| Previous changeset 7:bf1f4994f104 (2019-02-21) Next changeset 9:86737d0f7fab (2019-07-29) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 |
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modified:
bcftools_cnv.xml macros.xml test-data/stats.a.vcf |
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added:
test-data/cnv.vcf test-data/cnv_baf_only.vcf test-data/cnv_pairwise_summary.tab test-data/cnv_summary.tab test-data/color_chrs.dat test-data/color_chrs_unrelated.dat test-data/fasta_indexes.loc test-data/plugin_frameshifts.bed test-data/test-cache/23andme.fa test-data/test-cache/23andme.fa.fai test-data/test-cache/consensus.fa test-data/test-cache/consensus.fa.fai test-data/test-cache/csq.fa test-data/test-cache/csq.fa.fai test-data/test-cache/gvcf.fa test-data/test-cache/gvcf.fa.fai test-data/test-cache/mpileup.ref.fa test-data/test-cache/mpileup.ref.fa.fai test-data/test-cache/norm.fa test-data/test-cache/norm.fa.fai tool_data_table_conf.xml.test |
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removed:
test-data/mpileup.ref.fa.fai |
| b |
| diff -r bf1f4994f104 -r 13fe14c56f6d bcftools_cnv.xml --- a/bcftools_cnv.xml Thu Feb 21 16:10:57 2019 -0500 +++ b/bcftools_cnv.xml Wed Jun 05 13:19:54 2019 -0400 |
| [ |
| b'@@ -1,11 +1,13 @@\n <?xml version=\'1.0\' encoding=\'utf-8\'?>\n-<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@">\n- <description>Copy number variation caller, requires Illumina\'s B-allele frequency (BAF) and Log R Ratio intensity (LRR)</description>\n+<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy1">\n+ <description>Call copy number variation from VCF B-allele frequency (BAF) and Log R Ratio intensity (LRR) values</description>\n <macros>\n <token name="@EXECUTABLE@">cnv</token>\n <import>macros.xml</import>\n </macros>\n- <expand macro="requirements" />\n+ <expand macro="requirements">\n+ <expand macro="matplotlib_requirement" />\n+ </expand>\n <expand macro="version_command" />\n <command detect_errors="aggressive"><![CDATA[\n @PREPARE_ENV@\n@@ -16,59 +18,44 @@\n \n bcftools @EXECUTABLE@\n \n---output-dir cnv_tmp\n+#set $output_dir = \'cnv_tmp\'\n+--output-dir $output_dir\n \n ## General section\n-#set $section = $sec_general\n-#if $section.control_sample:\n- --control-sample "${section.control_sample}"\n+#set $query_sample = str($query_sample).strip()\n+#set $control_sample = str($control_sample).strip()\n+#if $control_sample:\n+ -c \'$control_sample\'\n #end if\n-#if $section.query_sample:\n- --query-sample "${section.query_sample}"\n+#if $query_sample:\n+ -s \'$query_sample\'\n #end if\n @AF_FILE@\n-\n-#if $section.plot_threshold:\n- --plot-threshold "${section.plot_threshold}"\n+#if str($plotting.generate_plots) != \'none\':\n+ -p ${plotting.plot_threshold}\n #end if\n \n ## HMM section\n #set $section = $sec_hmm\n-#if $section.aberrant_query or $section.aberrant_control:\n- #set $query_val = #if $section.aberrant_query then $section.aberrant_query else \'1.0\'#\n- #set $control_val = #if $section.aberrant_control then $section.aberrant_control else \'1.0\'#\n- --aberrant "${query_val},${control_val}"\n-#end if\n-#if $section.BAF_weight:\n- --BAF-weight "${section.BAF_weight}"\n-#end if\n-#if $section.BAF_dev_query or $section.BAF_dev_control:\n- #set $query_val = #if $section.BAF_dev_query then $section.BAF_dev_query else \'1.0\'#\n- #set $control_val = #if $section.BAF_dev_control then $section.BAF_dev_control else \'1.0\'#\n- --BAF-dev "${query_val},${control_val}"\n+--aberrant "${section.aberrant_query},${section.aberrant_control}"\n+#if str($section.aberrant_optimization.do_optimize) == \'yes\':\n+ --optimize ${section.aberrant_optimization.lower_bound}\n #end if\n-#if $section.LRR_weight:\n- --LRR-weight "${section.LRR_weight}"\n-#end if\n-#if $section.LRR_dev_query or $section.LRR_dev_control:\n- #set $query_val = #if $section.LRR_dev_query then $section.LRR_dev_query else \'1.0\'#\n- #set $control_val = #if $section.LRR_dev_control then $section.LRR_dev_control else \'1.0\'#\n- --LRR-dev "${query_val},${control_val}"\n-#end if\n-#if $section.LRR_smooth_win:\n- --LRR-smooth-win "${section.LRR_smooth_win}"\n-#end if\n-#if $section.optimize:\n- --optimize "${section.optimize}"\n+--BAF-weight ${section.score_usage.baf_weight}\n+--BAF-dev "${section.score_usage.baf_dev_query},${section.score_usage.baf_dev_control}"\n+--LRR-weight ${section.score_usage.lrr_weight}\n+#if str($section.score_usage.compute_on) == \'baf+lrr\':\n+ --LRR-dev "${section.score_usage.lrr_dev_query},${section.score_usage.lrr_dev_control}"\n+ --LRR-smooth-win ${section.score_usage.lrr_smooth_win}\n #end if\n #if $section.same_prob:\n- --same-prob "${section.same_prob}"\n+ --same-prob ${section.same_prob}\n #end if\n #if $section.err_prob:\n- --err-prob "${section.err_prob}"\n+ --err-prob ${section.err_prob}\n #end if\n #if $section.xy_prob:\n- --xy-prob "${section.xy_prob}"\n+ --xy-prob ${section.xy_prob}\n #end if\n \n ## Filter section\n@@ -78,85 +65,172 @@\n \n ## Primary Input/Outputs\n @INPUT_FILE@\n-&& mv $output_dir/cn.*.tab "$output_cn"\n-&& mv $output_dir/dat.*.tab "$output_dat"\n-&& mv $output_dir/summary.*.tab "$output_summary"\n-## && python $output_dir/plot.*.py\n+\n+&& mv $output_dir/cn.*.tab \'$output'..b'="Fraction of aberrant cells in control, defaults to 1." />\n- <param name="BAF_weight" type="float" value="1." min="0." max="1." label="Baf Weight" optional="True" help="relative contribution from BAF" />\n-\n- <param name="BAF_dev_query" type="float" value="" min="0." max="1." label="Baf Query Deviation" optional="true" \n- help="Expected BAF deviation in query, defaults to: 0.04" />\n- <param name="BAF_dev_control" type="float" value="" min="0." max="1." label="Baf Control Deviation" optional="true" \n- help="Expected BAF deviation in control, defaults to: 0.04" />\n-\n- <param name="LRR_weight" type="float" label="LRR Weight" optional="True" >\n- <help>\n- Relative contribution from LRR. \n- With noisy data, this option can have big effect on the number of calls produced. \n- In truly random noise (such as in simulated data), the value should be set high (1.0), i\n- but in the presence of systematic noise when LRR are not informative, lower values result in cleaner calls (0.2).\n- </help>\n- </param>\n- <param name="LRR_dev_query" type="float" value="" min="0." max="1." label="LRR Query Deviation" \n- help="Expected LRR deviation in query, default is: 0.2" />\n- <param name="LRR_dev_control" type="float" value="" min="0." max="1." label="LRR Control Deviation" \n- help="Expected LRR deviation in control, default is: 0.2" />\n- <param name="LRR_smooth_win" type="integer" label="Lrr Smooth Win" value="10" optional="True" \n- help="Window of LRR moving average smoothing" />\n-\n </section>\n </inputs>\n <outputs>\n <data name="output_cn" format="tabular" label="${input_file.name.rsplit(\'.\',1)[0]}.cn"/>\n- <data name="output_dat" format="tabular" label="${input_file.name.rsplit(\'.\',1)[0]}.dat"/>\n <data name="output_summary" format="tabular" label="${input_file.name.rsplit(\'.\',1)[0]}.summary"/>\n- <!-- add plot output -->\n- <!-- script has png per chr, html of images or collect into pdf?\n- <data name="output_plots" format="" />\n- -->\n+ <data name="output_plots" format="html" label="${input_file.name.rsplit(\'.