removed variables bulk type

git-svn-id: http://biopieces.googlecode.com/svn/trunk@487 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/add_ident b/bp_bin/add_ident
index 26497ef0c57afaf781a40cf210473f5fac5671fc..16bde7abc886bd719452c467dc08f27d4183b765 100755 (executable)
--- a/bp_bin/add_ident
+++ b/bp_bin/add_ident
@@ -33,7 +33,7 @@ use Maasha::Biopieces;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $key, $prefix, $i );
+my ( $options, $in, $out, $record, $key, $prefix, $i );
 
 $options = Maasha::Biopieces::parse_options(
     [
@@ -59,26 +59,22 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
     $i++;
 }
 
+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/align_pair_seq b/bp_bin/align_pair_seq
index 1f92640b15704b64900ebf52d4def7bdfc57a255..817ac256667fa84572f91725bbce810136d1cea0 100755 (executable)
--- a/bp_bin/align_pair_seq
+++ b/bp_bin/align_pair_seq
@@ -29,13 +29,12 @@
 use strict;
 use Maasha::Biopieces;
 use Maasha::AlignTwoSeq;
-use Data::Dumper;
 
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $count, $record, @records );
+my ( $options, $in, $out, $count, $record, @records );
 
 $options = Maasha::Biopieces::parse_options();
 
@@ -70,26 +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();
 }
 
 

diff --git a/bp_bin/align_seq b/bp_bin/align_seq
index 86ea57763f23f12d6e89d08188fb46a10e6593be..56a6e5467bbefc0a3dcccd2fe9c35bc514628645 100755 (executable)
--- a/bp_bin/align_seq
+++ b/bp_bin/align_seq
@@ -39,7 +39,7 @@ use constant {
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, @entries, $entry );
+my ( $options, $in, $out, $record, @entries, $entry );
 
 $options = Maasha::Biopieces::parse_options();
 

diff --git a/bp_bin/analyze_bed b/bp_bin/analyze_bed
index 47f21021ce306640086a31dcde4c9980630277bb..8548fa60840efed3d513eb18527c5a4f973cb45c 100755 (executable)
--- a/bp_bin/analyze_bed
+++ b/bp_bin/analyze_bed
@@ -34,7 +34,7 @@ use Maasha::UCSC;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record );
+my ( $options, $in, $out, $record );
 
 $options = Maasha::Biopieces::parse_options();
 

diff --git a/bp_bin/analyze_seq b/bp_bin/analyze_seq
index 1af08dcc47ee40f1988c69f42c97c2d688000078..6f76a9496e6041bf03189aa0ed56eb207c169104 100755 (executable)
--- a/bp_bin/analyze_seq
+++ b/bp_bin/analyze_seq
@@ -35,7 +35,7 @@ use Maasha::Seq;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $analysis );
+my ( $options, $in, $out, $record, $analysis );
 
 $options = Maasha::Biopieces::parse_options();
 

diff --git a/bp_bin/analyze_tags b/bp_bin/analyze_tags
index f21478d23621bda8e3d47f22066d24afbd2f1726..68f97ac890f18f33598b788fedcfb1acbf0ad4b6 100755 (executable)
--- a/bp_bin/analyze_tags
+++ b/bp_bin/analyze_tags
@@ -34,7 +34,7 @@ use Maasha::Seq;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, %len_hash, %clone_hash, $clones, $key, $tag_record );
+my ( $options, $in, $out, $record, %len_hash, %clone_hash, $clones, $key, $tag_record );
 
 $options = Maasha::Biopieces::parse_options();
 

diff --git a/bp_bin/analyze_vals b/bp_bin/analyze_vals
index 1ddd36fc52152869835615e4a07517aedc08a431..86e50e6cb5cbaee40fd4acb9aa9cf6ba0de6f000 100755 (executable)
--- a/bp_bin/analyze_vals
+++ b/bp_bin/analyze_vals
@@ -35,7 +35,7 @@ use Data::Dumper;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $analysis, $key, $len,
+my ( $options, $in, $out, $record, $analysis, $key, $len,
      %key_hash, $skip, $keys, $types, $counts, $mins, $maxs, $sums, $means );
 
 $options = Maasha::Biopieces::parse_options(

diff --git a/bp_bin/assemble_tag_contigs b/bp_bin/assemble_tag_contigs
index 8bdeda5880346993b9f7f0af46eff91d6ca4477a..898837eeb8f70022a683927b3656676642a3d1ee 100755 (executable)
--- a/bp_bin/assemble_tag_contigs
+++ b/bp_bin/assemble_tag_contigs
@@ -35,7 +35,7 @@ use Maasha::UCSC::BED;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $tmp_dir, $bed_file, $tag_file, $fh_in, $fh_out, 
+my ( $options, $in, $out, $tmp_dir, $bed_file, $tag_file, $fh_in, $fh_out, 
      $cols, $record, $bed_entry, $file_hash, $chr, $strand );
 
 $options = Maasha::Biopieces::parse_options(

diff --git a/bp_bin/blast_seq b/bp_bin/blast_seq
index 1823216f230a2188c10f7b7c2c0d01ddb35c8704..1534c77655b15653812ef459dc603e1fd5f664e1 100755 (executable)
--- a/bp_bin/blast_seq
+++ b/bp_bin/blast_seq
@@ -36,7 +36,7 @@ use Maasha::Fasta;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $tmp_dir, $tmp_in, $tmp_out, $q_type, $s_type, $record, $entry,
+my ( $options, $in, $out, $tmp_dir, $tmp_in, $tmp_out, $q_type, $s_type, $record, $entry,
      $fh_in, $fh_out, $program );
 
 $options = Maasha::Biopieces::parse_options(

diff --git a/bp_bin/blat_seq b/bp_bin/blat_seq
index bc5af18b8e51eaffb7b98d352499bdac07abef8a..9c3ffa7f879f6c4ef8932aba5633165af0ef176a 100755 (executable)
--- a/bp_bin/blat_seq
+++ b/bp_bin/blat_seq
@@ -37,7 +37,7 @@ use Maasha::UCSC::PSL;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $blat_args, $genome_file, $query_file, $fh_in, $fh_out,
+my ( $options, $in, $out, $record, $blat_args, $genome_file, $query_file, $fh_in, $fh_out,
      $tmp_dir, $type, $result_file, $entry );
 
 $options = Maasha::Biopieces::parse_options(

diff --git a/bp_bin/calc_bit_scores b/bp_bin/calc_bit_scores
index 9e98c2ec48ef8bf9d0aeb9cf6aa6a89fe82b15d1..6bb5374eb2be9e55fe6c31c5aa6847f1071cbf8e 100755 (executable)
--- a/bp_bin/calc_bit_scores
+++ b/bp_bin/calc_bit_scores
@@ -34,7 +34,7 @@ use Maasha::Seq;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $count, $i, $res, $type, $bit_max, %freq_hash, $bit_height, $bit_diff );
+my ( $options, $in, $out, $record, $count, $i, $res, $type, $bit_max, %freq_hash, $bit_height, $bit_diff );
 
