# HG changeset patch
# User iuc
# Date 1559754306 14400
# Node ID 693d81b3e1132f305153d4ed4424a8065965a081
# Parent  94a8d3db9b3fb125f82ee2f1ab1809e7bf9c464b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5

diff -r 94a8d3db9b3f -r 693d81b3e113 bcftools_plugin_frameshifts.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bcftools_plugin_frameshifts.xml	Wed Jun 05 13:05:06 2019 -0400
@@ -0,0 +1,100 @@
+<?xml version='1.0' encoding='utf-8'?>
+<tool name="bcftools @EXECUTABLE@" id="bcftools_plugin_@PLUGIN_ID@" version="@TOOL_VERSION@+galaxy1">
+    <description>plugin Annotate frameshift indels</description>
+    <macros>
+        <token name="@EXECUTABLE@">frameshifts</token>
+        <token name="@PLUGIN_ID@">frameshifts</token>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+    <command detect_errors="aggressive"><![CDATA[
+@PREPARE_ENV@
+@PREPARE_INPUT_FILE@
+#set $section = $sec_restrict
+@PREPARE_TARGETS_FILE@
+@PREPARE_REGIONS_FILE@
+## exons file needs to be bgzip and have tabix index
+bgzip -c $exons > exons.bed.gz &&
+tabix exons.bed.gz &&
+
+bcftools plugin @EXECUTABLE@
+## VCF input section
+#set $section = $sec_restrict
+@INCLUDE@
+@EXCLUDE@
+@REGIONS@
+@TARGETS@
+
+@OUTPUT_TYPE@
+@THREADS@
+
+## Primary Input/Outputs
+@INPUT_FILE@
+## Plugin options
+-- --exons exons.bed.gz
+> '$output_file'
+]]>
+    </command>
+    <inputs>
+        <expand macro="macro_input" />
+        <param name="exons" type="data" format="bed"
+        label="Exons File" help="BED file describing exons" />
+        <section name="sec_restrict" expanded="false" title="Restrict to">
+            <expand macro="macro_restrict" />
+            <expand macro="macro_restrict" type="target" label_type="Target" />
+            <expand macro="macro_include" />
+            <expand macro="macro_exclude" />
+        </section>
+        <expand macro="macro_select_output_type" />
+    </inputs>
+    <outputs>
+        <expand macro="macro_vcf_output" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_file" ftype="vcf" value="plugin1.vcf" />
+            <param name="exons" ftype="bed" value="plugin_frameshifts.bed" />
+            <param name="output_type" value="v" />
+            <output name="output_file" ftype="vcf">
+                <assert_contents>
+                    <has_line_matching expression="##INFO=&lt;ID=OOF,.+" />
+                    <has_line_matching expression="1&#09;3106154&#09;.&#09;CAAA&#09;C&#09;.+&#09;.+&#09;OOF=0.+" />
+                    <has_line_matching expression="1&#09;3106154&#09;.&#09;C&#09;CT&#09;.+&#09;.+&#09;OOF=1.+" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+=====================================
+ bcftools @EXECUTABLE@ plugin
+=====================================
+
+A simple tool to annotate the effect of indel variants.
+
+Adds an ``OOF`` (out-of-frame) subfield to the ``INFO`` field of indel records
+found in the input, where
+
+- ``OOF=1`` indicates that the indel results in a frameshift
+- ``OOF=0`` indicates an in-frame indel
+
+The information about indel effects is extracted from the ``BED`` input, which
+is supposed to describe the reference genome exons.
+
+If a variant record lists several ``ALT`` alleles, some of them indels, then
+``OOF`` will be a comma-separated list of status indicators. In the list a
+third ``OOF`` status code of ``-1`` will be used to indicate ``ALT`` alleles
+that are not associated with a change in sequence length or that don't affect
+an exon.
+
+The formal definition (added to the VCF header) of the ``OOF`` subfield is::
+
+  INFO=<ID=OOF,Number=A,Type=Integer,Description="Frameshift Indels: out-of-frame (1), in-frame (0), not-applicable (-1 or missing)">
+
+@REGIONS_HELP@
+@TARGETS_HELP@
+@EXPRESSIONS_HELP@
+
+    ]]></help>
+    <expand macro="citations" />
+</tool>
diff -r 94a8d3db9b3f -r 693d81b3e113 macros.xml
--- a/macros.xml	Thu Feb 21 16:00:10 2019 -0500
+++ b/macros.xml	Wed Jun 05 13:05:06 2019 -0400
@@ -1,13 +1,5 @@
 <macros>
   <token name="@TOOL_VERSION@">1.9</token>
-  <xml name="stdio">
-    <stdio>
-      <exit_code range="1:" />
-      <exit_code range=":-1" />
-      <regex match="Error:" />
-      <regex match="Exception:" />
-    </stdio>
-  </xml>
   <xml name="requirements">
     <requirements>
       <requirement type="package" version="@TOOL_VERSION@">bcftools</requirement>
@@ -18,6 +10,9 @@
   <xml name="samtools_requirement">
