# HG changeset patch
# User iuc
# Date 1492119943 14400
# Node ID a15210afaf1d248a434584277388388eb4fa8655
# Parent  c6071203aaa081cb395b37075f19c971da542e8e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e

diff -r c6071203aaa0 -r a15210afaf1d bcftools_plugin_impute_info.xml
--- a/bcftools_plugin_impute_info.xml	Sat Mar 11 18:02:08 2017 -0500
+++ b/bcftools_plugin_impute_info.xml	Thu Apr 13 17:45:43 2017 -0400
@@ -13,6 +13,7 @@
 @PREPARE_INPUT_FILE@
 #set $section = $sec_restrict
 @PREPARE_TARGETS_FILE@
+@PREPARE_REGIONS_FILE@
 
 bcftools plugin @EXECUTABLE@
 
@@ -28,7 +29,7 @@
 
 ## Primary Input/Outputs
 @INPUT_FILE@
-> "$output_file"
+> '$output_file'
 ]]>
     </command>
     <inputs>
diff -r c6071203aaa0 -r a15210afaf1d macros.xml
--- a/macros.xml	Sat Mar 11 18:02:08 2017 -0500
+++ b/macros.xml	Thu Apr 13 17:45:43 2017 -0400
@@ -1,5 +1,5 @@
 <macros>
-  <token name="@VERSION@">1.3.1</token>
+  <token name="@VERSION@">1.4.0</token>
   <xml name="stdio">
     <stdio>
       <exit_code range="1:" />
@@ -10,12 +10,14 @@
   </xml>
   <xml name="requirements">
     <requirements>
-      <requirement type="package" version="1.3.1">bcftools</requirement>
-      <!-- conda dependency -->
-      <requirement type="package" version="1.3.2">htslib</requirement>
+      <requirement type="package" version="1.4">bcftools</requirement>
+      <requirement type="package" version="1.4">htslib</requirement>
       <yield />
     </requirements>
   </xml>
+  <xml name="samtools_requirement">
+      <requirement type="package" version="1.3.1">samtools</requirement>
+  </xml>
   <xml name="version_command">
     <version_command>bcftools 2&gt;&amp;1 | grep 'Version:'</version_command>
   </xml>
@@ -245,7 +247,7 @@
   </xml>
   <token name="@OUTPUT_TYPE@">
 #if str($output_type) != "__none__":
-  --output-type "${output_type}"
+  --output-type '${output_type}'
 #end if
   </token>
 
@@ -279,14 +281,30 @@
         </when>
     </conditional>
   </xml>
+  <token name="@PREPARE_REGIONS_FILE@">
+<![CDATA[
+#set $regions_path = None
+#if 'regions' in $section
+  #if $section.regions.regions_src == 'regions_file' and $section.regions.regions_file:
+    #if $section.regions.regions_file.ext.startswith('bed'):
+      #set $regions_path = 'regions_file.bed'
+      ln -s '$section.regions.regions_file' $regions_path &&
+    #end if
+  #end if
+#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 $section.regions.regions_file:
-  --regions-file '$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/>
@@ -356,11 +374,11 @@
 
   <xml name="macro_samples">
       <param name="samples" type="text" value="" label="Samples" optional="true"
-             help="(-s) comma separated list of samples to annotate (or exclude with &quot;^&quot; prefix)">
+             help="(-s) comma separated list of samples to annotate (or exclude)">
           <validator type="regex" message="">^(\w+(,\w+)*)?$</validator>
       </param>
       <param name="invert_samples" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples"
-             help="inverts the query/filtering applied by Samples" />
+             help="inverts the query/filtering applied by Samples (adds &quot;^&quot; prefix to exclude)" />
       <param name="samples_file" type="data" format="tabular" label="Samples File" optional="True"
              help="(-S) file of samples to include" />
       <param name="invert_samples_file" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples File"
diff -r c6071203aaa0 -r a15210afaf1d test-data/csq.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/csq.fa	Thu Apr 13 17:45:43 2017 -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 c6071203aaa0 -r a15210afaf1d test-data/csq.gff3
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/csq.gff3	Thu Apr 13 17:45:43 2017 -0400
@@ -0,0 +1,40 @@
+##gff-version   3
+#! This file shows which fields are used and required by `bcftools +csq`. It is a trimmed version 
+#! of the GFF3 format, see an example of the full format here
+#!      ftp://ftp.ensembl.org/pub/grch37/release-84/gff3/homo_sapiens/
+#!
