# HG changeset patch
# User iuc
# Date 1492522436 14400
# Node ID 7adfd0589f49b395244f05c4419ee38534795ade
# Parent 20f0429a4bfeada59ddf1a6417e48f93e0ca7bca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1
diff -r 20f0429a4bfe -r 7adfd0589f49 readme.rst
--- a/readme.rst Mon Dec 19 11:56:53 2016 -0500
+++ b/readme.rst Tue Apr 18 09:33:56 2017 -0400
@@ -6,14 +6,6 @@
.. _SnpEff: http://snpeff.sourceforge.net/
-
-This repository let you automatically install SnpEff and SnpSift.
-This will use the default location for genome reference downloads from the ``snpEff.config`` file:
-
- data_dir = ~/snpEff/data/
-
-You can manually edit the installed ``snpEff.config`` file and change the location, or you can create a symbolic link to the desired data location from ``~/snpEff``.
-
The genome reference options used by the tools "SnpEff" (snpEff.xml) and "SnpEff Download" (snpEff_download.xml) are taken from the ``tool-data/snpeffect_genomedb.loc`` file.
You can fill this file by running the following command:
@@ -35,4 +27,3 @@
.. _Cingolani2012using: http://journal.frontiersin.org/Journal/10.3389/fgene.2012.00035/
Wrapper authors: Jim Johnson
-
diff -r 20f0429a4bfe -r 7adfd0589f49 snpEff.xml
--- a/snpEff.xml Mon Dec 19 11:56:53 2016 -0500
+++ b/snpEff.xml Tue Apr 18 09:33:56 2017 -0400
@@ -6,23 +6,20 @@
-
- "$snpeff_output";
+ '$input' > '$snpeff_output'
#if $statsFile:
+ &&
#import os
#set $genes_file = str($statsFile) + '.genes.txt'
#set $genes_file_name = os.path.split($genes_file)[-1]
- mkdir $statsFile.files_path;
- mv "$genes_file" #echo os.path.join($statsFile.files_path, $genes_file_name)#;
+ mkdir '$statsFile.files_path' &&
+ mv '$genes_file' '#echo os.path.join($statsFile.files_path, $genes_file_name)#'
#end if
#if $outputConditional.outputFormat == 'gatk' and $outputConditional.gatk_v1
+ &&
## Replace real SnpEff version with 2.0.5 to prevent this GATK 1.x error: "The version of SnpEff used to generate the SnpEff input file (x.x) is not currently supported by the GATK. Supported versions are: [2.0.5]"
- sed -i.bak -e 's/^\#\#SnpEffVersion="\(\S*\s\)/\#\#SnpEffVersion="2.0.5 - real is \1/' "$snpeff_output"
+ sed -i.bak -e 's/^\#\#SnpEffVersion="\(\S*\s\)/\#\#SnpEffVersion="2.0.5 - real is \1/' '$snpeff_output'
#end if
-]]>
-
+ ]]>
-
+
@@ -127,45 +124,34 @@
-
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+
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- These are available for only a few genomes
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- These are available for only a few genomes
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+
- value is not None and value.metadata.snpeff_version == "@SNPEFF_VERSION@"
+ value is not None and value.metadata.snpeff_version == "@SNPEFF_VERSION@"
-
-
- These are available for only a few genomes
-
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- These are available for only a few genomes
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@@ -287,12 +282,11 @@
-
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@@ -300,7 +294,7 @@
By default SnpEff simplifies all chromosome names. For instance 'chr1' is just '1'.
- You can prepend any string you want to the chromosome name.
