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Add -M option to bwakit

This commit is contained in:
Jacob Pfeil 2016-11-07 16:52:54 -08:00
parent 5961611c35
commit 9dfb9708db
1 changed files with 3 additions and 2 deletions
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5
bwakit/run-bwamem
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@ -5,7 +5,7 @@ use warnings;
use Getopt::Std; use Getopt::Std;
my %opts = (t=>1); my %opts = (t=>1);
getopts("PSadskHo:R:x:t:", \%opts); getopts("MPSadskHo:R:x:t:", \%opts);
die(' die('
Usage: run-bwamem [options] <idxbase> <file1> [file2] Usage: run-bwamem [options] <idxbase> <file1> [file2]
@ -24,6 +24,7 @@ Options: -o STR prefix for output files [inferred from
-S for BAM input, don\'t shuffle -S for BAM input, don\'t shuffle
-s sort the output alignment (via samtools; requring more RAM) -s sort the output alignment (via samtools; requring more RAM)
-k keep temporary files generated by typeHLA -k keep temporary files generated by typeHLA
-M mark shorter split hits as secondary
Examples: Examples:
@ -143,7 +144,7 @@ if ($is_bam) {
$cmd = "cat $ARGV[1] \\\n"; $cmd = "cat $ARGV[1] \\\n";
} }
my $bwa_opts = "-p " . ($opts{t} > 1? "-t$opts{t} " : "") . (defined($opts{x})? "-x $opts{x} " : "") . (defined($opts{R})? "-R'$opts{R}' " : ""); my $bwa_opts = "-p " . ($opts{t} > 1? "-t$opts{t} " : "") . (defined($opts{x})? "-x $opts{x} " : "") . (defined($opts{R})? "-R'$opts{R}' " : "") . (defined($opts{M})? "-M " : "");
$bwa_opts .= join(" ", @RG_lines) . " -C " if @RG_lines > 0; $bwa_opts .= join(" ", @RG_lines) . " -C " if @RG_lines > 0;
$cmd .= " | $root/trimadap 2> $prefix.log.trim \\\n" if defined($opts{a}); $cmd .= " | $root/trimadap 2> $prefix.log.trim \\\n" if defined($opts{a});