 $options = Maasha::Biopieces::parse_options();
 

diff --git a/bp_bin/calc_fixedstep b/bp_bin/calc_fixedstep
index 9c14f2ca49ed2ca2ae0bed582948926fee64b46e..cbb068a8ec42a7dc80e2bd86aa97dae7f45b3df8 100755 (executable)
--- a/bp_bin/calc_fixedstep
+++ b/bp_bin/calc_fixedstep
@@ -36,7 +36,7 @@ use Maasha::UCSC::Wiggle;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $tmp_dir, $bed_file, $fh_in, $fh_out,
+my ( $options, $in, $out, $record, $tmp_dir, $bed_file, $fh_in, $fh_out,
      $file_hash, $chr, $bed_entry, $fixedstep_file, $fixedstep_entry );
 
 $options = Maasha::Biopieces::parse_options(

diff --git a/bp_bin/complement_seq b/bp_bin/complement_seq
index 9ff22c8dd5449452a2fcee1212457a9cc5569990..38d1dae27056706b884fc7105c75cfd14fd0abb4 100755 (executable)
--- a/bp_bin/complement_seq
+++ b/bp_bin/complement_seq
@@ -34,7 +34,7 @@ use Maasha::Seq;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $type );
+my ( $options, $in, $out, $record, $type );
 
 $options = Maasha::Biopieces::parse_options();
 

diff --git a/bp_bin/compute b/bp_bin/compute
index 701c3d2ab5a6b7534046c8299785a61e66a29b73..299b787445e4bee7e6a89b9954e7fe3fe41b29df 100755 (executable)
--- a/bp_bin/compute
+++ b/bp_bin/compute
@@ -34,7 +34,7 @@ use Maasha::Biopieces;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $eval_key, @keys, $eval_val );
+my ( $options, $in, $out, $record, $eval_key, @keys, $eval_val );
 
 $options = Maasha::Biopieces::parse_options(
     [

diff --git a/bp_bin/count_records b/bp_bin/count_records
index 5ccc1e6a91532c38de7e6b31ccb2fdcbc67a34a1..3907e4f313c8aa684197fe8692d05518b925254d 100755 (executable)
--- a/bp_bin/count_records
+++ b/bp_bin/count_records
@@ -34,7 +34,7 @@ use Maasha::Biopieces;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $data_out, $count, $result, $line );
+my ( $options, $in, $out, $record, $data_out, $count, $result, $line );
 
 $options = Maasha::Biopieces::parse_options(
     [

diff --git a/bp_bin/count_vals b/bp_bin/count_vals
index 3beaeedcc3262f8a39537b3341324441a0d4539a..449fe81dfade7206e0d5ee023e376621d77f6913 100755 (executable)
--- a/bp_bin/count_vals
+++ b/bp_bin/count_vals
@@ -34,7 +34,7 @@ use Maasha::Biopieces;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $num, $record, %count_hash, @records, $tmp_dir, $tmp_file, $fh_out, $fh_in, $cache );
+my ( $options, $in, $out, $num, $record, %count_hash, @records, $tmp_dir, $tmp_file, $fh_out, $fh_in, $cache );
 
 $options = Maasha::Biopieces::parse_options(
     [

diff --git a/bp_bin/create_blast_db b/bp_bin/create_blast_db
index 79bd310ffad30eebfa8ef858778bd35cd9292dc1..9273af60a7976d6133ead3769dd546259f722867 100755 (executable)
--- a/bp_bin/create_blast_db
+++ b/bp_bin/create_blast_db
@@ -35,7 +35,7 @@ use Maasha::Biopieces;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $fh, $entry, $seq_type, $path );
+my ( $options, $in, $out, $record, $fh, $entry, $seq_type, $path );
 
 $options = Maasha::Biopieces::parse_options(
     [

diff --git a/bp_bin/create_vmatch_index b/bp_bin/create_vmatch_index
index f956745fbf1741cc2714f5fc14ea81107adaedaa..e6dc983a804cf0f9c0b2447177f617af57044773 100755 (executable)
--- a/bp_bin/create_vmatch_index
+++ b/bp_bin/create_vmatch_index
@@ -37,7 +37,7 @@ use Maasha::Fasta;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $default, $formats, $options, $in, $out, $record, $file_tmp, $fh_tmp, $type, $entry );
+my ( $default, $formats, $options, $in, $out, $record, $file_tmp, $fh_tmp, $type, $entry );
 
 $options = Maasha::Biopieces::parse_options(
     [

diff --git a/bp_bin/create_weight_matrix b/bp_bin/create_weight_matrix
index 44a211c2d180faaa1b0712c5feb6419f98c54777..8adffcf90edf31045b98c3731fce0090de2eae19 100755 (executable)
--- a/bp_bin/create_weight_matrix
+++ b/bp_bin/create_weight_matrix
@@ -34,7 +34,7 @@ use Maasha::Biopieces;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $count, $i, $res, %freq_hash, %res_hash, $freq );
+my ( $options, $in, $out, $record, $count, $i, $res, %freq_hash, %res_hash, $freq );
 
 $options = Maasha::Biopieces::parse_options(
     [

diff --git a/bp_bin/extract_seq b/bp_bin/extract_seq
index 95bc67025638d7e241b91f6af69f20df51a1cf24..c900bc77eef4d92afdf2492f15ccfec7d9fe57b6 100755 (executable)
--- a/bp_bin/extract_seq
+++ b/bp_bin/extract_seq
@@ -33,7 +33,7 @@ use Maasha::Biopieces;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $beg, $end, $len );
+my ( $options, $in, $out, $record, $beg, $end, $len );
 
 $options = Maasha::Biopieces::parse_options(
     [

diff --git a/bp_bin/flip_tab b/bp_bin/flip_tab
index 489e2b7514be7f0cd74c50671020f8e19ca61b46..605b27733c3f631202ec5cef00b96a7062b97754 100755 (executable)
--- a/bp_bin/flip_tab
+++ b/bp_bin/flip_tab
@@ -34,7 +34,7 @@ use Maasha::Matrix;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $key, $A, $B, @rows, @matrix, $row, $i );
+my ( $options, $in, $out, $record, $key, $A, $B, @rows, @matrix, $row, $i );
 
 $options = Maasha::Biopieces::parse_options();
 

diff --git a/bp_bin/fold_seq b/bp_bin/fold_seq
index cb144366855d27eb77ab244e0c7ac79262e5b863..701f900562d80fac4b3e2e05b0106c26e95f1c51 100755 (executable)
--- a/bp_bin/fold_seq
+++ b/bp_bin/fold_seq
@@ -33,7 +33,7 @@ use Maasha::Biopieces;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $type, $struct, $index );
+my ( $options, $in, $out, $record, $type, $struct, $index );
 
 $options = Maasha::Biopieces::parse_options();
 

diff --git a/bp_bin/format_genome b/bp_bin/format_genome
index 5e5b8def63955ed0ed6fc0885ced964f4fa2c92b..6ffa92d2b4ff7a603b2e17916227884df0be415a 100755 (executable)
--- a/bp_bin/format_genome
+++ b/bp_bin/format_genome
@@ -34,7 +34,7 @@ use Maasha::Biopieces;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $default, $formats, $options, $in, $out, $record, $data_out, $entry,
+my ( $default, $formats, $options, $in, $out, $record, $data_out, $entry,
      $genome, $dir, $fasta_dir, $phastcons_dir, $fh_out, $vals, $format, $tmp_dir );
 
 $tmp_dir = Maasha::Biopieces::get_tmpdir();