+ You can prepend any string you want to the chromosome name
^\S*$
@@ -308,93 +302,38 @@
-
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+
generate_stats == True
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diff -r 20f0429a4bfe -r 7adfd0589f49 snpEff_databases.xml
--- a/snpEff_databases.xml Mon Dec 19 11:56:53 2016 -0500
+++ b/snpEff_databases.xml Tue Apr 18 09:33:56 2017 -0400
@@ -1,4 +1,4 @@
-
+
snpEff_macros.xml
@@ -6,12 +6,9 @@
-
- "$snpeff_dbs"
-]]>
-
+ '$snpeff_dbs'
+ ]]>
@@ -27,11 +24,8 @@
-
+ ]]>
diff -r 20f0429a4bfe -r 7adfd0589f49 snpEff_download.xml
--- a/snpEff_download.xml Mon Dec 19 11:56:53 2016 -0500
+++ b/snpEff_download.xml Tue Apr 18 09:33:56 2017 -0400
@@ -6,14 +6,11 @@
-
-
-
+
-
+
@SNPEFF_DATABASE_URL@
\S+
@@ -32,11 +29,7 @@
-
+ ]]>
-
diff -r 20f0429a4bfe -r 7adfd0589f49 snpEff_macros.xml
--- a/snpEff_macros.xml Mon Dec 19 11:56:53 2016 -0500
+++ b/snpEff_macros.xml Tue Apr 18 09:33:56 2017 -0400
@@ -1,7 +1,7 @@
- snpEff
+ snpeff
@@ -10,22 +10,16 @@
- if [ -z "\$SNPEFF_JAR_PATH" ]; then export SNPEFF_JAR_PATH=\$(dirname \$(readlink -e \$(which snpEff))); fi
- 4.1
- SnpEff4.1
- https://snpeff-data.galaxyproject.org/databases/v4_1/
+ 4.3k
+ SnpEff4.3
+ https://sourceforge.net/projects/snpeff/files/databases/v4_3/
-
-For details about this tool, please go to:
- http://snpeff.sourceforge.net/SnpEff_manual.html
-
+For details about this tool, please go to: http://snpeff.sourceforge.net/SnpEff_manual.html
diff -r 20f0429a4bfe -r 7adfd0589f49 test-data/input.vcf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input.vcf Tue Apr 18 09:33:56 2017 -0400
@@ -0,0 +1,60 @@
+##fileformat=VCFv4.1
+##FORMAT=
+##contig=
+##reference=http://www.ncbi.nlm.nih.gov/nuccore/KJ660346.2
+#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT EBOV_2014_EM095 EBOV_2014_G3676 EBOV_2014_G3680 EBOV_2014_G3686 EBOV_2014_G3687 EBOV_2014_G3683 EBOV_2014_EM096 EBOV_2014_EM098 EBOV_2014_EM104 EBOV_2014_EM106 EBOV_2014_EM112 EBOV_2014_EM113 EBOV_2014_EM124 EBOV_2014_G3677 EBOV_2014_G3682 EBOV_2014_G3707 EBOV_2014_G3713 EBOV_2014_G3724 EBOV_2014_G3734 EBOV_2014_G3735 EBOV_2014_G3750 EBOV_2014_G3758 EBOV_2014_G3764 EBOV_2014_G3769 EBOV_2014_G3782 EBOV_2014_G3786 EBOV_2014_G3788 EBOV_2014_G3796 EBOV_2014_G3798 EBOV_2014_G3799 EBOV_2014_G3800 EBOV_2014_G3805 EBOV_2014_G3807 EBOV_2014_G3810 EBOV_2014_G3820 EBOV_2014_G3838 EBOV_2014_G3840 EBOV_2014_G3841 EBOV_2014_G3848 EBOV_2014_NM042 EBOV_2014_G3850 EBOV_2014_EM110 EBOV_2014_EM111 EBOV_2014_EM119 EBOV_2014_G3729 EBOV_2014_G3765 EBOV_2014_G3770 EBOV_2014_G3789 EBOV_2014_G3825 EBOV_2014_G3845 EBOV_2014_G3851 EBOV_2014_G3857 EBOV_2014_EM115 EBOV_2014_EM120 EBOV_2014_G3752 EBOV_2014_G3795 EBOV_2014_G3808 EBOV_2014_G3823 EBOV_2014_EM121 EBOV_2014_G3771 EBOV_2014_G3816 EBOV_2014_G3829 EBOV_2014_G3846 EBOV_2014_G3856 EBOV_2014_G3826 EBOV_2014_G3827 EBOV_2014_G3809 EBOV_2014_G3814 EBOV_2014_G3821 EBOV_2014_G3822 EBOV_2014_G3679 EBOV_2014_G3819 EBOV_2014_G3817 EBOV_2014_G3834 EBOV_2014_G3818 EBOV_2014_G3787 EBOV_2014_G3831 EBOV_2014_G3670 EBOV_2014_KJ660346 EBOV_2014_KJ660347 EBOV_2014_KJ660348
+KJ660346 572 . A G . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+KJ660346 800 . C T . . . GT 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0
+KJ660346 1024 . A C . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+KJ660346 1288 . A T . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0
+KJ660346 1492 . A G . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+KJ660346 1849 . C T . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1
+KJ660346 2124 . A G . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
+KJ660346 2185 . G A . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
+KJ660346 2341 . A G . . . GT 0 0 0 0 . 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0
+KJ660346 2364 . A G . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+KJ660346 2497 . A G . . . GT 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+KJ660346 2931 . G A . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1
+KJ660346 3116 . C G . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+KJ660346 3388 . T G . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0
+KJ660346 3638 . A G . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0
+KJ660346 4340 . C T . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0