\',1)[0]}.plots">\n+ <filter>plotting[\'generate_plots\'] != \'none\'</filter>\n+ </data>\n </outputs>\n- <tests />\n+ <tests>\n+ <test expect_num_outputs="3">\n+ <param name="input_file" ftype="vcf" value="cnv.vcf" />\n+ <output name="output_summary" file="cnv_summary.tab" compare="re_match" />\n+ </test>\n+ <test expect_num_outputs="2">\n+ <param name="input_file" ftype="vcf" value="cnv.vcf" />\n+ <conditional name="plotting">\n+ <param name="generate_plots" value="none" />\n+ </conditional>\n+ <output name="output_summary" file="cnv_summary.tab" compare="re_match" />\n+ </test>\n+ <test expect_num_outputs="3">\n+ <param name="input_file" ftype="vcf" value="cnv.vcf" />\n+ <param name="query_sample" value="test" />\n+ <param name="control_sample" value="test" />\n+ <output name="output_summary" file="cnv_pairwise_summary.tab" compare="re_match" />\n+ </test>\n+ <test expect_num_outputs="2">\n+ <param name="input_file" ftype="vcf" value="cnv_baf_only.vcf" />\n+ <conditional name="plotting">\n+ <param name="generate_plots" value="none" />\n+ </conditional>\n+ <conditional name="score_usage">\n+ <param name="compute_on" value="baf" />\n+ </conditional>\n+ <output name="output_summary" file="cnv_summary.tab" compare="re_match" />\n+ </test>\n+ </tests>\n <help><![CDATA[\n =====================================\n bcftools @EXECUTABLE@\n' |
| b |
| diff -r bf1f4994f104 -r 13fe14c56f6d macros.xml --- a/macros.xml Thu Feb 21 16:10:57 2019 -0500 +++ b/macros.xml Wed Jun 05 13:19:54 2019 -0400 |
| [ |
| b'@@ -1,13 +1,5 @@\n <macros>\n <token name="@TOOL_VERSION@">1.9</token>\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- </stdio>\n- </xml>\n <xml name="requirements">\n <requirements>\n <requirement type="package" version="@TOOL_VERSION@">bcftools</requirement>\n@@ -18,6 +10,9 @@\n <xml name="samtools_requirement">\n <requirement type="package" version="1.9">samtools</requirement>\n </xml>\n+ <xml name="matplotlib_requirement">\n+ <requirement type="package" version="3.1.0">matplotlib</requirement>\n+ </xml>\n <xml name="version_command">\n <version_command>bcftools 2>&1 | grep \'Version:\'</version_command>\n </xml>\n@@ -111,16 +106,45 @@\n $vcfs_list_file\n </token>\n \n+ <xml name="test_using_reference" token_select_from="history" token_ref="">\n+ <conditional name="reference_source">\n+ <param name="reference_source_selector" value="@SELECT_FROM@" />\n+ <param name="fasta_ref" ftype="fasta" value="@REF@" />\n+ </conditional>\n+ </xml>\n+\n <xml name="macro_fasta_ref">\n- <param name="fasta_ref" argument="--fasta-ref" type="data" format="data" optional="true" label="Reference sequence in FASTA format" />\n+ <conditional name="reference_source">\n+ <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">\n+ <option value="cached">Use a built-in genome</option>\n+ <option value="history">Use a genome from the history</option>\n+ </param>\n+ <when value="cached">\n+ <param name="fasta_ref" type="select" label="Reference genome">\n+ <options from_data_table="fasta_indexes">\n+ <filter type="data_meta" column="1" key="dbkey" ref="input_file" />\n+ <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file" />\n+ </options>\n+ </param>\n+ </when>\n+ <when value="history">\n+ <param name="fasta_ref" type="data" format="fasta" label="Reference genome" />\n+ </when>\n+ </conditional>\n </xml>\n <token name="@PREPARE_FASTA_REF@">\n <![CDATA[\n #set $input_fa_ref = None\n #if \'fasta_ref\' in $section and $section.fasta_ref:\n- #set $input_fa_ref = \'ref.fa\'\n- ln -s \'$section.fasta_ref\' $input_fa_ref &&\n- samtools faidx $input_fa_ref &&\n+ #if \'reference_source_selector\' in $section:\n+ #if str($section.reference_source_selector) == "history":\n+ #set $input_fa_ref = \'ref.fa\'\n+ ln -s \'$section.fasta_ref\' $input_fa_ref &&\n+ samtools faidx $input_fa_ref &&\n+ #else:\n+ #set $input_fa_ref = str($section.fasta_ref.fields.path)\n+ #end if\n+ #end if\n #end if\n ]]>\n </token>\n@@ -132,27 +156,6 @@\n #end if\n </token>\n \n- <xml name="macro_ref_fasta">\n- <conditional name="reference_source">\n- <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">\n- <option value="cached">Locally cached</option>\n- <option value="history">History</option>\n- </param>\n- <when value="cached">\n- <param name="ref_file" type="select" label="Select reference genome">\n- <options from_data_table="fasta_indexes">\n- <!