added use strict to all biopieces

git-svn-id: http://biopieces.googlecode.com/svn/trunk@558 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/add_ident b/bp_bin/add_ident
index f9cdac0ffd3ad299b697874cb4f9e40beb674777..57a644a445ec717cb7388dda2edc3743207b053a 100755 (executable)
--- a/bp_bin/add_ident
+++ b/bp_bin/add_ident
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 

diff --git a/bp_bin/align_pair_seq b/bp_bin/align_pair_seq
index bfa326bbd8eae9a16bfb38d23e015d949a3a0b44..1a9d673121ac4a66d3bbc555f3fcc0355b62d2c7 100755 (executable)
--- a/bp_bin/align_pair_seq
+++ b/bp_bin/align_pair_seq
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::AlignTwoSeq;

diff --git a/bp_bin/align_seq b/bp_bin/align_seq
index 7f880428c819e51d47cb9ff18218e30ebf15a03a..af114e1da2d78e1490cbf016fc10ab89a4656fe1 100755 (executable)
--- a/bp_bin/align_seq
+++ b/bp_bin/align_seq
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::Align;

diff --git a/bp_bin/analyze_bed b/bp_bin/analyze_bed
index 16c53d53e38a0c14a49e87f3f9aa469ac7addc3f..5895104553c09bb08cc860c203f37aedb8f59506 100755 (executable)
--- a/bp_bin/analyze_bed
+++ b/bp_bin/analyze_bed
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::UCSC;

diff --git a/bp_bin/analyze_seq b/bp_bin/analyze_seq
index 53a9d645af5c4524c66555944e1221d3efce6939..b6f7d8c50ca78c4c054a7f68936fcc2c75a8e8ff 100755 (executable)
--- a/bp_bin/analyze_seq
+++ b/bp_bin/analyze_seq
@@ -27,6 +27,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::Seq;

diff --git a/bp_bin/analyze_tags b/bp_bin/analyze_tags
index 63a0d326172d1d034be8ec24e5ba8d4ca5c195b1..181beb501b13b3b72b01a73e128144051419547c 100755 (executable)
--- a/bp_bin/analyze_tags
+++ b/bp_bin/analyze_tags
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::Seq;

diff --git a/bp_bin/analyze_vals b/bp_bin/analyze_vals
index 445b2db61afd05ee01e8df5110f93d1a3974f746..91da15a1a0055e67bc451339e5436874d7c31932 100755 (executable)
--- a/bp_bin/analyze_vals
+++ b/bp_bin/analyze_vals
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::Calc;

diff --git a/bp_bin/assemble_tag_contigs b/bp_bin/assemble_tag_contigs
index 758a0226bcfccbdc77ec9bbe8bf9bce4842d8848..9b605efbbb43e8cc92767662f8153dddd0f1367b 100755 (executable)
--- a/bp_bin/assemble_tag_contigs
+++ b/bp_bin/assemble_tag_contigs
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::Filesys;

diff --git a/bp_bin/bioscript b/bp_bin/bioscript
index 48dfec2f3b4408501c29576521b0d3d92d85664c..f2e4cbdc29801aa1fe884b000f1ea6622c433fe6 100755 (executable)
--- a/bp_bin/bioscript
+++ b/bp_bin/bioscript
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces qw( get_record put_record );
 use Data::Dumper;

diff --git a/bp_bin/biostat b/bp_bin/biostat
index 744710a1b91fec09d044bd674410e9d1268aa795..6a7d0406bc0fd1c7d5ceb3138e15068e1633b0d2 100755 (executable)
--- a/bp_bin/biostat
+++ b/bp_bin/biostat
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::Common;

diff --git a/bp_bin/blast_seq b/bp_bin/blast_seq
index 2f1254536bb3e54671c59a92e3e53496c7d7ab9a..55d05308ce6a7ef8d1ee9bf942c9bfbd9102dfa2 100755 (executable)
--- a/bp_bin/blast_seq
+++ b/bp_bin/blast_seq
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::Common;

diff --git a/bp_bin/blat_seq b/bp_bin/blat_seq
index 2fd60f6ed39060145e1f0657ffa1175a5e32db3d..220e7b3d61de86afb7878e70b815c966c0e20568 100755 (executable)
--- a/bp_bin/blat_seq
+++ b/bp_bin/blat_seq
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::Filesys;

