implementing status solution

git-svn-id: http://biopieces.googlecode.com/svn/trunk@488 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/add_ident b/bp_bin/add_ident
index 16bde7abc886bd719452c467dc08f27d4183b765..bbf6623727b09b3341997e34623a1c58df1f8e30 100755 (executable)
--- a/bp_bin/add_ident
+++ b/bp_bin/add_ident
@@ -82,4 +82,3 @@ END
 
 
 __END__
-

diff --git a/bp_bin/align_pair_seq b/bp_bin/align_pair_seq
index 817ac256667fa84572f91725bbce810136d1cea0..ebe340d693a73f897a0ff1007c95f48aecb1f041 100755 (executable)
--- a/bp_bin/align_pair_seq
+++ b/bp_bin/align_pair_seq
@@ -92,4 +92,3 @@ END
 
 
 __END__
-

diff --git a/bp_bin/align_seq b/bp_bin/align_seq
index 56a6e5467bbefc0a3dcccd2fe9c35bc514628645..469a97abd7910fe5e6db8a5de884f594c7c4ea2b 100755 (executable)
--- a/bp_bin/align_seq
+++ b/bp_bin/align_seq
@@ -73,26 +73,22 @@ foreach $entry ( @entries )
     }
 }
 
+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();
 }
 
 
@@ -100,4 +96,3 @@ END
 
 
 __END__
-

diff --git a/bp_bin/analyze_bed b/bp_bin/analyze_bed
index 8548fa60840efed3d513eb18527c5a4f973cb45c..544424f1be1f8d42e0181fa97b5ee9cdc659e5fd 100755 (executable)
--- a/bp_bin/analyze_bed
+++ b/bp_bin/analyze_bed
@@ -48,26 +48,22 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
     Maasha::Biopieces::put_record( $record, $out );
 }
 
+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();
 }
 
 
@@ -75,4 +71,3 @@ END
 
 
 __END__
-

diff --git a/bp_bin/analyze_seq b/bp_bin/analyze_seq
index 6f76a9496e6041bf03189aa0ed56eb207c169104..952fc4a8e3cec256b68e99ca967ed20e47c23263 100755 (executable)
--- a/bp_bin/analyze_seq
+++ b/bp_bin/analyze_seq
@@ -54,26 +54,22 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
     Maasha::Biopieces::put_record( $record, $out );
 }
 
+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();
 }
 
 
@@ -81,4 +77,3 @@ END
 
 
 __END__
-

diff --git a/bp_bin/analyze_tags b/bp_bin/analyze_tags
index 68f97ac890f18f33598b788fedcfb1acbf0ad4b6..cb2452326c38816b62e0c3ff70ae8b88fbb755e3 100755 (executable)
--- a/bp_bin/analyze_tags
+++ b/bp_bin/analyze_tags
@@ -74,26 +74,22 @@ foreach $key ( sort { $a <=> $b } keys %len_hash )
     Maasha::Biopieces::put_record( $tag_record, $out );
 }
 
+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();
 }
 
 
@@ -101,4 +97,3 @@ END
 
 
 __END__
-

diff --git a/bp_bin/analyze_vals b/bp_bin/analyze_vals
index 86e50e6cb5cbaee40fd4acb9aa9cf6ba0de6f000..d246ac76fa96945c0b02f04b2eabca0c232b1a21 100755 (executable)
--- a/bp_bin/analyze_vals
+++ b/bp_bin/analyze_vals
@@ -126,25 +126,22 @@ print "$maxs\n";
 print "$sums\n";
 print "$means\n";
 
+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();
 }
 
 

diff --git a/bp_bin/assemble_tag_contigs b/bp_bin/assemble_tag_contigs
index 898837eeb8f70022a683927b3656676642a3d1ee..9236586f351b7ad6bc999a1ce25fc5de95c5611e 100755 (executable)
--- a/bp_bin/assemble_tag_contigs
+++ b/bp_bin/assemble_tag_contigs
@@ -93,25 +93,22 @@ foreach $chr ( sort keys %{ $file_hash } )
 
 Maasha::Filesys::dir_remove( $tmp_dir );
 
+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();
 }
 
 
@@ -119,4 +116,3 @@ END
 
 
 __END__
-

diff --git a/bp_bin/blast_seq b/bp_bin/blast_seq
index 1534c77655b15653812ef459dc603e1fd5f664e1..2d06389d45132df3dbf92da07cede06537265bc8 100755 (executable)
--- a/bp_bin/blast_seq
+++ b/bp_bin/blast_seq
@@ -141,6 +141,9 @@ unlink $tmp_out;
 
 Maasha::Filesys::dir_remove( $tmp_dir );
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> SUBROUTINES <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
@@ -268,19 +271,13 @@ sub blast_tab2biopiece
 
 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();
 }
 
 
@@ -288,4 +285,3 @@ END
 
 
 __END__
-

diff --git a/bp_bin/blat_seq b/bp_bin/blat_seq
index 9c3ffa7f879f6c4ef8932aba5633165af0ef176a..4f68e0ebd720912b4ce43becf5c336adeb4ea0c9 100755 (executable)
--- a/bp_bin/blat_seq
+++ b/bp_bin/blat_seq
@@ -105,26 +105,22 @@ unlink $result_file;
 
 Maasha::Filesys::dir_remove( $tmp_dir );
 
+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();
 }
 
 
@@ -132,4 +128,3 @@ END
 
 
 __END__
-

diff --git a/bp_bin/calc_bit_scores b/bp_bin/calc_bit_scores
index 6bb5374eb2be9e55fe6c31c5aa6847f1071cbf8e..a6347019c2c1dcfb41fb89ea7403ac4218b6d20c 100755 (executable)
--- a/bp_bin/calc_bit_scores
+++ b/bp_bin/calc_bit_scores
@@ -85,25 +85,22 @@ for ( $i = 0; $i < keys %freq_hash; $i++ )
 
 Maasha::Biopieces::put_record( $record, $out );
 
+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();
 }
 
 
@@ -111,5 +108,3 @@ END
 
 
 __END__
-
-

diff --git a/bp_bin/calc_fixedstep b/bp_bin/calc_fixedstep
index cbb068a8ec42a7dc80e2bd86aa97dae7f45b3df8..27cae9f22fb64ca3a247800a5e8f26316d9d3f52 100755 (executable)
--- a/bp_bin/calc_fixedstep
+++ b/bp_bin/calc_fixedstep
@@ -95,25 +95,22 @@ foreach $chr ( sort keys %{ $file_hash } )
 