       <requirement type="package" version="1.9">samtools</requirement>
   </xml>
+  <xml name="matplotlib_requirement">
+      <requirement type="package" version="3.1.0">matplotlib</requirement>
+  </xml>
   <xml name="version_command">
     <version_command>bcftools 2&gt;&amp;1 | grep 'Version:'</version_command>
   </xml>
@@ -111,16 +106,45 @@
 $vcfs_list_file
   </token>
 
+  <xml name="test_using_reference" token_select_from="history" token_ref="">
+    <conditional name="reference_source">
+        <param name="reference_source_selector" value="@SELECT_FROM@" />
+        <param name="fasta_ref" ftype="fasta" value="@REF@" />
+    </conditional>
+  </xml>
+
   <xml name="macro_fasta_ref">
-    <param name="fasta_ref" argument="--fasta-ref" type="data" format="data" optional="true" label="Reference sequence in FASTA format" />
+    <conditional name="reference_source">
+        <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
+            <option value="cached">Use a built-in genome</option>
+            <option value="history">Use a genome from the history</option>
+        </param>
+        <when value="cached">
+            <param name="fasta_ref" type="select" label="Reference genome">
+                <options from_data_table="fasta_indexes">
+                    <filter type="data_meta" column="1" key="dbkey" ref="input_file" />
+                    <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file" />
+                </options>
+            </param>
+        </when>
+        <when value="history">
+            <param name="fasta_ref" type="data" format="fasta" label="Reference genome" />
+        </when>
+    </conditional>
   </xml>
   <token name="@PREPARE_FASTA_REF@">
 <![CDATA[
 #set $input_fa_ref = None
 #if 'fasta_ref' in $section and $section.fasta_ref:
-  #set $input_fa_ref = 'ref.fa'
-  ln -s '$section.fasta_ref' $input_fa_ref &&
-  samtools faidx $input_fa_ref &&
+  #if 'reference_source_selector' in $section:
+    #if str($section.reference_source_selector) == "history":
+      #set $input_fa_ref = 'ref.fa'
+      ln -s '$section.fasta_ref' $input_fa_ref &&
+      samtools faidx $input_fa_ref &&
+    #else:
+      #set $input_fa_ref = str($section.fasta_ref.fields.path)
+    #end if
+  #end if
 #end if
 ]]>
   </token>
@@ -132,27 +156,6 @@
 #end if
   </token>
 
-  <xml name="macro_ref_fasta">
-    <conditional name="reference_source">
-       <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
-         <option value="cached">Locally cached</option>
-         <option value="history">History</option>
-       </param>
-       <when value="cached">
-         <param name="ref_file" type="select" label="Select reference genome">
-           <options from_data_table="fasta_indexes">
-             <!--<filter type="data_meta" key="dbkey" ref="input_bam" column="value"/>-->
-           </options>
-           <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
-         </param>
-       </when>
-       <when value="history"> <!-- FIX ME!!!! -->
-         <param name="ref_file" type="data" format="fasta" label="Using reference file" />
-       </when>
-     </conditional>
-  </xml>
-
-
   <xml name="macro_AF_file">
     <param name="AF_file" argument="--AF-file" type="data" format="tabular" optional="true" label="Allele frequencies file" help="Tab-delimited file containing the columns CHR,POS,REF,ALT,AF" />
   </xml>
@@ -268,25 +271,97 @@
       </data>
   </xml>
 
-  <xml name="macro_regions">
-    <conditional name="regions">
-        <param name="regions_src" type="select" label="Regions">
-            <option value="__none__">None</option>
-            <option value="regions">regions</option>
-            <option value="regions_file">regions-file</option>
+  <xml name="macro_invert_targets">
+    <param name="invert_targets_file" type="boolean" truevalue="^" falsevalue=""
+    label="Invert Targets"
+    help="inverts the query/filtering applied by the targets" />
+  </xml>
+
+  <xml name="macro_restriction_spec" token_type="region" token_label_type="Region">
+    <repeat name="@TYPE@s" title="@LABEL_TYPE@ Filter" default="1" min="1">
+        <param name="chrom" type="text" label="@LABEL_TYPE@ chromosome">
+            <validator type="expression" message="A chromosome identifier is required when specifying a @LABEL_TYPE@ filter">value.strip()</validator>
+        </param>