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();
 }
 
 

diff --git a/bp_bin/get_genome_phastcons b/bp_bin/get_genome_phastcons
index 9fc75ee22684e71a7e50f220c9fa54d235d976aa..337c019851984f79c9c6a5b35f57b68b7ad59402 100755 (executable)
--- a/bp_bin/get_genome_phastcons
+++ b/bp_bin/get_genome_phastcons
@@ -35,7 +35,7 @@ use Maasha::UCSC;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $phastcons_file, $phastcons_index, $index, $fh_phastcons, $scores, $record );
+my ( $options, $in, $out, $phastcons_file, $phastcons_index, $index, $fh_phastcons, $scores, $record );
 
 $options = Maasha::Biopieces::parse_options(
     [

diff --git a/bp_bin/get_genome_seq b/bp_bin/get_genome_seq
index 68c52bd43c201724ec3844165342baba0602d083..bf0f787fa5317c4debd47c46e7007130b8e0826f 100755 (executable)
--- a/bp_bin/get_genome_seq
+++ b/bp_bin/get_genome_seq
@@ -35,7 +35,7 @@ use Maasha::Seq;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $genome_file, $index_file, $fh, $genome,
+my ( $options, $in, $out, $record, $genome_file, $index_file, $fh, $genome,
      $beg, $end, $len, $index_beg, $index_len, @begs, @lens, $index, $seq, $i, %lookup_hash );
 
 $options = Maasha::Biopieces::parse_options(

diff --git a/bp_bin/grab b/bp_bin/grab
index 6d2aabff4f5d55c4014202302565d3dc404c0f47..1fecf4303acbedefaa94b1ca18be8896fbbc5fde 100755 (executable)
--- a/bp_bin/grab
+++ b/bp_bin/grab
@@ -35,7 +35,7 @@ use Maasha::Patscan;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $keys, $vals_only, $keys_only, $invert,
+my ( $options, $in, $out, $record, $keys, $vals_only, $keys_only, $invert,
      $patterns, $regex, %lookup_hash, $key, $op, $val, $found );
 
 $options = Maasha::Biopieces::parse_options(

diff --git a/bp_bin/head_records b/bp_bin/head_records
index bc26919a47955b27652823de6ff9c3a35db52568..631973c0544158bb76005f7be4b4d56ffe6d0043 100755 (executable)
--- a/bp_bin/head_records
+++ b/bp_bin/head_records
@@ -33,7 +33,7 @@ use Maasha::Biopieces;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $count );
+my ( $options, $in, $out, $record, $count );
 
 $options = Maasha::Biopieces::parse_options(
     [

diff --git a/bp_bin/invert_align b/bp_bin/invert_align
index 413ab29f9d7d949b8194cf5b9aac51ce3ccdf03a..f8b330a13d1b8a2528f508891aa88de98a11e238 100755 (executable)
--- a/bp_bin/invert_align
+++ b/bp_bin/invert_align
@@ -39,7 +39,7 @@ use constant {
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, @entries );
+my ( $options, $in, $out, $record, @entries );
 
 $options = Maasha::Biopieces::parse_options(
     [

diff --git a/bp_bin/length_seq b/bp_bin/length_seq
index 2ca4b0f950ae56029513bb090cf8c9d2ecf75a11..b00eb3e875df0c3a95ea0281cccfd5552e52be62 100755 (executable)
--- a/bp_bin/length_seq
+++ b/bp_bin/length_seq
@@ -33,7 +33,7 @@ use Maasha::Biopieces;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $total );
+my ( $options, $in, $out, $record, $total );
 
 $options = Maasha::Biopieces::parse_options(
     [

diff --git a/bp_bin/length_vals b/bp_bin/length_vals
index 8bcb33ea968645e158e30760b077b86af9b08082..f9f1616cd9888700aab562d2eb7a857a618c0a77 100755 (executable)
--- a/bp_bin/length_vals
+++ b/bp_bin/length_vals
@@ -33,7 +33,7 @@ use Maasha::Biopieces;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $key );
+my ( $options, $in, $out, $record, $key );
 
 $options = Maasha::Biopieces::parse_options(
     [

diff --git a/bp_bin/list_biopieces b/bp_bin/list_biopieces
index b00e5af1b7c4d9e8466370fa1c33f3f0613263b9..f58f2e8cc265be843bef5cf9a5a9c99866c028a0 100755 (executable)
--- a/bp_bin/list_biopieces
+++ b/bp_bin/list_biopieces
@@ -35,7 +35,7 @@ use Maasha::Gwiki;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, @files, $file, $wiki, $program, $summary );
+my ( $options, @files, $file, $wiki, $program, $summary );
 
 $options = Maasha::Biopieces::parse_options();
 

diff --git a/bp_bin/list_genomes b/bp_bin/list_genomes
index b0e77a648cc045fa2e7be8b883f13c683e95df09..147d5c1def623caca7bcdbe793a6c7566d6e5cab 100755 (executable)
--- a/bp_bin/list_genomes
+++ b/bp_bin/list_genomes
@@ -34,7 +34,7 @@ use Maasha::Biopieces;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, @genomes, $genome, @formats, $format, %hash, %found, @row );
+my ( $options, @genomes, $genome, @formats, $format, %hash, %found, @row );
 
 $options = Maasha::Biopieces::parse_options();
 

diff --git a/bp_bin/match_seq b/bp_bin/match_seq
index 2b852f03ed7b5b44699d959ea8bdc1ae95c2cd67..0ce31eb39e675fea43196f07ad22a91bf25c1269 100755 (executable)
--- a/bp_bin/match_seq
+++ b/bp_bin/match_seq
@@ -35,7 +35,7 @@ use Maasha::Filesys;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, @entries, $results, $tmp_dir );
+my ( $options, $in, $out, $record, @entries, $results, $tmp_dir );
 
 $options = Maasha::Biopieces::parse_options(
     [

diff --git a/bp_bin/max_vals b/bp_bin/max_vals
index b8e91b41b482492154d1651f1b0b3d0b0591166d..7c760a5b1a2bffb63050f0abd9f40468d087fa9d 100755 (executable)
--- a/bp_bin/max_vals
+++ b/bp_bin/max_vals
@@ -33,7 +33,7 @@ use Maasha::Biopieces;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $key, $fh, %max_hash, $max_record );
+my ( $options, $in, $out, $record, $key, $fh, %max_hash, $max_record );
 
 $options = Maasha::Biopieces::parse_options(
     [

diff --git a/bp_bin/mean_vals b/bp_bin/mean_vals
index 60f7aaad4034badcd687417780ff6b7e84ac9ea7..fb073cdf0e19d7cf1f72ec7a94aa980d1ed135f9 100755 (executable)
--- a/bp_bin/mean_vals
+++ b/bp_bin/mean_vals
@@ -33,7 +33,7 @@ use Maasha::Biopieces;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $key, %sum_hash, %count_hash, $mean, $fh );
+my ( $options, $in, $out, $record, $key, %sum_hash, %count_hash, $mean, $fh );
 
 $options = Maasha::Biopieces::parse_options(
     [

diff --git a/bp_bin/median_vals b/bp_bin/median_vals
index 42dc410bacaefa313185e1f5879d8724b6c390fc..9428f9a2efd18dbaa6596f032c6178cdc04dcd2d 100755 (executable)
--- a/bp_bin/median_vals
+++ b/bp_bin/median_vals
@@ -34,7 +34,7 @@ use Maasha::Calc;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $key, %median_hash, $median, $fh );
+my ( $options, $in, $out, $record, $key, %median_hash, $median, $fh );
 