 Maasha::Filesys::dir_remove( $tmp_dir );
 
+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();
 }
 
 

diff --git a/bp_bin/complement_seq b/bp_bin/complement_seq
index 38d1dae27056706b884fc7105c75cfd14fd0abb4..6e7ba9053d58109f18a8ef6957f9e29f4571f7ad 100755 (executable)
--- a/bp_bin/complement_seq
+++ b/bp_bin/complement_seq
@@ -60,24 +60,22 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
 }
 
 
+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();
 }
 
 
@@ -85,5 +83,3 @@ END
 
 
 __END__
-
-

diff --git a/bp_bin/compute b/bp_bin/compute
index 299b787445e4bee7e6a89b9954e7fe3fe41b29df..6fbcdbb56c34162052d0d596dd77c2a6189556c7 100755 (executable)
--- a/bp_bin/compute
+++ b/bp_bin/compute
@@ -72,25 +72,22 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
     Maasha::Biopieces::put_record( $record, $out );
 }
 
+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();
 }
 
 

diff --git a/bp_bin/count_records b/bp_bin/count_records
index 3907e4f313c8aa684197fe8692d05518b925254d..6f97188f577f60e661c15a6cf632efc3553f5fe6 100755 (executable)
--- a/bp_bin/count_records
+++ b/bp_bin/count_records
@@ -75,25 +75,22 @@ Maasha::Biopieces::put_record( $result, $data_out );
 
 close $data_out;
 
+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();
 }
 
 

diff --git a/bp_bin/count_vals b/bp_bin/count_vals
index 449fe81dfade7206e0d5ee023e376621d77f6913..7f0fe503676d1a4bb2105815f14d390b16eacd95 100755 (executable)
--- a/bp_bin/count_vals
+++ b/bp_bin/count_vals
@@ -107,25 +107,22 @@ unlink $tmp_file;
 
 Maasha::Filesys::dir_remove( $tmp_dir );
 
+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();
 }
 
 

diff --git a/bp_bin/create_blast_db b/bp_bin/create_blast_db
index 9273af60a7976d6133ead3769dd546259f722867..58824690f97586108154fd551e8b42cee83d0a4f 100755 (executable)
--- a/bp_bin/create_blast_db
+++ b/bp_bin/create_blast_db
@@ -73,25 +73,22 @@ if ( $seq_type eq "protein" ) {
 
 unlink $path;
 
+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();
 }
 
 
@@ -99,4 +96,3 @@ END
 
 
 __END__
-

diff --git a/bp_bin/create_vmatch_index b/bp_bin/create_vmatch_index
index e6dc983a804cf0f9c0b2447177f617af57044773..0dc28c054410bde2f9d58cde7acd197b9795a41c 100755 (executable)
--- a/bp_bin/create_vmatch_index
+++ b/bp_bin/create_vmatch_index
@@ -75,25 +75,22 @@ if ( $type eq "protein" ) {
 
 unlink $file_tmp;
 
+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();
 }
 
 
@@ -101,5 +98,3 @@ END
 
 
 __END__
-
-

diff --git a/bp_bin/create_weight_matrix b/bp_bin/create_weight_matrix
index 8adffcf90edf31045b98c3731fce0090de2eae19..fa3cd776bd25e87ade3b37bc0ccbbd6ea10d207f 100755 (executable)
--- a/bp_bin/create_weight_matrix
+++ b/bp_bin/create_weight_matrix
@@ -87,25 +87,22 @@ foreach $res ( sort keys %res_hash )
     Maasha::Biopieces::put_record( $record, $out );
 }
 
+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();
 }
 
 

diff --git a/bp_bin/extract_seq b/bp_bin/extract_seq
index c900bc77eef4d92afdf2492f15ccfec7d9fe57b6..158804270a88ef4920acb7f41b34b63c9764bc23 100755 (executable)
--- a/bp_bin/extract_seq
+++ b/bp_bin/extract_seq
@@ -93,26 +93,22 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
     Maasha::Biopieces::put_record( $record, $out );
 }
 
+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();
 }
 
 
@@ -120,4 +116,3 @@ END
 
 
 __END__
-

diff --git a/bp_bin/flip_tab b/bp_bin/flip_tab
index 605b27733c3f631202ec5cef00b96a7062b97754..c24cf0f2df0f45a290e09c9dd9c7eeefda8457f6 100755 (executable)
--- a/bp_bin/flip_tab
+++ b/bp_bin/flip_tab
@@ -67,25 +67,22 @@ foreach $row ( @matrix )
     Maasha::Biopieces::put_record( $record, $out );
 }
 
+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();
 }
 
 

diff --git a/bp_bin/fold_seq b/bp_bin/fold_seq
index 701f900562d80fac4b3e2e05b0106c26e95f1c51..c8eba697e3023ca76811611407d4bbb96af6e6f8 100755 (executable)
--- a/bp_bin/fold_seq
+++ b/bp_bin/fold_seq
@@ -62,25 +62,22 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
     Maasha::Biopieces::put_record( $record, $out );
 }
 
+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();
 }
 
 

diff --git a/bp_bin/format_genome b/bp_bin/format_genome
index 6ffa92d2b4ff7a603b2e17916227884df0be415a..d5058cac84da12023a8619fea0746e0a04b1a56d 100755 (executable)
--- a/bp_bin/format_genome
+++ b/bp_bin/format_genome
@@ -114,25 +114,22 @@ foreach $format ( @{ $options->{ 'formats' } } )
 
 close $fh_out if $fh_out;
 
+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();
 }
 
 

diff --git a/bp_bin/get_genome_align b/bp_bin/get_genome_align
index 3b8bf43df599280049bdc4e1c26ef3ea68e1f371..b1e5c1d31a140637b515eb139c36dc6b4b19b173 100755 (executable)
--- a/bp_bin/get_genome_align
+++ b/bp_bin/get_genome_align
@@ -181,4 +181,3 @@ END
 
