| Previous changeset 7:19905c025d2a (2019-02-21) Next changeset 9:93bdd3bf5743 (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_norm.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 19905c025d2a -r 76655fe2c70e bcftools_norm.xml --- a/bcftools_norm.xml Thu Feb 21 15:57:55 2019 -0500 +++ b/bcftools_norm.xml Wed Jun 05 13:02:34 2019 -0400 |
| [ |
| b'@@ -1,5 +1,5 @@\n <?xml version=\'1.0\' encoding=\'utf-8\'?>\n-<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@">\n+<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy1">\n <description>Left-align and normalize indels; check if REF alleles match the reference; split multiallelic sites into multiple rows; recover multiallelics from multiple rows</description>\n <macros>\n <token name="@EXECUTABLE@">norm</token>\n@@ -12,7 +12,7 @@\n <command detect_errors="aggressive"><![CDATA[\n @PREPARE_ENV@\n @PREPARE_INPUT_FILE@\n-#set $section = $sec_ref\n+#set $section = $reference_source\n @PREPARE_FASTA_REF@\n #set $section = $sec_restrict\n @PREPARE_TARGETS_FILE@\n@@ -20,28 +20,21 @@\n \n bcftools @EXECUTABLE@\n \n-#set $section = $sec_ref\n+#set $section = $reference_source\n @FASTA_REF@\n-${section.do_not_normalize}\n-#if $section.check_ref:\n- --check-ref "${section.check_ref}"\n+--check-ref $check_ref\n+$normalize_indels\n+#if $rm_dup:\n+ --rm-dup "$rm_dup"\n #end if\n-\n-## Default section\n-#set $section = $sec_default\n-#if $section.rm_dup:\n- --rm-dup "${section.rm_dup}"\n+#if $multiallelics.mode:\n+ --multiallelics \'${multiallelics.mode}${multiallelics.multiallelic_types}\'\n #end if\n-#if $section.multiallelics:\n- #set $mtype = \'\'\n- #if $section.multiallelic_types:\n- #set $mtype = $section.multiallelic_types\n- #end if\n- --multiallelics "${section.multiallelics}${mtype}" \n+#if $multiallelics.mode == \'+\':\n+ ${multiallelics.strict_filter}\n #end if\n-${section.strict_filter}\n-#if $section.site_win:\n- --site-win "${section.site_win}"\n+#if $sec_default.site_win:\n+ --site-win ${sec_default.site_win}\n #end if\n \n #set $section = $sec_restrict\n@@ -58,49 +51,67 @@\n </command>\n <inputs>\n <expand macro="macro_input" />\n- <section name="sec_restrict" expanded="false" title="Restrict to">\n- <expand macro="macro_regions" />\n- <expand macro="macro_targets" />\n- </section>\n- <section name="sec_ref" expanded="false" title="Reference Options">\n- <expand macro="macro_fasta_ref" />\n- <param name="check_ref" type="select" label="Check REF" optional="true" \n- help="What to do when incorrect or missing REF allele is encountered">\n- <option value="e">check REF alleles and exit (e)</option>\n- <option value="w">warn (w)</option>\n- <option value="x">exclude (x)</option>\n- <option value="s">set bad sites (s)</option>\n- <option value="wx">warn and exclude (wx)</option>\n- <option value="ws">warn and set bad sites (ws)</option>\n- </param>\n- <param name="do_not_normalize" type="boolean" truevalue="--do-not-normalize" falsevalue="" label="Skip Normalization, just set REF allele" \n- help="Do not normalize indels, just fix or set the REF allele from the reference (-N, --do-not-normalize with -m or -c s)" />\n- </section>\n-\n- <section name="sec_default" expanded="false" title="Default Options">\n- <param name="rm_dup" type="select" label="Rm Dup" optional="true" \n- help="Remove duplicate snps|indels|both|any">\n- <option value="snps">snps</option>\n- <option value="indels">indels</option>\n- <option value="both">both</option>\n- <option value="any">any</option>\n- </param>\n- <param name="multiallelics" type="select" label="~multiallelics" optional="true">\n+ <expand macro="macro_fasta_ref" />\n+ <param name="check_ref" type="select" display="radio"\n+ label="When any REF allele does not match the reference genome base"\n+ help="Warnings about REF mismatches will be emitted to the standard\n+ error (stderr) stream, and it is recommended to check there for\n+ problems if you choose not to exit with an error immediately upo'..b'ptional="True" \n