| Previous changeset 7:a1213a0b7b66 (2019-02-21) Next changeset 9:df7585d6adb2 (2019-07-29) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 |
|
modified:
bcftools_gtcheck.xml macros.xml test-data/stats.a.vcf |
|
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 |
|
removed:
test-data/mpileup.ref.fa.fai |
| b |
| diff -r a1213a0b7b66 -r 833ad3665419 bcftools_gtcheck.xml --- a/bcftools_gtcheck.xml Thu Feb 21 16:00:59 2019 -0500 +++ b/bcftools_gtcheck.xml Wed Jun 05 13:05:47 2019 -0400 |
| b |
| @@ -1,5 +1,5 @@ <?xml version='1.0' encoding='utf-8'?> -<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@"> +<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy1"> <description>Check sample identity</description> <macros> <token name="@EXECUTABLE@">gtcheck</token> @@ -77,8 +77,8 @@ <inputs> <expand macro="macro_input" /> <section name="sec_restrict" expanded="false" title="Restrict to"> - <expand macro="macro_regions" /> - <expand macro="macro_targets" /> + <expand macro="macro_restrict" /> + <expand macro="macro_restrict" type="target" label_type="Target" /> </section> <section name="sec_default" expanded="true" title="Default Options"> <param name="genotypes" type="data" format="vcf,bcf" label="Genotypes to compare against" optional="True" |
| b |
| diff -r a1213a0b7b66 -r 833ad3665419 macros.xml --- a/macros.xml Thu Feb 21 16:00:59 2019 -0500 +++ b/macros.xml Wed Jun 05 13:05:47 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 a1213a0b7b66 -r 833ad3665419 test-data/cnv.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cnv.vcf Wed Jun 05 13:05:47 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 Ratio">\n+#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\ttest\n+10\t135656\trs10904561\tT\tG\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t0/1:0.0415:0.5176:0.543:0.661:0.9477\n+10\t135708\trs7917054\tG\tA\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t1/0:0.2441:0.501:0.742:0.659:0.9604\n+10\t178434\trs7089889\tT\tG\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t0/1:0.1440:0.4833:0.836:0.827:0.8884\n+10\t188805\trs12146291\tA\tG\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t0/1:0.2144:0.4715:0.776:0.743:0.9610\n+10\t203471\trs10903451\tA\tG\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t0/0:0.4201:0.0000:0.619:0.022:0.9337\n+10\t252693\trs2379078\tT\tC\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t0/0:-0.2673:0.0068:0.806:0.081:0.9018\n+10\t273344\trs2448378\tA\tC\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t0/0:-0.7407:0.0000:0.497:0.012:0.9411\n+10\t279248\trs2496278\tC\tA\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t1/0:-0.4228:0.6268:0.285:0.958:0.6772\n+10\t291134\trs10508201\tT\tC\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t0/1:0.1085:0.4723:0.317:0.444:0.9106\n+10\t293358\texm2249181\tA\tC\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t0/0:-0.0097:0.0044:1.507:0.061:0.3992\n+10\t313504\trs4880568\tC\tT\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t1/1:-0.5836:0.9803:0.017:0.321:0.9547\n+10\t317501\trs2018975\tC\tT\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t0/0:-0.3392:0:1.069:0.039:0.7852\n+10\t323283\trs3740304\tA\tG\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