adding bzip2 support in ruby

[biopieces.git] / bp_bin / write_bed

diff --git a/bp_bin/write_bed b/bp_bin/write_bed
index 34f88107b430e41b2fe63a05aa7845e9cc8b2590..5b1e1564934599c7cc475e075bdede71139f8f26 100755 (executable)
--- a/bp_bin/write_bed
+++ b/bp_bin/write_bed
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl -w
+#!/usr/bin/env perl
 
 # Copyright (C) 2007-2009 Martin A. Hansen.
 
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::UCSC::BED;
@@ -53,8 +54,6 @@ $fh = Maasha::Biopieces::write_stream( $options->{ 'data_out' }, $options->{ 'co
 
 while ( $record = Maasha::Biopieces::get_record( $in ) ) 
 {
-    $record = Maasha::UCSC::psl2record( $record ) if $record->{ 'tBaseInsert' }; # Dirty addition to allow Affy data from MySQL to be dumped
-
     if ( $bed_entry = Maasha::UCSC::BED::biopiece2bed( $record, $options->{ 'cols' } ) ) {
         Maasha::UCSC::BED::bed_entry_put( $bed_entry, $fh, $options->{ 'cols' }, $options->{ 'check' } );
     }