Removing core from all files which could use an alternative.
It seems we have others within the team that would like to use ensembl-io but will not because of the core dependency. This commit attempts to 1. Remove any use of Utils::Exception and replace it with Carp 2. Remove any use of Utils::IO work_with_file and replace it with an open 3. Remove any un-used import (there were a lot) Also this commit pulls up that simple_list.t is no longer a valid test because its dependencies are broken.
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- modules/Bio/EnsEMBL/IO/ColumnBasedParser.pm 2 additions, 2 deletionsmodules/Bio/EnsEMBL/IO/ColumnBasedParser.pm
- modules/Bio/EnsEMBL/IO/HubParser.pm 1 addition, 0 deletionsmodules/Bio/EnsEMBL/IO/HubParser.pm
- modules/Bio/EnsEMBL/IO/Parser.pm 8 additions, 9 deletionsmodules/Bio/EnsEMBL/IO/Parser.pm
- modules/Bio/EnsEMBL/IO/Parser/BLASTFormatter.pm 9 additions, 10 deletionsmodules/Bio/EnsEMBL/IO/Parser/BLASTFormatter.pm
- modules/Bio/EnsEMBL/IO/Parser/BaseVCF4.pm 5 additions, 5 deletionsmodules/Bio/EnsEMBL/IO/Parser/BaseVCF4.pm
- modules/Bio/EnsEMBL/IO/Parser/BigBed.pm 1 addition, 0 deletionsmodules/Bio/EnsEMBL/IO/Parser/BigBed.pm
- modules/Bio/EnsEMBL/IO/Parser/BigWig.pm 1 addition, 0 deletionsmodules/Bio/EnsEMBL/IO/Parser/BigWig.pm
- modules/Bio/EnsEMBL/IO/Parser/Pairwise.pm 0 additions, 1 deletionmodules/Bio/EnsEMBL/IO/Parser/Pairwise.pm
- modules/Bio/EnsEMBL/IO/Parser/PairwiseSimple.pm 0 additions, 1 deletionmodules/Bio/EnsEMBL/IO/Parser/PairwiseSimple.pm
- modules/Bio/EnsEMBL/IO/Parser/PairwiseTabix.pm 0 additions, 1 deletionmodules/Bio/EnsEMBL/IO/Parser/PairwiseTabix.pm
- modules/Bio/EnsEMBL/IO/Parser/VCF4.pm 0 additions, 1 deletionmodules/Bio/EnsEMBL/IO/Parser/VCF4.pm
- modules/Bio/EnsEMBL/IO/Parser/VCF4Tabix.pm 0 additions, 1 deletionmodules/Bio/EnsEMBL/IO/Parser/VCF4Tabix.pm
- modules/Bio/EnsEMBL/IO/TabixParser.pm 3 additions, 4 deletionsmodules/Bio/EnsEMBL/IO/TabixParser.pm
- modules/Bio/EnsEMBL/IO/TextParser.pm 4 additions, 5 deletionsmodules/Bio/EnsEMBL/IO/TextParser.pm
- modules/Bio/EnsEMBL/IO/TokenBasedParser.pm 2 additions, 3 deletionsmodules/Bio/EnsEMBL/IO/TokenBasedParser.pm
- modules/Bio/EnsEMBL/IO/TrackBasedParser.pm 1 addition, 1 deletionmodules/Bio/EnsEMBL/IO/TrackBasedParser.pm
- modules/Bio/EnsEMBL/IO/Translator.pm 0 additions, 2 deletionsmodules/Bio/EnsEMBL/IO/Translator.pm
- modules/Bio/EnsEMBL/IO/Translator/Feature.pm 1 addition, 1 deletionmodules/Bio/EnsEMBL/IO/Translator/Feature.pm
- modules/Bio/EnsEMBL/IO/Translator/Gene.pm 1 addition, 1 deletionmodules/Bio/EnsEMBL/IO/Translator/Gene.pm
- modules/Bio/EnsEMBL/IO/Translator/Transcript.pm 1 addition, 1 deletionmodules/Bio/EnsEMBL/IO/Translator/Transcript.pm
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