t0/1:0.1836:0.5588:1.053:1.110:0.8640\n+10\t326894\trs3125027\tT\tC\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t0/0:-0.0517:0.0005:1.300:0.026:0.8916\n+10\t327162\texm805022\tC\tT\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t0/0:-0.1197:0:0.995:0.015:0.5328\n+10\t329493\trs3815985\tC\tA\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t1/0:0.0480:0.5187:0.824:0.794:0.9109\n+10\t338553\trs3125031\tC\tT\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t1/0:-0.3387:0.4696:0.777:1.004:0.7901\n+10\t354301\trs35198327\tC\tT\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t1/0:-0.1338:0.4929:0.903:0.996:0.8546\n+10\t375475\tvariant.11341\tC\tT\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t0/0:-0.0747:0.000199999999999978:1.132:0.012:0.4773\n+10\t377161\trs7070654\tC\tT\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t0/0:0.1388:0:0.582:0.020:0.9458\n+10\t387060\trs7904155\tG\tA\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t1/1:0.0615:0.9945:0.080:1.883:0.8310\n+10\t390962\texm805090\tG\tA\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t0/0:-0.0087:9.9999999999989e-05:1.226:0.063:0.6950\n+10\t390983\texm805091\tG\tA\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t0/0:-0.3606:0:0.398:0.035:0.4585\n+10\t394615\texm805105\tG\tA\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t0/0:0.0170:0:1.345:0.020:0.4108\n+10\t402390\texm805131\tG\tC\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t0/0:0.0341:0.0000:1.127:0.023:0.8735\n+10\t403792\texm805136\tG\tC\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t0/0:-0.1428:0.0000:0.908:0.019:0.8483\n+10\t410501\texm805166\tC\tT\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t0/0:0.0189:0:1.162:0.050:0.4628\n+10\t413010\trs9787422\tC\tT\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t1/0:0.0871:0.5334:0.908:0.961:0.8338\n+10\t423555\trs12245012\tG\tA\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t0/0:0.1264:0.00149999999999995:1.658:0.040:0.8015\n+10\t423671\trs10904067\tC\tT\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t1/0:-0.3622:0.5566:0.326:0.370:0.9306\n+10\t431161\texm2271240\tC\tT\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t1/0:-0.0175:0.4838:0.935:1.004:0.8308\n+10\t435971\texm2249233\tT\tC\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t0/0:-0.2716:0.0000:1.217:0.042:0.3992\n+10\t435990\texm805214\tG\tA\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t0/0:-0.1427:0:1.107:0.031:0.4295\n+10\t453567\trs4881254\tC\tT\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t1/0:0.1831:0.5079:1.032:1.425:0.8149\n+10\t462885\trs10904173\tG\tA\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t1/0:-0.0930:0.4819:0.568:0.489:0.9332\n+10\t465046\texm805254\tG\tA\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t0/0:-0.1108:0:1.041:0.038:0.8704\n+10\t468599\trs12415961\tT\tC\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t0/1:0.1647:0.5021:1.192:0.825:0.8051\n+10\t486935\texm805280\tG\tC\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t0/0:-0.1369:0.0186:0.643:0.060:0.4804\n+10\t487973\trs4881313\tT\tC\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t0/1:0.0644:0.5628:0.747:0.992:0.8463\n+10\t521431\texm2271'..b'16650\tC\tT\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t0/0:0.0897:0:1.053:0.009:0.9557\n+11\t615782\trs17221309\tG\tA\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t0/0:0.2800:0.00319999999999998:1.764:0.035:0.7820\n+11\t635857\trs7069611\tT\tC\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t0/0:-0.0450:0.0013:0.593:0.017:0.9595\n+11\t669358\trs7898821\tG\tA\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t0/0:-0.1257:0:1.694:0.067:0.7270\n+11\t673037\trs816563\tC\tT\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t1/1:0.1368:0.9065:0.167:0.495:0.4895\n+11\t680428\trs2124585\tG\tA\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t1/0:-0.0590:0.5212:0.660:1.123:0.7133\n+11\t712617\trs17136372\tA\tC\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t1/1:-0.0174:0.9992:0.028:0.975:0.9556\n+11\t738630\trs1750792\tC\tT\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t0/0:0.0269:0:1.575:0.025:0.8126\n+11\t749238\trs553326\tG\tT\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t0/0:0.1758:0.00229999999999997:0.955:0.019:0.9300\n+11\t754033\trs2265090\tC\tA\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t0/0:-0.1347:0:1.181:0.025:0.9176\n+11\t757222\trs10904546\tA\tG\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t0/0:0.3035:0.0000:1.975:0.056:0.8047\n+11\t766105\trs7906313\tT\tC\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t0/0:-0.1672:0.0116:0.960:0.062:0.9381\n+11\t776027\trs11253377\tC\tT\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t1/1:-0.1474:0.9964:0.046:1.017:0.9087\n+11\t787896\trs1769242\tT\tC\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t0/0:0.2049:0.0000:0.965:0.029:0.9107\n+11\t800213\trs2254501\tG\tA\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t1/1:0.2422:0.9918:0.027:0.612:0.9374\n+11\t802445\trs1769215\tC\tT\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t0/0:0.0188:0.00370000000000004:0.859:0.024:0.9303\n+11\t803721\trs2790381\tC\tT\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t1/1:-0.0421:0.9798:0.029:0.485:0.9700\n+11\t811876\trs12414585\tG\tA\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t1/0:0.0717:0.516:0.374:0.276:0.9351\n+11\t813426\trs11253424\tC\tT\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t0/0:-0.5256:0:0.333:0.000:0.8993\n+11\t815149\trs7084027\tA\tG\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t1/1:0.3183:0.9944:0.037:1.547:0.8419\n+11\t820868\trs10752019\tC\tT\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t0/0:0.0749:0.0118:1.349:0.070:0.8882\n+11\t833528\texm2271241\tT\tG\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t0/1:-0.0329:0.4896:0.569:0.681:0.9348\n+11\t834736\trs4881530\tG\tA\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t0/0:-0.0453:0.00249999999999995:1.578:0.040:0.8076\n+11\t836115\trs11253444\tA\tG\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t0/1:-0.1380:0.5199:0.596:0.670:0.9248\n+11\t838179\trs1536337\tT\tC\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t0/0:-0.0534:0.0000:1.318:0.095:0.7967\n+11\t858022\trs9124\tC\tT\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t0/0:-0.5565:0:0.715:0.012:0.9397\n+11\t858924\texm805329\tG\tA\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