From 9dfb9708dba9e100db1b30c7c9caae1fb898e84c Mon Sep 17 00:00:00 2001
From: Jacob Pfeil <jpfeil@ucsc.edu>
Date: Mon, 7 Nov 2016 16:52:54 -0800
Subject: [PATCH] Add -M option to bwakit

---
 bwakit/run-bwamem | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/bwakit/run-bwamem b/bwakit/run-bwamem
index 462bafe..1dc61aa 100755
--- a/bwakit/run-bwamem
+++ b/bwakit/run-bwamem
@@ -5,7 +5,7 @@ use warnings;
 use Getopt::Std;
 
 my %opts = (t=>1);
-getopts("PSadskHo:R:x:t:", \%opts);
+getopts("MPSadskHo:R:x:t:", \%opts);
 
 die('
 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        sort the output alignment (via samtools; requring more RAM)
          -k        keep temporary files generated by typeHLA
+         -M        mark shorter split hits as secondary
 
 Examples:
 
@@ -143,7 +144,7 @@ if ($is_bam) {
 	$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;
 
 $cmd .= "  | $root/trimadap 2> $prefix.log.trim \\\n" if defined($opts{a});