| Previous changeset 12:d49d06d35683 (2013-08-21) |
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Commit message:
Uploaded |
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modified:
htseq.pl |
| b |
| 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 |
| b |
| @@ -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`; } |