+KJ660346 4505 . T C . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+KJ660346 4709 . T C . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+KJ660346 4759 . T C . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+KJ660346 4976 . C A . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0
+KJ660346 5461 . T C . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+KJ660346 6175 . G A . . . GT 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+KJ660346 6283 . T C . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1
+KJ660346 6909 . T A . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
+KJ660346 8280 . A G . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0
+KJ660346 8928 . A C . . . GT 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0
+KJ660346 9390 . A C . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+KJ660346 9536 . A G . . . GT 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+KJ660346 9923 . T C . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0
+KJ660346 10005 . G A . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0
+KJ660346 10218 . G A . . . GT 0 0 0 0 0 0 0 0 1 1 1 1 1 0 0 1 1 1 0 1 1 0 1 0 0 0 0 0 1 0 0 1 0 0 0 0 1 0 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 0 1 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 0 0 0 0 0 0
+KJ660346 10252 . A G . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0
+KJ660346 10268 . T C . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+KJ660346 10509 . C T . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+KJ660346 10743 . T C . . . GT 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+KJ660346 10801 . A G . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+KJ660346 11142 . G A . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+KJ660346 11811 . T C . . . GT 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
+KJ660346 11943 . G A . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0
+KJ660346 12878 . G A . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+KJ660346 12885 . A C . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 . . .
+KJ660346 13856 . G A . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1
+KJ660346 13923 . T C . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0
+KJ660346 14019 . T C . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 1 1 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0
+KJ660346 14232 . C T . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+KJ660346 15599 . G A . . . GT 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
+KJ660346 15660 . C T . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1
+KJ660346 15963 . G A . . . GT 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0
+KJ660346 16054 . T A . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0
+KJ660346 16455 . T C . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0
+KJ660346 16750 . T C . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+KJ660346 17142 . T C . . . GT 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0
+KJ660346 17985 . T C . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+KJ660346 18412 . T C . . . GT 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0
+KJ660346 18895 . C T . . . GT 0 0 0 0 0 0 0 . 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 . 0 0 0 0 0 0 0 0 . 0 0 0 0 . 0 . 0 0 0 . 0 0 0 0 0 0 0 0 0 0 0 0 0 0 . 0 0 0 0 0 0 0 0 0 0 0 1 1 1
diff -r 20f0429a4bfe -r 7adfd0589f49 test-data/vcf_homhet.vcf
--- a/test-data/vcf_homhet.vcf Mon Dec 19 11:56:53 2016 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,60 +0,0 @@
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-##FORMAT=
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-##source_20110319.1=/wsu/home/eq/eq83/eq8302/tools/vcftools/bin//vcf-merge s_1_ACAGTGA.vcf.gz s_1_CAGATCA.vcf.gz s_1_CGATGTA.vcf.gz s_1_CTTGTAA.vcf.gz s_1_GCCAATA.vcf.gz s_1_TGACCAA.vcf.gz
-##sourceFiles_20110319.1=0:s_1_ACAGTGA.vcf.gz,1:s_1_CAGATCA.vcf.gz,2:s_1_CGATGTA.vcf.gz,3:s_1_CTTGTAA.vcf.gz,4:s_1_GCCAATA.vcf.gz,5:s_1_TGACCAA.vcf.gz
-##INFO=
-##INFO=
-##INFO=
-#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT s_1_ACAGTGA_sort.bam s_1_CAGATCA_sort.bam s_1_CGATGTA_sort.bam s_1_CTTGTAA_sort.bam s_1_GCCAATA_sort.bam s_1_TGACCAA_sort.bam
-Y 3718196 . C T 7.59 . AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,2,0;DP=2;FQ=-33;G3=4.617e-16,8.575e-07,1;MQ=39;SF=1 GT:GQ:PL . 1/1:61:38,6,0 . . . .
