fixed a number of bugs in PSL

[biopieces.git] / bp_bin / blat_seq

diff --git a/bp_bin/blat_seq b/bp_bin/blat_seq
index e7dbc3a725e2d67b2065157cbcfcbbd34da657f7..342c5cd5a20c1602167b0c0057b8cb101e2b201d 100755 (executable)
--- a/bp_bin/blat_seq
+++ b/bp_bin/blat_seq
@@ -87,11 +87,15 @@ $blat_args .= " -q=$type";
 
 $result_file = "$tmp_dir/blat.psl";
 
-Maasha::Common::run( "blat", "$genome_file $query_file $blat_args $result_file > /dev/null 2>&1" );
+if ( $options->{ 'verbose' } ) {
+    Maasha::Common::run( "blat", "$genome_file $query_file $blat_args $result_file" );
+} else {
+    Maasha::Common::run( "blat", "$genome_file $query_file $blat_args $result_file > /dev/null 2>&1" );
+}
 
 unlink $query_file;
 
-$fh_in = Maasha::Filesys::file_read_opem( $result_file );
+$fh_in = Maasha::Filesys::file_read_open( $result_file );
 
 while ( $entry = Maasha::UCSC::PSL::psl_entry_get( $fh_in ) )
 {