# HG changeset patch
# User fcaramia
# Date 1418772279 18000
# Node ID 6324eefd9e9102fdb48c8c5c4112bf68f15995c2
# Parent  d49d06d35683aef968d6f8b178e1baaaffff0d31
Uploaded

diff -r d49d06d35683 -r 6324eefd9e91 htseq.pl
--- 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`;
 	}