+###
+1	.	gene	90	200	.	+	.	ID=gene:ENSG00000000001;Name=XYZ;biotype=protein_coding
+1	.	transcript	90	200	.	+	.	ID=transcript:ENST00000000001;Parent=gene:ENSG00000000001;biotype=protein_coding
+1	.	exon	90	110	.	+	.	Parent=transcript:ENST00000000001
+1	.	five_prime_UTR	90	98	.	+	.	Parent=transcript:ENST00000000001
+1	.	CDS	99	110	.	+	1	Parent=transcript:ENST00000000001
+1	.	exon	120	130	.	+	.	Parent=transcript:ENST00000000001
+1	.	CDS	120	130	.	+	1	Parent=transcript:ENST00000000001
+1	.	exon	140	150	.	+	.	Parent=transcript:ENST00000000001
+1	.	CDS	140	150	.	+	2	Parent=transcript:ENST00000000001
+1	.	exon	160	200	.	+	.	Parent=transcript:ENST00000000001
+1	.	CDS	160	171	.	+	0	Parent=transcript:ENST00000000001
+1	.	three_prime_UTR	172	200	.	+	.	Parent=transcript:ENST00000000001
+2	.	gene	80	200	.	-	.	ID=gene:ENSG00000000002;Name=ABC;biotype=protein_coding
+2	.	transcript	80	200	.	-	.	ID=transcript:ENST00000000002;Parent=gene:ENSG00000000002;biotype=protein_coding
+2	.	exon	80	110	.	-	.	Parent=transcript:ENST00000000002
+2	.	three_prime_UTR	80	98	.	-	.	Parent=transcript:ENST00000000002
+2	.	CDS	99	110	.	-	0	Parent=transcript:ENST00000000002
+2	.	exon	120	130	.	-	.	Parent=transcript:ENST00000000002
+2	.	CDS	120	130	.	-	2	Parent=transcript:ENST00000000002
+2	.	exon	140	150	.	-	.	Parent=transcript:ENST00000000002
+2	.	CDS	140	150	.	-	1	Parent=transcript:ENST00000000002
+2	.	exon	160	200	.	-	.	Parent=transcript:ENST00000000002
+2	.	CDS	160	171	.	-	1	Parent=transcript:ENST00000000002
+2	.	five_prime_UTR	172	200	.	-	.	Parent=transcript:ENST00000000002
+3	.	lincRNA_gene	20	50	.	-	.	ID=gene:ENSG00000000004;Name=mir-007;biotype=lincRNA
+3	.	lincRNA	20	50	.	-	.	ID=transcript:ENSG00000000004;Parent=gene:ENSG00000000004;biotype=lincRNA
+3	.	gene	100	200	.	-	.	ID=gene:ENSG00000000003;Name=QWRTY;biotype=protein_coding
+3	.	transcript	100	200	.	-	.	ID=transcript:ENST00000000003;Parent=gene:ENSG00000000003;biotype=protein_coding
+3	.	exon	100	110	.	-	.	Parent=transcript:ENST00000000003
+3	.	three_prime_UTR	100	105	.	-	.	Parent=transcript:ENST00000000003
+3	.	CDS	106	110	.	-	0	Parent=transcript:ENST00000000003
+3	.	exon	160	200	.	-	.	Parent=transcript:ENST00000000003
+3	.	CDS	160	171	.	-	0	Parent=transcript:ENST00000000003
+3	.	five_prime_UTR	172	200	.	-	.	Parent=transcript:ENST00000000003
diff -r c6071203aaa0 -r a15210afaf1d test-data/csq.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/csq.vcf	Thu Apr 13 17:45:43 2017 -0400
@@ -0,0 +1,40 @@
+##fileformat=VCFv4.2
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##INFO=<ID=EXP,Number=1,Type=String,Description="Expected consequence">
