Files

• CONTRIBUTING.md
• Changes
• LICENSE
• MANIFEST
• META.json
• META.yml
• Makefile.PL
• README
• lib/Bio/EnsEMBL.pm
• lib/Bio/EnsEMBL/AltAlleleGroup.pm
• lib/Bio/EnsEMBL/Analysis.pm
• lib/Bio/EnsEMBL/Analysis/PairAlign.pm
• lib/Bio/EnsEMBL/Analysis/Programs.pm
• lib/Bio/EnsEMBL/ApiVersion.pm
• lib/Bio/EnsEMBL/ArchiveStableId.pm
• lib/Bio/EnsEMBL/AssemblyExceptionFeature.pm
• lib/Bio/EnsEMBL/AssemblyMapper.pm
• lib/Bio/EnsEMBL/Attribute.pm
• lib/Bio/EnsEMBL/BaseAlignFeature.pm
• lib/Bio/EnsEMBL/Biotype.pm
• lib/Bio/EnsEMBL/CDS.pm
• lib/Bio/EnsEMBL/ChainedAssemblyMapper.pm
• lib/Bio/EnsEMBL/CircularSlice.pm
• lib/Bio/EnsEMBL/CoordSystem.pm
• lib/Bio/EnsEMBL/DB/ExternalFeatureFactoryI.pm
• lib/Bio/EnsEMBL/DBEntry.pm
• lib/Bio/EnsEMBL/DBLoader.pm
• lib/Bio/EnsEMBL/DBSQL/AltAlleleGroupAdaptor.pm
• lib/Bio/EnsEMBL/DBSQL/AnalysisAdaptor.pm
• lib/Bio/EnsEMBL/DBSQL/ArchiveStableIdAdaptor.pm
• lib/Bio/EnsEMBL/DBSQL/AssemblyExceptionFeatureAdaptor.pm
• lib/Bio/EnsEMBL/DBSQL/AssemblyMapperAdaptor.pm
• lib/Bio/EnsEMBL/DBSQL/AssemblySliceAdaptor.pm
• lib/Bio/EnsEMBL/DBSQL/AttributeAdaptor.pm
• lib/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm
• lib/Bio/EnsEMBL/DBSQL/BaseAlignFeatureAdaptor.pm
• lib/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm
• lib/Bio/EnsEMBL/DBSQL/BaseMetaContainer.pm
• lib/Bio/EnsEMBL/DBSQL/BaseSequenceAdaptor.pm
• lib/Bio/EnsEMBL/DBSQL/BiotypeAdaptor.pm
• lib/Bio/EnsEMBL/DBSQL/CoordSystemAdaptor.pm
• lib/Bio/EnsEMBL/DBSQL/DBAdaptor.pm
• lib/Bio/EnsEMBL/DBSQL/DBConnection.pm
• lib/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
• lib/Bio/EnsEMBL/DBSQL/DataFileAdaptor.pm
• lib/Bio/EnsEMBL/DBSQL/DensityFeatureAdaptor.pm
• lib/Bio/EnsEMBL/DBSQL/DensityTypeAdaptor.pm
• lib/Bio/EnsEMBL/DBSQL/DnaAlignFeatureAdaptor.pm
• lib/Bio/EnsEMBL/DBSQL/Driver.pm
• lib/Bio/EnsEMBL/DBSQL/Driver/Oracle.pm
• lib/Bio/EnsEMBL/DBSQL/Driver/Pg.pm
• lib/Bio/EnsEMBL/DBSQL/Driver/SQLite.pm
• lib/Bio/EnsEMBL/DBSQL/Driver/Sybase.pm
• lib/Bio/EnsEMBL/DBSQL/Driver/TestDummy.pm
• lib/Bio/EnsEMBL/DBSQL/Driver/mysql.pm
• lib/Bio/EnsEMBL/DBSQL/Driver/odbc.pm