 
 __END__
-

diff --git a/bp_bin/get_genome_phastcons b/bp_bin/get_genome_phastcons
index 337c019851984f79c9c6a5b35f57b68b7ad59402..24994abfe61a385d0bff5353fea67b542477b170 100755 (executable)
--- a/bp_bin/get_genome_phastcons
+++ b/bp_bin/get_genome_phastcons
@@ -101,26 +101,22 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
 
 close $fh_phastcons if $fh_phastcons;                                                                                                                                          
 
+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();
 }
 
 
@@ -128,4 +124,3 @@ END
 
 
 __END__
-

diff --git a/bp_bin/get_genome_seq b/bp_bin/get_genome_seq
index bf0f787fa5317c4debd47c46e7007130b8e0826f..b5ea5a70d73ed4c661693674d4ff713d383e5913 100755 (executable)
--- a/bp_bin/get_genome_seq
+++ b/bp_bin/get_genome_seq
@@ -191,26 +191,22 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
     Maasha::Biopieces::put_record( $record, $out );
 }
 
+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();
 }
 
 
@@ -218,4 +214,3 @@ END
 
 
 __END__
-

diff --git a/bp_bin/grab b/bp_bin/grab
index 1fecf4303acbedefaa94b1ca18be8896fbbc5fde..806ae1c10d2ad70c5a2708efce01f783e5dc14eb 100755 (executable)
--- a/bp_bin/grab
+++ b/bp_bin/grab
@@ -120,6 +120,8 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
     }
 }
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
 
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> SUBROUTINES <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
@@ -274,20 +276,13 @@ sub grab_eval
 
 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();
 }
 
 
@@ -295,4 +290,3 @@ END
 
 
 __END__
-

diff --git a/bp_bin/head_records b/bp_bin/head_records
index 631973c0544158bb76005f7be4b4d56ffe6d0043..d537501e3fc0aa042d3c972f0391f86d2a14e1a6 100755 (executable)
--- a/bp_bin/head_records
+++ b/bp_bin/head_records
@@ -55,26 +55,22 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
     last if $count == $options->{ "num" };
 }
 
+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();
 }
 
 
@@ -82,4 +78,3 @@ END
 
 
 __END__
-

diff --git a/bp_bin/invert_align b/bp_bin/invert_align
index f8b330a13d1b8a2528f508891aa88de98a11e238..84f17d357b9cf7a26b4b46de2ee9a89dfb247745 100755 (executable)
--- a/bp_bin/invert_align
+++ b/bp_bin/invert_align
@@ -66,26 +66,22 @@ Maasha::Align::align_invert( \@entries, $options->{ "soft" } );
 
 map { Maasha::Biopieces::put_record( { SEQ_NAME => $_->[ SEQ_NAME ], SEQ => $_->[ SEQ ] }, $out ) } @entries;
 
+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();
 }
 
 
@@ -93,4 +89,3 @@ END
 
 
 __END__
-

diff --git a/bp_bin/length_seq b/bp_bin/length_seq
index b00eb3e875df0c3a95ea0281cccfd5552e52be62..f7c3d95160a6a5f72d7d9a134f8c4ee107065b95 100755 (executable)
--- a/bp_bin/length_seq
+++ b/bp_bin/length_seq
@@ -58,26 +58,22 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
 
 Maasha::Biopieces::put_record( { TOTAL_SEQ_LEN => $total }, $out );
 
+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();
 }
 
 
@@ -85,4 +81,3 @@ END
 
 
 __END__
-

diff --git a/bp_bin/length_vals b/bp_bin/length_vals
index f9f1616cd9888700aab562d2eb7a857a618c0a77..99a3c2b3ecbad99dfb513fab72d4c2c0d1c30f42 100755 (executable)
--- a/bp_bin/length_vals
+++ b/bp_bin/length_vals
@@ -56,26 +56,22 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
     Maasha::Biopieces::put_record( $record, $out );
 }
 
+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();
 }
 
 
@@ -83,4 +79,3 @@ END
 
 
 __END__
-

diff --git a/bp_bin/list_biopieces b/bp_bin/list_biopieces
index f58f2e8cc265be843bef5cf9a5a9c99866c028a0..a51a2ade81919687c2f550a65250fb2a06662cee 100755 (executable)
--- a/bp_bin/list_biopieces
+++ b/bp_bin/list_biopieces
@@ -62,16 +62,13 @@ foreach $file ( sort @files )
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
+
 END
 {
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
@@ -79,5 +76,3 @@ END
 
 
 __END__
-
-

diff --git a/bp_bin/list_genomes b/bp_bin/list_genomes
index 147d5c1def623caca7bcdbe793a6c7566d6e5cab..7a4f4577b30d0497eeeb62bcf466fdcb330ba7b0 100755 (executable)
--- a/bp_bin/list_genomes
+++ b/bp_bin/list_genomes
@@ -85,16 +85,13 @@ foreach $genome ( sort keys %hash )
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
+
 END
 {
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
@@ -102,5 +99,3 @@ END
 
 
 __END__
-
-

diff --git a/bp_bin/match_seq b/bp_bin/match_seq
index 0ce31eb39e675fea43196f07ad22a91bf25c1269..b418f3c1ff91bb832dab5afa3dffd5ec61983e5c 100755 (executable)
--- a/bp_bin/match_seq
+++ b/bp_bin/match_seq
@@ -73,26 +73,22 @@ elsif ( @entries == 2 )
 
 Maasha::Filesys::dir_remove( $tmp_dir );
 
+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();
 }
 
 
@@ -100,4 +96,3 @@ END
 
 
 __END__
-

diff --git a/bp_bin/max_vals b/bp_bin/max_vals
index 7c760a5b1a2bffb63050f0abd9f40468d087fa9d..49e6fedea525b6b59363c702d7b1d847502775ef 100755 (executable)
--- a/bp_bin/max_vals
+++ b/bp_bin/max_vals
@@ -74,26 +74,22 @@ Maasha::Biopieces::put_record( $max_record, $fh );
 
 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();
 }
 
 
@@ -101,4 +97,3 @@ END
 
 
 __END__
-

diff --git a/bp_bin/mean_vals b/bp_bin/mean_vals
index fb073cdf0e19d7cf1f72ec7a94aa980d1ed135f9..654c4fe337de2c41ac7d8ab62bbe47a9cd3c3ae9 100755 (executable)
--- a/bp_bin/mean_vals
+++ b/bp_bin/mean_vals
@@ -75,26 +75,22 @@ foreach $key ( @{ $options->{ "keys" } } )
 