help="(-w, --site-win) Buffer for sorting lines which changed position during realignment" />\n </section>\n-\n <expand macro="macro_select_output_type" />\n </inputs>\n <outputs>\n@@ -109,7 +120,21 @@\n <tests>\n <test>\n <param name="input_file" ftype="vcf" value="norm.vcf" />\n- <param name="fasta_ref" ftype="fasta" value="norm.fa" />\n+ <expand macro="test_using_reference" ref="norm.fa" />\n+ <param name="normalize_indels" value="true" />\n+ <param name="output_type" value="v" />\n+ <output name="output_file">\n+ <assert_contents>\n+ <has_text text="T,TAACCCTA" />\n+ <not_has_text text="TAA,TAACCCTAAA" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+\n+ <test>\n+ <param name="input_file" ftype="vcf" dbkey="?" value="norm.vcf" />\n+ <expand macro="test_using_reference" select_from="cached" ref="norm" />\n+ <param name="normalize_indels" value="true" />\n <param name="output_type" value="v" />\n <output name="output_file">\n <assert_contents>\n@@ -121,7 +146,10 @@\n \n <test>\n <param name="input_file" ftype="vcf" value="norm.split.vcf" />\n- <param name="multiallelics" value="-" />\n+ <expand macro="test_using_reference" ref="norm.fa" />\n+ <conditional name="multiallelics">\n+ <param name="mode" value="-" />\n+ </conditional>\n <param name="output_type" value="v" />\n <output name="output_file">\n <assert_contents>\n@@ -134,8 +162,11 @@\n \n <test>\n <param name="input_file" ftype="vcf" value="norm.split.vcf" />\n- <param name="fasta_ref" ftype="fasta" value="norm.fa" />\n- <param name="multiallelics" value="-" />\n+ <expand macro="test_using_reference" ref="norm.fa" />\n+ <param name="normalize_indels" value="true" />\n+ <conditional name="multiallelics">\n+ <param name="mode" value="-" />\n+ </conditional>\n <param name="output_type" value="v" />\n <output name="output_file">\n <assert_contents>\n@@ -148,7 +179,10 @@\n \n <test>\n <param name="input_file" ftype="vcf" value="norm.merge.vcf" />\n- <param name="multiallelics" value="+" />\n+ <expand macro="test_using_reference" ref="norm.fa" />\n+ <conditional name="multiallelics">\n+ <param name="mode" value="+" />\n+ </conditional>\n <param name="output_type" value="v" />\n <output name="output_file">\n <assert_contents>\n@@ -159,8 +193,11 @@\n </test>\n <test>\n <param name="input_file" ftype="vcf" value="norm.merge.vcf" />\n- <param name="multiallelics" value="+" />\n- <param name="strict_filter" value="true" />\n+ <expand macro="test_using_reference" ref="norm.fa" />\n+ <conditional name="multiallelics">\n+ <param name="mode" value="+" />\n+ <param name="strict_filter" value="true" />\n+ </conditional>\n <param name="output_type" value="v" />\n <output name="output_file">\n <assert_contents>\n@@ -172,9 +209,8 @@\n \n <test>\n <param name="input_file" ftype="vcf" value="norm.setref.vcf" />\n- <param name="fasta_ref" ftype="fasta" value="norm.fa" />\n- <param name="do_not_normalize" value="true" />\n- <param name="check_ref" value="s" />\n+ <expand macro="test_using_reference" ref="norm.fa" />\n+ <param name="check_ref" value="ws" />\n <param name="output_type" value="v" />\n <output name="output_file">\n <assert_contents>\n' |
| b |
| diff -r 19905c025d2a -r 76655fe2c70e macros.xml --- a/macros.xml Thu Feb 21 15:57:55 2019 -0500 +++ b/macros.xml Wed Jun 05 13:02:34 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 19905c025d2a -r 76655fe2c70e test-data/cnv.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cnv.vcf Wed Jun 05 13:02:34 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 19905c025d2a -r 76655fe2c70e 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 13:02:34 2019 -0400 |
| b |
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|
| b |