• lib/Bio/EnsEMBL/DBSQL/ExonAdaptor.pm
• lib/Bio/EnsEMBL/DBSQL/FastaSequenceAdaptor.pm
• lib/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
• lib/Bio/EnsEMBL/DBSQL/GenomeContainer.pm
• lib/Bio/EnsEMBL/DBSQL/IntronSupportingEvidenceAdaptor.pm
• lib/Bio/EnsEMBL/DBSQL/KaryotypeBandAdaptor.pm
• lib/Bio/EnsEMBL/DBSQL/MergedAdaptor.pm
• lib/Bio/EnsEMBL/DBSQL/MetaContainer.pm
• lib/Bio/EnsEMBL/DBSQL/MetaCoordContainer.pm
• lib/Bio/EnsEMBL/DBSQL/MiscFeatureAdaptor.pm
• lib/Bio/EnsEMBL/DBSQL/MiscSetAdaptor.pm
• lib/Bio/EnsEMBL/DBSQL/OntologyDBAdaptor.pm
• lib/Bio/EnsEMBL/DBSQL/OntologyTermAdaptor.pm
• lib/Bio/EnsEMBL/DBSQL/OperonAdaptor.pm
• lib/Bio/EnsEMBL/DBSQL/OperonTranscriptAdaptor.pm
• lib/Bio/EnsEMBL/DBSQL/PredictionExonAdaptor.pm
• lib/Bio/EnsEMBL/DBSQL/PredictionTranscriptAdaptor.pm
• lib/Bio/EnsEMBL/DBSQL/ProteinAlignFeatureAdaptor.pm
• lib/Bio/EnsEMBL/DBSQL/ProteinFeatureAdaptor.pm
• lib/Bio/EnsEMBL/DBSQL/ProxyDBConnection.pm
• lib/Bio/EnsEMBL/DBSQL/RNAProductAdaptor.pm
• lib/Bio/EnsEMBL/DBSQL/RepeatConsensusAdaptor.pm
• lib/Bio/EnsEMBL/DBSQL/RepeatFeatureAdaptor.pm
• lib/Bio/EnsEMBL/DBSQL/SeqRegionSynonymAdaptor.pm
• lib/Bio/EnsEMBL/DBSQL/SequenceAdaptor.pm
• lib/Bio/EnsEMBL/DBSQL/SimpleFeatureAdaptor.pm
• lib/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
• lib/Bio/EnsEMBL/DBSQL/StatementHandle.pm
• lib/Bio/EnsEMBL/DBSQL/Support/BaseCache.pm
• lib/Bio/EnsEMBL/DBSQL/Support/FullIdCache.pm
• lib/Bio/EnsEMBL/DBSQL/Support/LruIdCache.pm
• lib/Bio/EnsEMBL/DBSQL/SupportingFeatureAdaptor.pm
• lib/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
• lib/Bio/EnsEMBL/DBSQL/TranscriptSupportingFeatureAdaptor.pm
• lib/Bio/EnsEMBL/DBSQL/TranslationAdaptor.pm
• lib/Bio/EnsEMBL/DBSQL/UnmappedObjectAdaptor.pm
• lib/Bio/EnsEMBL/DataFile.pm
• lib/Bio/EnsEMBL/DensityFeature.pm
• lib/Bio/EnsEMBL/DensityFeatureSet.pm
• lib/Bio/EnsEMBL/DensityPlot/BinValue.pm
• lib/Bio/EnsEMBL/DensityPlot/BinValueSet.pm
• lib/Bio/EnsEMBL/DensityType.pm
• lib/Bio/EnsEMBL/DnaDnaAlignFeature.pm
• lib/Bio/EnsEMBL/DnaPepAlignFeature.pm
• lib/Bio/EnsEMBL/Exon.pm
• lib/Bio/EnsEMBL/ExonTranscript.pm