 $options = Maasha::Biopieces::parse_options(
     [

diff --git a/bp_bin/merge_records b/bp_bin/merge_records
index cdfe46e88ce6c02f87695fb6f5d11e2c2b06785d..39f09e2df8cde1e367e0993e37463cd6ef95aed0 100755 (executable)
--- a/bp_bin/merge_records
+++ b/bp_bin/merge_records
@@ -35,7 +35,7 @@ use Maasha::Filesys;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $tmp_dir, $file1, $file2, $fh1, $fh2,
+my ( $options, $in, $out, $record, $tmp_dir, $file1, $file2, $fh1, $fh2,
      $key1, $key2, @keys1, @keys2, @vals1, @vals2, $num1, $num2, $num, $cmp, $i );
 
 $options = Maasha::Biopieces::parse_options(

diff --git a/bp_bin/merge_vals b/bp_bin/merge_vals
index f53d99abbf586b022a2625a94d37bbdc7fc4c0fa..c751a4d8902139790f30812defbd08ba27245ee7 100755 (executable)
--- a/bp_bin/merge_vals
+++ b/bp_bin/merge_vals
@@ -33,7 +33,7 @@ use Maasha::Biopieces;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, @join, $i );
+my ( $options, $in, $out, $record, @join, $i );
 
 $options = Maasha::Biopieces::parse_options(
     [

diff --git a/bp_bin/min_vals b/bp_bin/min_vals
index 77dc832d0d0999bd4893709f22ab3363e26044ca..34024b1fd2ef1a911ea4468a310e092ae6b5801a 100755 (executable)
--- a/bp_bin/min_vals
+++ b/bp_bin/min_vals
@@ -33,7 +33,7 @@ use Maasha::Biopieces;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $key, $fh, %min_hash, $min_record );
+my ( $options, $in, $out, $record, $key, $fh, %min_hash, $min_record );
 
 $options = Maasha::Biopieces::parse_options(
     [

diff --git a/bp_bin/oligo_freq b/bp_bin/oligo_freq
index 7631103faac9544b07d88c8c1333f4448bea5f37..e179d8dd218855831e48b8c4c81b765150f9bf74 100755 (executable)
--- a/bp_bin/oligo_freq
+++ b/bp_bin/oligo_freq
@@ -33,7 +33,7 @@ use Maasha::Biopieces;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, @freq_table, %oligos );
+my ( $options, $in, $out, $record, @freq_table, %oligos );
 
 $options = Maasha::Biopieces::parse_options(
     [

diff --git a/bp_bin/patscan_seq b/bp_bin/patscan_seq
index 800eac7e2b25312468bced78c4e95184543c703f..60a5cae0bdbc18fc9450bc06d1dc9771ebed2572 100755 (executable)
--- a/bp_bin/patscan_seq
+++ b/bp_bin/patscan_seq
@@ -41,7 +41,7 @@ use constant {
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, @args, $arg, $type, $tmp_dir,
+my ( $options, $in, $out, $record, @args, $arg, $type, $tmp_dir,
      $seq_file, $pat_file, $out_file, $fh_in, $fh_out, $patterns, $pattern, $entry, $result, %head_hash, $i );
 
 $options = Maasha::Biopieces::parse_options(

diff --git a/bp_bin/plot_chrdist b/bp_bin/plot_chrdist
index dd1213638373fd58db59077b8b4767b16b4e3282..df4db5a7e7cb07b2abc729065d109383a7c0ca53 100755 (executable)
--- a/bp_bin/plot_chrdist
+++ b/bp_bin/plot_chrdist
@@ -34,7 +34,7 @@ use Maasha::Plot;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $default, $terminals, $record, %data_hash, @data_list, $elem, $sort_key, $count, $result, $fh );
+my ( $options, $in, $out, $default, $terminals, $record, %data_hash, @data_list, $elem, $sort_key, $count, $result, $fh );
 
 $default   = "Chromosome Distribution";
 $terminals = "dumb,x11,aqua,post,svg";

diff --git a/bp_bin/plot_histogram b/bp_bin/plot_histogram
index 989222e299c5dad742fe79e75ab5eb5791e37d7c..9eccb6812bade735d8ae4b21ec54e0a92b1c1227 100755 (executable)
--- a/bp_bin/plot_histogram
+++ b/bp_bin/plot_histogram
@@ -34,7 +34,7 @@ use Maasha::Plot;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $default, $terminals, $record, %data_hash, $max, @data_list, $i, $result, $fh );
+my ( $options, $in, $out, $default, $terminals, $record, %data_hash, $max, @data_list, $i, $result, $fh );
 
 $default   = "Histogram";
 $terminals = "dumb,x11,aqua,post,svg";

diff --git a/bp_bin/plot_karyogram b/bp_bin/plot_karyogram
index 5e6c015d83fa24ba1ba8df1928bada9eae570944..9adf2f8427bcd1065a93f86f9579474aec9df88f 100755 (executable)
--- a/bp_bin/plot_karyogram
+++ b/bp_bin/plot_karyogram
@@ -34,7 +34,7 @@ use Maasha::Plot;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, @data, $fh, $result, %data_hash );
+my ( $options, $in, $out, $record, @data, $fh, $result, %data_hash );
 
 $options = Maasha::Biopieces::parse_options(
     [

diff --git a/bp_bin/plot_lendist b/bp_bin/plot_lendist
index 0197aca2758f78d8e9c5c6788172449c83c1cc2b..a2fb9ccfb03ef338d41974acd8325d9cb04d6772 100755 (executable)
--- a/bp_bin/plot_lendist
+++ b/bp_bin/plot_lendist
@@ -35,7 +35,7 @@ use Maasha::Calc;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $default, $terminals, $record, %data_hash, $max, @data_list, $i, $result, $fh );
+my ( $options, $in, $out, $default, $terminals, $record, %data_hash, $max, @data_list, $i, $result, $fh );
 
 $default   = "Length Distribution";
 $terminals = "dumb,x11,aqua,post,svg";

diff --git a/bp_bin/plot_matches b/bp_bin/plot_matches
index a2d97cf76b02aead93c80caa1041a3e493a80676..f383da8ad2c39e0ef4bdfb406fd81eeea10623ad 100755 (executable)
--- a/bp_bin/plot_matches
+++ b/bp_bin/plot_matches
@@ -36,7 +36,7 @@ use IPC::Open2;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $default, $terminals, $record, @data, $fh, $result, %data_hash, $tmp_dir );
+my ( $options, $in, $out, $default, $terminals, $record, @data, $fh, $result, %data_hash, $tmp_dir );
 
 $default   = "plot_matches";
 $terminals = "dumb,x11,aqua,post,svg";

diff --git a/bp_bin/plot_phastcons_profiles b/bp_bin/plot_phastcons_profiles
index 52489f5c5e668539c1ab491f19bade47951e8702..caf444f629b7ae38fb5d53cd1d9888737ffac48a 100755 (executable)
--- a/bp_bin/plot_phastcons_profiles
+++ b/bp_bin/plot_phastcons_profiles
@@ -37,7 +37,7 @@ use Maasha::UCSC;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $default, $terminals, $phastcons_file, $phastcons_index,
+my ( $options, $in, $out, $default, $terminals, $phastcons_file, $phastcons_index,
      $index, $fh_phastcons, $record, $scores, $AoA, $plot, $fh, $tmp_dir );
 