diff --git a/bp_bin/calc_bit_scores b/bp_bin/calc_bit_scores
index 9de170d172071c0b73149db1e81282890b266d4e..4b930c30c1c8e911431e11cc749e3c7d24e04a61 100755 (executable)
--- a/bp_bin/calc_bit_scores
+++ b/bp_bin/calc_bit_scores
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::Seq;

diff --git a/bp_bin/calc_fixedstep b/bp_bin/calc_fixedstep
index 27628fe1fe2b90818f87a13db6e6dea731c264ac..49c9a76d207b9581ff8c4e2fc975ece8de7ef7b4 100755 (executable)
--- a/bp_bin/calc_fixedstep
+++ b/bp_bin/calc_fixedstep
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::Filesys;

diff --git a/bp_bin/complement_seq b/bp_bin/complement_seq
index 193d9e4838be10f0a19dfe9e2b2046571aa52c0d..348e0580640c1e2a97c18cbd156d543bd08e67cc 100755 (executable)
--- a/bp_bin/complement_seq
+++ b/bp_bin/complement_seq
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::Seq;

diff --git a/bp_bin/compute b/bp_bin/compute
index 359becd34640a9b04859d5f0adc0accecbb4f80e..0b2e280c30203114b4ec8bc32eaa71181301cfe8 100755 (executable)
--- a/bp_bin/compute
+++ b/bp_bin/compute
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Common;
 use Maasha::Biopieces;

diff --git a/bp_bin/count_records b/bp_bin/count_records
index 28b615704180d5baec317bc466079055e5529a81..cbe5f0dba6226fc39b6670831c6f9a8f0f6178bd 100755 (executable)
--- a/bp_bin/count_records
+++ b/bp_bin/count_records
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Fasta;
 use Maasha::Biopieces;

diff --git a/bp_bin/count_vals b/bp_bin/count_vals
index 377af3581d69fc394fca3b7850ae3a47f8ef7550..8081e5c98e661cddd658cb760af0bc3b3548e70f 100755 (executable)
--- a/bp_bin/count_vals
+++ b/bp_bin/count_vals
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Filesys;
 use Maasha::Biopieces;

diff --git a/bp_bin/create_blast_db b/bp_bin/create_blast_db
index eee83577297c8c7199b93aa824e822cbeec6f960..8dc857edcfc030f6bde855a3fc80644e59d8af8d 100755 (executable)
--- a/bp_bin/create_blast_db
+++ b/bp_bin/create_blast_db
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Seq;
 use Maasha::Fasta;

diff --git a/bp_bin/create_vmatch_index b/bp_bin/create_vmatch_index
index aed4ca7b2608bb349e11ff92c024f7e52fcc68e5..f27e255648b7609d89f4ae8bb1504266a101cee0 100755 (executable)
--- a/bp_bin/create_vmatch_index
+++ b/bp_bin/create_vmatch_index
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Common;
 use Maasha::Biopieces;

diff --git a/bp_bin/create_weight_matrix b/bp_bin/create_weight_matrix
index 8c5089b30743a6c15e90b9ae12736955c89af1c5..ac7d12c4baa5936f41f3ae90dbb0cbc108625fc7 100755 (executable)
--- a/bp_bin/create_weight_matrix
+++ b/bp_bin/create_weight_matrix
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Common;
 use Maasha::Biopieces;

diff --git a/bp_bin/extract_seq b/bp_bin/extract_seq
index ee1a004d1bb56d16b75a42507204a0047d8c360c..d5760d5a76f7cf31b8e91e3f409f7921dd254af0 100755 (executable)
--- a/bp_bin/extract_seq
+++ b/bp_bin/extract_seq
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 

diff --git a/bp_bin/flip_tab b/bp_bin/flip_tab
index 7f520bc6bad70d7a0a660ff7a1ef5a2f5099d133..74fca2ea1ea261881f42d62a61be402555b67c68 100755 (executable)
--- a/bp_bin/flip_tab
+++ b/bp_bin/flip_tab
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::Matrix;

diff --git a/bp_bin/fold_seq b/bp_bin/fold_seq
index 656310748412d6c037c2e91ad0e2c6479e065de4..1207cfe9bc46a84c476f64003bdd203f0f116016 100755 (executable)
--- a/bp_bin/fold_seq
+++ b/bp_bin/fold_seq
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 

diff --git a/bp_bin/format_genome b/bp_bin/format_genome
index 844e5af6c20a86f419bab1055b205bf17c0ebede..dbd4182ce02c18cddba67faf12f62fe3f6a670c7 100755 (executable)
--- a/bp_bin/format_genome
+++ b/bp_bin/format_genome
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Fasta;
 use Maasha::Biopieces;