• lib/Bio/EnsEMBL/External/ExternalFeatureAdaptor.pm
• lib/Bio/EnsEMBL/Feature.pm
• lib/Bio/EnsEMBL/FeaturePair.pm
• lib/Bio/EnsEMBL/Gene.pm
• lib/Bio/EnsEMBL/Genome.pm
• lib/Bio/EnsEMBL/IdMapping/Archiver.pm
• lib/Bio/EnsEMBL/IdMapping/BaseObject.pm
• lib/Bio/EnsEMBL/IdMapping/Cache.pm
• lib/Bio/EnsEMBL/IdMapping/Entry.pm
• lib/Bio/EnsEMBL/IdMapping/ExonScoreBuilder.pm
• lib/Bio/EnsEMBL/IdMapping/GeneScoreBuilder.pm
• lib/Bio/EnsEMBL/IdMapping/InternalIdMapper.pm
• lib/Bio/EnsEMBL/IdMapping/InternalIdMapper/BaseMapper.pm
• lib/Bio/EnsEMBL/IdMapping/InternalIdMapper/EnsemblExonGeneric.pm
• lib/Bio/EnsEMBL/IdMapping/InternalIdMapper/EnsemblGeneGeneric.pm
• lib/Bio/EnsEMBL/IdMapping/InternalIdMapper/EnsemblTranscriptGeneric.pm
• lib/Bio/EnsEMBL/IdMapping/MappingList.pm
• lib/Bio/EnsEMBL/IdMapping/ResultAnalyser.pm
• lib/Bio/EnsEMBL/IdMapping/ScoreBuilder.pm
• lib/Bio/EnsEMBL/IdMapping/ScoredMappingMatrix.pm
• lib/Bio/EnsEMBL/IdMapping/Serialisable.pm
• lib/Bio/EnsEMBL/IdMapping/StableIdGenerator/AedesAegypti.pm
• lib/Bio/EnsEMBL/IdMapping/StableIdGenerator/AnophelesGambiae.pm
• lib/Bio/EnsEMBL/IdMapping/StableIdGenerator/EnsemblGeneric.pm
• lib/Bio/EnsEMBL/IdMapping/StableIdGenerator/PristionchusPacificus.pm
• lib/Bio/EnsEMBL/IdMapping/StableIdMapper.pm
• lib/Bio/EnsEMBL/IdMapping/SyntenyFramework.pm
• lib/Bio/EnsEMBL/IdMapping/SyntenyRegion.pm
• lib/Bio/EnsEMBL/IdMapping/TinyExon.pm
• lib/Bio/EnsEMBL/IdMapping/TinyFeature.pm
• lib/Bio/EnsEMBL/IdMapping/TinyGene.pm
• lib/Bio/EnsEMBL/IdMapping/TinyTranscript.pm
• lib/Bio/EnsEMBL/IdMapping/TinyTranslation.pm
• lib/Bio/EnsEMBL/IdMapping/TranscriptScoreBuilder.pm
• lib/Bio/EnsEMBL/IdentityXref.pm
• lib/Bio/EnsEMBL/Intron.pm
• lib/Bio/EnsEMBL/IntronSupportingEvidence.pm
• lib/Bio/EnsEMBL/KaryotypeBand.pm
• lib/Bio/EnsEMBL/LRGSlice.pm
• lib/Bio/EnsEMBL/MANE.pm
• lib/Bio/EnsEMBL/Map/DBSQL/DitagAdaptor.pm
• lib/Bio/EnsEMBL/Map/DBSQL/DitagFeatureAdaptor.pm
• lib/Bio/EnsEMBL/Map/DBSQL/MarkerAdaptor.pm
• lib/Bio/EnsEMBL/Map/DBSQL/MarkerFeatureAdaptor.pm
• lib/Bio/EnsEMBL/Map/Ditag.pm
• lib/Bio/EnsEMBL/Map/DitagFeature.pm
