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Change for Chris: don't depend on other Perl modules. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4053 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2010-08-17 22:19:13 +00:00
parent cb74806bb5
commit 1c3f2be829
1 changed files with 12 additions and 7 deletions
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19
perl/AnnotateVCFwithMAF.pl
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@ -1,11 +1,19 @@
#!/usr/bin/perl -w #!/usr/bin/perl -w
use strict; use strict;
use lib "$ENV{'STING_DIR'}/perl";
use StingArgs;
use Data::Dumper;
my %args = &getCommandArguments("VCF_IN" => undef, "MAF_IN" => undef, "VCF_OUT" => "/dev/stdout"); sub usage {
print "Usage: $0 <input.vcf> <input.maf> <output.vcf>\n";
print "This program takes an annotated MAF file and propagates the annotations to the VCF file.\n";
exit(1);
}
my %args;
($args{'VCF_IN'}, $args{'MAF_IN'}, $args{'VCF_OUT'}) = @ARGV;
if (!defined($args{'VCF_IN'}) || !defined($args{'MAF_IN'}) || !defined($args{'VCF_OUT'})) {
&usage();
}
my %ignoreEntries = ( my %ignoreEntries = (
'normal_barcode' => 1, 'normal_barcode' => 1,
@ -37,13 +45,10 @@ while (my $mafline = <MAF_IN>) {
my $locus = "$mafentry{'chr'}:$mafentry{'start'}"; my $locus = "$mafentry{'chr'}:$mafentry{'start'}";
if (exists($mafentry{$locus})) { if (exists($mafentry{$locus})) {
print "Locus $locus already spoken for!\n"; print "Locus $locus already spoken for!\n";
print Dumper(\%mafentry);
exit(1); exit(1);
} }
$maf{$locus} = \%mafentry; $maf{$locus} = \%mafentry;
#print Dumper(\%mafentry);
} }
close(MAF_IN); close(MAF_IN);