diff --git a/bp_bin/get_genome_align b/bp_bin/get_genome_align
index 664e6b5f66134959624f88a460d55d5251ae360a..566ea6e365072e40f388b27a6b9784e503547439 100755 (executable)
--- a/bp_bin/get_genome_align
+++ b/bp_bin/get_genome_align
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::Common;

diff --git a/bp_bin/get_genome_phastcons b/bp_bin/get_genome_phastcons
index 0790bb0b731e6783116f6fe210458ddf5f19cff7..8531d269e2708ce5dfdf205fde8621100791be62 100755 (executable)
--- a/bp_bin/get_genome_phastcons
+++ b/bp_bin/get_genome_phastcons
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::Filesys;

diff --git a/bp_bin/get_genome_seq b/bp_bin/get_genome_seq
index 5292b72f58efe1f98933e11b19a44d5c7e3a4193..dbbc9d414287f96dada2dea518082293f9915342 100755 (executable)
--- a/bp_bin/get_genome_seq
+++ b/bp_bin/get_genome_seq
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::Filesys;

diff --git a/bp_bin/grab b/bp_bin/grab
index 1be030a34e1ab4b451f386d5ad8443a3959436f9..8728f81a352868047b72b964c3104c8c08266e7a 100755 (executable)
--- a/bp_bin/grab
+++ b/bp_bin/grab
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::Common;

diff --git a/bp_bin/head_records b/bp_bin/head_records
index 9ae391816cf5574b55f96e31e4159244c61a9c3e..d88c2228aef9abc01deb3a62a3b83e5b7a308dfd 100755 (executable)
--- a/bp_bin/head_records
+++ b/bp_bin/head_records
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 

diff --git a/bp_bin/indel_seq b/bp_bin/indel_seq
index 4fe3d3d4877cb6a1f9099a5644ce54f87eb147f2..f5288d69f4ead4b9e102004f90e69c7335b968ce 100755 (executable)
--- a/bp_bin/indel_seq
+++ b/bp_bin/indel_seq
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Common;
 use Maasha::Biopieces;

diff --git a/bp_bin/invert_align b/bp_bin/invert_align
index 28ccac0191f64645af70dd99941bfb0c0385cf86..e798687eb82bf0de598d8aaedbfb5f3517b299ff 100755 (executable)
--- a/bp_bin/invert_align
+++ b/bp_bin/invert_align
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::Align;

diff --git a/bp_bin/length_seq b/bp_bin/length_seq
index 4a9433383b85882a483cd8860c9663d32b864598..4e8d0e37a72efae555ab0029152e50675e031c75 100755 (executable)
--- a/bp_bin/length_seq
+++ b/bp_bin/length_seq
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 

diff --git a/bp_bin/length_vals b/bp_bin/length_vals
index b7ed3c43c7b86e2eedc1f6fc939979ca1a024291..29451b83baae76015845385886b968d5a5e93a9a 100755 (executable)
--- a/bp_bin/length_vals
+++ b/bp_bin/length_vals
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 

diff --git a/bp_bin/list_biopieces b/bp_bin/list_biopieces
index bf17d01b0271d9455c9ac08e7bb7402e13a9de50..e36d52e2cfd4086cb2aec26267aedf92ef459a95 100755 (executable)
--- a/bp_bin/list_biopieces
+++ b/bp_bin/list_biopieces
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Common;
 use Maasha::Biopieces;

diff --git a/bp_bin/list_genomes b/bp_bin/list_genomes
index 2c8fb1d79e313f8ae928a8fe8672d29d1d4cc50c..f5e6d4d8e4ec1f27675127829e28af25a5ed97b6 100755 (executable)
--- a/bp_bin/list_genomes
+++ b/bp_bin/list_genomes
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Common;
 use Maasha::Biopieces;

diff --git a/bp_bin/match_seq b/bp_bin/match_seq
index dd1ac6392177bb799d47d00d2e124b16350ffc72..bb95a3f14fd14fe70561ba75fdb8338e1755a4f6 100755 (executable)
--- a/bp_bin/match_seq
+++ b/bp_bin/match_seq
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::Match;

diff --git a/bp_bin/max_vals b/bp_bin/max_vals
index 4d42fcfc5e89febc4075d03652f3ee411e338413..4cb794b8019cca8d487004a8a623dd3256ea75ca 100755 (executable)
--- a/bp_bin/max_vals
+++ b/bp_bin/max_vals
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 

