diff --git a/src/perllib/CiceroExtTools.pm b/src/perllib/CiceroExtTools.pm index 40fa83a..77b598f 100755 --- a/src/perllib/CiceroExtTools.pm +++ b/src/perllib/CiceroExtTools.pm @@ -163,7 +163,8 @@ sub run { croak "Please check BLAT server is correctly configured or running.\n" if($test != 0); print STDERR "\ntest=$test\t", join(" ", ($self->{PRG}, $self->{BIT2_DIR}, $param{-QUERY}, $unsorted_psl, $options)), "\n" if($debug); # Sort the output PSL file from BLAT. - `sort -k 11,11nr -k 10,10d -k 14,14d -k 1,1nr $unsorted_psl -o $psl_file`; + # Sort by query sequence, score, chromosome + `sort -k 11,11nr -k 10,10d -k 1,1nr -k 14,14d $unsorted_psl -o $psl_file`; if ($?){ my $err = $!; print STDERR "Error sorting blat output: $err\n"; @@ -968,7 +969,8 @@ sub overhang_remapping { print STDERR "test=$test\t", join(" ", ($blat_prefix, $contig_file, $unsorted_psl, $options)), "\n" if($debug); return unless(-s $unsorted_psl); - `sort -k 10,10d -k 14,14d -k 1,1nr $unsorted_psl -o $psl_file`; + # Sort by query sequence, score, chromosome + `sort -k 10,10d -k 1,1nr -k 14,14d $unsorted_psl -o $psl_file`; if ($?){ my $err = $!; print STDERR "Error sorting blat output: $err\n";