comparison DC_Genotyper.pl @ 20:8262299f8f3c draft

Fixed loading of dbsnp after bcftools-tabix switch.

19:8938f339ed37

	open SNP, ">$wd/dbsnp.txt";
	## dummy line on chr zero to prevent R issues on empty file.
	print SNP "chr0\t1\t.\tA\tT\n";
	close SNP;
}

## now process the bam file.
mkdir "$wd/WIGS/";
my $bam :shared;
$bam = $opts{'b'};

20:8262299f8f3c

	open SNP, ">$wd/dbsnp.txt";
	## dummy line on chr zero to prevent R issues on empty file.
	print SNP "chr0\t1\t.\tA\tT\n";
	close SNP;
}
open IN, "$wd/dbsnp.txt";
while (<IN>) {
	chomp;
	my @p = split(/\t/,$_);
	$dbsnp{$p[0].'-'.$p[1]} = $p[3].'-'.$p[4].'-'.$p[2];
}
close IN;

## now process the bam file.
mkdir "$wd/WIGS/";
my $bam :shared;
$bam = $opts{'b'};