 $default   = "PhastCons Profiles";

diff --git a/bp_bin/plot_seqlogo b/bp_bin/plot_seqlogo
index 0a2d5d4bc40a563194887cec344e471bfd20735c..e9be5a6b2fae5df2b959f8691d6853b772acd9a8 100755 (executable)
--- a/bp_bin/plot_seqlogo
+++ b/bp_bin/plot_seqlogo
@@ -34,7 +34,7 @@ use Maasha::Plot;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, @entries, $logo, $fh );
+my ( $options, $in, $out, $record, @entries, $logo, $fh );
 
 $options = Maasha::Biopieces::parse_options(
     [

diff --git a/bp_bin/print_wiki b/bp_bin/print_wiki
index 578aa8e086dafda132b0f4806dbded6c64dad870..b13d514436e348880de788e1b8d16ee006a2e6cc 100755 (executable)
--- a/bp_bin/print_wiki
+++ b/bp_bin/print_wiki
@@ -34,7 +34,7 @@ use Maasha::Gwiki;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $default, $wiki, $lines );
+my ( $options, $default, $wiki, $lines );
 
 $default = $ENV{ 'BP_DIR' } . "/bp_usage/" . ( split "/", $0 )[ -1 ]. ".wiki";
 

diff --git a/bp_bin/random_records b/bp_bin/random_records
index f45f942028a7e730067999550747a05068c8733d..5c4595cc222b250b722b9b0270ea7cec601489b2 100755 (executable)
--- a/bp_bin/random_records
+++ b/bp_bin/random_records
@@ -34,7 +34,7 @@ use Maasha::Filesys;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $tmp_dir, $tmp_file, $fh_out, $fh_in, $count, $i, %rand_hash, $rand, $max );
+my ( $options, $in, $out, $record, $tmp_dir, $tmp_file, $fh_out, $fh_in, $count, $i, %rand_hash, $rand, $max );
 
 $options = Maasha::Biopieces::parse_options(
     [

diff --git a/bp_bin/read_2bit b/bp_bin/read_2bit
index 25f0193ba82bdc4869bc4e66be9c0a119703fecb..63bb7e1988f72efa502216edb28eabb9b42ac489 100755 (executable)
--- a/bp_bin/read_2bit
+++ b/bp_bin/read_2bit
@@ -35,7 +35,7 @@ use Maasha::TwoBit;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $file, $data_in, $mask, $toc, $line, $num );
+my ( $options, $in, $out, $record, $file, $data_in, $mask, $toc, $line, $num );
 
 $options = Maasha::Biopieces::parse_options(
     [

diff --git a/bp_bin/read_bed b/bp_bin/read_bed
index 18c5c226fe1b5f892e7d07dfb3b36b0317a3df65..551d86e10662ca48ca63825775d68539c74702c7 100755 (executable)
--- a/bp_bin/read_bed
+++ b/bp_bin/read_bed
@@ -35,7 +35,7 @@ use Maasha::UCSC::BED;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $file, $record, $bed_entry, $data_in, $num );
+my ( $options, $in, $out, $file, $record, $bed_entry, $data_in, $num );
 
 $options = Maasha::Biopieces::parse_options(
     [

diff --git a/bp_bin/read_blast_tab b/bp_bin/read_blast_tab
index 2ed0a55ca02047022b38716c8ebc74b803bd4257..fcf53ae34b001b5aee5f0f1c6e13c6adae8e5f94 100755 (executable)
--- a/bp_bin/read_blast_tab
+++ b/bp_bin/read_blast_tab
@@ -34,7 +34,7 @@ use Maasha::Filesys;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $file, $record, $line, @fields, $data_in, $num );
+my ( $options, $in, $out, $file, $record, $line, @fields, $data_in, $num );
 
 $options = Maasha::Biopieces::parse_options(
     [

diff --git a/bp_bin/read_embl b/bp_bin/read_embl
index e0ba8b76b98acb61a0d60e6d4a091a63625db64b..80cc39ab791652f7a9539e8f2f3b4a6dc444b98a 100755 (executable)
--- a/bp_bin/read_embl
+++ b/bp_bin/read_embl
@@ -35,7 +35,7 @@ use Maasha::EMBL;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, %options2, $file, $data_in, $num, $entry, $record );
+my ( $options, $in, $out, %options2, $file, $data_in, $num, $entry, $record );
 
 $options = Maasha::Biopieces::parse_options(
     [

diff --git a/bp_bin/read_fasta b/bp_bin/read_fasta
index 9449a0d68cfbc2e00147ad381e656bde142fed88..17a26df65c136640692aede7b15355ca312a66e7 100755 (executable)
--- a/bp_bin/read_fasta
+++ b/bp_bin/read_fasta
@@ -35,7 +35,7 @@ use Maasha::Fasta;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $data_in, $num, $entry );
+my ( $options, $in, $out, $record, $data_in, $num, $entry );
 
 $options = Maasha::Biopieces::parse_options(
     [
@@ -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();
 }
 
 
@@ -97,3 +94,4 @@ END
 
 
 __END__
+

diff --git a/bp_bin/read_fixedstep b/bp_bin/read_fixedstep
index 93b462966a26ba84bc664c52dc74bdd5734c855a..794599bdf8315650fddaec148b4dd57028d528a3 100755 (executable)
--- a/bp_bin/read_fixedstep
+++ b/bp_bin/read_fixedstep
@@ -35,7 +35,7 @@ use Maasha::UCSC::Wiggle;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $data_in, $num, $entry );
+my ( $options, $in, $out, $record, $data_in, $num, $entry );
 
 $options = Maasha::Biopieces::parse_options(
     [

diff --git a/bp_bin/read_gff b/bp_bin/read_gff
index 411c2a6d1b6b556876f1dd5efe3289f20693ff01..f7162a1118df43af98e5311f95c51eb0fd8a06df 100755 (executable)
--- a/bp_bin/read_gff
+++ b/bp_bin/read_gff
@@ -35,7 +35,7 @@ use Maasha::GFF;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $data_in, $num, $entry );
+my ( $options, $in, $out, $record, $data_in, $num, $entry );
 
 $options = Maasha::Biopieces::parse_options(
     [

diff --git a/bp_bin/read_mysql b/bp_bin/read_mysql
index 003320767033cb5c0b370c98989434f4341eba59..b79458bcf200cbf7462f40b96dfa8d6e164df977 100755 (executable)
--- a/bp_bin/read_mysql
+++ b/bp_bin/read_mysql
@@ -35,7 +35,7 @@ use Maasha::UCSC;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $default_user, $default_password, $options, $in, $out, $record, $dbh, $results );
+my ( $default_user, $default_password, $options, $in, $out, $record, $dbh, $results );
 
 $default_user     = Maasha::UCSC::ucsc_get_user();
 $default_password = Maasha::UCSC::ucsc_get_password();

diff --git a/bp_bin/read_psl b/bp_bin/read_psl
index e2aa4375b919b692381bbeb4c410fe12a31e9c17..c7183ee9b3cc95242bd26d259353d772fcb0dac3 100755 (executable)
--- a/bp_bin/read_psl
+++ b/bp_bin/read_psl
@@ -35,7 +35,7 @@ use Maasha::UCSC::PSL;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $data_in, $num, $entry );
+my ( $options, $in, $out, $record, $data_in, $num, $entry );
 