+        <param name="start" type="text" label="@LABEL_TYPE@ start position">
+            <validator type="expression" message="an integer number is required">not value or value.isdigit()</validator>
+        </param>
+        <param name="stop" type="text" label="@LABEL_TYPE@ end position">
+            <validator type="expression" message="an integer number is required">not value or value.isdigit()</validator>
+        </param>
+        <yield />
+    </repeat>
+  </xml>
+
+  <xml name="macro_restrictions_file" token_type="region" token_label_type="Region">
+    <param name="@TYPE@s_file" type="data" format="tabular" label="@LABEL_TYPE@s File" help="restrict to @LABEL_TYPE@s listed in a file" />
+  </xml>
+
+  <xml name="macro_restrict" token_type="region" token_label_type="Region" >
+    <conditional name="@TYPE@s">
+        <param name="@TYPE@s_src" type="select" label="@LABEL_TYPE@s">
+            <option value="__none__">Do not restrict to @LABEL_TYPE@s</option>
+            <option value="@TYPE@s">Specify one or more @LABEL_TYPE@(s) directly</option>
+            <option value="@TYPE@s_file">Operate on @LABEL_TYPE@s specified in a history dataset</option>
         </param>
         <when value="__none__"/>
-        <when value="regions">
-            <param name="regions" type="text" value="" optional="true" label="Restrict to comma-separated list of regions"
-                   help="Each region is specifed as: chr or chr:pos or chr:from-to">
-                 <validator type="regex" message="">^(\w+(:\d+(-\d+)?)?(,\w+(:\d+(-\d+)?)?)*)?$</validator>
-            </param>
+        <when value="@TYPE@s">
+            <expand macro="macro_restriction_spec" type="@TYPE@" label_type="@LABEL_TYPE@" />
+            <yield />
         </when>
-        <when value="regions_file">
-            <param name="regions_file" type="data" format="vcf,bed,tabular" optional="true" label="Regions file" help="Restrict to regions listed in a file" />
-        </when>
+        <when value="@TYPE@s_file">
+            <expand macro="macro_restrictions_file" type="@TYPE@" label_type="@LABEL_TYPE@" />
+            <yield />
+        </when>        
     </conditional>
   </xml>
+
+  <token name="@PARSE_INTERVALS@">
+<![CDATA[
+#set $components = []
+#for $i in $intervals:
+  #set $chrom = str($i.chrom).strip()
+  #set $start = str($i.start).strip()
+  #set $stop = str($i.stop).strip()
+  #if $start or $stop:
+    $components.append($chrom + ':' + ($start or '0') + '-' + $stop)
+  #else:
+    $components.append($chrom)
+  #end if
+#end for
+#set $intervals_spec = ','.join($components)
+]]>
+  </token>
+  
+  <token name="@REGIONS@">
+<![CDATA[
+#if $section.regions.regions_src == 'regions':
+  #set $intervals = $section.regions.regions
+  @PARSE_INTERVALS@
+  --regions '$intervals_spec'
+#elif $section.regions.regions_src == 'regions_file' and $section.regions.regions_file:
+  #if $regions_path is not None:
+    --regions-file '$regions_path'
+  #else:
+    --regions-file '$section.regions.regions_file'
+  #end if
+#end if
+]]>
+  </token>
+  
+  <token name="@TARGETS@">
+<![CDATA[
+#if $targets_path:
+  --targets-file "${section.targets.invert_targets_file}${targets_path}"
+#elif $section.targets.targets_src == 'targets':
+  #set $intervals = $section.targets.targets
+  @PARSE_INTERVALS@
+  --targets '${section.targets.invert_targets_file}$intervals_spec'
+#elif $section.targets.targets_src == 'targets_file' and $section.targets.targets_file:
+  --targets-file "${section.targets.invert_targets_file}${section.targets.targets_file}"
+#end if
+]]>
+  </token>
+
   <token name="@PREPARE_REGIONS_FILE@">
 <![CDATA[
 #set $regions_path = None
@@ -300,23 +375,7 @@
 #end if
 ]]>
   </token>
-  <token name="@REGIONS@">
-#if $section.regions.regions_src == 'regions' and $section.regions.regions != '':
-  --regions '$section.regions.regions'
-#elif $section.regions.regions_src == 'regions_file' and $section.regions.regions_file:
-  #if $regions_path is not None:
-    --regions-file '$regions_path'
-  #else:
-    --regions-file '$section.regions.regions_file'
-  #end if
-#end if
-  </token>
-  <xml name="macro_targets_file">
-            <param name="targets_file" type="data" format="tabular" label="Targets File" help="restrict to targets listed in a file" >
-              <yield/>
-            </param>