t0/0:-0.0866:0:0.873:0.021:0.9056\n+11\t859047\texm805338\tC\tA\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t0/0:0.1868:0:0.917:0.007:0.5296\n+11\t860687\texm805350\tC\tT\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t0/0:-0.1509:0:1.172:0.059:0.3777\n+11\t860726\texm805354\tT\tC\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t0/0:-0.0224:0.0000:2.255:0.138:0.3747\n+11\t860970\texm805360\tA\tG\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t0/0:-0.1069:0.0000:1.859:0.070:0.7352\n+11\t871110\texm805378\tG\tC\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t0/0:0.0701:0.0000:1.373:0.002:0.4607\n+11\t871746\texm805386\tG\tA\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t0/0:-0.1743:0.00239999999999996:0.597:0.017:0.5312\n+11\t875350\texm805392\tG\tA\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t0/0:0.1814:0:0.924:0.018:0.5191\n+11\t888899\texm805400\tC\tT\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t0/0:0.0585:0.00470000000000004:1.182:0.028:0.5116\n+11\t888916\texm805401\tT\tC\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t0/0:0.1408:0.0000:1.480:0.041:0.4128\n+11\t894838\trs12249828\tC\tT\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t1/0:0.2119:0.4839:1.145:1.256:0.8432\n+11\t903950\trs11253471\tA\tG\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t0/1:-0.0047:0.4747:0.562:0.549:0.9470\n+11\t909757\texm805413\tG\tA\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t0/0:0.0614:0:1.538:0.027:0.4097\n+11\t909766\texm805415\tG\tA\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t0/0:0.0578:0:1.502:0.023:0.4128\n+11\t910074\texm805420\tC\tT\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t0/0:-0.0503:0.0071:1.001:0.057:0.5002\n+11\t910081\texm805421\tC\tT\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t0/0:-0.1352:0.002:1.125:0.033:0.4254\n+11\t927331\trs11253489\tG\tA\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t1/0:0.0370:0.5325:0.976:1.435:0.7729\n+11\t931618\texm805430\tG\tA\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t0/0:0.0474:0:1.222:0.009:0.4871\n+11\t931631\texm805431\tC\tT\t.\t.\t.\tGT:LRR:BAF:IA:IB:GC\t0/0:-0.0819:0.00390000000000001:0.827:0.023:0.5296\n' |
| b |
| diff -r a1213a0b7b66 -r 833ad3665419 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 13:05:47 2019 -0400 |
| b |
| b'@@ -0,0 +1,188 @@\n+##fileformat=VCFv4.2\n+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n+##FORMAT=<ID=BAF,Number=1,Type=Float,Description="B Allele Frequency">\n+#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\ttest\n+10\t135656\trs10904561\tT\tG\t.\t.\t.\tGT:BAF\t0/1:0.5176\n+10\t135708\trs7917054\tG\tA\t.\t.\t.\tGT:BAF\t1/0:0.501\n+10\t178434\trs7089889\tT\tG\t.\t.\t.\tGT:BAF\t0/1:0.4833\n+10\t188805\trs12146291\tA\tG\t.\t.\t.\tGT:BAF\t0/1:0.4715\n+10\t203471\trs10903451\tA\tG\t.\t.\t.\tGT:BAF\t0/0:0.0000\n+10\t252693\trs2379078\tT\tC\t.\t.\t.\tGT:BAF\t0/0:0.0068\n+10\t273344\trs2448378\tA\tC\t.\t.\t.\tGT:BAF\t0/0:0.0000\n+10\t279248\trs2496278\tC\tA\t.\t.\t.\tGT:BAF\t1/0:0.6268\n+10\t291134\trs10508201\tT\tC\t.\t.\t.\tGT:BAF\t0/1:0.4723\n+10\t293358\texm2249181\tA\tC\t.\t.\t.\tGT:BAF\t0/0:0.0044\n+10\t313504\trs4880568\tC\tT\t.\t.\t.