 $options = Maasha::Biopieces::parse_options(
     [

diff --git a/bp_bin/read_soft b/bp_bin/read_soft
index f83aab7a1096804559bcd6e226c1a1c95881c7f2..c51ba9051eeec77a77dec273fd31d53b70d477b7 100755 (executable)
--- a/bp_bin/read_soft
+++ b/bp_bin/read_soft
@@ -36,7 +36,7 @@ use Maasha::NCBI;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $data_in, $num, $entry, $records, $soft_index,
+my ( $options, $in, $out, $record, $data_in, $num, $entry, $records, $soft_index,
      $fh, @platforms, $plat_table, @samples, $sample, $old_end, $skip, $file );
 
 $options = Maasha::Biopieces::parse_options(

diff --git a/bp_bin/read_solexa b/bp_bin/read_solexa
index 34fd6e9cc64e8540995efb535e6b4d064300357a..b35c21c66dc16b10e09af29118e69f75d6c5c4de 100755 (executable)
--- a/bp_bin/read_solexa
+++ b/bp_bin/read_solexa
@@ -35,7 +35,7 @@ use Maasha::Solexa;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $data_in, $num, $entry, @seqs, @scores, $i );
+my ( $options, $in, $out, $record, $data_in, $num, $entry, @seqs, @scores, $i );
 
 $options = Maasha::Biopieces::parse_options(
     [

diff --git a/bp_bin/read_solid b/bp_bin/read_solid
index 2d6ccf9f91eea4c531842562a7ef9c179a4ce724..b39e596177f7f99e3994878f0ac51e1e29998bc1 100755 (executable)
--- a/bp_bin/read_solid
+++ b/bp_bin/read_solid
@@ -36,7 +36,7 @@ use Maasha::Calc;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $data_in, $num, $entry, $i,
+my ( $options, $in, $out, $record, $data_in, $num, $entry, $i,
      $seq_name, $seq_cs, $line, $seq_qual, @scores, @seqs );
 
 $options = Maasha::Biopieces::parse_options(

diff --git a/bp_bin/read_stockholm b/bp_bin/read_stockholm
index 530ddd4bcb1c52e785da3aa682c2a27cf6a0512e..f883d410d22c5f8234b4977c6baff7cc44fa31e9 100755 (executable)
--- a/bp_bin/read_stockholm
+++ b/bp_bin/read_stockholm
@@ -35,7 +35,7 @@ use Maasha::Stockholm;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $num, $entry, $data_in, $record_anno, $key, $seq, $record_align );
+my ( $options, $in, $out, $record, $num, $entry, $data_in, $record_anno, $key, $seq, $record_align );
 
 $options = Maasha::Biopieces::parse_options(
     [

diff --git a/bp_bin/read_tab b/bp_bin/read_tab
index b6c82ab0de6ede21482689650a08339f2ad6c049..152c0d5f26fd8e715afc2b8a6c26ff7dbc6eab56 100755 (executable)
--- a/bp_bin/read_tab
+++ b/bp_bin/read_tab
@@ -35,7 +35,7 @@ use Maasha::Biopieces;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $data_in, $num, $skip, $line, @fields, @fields2, $i );
+my ( $options, $in, $out, $record, $data_in, $num, $skip, $line, @fields, @fields2, $i );
 
 $options = Maasha::Biopieces::parse_options(
     [

diff --git a/bp_bin/read_ucsc_config b/bp_bin/read_ucsc_config
index 35e6d2de5dc702ccdd4617f18c9fc514468119ea..a62000b776366f34630baf68a80f19db1a1a0dbe 100755 (executable)
--- a/bp_bin/read_ucsc_config
+++ b/bp_bin/read_ucsc_config
@@ -35,7 +35,7 @@ use Maasha::UCSC;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $data_in, $num, $entry );
+my ( $options, $in, $out, $record, $data_in, $num, $entry );
 
 $options = Maasha::Biopieces::parse_options(
     [

diff --git a/bp_bin/remove_adaptor b/bp_bin/remove_adaptor
index 118bab32f6636cee4ff22e6fec72babde6874fd8..d9898292277f4efaf4783e0ffb07ac9e417f5e24 100755 (executable)
--- a/bp_bin/remove_adaptor
+++ b/bp_bin/remove_adaptor
@@ -34,7 +34,7 @@ use Maasha::Common;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $adaptor, $seq, $adaptor_len,
+my ( $options, $in, $out, $record, $adaptor, $seq, $adaptor_len,
      $seq_len, $offset, $max_match, $max_mismatch, $pos );
 
 $options = Maasha::Biopieces::parse_options(

diff --git a/bp_bin/remove_indels b/bp_bin/remove_indels
index f1677c5909c5881557da3af70253e680b486cc2c..e476694a7c77b2bdcb40c59004aa4430938b89fe 100755 (executable)
--- a/bp_bin/remove_indels
+++ b/bp_bin/remove_indels
@@ -33,7 +33,7 @@ use Maasha::Biopieces;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record );
+my ( $options, $in, $out, $record );
 
 $options = Maasha::Biopieces::parse_options();
 

diff --git a/bp_bin/remove_keys b/bp_bin/remove_keys
index 5324bf53ccd17837ef012785782f66aa15113ffc..0683dceebda3cad81f432460cbc8eda42901988b 100755 (executable)
--- a/bp_bin/remove_keys
+++ b/bp_bin/remove_keys
@@ -33,7 +33,7 @@ use Maasha::Biopieces;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $new_record );
+my ( $options, $in, $out, $record, $new_record );
 
 $options = Maasha::Biopieces::parse_options(
     [

diff --git a/bp_bin/remove_mysql_tables b/bp_bin/remove_mysql_tables
index b2e9e34a153f3f8738fd6fbf2d43a4b703703adb..28751697a5cb66b4b4fa7e48d3cadc3ddba9bf99 100755 (executable)
--- a/bp_bin/remove_mysql_tables
+++ b/bp_bin/remove_mysql_tables
@@ -36,7 +36,7 @@ use Maasha::UCSC;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, %table_hash, $dbh, $table );
+my ( $options, $in, $out, $record, %table_hash, $dbh, $table );
 
 $options = Maasha::Biopieces::parse_options(
     [

diff --git a/bp_bin/remove_ucsc_tracks b/bp_bin/remove_ucsc_tracks
index 82db5d5c9cdae031365f1d172506d2be6b3f9ee9..ca565750a02eb9134746837f19e21db30a01794d 100755 (executable)
--- a/bp_bin/remove_ucsc_tracks
+++ b/bp_bin/remove_ucsc_tracks
@@ -36,7 +36,7 @@ use Maasha::UCSC;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $conf_file, %track_hash, $fh_in, $fh_out, $track, @tracks, $dbh, @new_tracks );
+my ( $options, $in, $out, $record, $conf_file, %track_hash, $fh_in, $fh_out, $track, @tracks, $dbh, @new_tracks );
 
 $conf_file = $ENV{ 'HOME' } . "/ucsc/my_tracks.ra";
 

diff --git a/bp_bin/rename_keys b/bp_bin/rename_keys
index 5a8b2217b09caedb2064f2165704ddb83b716fff..4a804d496d9ab14c7dc001f0a1520c3f4e0cd676 100755 (executable)
--- a/bp_bin/rename_keys
+++ b/bp_bin/rename_keys
@@ -33,7 +33,7 @@ use Maasha::Biopieces;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record );
+my ( $options, $in, $out, $record );
 