+##contig=<ID=1,length=2147483647>
+##contig=<ID=2,length=2147483647>
+##contig=<ID=3,length=2147483647>
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SmplAAA	SmplBBB
+1	90	.	C	T	.	.	EXP=5_prime_utr|XYZ|ENST00000000001|protein_coding	GT	1|0	1|1
+1	102	.	C	T	1	.	EXP=synonymous|XYZ|ENST00000000001|protein_coding|+|1Y|102C>T	GT	1|0	1|0
+1	103	.	G	A	1	.	EXP=missense|XYZ|ENST00000000001|protein_coding|+|2V>2I|103G>A	GT	1|0	0|0
+1	103	.	G	C	1	.	EXP=missense|XYZ|ENST00000000001|protein_coding|+|2V>2L|103G>C	GT	0|0	1|0
+1	107	.	G	A	1	.	EXP=missense|XYZ|ENST00000000001|protein_coding|+|3R>3Q|107G>A+108T>A	GT	1|0	1|0
+1	108	.	T	A	1	.	EXP=splice_region|XYZ|ENST00000000001|protein_coding,@107	GT	1|0	1|0
+1	121	.	ACG	A	.	.	EXP=inframe_deletion|XYZ|ENST00000000001|protein_coding|+|5TY>5I|121ACG>A+124TA>T,splice_region|XYZ|ENST00000000001|protein_coding	GT	1|0	1|0
+1	124	.	TA	T	.	.	EXP=@121	GT	1|0	1|0
+1	128	.	T	C	1	.	EXP=missense|XYZ|ENST00000000001|protein_coding|+|7V>6A|128T>C+129A>C,splice_region|XYZ|ENST00000000001|protein_coding	GT	1|0	0/0
+1	129	.	A	C	1	.	EXP=splice_region|XYZ|ENST00000000001|protein_coding,@128	GT	1|0	0/0
+1	140	.	TA	AACG	.	.	EXP=inframe_insertion|XYZ|ENST00000000001|protein_coding|+|8LR>7QRR|140TA>AACG+142C>CC,splice_region|XYZ|ENST00000000001|protein_coding	GT	1|0	0|0
+1	142	.	C	CC	.	.	EXP=splice_region|XYZ|ENST00000000001|protein_coding,@140	GT	1|0	0|0
+1	145	.	AC	TA	.	.	EXP=stop_gained|XYZ|ENST00000000001|protein_coding|+|10T>10*|145AC>TA	GT	1|0	0|0
+1	160	.	TA	T	.	.	EXP=*frameshift|XYZ|ENST00000000001|protein_coding|+|12YVRT>12SYV|160TA>T,splice_region|XYZ|ENST00000000001|protein_coding	GT	1|0	0|0
+1	190	.	C	T	.	.	EXP=3_prime_utr|XYZ|ENST00000000001|protein_coding	GT	1|0	0|0
+2	97	.	A	C	.	.	EXP=3_prime_utr|ABC|ENST00000000002|protein_coding	GT	1|0	0|0
+2	105	.	AC	A	.	.	EXP=@121	GT	1|0	0|0
+2	121	.	AC	A	.	.	EXP=frameshift|ABC|ENST00000000002|protein_coding|-|11VVRTY>11*|105AC>A+121AC>A,splice_region|ABC|ENST00000000002|protein_coding	GT	1|0	0|0
+2	126	.	C	CTT	.	.	EXP=@127	GT	1|0	0|0
+2	127	.	G	GG	.	.	EXP=inframe_insertion|ABC|ENST00000000002|protein_coding|-|9T>8TK|126C>CTT+127G>GG	GT	1|0	0|0
+2	144	.	TAC	T	.	.	EXP=@148	GT	1|0	0|0
+2	148	.	TA	T	.	.	EXP=inframe_deletion|ABC|ENST00000000002|protein_coding|-|5YV>5T|144TAC>T+148TA>T,splice_region|ABC|ENST00000000002|protein_coding	GT	1|0	0|0
+2	164	.	T	G	.	.	EXP=missense|ABC|ENST00000000002|protein_coding|-|3T>3P|164T>G	GT	1|0	0|0
+2	165	.	A	C	.	.	EXP=synonymous|ABC|ENST00000000002|protein_coding|-|2R|165A>C	GT	1|0	0|0
+2	169	.	A	G	.	.	EXP=@170	GT	1|0	0|0
