refactoring of assemble_pairs

[biopieces.git] / bp_bin / get_genome_align

diff --git a/bp_bin/get_genome_align b/bp_bin/get_genome_align
index a346b9c11c9f3c3854924359df889d3223bcf731..566ea6e365072e40f388b27a6b9784e503547439 100755 (executable)
--- a/bp_bin/get_genome_align
+++ b/bp_bin/get_genome_align
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl -w
+#!/usr/bin/env perl
 
 # Copyright (C) 2007-2009 Martin A. Hansen.
 
@@ -26,17 +26,17 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::Common;
 use Maasha::UCSC;
-use Maasha::Filesys;
 
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $tmp_dir, $maf_track, $align, $align_num, $beg, $end, $len, $entry );
+my ( $options, $in, $out, $record, $tmp_dir, $maf_track, $align, $align_num, $beg, $end, $len, $entry );
 
 $options = Maasha::Biopieces::parse_options(
     [
@@ -117,7 +117,8 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
     $align_num++;
 }
 
-Maasha::Filesys::dir_remove( $tmp_dir );
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
 
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> SUBROUTINES <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
@@ -164,20 +165,13 @@ sub maf_track
 
 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();
 }
 
 
@@ -185,4 +179,3 @@ END
 
 
 __END__
-