\tGT:BAF\t1/1:0.9803\n+10\t317501\trs2018975\tC\tT\t.\t.\t.\tGT:BAF\t0/0:0\n+10\t323283\trs3740304\tA\tG\t.\t.\t.\tGT:BAF\t0/1:0.5588\n+10\t326894\trs3125027\tT\tC\t.\t.\t.\tGT:BAF\t0/0:0.0005\n+10\t327162\texm805022\tC\tT\t.\t.\t.\tGT:BAF\t0/0:0\n+10\t329493\trs3815985\tC\tA\t.\t.\t.\tGT:BAF\t1/0:0.5187\n+10\t338553\trs3125031\tC\tT\t.\t.\t.\tGT:BAF\t1/0:0.4696\n+10\t354301\trs35198327\tC\tT\t.\t.\t.\tGT:BAF\t1/0:0.4929\n+10\t375475\tvariant.11341\tC\tT\t.\t.\t.\tGT:BAF\t0/0:0.000199999999999978\n+10\t377161\trs7070654\tC\tT\t.\t.\t.\tGT:BAF\t0/0:0\n+10\t387060\trs7904155\tG\tA\t.\t.\t.\tGT:BAF\t1/1:0.9945\n+10\t390962\texm805090\tG\tA\t.\t.\t.\tGT:BAF\t0/0:9.9999999999989e-05\n+10\t390983\texm805091\tG\tA\t.\t.\t.\tGT:BAF\t0/0:0\n+10\t394615\texm805105\tG\tA\t.\t.\t.\tGT:BAF\t0/0:0\n+10\t402390\texm805131\tG\tC\t.\t.\t.\tGT:BAF\t0/0:0.0000\n+10\t403792\texm805136\tG\tC\t.\t.\t.\tGT:BAF\t0/0:0.0000\n+10\t410501\texm805166\tC\tT\t.\t.\t.\tGT:BAF\t0/0:0\n+10\t413010\trs9787422\tC\tT\t.\t.\t.\tGT:BAF\t1/0:0.5334\n+10\t423555\trs12245012\tG\tA\t.\t.\t.\tGT:BAF\t0/0:0.00149999999999995\n+10\t423671\trs10904067\tC\tT\t.\t.\t.\tGT:BAF\t1/0:0.5566\n+10\t431161\texm2271240\tC\tT\t.\t.\t.\tGT:BAF\t1/0:0.4838\n+10\t435971\texm2249233\tT\tC\t.\t.\t.\tGT:BAF\t0/0:0.0000\n+10\t435990\texm805214\tG\tA\t.\t.\t.\tGT:BAF\t0/0:0\n+10\t453567\trs4881254\tC\tT\t.\t.\t.\tGT:BAF\t1/0:0.5079\n+10\t462885\trs10904173\tG\tA\t.\t.\t.\tGT:BAF\t1/0:0.4819\n+10\t465046\texm805254\tG\tA\t.\t.\t.\tGT:BAF\t0/0:0\n+10\t468599\trs12415961\tT\tC\t.\t.\t.\tGT:BAF\t0/1:0.5021\n+10\t486935\texm805280\tG\tC\t.\t.\t.\tGT:BAF\t0/0:0.0186\n+10\t487973\trs4881313\tT\tC\t.\t.\t.\tGT:BAF\t0/1:0.5628\n+10\t521431\texm2271370\tC\tT\t.\t.\t.\tGT:BAF\t1/1:0.9952\n+10\t521723\trs4881336\tC\tT\t.\t.\t.\tGT:BAF\t1/1:1\n+10\t547567\trs816599\tA\tG\t.\t.\t.\tGT:BAF\t1/1:1.0000\n+10\t554186\trs12251997\tC\tT\t.\t.\t.\tGT:BAF\t0/0:0.00309999999999999\n+10\t556129\trs10466270\tA\tG\t.\t.\t.\tGT:BAF\t0/1:0.5142\n+10\t566379\trs11252926\tC\tT\t.\t.\t.\tGT:BAF\t1/0:0.5024\n+10\t588406\trs10904450\tA\tG\t.\t.\t.\tGT:BAF\t0/0:0.0006\n+10\t592283\trs816646\tG\tA\t.\t.\t.\tGT:BAF\t1/0:0.5006\n+10\t601089\trs816650\tC\tT\t.\t.\t.\tGT:BAF\t0/0:0\n+10\t615782\trs17221309\tG\tA\t.\t.\t.\tGT:BAF\t0/0:0.00319999999999998\n+10\t635857\trs7069611\tT\tC\t.\t.\t.\tGT:BAF\t0/0:0.0013\n+10\t669358\trs7898821\tG\tA\t.\t.\t.\tGT:BAF\t0/0:0\n+10\t673037\trs816563\tC\tT\t.\t.\t.\tGT:BAF\t1/1:0.9065\n+10\t680428\trs2124585\tG\tA\t.\t.\t.\tGT:BAF\t1/0:0.5212\n+10\t712617\trs17136372\tA\tC\t.\t.\t.\tGT:BAF\t1/1:0.9992\n+10\t738630\trs1750792\tC\tT\t.\t.\t.\tGT:BAF\t0/0:0\n+10\t749238\trs553326\tG\tT\t.\t.\t.\tGT:BAF\t0/0:0.00229999999999997\n+10\t754033\trs2265090\tC\tA\t.\t.\t.\tGT:BAF\t0/0:0\n+10\t757222\trs10904546\tA\tG\t.\t.\t.\tGT:BAF\t0/0:0.0000\n+10\t766105\trs7906313\tT\tC\t.\t.\t.\tGT:BAF\t0/0:0.0116\n+10\t776027\trs11253377\tC\tT\t.\t.\t.\tGT:BAF\t1/1:0.9964\n+10\t787896\trs1769242\tT\tC\t.\t.\t.\tGT:BAF\t0/0:0.0000\n+10\t800213\trs2254501\tG\tA\t.\t.\t.\tGT:BAF\t1/1:0.9918\n+10\t802445\trs1769215\tC\tT\t.\t.\t.\tGT:BAF\t0/0:0.00370000000000004\n+10\t803721\trs2790381\tC\tT\t.\t.\t.\tGT:BAF\t1/1:0.9798\n+10\t811876\trs12414585\tG\tA\t.\t.\t.\tGT:BAF\t1/0:0.516\n+10\t813426\trs11253424\tC\tT\t.