 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();
 }
 
 
@@ -102,4 +98,3 @@ END
 
 
 __END__
-

diff --git a/bp_bin/median_vals b/bp_bin/median_vals
index 9428f9a2efd18dbaa6596f032c6178cdc04dcd2d..c1b8013bc9d5c8307463da2493bc3afa038b2e3c 100755 (executable)
--- a/bp_bin/median_vals
+++ b/bp_bin/median_vals
@@ -71,26 +71,22 @@ foreach $key ( @{ $options->{ "keys" } } )
 
 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();
 }
 
 
@@ -98,4 +94,3 @@ END
 
 
 __END__
-

diff --git a/bp_bin/merge_records b/bp_bin/merge_records
index 39f09e2df8cde1e367e0993e37463cd6ef95aed0..ad0d06e435827275e12735650d744a01bbe40ccc 100755 (executable)
--- a/bp_bin/merge_records
+++ b/bp_bin/merge_records
@@ -203,26 +203,22 @@ if ( $num2 > 0 and $options->{ 'merge' } =~ /^(BorA|BnotA)$/ )
 
 Maasha::Filesys::dir_remove( $tmp_dir );
 
+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();
 }
 
 
@@ -230,4 +226,3 @@ END
 
 
 __END__
-

diff --git a/bp_bin/merge_vals b/bp_bin/merge_vals
index c751a4d8902139790f30812defbd08ba27245ee7..9979d074a9690f32d21834fa95941f52bd9b1475 100755 (executable)
--- a/bp_bin/merge_vals
+++ b/bp_bin/merge_vals
@@ -61,26 +61,22 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
     Maasha::Biopieces::put_record( $record, $out );
 }
 
+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();
 }
 
 
@@ -88,4 +84,3 @@ END
 
 
 __END__
-

diff --git a/bp_bin/min_vals b/bp_bin/min_vals
index 34024b1fd2ef1a911ea4468a310e092ae6b5801a..7eeb7a6a4351a4431ae53c0bcb6c552e6c4320c5 100755 (executable)
--- a/bp_bin/min_vals
+++ b/bp_bin/min_vals
@@ -74,26 +74,22 @@ Maasha::Biopieces::put_record( $min_record, $fh );
 
 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();
 }
 
 
@@ -101,4 +97,3 @@ END
 
 
 __END__
-

diff --git a/bp_bin/oligo_freq b/bp_bin/oligo_freq
index e179d8dd218855831e48b8c4c81b765150f9bf74..d6606102ea892f01e8d260fc6d503200c6ead00e 100755 (executable)
--- a/bp_bin/oligo_freq
+++ b/bp_bin/oligo_freq
@@ -71,26 +71,22 @@ if ( defined $options->{ "all" } )
     map { Maasha::Biopieces::put_record( $_, $out ) } @freq_table;
 }
 
+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();
 }
 
 
@@ -98,4 +94,3 @@ END
 
 
 __END__
-

diff --git a/bp_bin/patscan_seq b/bp_bin/patscan_seq
index 60a5cae0bdbc18fc9450bc06d1dc9771ebed2572..d6b9c1b60322b13824f5a25bc61f0d59d00a8f9b 100755 (executable)
--- a/bp_bin/patscan_seq
+++ b/bp_bin/patscan_seq
@@ -139,6 +139,9 @@ unlink $seq_file if not $options->{ 'genome' };
 
 Maasha::Filesys::dir_remove( $tmp_dir );
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> SUBROUTINES <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
@@ -219,20 +222,13 @@ sub pat_write
 
 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();
 }
 
 
@@ -240,4 +236,3 @@ END
 
 
 __END__
-

diff --git a/bp_bin/plot_chrdist b/bp_bin/plot_chrdist
index df4db5a7e7cb07b2abc729065d109383a7c0ca53..16b86a6f1e3b853eece51309e981f1de768ef720 100755 (executable)
--- a/bp_bin/plot_chrdist
+++ b/bp_bin/plot_chrdist
@@ -97,26 +97,22 @@ print $fh "$_\n" foreach @{ $result };
 
 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();
 }
 
 
@@ -124,4 +120,3 @@ END
 
 
 __END__
-

diff --git a/bp_bin/plot_histogram b/bp_bin/plot_histogram
index 9eccb6812bade735d8ae4b21ec54e0a92b1c1227..74ba7486e2feaef842e5d7f99a04776fb95589ad 100755 (executable)
--- a/bp_bin/plot_histogram
+++ b/bp_bin/plot_histogram
@@ -76,26 +76,22 @@ print $fh "$_\n" foreach @{ $result };
 
 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();
 }
 
 
@@ -103,4 +99,3 @@ END
 
 
 __END__
-

diff --git a/bp_bin/plot_karyogram b/bp_bin/plot_karyogram
index 9adf2f8427bcd1065a93f86f9579474aec9df88f..e9542ca40979c4ca95584e20a77471fca8f6fada 100755 (executable)
--- a/bp_bin/plot_karyogram
+++ b/bp_bin/plot_karyogram
@@ -69,26 +69,22 @@ print $fh $result;
 
 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();
 }
 
 
@@ -96,4 +92,3 @@ END
 
 
 __END__
-

diff --git a/bp_bin/plot_lendist b/bp_bin/plot_lendist
index a2fb9ccfb03ef338d41974acd8325d9cb04d6772..a515f5c8c797fdcf7aadcabb1bcb4d203a0df2a4 100755 (executable)
--- a/bp_bin/plot_lendist
+++ b/bp_bin/plot_lendist
@@ -76,26 +76,22 @@ print $fh "$_\n" foreach @{ $result };
 
 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();
 }
 
 
@@ -103,4 +99,3 @@ END
 
 
 __END__
-

diff --git a/bp_bin/plot_matches b/bp_bin/plot_matches
index f383da8ad2c39e0ef4bdfb406fd81eeea10623ad..9bdb0874693885ffb9ce5bdadfeb991c42ab5ec2 100755 (executable)
--- a/bp_bin/plot_matches
+++ b/bp_bin/plot_matches
@@ -80,6 +80,9 @@ close $fh;
 
 Maasha::Filesys::dir_remove( $tmp_dir );
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> SUBROUTINES <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
@@ -189,20 +192,13 @@ sub dotplot_matches
 
