use warnings

modules/Bio/EnsEMBL/IO/Adaptor/BAMAdaptor.pm

@@ -18,7 +18,9 @@ limitations under the License.
 =cut
 
 package Bio::EnsEMBL::IO::Adaptor::BAMAdaptor;
+
 use strict;
+use warnings;
 
 use Bio::EnsEMBL::Feature;
 use Data::Dumper;

modules/Bio/EnsEMBL/IO/Adaptor/BigBedAdaptor.pm

@@ -18,8 +18,9 @@ limitations under the License.
 =cut
 
 package Bio::EnsEMBL::IO::Adaptor::BigBedAdaptor;
-use strict;
 
+use strict;
+use warnings;
 
 #########################################################################
 # DEPRECATED MODULE - please use Bio::EnsEMBL::IO::Parser::BigBed instead

modules/Bio/EnsEMBL/IO/Adaptor/BigWigAdaptor.pm

@@ -18,7 +18,9 @@ limitations under the License.
 =cut
 
 package Bio::EnsEMBL::IO::Adaptor::BigWigAdaptor;
+
 use strict;
+use warnings;
 
 #########################################################################
 # DEPRECATED MODULE - please use Bio::EnsEMBL::IO::Parser::BigBed instead

modules/Bio/EnsEMBL/IO/Adaptor/HTSAdaptor.pm

@@ -18,7 +18,9 @@ limitations under the License.
 =cut
 
 package Bio::EnsEMBL::IO::Adaptor::HTSAdaptor;
+
 use strict;
+use warnings;
 
 use Bio::EnsEMBL::Feature;
 use Data::Dumper;

modules/Bio/EnsEMBL/IO/Adaptor/PairwiseAdaptor.pm

@@ -23,8 +23,8 @@ package Bio::EnsEMBL::IO::Adaptor::PairwiseAdaptor;
 # No longer in use by the webcode; will be removed in November 2016
 ####################################################################
 
-
 use strict;
+use warnings;
 
 use Bio::EnsEMBL::IO::Parser::PairwiseTabix;
 

modules/Bio/EnsEMBL/IO/Adaptor/VCFAdaptor.pm

@@ -18,7 +18,9 @@ limitations under the License.
 =cut
 
 package Bio::EnsEMBL::IO::Adaptor::VCFAdaptor;
+
 use strict;
+use warnings;
 
 use EnsEMBL::Web::Utils::FormatText qw(date_format);
 use File::Path qw(make_path);

modules/Bio/EnsEMBL/IO/NamedColours.pm

@@ -18,7 +18,9 @@ limitations under the License.
 =cut
 
 package Bio::EnsEMBL::IO::NamedColours;
+
 use strict;
+use warnings;
 
 ## Simple package to return the Unix named colours
 

modules/Bio/EnsEMBL/Utils/ColourMap.pm

@@ -18,7 +18,9 @@ limitations under the License.
 =cut
 
 package Bio::EnsEMBL::Utils::ColourMap;
+
 use strict;
+use warnings;
 
 use Bio::EnsEMBL::Utils::NamedColours;
 

modules/Bio/EnsEMBL/Utils/NamedColours.pm

@@ -18,7 +18,9 @@ limitations under the License.
 =cut
 
 package Bio::EnsEMBL::Utils::NamedColours;
+
 use strict;
+use warnings;
 
 ## Simple package to return the Unix named colours
 ## plus other ones... it is a really just list of colours

modules/Bio/EnsEMBL/Utils/RDF/Mapper.pm

@@ -37,6 +37,7 @@ Bio::EnsEMBL::Utils::RDF::Mapper
 package Bio::EnsEMBL::Utils::RDF::Mapper;
 
 use strict;
+use warnings;
 use JSON qw/decode_json/;
 use IO::File;
 

modules/EnsEMBL/Web/File/Utils.pm

@@ -22,6 +22,7 @@ package EnsEMBL::Web::File::Utils;
 ### Library for location-independent file functions such as compression support
 
 use strict;
+use warnings;
 
 use Compress::Zlib qw//;
 use Compress::Bzip2;

modules/EnsEMBL/Web/File/Utils/IO.pm

@@ -55,6 +55,7 @@ package EnsEMBL::Web::File::Utils::IO;
 ### }
 
 use strict;
+use warnings;
 
 use Bio::EnsEMBL::Utils::IO qw(:all);
 use Bio::EnsEMBL::Utils::Exception qw(throw);

modules/EnsEMBL/Web/File/Utils/TrackHub.pm

@@ -23,6 +23,7 @@ package EnsEMBL::Web::File::Utils::TrackHub;
 ### which also fetches each file in the trackhub configuration
 
 use strict;
+use warnings;
 
 use Digest::MD5 qw(md5_hex);
 

modules/EnsEMBL/Web/File/Utils/URL.pm

@@ -33,6 +33,7 @@ package EnsEMBL::Web::File::Utils::URL;
 ### can access site-wide parameters such as proxies
 
 use strict;
+use warnings;
 
 use HTTP::Tiny;
 use LWP::UserAgent;