--<filter type="data_meta" key="dbkey" ref="input_bam" column="value"/>-->\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"> <!-- FIX ME!!!! -->\n- <param name="ref_file" type="data" format="fasta" label="Using reference file" />\n- </when>\n- </conditional>\n- </xml>\n-\n-\n <xml name="macro_AF_file">\n <param name="AF_file" argument="--AF-file" type="data" format="tabular'..b'in($components)\n+]]>\n+ </token>\n+ \n+ <token name="@REGIONS@">\n+<![CDATA[\n+#if $section.regions.regions_src == \'regions\':\n+ #set $intervals = $section.regions.regions\n+ @PARSE_INTERVALS@\n+ --regions \'$intervals_spec\'\n+#elif $section.regions.regions_src == \'regions_file\' and $section.regions.regions_file:\n+ #if $regions_path is not None:\n+ --regions-file \'$regions_path\'\n+ #else:\n+ --regions-file \'$section.regions.regions_file\'\n+ #end if\n+#end if\n+]]>\n+ </token>\n+ \n+ <token name="@TARGETS@">\n+<![CDATA[\n+#if $targets_path:\n+ --targets-file "${section.targets.invert_targets_file}${targets_path}"\n+#elif $section.targets.targets_src == \'targets\':\n+ #set $intervals = $section.targets.targets\n+ @PARSE_INTERVALS@\n+ --targets \'${section.targets.invert_targets_file}$intervals_spec\'\n+#elif $section.targets.targets_src == \'targets_file\' and $section.targets.targets_file:\n+ --targets-file "${section.targets.invert_targets_file}${section.targets.targets_file}"\n+#end if\n+]]>\n+ </token>\n+\n <token name="@PREPARE_REGIONS_FILE@">\n <![CDATA[\n #set $regions_path = None\n@@ -300,23 +375,7 @@\n #end if\n ]]>\n </token>\n- <token name="@REGIONS@">\n-#if $section.regions.regions_src == \'regions\' and $section.regions.regions != \'\':\n- --regions \'$section.regions.regions\'\n-#elif $section.regions.regions_src == \'regions_file\' and $section.regions.regions_file:\n- #if $regions_path is not None:\n- --regions-file \'$regions_path\'\n- #else:\n- --regions-file \'$section.regions.regions_file\'\n- #end if\n-#end if\n- </token>\n- <xml name="macro_targets_file">\n- <param name="targets_file" type="data" format="tabular" label="Targets File" help="restrict to targets listed in a file" >\n- <yield/>\n- </param>\n- <param name="invert_targets_file" type="boolean" truevalue="^" falsevalue="" label="Invert Targets" help="inverts the query/filtering applied by the target file selection" />\n- </xml>\n+\n <token name="@PREPARE_TARGETS_FILE@">\n <![CDATA[\n #set $targets_path = None\n@@ -333,6 +392,7 @@\n #end if\n ]]>\n </token>\n+\n <token name="@TARGETS_FILE@">\n <![CDATA[\n #if $targets_path is not None:\n@@ -343,41 +403,6 @@\n ]]>\n </token>\n \n- <xml name="macro_targets">\n- <conditional name="targets">\n- <param name="targets_src" type="select" label="Targets">\n- <option value="__none__">None</option>\n- <option value="targets">targets</option>\n- <option value="targets_file">targets-file</option>\n- </param>\n- <when value="__none__"/>\n- <when value="targets">\n- <param name="targets" type="text" value="" optional="true" label="Restrict to comma-separated list of targets"\n- help="Each target is specifed as: chr or chr:pos or chr:from-to">\n- <validator type="regex" message="">^(\\w+(:\\d+(-\\d+)?)?(,\\w+(:\\d+(-\\d+)?)?)*)?$</validator>\n- </param>\n- <param name="invert_targets_file" type="boolean" truevalue="^" falsevalue="" label="Invert Targets" help="inverts the query/filtering applied by the targets" />\n- </when>\n- <when value="targets_file">\n- <expand macro="macro_targets_file">\n- </expand>\n- </when>\n- </conditional>\n- </xml>\n- <token name="@TARGETS@">\n-<![CDATA[\n-#if $targets_path:\n- --targets-file "${section.targets.invert_targets_file}${targets_path}"\n-#else:\n- #if $section.targets.targets_src == \'targets\' and $section.targets.targets != \'\':\n- --targets \'${section.targets.invert_targets_file}${section.targets.targets}\'\n- #elif $section.targets.targets_src == \'targets_file\' and $section.targets.targets_file:\n- --targets-file "${section.targets.invert_targets_file}${section.targets.targets_file}"\n- #end if\n-#end if\n-]]>\n- </token>\n-\n <xml name="macro_samples">\n <param argument="--samples" type="text" value="" optional="true" label="Samples"\n help="Comma separated list of samples to annotate (or exclude)">\n' |