 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();
 }
 
 
@@ -210,4 +206,3 @@ END
 
 
 __END__
-

diff --git a/bp_bin/plot_phastcons_profiles b/bp_bin/plot_phastcons_profiles
index caf444f629b7ae38fb5d53cd1d9888737ffac48a..b1af87bb4f8e2b1325cdd57939e70d7ef37889e6 100755 (executable)
--- a/bp_bin/plot_phastcons_profiles
+++ b/bp_bin/plot_phastcons_profiles
@@ -101,26 +101,22 @@ close $fh;
 
 Maasha::Filesys::dir_remove( $tmp_dir );
 
+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();
 }
 
 
@@ -128,4 +124,3 @@ END
 
 
 __END__
-

diff --git a/bp_bin/plot_seqlogo b/bp_bin/plot_seqlogo
index e9be5a6b2fae5df2b959f8691d6853b772acd9a8..34a533f969a36034c6c3954c99dfb06c531a6ca2 100755 (executable)
--- a/bp_bin/plot_seqlogo
+++ b/bp_bin/plot_seqlogo
@@ -63,26 +63,22 @@ print $fh $logo;
 
 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();
 }
 
 
@@ -90,4 +86,3 @@ END
 
 
 __END__
-

diff --git a/bp_bin/print_wiki b/bp_bin/print_wiki
index b13d514436e348880de788e1b8d16ee006a2e6cc..1c36c1096be2b46dfa5c1148306fdf9e2222eb38 100755 (executable)
--- a/bp_bin/print_wiki
+++ b/bp_bin/print_wiki
@@ -62,21 +62,17 @@ print STDERR "$_\n" foreach @{ $lines };
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
 
 END
 {
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
+
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 __END__
-

diff --git a/bp_bin/random_records b/bp_bin/random_records
index 5c4595cc222b250b722b9b0270ea7cec601489b2..83ac80d858b8dfb942f6a801c4e683800e18e0bc 100755 (executable)
--- a/bp_bin/random_records
+++ b/bp_bin/random_records
@@ -98,26 +98,22 @@ close $fh_in;
 unlink $tmp_file;
 Maasha::Filesys::dir_remove( $tmp_dir );
 
+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();
 }
 
 
@@ -125,4 +121,3 @@ END
 
 
 __END__
-

diff --git a/bp_bin/read_2bit b/bp_bin/read_2bit
index 63bb7e1988f72efa502216edb28eabb9b42ac489..ab2816a8c1fa42cdc53aa4141b19c4f920b5af84 100755 (executable)
--- a/bp_bin/read_2bit
+++ b/bp_bin/read_2bit
@@ -82,25 +82,22 @@ NUM:
 
 close $data_in if $data_in;
 
+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();
 }
 
 

diff --git a/bp_bin/read_bed b/bp_bin/read_bed
index 551d86e10662ca48ca63825775d68539c74702c7..177d1c7855524e7c06afeeaf46420321e523d93a 100755 (executable)
--- a/bp_bin/read_bed
+++ b/bp_bin/read_bed
@@ -73,25 +73,22 @@ if ( $options->{ 'data_in' } )
     close $data_in;
 }
 
+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();
 }
 
 

diff --git a/bp_bin/read_blast_tab b/bp_bin/read_blast_tab
index fcf53ae34b001b5aee5f0f1c6e13c6adae8e5f94..d5aaf8aed6dc1377efe74bd69820bdb78a2a083d 100755 (executable)
--- a/bp_bin/read_blast_tab
+++ b/bp_bin/read_blast_tab
@@ -99,25 +99,22 @@ if ( $options->{ 'data_in' } )
     close $data_in;
 }
 
+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();
 }
 
 

diff --git a/bp_bin/read_embl b/bp_bin/read_embl
index 80cc39ab791652f7a9539e8f2f3b4a6dc444b98a..7197794e8c0a0415e38f35b32204f5c6c024fe02 100755 (executable)
--- a/bp_bin/read_embl
+++ b/bp_bin/read_embl
@@ -106,25 +106,22 @@ if ( $options->{ 'data_in' } )
     close $data_in;
 }
 
+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();
 }
 
 

diff --git a/bp_bin/read_fasta b/bp_bin/read_fasta
index 17a26df65c136640692aede7b15355ca312a66e7..1c350698a6b1579ad8e605596ead58ed4641dc19 100755 (executable)
--- a/bp_bin/read_fasta
+++ b/bp_bin/read_fasta
@@ -94,4 +94,3 @@ END
 
 
 __END__
-

diff --git a/bp_bin/read_fixedstep b/bp_bin/read_fixedstep
index 794599bdf8315650fddaec148b4dd57028d528a3..16ad12f6d73fe0e8cf71230af53f7ea08924abaf 100755 (executable)
--- a/bp_bin/read_fixedstep
+++ b/bp_bin/read_fixedstep
@@ -71,25 +71,22 @@ if ( $options->{ 'data_in' } )
     close $data_in;
 }
 
+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();
 }
 
 

diff --git a/bp_bin/read_gff b/bp_bin/read_gff
index f7162a1118df43af98e5311f95c51eb0fd8a06df..3901757e16980816ca9f7b9c2afb8a742f621132 100755 (executable)
--- a/bp_bin/read_gff
+++ b/bp_bin/read_gff
@@ -69,25 +69,22 @@ if ( $options->{ 'data_in' } )
     close $data_in;
 }
 
+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();
 }
 
 

diff --git a/bp_bin/read_mysql b/bp_bin/read_mysql
index b79458bcf200cbf7462f40b96dfa8d6e164df977..f0ce4def8715113e9774d2557062597e8c2fb165 100755 (executable)
--- a/bp_bin/read_mysql
+++ b/bp_bin/read_mysql
@@ -64,25 +64,22 @@ Maasha::SQL::disconnect( $dbh );
 
 map { Maasha::Biopieces::put_record( $_ ) } @{ $results };
 
+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();
 }
 
 

diff --git a/bp_bin/read_psl b/bp_bin/read_psl
index c7183ee9b3cc95242bd26d259353d772fcb0dac3..866b99bc3343944eadeaafd60b60ef4788ea49ea 100755 (executable)
--- a/bp_bin/read_psl
+++ b/bp_bin/read_psl
@@ -69,25 +69,22 @@ if ( $options->{ 'data_in' } )
     close $data_in;
 }
 