\t.\t.\tGT:BAF\t0/0:0\n+10\t815149\trs7084027\tA\tG\t.\t.\t.\tGT:BAF\t1/1:0.9944\n+10\t820868\trs10752019\tC\tT\t.\t.\t.\tGT:BAF\t0/0:0.0118\n+10\t833528\texm2271241\tT\tG\t.\t.\t.\tGT:BAF\t0/1:0.4896\n+10\t834736\trs4881530\tG\tA\t.\t.\t.\tGT:BAF\t0/0:0.00249999999999995\n+10\t836115\trs11253444\tA\tG\t.\t.\t.\tGT:BAF\t0/1:0.5199\n+10\t838179\trs1536337\tT\tC\t.\t.\t.\tGT:BAF\t0/0:0.0000\n+10\t858022\trs9124\tC\tT\t.\t.\t.\tGT:BAF\t0/0:0\n+10\t858924\texm805329\tG\tA\t.\t.\t.\tGT:BAF\t0/0:0\n+10\t859047\texm805338\tC\tA\t.\t.\t.\tGT:BAF\t0/0:0\n+10\t860687\texm805350\tC\tT\t.\t.\t.\tGT:BAF\t0/0:0\n+10\t860726\texm'..b'\tT\t.\t.\t.\tGT:BAF\t0/0:0\n+11\t323283\trs3740304\tA\tG\t.\t.\t.\tGT:BAF\t0/1:0.5588\n+11\t326894\trs3125027\tT\tC\t.\t.\t.\tGT:BAF\t0/0:0.0005\n+11\t327162\texm805022\tC\tT\t.\t.\t.\tGT:BAF\t0/0:0\n+11\t329493\trs3815985\tC\tA\t.\t.\t.\tGT:BAF\t1/0:0.5187\n+11\t338553\trs3125031\tC\tT\t.\t.\t.\tGT:BAF\t1/0:0.4696\n+11\t354301\trs35198327\tC\tT\t.\t.\t.\tGT:BAF\t1/0:0.4929\n+11\t375475\tvariant.11341\tC\tT\t.\t.\t.\tGT:BAF\t0/0:0.000199999999999978\n+11\t377161\trs7070654\tC\tT\t.\t.\t.\tGT:BAF\t0/0:0\n+11\t387060\trs7904155\tG\tA\t.\t.\t.\tGT:BAF\t1/1:0.9945\n+11\t390962\texm805090\tG\tA\t.\t.\t.\tGT:BAF\t0/0:9.9999999999989e-05\n+11\t390983\texm805091\tG\tA\t.\t.\t.\tGT:BAF\t0/0:0\n+11\t394615\texm805105\tG\tA\t.\t.\t.\tGT:BAF\t0/0:0\n+11\t402390\texm805131\tG\tC\t.\t.\t.\tGT:BAF\t0/0:0.0000\n+11\t403792\texm805136\tG\tC\t.\t.\t.\tGT:BAF\t0/0:0.0000\n+11\t410501\texm805166\tC\tT\t.\t.\t.\tGT:BAF\t0/0:0\n+11\t413010\trs9787422\tC\tT\t.\t.\t.\tGT:BAF\t1/0:0.5334\n+11\t423555\trs12245012\tG\tA\t.\t.\t.\tGT:BAF\t0/0:0.00149999999999995\n+11\t423671\trs10904067\tC\tT\t.\t.\t.\tGT:BAF\t1/0:0.5566\n+11\t431161\texm2271240\tC\tT\t.\t.\t.\tGT:BAF\t1/0:0.4838\n+11\t435971\texm2249233\tT\tC\t.\t.\t.\tGT:BAF\t0/0:0.0000\n+11\t435990\texm805214\tG\tA\t.\t.\t.\tGT:BAF\t0/0:0\n+11\t453567\trs4881254\tC\tT\t.\t.\t.\tGT:BAF\t1/0:0.5079\n+11\t462885\trs10904173\tG\tA\t.\t.\t.\tGT:BAF\t1/0:0.4819\n+11\t465046\texm805254\tG\tA\t.\t.\t.\tGT:BAF\t0/0:0\n+11\t468599\trs12415961\tT\tC\t.\t.\t.\tGT:BAF\t0/1:0.5021\n+11\t486935\texm805280\tG\tC\t.\t.\t.\tGT:BAF\t0/0:0.0186\n+11\t487973\trs4881313\tT\tC\t.\t.\t.\tGT:BAF\t0/1:0.5628\n+11\t521431\texm2271370\tC\tT\t.\t.\t.\tGT:BAF\t1/1:0.9952\n+11\t521723\trs4881336\tC\tT\t.\t.\t.\tGT:BAF\t1/1:1\n+11\t547567\trs816599\tA\tG\t.\t.\t.\tGT:BAF\t1/1:1.0000\n+11\t554186\trs12251997\tC\tT\t.\t.\t.\tGT:BAF\t0/0:0.00309999999999999\n+11\t556129\trs10466270\tA\tG\t.\t.\t.\tGT:BAF\t0/1:0.5142\n+11\t566379\trs11252926\tC\tT\t.\t.\t.\tGT:BAF\t1/0:0.5024\n+11\t588406\trs10904450\tA\tG\t.\t.\t.\tGT:BAF\t0/0:0.0006\n+11\t592283\trs816646\tG\tA\t.\t.\t.\tGT:BAF\t1/0:0.5006\n+11\t601089\trs816650\tC\tT\t.\t.\t.\tGT:BAF\t0/0:0\n+11\t615782\trs17221309\tG\tA\t.\t.\t.\tGT:BAF\t0/0:0.00319999999999998\n+11\t635857\trs7069611\tT\tC\t.\t.\t.\tGT:BAF\t0/0:0.0013\n+11\t669358\trs7898821\tG\tA\t.\t.\t.\tGT:BAF\t0/0:0\n+11\t673037\trs816563\tC\tT\t.\t.\t.\tGT:BAF\t1/1:0.9065\n+11\t680428\trs2124585\tG\tA\t.\t.\t.\tGT:BAF\t1/0:0.5212\n+11\t712617\trs17136372\tA\tC\t.\t.\t.\tGT:BAF\t1/1:0.9992\n+11\t738630\trs1750792\tC\tT\t.\t.\t.