-            <param name="invert_targets_file" type="boolean" truevalue="^" falsevalue="" label="Invert Targets" help="inverts the query/filtering applied by the target file selection" />
-  </xml>
+
   <token name="@PREPARE_TARGETS_FILE@">
 <![CDATA[
 #set $targets_path = None
@@ -333,6 +392,7 @@
 #end if
 ]]>
   </token>
+
   <token name="@TARGETS_FILE@">
 <![CDATA[
 #if $targets_path is not None:
@@ -343,41 +403,6 @@
 ]]>
   </token>
 
-  <xml name="macro_targets">
-    <conditional name="targets">
-        <param name="targets_src" type="select" label="Targets">
-            <option value="__none__">None</option>
-            <option value="targets">targets</option>
-            <option value="targets_file">targets-file</option>
-        </param>
-        <when value="__none__"/>
-        <when value="targets">
-            <param name="targets" type="text" value="" optional="true" label="Restrict to comma-separated list of targets"
-                   help="Each target is specifed as: chr or chr:pos or chr:from-to">
-                 <validator type="regex" message="">^(\w+(:\d+(-\d+)?)?(,\w+(:\d+(-\d+)?)?)*)?$</validator>
-            </param>
-            <param name="invert_targets_file" type="boolean" truevalue="^" falsevalue="" label="Invert Targets" help="inverts the query/filtering applied by the targets" />
-        </when>
-        <when value="targets_file">
-            <expand macro="macro_targets_file">
-            </expand>
-        </when>
-    </conditional>
-  </xml>
-  <token name="@TARGETS@">
-<![CDATA[
-#if $targets_path:
-  --targets-file "${section.targets.invert_targets_file}${targets_path}"
-#else:
-  #if $section.targets.targets_src == 'targets' and $section.targets.targets != '':
-    --targets '${section.targets.invert_targets_file}${section.targets.targets}'
-  #elif $section.targets.targets_src == 'targets_file' and $section.targets.targets_file:
-    --targets-file "${section.targets.invert_targets_file}${section.targets.targets_file}"
-  #end if
-#end if
-]]>
-  </token>
-
   <xml name="macro_samples">
       <param argument="--samples" type="text" value="" optional="true" label="Samples"
              help="Comma separated list of samples to annotate (or exclude)">
diff -r 94a8d3db9b3f -r 693d81b3e113 test-data/cnv.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cnv.vcf	Wed Jun 05 13:05:06 2019 -0400
@@ -0,0 +1,192 @@
+##fileformat=VCFv4.2
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GC,Number=1,Type=Float,Description="GenCall score">
+##FORMAT=<ID=IA,Number=1,Type=Float,Description="Intensity of the A Allele">
+##FORMAT=<ID=IB,Number=1,Type=Float,Description="Intensity of the B Allele">
+##FORMAT=<ID=BAF,Number=1,Type=Float,Description="B Allele Frequency">
+##FORMAT=<ID=LRR,Number=1,Type=Float,Description="Log R Ratio">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	test
+10	135656	rs10904561	T	G	.	.	.	GT:LRR:BAF:IA:IB:GC	0/1:0.0415:0.5176:0.543:0.661:0.9477
+10	135708	rs7917054	G	A	.	.	.	GT:LRR:BAF:IA:IB:GC	1/0:0.2441:0.501:0.742:0.659:0.9604
+10	178434	rs7089889	T	G	.	.	.	GT:LRR:BAF:IA:IB:GC	0/1:0.1440:0.4833:0.836:0.827:0.8884
+10	188805	rs12146291	A	G	.	.	.	GT:LRR:BAF:IA:IB:GC	0/1:0.2144:0.4715:0.776:0.743:0.9610
+10	203471	rs10903451	A	G	.	.	.	GT:LRR:BAF:IA:IB:GC	0/0:0.4201:0.0000:0.619:0.022:0.9337
+10	252693	rs2379078	T	C	.	.	.	GT:LRR:BAF:IA:IB:GC	0/0:-0.2673:0.0068:0.806:0.081:0.9018
+10	273344	rs2448378	A	C	.	.	.	GT:LRR:BAF:IA:IB:GC	0/0:-0.7407:0.0000:0.497:0.012:0.9411
+10	279248	rs2496278	C	A	.	.	.	GT:LRR:BAF:IA:IB:GC	1/0:-0.4228:0.6268:0.285:0.958:0.6772
+10	291134	rs10508201	T	C	.	.	.	GT:LRR:BAF:IA:IB:GC	0/1:0.1085:0.4723:0.317:0.444:0.9106
+10	293358	exm2249181	A	C	.	.	.	GT:LRR:BAF:IA:IB:GC	0/0:-0.0097:0.0044:1.507:0.061:0.3992
+10	313504	rs4880568	C	T	.	.	.	GT:LRR:BAF:IA:IB:GC	1/1:-0.5836:0.9803:0.017:0.321:0.9547
+10	317501	rs2018975	C	T	.	.	.	GT:LRR:BAF:IA:IB:GC	0/0:-0.3392:0:1.069:0.039:0.7852
+10	323283	rs3740304	A	G	.	.	.	GT:LRR:BAF:IA:IB:GC	0/1:0.1836:0.5588:1.053:1.110:0.8640
+10	326894	rs3125027	T	C	.	.	.	GT:LRR:BAF:IA:IB:GC	0/0:-0.0517:0.0005:1.300:0.026:0.8916
+10	327162	exm805022	C	T	.	.	.	GT:LRR:BAF:IA:IB:GC	0/0:-0.1197:0:0.995:0.015:0.5328
+10	329493	rs3815985	C	A	.	.	.	GT:LRR:BAF:IA:IB:GC	1/0:0.0480:0.5187:0.824:0.794:0.9109
+10	338553	rs3125031	C	T	.	.	.	GT:LRR:BAF:IA:IB:GC	1/0:-0.3387:0.4696:0.777:1.004:0.7901
+10	354301	rs35198327	C	T	.	.	.	GT:LRR:BAF:IA:IB:GC	1/0:-0.1338:0.4929:0.903:0.996:0.8546
