Mercurial > repos > fcaramia > edger

changeset 13:6324eefd9e91 draft default tip

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Uploaded
author fcaramia
date Tue, 16 Dec 2014 18:24:39 -0500
parents d49d06d35683
children
files htseq.pl
diffstat 1 files changed, 2 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/htseq.pl	Wed Aug 21 22:13:23 2013 -0400
+++ b/htseq.pl	Tue Dec 16 18:24:39 2014 -0500
@@ -56,10 +56,10 @@
 	my $COMM;
 	my $file_type = `file $input_file`;
 	if(grep /text$/, $file_type ) {
-		$COMM = "htseq-count -q -m $OPTIONS{m} -s $OPTIONS{s} -a $OPTIONS{a} -t $OPTIONS{t} -i $OPTIONS{i} $input_file $OPTIONS{g}";
+		$COMM = "htseq-count -r -q -m $OPTIONS{m} -s $OPTIONS{s} -a $OPTIONS{a} -t $OPTIONS{t} -i $OPTIONS{i} $input_file $OPTIONS{g}";
 		@htseq = `$COMM`;
 	} else {
-		$COMM = "samtools view $input_file | htseq-count -q -m $OPTIONS{m} -s $OPTIONS{s} -a $OPTIONS{a} -t $OPTIONS{t} -i $OPTIONS{i} - $OPTIONS{g}";
+		$COMM = "samtools view $input_file | htseq-count -r -q -m $OPTIONS{m} -s $OPTIONS{s} -a $OPTIONS{a} -t $OPTIONS{t} -i $OPTIONS{i} - $OPTIONS{g}";
 		@htseq = `$COMM`;
 	}