| diff -r 19905c025d2a -r 76655fe2c70e 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 13:02:34 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 19905c025d2a -r 76655fe2c70e test-data/cnv_summary.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cnv_summary.tab Wed Jun 05 13:02:34 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 19905c025d2a -r 76655fe2c70e test-data/color_chrs.dat --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/color_chrs.dat Wed Jun 05 13:02:34 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 19905c025d2a -r 76655fe2c70e 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 13:02:34 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 19905c025d2a -r 76655fe2c70e test-data/fasta_indexes.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fasta_indexes.loc Wed Jun 05 13:02:34 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 19905c025d2a -r 76655fe2c70e test-data/mpileup.ref.fa.fai --- a/test-data/mpileup.ref.fa.fai Thu Feb 21 15:57:55 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 19905c025d2a -r 76655fe2c70e test-data/plugin_frameshifts.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plugin_frameshifts.bed Wed Jun 05 13:02:34 2019 -0400 |
| b |
| @@ -0,0 +1,1 @@ +1 3106150 3106160 |
| b |
| diff -r 19905c025d2a -r 76655fe2c70e test-data/stats.a.vcf --- a/test-data/stats.a.vcf Thu Feb 21 15:57:55 2019 -0500 +++ b/test-data/stats.a.vcf Wed Jun 05 13:02:34 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 19905c025d2a -r 76655fe2c70e 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 13:02:34 2019 -0400 |
| b |
| @@ -0,0 +1,14 @@ +>1 +CACGTNACGGCTGAAGTCCAAGGTAC +CGTATCGAGTTCACAGTCGATAGCTC +GATCGATAGCATCGCTAGCNNNACTA +CGATCGATCGCTCTCCGTAACACTCA +AAAACGATCGATCGACTGCTCTTTAG +CGATGACTTTAGGGGAAAAA +>2 +CGCTCAGCCGTACAGCCGAGCAGGAC +ACGCTATTTTAGATCGACTGGCTNNG +CGCTAGCTACGCTTTAGCACGAGAA +>Y +NNNGCATACGTGTCCATCACGATGAT +AGCGATGATCGATC |
| b |
| diff -r 19905c025d2a -r 76655fe2c70e 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 13:02:34 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 19905c025d2a -r 76655fe2c70e 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 13:02:34 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 19905c025d2a -r 76655fe2c70e 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 13:02:34 2019 -0400 |
| b |
| @@ -0,0 +1,2 @@ +1:2-501 500 9 60 61 +2 501 521 60 61 |
| b |
| diff -r 19905c025d2a -r 76655fe2c70e 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 13:02:34 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 19905c025d2a -r 76655fe2c70e 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 13:02:34 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 19905c025d2a -r 76655fe2c70e 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 13:02:34 2019 -0400 |
| b |
| @@ -0,0 +1,9 @@ +>22 +NNNNNNNNCCTTGGCCAAGTCACTTCCTCCTTCAGGAACATTGCAGTGGGCCTAAGTGCC +TCCTCTCGGGACTGGTATGGGGACGGTCATGCAATCTGGACAACATTCACCTTTAAAAGT +TTATTGATCTTTTGTGACATGCACGTGGGTTCCCAGTAGCAAGAAACTAAAGGGTCGCAG +GCCGGTTTCTGCTAATTTCTTTAATTCCAAGACAGTCTCAAATATTTTCTTATTAACTTC +CTGGAGGGAGGCTTATCATTCTCTCTTTTGGATGATTCTAAGTACCAGCTAAAATACAGC +TATCATTCATTTTCCTTGATTTGGGAGCCTAATTTCTTTAATTTAGTATGCAAGAAAACC +AATTTGGAAATATCAACTGTTTTGGAAACCTTAGACCTAGGTCATCCTTAGTAAGATCTT +CCCATTTATATAAATACTTGCAAGTAGTAGTGCCATAATT |
| b |
| diff -r 19905c025d2a -r 76655fe2c70e 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 13:02:34 2019 -0400 |
| b |
| @@ -0,0 +1,1 @@ +22 460 4 60 61 |
| b |
| diff -r 19905c025d2a -r 76655fe2c70e 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 13:02:34 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 19905c025d2a -r 76655fe2c70e 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 13:02:34 2019 -0400 |
| b |
| @@ -0,0 +1,1 @@ +17 4200 14 60 61 |
| b |
| diff -r 19905c025d2a -r 76655fe2c70e 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 13:02:34 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 19905c025d2a -r 76655fe2c70e 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 13:02:34 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 19905c025d2a -r 76655fe2c70e 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 13:02:34 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> |