ported bwa_seq to ruby for better SAM support

[biopieces.git] / bp_bin / write_fixedstep

diff --git a/bp_bin/write_fixedstep b/bp_bin/write_fixedstep
index 5de9a6bcde74eb82eca8d7a274b6fae6b2c6b011..a80bf0f810aa7a5af12e34f2c304e8076de22f19 100755 (executable)
--- a/bp_bin/write_fixedstep
+++ b/bp_bin/write_fixedstep
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl -w
+#!/usr/bin/env perl
 
 # Copyright (C) 2007-2009 Martin A. Hansen.
 
@@ -26,7 +26,9 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
+use Data::Dumper;
 use Maasha::Biopieces;
 use Maasha::UCSC::Wiggle;
 
@@ -60,25 +62,22 @@ 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();
 }