+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();
 }
 
 

diff --git a/bp_bin/read_soft b/bp_bin/read_soft
index c51ba9051eeec77a77dec273fd31d53b70d477b7..dfbf9f387a77683023180284d0b61979ef31eb88 100755 (executable)
--- a/bp_bin/read_soft
+++ b/bp_bin/read_soft
@@ -103,25 +103,22 @@ NUM:
 close $data_in if $data_in;
 close $fh if $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();
 }
 
 

diff --git a/bp_bin/read_solexa b/bp_bin/read_solexa
index b35c21c66dc16b10e09af29118e69f75d6c5c4de..f509aa49f0d49c014a93fec79461911411e70a76 100755 (executable)
--- a/bp_bin/read_solexa
+++ b/bp_bin/read_solexa
@@ -89,25 +89,22 @@ if ( $options->{ 'data_in' } )
     close $data_in;
 }
 
+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();
 }
 
 

diff --git a/bp_bin/read_solid b/bp_bin/read_solid
index b39e596177f7f99e3994878f0ac51e1e29998bc1..cfcd4e6ef834244db16e6f0491292fec8b07f6c2 100755 (executable)
--- a/bp_bin/read_solid
+++ b/bp_bin/read_solid
@@ -93,25 +93,22 @@ if ( $options->{ 'data_in' } )
     close $data_in;
 }
 
+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();
 }
 
 

diff --git a/bp_bin/read_stockholm b/bp_bin/read_stockholm
index f883d410d22c5f8234b4977c6baff7cc44fa31e9..177ded535bc1a7c41826455bef469cc13848f13a 100755 (executable)
--- a/bp_bin/read_stockholm
+++ b/bp_bin/read_stockholm
@@ -91,6 +91,8 @@ if ( $options->{ 'data_in' } )
     close $data_in;
 }
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
 
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
@@ -98,19 +100,13 @@ if ( $options->{ 'data_in' } )
 
 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();
 }
 
 

diff --git a/bp_bin/read_tab b/bp_bin/read_tab
index 152c0d5f26fd8e715afc2b8a6c26ff7dbc6eab56..0fda36bedd3aebc05a4c31cb1eeb1ae4a310ba2c 100755 (executable)
--- a/bp_bin/read_tab
+++ b/bp_bin/read_tab
@@ -104,25 +104,22 @@ if ( $options->{ 'data_in' } )
     close $data_in;
 }
 
+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();
 }
 
 
@@ -130,7 +127,3 @@ END
 
 
 __END__
-
-
-
-

diff --git a/bp_bin/read_ucsc_config b/bp_bin/read_ucsc_config
index a62000b776366f34630baf68a80f19db1a1a0dbe..a07a99f6041514043f71a10f04688351bad39807 100755 (executable)
--- a/bp_bin/read_ucsc_config
+++ b/bp_bin/read_ucsc_config
@@ -71,25 +71,22 @@ if ( $options->{ 'data_in' } )
     close $data_in;
 }
 
+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();
 }
 
 

diff --git a/bp_bin/remove_adaptor b/bp_bin/remove_adaptor
index d9898292277f4efaf4783e0ffb07ac9e417f5e24..a07a719ea69ef773b4f29a91b1a21a42ac24e54f 100755 (executable)
--- a/bp_bin/remove_adaptor
+++ b/bp_bin/remove_adaptor
@@ -94,26 +94,22 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
     }
 }
 
+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();
 }
 
 
@@ -121,4 +117,3 @@ END
 
 
 __END__
-

diff --git a/bp_bin/remove_indels b/bp_bin/remove_indels
index e476694a7c77b2bdcb40c59004aa4430938b89fe..5d350e09851c8a81dd0b807f0256666d0ffa3ac2 100755 (executable)
--- a/bp_bin/remove_indels
+++ b/bp_bin/remove_indels
@@ -47,26 +47,22 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
     Maasha::Biopieces::put_record( $record, $out );
 }
 
+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();
 }
 
 
@@ -74,4 +70,3 @@ END
 
 
 __END__
-

diff --git a/bp_bin/remove_keys b/bp_bin/remove_keys
index 0683dceebda3cad81f432460cbc8eda42901988b..03c6bcba8b93af9e009da9f34419112fc023fc60 100755 (executable)
--- a/bp_bin/remove_keys
+++ b/bp_bin/remove_keys
@@ -61,26 +61,22 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
     Maasha::Biopieces::put_record( $record, $out ) if keys %{ $record };
 }
 
+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();
 }
 
 
@@ -88,4 +84,3 @@ END
 
 
 __END__
-

diff --git a/bp_bin/remove_mysql_tables b/bp_bin/remove_mysql_tables
index 28751697a5cb66b4b4fa7e48d3cadc3ddba9bf99..64450f41580bffb4ec8b0f5cfac6b0b9aeb3c71b 100755 (executable)
--- a/bp_bin/remove_mysql_tables
+++ b/bp_bin/remove_mysql_tables
@@ -84,26 +84,22 @@ foreach $table ( sort keys %table_hash )
 
 Maasha::SQL::disconnect( $dbh );
 
+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();
 }
 
 
@@ -111,4 +107,3 @@ END
 
 
 __END__
-

diff --git a/bp_bin/remove_ucsc_tracks b/bp_bin/remove_ucsc_tracks
index ca565750a02eb9134746837f19e21db30a01794d..e4005022b2371402afbafd3b715f449e8d248af3 100755 (executable)
--- a/bp_bin/remove_ucsc_tracks
+++ b/bp_bin/remove_ucsc_tracks
@@ -116,26 +116,22 @@ Maasha::SQL::disconnect( $dbh );
 
 Maasha::Common::run( "ucscMakeTracks.pl", "-b > /dev/null 2>&1" );
 
+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();
 }
 
 
@@ -143,4 +139,3 @@ END
 
 
 __END__
-

diff --git a/bp_bin/rename_keys b/bp_bin/rename_keys
index 4a804d496d9ab14c7dc001f0a1520c3f4e0cd676..a792544450d90e8087217a5e376c212f337f9eeb 100755 (executable)
--- a/bp_bin/rename_keys
+++ b/bp_bin/rename_keys
@@ -56,26 +56,22 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
     Maasha::Biopieces::put_record( $record, $out );
 }
 
