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2024 update
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jamie-m-a committed Jan 26, 2024
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2 changes: 1 addition & 1 deletion INSTALL.pl
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=head1 LICENSE
Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Copyright [2016-2023] EMBL-European Bioinformatics Institute
Copyright [2016-2024] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion LICENSE
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identification within third-party archives.

Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Copyright [2016-2023] EMBL-European Bioinformatics Institute
Copyright [2016-2024] EMBL-European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion convert_cache.pl
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#!/usr/bin/env perl
# Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
# Copyright [2016-2023] EMBL-European Bioinformatics Institute
# Copyright [2016-2024] EMBL-European Bioinformatics Institute
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion filter_vep
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=head1 LICENSE
Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Copyright [2016-2023] EMBL-European Bioinformatics Institute
Copyright [2016-2024] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion haplo
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#!/usr/bin/env perl
# Copyright [2016-2023] EMBL-European Bioinformatics Institute
# Copyright [2016-2024] EMBL-European Bioinformatics Institute
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion modules/Bio/EnsEMBL/VEP/AnnotationSource.pm
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=head1 LICENSE
Copyright [2016-2023] EMBL-European Bioinformatics Institute
Copyright [2016-2024] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion modules/Bio/EnsEMBL/VEP/AnnotationSource/Cache.pm
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=head1 LICENSE
Copyright [2016-2023] EMBL-European Bioinformatics Institute
Copyright [2016-2024] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion modules/Bio/EnsEMBL/VEP/AnnotationSource/Cache/BaseCacheVariation.pm
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=head1 LICENSE
Copyright [2016-2023] EMBL-European Bioinformatics Institute
Copyright [2016-2024] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion modules/Bio/EnsEMBL/VEP/AnnotationSource/Cache/BaseSerialized.pm
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=head1 LICENSE
Copyright [2016-2023] EMBL-European Bioinformatics Institute
Copyright [2016-2024] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion modules/Bio/EnsEMBL/VEP/AnnotationSource/Cache/RegFeat.pm
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=head1 LICENSE
Copyright [2016-2023] EMBL-European Bioinformatics Institute
Copyright [2016-2024] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion modules/Bio/EnsEMBL/VEP/AnnotationSource/Cache/Transcript.pm
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=head1 LICENSE
Copyright [2016-2023] EMBL-European Bioinformatics Institute
Copyright [2016-2024] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion modules/Bio/EnsEMBL/VEP/AnnotationSource/Cache/Variation.pm
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=head1 LICENSE
Copyright [2016-2023] EMBL-European Bioinformatics Institute
Copyright [2016-2024] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion modules/Bio/EnsEMBL/VEP/AnnotationSource/Cache/VariationTabix.pm
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=head1 LICENSE
Copyright [2016-2023] EMBL-European Bioinformatics Institute
Copyright [2016-2024] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion modules/Bio/EnsEMBL/VEP/AnnotationSource/Database.pm
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=head1 LICENSE
Copyright [2016-2023] EMBL-European Bioinformatics Institute
Copyright [2016-2024] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion modules/Bio/EnsEMBL/VEP/AnnotationSource/Database/RegFeat.pm
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=head1 LICENSE
Copyright [2016-2023] EMBL-European Bioinformatics Institute
Copyright [2016-2024] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion modules/Bio/EnsEMBL/VEP/AnnotationSource/Database/StructuralVariation.pm
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=head1 LICENSE
Copyright [2016-2023] EMBL-European Bioinformatics Institute
Copyright [2016-2024] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion modules/Bio/EnsEMBL/VEP/AnnotationSource/Database/Transcript.pm
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=head1 LICENSE
Copyright [2016-2023] EMBL-European Bioinformatics Institute
Copyright [2016-2024] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion modules/Bio/EnsEMBL/VEP/AnnotationSource/Database/Variation.pm
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=head1 LICENSE
Copyright [2016-2023] EMBL-European Bioinformatics Institute
Copyright [2016-2024] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion modules/Bio/EnsEMBL/VEP/AnnotationSource/File.pm
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=head1 LICENSE
Copyright [2016-2023] EMBL-European Bioinformatics Institute
Copyright [2016-2024] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion modules/Bio/EnsEMBL/VEP/AnnotationSource/File/BED.pm
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=head1 LICENSE
Copyright [2016-2023] EMBL-European Bioinformatics Institute
Copyright [2016-2024] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion modules/Bio/EnsEMBL/VEP/AnnotationSource/File/BaseGXF.pm
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=head1 LICENSE
Copyright [2016-2023] EMBL-European Bioinformatics Institute
Copyright [2016-2024] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion modules/Bio/EnsEMBL/VEP/AnnotationSource/File/BigWig.pm
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=head1 LICENSE
Copyright [2016-2023] EMBL-European Bioinformatics Institute
Copyright [2016-2024] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion modules/Bio/EnsEMBL/VEP/AnnotationSource/File/GFF.pm
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=head1 LICENSE
Copyright [2016-2023] EMBL-European Bioinformatics Institute
Copyright [2016-2024] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion modules/Bio/EnsEMBL/VEP/AnnotationSource/File/GTF.pm
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=head1 LICENSE