-Y 3720217 . A G 8.65 . AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,0,1;DP=2;FQ=-30;G3=4.415e-15,5.291e-06,1;MQ=38;SF=5 GT:GQ:PL . . . . . 1/1:53:38,3,0
-Y 3720581 . A G 7.80 . AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,1,0;DP=1;FQ=-30;G3=5.56e-15,5.291e-06,1;MQ=44;SF=1 GT:GQ:PL . 1/1:53:37,3,0 . . . .
-Y 3721154 . A G 13.90 . AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,2,0;DP=2;FQ=-33;G3=9.194e-17,8.566e-07,1;MQ=37;SF=3 GT:GQ:PL . . . 1/1:61:45,6,0 . .
-Y 3721230 . C G 21.80 . AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,0,2;DP=2;FQ=-33;G3=1.456e-17,8.564e-07,1;MQ=29;SF=3 GT:GQ:PL . . . 1/1:61:53,6,0 . .
-Y 3744605 . C A 3.98 . AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,0,2;DP=2;FQ=-33;G3=1.468e-15,8.599e-07,1;MQ=19;SF=2 GT:GQ:PL . . 1/1:61:33,6,0 . . .
-Y 4433091 . T C 11.10 . AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,2,0;DP=2;FQ=-33;G3=1.835e-16,8.568e-07,1;MQ=23;SF=5 GT:GQ:PL . . . . . 1/1:61:42,6,0
-Y 9945223 . ATTT ATTTT 19.80 . AC=4;AF1=1;AN=4;CI95=0.5,1;DP4=0,0,0,2;DP=2;FQ=-40.5;G3=2.906e-18,8.564e-07,1;INDEL;MQ=45;SF=0,2 GT:GQ:PL 1/1:61:60,6,0 . 1/1:61:57,6,0 . . .
-Y 9987395 . TTAT TT 80.40 . AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,1,2;DP=3;FQ=-43.5;G3=5.464e-26,5.886e-08,1;INDEL;MQ=43;SF=5 GT:GQ:PL . . . . . 1/1:72:120,9,0
-Y 10011604 . C CTT 119.17 . AC=12;AF1=1;AN=12;CI95=1,1;DP4=0,0,7,0;DP=9;FQ=-55.5;G3=4.948e-32,3.15e-11,1;INDEL;MQ=33;SF=0,1,2,3,4,5 GT:GQ:PL 1/1:99:139,21,0 1/1:96:134,24,0 1/1:99:168,36,0 1/1:99:159,45,0 1/1:99:185,33,0 1/1:99:175,39,0
-Y 10011748 . GAAAAAA GAAAAAAA 23.70 . AC=6;AF1=0.5;AN=12;CI95=0.5,0.5;DP4=12,12,11,10;DP=51;FQ=33.5;G3=1.256e-14,1,1.991e-19;INDEL;MQ=33;PV4=1,0.49,0.012,0.2;SF=0,1,2,3,4,5 GT:GQ:PL 0/0:71:68,0,92 1/1:55:52,0,77 1/1:71:69,0,75 1/1:69:66,0,79 1/1:56:53,0,80 1/1:62:59,0,98
-Y 10011894 . ATTATTTATTT ATTATTT 58.62 . AC=4;AF1=0.5;AN=8;CI95=0.5,0.5;DP4=4,11,0,6;DP=34;FQ=32.5;G3=1.991e-14,1,7.924e-52;INDEL;MQ=35;PV4=0.28,0.049,0.14,0.2;SF=1,3,4,5 GT:GQ:PL . 0/0:70:67,0,254 . 1/1:99:152,0,255 1/1:83:80,0,255 1/1:89:86,0,255
-Y 10011930 . ACT A 90.85 . AC=2;AF1=0.5;AN=4;CI95=0.5,0.5;DP4=2,6,1,3;DP=17;FQ=16.6;G3=3.155e-11,1,1.991e-34;INDEL;MQ=35;PV4=1,0.00044,0.33,1;SF=0,5 GT:GQ:PL 0/0:54:51,0,167 . . . . 0/0:99:206,0,255
-Y 10011935 . C CT 83.83 . AC=3;AF1=0.5;AN=6;CI95=0.5,0.5;DP4=1,8,2,5;DP=23;FQ=90.3;G3=1.256e-28,1,5e-26;INDEL;MQ=39;PV4=0.55,1,0.15,1;SF=1,2,4 GT:GQ:PL . 0/0:99:138,0,125 1/1:92:89,0,148 . 1/1:99:138,0,171 .