diff --git a/bp_bin/mean_vals b/bp_bin/mean_vals
index 45a17079ca9bd5eb517a272a53e5f5cc5260a843..f29a4fce3c84e573ab103f04fb2fbf0cf3f96a38 100755 (executable)
--- a/bp_bin/mean_vals
+++ b/bp_bin/mean_vals
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 

diff --git a/bp_bin/median_vals b/bp_bin/median_vals
index 9256cf5fc2b5a17c1dfdfe82937ababee975a8be..91cdd36d8b895b03219063f8aa6abd763e8e671b 100755 (executable)
--- a/bp_bin/median_vals
+++ b/bp_bin/median_vals
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::Calc;

diff --git a/bp_bin/merge_records b/bp_bin/merge_records
index a452c7a80d405a223ed5b4848eeb8c27e474bdd4..7294590598566fc418fbf67fdd9c11f0d219ebb5 100755 (executable)
--- a/bp_bin/merge_records
+++ b/bp_bin/merge_records
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::Common;

diff --git a/bp_bin/merge_vals b/bp_bin/merge_vals
index c6c6cfeaed7d267668a9c6163a14367e6b785b2f..963fbfc5e947838ffe8a25067e5c0db65bd2f6fc 100755 (executable)
--- a/bp_bin/merge_vals
+++ b/bp_bin/merge_vals
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 

diff --git a/bp_bin/min_vals b/bp_bin/min_vals
index ed355d4d7a857b521d4713f96bacddc67d8adf90..bff25a7464286ddb6f9b8286e0a1e19c79c433db 100755 (executable)
--- a/bp_bin/min_vals
+++ b/bp_bin/min_vals
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 

diff --git a/bp_bin/mutate_seq b/bp_bin/mutate_seq
index 2000e9da9e9655c6509d24865bcd8fded7231e17..b77ffcf4561b71e10889dd2a6def354417d899e4 100755 (executable)
--- a/bp_bin/mutate_seq
+++ b/bp_bin/mutate_seq
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Common;
 use Maasha::Biopieces;

diff --git a/bp_bin/oligo_freq b/bp_bin/oligo_freq
index 008bcbebb691f672f3d8648eb89d20c33dafa38a..53029b661c1c70be8e64215c1ec98e49834a9129 100755 (executable)
--- a/bp_bin/oligo_freq
+++ b/bp_bin/oligo_freq
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 

diff --git a/bp_bin/patscan_seq b/bp_bin/patscan_seq
index 07dd685d7b146e357475521497fbf6b15fac767a..2d828f694cf852064326f59b43261d8922e1df76 100755 (executable)
--- a/bp_bin/patscan_seq
+++ b/bp_bin/patscan_seq
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::Common;

diff --git a/bp_bin/plot_chrdist b/bp_bin/plot_chrdist
index 172d3dc7f556526c17547205a127e16117402397..9e3ba416f1b3c45864a7448b9118dc26f38833aa 100755 (executable)
--- a/bp_bin/plot_chrdist
+++ b/bp_bin/plot_chrdist
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::Plot;

diff --git a/bp_bin/plot_histogram b/bp_bin/plot_histogram
index f04068fa32ed9a7570b6b9d69b53b2231b7dbac5..4950305b8aede84ba0a131644860836bb992abd0 100755 (executable)
--- a/bp_bin/plot_histogram
+++ b/bp_bin/plot_histogram
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::Plot;

diff --git a/bp_bin/plot_karyogram b/bp_bin/plot_karyogram
index a48619031af1f6d1aedf28617d1035097314841a..2e3748be5a113282cc3997c8862744cbe19d137d 100755 (executable)
--- a/bp_bin/plot_karyogram
+++ b/bp_bin/plot_karyogram
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::Plot;

diff --git a/bp_bin/plot_lendist b/bp_bin/plot_lendist
index 0138c669232fae480898e1de592831a260e2b91e..dfc0abb390dfeb60f91eaceb9333658dd135e3f0 100755 (executable)
--- a/bp_bin/plot_lendist
+++ b/bp_bin/plot_lendist
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::Plot;

diff --git a/bp_bin/plot_matches b/bp_bin/plot_matches
index 3aa016efb19f7c99f791d70518c90272a5f3edce..3fc25ad2f871c11799007229d859c3e9673ecaa1 100755 (executable)
--- a/bp_bin/plot_matches
+++ b/bp_bin/plot_matches
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::Plot;

