From 84ddadca64f8abc9792fa434ecb874839f727603 Mon Sep 17 00:00:00 2001
From: kiran <kiran@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 8 Sep 2010 03:09:08 +0000
Subject: [PATCH] One more fix: exclude input VCF file's directory name from
 the output file.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4226 348d0f76-0448-11de-a6fe-93d51630548a
---
 perl/AnnotateVCFwithMAF.pl | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/perl/AnnotateVCFwithMAF.pl b/perl/AnnotateVCFwithMAF.pl
index 5dc37be2e..89dda2de0 100755
--- a/perl/AnnotateVCFwithMAF.pl
+++ b/perl/AnnotateVCFwithMAF.pl
@@ -2,6 +2,7 @@
 
 use strict;
 use Data::Dumper;
+use File::Basename;
 
 sub usage {
     print "Usage: $0 <input.vcf> <input.maf> <output.vcf>\n";
@@ -16,7 +17,7 @@ if (!defined($args{'VCF_IN'}) || !defined($args{'MAF_IN'})) {
     &usage();
 }
 
-($args{'VCF_OUT'} = $args{'VCF_IN'}) =~ s/\.vcf/.maf_annotated.vcf/;
+($args{'VCF_OUT'} = basename($args{'VCF_IN'})) =~ s/\.vcf/.maf_annotated.vcf/;
 
 my %ignoreEntries = (
     'normal_barcode' => 1,