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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
This commit is contained in:
kiran 2010-09-07 21:07:46 +00:00
parent 501f6a0e14
commit bd878565f6
1 changed files with 4 additions and 2 deletions
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6
perl/AnnotateVCFwithMAF.pl
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@ -10,12 +10,14 @@ sub usage {
} }
my %args; 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(); &usage();
} }
($args{'VCF_OUT'} = $args{'VCF_IN'}) =~ s/\.vcf/.maf_annotated.vcf/;
my %ignoreEntries = ( my %ignoreEntries = (
'normal_barcode' => 1, 'normal_barcode' => 1,
'tumor_barcode' => 1, 'tumor_barcode' => 1,