+2	170	.	C	T	.	.	EXP=missense|ABC|ENST00000000002|protein_coding|-|1V>1T|169A>G+170C>T	GT	1|0	0|0
+2	199	.	G	T	.	.	EXP=5_prime_utr|ABC|ENST00000000002|protein_coding	GT	1|0	0|0
+3	20	.	T	A	.	.	EXP=non_coding|mir-007||lincRNA	GT	1|0	0|0
+3	109	.	ACGTACGT	A	1	.	EXP=splice_acceptor|QWRTY|ENST00000000003|protein_coding	GT	1|0	0|0
+3	113	.	A	T	.	.	EXP=splice_region|QWRTY|ENST00000000003|protein_coding	GT	1|0	0|0
+3	120	.	T	A	.	.	EXP=intron|QWRTY||protein_coding	GT	1|0	0|0
+3	152	.	T	A	.	.	EXP=splice_region|QWRTY|ENST00000000003|protein_coding	GT	1|0	0|0
+3	159	.	G	A	.	.	EXP=splice_donor|QWRTY|ENST00000000003|protein_coding	GT	1|0	0|0
diff -r c6071203aaa0 -r a15210afaf1d test-data/mpileup.1.bam
Binary file test-data/mpileup.1.bam has changed
diff -r c6071203aaa0 -r a15210afaf1d test-data/mpileup.1.bam.bai
Binary file test-data/mpileup.1.bam.bai has changed
diff -r c6071203aaa0 -r a15210afaf1d test-data/mpileup.2.bam
Binary file test-data/mpileup.2.bam has changed
diff -r c6071203aaa0 -r a15210afaf1d test-data/mpileup.2.bam.bai
Binary file test-data/mpileup.2.bam.bai has changed
diff -r c6071203aaa0 -r a15210afaf1d test-data/mpileup.3.bam
Binary file test-data/mpileup.3.bam has changed
diff -r c6071203aaa0 -r a15210afaf1d test-data/mpileup.3.bam.bai
Binary file test-data/mpileup.3.bam.bai has changed
diff -r c6071203aaa0 -r a15210afaf1d test-data/mpileup.3.cram
Binary file test-data/mpileup.3.cram has changed
diff -r c6071203aaa0 -r a15210afaf1d test-data/mpileup.4.bam
Binary file test-data/mpileup.4.bam has changed
diff -r c6071203aaa0 -r a15210afaf1d test-data/mpileup.ref.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mpileup.ref.fa	Thu Apr 13 17:45:43 2017 -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 c6071203aaa0 -r a15210afaf1d test-data/mpileup.ref.fa.fai
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mpileup.ref.fa.fai	Thu Apr 13 17:45:43 2017 -0400
@@ -0,0 +1,1 @@
+17	4200	14	60	61
diff -r c6071203aaa0 -r a15210afaf1d test-data/mpileup.regions.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mpileup.regions.bed	Thu Apr 13 17:45:43 2017 -0400
@@ -0,0 +1,1 @@
+17	99	110
diff -r c6071203aaa0 -r a15210afaf1d test-data/mpileup.regions.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mpileup.regions.tab	Thu Apr 13 17:45:43 2017 -0400
@@ -0,0 +1,1 @@
+17	100	110
diff -r c6071203aaa0 -r a15210afaf1d test-data/roh.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/roh.vcf	Thu Apr 13 17:45:43 2017 -0400
@@ -0,0 +1,8895 @@
+##fileformat=VCFv4.2
+##reference=test
+##contig=<ID=1,length=249250621>
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	sample