+10	375475	variant.11341	C	T	.	.	.	GT:LRR:BAF:IA:IB:GC	0/0:-0.0747:0.000199999999999978:1.132:0.012:0.4773
+10	377161	rs7070654	C	T	.	.	.	GT:LRR:BAF:IA:IB:GC	0/0:0.1388:0:0.582:0.020:0.9458
+10	387060	rs7904155	G	A	.	.	.	GT:LRR:BAF:IA:IB:GC	1/1:0.0615:0.9945:0.080:1.883:0.8310
+10	390962	exm805090	G	A	.	.	.	GT:LRR:BAF:IA:IB:GC	0/0:-0.0087:9.9999999999989e-05:1.226:0.063:0.6950
+10	390983	exm805091	G	A	.	.	.	GT:LRR:BAF:IA:IB:GC	0/0:-0.3606:0:0.398:0.035:0.4585
+10	394615	exm805105	G	A	.	.	.	GT:LRR:BAF:IA:IB:GC	0/0:0.0170:0:1.345:0.020:0.4108
+10	402390	exm805131	G	C	.	.	.	GT:LRR:BAF:IA:IB:GC	0/0:0.0341:0.0000:1.127:0.023:0.8735
+10	403792	exm805136	G	C	.	.	.	GT:LRR:BAF:IA:IB:GC	0/0:-0.1428:0.0000:0.908:0.019:0.8483
+10	410501	exm805166	C	T	.	.	.	GT:LRR:BAF:IA:IB:GC	0/0:0.0189:0:1.162:0.050:0.4628
+10	413010	rs9787422	C	T	.	.	.	GT:LRR:BAF:IA:IB:GC	1/0:0.0871:0.5334:0.908:0.961:0.8338
+10	423555	rs12245012	G	A	.	.	.	GT:LRR:BAF:IA:IB:GC	0/0:0.1264:0.00149999999999995:1.658:0.040:0.8015
+10	423671	rs10904067	C	T	.	.	.	GT:LRR:BAF:IA:IB:GC	1/0:-0.3622:0.5566:0.326:0.370:0.9306
+10	431161	exm2271240	C	T	.	.	.	GT:LRR:BAF:IA:IB:GC	1/0:-0.0175:0.4838:0.935:1.004:0.8308
+10	435971	exm2249233	T	C	.	.	.	GT:LRR:BAF:IA:IB:GC	0/0:-0.2716:0.0000:1.217:0.042:0.3992
+10	435990	exm805214	G	A	.	.	.	GT:LRR:BAF:IA:IB:GC	0/0:-0.1427:0:1.107:0.031:0.4295
+10	453567	rs4881254	C	T	.	.	.	GT:LRR:BAF:IA:IB:GC	1/0:0.1831:0.5079:1.032:1.425:0.8149
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+11	820868	rs10752019	C	T	.	.	.	GT:LRR:BAF:IA:IB:GC	0/0:0.0749:0.0118:1.349:0.070:0.8882
+11	833528	exm2271241	T	G	.	.	.	GT:LRR:BAF:IA:IB:GC	0/1:-0.0329:0.4896:0.569:0.681:0.9348
+11	834736	rs4881530	G	A	.	.	.	GT:LRR:BAF:IA:IB:GC	0/0:-0.0453:0.00249999999999995:1.578:0.040:0.8076
+11	836115	rs11253444	A	G	.	.	.	GT:LRR:BAF:IA:IB:GC	0/1:-0.1380:0.5199:0.596:0.670:0.9248
+11	838179	rs1536337	T	C	.	.	.	GT:LRR:BAF:IA:IB:GC	0/0:-0.0534:0.0000:1.318:0.095:0.7967
+11	858022	rs9124	C	T	.	.	.	GT:LRR:BAF:IA:IB:GC	0/0:-0.5565:0:0.715:0.012:0.9397
+11	858924	exm805329	G	A	.	.	.	GT:LRR:BAF:IA:IB:GC	0/0:-0.0866:0:0.873:0.021:0.9056
+11	859047	exm805338	C	A	.	.	.	GT:LRR:BAF:IA:IB:GC	0/0:0.1868:0:0.917:0.007:0.5296
+11	860687	exm805350	C	T	.	.	.	GT:LRR:BAF:IA:IB:GC	0/0:-0.1509:0:1.172:0.059:0.3777
+11	860726	exm805354	T	C	.	.	.	GT:LRR:BAF:IA:IB:GC	0/0:-0.0224:0.0000:2.255:0.138:0.3747
+11	860970	exm805360	A	G	.	.	.	GT:LRR:BAF:IA:IB:GC	0/0:-0.1069:0.0000:1.859:0.070:0.7352
+11	871110	exm805378	G	C	.	.	.	GT:LRR:BAF:IA:IB:GC	0/0:0.0701:0.0000:1.373:0.002:0.4607
+11	871746	exm805386	G	A	.	.	.	GT:LRR:BAF:IA:IB:GC	0/0:-0.1743:0.00239999999999996:0.597:0.017:0.5312
+11	875350	exm805392	G	A	.	.	.	GT:LRR:BAF:IA:IB:GC	0/0:0.1814:0:0.924:0.018:0.5191
+11	888899	exm805400	C	T	.	.	.	GT:LRR:BAF:IA:IB:GC	0/0:0.0585:0.00470000000000004:1.182:0.028:0.5116
+11	888916	exm805401	T	C	.	.	.	GT:LRR:BAF:IA:IB:GC	0/0:0.1408:0.0000:1.480:0.041:0.4128
+11	894838	rs12249828	C	T	.	.	.	GT:LRR:BAF:IA:IB:GC	1/0:0.2119:0.4839:1.145:1.256:0.8432
+11	903950	rs11253471	A	G	.	.	.	GT:LRR:BAF:IA:IB:GC	0/1:-0.0047:0.4747:0.562:0.549:0.9470
+11	909757	exm805413	G	A	.	.	.	GT:LRR:BAF:IA:IB:GC	0/0:0.0614:0:1.538:0.027:0.4097
+11	909766	exm805415	G	A	.	.	.	GT:LRR:BAF:IA:IB:GC	0/0:0.0578:0:1.502:0.023:0.4128
+11	910074	exm805420	C	T	.	.	.	GT:LRR:BAF:IA:IB:GC	0/0:-0.0503:0.0071:1.001:0.057:0.5002
+11	910081	exm805421	C	T	.	.	.	GT:LRR:BAF:IA:IB:GC	0/0:-0.1352:0.002:1.125:0.033:0.4254
+11	927331	rs11253489	G	A	.	.	.	GT:LRR:BAF:IA:IB:GC	1/0:0.0370:0.5325:0.976:1.435:0.7729
+11	931618	exm805430	G	A	.	.	.	GT:LRR:BAF:IA:IB:GC	0/0:0.0474:0:1.222:0.009:0.4871
+11	931631	exm805431	C	T	.	.	.	GT:LRR:BAF:IA:IB:GC	0/0:-0.0819:0.00390000000000001:0.827:0.023:0.5296
diff -r 94a8d3db9b3f -r 693d81b3e113 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 13:05:06 2019 -0400
@@ -0,0 +1,188 @@
+##fileformat=VCFv4.2
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=BAF,Number=1,Type=Float,Description="B Allele Frequency">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	test
+10	135656	rs10904561	T	G	.	.	.	GT:BAF	0/1:0.5176
+10	135708	rs7917054	G	A	.	.	.	GT:BAF	1/0:0.501
+10	178434	rs7089889	T	G	.	.	.	GT:BAF	0/1:0.4833
+10	188805	rs12146291	A	G	.	.	.	GT:BAF	0/1:0.4715
+10	203471	rs10903451	A	G	.	.	.	GT:BAF	0/0:0.0000
+10	252693	rs2379078	T	C	.	.	.	GT:BAF	0/0:0.0068
+10	273344	rs2448378	A	C	.	.	.	GT:BAF	0/0:0.0000
