removed variables bulk type

[biopieces.git] / bp_bin / get_genome_align

diff --git a/bp_bin/get_genome_align b/bp_bin/get_genome_align
index a346b9c11c9f3c3854924359df889d3223bcf731..3b8bf43df599280049bdc4e1c26ef3ea68e1f371 100755 (executable)
--- a/bp_bin/get_genome_align
+++ b/bp_bin/get_genome_align
@@ -36,7 +36,7 @@ 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(
     [
@@ -119,6 +119,9 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
 
 Maasha::Filesys::dir_remove( $tmp_dir );
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> SUBROUTINES <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
@@ -164,20 +167,13 @@ 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();
 }