+1	14907	.	A	G	.	PASS	.	GT	0/1
+1	14930	.	A	G	.	PASS	.	GT	0/1
+1	15211	.	T	G	.	PASS	.	GT	0/1
+1	16378	.	T	C	.	PASS	.	GT	0/1
+1	69511	.	A	G	.	PASS	.	GT	1/1
+1	129285	.	G	A	.	PASS	.	GT	0/1
+1	133129	.	G	A	.	PASS	.	GT	0/1
+1	133483	.	G	T	.	PASS	.	GT	0/1
+1	136048	.	C	T	.	PASS	.	GT	0/1
+1	753405	.	C	A	.	PASS	.	GT	1/1
+1	753425	.	T	C	.	PASS	.	GT	1/1
+1	753474	.	C	G	.	PASS	.	GT	0/1
+1	808631	.	G	A	.	PASS	.	GT	1/1
+1	808922	.	G	A	.	PASS	.	GT	0/1
+1	808928	.	C	T	.	PASS	.	GT	0/1
+1	814668	.	C	T	.	PASS	.	GT	1/1
+1	824094	.	G	A	.	PASS	.	GT	1/1
+1	866319	.	G	A	.	PASS	.	GT	1/1
+1	876499	.	A	G	.	PASS	.	GT	1/1
+1	880238	.	A	G	.	PASS	.	GT	1/1
+1	881627	.	G	A	.	PASS	.	GT	0/1
+1	881918	.	G	A	.	PASS	.	GT	0/1
+1	883625	.	A	G	.	PASS	.	GT	1/1
+1	887560	.	A	C	.	PASS	.	GT	1/1
+1	887801	.	A	G	.	PASS	.	GT	1/1
+1	888639	.	T	C	.	PASS	.	GT	1/1
+1	888659	.	T	C	.	PASS	.	GT	1/1
+1	889158	.	G	C	.	PASS	.	GT	1/1
+1	892745	.	G	A	.	PASS	.	GT	1/1
+1	894573	.	G	A	.	PASS	.	GT	1/1
+1	897325	.	G	C	.	PASS	.	GT	1/1
+1	897564	.	T	C	.	PASS	.	GT	1/1
+1	898323	.	T	C	.	PASS	.	GT	1/1
+1	900505	.	G	C	.	PASS	.	GT	0/1
+1	908823	.	G	A	.	PASS	.	GT	0/1
+1	909238	.	G	C	.	PASS	.	GT	0/1
+1	909309	.	T	C	.	PASS	.	GT	0/1
+1	909419	.	C	T	.	PASS	.	GT	0/1
+1	909555	.	A	G	.	PASS	.	GT	1/1
+1	909768	.	A	G	.	PASS	.	GT	1/1
+1	911916	.	C	T	.	PASS	.	GT	0/1
+1	914876	.	T	C	.	PASS	.	GT	1/1
+1	915227	.	A	G	.	PASS	.	GT	1/1
+1	943468	.	T	C	.	PASS	.	GT	0/1
+1	943687	.	G	C	.	PASS	.	GT	1/1
+1	948870	.	C	G	.	PASS	.	GT	1/1
+1	948921	.	T	C	.	PASS	.	GT	1/1
+1	949235	.	G	A	.	PASS	.	GT	1/1
+1	949608	.	G	A	.	PASS	.	GT	1/1
+1	949654	.	A	G	.	PASS	.	GT	1/1
+1	949925	.	C	T	.	PASS	.	GT	1/1
+1	951628	.	A	T	.	PASS	.	GT	1/1
+1	957640	.	C	T	.	PASS	.	GT	0/1
+1	957898	.	G	T	.	PASS	.	GT	0/1
+1	977203	.	G	C	.	PASS	.	GT	1/1
+1	977330	.	T	C	.	PASS	.	GT	1/1
+1	977570	.	G	A	.	PASS	.	GT	1/1
+1	979748	.	A	T	.	PASS	.	GT	0/1
+1	980460	.	G	A	.	PASS	.	GT	0/1
+1	981087	.	A	G	.	PASS	.	GT	1/1
+1	982722	.	A	G	.	PASS	.	GT	0/1
+1	982941	.	T	C	.	PASS	.	GT	1/1
+1	982994	.	T	C	.	PASS	.	GT	0/1
+1	985797	.	A	G	.	PASS	.	GT	0/1
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+1	986286	.	C	T	.	PASS	.	GT	0/1
+1	986443	.	C	T	.	PASS	.	GT	0/1
+1	987200	.	C	T	.	PASS	.	GT	0/1
+1	1019841	.	G	A	.	PASS	.	GT	0/1
+1	1021415	.	A	G	.	PASS	.	GT	0/1
+1	1102563	.	G	A	.	PASS	.	GT	0/1
+1	1119657	.	G	C	.	PASS	.	GT	1/1
+1	1158631	.	A	G	.	PASS	.	GT	1/1
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+1	1246004	.	A	G	.	PASS	.	GT	1/1
+1	1249187	.	G	A	.	PASS	.	GT	1/1
+1	1254136	.	G	A	.	PASS	.	GT	1/1
+1	1254436	.	A	G	.	PASS	.	GT	1/1
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+1	1262591	.	C	T	.	PASS	.	GT	0/1