 $options = Maasha::Biopieces::parse_options(
     [

diff --git a/bp_bin/reverse_seq b/bp_bin/reverse_seq
index 95e122a53bdca370b2d63918b94b1a1c97c9d7a0..7d2052da33bd11c4a425e9c2bba07259abe1b78a 100755 (executable)
--- a/bp_bin/reverse_seq
+++ b/bp_bin/reverse_seq
@@ -33,7 +33,7 @@ use Maasha::Biopieces;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record );
+my ( $options, $in, $out, $record );
 
 $options = Maasha::Biopieces::parse_options();
 

diff --git a/bp_bin/shuffle_seq b/bp_bin/shuffle_seq
index a3cb9234426abe24f8ed6501d4c8d8b9a818f88b..05932c45e8f757bc87a2215272ab922697ddbfb6 100755 (executable)
--- a/bp_bin/shuffle_seq
+++ b/bp_bin/shuffle_seq
@@ -34,7 +34,7 @@ use Maasha::Seq;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record );
+my ( $options, $in, $out, $record );
 
 $options = Maasha::Biopieces::parse_options();
 

diff --git a/bp_bin/soap_seq b/bp_bin/soap_seq
index 181e4fd6eac380cb5e57debb1e06c0027460bd4c..f99bbb3c3b76ea364027569ac3a95eab257b4d76 100755 (executable)
--- a/bp_bin/soap_seq
+++ b/bp_bin/soap_seq
@@ -36,7 +36,7 @@ use Maasha::Fasta;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $tmp_dir, $tmp_in, $tmp_out, $fh_out, $record, $entry, $count, $args, $line, @fields );
+my ( $options, $in, $out, $tmp_dir, $tmp_in, $tmp_out, $fh_out, $record, $entry, $count, $args, $line, @fields );
 
 $options = Maasha::Biopieces::parse_options(
     [

diff --git a/bp_bin/sort_records b/bp_bin/sort_records
index 9c551b097dbb775ff8864869ac01b781a8770aa4..13bd4eb379043d81a0ca82d5b1a050dbfc5e10b0 100755 (executable)
--- a/bp_bin/sort_records
+++ b/bp_bin/sort_records
@@ -33,7 +33,7 @@ use Maasha::Biopieces;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, @keys, $key, @sort_cmd, $sort_str, $sort_sub, @records, $record, $i, $ok );
+my ( $options, $in, $out, @keys, $key, @sort_cmd, $sort_str, $sort_sub, @records, $record, $i, $ok );
 
 $options = Maasha::Biopieces::parse_options(
     [

diff --git a/bp_bin/split_bed b/bp_bin/split_bed
index 47e2947747c7db594268f427e3b471d6f3a7d410..97cbaf6a7cb79670ac4f8ce59ffbac7ab064853d 100755 (executable)
--- a/bp_bin/split_bed
+++ b/bp_bin/split_bed
@@ -33,7 +33,7 @@ use Maasha::Biopieces;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $new_record, $i );
+my ( $options, $in, $out, $record, $new_record, $i );
 
 $options = Maasha::Biopieces::parse_options(
     [

diff --git a/bp_bin/split_seq b/bp_bin/split_seq
index 93ed6c72f1875475cfd4b80ac4fdba206f1f6491..776a79bfcc4fe69b96c4c1419b0e5c340821792e 100755 (executable)
--- a/bp_bin/split_seq
+++ b/bp_bin/split_seq
@@ -33,7 +33,7 @@ use Maasha::Biopieces;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $new_record, $i, $subseq, %lookup );
+my ( $options, $in, $out, $record, $new_record, $i, $subseq, %lookup );
 
 $options = Maasha::Biopieces::parse_options(
     [

diff --git a/bp_bin/sum_vals b/bp_bin/sum_vals
index 2a69acda842780d6041bb7dd1b734cc2e3458945..1da7130473ca5bc70607954eea3c7ed23df2dd3b 100755 (executable)
--- a/bp_bin/sum_vals
+++ b/bp_bin/sum_vals
@@ -33,7 +33,7 @@ use Maasha::Biopieces;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $key, %sum_hash, $fh );
+my ( $options, $in, $out, $record, $key, %sum_hash, $fh );
 
 $options = Maasha::Biopieces::parse_options(
     [

diff --git a/bp_bin/tile_seq b/bp_bin/tile_seq
index 500f70530b04be7d6a8298ee21726443ad76bc70..a90f1e40e5c86f0273c90b7f58e72fcfac5ff238 100755 (executable)
--- a/bp_bin/tile_seq
+++ b/bp_bin/tile_seq
@@ -39,7 +39,7 @@ use constant {
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $first, $ref_entry, @entries );
+my ( $options, $in, $out, $record, $first, $ref_entry, @entries );
 
 $options = Maasha::Biopieces::parse_options(
     [

diff --git a/bp_bin/translate_seq b/bp_bin/translate_seq
index 445d5457ed893aaf83063b54df064389e29c561b..21452b901c22ba142713e69698331c615308f8cf 100755 (executable)
--- a/bp_bin/translate_seq
+++ b/bp_bin/translate_seq
@@ -34,7 +34,7 @@ use Maasha::Seq;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $frame, %new_record );
+my ( $options, $in, $out, $record, $frame, %new_record );
 
 $options = Maasha::Biopieces::parse_options(
     [

diff --git a/bp_bin/transliterate_seq b/bp_bin/transliterate_seq
index 9e10b65cd783bd5e7d7349915a1631fbd8dfb690..44c60ff55263a9a21d7dbbeb3cbbf8ec749cb427 100755 (executable)
--- a/bp_bin/transliterate_seq
+++ b/bp_bin/transliterate_seq
@@ -33,7 +33,7 @@ use Maasha::Biopieces;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $search, $replace, $delete );
+my ( $options, $in, $out, $record, $search, $replace, $delete );
 
 $options = Maasha::Biopieces::parse_options(
     [

diff --git a/bp_bin/transliterate_vals b/bp_bin/transliterate_vals
index 94312394f3b4b1dee80a9f28b96b1006e694d95c..091aa9d9f53873a0a28e21cbd8e87a4feaed0bd3 100755 (executable)
--- a/bp_bin/transliterate_vals
+++ b/bp_bin/transliterate_vals
@@ -33,7 +33,7 @@ use Maasha::Biopieces;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $search, $replace, $delete, $key );
+my ( $options, $in, $out, $record, $search, $replace, $delete, $key );
 
 $options = Maasha::Biopieces::parse_options(
     [

diff --git a/bp_bin/uniq_vals b/bp_bin/uniq_vals
index c27461d9680bc8587345634ec6eaae9e5bdbc204..93fd3be92fc3737e5e6a5dc119b1978a12109ce8 100755 (executable)
--- a/bp_bin/uniq_vals
+++ b/bp_bin/uniq_vals
@@ -33,7 +33,7 @@ use Maasha::Biopieces;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, %hash, $record );
+my ( $options, $in, $out, %hash, $record );
 
 $options = Maasha::Biopieces::parse_options(
     [

diff --git a/bp_bin/upload_to_ucsc b/bp_bin/upload_to_ucsc
index e4c206e8707b198316965cdae4208124466602ad..5fa6c3e633ba51d7462bdcfe5154b338a93b5c97 100755 (executable)
--- a/bp_bin/upload_to_ucsc
+++ b/bp_bin/upload_to_ucsc
@@ -39,7 +39,7 @@ use Maasha::UCSC::BED;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $tmp_dir, $file, $wib_file, $wig_file, $wib_dir, $fh_out, $i, $first, $format, $type, $columns, $append, $entry );
+my ( $options, $in, $out, $record, $tmp_dir, $file, $wib_file, $wig_file, $wib_dir, $fh_out, $i, $first, $format, $type, $columns, $append, $entry );
 
