From bd878565f6350b0148a3680baee508333ea620e2 Mon Sep 17 00:00:00 2001
From: kiran <kiran@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 7 Sep 2010 21:07:46 +0000
Subject: [PATCH] Change for Firehose: infers output path from the input VCF,
 so that we don't have to change a whole bunch of stuff so that Firehose knows
 where to expect the output file.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4221 348d0f76-0448-11de-a6fe-93d51630548a
---
 perl/AnnotateVCFwithMAF.pl | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/perl/AnnotateVCFwithMAF.pl b/perl/AnnotateVCFwithMAF.pl
index cd17060b9..5dc37be2e 100755
--- a/perl/AnnotateVCFwithMAF.pl
+++ b/perl/AnnotateVCFwithMAF.pl
@@ -10,12 +10,14 @@ sub usage {
 }
 
 my %args;
-($args{'VCF_IN'}, $args{'MAF_IN'}, $args{'VCF_OUT'}) = @ARGV;
+($args{'VCF_IN'}, $args{'MAF_IN'}) = @ARGV;
 
-if (!defined($args{'VCF_IN'}) || !defined($args{'MAF_IN'}) || !defined($args{'VCF_OUT'})) {
+if (!defined($args{'VCF_IN'}) || !defined($args{'MAF_IN'})) {
     &usage();
 }
 
+($args{'VCF_OUT'} = $args{'VCF_IN'}) =~ s/\.vcf/.maf_annotated.vcf/;
+
 my %ignoreEntries = (
     'normal_barcode' => 1,
     'tumor_barcode' => 1,