+1	1262966	.	C	T	.	PASS	.	GT	1/1
+1	1263144	.	G	A	.	PASS	.	GT	0/1
+1	1263457	.	T	C	.	PASS	.	GT	1/1
+1	1268847	.	T	G	.	PASS	.	GT	1/1
+1	1269554	.	T	C	.	PASS	.	GT	1/1
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+1	1275291	.	G	A	.	PASS	.	GT	0/1
+1	1277533	.	T	C	.	PASS	.	GT	1/1
+1	1278237	.	T	C	.	PASS	.	GT	1/1
+1	1284490	.	G	A	.	PASS	.	GT	1/1
+1	1289911	.	G	A	.	PASS	.	GT	1/1
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+1	1296691	.	C	G	.	PASS	.	GT	0/1
+1	1296818	.	C	G	.	PASS	.	GT	1/1
+1	1308982	.	A	G	.	PASS	.	GT	1/1
+1	1314172	.	C	T	.	PASS	.	GT	1/1
+1	1314245	.	C	T	.	PASS	.	GT	1/1
+1	1387667	.	C	G	.	PASS	.	GT	1/1
+1	1395983	.	T	C	.	PASS	.	GT	1/1
+1	1469546	.	G	A	.	PASS	.	GT	0/1
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+1	1560103	.	C	T	.	PASS	.	GT	1/1
+1	1562437	.	C	G	.	PASS	.	GT	0/1
+1	1562536	.	G	A	.	PASS	.	GT	1/1
+1	1562895	.	C	T	.	PASS	.	GT	1/1
+1	1574019	.	A	G	.	PASS	.	GT	0/1
+1	1574076	.	G	A	.	PASS	.	GT	0/1
+1	1575616	.	T	C	.	PASS	.	GT	1/1
+1	1575836	.	C	G	.	PASS	.	GT	0/1
+1	1576636	.	G	A	.	PASS	.	GT	1/1
+1	1580738	.	T	A	.	PASS	.	GT	0/1
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+1	1581926	.	G	T	.	PASS	.	GT	0/1
+1	1582106	.	T	C	.	PASS	.	GT	0/1
+1	1582202	.	C	T	.	PASS	.	GT	0/1
+1	1585597	.	A	G	.	PASS	.	GT	1/1
+1	1585642	.	G	T	.	PASS	.	GT	1/1
+1	1586752	.	T	C	.	PASS	.	GT	0/1
+1	1635004	.	T	C	.	PASS	.	GT	1/1
+1	1635619	.	T	C	.	PASS	.	GT	0/1
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+1	1647686	.	A	C	.	PASS	.	GT	1/1
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+1	1649740	.	C	T	.	PASS	.	GT	1/1
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+1	1650845	.	G	A	.	PASS	.	GT	0/1
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+1	1651063	.	T	C	.	PASS	.	GT	0/1
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+1	1653028	.	C	T	.	PASS	.	GT	1/1
+1	1653303	.	T	C	.	PASS	.	GT	1/1
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+1	1886859	.	C	T	.	PASS	.	GT	0/1
+1	1887019	.	A	G	.	PASS	.	GT	1/1
+1	1887245	.	G	A	.	PASS	.	GT	0/1
+1	1888193	.	C	A	.	PASS	.	GT	0/1
+1	1895177	.	C	T	.	PASS	.	GT	0/1
+1	1896223	.	C	T	.	PASS	.	GT	0/1
+1	1897753	.	C	G	.	PASS	.	GT	0/1
+1	1900232	.	T	C	.	PASS	.	GT	0/1
+1	1900332	.	A	G	.	PASS	.	GT	0/1
+1	1900339	.	A	G	.	PASS	.	GT	0/1
+1	1903303	.	C	T	.	PASS	.	GT	0/1
+1	1916890	.	C	T	.	PASS	.	GT	0/1
+1	1918488	.	A	G	.	PASS	.	GT	0/1
+1	1918535	.	A	T	.	PASS	.	GT	0/1
+1	1922303	.	C	T	.	PASS	.	GT	0/1
+1	1956362	.	G	A	.	PASS	.	GT	0/1
+1	1957037	.	T	C	.	PASS	.	GT	0/1
+1	1960926	.	T	C	.	PASS	.	GT	1/1
+1	2118539	.	T	C	.	PASS	.	GT	1/1
+1	2121118	.	C	T	.	PASS	.	GT	1/1