| b |
| diff -r bf1f4994f104 -r 13fe14c56f6d test-data/cnv.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cnv.vcf Wed Jun 05 13:19:54 2019 -0400 |
| b |
| b'@@ -0,0 +1,192 @@\n+##fileformat=VCFv4.2\n+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n+##FORMAT=<ID=GC,Number=1,Type=Float,Description="GenCall score">\n+##FORMAT=<ID=IA,Number=1,Type=Float,Description="Intensity of the A Allele">\n+##FORMAT=<ID=IB,Number=1,Type=Float,Description="Intensity of the B Allele">\n+##FORMAT=<ID=BAF,Number=1,Type=Float,Description="B Allele Frequency">\n+##FORMAT=<ID=LRR,Number=1,Type=Float,Description="Log R 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|
| b |
| diff -r bf1f4994f104 -r 13fe14c56f6d test-data/cnv_baf_only.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cnv_baf_only.vcf Wed Jun 05 13:19:54 2019 -0400 |
| b |
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|
| b |
| diff -r bf1f4994f104 -r 13fe14c56f6d test-data/cnv_pairwise_summary.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cnv_pairwise_summary.tab Wed Jun 05 13:19:54 2019 -0400 |
| b |
| @@ -0,0 +1,6 @@ +# This file was produced by: bcftools cnv* +# The command line was: bcftools cnv .+ test .+ test * +# +# RG, Regions * +RG 10 135656 931631 2 2 21.7 92 27 92 27 +RG 11 135656 931631 2 2 21.7 92 27 92 27 |
| b |
| diff -r bf1f4994f104 -r 13fe14c56f6d test-data/cnv_summary.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cnv_summary.tab Wed Jun 05 13:19:54 2019 -0400 |
| b |
| @@ -0,0 +1,7 @@ +# RG, Regions * +# This file was produced by: bcftools cnv* +# The command line was: bcftools cnv * +# +# RG, Regions * +RG 10 135656 931631 2 22.6 92 27 +RG 11 135656 931631 2 22.6 92 27 |
| b |
| diff -r bf1f4994f104 -r 13fe14c56f6d test-data/color_chrs.dat --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/color_chrs.dat Wed Jun 05 13:19:54 2019 -0400 |
| [ |
| @@ -0,0 +1,5 @@ +# SG, shared segment [2]Chromosome [3]Start [4]End [5]B:1 [6]B:2 +# SW, number of switches [3]Sample [4]Chromosome [5]nHets [5]nSwitches [6]switch rate +SG 1 1 999 A:1 C:1 +SW A 1 0 0 0.000000 +SW C 1 0 0 0.000000 |
| b |
| diff -r bf1f4994f104 -r 13fe14c56f6d test-data/color_chrs_unrelated.dat --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/color_chrs_unrelated.dat Wed Jun 05 13:19:54 2019 -0400 |
| [ |
| @@ -0,0 +1,5 @@ +# SG, shared segment [2]Chromosome [3]Start [4]End [5]B:1 [6]B:2 +# SW, number of switches [3]Sample [4]Chromosome [5]nHets [5]nSwitches [6]switch rate +SG 1 1 999 A:1 - +SW A 1 0 0 0.000000 +SW (null) 1 0 0 0.000000 |
| b |
| diff -r bf1f4994f104 -r 13fe14c56f6d test-data/fasta_indexes.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fasta_indexes.loc Wed Jun 05 13:19:54 2019 -0400 |
| b |
| @@ -0,0 +1,6 @@ +23andme ? test genome ${__HERE__}/test-cache/23andme.fa +consensus ? test genome ${__HERE__}/test-cache/consensus.fa +csq ? test genome ${__HERE__}/test-cache/csq.fa +gvcf ? test genome ${__HERE__}/test-cache/gvcf.fa +mpileup ? test genome ${__HERE__}/test-cache/mpileup.ref.fa +norm ? test genome ${__HERE__}/test-cache/norm.fa |
| b |
| diff -r bf1f4994f104 -r 13fe14c56f6d test-data/mpileup.ref.fa.fai --- a/test-data/mpileup.ref.fa.fai Thu Feb 21 16:10:57 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,1 +0,0 @@ -17 4200 14 60 61 |
| b |