diff --git a/bp_bin/plot_phastcons_profiles b/bp_bin/plot_phastcons_profiles
index 89835c32e4a28e3be351baaeb468cb8ea571f7ab..82db05615e68b84eb264b83f2e0a59099c61c22f 100755 (executable)
--- a/bp_bin/plot_phastcons_profiles
+++ b/bp_bin/plot_phastcons_profiles
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::Plot;

diff --git a/bp_bin/plot_seqlogo b/bp_bin/plot_seqlogo
index ce30a7341f3a03af655c1f73d5926159c570bee5..3495c9e5ae54279d0a396ee07bd0f767b0585daf 100755 (executable)
--- a/bp_bin/plot_seqlogo
+++ b/bp_bin/plot_seqlogo
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::Plot;

diff --git a/bp_bin/print_wiki b/bp_bin/print_wiki
index 1c581d2cf0cf191a891f8dc8f92915485e557238..f766c8b861dd177607e5aa58cd1cb8a829a7804a 100755 (executable)
--- a/bp_bin/print_wiki
+++ b/bp_bin/print_wiki
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::Gwiki;

diff --git a/bp_bin/random_records b/bp_bin/random_records
index 12986d1b05eeb4a29e26313c661c2372739a1f22..b700dc19a22ef646d32d262ecb255533a5f29218 100755 (executable)
--- a/bp_bin/random_records
+++ b/bp_bin/random_records
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::Filesys;

diff --git a/bp_bin/read_2bit b/bp_bin/read_2bit
index fe5878e6c7e1be91beed0c66569288210a0350c1..7eebe05309df6b0d26004332d38e270b23f94cee 100755 (executable)
--- a/bp_bin/read_2bit
+++ b/bp_bin/read_2bit
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::Filesys;

diff --git a/bp_bin/read_bed b/bp_bin/read_bed
index 8d270cb505f08b01e2b7e1c11b870f9cdb833d52..28157493dc824fa4c2b1b84f3539ecc33cf8532c 100755 (executable)
--- a/bp_bin/read_bed
+++ b/bp_bin/read_bed
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::Filesys;

diff --git a/bp_bin/read_blast_tab b/bp_bin/read_blast_tab
index 61aabc6c0656b98b1f2ce8d2eadc70537e122a68..26d40890f02ee2327158e338dec67c7a1c486dee 100755 (executable)
--- a/bp_bin/read_blast_tab
+++ b/bp_bin/read_blast_tab
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::Filesys;

diff --git a/bp_bin/read_embl b/bp_bin/read_embl
index 50b24e51d161d2e73eb3a1d93e00b747a78db31b..496a5d8f85594e4119ab5960690b6ef0016f75b4 100755 (executable)
--- a/bp_bin/read_embl
+++ b/bp_bin/read_embl
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::Filesys;

diff --git a/bp_bin/read_fasta b/bp_bin/read_fasta
index 488465dfd24739616ed1ecc4a46cd4c3e7966e56..91d8ad2a921d26542203d192e0ef145df22b6dfc 100755 (executable)
--- a/bp_bin/read_fasta
+++ b/bp_bin/read_fasta
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::Filesys;

diff --git a/bp_bin/read_fixedstep b/bp_bin/read_fixedstep
index 932ebe69b12d0bb509e3ab88ba91bd3a818c3b9b..64d949c8b41a009e93cafef94cf9950ce9a05bc8 100755 (executable)
--- a/bp_bin/read_fixedstep
+++ b/bp_bin/read_fixedstep
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::Filesys;

diff --git a/bp_bin/read_gff b/bp_bin/read_gff
index d3785b64c0c8f8ba06743f47f44b74b957fbb8e5..b3d36db6ebe6a022fb898fefaf067d0ff8318124 100755 (executable)
--- a/bp_bin/read_gff
+++ b/bp_bin/read_gff
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::Filesys;

diff --git a/bp_bin/read_mysql b/bp_bin/read_mysql
index 8abc9087434cb1a0a49598515d7d15fbfa535981..ff96a81ee6bd4d00926e1991b38fa51a24e207db 100755 (executable)
--- a/bp_bin/read_mysql
+++ b/bp_bin/read_mysql
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::SQL;

diff --git a/bp_bin/read_psl b/bp_bin/read_psl
index bcba5ee63dfa8456ec5ed853c9a94c529c63130c..0d7fe35e10270a0909c41fe6c06116eeef4e030d 100755 (executable)
--- a/bp_bin/read_psl
+++ b/bp_bin/read_psl
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::Filesys;

diff --git a/bp_bin/read_soft b/bp_bin/read_soft
index 9e44f59ef355885cd6366aac6a84553c86e020ec..78adc841349450c3d2930fbf3afc3c74f6f335c6 100755 (executable)
--- a/bp_bin/read_soft
+++ b/bp_bin/read_soft
@@ -27,6 +27,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::Filesys;

diff --git a/bp_bin/read_solexa b/bp_bin/read_solexa
index fb3a988c6657aea219f9985dcb2cbaa425d64793..dc5d237523414d9effc0b47f404b861a7ffdd50b 100755 (executable)
--- a/bp_bin/read_solexa
+++ b/bp_bin/read_solexa
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::Filesys;

diff --git a/bp_bin/read_solid b/bp_bin/read_solid
index 8a6661805f573d742d02d072290a8da02437be26..193cd52657dc6bcdb4911fdbfb8f1a01b764bd5a 100755 (executable)
--- a/bp_bin/read_solid
+++ b/bp_bin/read_solid
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::Filesys;

diff --git a/bp_bin/read_stockholm b/bp_bin/read_stockholm
index 400c8a72378e6c19e4a05ba881478af0e447db6c..597e9e9b72f867636fea7593db052e4211610520 100755 (executable)
--- a/bp_bin/read_stockholm
+++ b/bp_bin/read_stockholm
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::Filesys;

diff --git a/bp_bin/read_tab b/bp_bin/read_tab
index cf37a12b3b3496136a152d6cf86b5fa52415b711..3c782303d101c2da9d14afaebab7dac2f9857119 100755 (executable)
--- a/bp_bin/read_tab
+++ b/bp_bin/read_tab
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Filesys;
 use Maasha::Biopieces;

diff --git a/bp_bin/read_ucsc_config b/bp_bin/read_ucsc_config
index fed3f83d944729dba0871b9ddd62fc11c596487a..4317ae394b8e60e69ff81608d1584fa8969c7251 100755 (executable)
--- a/bp_bin/read_ucsc_config
+++ b/bp_bin/read_ucsc_config
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::Filesys;

diff --git a/bp_bin/remove_adaptor b/bp_bin/remove_adaptor
index f037055ad08e6a840830eca2e31ae5f396b0a289..14a7f896d46e9cbb23d2e6c6256bd2623964c3e3 100755 (executable)
--- a/bp_bin/remove_adaptor
+++ b/bp_bin/remove_adaptor
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::Common;

diff --git a/bp_bin/remove_indels b/bp_bin/remove_indels
index 59bbd4f92b932073a7fdaecd211d410712e18f7e..3156b44d60c29fa7418033c31868c1aec0546282 100755 (executable)
--- a/bp_bin/remove_indels
+++ b/bp_bin/remove_indels
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 

diff --git a/bp_bin/remove_keys b/bp_bin/remove_keys
index a61e763c67a1d32843f336ae3459a43897dcc123..6e0004354d2aa1c67e58a82ac99ee86656ae91c7 100755 (executable)
--- a/bp_bin/remove_keys
+++ b/bp_bin/remove_keys
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 

diff --git a/bp_bin/remove_mysql_tables b/bp_bin/remove_mysql_tables
index b25b79dd22ce8554b233c7b9c3ec3f6fafae377f..1419cbc5b0889fa33f7d1ee03f3bbf8757365c0e 100755 (executable)
--- a/bp_bin/remove_mysql_tables
+++ b/bp_bin/remove_mysql_tables
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::Common;

diff --git a/bp_bin/remove_ucsc_tracks b/bp_bin/remove_ucsc_tracks
index 52d7ee6dbe345d25be40240e9a1500af37e6437c..4148da8f30242fe87b090120489b8f69cc2071ea 100755 (executable)
--- a/bp_bin/remove_ucsc_tracks
+++ b/bp_bin/remove_ucsc_tracks
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::Common;

diff --git a/bp_bin/rename_keys b/bp_bin/rename_keys
index b8d85be212e8019a2f2c9e00c922fee5cf5a625b..b0dc229a983f231d91c9406abc1538c8111aa055 100755 (executable)
--- a/bp_bin/rename_keys
+++ b/bp_bin/rename_keys
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 

diff --git a/bp_bin/reverse_seq b/bp_bin/reverse_seq
index 7d137272a4f7aa0b20e238078920628565d03e4f..019245e1e5c1a57d713b35bd8a335b1d71289ffa 100755 (executable)
--- a/bp_bin/reverse_seq
+++ b/bp_bin/reverse_seq
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 