+10	279248	rs2496278	C	A	.	.	.	GT:BAF	1/0:0.6268
+10	291134	rs10508201	T	C	.	.	.	GT:BAF	0/1:0.4723
+10	293358	exm2249181	A	C	.	.	.	GT:BAF	0/0:0.0044
+10	313504	rs4880568	C	T	.	.	.	GT:BAF	1/1:0.9803
+10	317501	rs2018975	C	T	.	.	.	GT:BAF	0/0:0
+10	323283	rs3740304	A	G	.	.	.	GT:BAF	0/1:0.5588
+10	326894	rs3125027	T	C	.	.	.	GT:BAF	0/0:0.0005
+10	327162	exm805022	C	T	.	.	.	GT:BAF	0/0:0
+10	329493	rs3815985	C	A	.	.	.	GT:BAF	1/0:0.5187
+10	338553	rs3125031	C	T	.	.	.	GT:BAF	1/0:0.4696
+10	354301	rs35198327	C	T	.	.	.	GT:BAF	1/0:0.4929
+10	375475	variant.11341	C	T	.	.	.	GT:BAF	0/0:0.000199999999999978
+10	377161	rs7070654	C	T	.	.	.	GT:BAF	0/0:0
+10	387060	rs7904155	G	A	.	.	.	GT:BAF	1/1:0.9945
+10	390962	exm805090	G	A	.	.	.	GT:BAF	0/0:9.9999999999989e-05
+10	390983	exm805091	G	A	.	.	.	GT:BAF	0/0:0
+10	394615	exm805105	G	A	.	.	.	GT:BAF	0/0:0
+10	402390	exm805131	G	C	.	.	.	GT:BAF	0/0:0.0000
+10	403792	exm805136	G	C	.	.	.	GT:BAF	0/0:0.0000
+10	410501	exm805166	C	T	.	.	.	GT:BAF	0/0:0
+10	413010	rs9787422	C	T	.	.	.	GT:BAF	1/0:0.5334
+10	423555	rs12245012	G	A	.	.	.	GT:BAF	0/0:0.00149999999999995
+10	423671	rs10904067	C	T	.	.	.	GT:BAF	1/0:0.5566
+10	431161	exm2271240	C	T	.	.	.	GT:BAF	1/0:0.4838
+10	435971	exm2249233	T	C	.	.	.	GT:BAF	0/0:0.0000
+10	435990	exm805214	G	A	.	.	.	GT:BAF	0/0:0
+10	453567	rs4881254	C	T	.	.	.	GT:BAF	1/0:0.5079
+10	462885	rs10904173	G	A	.	.	.	GT:BAF	1/0:0.4819
+10	465046	exm805254	G	A	.	.	.	GT:BAF	0/0:0
+10	468599	rs12415961	T	C	.	.	.	GT:BAF	0/1:0.5021
+10	486935	exm805280	G	C	.	.	.	GT:BAF	0/0:0.0186
+10	487973	rs4881313	T	C	.	.	.	GT:BAF	0/1:0.5628
+10	521431	exm2271370	C	T	.	.	.	GT:BAF	1/1:0.9952
+10	521723	rs4881336	C	T	.	.	.	GT:BAF	1/1:1
+10	547567	rs816599	A	G	.	.	.	GT:BAF	1/1:1.0000
+10	554186	rs12251997	C	T	.	.	.	GT:BAF	0/0:0.00309999999999999
+10	556129	rs10466270	A	G	.	.	.	GT:BAF	0/1:0.5142
+10	566379	rs11252926	C	T	.	.	.	GT:BAF	1/0:0.5024
+10	588406	rs10904450	A	G	.	.	.	GT:BAF	0/0:0.0006
+10	592283	rs816646	G	A	.	.	.	GT:BAF	1/0:0.5006
+10	601089	rs816650	C	T	.	.	.	GT:BAF	0/0:0
+10	615782	rs17221309	G	A	.	.	.	GT:BAF	0/0:0.00319999999999998
+10	635857	rs7069611	T	C	.	.	.	GT:BAF	0/0:0.0013
+10	669358	rs7898821	G	A	.	.	.	GT:BAF	0/0:0
+10	673037	rs816563	C	T	.	.	.	GT:BAF	1/1:0.9065
+10	680428	rs2124585	G	A	.	.	.	GT:BAF	1/0:0.5212
+10	712617	rs17136372	A	C	.	.	.	GT:BAF	1/1:0.9992
+10	738630	rs1750792	C	T	.	.	.	GT:BAF	0/0:0
+10	749238	rs553326	G	T	.	.	.	GT:BAF	0/0:0.00229999999999997
+10	754033	rs2265090	C	A	.	.	.	GT:BAF	0/0:0
+10	757222	rs10904546	A	G	.	.	.	GT:BAF	0/0:0.0000
+10	766105	rs7906313	T	C	.	.	.	GT:BAF	0/0:0.0116
+10	776027	rs11253377	C	T	.	.	.	GT:BAF	1/1:0.9964
+10	787896	rs1769242	T	C	.	.	.	GT:BAF	0/0:0.0000
+10	800213	rs2254501	G	A	.	.	.	GT:BAF	1/1:0.9918
+10	802445	rs1769215	C	T	.	.	.	GT:BAF	0/0:0.00370000000000004
+10	803721	rs2790381	C	T	.	.	.	GT:BAF	1/1:0.9798
+10	811876	rs12414585	G	A	.	.	.	GT:BAF	1/0:0.516
+10	813426	rs11253424	C	T	.	.	.	GT:BAF	0/0:0
+10	815149	rs7084027	A	G	.	.	.	GT:BAF	1/1:0.9944
+10	820868	rs10752019	C	T	.	.	.	GT:BAF	0/0:0.0118
+10	833528	exm2271241	T	G	.	.	.	GT:BAF	0/1:0.4896
+10	834736	rs4881530	G	A	.	.	.	GT:BAF	0/0:0.00249999999999995
+10	836115	rs11253444	A	G	.	.	.	GT:BAF	0/1:0.5199
+10	838179	rs1536337	T	C	.	.	.	GT:BAF	0/0:0.0000
+10	858022	rs9124	C	T	.	.	.	GT:BAF	0/0:0
+10	858924	exm805329	G	A	.	.	.	GT:BAF	0/0:0
+10	859047	exm805338	C	A	.	.	.	GT:BAF	0/0:0
+10	860687	exm805350	C	T	.	.	.	GT:BAF	0/0:0
+10	860726	exm805354	T	C	.	.	.	GT:BAF	0/0:0.0000
+10	860970	exm805360	A	G	.	.	.	GT:BAF	0/0:0.0000
+10	871110	exm805378	G	C	.	.	.	GT:BAF	0/0:0.0000
+10	871746	exm805386	G	A	.	.	.	GT:BAF	0/0:0.00239999999999996
+10	875350	exm805392	G	A	.	.	.	GT:BAF	0/0:0
+10	888899	exm805400	C	T	.	.	.	GT:BAF	0/0:0.00470000000000004
+10	888916	exm805401	T	C	.	.	.	GT:BAF	0/0:0.0000
+10	894838	rs12249828	C	T	.	.	.	GT:BAF	1/0:0.4839
+10	903950	rs11253471	A	G	.	.	.	GT:BAF	0/1:0.4747
+10	909757	exm805413	G	A	.	.	.	GT:BAF	0/0:0
+10	909766	exm805415	G	A	.	.	.	GT:BAF	0/0:0
+10	910074	exm805420	C	T	.	.	.	GT:BAF	0/0:0.0071
+10	910081	exm805421	C	T	.	.	.	GT:BAF	0/0:0.002
+10	927331	rs11253489	G	A	.	.	.	GT:BAF	1/0:0.5325
+10	931618	exm805430	G	A	.	.	.	GT:BAF	0/0:0
+10	931631	exm805431	C	T	.	.	.	GT:BAF	0/0:0.00390000000000001
+11	135656	rs10904561	T	G	.	.	.	GT:BAF	0/1:0.5176
+11	135708	rs7917054	G	A	.	.	.	GT:BAF	1/0:0.501
+11	178434	rs7089889	T	G	.	.	.	GT:BAF	0/1:0.4833
+11	188805	rs12146291	A	G	.	.	.	GT:BAF	0/1:0.4715