\tGT:BAF\t0/0:0\n+11\t749238\trs553326\tG\tT\t.\t.\t.\tGT:BAF\t0/0:0.00229999999999997\n+11\t754033\trs2265090\tC\tA\t.\t.\t.\tGT:BAF\t0/0:0\n+11\t757222\trs10904546\tA\tG\t.\t.\t.\tGT:BAF\t0/0:0.0000\n+11\t766105\trs7906313\tT\tC\t.\t.\t.\tGT:BAF\t0/0:0.0116\n+11\t776027\trs11253377\tC\tT\t.\t.\t.\tGT:BAF\t1/1:0.9964\n+11\t787896\trs1769242\tT\tC\t.\t.\t.\tGT:BAF\t0/0:0.0000\n+11\t800213\trs2254501\tG\tA\t.\t.\t.\tGT:BAF\t1/1:0.9918\n+11\t802445\trs1769215\tC\tT\t.\t.\t.\tGT:BAF\t0/0:0.00370000000000004\n+11\t803721\trs2790381\tC\tT\t.\t.\t.\tGT:BAF\t1/1:0.9798\n+11\t811876\trs12414585\tG\tA\t.\t.\t.\tGT:BAF\t1/0:0.516\n+11\t813426\trs11253424\tC\tT\t.\t.\t.\tGT:BAF\t0/0:0\n+11\t815149\trs7084027\tA\tG\t.\t.\t.\tGT:BAF\t1/1:0.9944\n+11\t820868\trs10752019\tC\tT\t.\t.\t.\tGT:BAF\t0/0:0.0118\n+11\t833528\texm2271241\tT\tG\t.\t.\t.\tGT:BAF\t0/1:0.4896\n+11\t834736\trs4881530\tG\tA\t.\t.\t.\tGT:BAF\t0/0:0.00249999999999995\n+11\t836115\trs11253444\tA\tG\t.\t.\t.\tGT:BAF\t0/1:0.5199\n+11\t838179\trs1536337\tT\tC\t.\t.\t.\tGT:BAF\t0/0:0.0000\n+11\t858022\trs9124\tC\tT\t.\t.\t.\tGT:BAF\t0/0:0\n+11\t858924\texm805329\tG\tA\t.\t.\t.\tGT:BAF\t0/0:0\n+11\t859047\texm805338\tC\tA\t.\t.\t.\tGT:BAF\t0/0:0\n+11\t860687\texm805350\tC\tT\t.\t.\t.\tGT:BAF\t0/0:0\n+11\t860726\texm805354\tT\tC\t.\t.\t.\tGT:BAF\t0/0:0.0000\n+11\t860970\texm805360\tA\tG\t.\t.\t.\tGT:BAF\t0/0:0.0000\n+11\t871110\texm805378\tG\tC\t.\t.\t.\tGT:BAF\t0/0:0.0000\n+11\t871746\texm805386\tG\tA\t.\t.\t.\tGT:BAF\t0/0:0.00239999999999996\n+11\t875350\texm805392\tG\tA\t.\t.\t.\tGT:BAF\t0/0:0\n+11\t888899\texm805400\tC\tT\t.\t.\t.\tGT:BAF\t0/0:0.00470000000000004\n+11\t888916\texm805401\tT\tC\t.\t.\t.\tGT:BAF\t0/0:0.0000\n+11\t894838\trs12249828\tC\tT\t.\t.\t.\tGT:BAF\t1/0:0.4839\n+11\t903950\trs11253471\tA\tG\t.\t.\t.\tGT:BAF\t0/1:0.4747\n+11\t909757\texm805413\tG\tA\t.\t.\t.\tGT:BAF\t0/0:0\n+11\t909766\texm805415\tG\tA\t.\t.\t.\tGT:BAF\t0/0:0\n+11\t910074\texm805420\tC\tT\t.\t.\t.\tGT:BAF\t0/0:0.0071\n+11\t910081\texm805421\tC\tT\t.\t.\t.\tGT:BAF\t0/0:0.002\n+11\t927331\trs11253489\tG\tA\t.\t.\t.\tGT:BAF\t1/0:0.5325\n+11\t931618\texm805430\tG\tA\t.\t.\t.\tGT:BAF\t0/0:0\n+11\t931631\texm805431\tC\tT\t.\t.\t.\tGT:BAF\t0/0:0.00390000000000001\n' |
| b |
| diff -r a1213a0b7b66 -r 833ad3665419 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 13:05:47 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 a1213a0b7b66 -r 833ad3665419 test-data/cnv_summary.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cnv_summary.tab Wed Jun 05 13:05:47 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 a1213a0b7b66 -r 833ad3665419 test-data/color_chrs.dat --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/color_chrs.dat Wed Jun 05 13:05:47 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 a1213a0b7b66 -r 833ad3665419 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 13:05:47 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 a1213a0b7b66 -r 833ad3665419 test-data/fasta_indexes.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fasta_indexes.loc Wed Jun 05 13:05:47 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 a1213a0b7b66 -r 833ad3665419 test-data/mpileup.ref.fa.fai --- a/test-data/mpileup.ref.fa.fai Thu Feb 21 16:00:59 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 a1213a0b7b66 -r 833ad3665419 test-data/plugin_frameshifts.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plugin_frameshifts.bed Wed Jun 05 13:05:47 2019 -0400 |