| diff -r bf1f4994f104 -r 13fe14c56f6d test-data/plugin_frameshifts.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plugin_frameshifts.bed Wed Jun 05 13:19:54 2019 -0400 |
| b |
| @@ -0,0 +1,1 @@ +1 3106150 3106160 |
| b |
| diff -r bf1f4994f104 -r 13fe14c56f6d test-data/stats.a.vcf --- a/test-data/stats.a.vcf Thu Feb 21 16:10:57 2019 -0500 +++ b/test-data/stats.a.vcf Wed Jun 05 13:19:54 2019 -0400 |
| b |
| @@ -3,6 +3,6 @@ ##contig=<ID=1,assembly=b37,length=249250621> ##reference=file:///lustre/scratch105/projects/g1k/ref/main_project/human_g1k_v37.fasta #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A B C -1 1000 . G A . PASS . GT 0/0 0/1 1/1 -1 1001 . G A . PASS . GT 0/0 0/1 1/1 -1 1002 . G A . PASS . GT 0/0 0/1 1/1 +1 1000 . G A . PASS . GT 0|0 0|1 1|1 +1 1001 . G A . PASS . GT 0/0 0|1 1|1 +1 1002 . G A . PASS . GT 0|0 0|1 1|1 |
| b |
| diff -r bf1f4994f104 -r 13fe14c56f6d test-data/test-cache/23andme.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-cache/23andme.fa Wed Jun 05 13:19:54 2019 -0400 |
| b |
| @@ -0,0 +1,14 @@ +>1 +CACGTNACGGCTGAAGTCCAAGGTAC +CGTATCGAGTTCACAGTCGATAGCTC +GATCGATAGCATCGCTAGCNNNACTA +CGATCGATCGCTCTCCGTAACACTCA +AAAACGATCGATCGACTGCTCTTTAG +CGATGACTTTAGGGGAAAAA +>2 +CGCTCAGCCGTACAGCCGAGCAGGAC +ACGCTATTTTAGATCGACTGGCTNNG +CGCTAGCTACGCTTTAGCACGAGAA +>Y +NNNGCATACGTGTCCATCACGATGAT +AGCGATGATCGATC |
| b |
| diff -r bf1f4994f104 -r 13fe14c56f6d test-data/test-cache/23andme.fa.fai --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-cache/23andme.fa.fai Wed Jun 05 13:19:54 2019 -0400 |
| b |
| @@ -0,0 +1,3 @@ +1 150 3 26 27 +2 77 162 26 27 +Y 40 245 26 27 |
| b |
| diff -r bf1f4994f104 -r 13fe14c56f6d test-data/test-cache/consensus.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-cache/consensus.fa Wed Jun 05 13:19:54 2019 -0400 |
| b |
| @@ -0,0 +1,20 @@ +>1:2-501 +TACCATATGTGACATATAAAAAAGAACATAACCTACGTATCAACTAAAGTGGTTGTTTGC +AGAAAAGGAAGACTTAAAAAGAGTCAGTACTAACCTACATAATATATACAATGTTCATTA +AATAATAAAATGAGCTCATCATACTTAGGTCATCATAAATATATCTGAAATTCACAAATA +TTGATCAAATGGTAAAATAGACAAGTAGATTTTAATAGGTTAAACAATTACTGATTCTCT +TGAAAGAATAAATTTAATATGAGACCTATTTCATTATAATGAACTCACAAATTAGAAACT +TCACACTGGGGGCTGGAGAGATGGCTCAGTAGTTAAGAACACTGACTGCTCTTCTGAAGG +TCCTGAGTTCAAATCCCAGCAACCACATGGTGACTTACAACCATCTGTAATGACATCTGA +TGCCCTCTGGTGTGTCTGAAGACAGCTACAGTGTACTTACATAAAATAATAAATAAATCT +TTAAAAACAAAAAAAAAGAA +>2 +GAAGATCTTTTCCTTATTAAGGATCTGAAGCTCTGTAGATTTGTATTCTATTAAACATGG +AGAGATTAGTGATTTTCCATATTCTTTAAGTCATTTTAGAGTAATGTGTTCTTAAGATAA +ATCAGAAAAACAAAAACTTGTGCTTTCCTGTTTGAAAAACAAACAGCTGTGGGGAATGGT +GTCGGGACAGCCTTTTTATAAAATTTTTCTAAATAATGTTGAGGCTTTGATACGTCAAAG +TTATATTTCAAATGGAATCACTTAGACCTCGTTTCTGAGTGTCAATGGCCATATTGGGGA +TTTGCTGCTGCCAATGACAGCACACCCTGGGAATGCCCCAACTACTTACTACAAAGCAGT +GTTACATGGAGAAGATCTTCAAGAGTCTTTTTGCTAGATCTTTCCTTGGCTTTTGATGTG +ACTCCTCTCAATAAAATCCACAGTAATATAGTGAGTGGTCTCCTGCTCCAAACCAGTATT +TCAGACACAGTTAATCCAGAC |
| b |
| diff -r bf1f4994f104 -r 13fe14c56f6d test-data/test-cache/consensus.fa.fai --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-cache/consensus.fa.fai Wed Jun 05 13:19:54 2019 -0400 |
| b |
| @@ -0,0 +1,2 @@ +1:2-501 500 9 60 61 +2 501 521 60 61 |
| b |
| diff -r bf1f4994f104 -r 13fe14c56f6d test-data/test-cache/csq.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-cache/csq.fa Wed Jun 05 13:19:54 2019 -0400 |
| b |
| @@ -0,0 +1,34 @@ +>1 +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT +>2 +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT +>3 +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT + |
| b |
| diff -r bf1f4994f104 -r 13fe14c56f6d test-data/test-cache/csq.fa.fai --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-cache/csq.fa.fai Wed Jun 05 13:19:54 2019 -0400 |
| b |
| @@ -0,0 +1,3 @@ +1 600 3 60 61 +2 600 616 60 61 +3 600 1229 60 61 |
| b |
| diff -r bf1f4994f104 -r 13fe14c56f6d test-data/test-cache/gvcf.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-cache/gvcf.fa Wed Jun 05 13:19:54 2019 -0400 |
