Merge pull request lh3#129 from lexentbio/bwakit_fix_sort

Fix output file parameter for samtools sort
mza0150 · Jul 30, 2017 · 5d15c8b · 5d15c8b
2 parents 950ea8c + 7a77cc4
commit 5d15c8b
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/bwakit/run-bwamem b/bwakit/run-bwamem
@@ -164,7 +164,7 @@ 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";