From 7a77cc478565d152e46fb8e9b4256891555cc058 Mon Sep 17 00:00:00 2001
From: Ram Yalamanchili <ramyinc@gmail.com>
Date: Thu, 18 May 2017 15:23:05 -0700
Subject: [PATCH] Fix output file parameter for samtools sort

samtools sort v0.7.15+ requires -o flag to specify the output file
---
 bwakit/run-bwamem | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bwakit/run-bwamem b/bwakit/run-bwamem
index 462bafe..93e88bd 100755
--- a/bwakit/run-bwamem
+++ b/bwakit/run-bwamem
@@ -163,7 +163,7 @@ if (-f "$ARGV[0].alt" && !defined($opts{P})) {
 }
 
 my $t_sort = $opts{t} < 4? $opts{t} : 4;
-$cmd .= defined($opts{s})? "  | $root/samtools sort -@ $t_sort -m1G - $prefix.aln;\n" : "  | $root/samtools view -1 - > $prefix.aln.bam;\n";
+$cmd .= defined($opts{s})? "  | $root/samtools sort -@ $t_sort -m1G - -o $prefix.aln.bam;\n" : "  | $root/samtools view -1 - > $prefix.aln.bam;\n";
 
 if ($has_hla && defined($opts{H}) && (!defined($opts{x}) || $opts{x} eq 'intractg')) {
 	$cmd .= "$root/run-HLA ". (defined($opts{x}) && $opts{x} eq 'intractg'? "-A " : "") . "$prefix.hla > $prefix.hla.top 2> $prefix.log.hla;\n";