| b |
| @@ -0,0 +1,1 @@ +1 3106150 3106160 |
| b |
| diff -r a1213a0b7b66 -r 833ad3665419 test-data/stats.a.vcf --- a/test-data/stats.a.vcf Thu Feb 21 16:00:59 2019 -0500 +++ b/test-data/stats.a.vcf Wed Jun 05 13:05:47 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 a1213a0b7b66 -r 833ad3665419 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 13:05:47 2019 -0400 |
| b |
| @@ -0,0 +1,14 @@ +>1 +CACGTNACGGCTGAAGTCCAAGGTAC +CGTATCGAGTTCACAGTCGATAGCTC +GATCGATAGCATCGCTAGCNNNACTA +CGATCGATCGCTCTCCGTAACACTCA +AAAACGATCGATCGACTGCTCTTTAG +CGATGACTTTAGGGGAAAAA +>2 +CGCTCAGCCGTACAGCCGAGCAGGAC +ACGCTATTTTAGATCGACTGGCTNNG +CGCTAGCTACGCTTTAGCACGAGAA +>Y +NNNGCATACGTGTCCATCACGATGAT +AGCGATGATCGATC |
| b |
| diff -r a1213a0b7b66 -r 833ad3665419 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 13:05:47 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 a1213a0b7b66 -r 833ad3665419 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 13:05:47 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 a1213a0b7b66 -r 833ad3665419 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 13:05:47 2019 -0400 |
| b |
| @@ -0,0 +1,2 @@ +1:2-501 500 9 60 61 +2 501 521 60 61 |
| b |
| diff -r a1213a0b7b66 -r 833ad3665419 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 13:05:47 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 a1213a0b7b66 -r 833ad3665419 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 13:05:47 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 a1213a0b7b66 -r 833ad3665419 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 13:05:47 2019 -0400 |
| b |
| @@ -0,0 +1,9 @@ +>22 +NNNNNNNNCCTTGGCCAAGTCACTTCCTCCTTCAGGAACATTGCAGTGGGCCTAAGTGCC +TCCTCTCGGGACTGGTATGGGGACGGTCATGCAATCTGGACAACATTCACCTTTAAAAGT +TTATTGATCTTTTGTGACATGCACGTGGGTTCCCAGTAGCAAGAAACTAAAGGGTCGCAG +GCCGGTTTCTGCTAATTTCTTTAATTCCAAGACAGTCTCAAATATTTTCTTATTAACTTC +CTGGAGGGAGGCTTATCATTCTCTCTTTTGGATGATTCTAAGTACCAGCTAAAATACAGC +TATCATTCATTTTCCTTGATTTGGGAGCCTAATTTCTTTAATTTAGTATGCAAGAAAACC +AATTTGGAAATATCAACTGTTTTGGAAACCTTAGACCTAGGTCATCCTTAGTAAGATCTT +CCCATTTATATAAATACTTGCAAGTAGTAGTGCCATAATT |
| b |
| diff -r a1213a0b7b66 -r 833ad3665419 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 13:05:47 2019 -0400 |
| b |
| @@ -0,0 +1,1 @@ +22 460 4 60 61 |
| b |
| diff -r a1213a0b7b66 -r 833ad3665419 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 13:05:47 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 a1213a0b7b66 -r 833ad3665419 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 13:05:47 2019 -0400 |
| b |
| @@ -0,0 +1,1 @@ +17 4200 14 60 61 |
| b |
| diff -r a1213a0b7b66 -r 833ad3665419 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 13:05:47 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 a1213a0b7b66 -r 833ad3665419 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 13:05:47 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 a1213a0b7b66 -r 833ad3665419 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 13:05:47 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> |