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Fix output file parameter for samtools sort #129

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merged 1 commit into from Jul 30, 2017
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Fix output file parameter for samtools sort #129

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2 changes: 1 addition & 1 deletion bwakit/run-bwamem
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Original file line number Diff line number Diff line change
Expand Up @@ -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";
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