removed debug message

[biopieces.git] / bp_bin / write_bed

diff --git a/bp_bin/write_bed b/bp_bin/write_bed
index 38b8704c3c8d71542f8cf3f695114b1788045c7c..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' } );
     }
@@ -64,25 +63,22 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
 
 close $fh;
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
+
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }