From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Sat, 6 Jun 2009 15:40:49 +0000 (+0000)
Subject: removed variables bulk type
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=b607bb9d6e4adcebd9f9e128aacc91a212010ee0;p=biopieces.git

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 26497ef..16bde7a 100755
--- 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 1f92640..817ac25 100755
--- 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 86ea577..56a6e54 100755
--- 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 47f2102..8548fa6 100755
--- 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 1af08dc..6f76a94 100755
--- 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 f21478d..68f97ac 100755
--- 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 1ddd36f..86e50e6 100755
--- 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 8bdeda5..898837e 100755
--- 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 1823216..1534c77 100755
--- 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 bc5af18..9c3ffa7 100755
--- 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 9e98c2e..6bb5374 100755
--- 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 9c14f2c..cbb068a 100755
--- 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 9ff22c8..38d1dae 100755
--- 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 701c3d2..299b787 100755
--- 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 5ccc1e6..3907e4f 100755
--- 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 3beaeed..449fe81 100755
--- 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 79bd310..9273af6 100755
--- 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 f956745..e6dc983 100755
--- 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 44a211c..8adffcf 100755
--- 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 95bc670..c900bc7 100755
--- 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 489e2b7..605b277 100755
--- 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 cb14436..701f900 100755
--- 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 5e5b8de..6ffa92d 100755
--- 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 a346b9c..3b8bf43 100755
--- 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 9fc75ee..337c019 100755
--- 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 68c52bd..bf0f787 100755
--- 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 6d2aabf..1fecf43 100755
--- 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 bc26919..631973c 100755
--- 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 413ab29..f8b330a 100755
--- 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 2ca4b0f..b00eb3e 100755
--- 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 8bcb33e..f9f1616 100755
--- 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 b00e5af..f58f2e8 100755
--- 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 b0e77a6..147d5c1 100755
--- 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 2b852f0..0ce31eb 100755
--- 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 b8e91b4..7c760a5 100755
--- 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 60f7aaa..fb073cd 100755
--- 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 42dc410..9428f9a 100755
--- 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 cdfe46e..39f09e2 100755
--- 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 f53d99a..c751a4d 100755
--- 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 77dc832..34024b1 100755
--- 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 7631103..e179d8d 100755
--- 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 800eac7..60a5cae 100755
--- 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 dd12136..df4db5a 100755
--- 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 989222e..9eccb68 100755
--- 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 5e6c015..9adf2f8 100755
--- 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 0197aca..a2fb9cc 100755
--- 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 a2d97cf..f383da8 100755
--- 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 52489f5..caf444f 100755
--- 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 0a2d5d4..e9be5a6 100755
--- 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 578aa8e..b13d514 100755
--- 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 f45f942..5c4595c 100755
--- 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 25f0193..63bb7e1 100755
--- 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 18c5c22..551d86e 100755
--- 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 2ed0a55..fcf53ae 100755
--- 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 e0ba8b7..80cc39a 100755
--- 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 9449a0d..17a26df 100755
--- 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 93b4629..794599b 100755
--- 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 411c2a6..f7162a1 100755
--- 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 0033207..b79458b 100755
--- 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 e2aa437..c7183ee 100755
--- 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 f83aab7..c51ba90 100755
--- 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 34fd6e9..b35c21c 100755
--- 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 2d6ccf9..b39e596 100755
--- 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 530ddd4..f883d41 100755
--- 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 b6c82ab..152c0d5 100755
--- 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 35e6d2d..a62000b 100755
--- 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 118bab3..d989829 100755
--- 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 f1677c5..e476694 100755
--- 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 5324bf5..0683dce 100755
--- 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 b2e9e34..2875169 100755
--- 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 82db5d5..ca56575 100755
--- 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 5a8b221..4a804d4 100755
--- 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 95e122a..7d2052d 100755
--- 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 a3cb923..05932c4 100755
--- 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 181e4fd..f99bbb3 100755
--- 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 9c551b0..13bd4eb 100755
--- 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 47e2947..97cbaf6 100755
--- 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 93ed6c7..776a79b 100755
--- 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 2a69acd..1da7130 100755
--- 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 500f705..a90f1e4 100755
--- 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 445d545..21452b9 100755
--- 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 9e10b65..44c60ff 100755
--- 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 9431239..091aa9d 100755
--- 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 c27461d..93fd3be 100755
--- 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 e4c206e..5fa6c3e 100755
--- 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 703d383..3a9c89b 100755
--- 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 96d4263..0cddbe0 100755
--- 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 1a1f756..459f852 100755
--- 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 dcbe345..d978bd4 100755
--- 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 ceabb1b..38b8704 100755
--- 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 f72f718..27f164a 100755
--- 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 51cfec0..f71aa26 100755
--- 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 3c30074..5de9a6b 100755
--- 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 975b369..43c85d4 100755
--- 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 7a71e51..b467e55 100755
--- 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 bc6fbd9..e20794d 100755
--- 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 b566281..efd4dd0 100755
--- 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(
     [