diff --git a/bp_bin/shuffle_seq b/bp_bin/shuffle_seq
index 11d4c91312ae0cf1de7933d4da274e94c39995fe..165fbda967f8ac5a510e670ecf6192cb7d6a0c55 100755 (executable)
--- a/bp_bin/shuffle_seq
+++ b/bp_bin/shuffle_seq
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::Seq;

diff --git a/bp_bin/soap_seq b/bp_bin/soap_seq
index 67d53e9dd47d258f167825e0252e153b6f6bc9fe..e6417f562eb9512db230f293f4bfefaa699b0ced 100755 (executable)
--- a/bp_bin/soap_seq
+++ b/bp_bin/soap_seq
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::Common;

diff --git a/bp_bin/sort_records b/bp_bin/sort_records
index f6e4234032046ce68d020a5ec9c3a1b1e4aa1db5..af8edbc8c189489eb1a32d65043af37d1551f32a 100755 (executable)
--- a/bp_bin/sort_records
+++ b/bp_bin/sort_records
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 

diff --git a/bp_bin/split_bed b/bp_bin/split_bed
index 5fbdf4027af91f2695060ee8469699f35f6a8d68..bd708a4d20a341c3f5515a6e3d6d99ebd42fc540 100755 (executable)
--- a/bp_bin/split_bed
+++ b/bp_bin/split_bed
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 

diff --git a/bp_bin/split_seq b/bp_bin/split_seq
index b8aa503c3c28a7950f9b6f1a97588881e7b8bd6b..518565d299481bd69baab910f82d3133339dae2a 100755 (executable)
--- a/bp_bin/split_seq
+++ b/bp_bin/split_seq
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 

diff --git a/bp_bin/split_vals b/bp_bin/split_vals
index f6545234a2c5b98e9b0a27d3ebdcea884dbe34d3..93cac4a118b087f485c8c5d44b06b6545ce26a8a 100755 (executable)
--- a/bp_bin/split_vals
+++ b/bp_bin/split_vals
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 

diff --git a/bp_bin/sum_vals b/bp_bin/sum_vals
index 2db00ff85dae1e9eda99bf4f24e3daa91b785466..b672de388c88b63dee2901f477fb66acffd49e1f 100755 (executable)
--- a/bp_bin/sum_vals
+++ b/bp_bin/sum_vals
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 

diff --git a/bp_bin/tile_seq b/bp_bin/tile_seq
index d0f95622fad6d40b01c571e358c775a0da155491..9a7dcfd8410bf139e62ce76c200428edc9f92890 100755 (executable)
--- a/bp_bin/tile_seq
+++ b/bp_bin/tile_seq
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::Align;

diff --git a/bp_bin/translate_seq b/bp_bin/translate_seq
index 663012b29ec5aa7501607fed90782498f609fe42..ba6b07f696d8d21cca3b3e395c49bc4fa63ec477 100755 (executable)
--- a/bp_bin/translate_seq
+++ b/bp_bin/translate_seq
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::Seq;

diff --git a/bp_bin/transliterate_seq b/bp_bin/transliterate_seq
index a53c62ad95d9cfbb57bfd314857575cf96d2befd..a81d328d9a99ac54936a086caff7c03c3b7f993d 100755 (executable)
--- a/bp_bin/transliterate_seq
+++ b/bp_bin/transliterate_seq
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 

diff --git a/bp_bin/transliterate_vals b/bp_bin/transliterate_vals
index 502939a8c811f750ea23ad7e6211aeeee9c30572..3877ad44ab91aefd6655454da9b8e7d44545c47d 100755 (executable)
--- a/bp_bin/transliterate_vals
+++ b/bp_bin/transliterate_vals
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 

diff --git a/bp_bin/uniq_vals b/bp_bin/uniq_vals
index c9bf842bc78a4a2e409bcd12a870dc8c6da25a97..0bc6ce0aa8adcf017fe1742a07892e29b7e663f2 100755 (executable)
--- a/bp_bin/uniq_vals
+++ b/bp_bin/uniq_vals
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 

diff --git a/bp_bin/upload_to_ucsc b/bp_bin/upload_to_ucsc
index 72ef8c43d85f77c5ede0be02ccf2bca92cfb3431..aac49282267a919c50d2fb82380fc6bfa1241352 100755 (executable)
--- a/bp_bin/upload_to_ucsc
+++ b/bp_bin/upload_to_ucsc
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Common;
 use Maasha::Biopieces;