 $options = Maasha::Biopieces::parse_options(
     [

diff --git a/bp_bin/uppercase_seq b/bp_bin/uppercase_seq
index 703d383b724220e098a1a47dae4d1535bc2f9532..3a9c89bf724b5b14b86b621403eb88c10fc9fe53 100755 (executable)
--- a/bp_bin/uppercase_seq
+++ b/bp_bin/uppercase_seq
@@ -33,7 +33,7 @@ use Maasha::Biopieces;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record );
+my ( $options, $in, $out, $record );
 
 $options = Maasha::Biopieces::parse_options();
 

diff --git a/bp_bin/vmatch_seq b/bp_bin/vmatch_seq
index 96d4263cf00e60da4c86858b2b08c8f466b8e7d6..0cddbe0e696dfcedcdf219fb51502d9954bf7ba1 100755 (executable)
--- a/bp_bin/vmatch_seq
+++ b/bp_bin/vmatch_seq
@@ -38,7 +38,7 @@ use Maasha::Fasta;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, @index_files, $tmp_dir, $query_file, $fh_out, $fh_in, $record, $entry,
+my ( $options, $in, $out, @index_files, $tmp_dir, $query_file, $fh_out, $fh_in, $record, $entry,
      $vmatch_args, $result_file, $count_hash );
 
 $options = Maasha::Biopieces::parse_options(

diff --git a/bp_bin/write_2bit b/bp_bin/write_2bit
index 1a1f756d570ef833b72512b72514ddc40830d4a9..459f852c3c6fe55f3edd0c1e1a39d1199c1aa6c1 100755 (executable)
--- a/bp_bin/write_2bit
+++ b/bp_bin/write_2bit
@@ -39,7 +39,7 @@ use Maasha::TwoBit;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $mask, $tmp_dir, $tmp_file, $fh_tmp, $fh_in, $fh_out, $entry );
+my ( $options, $in, $out, $record, $mask, $tmp_dir, $tmp_file, $fh_tmp, $fh_in, $fh_out, $entry );
 
 $options = Maasha::Biopieces::parse_options(
     [

diff --git a/bp_bin/write_align b/bp_bin/write_align
index dcbe3452a4c413d289721b70244911659726e0a4..d978bd4c7e436ca6ace7eb1c9350007e7a6cf948 100755 (executable)
--- a/bp_bin/write_align
+++ b/bp_bin/write_align
@@ -34,7 +34,7 @@ use Maasha::Align;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $data_out, @entries );
+my ( $options, $in, $out, $record, $data_out, @entries );
 
 $options = Maasha::Biopieces::parse_options(
     [

diff --git a/bp_bin/write_bed b/bp_bin/write_bed
index ceabb1b286c57560e42b764744941575f508345c..38b8704c3c8d71542f8cf3f695114b1788045c7c 100755 (executable)
--- a/bp_bin/write_bed
+++ b/bp_bin/write_bed
@@ -34,7 +34,7 @@ use Maasha::UCSC::BED;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $fh, $record, $bed_entry, $new_record );
+my ( $options, $in, $out, $fh, $record, $bed_entry, $new_record );
 
 $options = Maasha::Biopieces::parse_options(
     [

diff --git a/bp_bin/write_blast b/bp_bin/write_blast
index f72f71874c0bd9391cdf313daea5926098e8be34..27f164aef21d6d77622c8aa3995d453124269c62 100755 (executable)
--- a/bp_bin/write_blast
+++ b/bp_bin/write_blast
@@ -34,7 +34,7 @@ use Maasha::Biopieces;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $first, $entry, $data_out );
+my ( $options, $in, $out, $record, $first, $entry, $data_out );
 
 $options = Maasha::Biopieces::parse_options(
     [

diff --git a/bp_bin/write_fasta b/bp_bin/write_fasta
index 51cfec07a5c7c67af38c8d1fc2c8ee061cc0ccc3..f71aa26047f7758d49d136e8e3db6ad78fb150a5 100755 (executable)
--- a/bp_bin/write_fasta
+++ b/bp_bin/write_fasta
@@ -34,7 +34,7 @@ use Maasha::Biopieces;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $data_out, $entry );
+my ( $options, $in, $out, $record, $data_out, $entry );
 
 $options = Maasha::Biopieces::parse_options(
     [

diff --git a/bp_bin/write_fixedstep b/bp_bin/write_fixedstep
index 3c3007438773f1d500ab4b094c8db61527af1c39..5de9a6bcde74eb82eca8d7a274b6fae6b2c6b011 100755 (executable)
--- a/bp_bin/write_fixedstep
+++ b/bp_bin/write_fixedstep
@@ -34,7 +34,7 @@ use Maasha::UCSC::Wiggle;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $fh, $record, $entry );
+my ( $options, $in, $out, $fh, $record, $entry );
 
 $options = Maasha::Biopieces::parse_options(
     [

diff --git a/bp_bin/write_psl b/bp_bin/write_psl
index 975b3692a2c44aead630be9075af2e714b1ac46c..43c85d485af0313dc43771328395eb0619944ef4 100755 (executable)
--- a/bp_bin/write_psl
+++ b/bp_bin/write_psl
@@ -34,7 +34,7 @@ use Maasha::UCSC::PSL;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $fh, $record, @output, $first );
+my ( $options, $in, $out, $fh, $record, @output, $first );
 
 $options = Maasha::Biopieces::parse_options(
     [

diff --git a/bp_bin/write_solid b/bp_bin/write_solid
index 7a71e51637df9cd1204e1c00339bbfc804356f84..b467e558101a197189179ff5625dd74ed7592a4e 100755 (executable)
--- a/bp_bin/write_solid
+++ b/bp_bin/write_solid
@@ -35,7 +35,7 @@ use Maasha::Solid;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $fh, $entry );
+my ( $options, $in, $out, $record, $fh, $entry );
 
 $options = Maasha::Biopieces::parse_options(
     [

diff --git a/bp_bin/write_tab b/bp_bin/write_tab
index bc6fbd9e04e21fd8f103f507b28523eb633267f3..e20794db2189e5d58ed4a816345e3aadbeee7ce6 100755 (executable)
--- a/bp_bin/write_tab
+++ b/bp_bin/write_tab
@@ -34,7 +34,7 @@ use Maasha::Biopieces;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $data_out, @vals, $ok, $key, @keys, $A, $B, %no_keys, $sort_keys, $check_sort );
+my ( $options, $in, $out, $record, $data_out, @vals, $ok, $key, @keys, $A, $B, %no_keys, $sort_keys, $check_sort );
 
 $options = Maasha::Biopieces::parse_options(
     [

diff --git a/bp_bin/write_ucsc_config b/bp_bin/write_ucsc_config
index b566281727fb014479cd122eabeabeb9fbeb16e1..efd4dd0a81566538ad7f45a9e33f3dd3e5dcdde9 100755 (executable)
--- a/bp_bin/write_ucsc_config
+++ b/bp_bin/write_ucsc_config
@@ -34,7 +34,7 @@ use Maasha::UCSC;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $fh );
+my ( $options, $in, $out, $record, $fh );
 
 $options = Maasha::Biopieces::parse_options(
     [