Repository 'bcftools_cnv'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv

Changeset 8:13fe14c56f6d (2019-06-05)
Previous changeset 7:bf1f4994f104 (2019-02-21) Next changeset 9:86737d0f7fab (2019-07-29)
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
modified:
bcftools_cnv.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 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&gt;&amp;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
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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
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\trs38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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>