• lib/Bio/EnsEMBL/Map/MapLocation.pm
• lib/Bio/EnsEMBL/Map/Marker.pm
• lib/Bio/EnsEMBL/Map/MarkerFeature.pm
• lib/Bio/EnsEMBL/Map/MarkerSynonym.pm
• lib/Bio/EnsEMBL/MappedSlice.pm
• lib/Bio/EnsEMBL/MappedSliceContainer.pm
• lib/Bio/EnsEMBL/Mapper.pm
• lib/Bio/EnsEMBL/Mapper/Coordinate.pm
• lib/Bio/EnsEMBL/Mapper/Gap.pm
• lib/Bio/EnsEMBL/Mapper/IndelCoordinate.pm
• lib/Bio/EnsEMBL/Mapper/IndelPair.pm
• lib/Bio/EnsEMBL/Mapper/Pair.pm
• lib/Bio/EnsEMBL/Mapper/RangeRegistry.pm
• lib/Bio/EnsEMBL/Mapper/Unit.pm
• lib/Bio/EnsEMBL/MicroRNA.pm
• lib/Bio/EnsEMBL/MiscFeature.pm
• lib/Bio/EnsEMBL/MiscSet.pm
• lib/Bio/EnsEMBL/OntologyTerm.pm
• lib/Bio/EnsEMBL/OntologyXref.pm
• lib/Bio/EnsEMBL/Operon.pm
• lib/Bio/EnsEMBL/OperonTranscript.pm
• lib/Bio/EnsEMBL/PaddedSlice.pm
• lib/Bio/EnsEMBL/PepDnaAlignFeature.pm
• lib/Bio/EnsEMBL/PredictionExon.pm
• lib/Bio/EnsEMBL/PredictionTranscript.pm
• lib/Bio/EnsEMBL/ProjectionSegment.pm
• lib/Bio/EnsEMBL/ProteinFeature.pm
• lib/Bio/EnsEMBL/RNAProduct.pm
• lib/Bio/EnsEMBL/Registry.pm
• lib/Bio/EnsEMBL/RepeatConsensus.pm
• lib/Bio/EnsEMBL/RepeatFeature.pm
• lib/Bio/EnsEMBL/RepeatMaskedSlice.pm
• lib/Bio/EnsEMBL/SeqEdit.pm
• lib/Bio/EnsEMBL/SeqFeature.pm
• lib/Bio/EnsEMBL/SeqRegionSynonym.pm
• lib/Bio/EnsEMBL/SimpleFeature.pm
• lib/Bio/EnsEMBL/Slice.pm
• lib/Bio/EnsEMBL/StableIdEvent.pm
• lib/Bio/EnsEMBL/StableIdHistoryTree.pm
• lib/Bio/EnsEMBL/StopCodonReadthroughEdit.pm
• lib/Bio/EnsEMBL/Storable.pm
• lib/Bio/EnsEMBL/SubSlicedFeature.pm
• lib/Bio/EnsEMBL/TopLevelAssemblyMapper.pm
• lib/Bio/EnsEMBL/Transcript.pm
• lib/Bio/EnsEMBL/TranscriptFactory.pm
• lib/Bio/EnsEMBL/TranscriptMapper.pm
• lib/Bio/EnsEMBL/Translation.pm
• lib/Bio/EnsEMBL/UTR.pm
• lib/Bio/EnsEMBL/UnmappedObject.pm
• lib/Bio/EnsEMBL/Upstream.pm
• lib/Bio/EnsEMBL/Utils/Argument.pm
• lib/Bio/EnsEMBL/Utils/AssemblyProjector.pm
• lib/Bio/EnsEMBL/Utils/BitString.pm
• lib/Bio/EnsEMBL/Utils/Cache.pm
• lib/Bio/EnsEMBL/Utils/CigarString.pm
• lib/Bio/EnsEMBL/Utils/CliHelper.pm
• lib/Bio/EnsEMBL/Utils/ConfParser.pm
• lib/Bio/EnsEMBL/Utils/ConfigRegistry.pm