+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();
 }
 
 
@@ -83,4 +79,3 @@ END
 
 
 __END__
-

diff --git a/bp_bin/reverse_seq b/bp_bin/reverse_seq
index 7d2052da33bd11c4a425e9c2bba07259abe1b78a..1b331c9670d227c450b46fded099aa256cf62bba 100755 (executable)
--- a/bp_bin/reverse_seq
+++ b/bp_bin/reverse_seq
@@ -47,24 +47,22 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
     Maasha::Biopieces::put_record( $record, $out );
 }
 
+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();
 }
 
 

diff --git a/bp_bin/shuffle_seq b/bp_bin/shuffle_seq
index 05932c45e8f757bc87a2215272ab922697ddbfb6..e7913971901b93525decb2176e5cd0c7319db099 100755 (executable)
--- a/bp_bin/shuffle_seq
+++ b/bp_bin/shuffle_seq
@@ -48,24 +48,22 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
     Maasha::Biopieces::put_record( $record, $out );
 }
 
+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();
 }
 
 

diff --git a/bp_bin/soap_seq b/bp_bin/soap_seq
index f99bbb3c3b76ea364027569ac3a95eab257b4d76..7adb6a969e5f91f0a2ddf4738692e1f3343f01ff 100755 (executable)
--- a/bp_bin/soap_seq
+++ b/bp_bin/soap_seq
@@ -126,25 +126,22 @@ unlink $tmp_out;
 
 Maasha::Filesys::dir_remove( $tmp_dir );
 
+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();
 }
 
 
@@ -152,4 +149,3 @@ END
 
 
 __END__
-

diff --git a/bp_bin/sort_records b/bp_bin/sort_records
index 13bd4eb379043d81a0ca82d5b1a050dbfc5e10b0..c9b3085269545dccdb9fe409f9bfb1b0f155f22c 100755 (executable)
--- a/bp_bin/sort_records
+++ b/bp_bin/sort_records
@@ -87,26 +87,22 @@ else
     }
 }
 
+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();
 }
 
 
@@ -114,4 +110,3 @@ END
 
 
 __END__
-

diff --git a/bp_bin/split_bed b/bp_bin/split_bed
index 97cbaf6a7cb79670ac4f8ce59ffbac7ab064853d..d344a3c7b23ae2dac1fdb476a37f94935cd988ee 100755 (executable)
--- a/bp_bin/split_bed
+++ b/bp_bin/split_bed
@@ -71,26 +71,22 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
     }
 }
 
+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();
 }
 
 
@@ -98,4 +94,3 @@ END
 
 
 __END__
-

diff --git a/bp_bin/split_seq b/bp_bin/split_seq
index 776a79bfcc4fe69b96c4c1419b0e5c340821792e..7c4c5980a6e4162bc8e85262a629f7ee63a9cd16 100755 (executable)
--- a/bp_bin/split_seq
+++ b/bp_bin/split_seq
@@ -77,26 +77,22 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
     }
 }
 
+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();
 }
 
 
@@ -104,4 +100,3 @@ END
 
 
 __END__
-

diff --git a/bp_bin/split_vals b/bp_bin/split_vals
index f7249f864d9332d84f8ba6cde82617827eb35dbd..77194a3ef01fb46c1495254e1bd43800adae764d 100755 (executable)
--- a/bp_bin/split_vals
+++ b/bp_bin/split_vals
@@ -91,4 +91,3 @@ END
 
 
 __END__
-

diff --git a/bp_bin/sum_vals b/bp_bin/sum_vals
index 1da7130473ca5bc70607954eea3c7ed23df2dd3b..b0b150a4ed6322ae3888bb26f3c7b924927dc3b8 100755 (executable)
--- a/bp_bin/sum_vals
+++ b/bp_bin/sum_vals
@@ -66,26 +66,22 @@ foreach $key ( @{ $options->{ "keys" } } ) {
 
 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();
 }
 
 
@@ -93,4 +89,3 @@ END
 
 
 __END__
-

diff --git a/bp_bin/tile_seq b/bp_bin/tile_seq
index a90f1e40e5c86f0273c90b7f58e72fcfac5ff238..139a6f255d97c8fa985f07a7fba32c91dd290ec1 100755 (executable)
--- a/bp_bin/tile_seq
+++ b/bp_bin/tile_seq
@@ -78,26 +78,22 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
 
 map { Maasha::Biopieces::put_record( { SEQ_NAME => $_->[ SEQ_NAME ], SEQ => $_->[ SEQ ] }, $out ) } @entries;
 
+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();
 }
 
 
@@ -105,4 +101,3 @@ END
 
 
 __END__
-

diff --git a/bp_bin/translate_seq b/bp_bin/translate_seq
index 21452b901c22ba142713e69698331c615308f8cf..9627c9d05deba5ac6c018848a522434ff3ad2989 100755 (executable)
--- a/bp_bin/translate_seq
+++ b/bp_bin/translate_seq
@@ -69,26 +69,22 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
     }
 }
 
+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();
 }
 
 
@@ -96,4 +92,3 @@ END
 
 
 __END__
-

diff --git a/bp_bin/transliterate_seq b/bp_bin/transliterate_seq
index 44c60ff55263a9a21d7dbbeb3cbbf8ec749cb427..2908163708a2c9d3570ead04a2d82145f021b4f2 100755 (executable)
--- a/bp_bin/transliterate_seq
+++ b/bp_bin/transliterate_seq
@@ -64,26 +64,22 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
     Maasha::Biopieces::put_record( $record, $out );
 }
 
+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();
 }
 
 
@@ -91,4 +87,3 @@ END
 
 
 __END__
-

diff --git a/bp_bin/transliterate_vals b/bp_bin/transliterate_vals
index 091aa9d9f53873a0a28e21cbd8e87a4feaed0bd3..546652cd3c42a9ad30f8f69a12756d62fc7cb5f7 100755 (executable)
--- a/bp_bin/transliterate_vals
+++ b/bp_bin/transliterate_vals
@@ -68,26 +68,22 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
     Maasha::Biopieces::put_record( $record, $out );
 }
 