Copyright [2016-2023] EMBL-European Bioinformatics Institute
Copyright [2016-2024] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion modules/Bio/EnsEMBL/VEP/AnnotationSource/File/VCF.pm
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=head1 LICENSE
Copyright [2016-2023] EMBL-European Bioinformatics Institute
Copyright [2016-2024] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm
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=head1 LICENSE
Copyright [2016-2023] EMBL-European Bioinformatics Institute
Copyright [2016-2024] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion modules/Bio/EnsEMBL/VEP/AnnotationType/RegFeat.pm
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=head1 LICENSE
Copyright [2016-2023] EMBL-European Bioinformatics Institute
Copyright [2016-2024] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion modules/Bio/EnsEMBL/VEP/AnnotationType/Transcript.pm
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=head1 LICENSE
Copyright [2016-2023] EMBL-European Bioinformatics Institute
Copyright [2016-2024] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion modules/Bio/EnsEMBL/VEP/AnnotationType/Variation.pm
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=head1 LICENSE
Copyright [2016-2023] EMBL-European Bioinformatics Institute
Copyright [2016-2024] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion modules/Bio/EnsEMBL/VEP/BaseRunner.pm
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=head1 LICENSE
Copyright [2016-2023] EMBL-European Bioinformatics Institute
Copyright [2016-2024] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion modules/Bio/EnsEMBL/VEP/BaseVEP.pm
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=head1 LICENSE
Copyright [2016-2023] EMBL-European Bioinformatics Institute
Copyright [2016-2024] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion modules/Bio/EnsEMBL/VEP/CacheDir.pm
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=head1 LICENSE
Copyright [2016-2023] EMBL-European Bioinformatics Institute
Copyright [2016-2024] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion modules/Bio/EnsEMBL/VEP/Config.pm
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=head1 LICENSE
Copyright [2016-2023] EMBL-European Bioinformatics Institute
Copyright [2016-2024] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion modules/Bio/EnsEMBL/VEP/Constants.pm
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=head1 LICENSE
Copyright [2016-2023] EMBL-European Bioinformatics Institute
Copyright [2016-2024] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion modules/Bio/EnsEMBL/VEP/FilterSet.pm
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=head1 LICENSE
Copyright [2016-2023] EMBL-European Bioinformatics Institute
Copyright [2016-2024] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion modules/Bio/EnsEMBL/VEP/Haplo/AnnotationSource/Cache/Transcript.pm
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=head1 LICENSE
Copyright [2016-2023] EMBL-European Bioinformatics Institute
Copyright [2016-2024] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion modules/Bio/EnsEMBL/VEP/Haplo/AnnotationSource/Database/Transcript.pm
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=head1 LICENSE
Copyright [2016-2023] EMBL-European Bioinformatics Institute
Copyright [2016-2024] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion modules/Bio/EnsEMBL/VEP/Haplo/AnnotationSource/File/GFF.pm
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=head1 LICENSE
Copyright [2016-2023] EMBL-European Bioinformatics Institute
Copyright [2016-2024] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion modules/Bio/EnsEMBL/VEP/Haplo/AnnotationSource/File/GTF.pm
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=head1 LICENSE
Copyright [2016-2023] EMBL-European Bioinformatics Institute
Copyright [2016-2024] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion modules/Bio/EnsEMBL/VEP/Haplo/AnnotationType/Transcript.pm
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=head1 LICENSE
Copyright [2016-2023] EMBL-European Bioinformatics Institute
Copyright [2016-2024] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion modules/Bio/EnsEMBL/VEP/Haplo/InputBuffer.pm
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=head1 LICENSE
Copyright [2016-2023] EMBL-European Bioinformatics Institute
Copyright [2016-2024] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion modules/Bio/EnsEMBL/VEP/Haplo/Parser/VCF.pm
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=head1 LICENSE
Copyright [2016-2023] EMBL-European Bioinformatics Institute
Copyright [2016-2024] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion modules/Bio/EnsEMBL/VEP/Haplo/Runner.pm
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=head1 LICENSE
Copyright [2016-2023] EMBL-European Bioinformatics Institute
Copyright [2016-2024] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion modules/Bio/EnsEMBL/VEP/InputBuffer.pm
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=head1 LICENSE
Copyright [2016-2023] EMBL-European Bioinformatics Institute
Copyright [2016-2024] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion modules/Bio/EnsEMBL/VEP/OutputFactory.pm
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=head1 LICENSE
Copyright [2016-2023] EMBL-European Bioinformatics Institute
Copyright [2016-2024] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion modules/Bio/EnsEMBL/VEP/OutputFactory/BaseTab.pm
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=head1 LICENSE
Copyright [2016-2023] EMBL-European Bioinformatics Institute
Copyright [2016-2024] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion modules/Bio/EnsEMBL/VEP/OutputFactory/JSON.pm
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=head1 LICENSE
Copyright [2016-2023] EMBL-European Bioinformatics Institute
Copyright [2016-2024] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion modules/Bio/EnsEMBL/VEP/OutputFactory/Tab.pm
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=head1 LICENSE
Copyright [2016-2023] EMBL-European Bioinformatics Institute
Copyright [2016-2024] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
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2 changes: 1 addition & 1 deletion modules/Bio/EnsEMBL/VEP/OutputFactory/VCF.pm
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=head1 LICENSE
Copyright [2016-2023] EMBL-European Bioinformatics Institute
Copyright [2016-2024] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
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