@ -0,0 +1,3 @@ +16569 1 11 +0 gi|251831106|ref|NC_012920.1| (null) +0 16569 1 |
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| diff -r 000000000000 -r 82217dccdbcf test-data/test-cache/bwa-mem-mt-genome.fa.bwt.2bit.64 |
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| Binary file test-data/test-cache/bwa-mem-mt-genome.fa.bwt.2bit.64 has changed |
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| diff -r 000000000000 -r 82217dccdbcf test-data/test-cache/bwa-mem-mt-genome.fa.pac |
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| Binary file test-data/test-cache/bwa-mem-mt-genome.fa.pac has changed |
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| diff -r 000000000000 -r 82217dccdbcf tool-data/bwa_mem2_index.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/bwa_mem2_index.loc.sample Fri Oct 08 10:19:48 2021 +0000 |
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| @@ -0,0 +1,38 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of BWA indexed sequences data files. You will need +#to create these data files and then create a bwa_index.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The bwa_index.loc +#file has this format (longer white space characters are TAB characters): +# +#<unique_build_id> <dbkey> <display_name> <file_path> +# +#So, for example, if you had phiX indexed stored in +#/depot/data2/galaxy/phiX/base/, +#then the bwa_index.loc entry would look like this: +# +#phiX174 phiX phiX Pretty /depot/data2/galaxy/phiX/base/phiX.fa +# +#and your /depot/data2/galaxy/phiX/base/ directory +#would contain phiX.fa.* files: +# +#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 phiX.fa.amb +#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 phiX.fa.ann +#-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 phiX.fa.bwt +#...etc... +# +#Your bwa_index.loc file should include an entry per line for each +#index set you have stored. The "file" in the path does not actually +#exist, but it is the prefix for the actual index files. For example: +# +#phiX174 phiX phiX174 /depot/data2/galaxy/phiX/base/phiX.fa +#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/hg18/base/hg18canon.fa +#hg18full hg18 hg18 Full /depot/data2/galaxy/hg18/base/hg18full.fa +#/orig/path/hg19.fa hg19 hg19 /depot/data2/galaxy/hg19/base/hg19.fa +#...etc... +# +#Note that for backwards compatibility with workflows, the unique ID of +#an entry must be the path that was in the original loc file, because that +#is the value stored in the workflow for that parameter. That is why the +#hg19 entry above looks odd. New genomes can be better-looking. +# |
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| diff -r 000000000000 -r 82217dccdbcf tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Fri Oct 08 10:19:48 2021 +0000 |
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| @@ -0,0 +1,8 @@ +<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> +<tables> + <!-- Locations of indexes in the BWA-MEM2 mapper format--> + <table name="bwa_mem2_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/bwa_mem_index.loc" /> + </table> +</tables> |
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| diff -r 000000000000 -r 82217dccdbcf tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Fri Oct 08 10:19:48 2021 +0000 |
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| @@ -0,0 +1,8 @@ +<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> +<tables> + <!-- Locations of indexes in the BWA-MEM2 mapper format--> + <table name="bwa_mem2_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="${__HERE__}/test-data/bwa_mem2_index.loc" /> + </table> +</tables> |