• lib/Bio/EnsEMBL/Utils/ConversionSupport.pm
• lib/Bio/EnsEMBL/Utils/Converter.pm
• lib/Bio/EnsEMBL/Utils/Converter/bio_ens.pm
• lib/Bio/EnsEMBL/Utils/Converter/bio_ens_analysis.pm
• lib/Bio/EnsEMBL/Utils/Converter/bio_ens_exon.pm
• lib/Bio/EnsEMBL/Utils/Converter/bio_ens_featurePair.pm
• lib/Bio/EnsEMBL/Utils/Converter/bio_ens_gene.pm
• lib/Bio/EnsEMBL/Utils/Converter/bio_ens_hit.pm
• lib/Bio/EnsEMBL/Utils/Converter/bio_ens_hsp.pm
• lib/Bio/EnsEMBL/Utils/Converter/bio_ens_predictionExon.pm
• lib/Bio/EnsEMBL/Utils/Converter/bio_ens_predictionGene.pm
• lib/Bio/EnsEMBL/Utils/Converter/bio_ens_seqFeature.pm
• lib/Bio/EnsEMBL/Utils/Converter/bio_ens_transcript.pm
• lib/Bio/EnsEMBL/Utils/Converter/ens_bio.pm
• lib/Bio/EnsEMBL/Utils/Converter/ens_bio_featurePair.pm
• lib/Bio/EnsEMBL/Utils/Converter/ens_bio_seqFeature.pm
• lib/Bio/EnsEMBL/Utils/EasyArgv.pm
• lib/Bio/EnsEMBL/Utils/Eprof.pm
• lib/Bio/EnsEMBL/Utils/EprofStack.pm
• lib/Bio/EnsEMBL/Utils/Exception.pm
• lib/Bio/EnsEMBL/Utils/IO.pm
• lib/Bio/EnsEMBL/Utils/Interval.pm
• lib/Bio/EnsEMBL/Utils/Iterator.pm
• lib/Bio/EnsEMBL/Utils/Logger.pm
• lib/Bio/EnsEMBL/Utils/Net.pm
• lib/Bio/EnsEMBL/Utils/PolyA.pm
• lib/Bio/EnsEMBL/Utils/Proxy.pm
• lib/Bio/EnsEMBL/Utils/RNAProductTypeMapper.pm
• lib/Bio/EnsEMBL/Utils/Scalar.pm
• lib/Bio/EnsEMBL/Utils/SchemaConversion.pm
• lib/Bio/EnsEMBL/Utils/ScriptUtils.pm
• lib/Bio/EnsEMBL/Utils/SeqDumper.pm
• lib/Bio/EnsEMBL/Utils/SeqRegionCache.pm
• lib/Bio/EnsEMBL/Utils/Sequence.pm
• lib/Bio/EnsEMBL/Utils/Slice.pm
• lib/Bio/EnsEMBL/Utils/SqlHelper.pm
• lib/Bio/EnsEMBL/Utils/TranscriptSelector.pm
• lib/Bio/EnsEMBL/Utils/Tree/Interval/Immutable.pm
• lib/Bio/EnsEMBL/Utils/Tree/Interval/Immutable/Node.pm
• lib/Bio/EnsEMBL/Utils/Tree/Interval/Mutable.pm
• lib/Bio/EnsEMBL/Utils/Tree/Interval/Mutable/Node.pm
• lib/Bio/EnsEMBL/Utils/Tree/Interval/Mutable/PP.pm
• lib/Bio/EnsEMBL/Utils/URI.pm
• lib/Bio/EnsEMBL/Utils/VegaCuration/Gene.pm
• lib/Bio/EnsEMBL/Utils/VegaCuration/Transcript.pm
• lib/Bio/EnsEMBL/Utils/VegaCuration/Translation.pm
• lib/Bio/EnsEMBL/Utils/ensembl_init.example
• xt/release/changes_has_content.t