+1	2234251	.	A	G	.	PASS	.	GT	0/1
+1	2234632	.	G	A	.	PASS	.	GT	0/1
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+1	2311393	.	A	G	.	PASS	.	GT	0/1
+1	2328501	.	T	G	.	PASS	.	GT	0/1
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+1	2332391	.	C	T	.	PASS	.	GT	0/1
+1	2338126	.	C	A	.	PASS	.	GT	0/1
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+1	2431057	.	C	T	.	PASS	.	GT	0/1
+1	2436778	.	A	G	.	PASS	.	GT	0/1
+1	2441358	.	T	C	.	PASS	.	GT	0/1
+1	2442953	.	C	A	.	PASS	.	GT	0/1
+1	2443212	.	G	A	.	PASS	.	GT	0/1
+1	2444226	.	C	T	.	PASS	.	GT	0/1
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diff -r c6071203aaa0 -r a15210afaf1d tool-data/fasta_indexes.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/fasta_indexes.loc.sample	Thu Apr 13 17:45:43 2017 -0400
@@ -0,0 +1,29 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of Samtools indexed sequences data files.  You will need
+#to create these data files and then create a fasta_indexes.loc file
+#similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The fasta_indexes.loc
+#file has this format (white space characters are TAB characters):
+#
+# <unique_build_id>	<dbkey>	<display_name>	<file_base_path>
+#
+#So, for example, if you had hg19 Canonical indexed stored in
+#
+# /depot/data2/galaxy/hg19/sam/,
+#
+#then the fasta_indexes.loc entry would look like this:
+#
+#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/depot/data2/galaxy/hg19/sam/hg19canon.fa
+#
+#and your /depot/data2/galaxy/hg19/sam/ directory
+#would contain hg19canon.fa and hg19canon.fa.fai files.
+#
+#Your fasta_indexes.loc file should include an entry per line for
+#each index set you have stored.  The file in the path does actually
+#exist, but it should never be directly used. Instead, the name serves
+#as a prefix for the index file.  For example:
+#
+#hg18canon	hg18	Human (Homo sapiens): hg18 Canonical	/depot/data2/galaxy/hg18/sam/hg18canon.fa
+#hg18full	hg18	Human (Homo sapiens): hg18 Full	/depot/data2/galaxy/hg18/sam/hg18full.fa
+#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/depot/data2/galaxy/hg19/sam/hg19canon.fa
+#hg19full	hg19	Human (Homo sapiens): hg19 Full	/depot/data2/galaxy/hg19/sam/hg19full.fa
diff -r c6071203aaa0 -r a15210afaf1d tool_data_table_conf.xml.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Thu Apr 13 17:45:43 2017 -0400
@@ -0,0 +1,8 @@
+<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc-->
+<tables>
+    <!-- Location of SAMTools indexes for FASTA files -->
+    <table name="fasta_indexes" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/fasta_indexes.loc" />
+    </table>
+</tables>