-Y 10011966 . ATT AT 79.38 . AC=6;AF1=0.5;AN=12;CI95=0.5,0.5;DP4=1,6,0,2;DP=14;FQ=5.09;G3=1.991e-12,1,1.256e-28;INDEL;MQ=38;PV4=1,1,0.46,0.088;SF=0,1,2,3,4,5 GT:GQ:PL 1/1:41:38,0,92 1/1:76:73,0,109 1/1:99:181,0,109 1/1:99:114,0,103 1/1:99:139,0,171 1/1:99:155,0,144
-Y 10028061 . CA CAA 28.40 . AC=4;AF1=1;AN=4;CI95=0.5,1;DP4=0,0,2,1;DP=9;FQ=-43.5;G3=2.739e-22,5.886e-08,1;INDEL;MQ=37;SF=4,5 GT:GQ:PL . . . . 1/1:72:83,9,0 0/0:61:52,6,0
-Y 10029194 . CA C 73.47 . AC=10;AF1=0.7304;AN=12;CI95=0.5,1;DP4=2,0,7,3;DP=19;FQ=-32.5;G3=2.922e-150,0.9991,0.000854;INDEL;MQ=25;PV4=1,0.4,1,0.23;SF=0,1,2,3,4,5 GT:GQ:PL 0/0:3:93,0,2 1/1:85:100,17,0 1/1:99:181,36,0 1/1:90:107,18,0 1/1:3:104,0,2 1/1:70:90,10,0
-Y 10029452 . CAA CAAA 7.26 . AC=4;AF1=1;AN=4;CI95=0.5,1;DP4=0,0,4,0;DP=13;FQ=-46.5;G3=2.341e-18,6.106e-08,1;INDEL;MQ=26;SF=3,4 GT:GQ:PL . . . 1/1:72:50,12,0 1/1:72:42,12,0 .
-Y 10037877 . GCCC GCCCC 14.40 . AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,0,2;DP=3;FQ=-40.5;G3=1.456e-17,8.564e-07,1;INDEL;MQ=29;SF=2 GT:GQ:PL . . 1/1:61:53,6,0 . . .
-Y 13266272 . TTTT TTTTATTT 51.50 . AC=1;AF1=0.5;AN=2;CI95=0.5,0.5;DP4=5,1,7,0;DP=15;FQ=54.5;G3=7.924e-19,1,3.155e-24;INDEL;MQ=30;PV4=0.46,1,0.078,0.00035;SF=3 GT:GQ:PL . . . 0/0:92:89,0,116 . .
-Y 13268110 . GC GCC 3.66 . AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,2,0;DP=2;FQ=-40.5;G3=2.911e-16,8.571e-07,1;INDEL;MQ=23;SF=2 GT:GQ:PL . . 1/1:61:40,6,0 . . .