| b |
| @@ -0,0 +1,9 @@ +>22 +NNNNNNNNCCTTGGCCAAGTCACTTCCTCCTTCAGGAACATTGCAGTGGGCCTAAGTGCC +TCCTCTCGGGACTGGTATGGGGACGGTCATGCAATCTGGACAACATTCACCTTTAAAAGT +TTATTGATCTTTTGTGACATGCACGTGGGTTCCCAGTAGCAAGAAACTAAAGGGTCGCAG +GCCGGTTTCTGCTAATTTCTTTAATTCCAAGACAGTCTCAAATATTTTCTTATTAACTTC +CTGGAGGGAGGCTTATCATTCTCTCTTTTGGATGATTCTAAGTACCAGCTAAAATACAGC +TATCATTCATTTTCCTTGATTTGGGAGCCTAATTTCTTTAATTTAGTATGCAAGAAAACC +AATTTGGAAATATCAACTGTTTTGGAAACCTTAGACCTAGGTCATCCTTAGTAAGATCTT +CCCATTTATATAAATACTTGCAAGTAGTAGTGCCATAATT |
| b |
| diff -r bf1f4994f104 -r 13fe14c56f6d test-data/test-cache/gvcf.fa.fai --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-cache/gvcf.fa.fai Wed Jun 05 13:19:54 2019 -0400 |
| b |
| @@ -0,0 +1,1 @@ +22 460 4 60 61 |
| b |
| diff -r bf1f4994f104 -r 13fe14c56f6d test-data/test-cache/mpileup.ref.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-cache/mpileup.ref.fa Wed Jun 05 13:19:54 2019 -0400 |
| b |
| @@ -0,0 +1,71 @@ +>17 17:1-4200 +AAGCTTCTCACCCTGTTCCTGCATAGATAATTGCATGACAATTGCCTTGTCCCTGCTGAA +TGTGCTCTGGGGTCTCTGGGGTCTCACCCACGACCAACTCCCTGGGCCTGGCACCAGGGA +GCTTAACAAACATCTGTCCAGCGAATACCTGCATCCCTAGAAGTGAAGCCACCGCCCAAA +GACACGCCCATGTCCAGCTTAACCTGCATCCCTAGAAGTGAAGGCACCGCCCAAAGACAC +GCCCATGTCCAGCTTATTCTGCCCAGTTCCTCTCCAGAAAGGCTGCATGGTTGACACACA +GTGCCTGCGACAAAGCTGAATGCTATCATTTAAAAACTCCTTGCTGGTTTGAGAGGCAGA +AAATGATATCTCATAGTTGCTTTACTTTGCATATTTTAAAATTGTGACTTTCATGGCATA +AATAATACTGGTTTATTACAGAAGCACTAGAAAATGCATGTGGACAAAAGTTGGGATTAG +GAGAGAGAAATGAAGACATATGTCCACACAAAAACCTGTTCATTGCAGCTTTCTACCATC +ACCAAAAATTGCAAACAACCACACGCCCTTCAACTGGGGAACTCATCAACAACAAACTTG +TGGTTTACCCACACAATGGAAGACCACTTAGCAACAAAAAGGACCAAACTCCTGGTACAT +GCAACTGACAGATGAATCTCAAACGCATTCCTCCGTGTGAAAGAAGCCGGACTCACAGGG +CAACACACTATCTGACTGTTTCATGGGAAAGTCTGGAAACGGCAACACCATTGAGACAGA +AAACAGGTGAGTGGTTGCCTGGGGCCAGGGAACTTTCTGGGGTCATATTCTCTGTGTTGA +TTCTGGTGGTGGAAACAAGACTGTCCCAGCCTGGGTGATACAGCGAGACCCCATCTCTAC +CAAAAAATTAAAAATTAGCTGGGCATGGTGGTGCATGCCTGTAGTCCCAGCTATTCACAG +TGCTGAGGTGGGAAGATGCTTGAGCCCAGGAGTTCAAGGCTGCAATGAGCTATGATTGCG +CCACTGCACTTTGGCCTGGACAACAGAGCAAAACCCTGTCTCTAAAAAAAGAAAAGAAAA +GAAAAACTCACTGGATATGAATGATACAGGTTGAGGATCCATTATCTGAAATGCTTGGAC +CAGATGTTTTGAATTTTGGATTTTTTCATATTTTGTAATCTTTGCAGTATATTTACCAGT +TCAGCATCCCTAACTCAAAAATTCAAAAATCTGAAATCCCAAACGCGCCAATAAGCATTC +CCTTTGAGCGTCATGTCGGTGCTTGGAATGTTTGGGGTTTTGGATTTACAGCTTTGGGAC +GCTCAACCTGTACCTCAATAAACCTGATTTTAAAAAAGTTTGGGGGGATTCCCCTAAGCC +CGCCACCCGGAGACAGCGGATTTCCTTAGTTACTTACTATGCTCCTTGGCCATTTCTCTA +GGTATTGGTATATTGTGTCTGCTGTGAACTGTCCTTGGCCTGTTTGGTGACGGGTGAGGA +GCAGGGACAGAAGGGTCCTGCGTGCCCTGCCTTCACAAGCCCCTGGAAGGAAAGTTGTTT +TGGGATCTCTGCACCCTCAGCCTGGACAACTTGTGCCCATCTGGTGACCCCTCACTCAGC +CACCAGACTTCCACGACAGGCTCCAGCCTCGGCACCTTCAGCCATGGACAGTTCCGCCAG +CGTTGCCCTCTGTTCTGCTGTTTTCTCTACCAGAAGTGCCCTTCCCTCCTCACCTGACCA +CTCTGGGGAAATCCCTCAGCACCCTCCCTGAGCATACCCTACTCTGGCACAAGCCCACCC +TGCAAAGCCCCTGAGGCCCGCCCTGTGGCGTCTCTCCCTCCCTTGCTGTCAGGACAGTGG +TCCTGGCCACCGGGGCTCACGGAGCCGCCCTGTGCCGTGTACCTCTGAGCCCTCTGCACA +GTGCCTTCTGCTTGCCTGTGGCTTTGAGAAGAAACCCCTTCTGGTTATACATAAGACAGC +CAGAGAAGGGAGTTGCCCAGGGTGGCACAGCACGTTGCTGCCAGTTACTGCCATTTTCAC +GGGCATGAAATGGAGATAACAACAGGAGCGACCGCACAGGCTGCTGAGCGCGTCACACGC +AGCCATCGCGCAGCTCAGGGATATTACGTGTAACTCGACATGTCAGCGATTGTCACAGGC +ACTGCTACTCCTGGGGTTTTCCATCAAACCCTCAAGAGCTGGGCCTGGGGTCAACTTCCG +GCCTGGGGAAACTGGGGCAAGTATCACCAGAGATGAGCTTTATAAAAATAATGGTGCTAG +CTGGGCATGGTGGCTTGCACCTGTAATCCCAGCACTTTGGGAGGCCGAGCTAGGAGGATC +GTTTGAGTCCAGCAGTTTGAGACCAGCCTGGCCAATACGGCAAAACCCAGTCTCTACAAA +AAATACAAAAAACAACTAGCCAGGCGTGGTGGTGCACACCTGTAGTCCCAGCTACTCAGG +AGGCTGAGGGGGAAGGACTGCTTGAGCCCAGGAGTTTGAGGCTGCTGTGAGCTGTGATCG +CATCACTGCATTCCAGCCCGGTGACAGAGTGAGTCACTGTCTCAAAAAAGAAAGGAAGAA +ATAAAGAAAACAAATAAAAATAATAGTGCAGACAAAAGGCCTTGACCCATCTAGCTTTGG +CCCTCAGCATCAACCGCTAGATACGTCCCTCCCTTTCTTCTGGGGCACAGGTCACACTCT +CTTCCAGGTCTAGGATGCAGCTGAGGGGTGCCCCTCTTACCATCTAATCTGTGCCCTTAT +TTCCTCTGCTTTAGTGAGGAAGAGGCCCCTGGTCCATGAAGGGGCCTTTCAGAGACGGGG +ACCCCTGAGGAGCCCCGAGCAGCAGCCGTCGTGTCTCACCCAGGGTGTCTGAAACAGATG +TGGAGGTCTCGGGTGAGGCGTGGCTCAGATACAGGGAGTGGCCCACAGCTCGGCCTGTCT +TTGAAAGGCCACGTGACCTGGCCCACGGCTGGCAGGTGGGACCCAGCTGCAGGGGTCCAG +CAGCACCCACAGCAGCCACCTGTGGCAGGGAGGAGCTTGTGGTACAGTGGACAGGCCCTG +CCCAGATGGCCCCCCGCCTGCCTGTGGAAGTTGACCAGACCATCTGTCACAGCAGGTAAG +ACTCTGCTTTCTGGGCAACCCAGCAGGTGACCCTGGAATTCCTGTCCATCTGGCAGGTGG +GCATTGAAACTGGTTTAAAAATGTCACACCATAGGCCGGGCACAGTGGCTCACGCCTGTA +ATCCCAGCCCTTTGGGAGGCCAGGGTGGGTGGATCACTTGAGGTCAGGAGTTCAAGACCA +GCCTGGCCAACATGGTGAAACCCCGTCTACTAAAAATACAAAAATTAGCCTGGCGTGGTG +GCGCATGCCTGTAATCCCAGCTACTTGGGAAGCTGAGGGATGAGAACTGCTTGAACCTGG +GAGGCAGACGTTGCAGTGAGCTGAGATCACGCCACTGCACTCCAGCCTGGGCAACAGAGT +AAGACTCTGTCTCAAAAAAAAAAAAATCACACCATTTTGGCTTCAGATTGCATATCCTCC +TGCAAGGATATATACGCGTGAAATTCAAGTCAATGACAAATCAGAAGAAAAAACATATAT +ATACGCAAACCAGTATCCTACTGTGTGTGTCGTTTGTTGTGTTTTCGACAGCTGTCCGTG +TTATAATAATTCCTCTAGTTCAAATTTATTCATTTTTAACTTCATAGTACCACATTCTAC +ACACTGCCCATGTCCCCTCAAGCTTCCCCTGGCTCCTGCAACCACAAATCTACTCTCTGC +CTCTGTGGGTTGACCTATTCTGGACACGTCATAGAAATAGAGTCCTGCAACACGTGGCCG +TCTGTGTCTGGCTTCTCTCGCTTAGCATCTTGTTTCCAAGGTCCTCCCACAGTGTAGCAT +GCACCTGCTACACTCCTTCTTAGGGCTGATATTCCACGCACCTGCTACACTCCTTCTTAT +GGCTGATATTCCACGCACCTGCTACACTCCTTCTTAGGGCTGATATTCCACACACCCGCT +ACACTCCTTCTTAGGGCTGATATTCCACGCACCCGCTACACTCCTTCTTAGGGCTGATAT +TCCACGCACCTGCTACACTCCTTCTTAGGGCTGATATTCCACGCACCTGCTACACTCCTT +CTTAGGGCTGATATTCCACGCACCTGCTACACTCCTTCTTAGGGCTGATATTCCACGCAC |
| b |
| diff -r bf1f4994f104 -r 13fe14c56f6d test-data/test-cache/mpileup.ref.fa.fai --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-cache/mpileup.ref.fa.fai Wed Jun 05 13:19:54 2019 -0400 |
| b |
| @@ -0,0 +1,1 @@ +17 4200 14 60 61 |
| b |
| diff -r bf1f4994f104 -r 13fe14c56f6d test-data/test-cache/norm.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-cache/norm.fa Wed Jun 05 13:19:54 2019 -0400 |
| b |
| @@ -0,0 +1,26 @@ +>20 20:1339000-1339300 +AGGATGGGGCTCATTAATAGAGCTCCACTTGTCTCCAGAATCACTGGTGAGGAAGGGGAG +TGTTGCCCCCACATTCGTGCACAGCAGGGATGGTTCACCGAACTCCACACCAGTCTCTGC +AGAGCCTGTTGGGGAGAGGAGGGCTGTGGTTTCTTTGATGGTGTTCACCTGGAGTAGAGC +AAGTATTGTCAAAAGGGTCATCCTCGGAGGTTGCAGTGAGCCGAGATCGCACCATTGCAC +TGCAGCCTGGGAGACAGAGCAAGACTCCATCTCAAAAAAAAAAAAAAAAAAAAAGGCCAT +C +>1 1:10143-10443 +CTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCTAACCCTAACCCTAACCCTAACC +CTAACCCTAACCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAAACCCTAAACCCTA +ACCCTAACCCTAACCCTAACCCTAACCCCAACCCCAACCCCAACCCCAACCCCAACCCCA +ACCCTAACCCCTAACCCTAACCCTAACCCTACCCTAACCCTAACCCTAACCCTAACCCTA +ACCCTAACCCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCC +>2 1:1382388-1382602 +GGGCGTCTCATAGCTGGAGCAATGGCGAGCGCCTGGACAAGGGAGGGGAAGGGGTTCTTA +TTACTGACGCGGGTAGCCCCTACTGCTGTGTGGTTCCCCTATTTTTTTTTTTTTCTTTTT +GAGACGGAGTCTCGCTCTGTCACCCAGGCTGGAGTGCAGTGGCACAATCTCGGCTCACTG +CAAGCTCCACCTCCTGGGTTCACGCCATTCTCCTG +>3 madeup +ACTGGACACGTGGACACACACACACACACACACACACACACAGTCAAACCACCTACCAGA +>4 20:8917026-8917085 +TCCCCTCTTGACCTCTCTCTATTTTTTTTTTTTTTTCTGAGATGGATTTTTGCTCTTGTT +>5 20:18724313-18724343 +GTCTCAAAAAAAAAAAAAAAAAAAAGAAAAG +>21 +TTTATTATTATTATTATTAAATTGAATTTATTTAGTGTACATACATTCATGTGTATTGTG |
| b |
| diff -r bf1f4994f104 -r 13fe14c56f6d test-data/test-cache/norm.fa.fai --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-cache/norm.fa.fai Wed Jun 05 13:19:54 2019 -0400 |
| b |
| @@ -0,0 +1,7 @@ +20 301 23 60 61 +1 300 347 60 61 +2 215 673 60 61 +3 60 902 60 61 +4 60 985 60 61 +5 31 1070 31 32 +21 60 1106 60 61 |
| b |
| diff -r bf1f4994f104 -r 13fe14c56f6d tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Wed Jun 05 13:19:54 2019 -0400 |
| b |
| @@ -0,0 +1,7 @@ +<tables> + <!-- Locations of FASTA index ffiles for testing --> + <table name="fasta_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="${__HERE__}/test-data/fasta_indexes.loc" /> + </table> +</tables> |