+11	203471	rs10903451	A	G	.	.	.	GT:BAF	0/0:0.0000
+11	252693	rs2379078	T	C	.	.	.	GT:BAF	0/0:0.0068
+11	273344	rs2448378	A	C	.	.	.	GT:BAF	0/0:0.0000
+11	279248	rs2496278	C	A	.	.	.	GT:BAF	1/0:0.6268
+11	291134	rs10508201	T	C	.	.	.	GT:BAF	0/1:0.4723
+11	293358	exm2249181	A	C	.	.	.	GT:BAF	0/0:0.0044
+11	313504	rs4880568	C	T	.	.	.	GT:BAF	1/1:0.9803
+11	317501	rs2018975	C	T	.	.	.	GT:BAF	0/0:0
+11	323283	rs3740304	A	G	.	.	.	GT:BAF	0/1:0.5588
+11	326894	rs3125027	T	C	.	.	.	GT:BAF	0/0:0.0005
+11	327162	exm805022	C	T	.	.	.	GT:BAF	0/0:0
+11	329493	rs3815985	C	A	.	.	.	GT:BAF	1/0:0.5187
+11	338553	rs3125031	C	T	.	.	.	GT:BAF	1/0:0.4696
+11	354301	rs35198327	C	T	.	.	.	GT:BAF	1/0:0.4929
+11	375475	variant.11341	C	T	.	.	.	GT:BAF	0/0:0.000199999999999978
+11	377161	rs7070654	C	T	.	.	.	GT:BAF	0/0:0
+11	387060	rs7904155	G	A	.	.	.	GT:BAF	1/1:0.9945
+11	390962	exm805090	G	A	.	.	.	GT:BAF	0/0:9.9999999999989e-05
+11	390983	exm805091	G	A	.	.	.	GT:BAF	0/0:0
+11	394615	exm805105	G	A	.	.	.	GT:BAF	0/0:0
+11	402390	exm805131	G	C	.	.	.	GT:BAF	0/0:0.0000
+11	403792	exm805136	G	C	.	.	.	GT:BAF	0/0:0.0000
+11	410501	exm805166	C	T	.	.	.	GT:BAF	0/0:0
+11	413010	rs9787422	C	T	.	.	.	GT:BAF	1/0:0.5334
+11	423555	rs12245012	G	A	.	.	.	GT:BAF	0/0:0.00149999999999995
+11	423671	rs10904067	C	T	.	.	.	GT:BAF	1/0:0.5566
+11	431161	exm2271240	C	T	.	.	.	GT:BAF	1/0:0.4838
+11	435971	exm2249233	T	C	.	.	.	GT:BAF	0/0:0.0000
+11	435990	exm805214	G	A	.	.	.	GT:BAF	0/0:0
+11	453567	rs4881254	C	T	.	.	.	GT:BAF	1/0:0.5079
+11	462885	rs10904173	G	A	.	.	.	GT:BAF	1/0:0.4819
+11	465046	exm805254	G	A	.	.	.	GT:BAF	0/0:0
+11	468599	rs12415961	T	C	.	.	.	GT:BAF	0/1:0.5021
+11	486935	exm805280	G	C	.	.	.	GT:BAF	0/0:0.0186
+11	487973	rs4881313	T	C	.	.	.	GT:BAF	0/1:0.5628
+11	521431	exm2271370	C	T	.	.	.	GT:BAF	1/1:0.9952
+11	521723	rs4881336	C	T	.	.	.	GT:BAF	1/1:1
+11	547567	rs816599	A	G	.	.	.	GT:BAF	1/1:1.0000
+11	554186	rs12251997	C	T	.	.	.	GT:BAF	0/0:0.00309999999999999
+11	556129	rs10466270	A	G	.	.	.	GT:BAF	0/1:0.5142
+11	566379	rs11252926	C	T	.	.	.	GT:BAF	1/0:0.5024
+11	588406	rs10904450	A	G	.	.	.	GT:BAF	0/0:0.0006
+11	592283	rs816646	G	A	.	.	.	GT:BAF	1/0:0.5006
+11	601089	rs816650	C	T	.	.	.	GT:BAF	0/0:0
+11	615782	rs17221309	G	A	.	.	.	GT:BAF	0/0:0.00319999999999998
+11	635857	rs7069611	T	C	.	.	.	GT:BAF	0/0:0.0013
+11	669358	rs7898821	G	A	.	.	.	GT:BAF	0/0:0
+11	673037	rs816563	C	T	.	.	.	GT:BAF	1/1:0.9065
+11	680428	rs2124585	G	A	.	.	.	GT:BAF	1/0:0.5212
+11	712617	rs17136372	A	C	.	.	.	GT:BAF	1/1:0.9992
+11	738630	rs1750792	C	T	.	.	.	GT:BAF	0/0:0
+11	749238	rs553326	G	T	.	.	.	GT:BAF	0/0:0.00229999999999997
+11	754033	rs2265090	C	A	.	.	.	GT:BAF	0/0:0
+11	757222	rs10904546	A	G	.	.	.	GT:BAF	0/0:0.0000
+11	766105	rs7906313	T	C	.	.	.	GT:BAF	0/0:0.0116
+11	776027	rs11253377	C	T	.	.	.	GT:BAF	1/1:0.9964
+11	787896	rs1769242	T	C	.	.	.	GT:BAF	0/0:0.0000
+11	800213	rs2254501	G	A	.	.	.	GT:BAF	1/1:0.9918
+11	802445	rs1769215	C	T	.	.	.	GT:BAF	0/0:0.00370000000000004
+11	803721	rs2790381	C	T	.	.	.	GT:BAF	1/1:0.9798
+11	811876	rs12414585	G	A	.	.	.	GT:BAF	1/0:0.516
+11	813426	rs11253424	C	T	.	.	.	GT:BAF	0/0:0
+11	815149	rs7084027	A	G	.	.	.	GT:BAF	1/1:0.9944
+11	820868	rs10752019	C	T	.	.	.	GT:BAF	0/0:0.0118
+11	833528	exm2271241	T	G	.	.	.	GT:BAF	0/1:0.4896
+11	834736	rs4881530	G	A	.	.	.	GT:BAF	0/0:0.00249999999999995
+11	836115	rs11253444	A	G	.	.	.	GT:BAF	0/1:0.5199
+11	838179	rs1536337	T	C	.	.	.	GT:BAF	0/0:0.0000
+11	858022	rs9124	C	T	.	.	.	GT:BAF	0/0:0
+11	858924	exm805329	G	A	.	.	.	GT:BAF	0/0:0
+11	859047	exm805338	C	A	.	.	.	GT:BAF	0/0:0
+11	860687	exm805350	C	T	.	.	.	GT:BAF	0/0:0
+11	860726	exm805354	T	C	.	.	.	GT:BAF	0/0:0.0000
+11	860970	exm805360	A	G	.	.	.	GT:BAF	0/0:0.0000
+11	871110	exm805378	G	C	.	.	.	GT:BAF	0/0:0.0000
+11	871746	exm805386	G	A	.	.	.	GT:BAF	0/0:0.00239999999999996
+11	875350	exm805392	G	A	.	.	.	GT:BAF	0/0:0
+11	888899	exm805400	C	T	.	.	.	GT:BAF	0/0:0.00470000000000004
+11	888916	exm805401	T	C	.	.	.	GT:BAF	0/0:0.0000
+11	894838	rs12249828	C	T	.	.	.	GT:BAF	1/0:0.4839
+11	903950	rs11253471	A	G	.	.	.	GT:BAF	0/1:0.4747
+11	909757	exm805413	G	A	.	.	.	GT:BAF	0/0:0
+11	909766	exm805415	G	A	.	.	.	GT:BAF	0/0:0
+11	910074	exm805420	C	T	.	.	.	GT:BAF	0/0:0.0071
+11	910081	exm805421	C	T	.	.	.	GT:BAF	0/0:0.002
+11	927331	rs11253489	G	A	.	.	.	GT:BAF	1/0:0.5325
+11	931618	exm805430	G	A	.	.	.	GT:BAF	0/0:0
+11	931631	exm805431	C	T	.	.	.	GT:BAF	0/0:0.00390000000000001
