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fast-bwa
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option to skip ALT

This commit is contained in:
Heng Li 2016-03-16 16:06:49 -04:00
parent 83662032a2
commit 2c078eb667
1 changed files with 2 additions and 2 deletions
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4
bwakit/run-bwamem
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@ -5,7 +5,7 @@ use warnings;
use Getopt::Std;
my %opts = (t=>1);
getopts("SadskHo:R:x:t:", \%opts);
getopts("PSadskHo:R:x:t:", \%opts);
die('
Usage: run-bwamem [options] <idxbase> <file1> [file2]
@ -151,7 +151,7 @@ $cmd .= " | $root/bwa mem $bwa_opts$ARGV[0] - 2> $prefix.log.bwamem \\\n";
$cmd .= " | $root/samblaster 2> $prefix.log.dedup \\\n" if defined($opts{d});
my $has_hla = 0;
if (-f "$ARGV[0].alt") {
if (-f "$ARGV[0].alt" && !defined($opts{P})) {
my $fh;
open($fh, "$ARGV[0].alt") || die;
while (<$fh>) {