zzh
/
fast-bwa
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Fix output file parameter for samtools sort 

samtools sort v0.7.15+ requires -o flag to specify the output file
This commit is contained in:
Ram Yalamanchili 2017-05-18 15:23:05 -07:00
parent 5961611c35
commit 7a77cc4785
1 changed files with 1 additions and 1 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
bwakit/run-bwamem
View File

@ -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";