-Y 13292082 . TCCCCCCCCCC TCCCCCCC 14.40 . AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,0,2;DP=2;FQ=-40.5;G3=1.456e-17,8.564e-07,1;INDEL;MQ=29;SF=3 GT:GQ:PL . . . 1/1:61:53,6,0 . .
-Y 13297070 . AGGTGGTGGTGGT AGGTGGTGGT 12.70 . AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,0,1;DP=1;FQ=-37.5;G3=2.782e-16,5.287e-06,1;INDEL;MQ=50;SF=5 GT:GQ:PL . . . . . 1/1:53:50,3,0
-Y 13312198 . CGGGGG CGGGG 14.87 . AC=5;AF1=1;AN=6;CI95=0.5,1;DP4=2,0,10,0;DP=12;FQ=-43.5;G3=1.373e-19,5.886e-08,1;INDEL;MQ=24;PV4=1,0.44,1,0.019;SF=1,4,5 GT:GQ:PL . 1/1:72:56,9,0 . . 1/1:70:57,10,0 1/1:44:48,0,42
-Y 13312608 . CA CAA 22.50 . AC=1;AF1=0.5032;AN=2;CI95=0.5,0.5;DP4=2,0,7,0;DP=16;FQ=-15.6;G3=4.937e-25,1,1.272e-08;INDEL;MQ=24;PV4=1,1,0.093,1;SF=2 GT:GQ:PL . . 0/0:22:60,0,19 . . .
-Y 13402810 . TAGAGA TAGA 29.80 . AC=4;AF1=1;AN=4;CI95=0.5,1;DP4=0,0,1,1;DP=2;FQ=-40.5;G3=7.299e-19,8.564e-07,1;INDEL;MQ=33;SF=0,2 GT:GQ:PL 1/1:61:66,6,0 . 1/1:72:72,9,0 . . .
-Y 21153016 . AG ATG 213.83 . AC=12;AF1=1;AN=12;CI95=1,1;DP4=0,0,6,9;DP=15;FQ=-79.5;G3=7.905e-54,1e-18,1;INDEL;MQ=43;SF=0,1,2,3,4,5 GT:GQ:PL 1/1:99:255,45,0 1/1:99:.,.,0 1/1:99:255,87,0 1/1:99:.,.,0 1/1:99:255,78,0 1/1:99:.,.,0
-Y 21153067 . CCA C 46.50 . AC=1;AF1=0.5;AN=2;CI95=0.5,0.5;DP4=8,4,5,0;DP=18;FQ=49.5;G3=7.924e-18,1,5e-52;INDEL;MQ=39;PV4=0.26,0.08,0.035,1;SF=3 GT:GQ:PL . . . 0/0:87:84,0,255 . .
-Y 26325233 . TGAGAGAGAGAGA TGAGAGAGAGA 22.20 . AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,2,0;DP=2;FQ=-40.5;G3=2.308e-18,8.564e-07,1;INDEL;MQ=33;SF=0 GT:GQ:PL 1/1:61:61,6,0 . . . . .
-Y 28588049 . ACATCAT ACAT 7.35 . AC=4;AF1=1;AN=4;CI95=0.5,1;DP4=0,0,1,0;DP=1;FQ=-37.5;G3=1.108e-15,5.288e-06,1;INDEL;MQ=44;SF=1,3 GT:GQ:PL . 1/1:53:44,3,0 . 1/1:53:44,3,0 . .
-Y 59030478 . AAAACAAACAAACAAACAAACAAACAAA AAAACAAACAAACAAA 14.40 . AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,0,2;DP=2;FQ=-40.5;G3=1.456e-17,8.564e-07,1;INDEL;MQ=29;SF=2 GT:GQ:PL . . 1/1:61:53,6,0 . . .
-Y 59032947 . GTT GTTT 28.20 . AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,0,2;DP=2;FQ=-40.5;G3=5.798e-19,8.564e-07,1;INDEL;MQ=37;SF=5 GT:GQ:PL . . . . . 1/1:61:67,6,0
diff -r 20f0429a4bfe -r 7adfd0589f49 tool_dependencies.xml
--- a/tool_dependencies.xml Mon Dec 19 11:56:53 2016 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-
-
-
-
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