comparison DC_Genotyper.pl @ 12:8cc26598eeac draft

Uploaded

11:845a87ad254a

####################
## get paramaters ##
####################
# t: target file
# b: bam file
# R: 2bit version of reference fasta.
# p: number of threads.
# s: dbsnp file
# m: minimal coverage (defaults 400x)
# P: ploidy
# a: outfile for allele distributions

my $twobit :shared;
my $igvgenome :shared;
if (!defined($opts{'R'})) {
	die("Reference Genomes not specified\n");
}
my @refgenomes = split(",",$opts{'r'});
if (!-e $refgenomes[0]) {
	die("'$refgenomes[0]' is not a valid file path.");
}
else {
	$twobit = $refgenomes[0];

12:8cc26598eeac

####################
## get paramaters ##
####################
# t: target file
# b: bam file
# R: reference genome files for twobit and IGV.
# p: number of threads.
# s: dbsnp file
# m: minimal coverage (defaults 400x)
# P: ploidy
# a: outfile for allele distributions

my $twobit :shared;
my $igvgenome :shared;
if (!defined($opts{'R'})) {
	die("Reference Genomes not specified\n");
}
my @refgenomes = split(",",$opts{'R'});
if (!-e $refgenomes[0]) {
	die("'$refgenomes[0]' is not a valid file path.");
}
else {
	$twobit = $refgenomes[0];