diff -r 94a8d3db9b3f -r 693d81b3e113 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 13:05:06 2019 -0400
@@ -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
diff -r 94a8d3db9b3f -r 693d81b3e113 test-data/cnv_summary.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cnv_summary.tab	Wed Jun 05 13:05:06 2019 -0400
@@ -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
diff -r 94a8d3db9b3f -r 693d81b3e113 test-data/color_chrs.dat
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/color_chrs.dat	Wed Jun 05 13:05:06 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
diff -r 94a8d3db9b3f -r 693d81b3e113 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 13:05:06 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
diff -r 94a8d3db9b3f -r 693d81b3e113 test-data/fasta_indexes.loc
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fasta_indexes.loc	Wed Jun 05 13:05:06 2019 -0400
@@ -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
diff -r 94a8d3db9b3f -r 693d81b3e113 test-data/mpileup.ref.fa.fai
--- a/test-data/mpileup.ref.fa.fai	Thu Feb 21 16:00:10 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-17	4200	14	60	61
diff -r 94a8d3db9b3f -r 693d81b3e113 test-data/plugin_frameshifts.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/plugin_frameshifts.bed	Wed Jun 05 13:05:06 2019 -0400
@@ -0,0 +1,1 @@
+1	3106150	3106160
diff -r 94a8d3db9b3f -r 693d81b3e113 test-data/stats.a.vcf
--- a/test-data/stats.a.vcf	Thu Feb 21 16:00:10 2019 -0500
+++ b/test-data/stats.a.vcf	Wed Jun 05 13:05:06 2019 -0400
@@ -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
diff -r 94a8d3db9b3f -r 693d81b3e113 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 13:05:06 2019 -0400
@@ -0,0 +1,14 @@
+>1
+CACGTNACGGCTGAAGTCCAAGGTAC
+CGTATCGAGTTCACAGTCGATAGCTC
+GATCGATAGCATCGCTAGCNNNACTA
+CGATCGATCGCTCTCCGTAACACTCA
+AAAACGATCGATCGACTGCTCTTTAG
+CGATGACTTTAGGGGAAAAA
+>2
+CGCTCAGCCGTACAGCCGAGCAGGAC
+ACGCTATTTTAGATCGACTGGCTNNG
+CGCTAGCTACGCTTTAGCACGAGAA
+>Y
+NNNGCATACGTGTCCATCACGATGAT
+AGCGATGATCGATC
diff -r 94a8d3db9b3f -r 693d81b3e113 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 13:05:06 2019 -0400
@@ -0,0 +1,3 @@
+1	150	3	26	27
+2	77	162	26	27
+Y	40	245	26	27
diff -r 94a8d3db9b3f -r 693d81b3e113 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 13:05:06 2019 -0400
@@ -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
diff -r 94a8d3db9b3f -r 693d81b3e113 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 13:05:06 2019 -0400
@@ -0,0 +1,2 @@
+1:2-501	500	9	60	61
+2	501	521	60	61
diff -r 94a8d3db9b3f -r 693d81b3e113 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 13:05:06 2019 -0400
@@ -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
+
diff -r 94a8d3db9b3f -r 693d81b3e113 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 13:05:06 2019 -0400
@@ -0,0 +1,3 @@
+1	600	3	60	61
+2	600	616	60	61
+3	600	1229	60	61
diff -r 94a8d3db9b3f -r 693d81b3e113 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 13:05:06 2019 -0400
@@ -0,0 +1,9 @@
+>22
+NNNNNNNNCCTTGGCCAAGTCACTTCCTCCTTCAGGAACATTGCAGTGGGCCTAAGTGCC
+TCCTCTCGGGACTGGTATGGGGACGGTCATGCAATCTGGACAACATTCACCTTTAAAAGT
+TTATTGATCTTTTGTGACATGCACGTGGGTTCCCAGTAGCAAGAAACTAAAGGGTCGCAG
+GCCGGTTTCTGCTAATTTCTTTAATTCCAAGACAGTCTCAAATATTTTCTTATTAACTTC
+CTGGAGGGAGGCTTATCATTCTCTCTTTTGGATGATTCTAAGTACCAGCTAAAATACAGC
+TATCATTCATTTTCCTTGATTTGGGAGCCTAATTTCTTTAATTTAGTATGCAAGAAAACC
+AATTTGGAAATATCAACTGTTTTGGAAACCTTAGACCTAGGTCATCCTTAGTAAGATCTT
+CCCATTTATATAAATACTTGCAAGTAGTAGTGCCATAATT
diff -r 94a8d3db9b3f -r 693d81b3e113 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 13:05:06 2019 -0400
@@ -0,0 +1,1 @@
+22	460	4	60	61
diff -r 94a8d3db9b3f -r 693d81b3e113 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 13:05:06 2019 -0400
@@ -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
diff -r 94a8d3db9b3f -r 693d81b3e113 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 13:05:06 2019 -0400
@@ -0,0 +1,1 @@
+17	4200	14	60	61
diff -r 94a8d3db9b3f -r 693d81b3e113 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 13:05:06 2019 -0400
@@ -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
diff -r 94a8d3db9b3f -r 693d81b3e113 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 13:05:06 2019 -0400
@@ -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
diff -r 94a8d3db9b3f -r 693d81b3e113 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 13:05:06 2019 -0400
@@ -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>