+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();
 }
 
 
@@ -95,4 +91,3 @@ END
 
 
 __END__
-

diff --git a/bp_bin/uniq_vals b/bp_bin/uniq_vals
index 93fd3be92fc3737e5e6a5dc119b1978a12109ce8..f01be818cd60156d87011654f5deab0c61d2c12b 100755 (executable)
--- a/bp_bin/uniq_vals
+++ b/bp_bin/uniq_vals
@@ -70,26 +70,22 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
     }
 }
 
+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();
 }
 
 
@@ -97,4 +93,3 @@ END
 
 
 __END__
-

diff --git a/bp_bin/upload_to_ucsc b/bp_bin/upload_to_ucsc
index 5fa6c3e633ba51d7462bdcfe5154b338a93b5c97..25c310358555e31c72ffab5dd25b0d31736d43ec 100755 (executable)
--- a/bp_bin/upload_to_ucsc
+++ b/bp_bin/upload_to_ucsc
@@ -228,26 +228,22 @@ Maasha::UCSC::ucsc_update_config( $options, $type );
 
 Maasha::Filesys::dir_remove( $tmp_dir );
 
+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();
 }
 
 
@@ -255,4 +251,3 @@ END
 
 
 __END__
-

diff --git a/bp_bin/uppercase_seq b/bp_bin/uppercase_seq
index 3a9c89bf724b5b14b86b621403eb88c10fc9fe53..5e1ec7b2c781e3721d7d7392424f2daa7484c14e 100755 (executable)
--- a/bp_bin/uppercase_seq
+++ b/bp_bin/uppercase_seq
@@ -47,24 +47,22 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
     Maasha::Biopieces::put_record( $record, $out );
 }
 
+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();
 }
 
 

diff --git a/bp_bin/vmatch_seq b/bp_bin/vmatch_seq
index 0cddbe0e696dfcedcdf219fb51502d9954bf7ba1..4d54dc9de7cf8f823afb1f47977f8c00f7cb9cc9 100755 (executable)
--- a/bp_bin/vmatch_seq
+++ b/bp_bin/vmatch_seq
@@ -268,25 +268,22 @@ sub vmatch_get_entry
     }
 }
 
+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();
 }
 
 
@@ -294,4 +291,3 @@ END
 
 
 __END__
-

diff --git a/bp_bin/write_2bit b/bp_bin/write_2bit
index 459f852c3c6fe55f3edd0c1e1a39d1199c1aa6c1..3929bba7ec509b5a4d48d6e06e9c3829e9653061 100755 (executable)
--- a/bp_bin/write_2bit
+++ b/bp_bin/write_2bit
@@ -84,25 +84,22 @@ unlink $tmp_file;
 
 Maasha::Filesys::dir_remove( $tmp_dir );
 
+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();
 }
 
 

diff --git a/bp_bin/write_align b/bp_bin/write_align
index d978bd4c7e436ca6ace7eb1c9350007e7a6cf948..3963d945be3bc5e889c1d56b49928b0e9606b67c 100755 (executable)
--- a/bp_bin/write_align
+++ b/bp_bin/write_align
@@ -68,25 +68,22 @@ if ( scalar( @entries ) == 2 ) {
 
 close $data_out;
 
+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();
 }
 
 

diff --git a/bp_bin/write_bed b/bp_bin/write_bed
index 38b8704c3c8d71542f8cf3f695114b1788045c7c..34f88107b430e41b2fe63a05aa7845e9cc8b2590 100755 (executable)
--- a/bp_bin/write_bed
+++ b/bp_bin/write_bed
@@ -64,25 +64,22 @@ 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();
 }
 
 

diff --git a/bp_bin/write_blast b/bp_bin/write_blast
index 27f164aef21d6d77622c8aa3995d453124269c62..ecf086215cc43884936c3dfd7cee8c1e1eb51f12 100755 (executable)
--- a/bp_bin/write_blast
+++ b/bp_bin/write_blast
@@ -70,8 +70,11 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
 
 close $data_out;
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
 
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> SUBROUTINES <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 sub biopiece2blast_tab
@@ -123,19 +126,13 @@ sub biopiece2blast_tab
 
 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();
 }
 
 

diff --git a/bp_bin/write_fasta b/bp_bin/write_fasta
index f71aa26047f7758d49d136e8e3db6ad78fb150a5..a2f68c6c0d45598cec07bee76f68194f9195fdd1 100755 (executable)
--- a/bp_bin/write_fasta
+++ b/bp_bin/write_fasta
@@ -61,25 +61,22 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
 
 close $data_out;
 
+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();
 }
 
 

diff --git a/bp_bin/write_fixedstep b/bp_bin/write_fixedstep
index 5de9a6bcde74eb82eca8d7a274b6fae6b2c6b011..7fbd8f9eecc8f23fec5774ef88d5dbe39da4b1b5 100755 (executable)
--- a/bp_bin/write_fixedstep
+++ b/bp_bin/write_fixedstep
@@ -60,25 +60,22 @@ 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();
 }
 
 

diff --git a/bp_bin/write_psl b/bp_bin/write_psl
index 43c85d485af0313dc43771328395eb0619944ef4..404e21aea0fbbccb31e2b30d468d5fc5a07c9ec0 100755 (executable)
--- a/bp_bin/write_psl
+++ b/bp_bin/write_psl
@@ -65,25 +65,22 @@ 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();
 }
 
 

diff --git a/bp_bin/write_solid b/bp_bin/write_solid
index b467e558101a197189179ff5625dd74ed7592a4e..f999c8bda28f0639c3c34461dabe2a01b774a453 100755 (executable)
--- a/bp_bin/write_solid
+++ b/bp_bin/write_solid
@@ -65,25 +65,22 @@ 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();
 }
 
 

diff --git a/bp_bin/write_tab b/bp_bin/write_tab
index e20794db2189e5d58ed4a816345e3aadbeee7ce6..eab15ff00d589b42a35a087950a9a3ca121da4da 100755 (executable)
--- a/bp_bin/write_tab
+++ b/bp_bin/write_tab
@@ -123,25 +123,22 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
 
 close $data_out;
 
+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();
 }
 
 

diff --git a/bp_bin/write_ucsc_config b/bp_bin/write_ucsc_config
index efd4dd0a81566538ad7f45a9e33f3dd3e5dcdde9..c8d2df31036065393bed211666f2d6f956b08dd9 100755 (executable)
--- a/bp_bin/write_ucsc_config
+++ b/bp_bin/write_ucsc_config
@@ -58,25 +58,22 @@ 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();
 }