diff --git a/bp_bin/uppercase_seq b/bp_bin/uppercase_seq
index 3b4b941b0bfd9cb7ef943b5e713686d6c1f4ddd5..e5acdf8b9cd6dd65511b44b907c305e30fd414d6 100755 (executable)
--- a/bp_bin/uppercase_seq
+++ b/bp_bin/uppercase_seq
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 

diff --git a/bp_bin/vmatch_seq b/bp_bin/vmatch_seq
index 9b8f952ccd9aa223ddd26df1fc41a30766b88337..c02b98d1f8d895fa0791c8f057e7ffc02081a9cf 100755 (executable)
--- a/bp_bin/vmatch_seq
+++ b/bp_bin/vmatch_seq
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Data::Dumper;
 use Maasha::Biopieces;

diff --git a/bp_bin/write_2bit b/bp_bin/write_2bit
index 1f1575e715d43d3b9995d784ef4ecd03adaf64c7..12e330dbbd872bddc468bc8361d36d6152502b34 100755 (executable)
--- a/bp_bin/write_2bit
+++ b/bp_bin/write_2bit
@@ -29,6 +29,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Fasta;
 use Maasha::Biopieces;

diff --git a/bp_bin/write_align b/bp_bin/write_align
index 4692f86955e9d69ea889ed1a58746267a3a6a273..f0a0598d68aeff4d5e92e11bd2fb539749401cc0 100755 (executable)
--- a/bp_bin/write_align
+++ b/bp_bin/write_align
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::Align;

diff --git a/bp_bin/write_bed b/bp_bin/write_bed
index 3b486fd050419accd35163851b6b04983db5f268..51cdc758225af677fab9ee31c3f7f0fbb6ef116f 100755 (executable)
--- a/bp_bin/write_bed
+++ b/bp_bin/write_bed
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::UCSC::BED;

diff --git a/bp_bin/write_blast b/bp_bin/write_blast
index ba65a2b0698222f8c5001a6fefb6187e58b8deda..b3f6c72180565265e34713903c184bf37e72c325 100755 (executable)
--- a/bp_bin/write_blast
+++ b/bp_bin/write_blast
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Fasta;
 use Maasha::Biopieces;

diff --git a/bp_bin/write_fasta b/bp_bin/write_fasta
index b6dd3440b469d659ca847f570f2610cf1267383b..52f8a7011089f04b3052aaad2bc0d08b53c85ac6 100755 (executable)
--- a/bp_bin/write_fasta
+++ b/bp_bin/write_fasta
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Fasta;
 use Maasha::Biopieces;

diff --git a/bp_bin/write_fixedstep b/bp_bin/write_fixedstep
index 97f8f2128fccca27e2ffd428593c3bf16c9ef48e..f79873d88259b85b58576c9d07e929d0b6d0b892 100755 (executable)
--- a/bp_bin/write_fixedstep
+++ b/bp_bin/write_fixedstep
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::UCSC::Wiggle;

diff --git a/bp_bin/write_psl b/bp_bin/write_psl
index 6ff8fef11683d277f5a7447a9d26c27526f48915..776676d782a8d80202c4293130e111bf7d3a0bd4 100755 (executable)
--- a/bp_bin/write_psl
+++ b/bp_bin/write_psl
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::UCSC::PSL;

diff --git a/bp_bin/write_solid b/bp_bin/write_solid
index 01b8220457b80918b055d8cfa8c70725ba6e2bb6..7723f768fd35cbf8fa4b58947a47df619dd40e84 100755 (executable)
--- a/bp_bin/write_solid
+++ b/bp_bin/write_solid
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::Fasta;

diff --git a/bp_bin/write_tab b/bp_bin/write_tab
index 2ed2ce8310f57ccf28e89a68aade8924ada40e2e..b512d9469c07a73018359571244082629c4be3f2 100755 (executable)
--- a/bp_bin/write_tab
+++ b/bp_bin/write_tab
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Fasta;
 use Maasha::Biopieces;

diff --git a/bp_bin/write_ucsc_config b/bp_bin/write_ucsc_config
index 5d2e2d5096c125b1dbfeb30449f5b168e485c719..2c8654a2d5f2ef1369d328462b861bd8461809dd 100755 (executable)
--- a/bp_bin/write_ucsc_config
+++ b/bp_bin/write_ucsc_config
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::UCSC;