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  1. 04 Nov, 2009 11 commits
    • Ian Longden's avatar
      XrefMapper/XrefLoader.pm · 9c6ea761
      Ian Longden authored
      9c6ea761
    • Ian Longden's avatar
      new faster sql · 99ff8cb8
      Ian Longden authored
      99ff8cb8
    • Ian Longden's avatar
      New official naming subs · 5ef55fec
      Ian Longden authored
      5ef55fec
    • Ian Longden's avatar
      get hgnc descriptions etc · 235cfc9d
      Ian Longden authored
      235cfc9d
    • Ian Longden's avatar
      possible new order for priority of HGNC · c29e0f28
      Ian Longden authored
      c29e0f28
    • cvs2git's avatar
      This commit was manufactured by cvs2svn to create branch 'HGNC_new'. · e4d8dcbb
      cvs2git authored
      Sprout from master 2009-11-04 10:12:45 UTC Ian Longden <ianl@sanger.ac.uk> 'update staging databases etc'
      Delete:
          LICENSE
          docs/ensembl_changes_spec.txt
          docs/ensembl_das/Homo_sapiens.ini
          docs/ensembl_das/demo.ini
          docs/ensembl_das/demo.pm
          docs/ensembl_das/ensembl-das.pdf
          docs/ensembl_das/ensembl-das.sxw
          docs/schema_description/README
          docs/schema_description/process-saxon.bat
          docs/schema_description/process-saxon.sh
          docs/schema_description/schema_description.dtd
          docs/schema_description/schema_description.html
          docs/schema_description/tables.html
          docs/schema_description/tables.txt
          docs/schema_description/tables.xml
          docs/schema_description/xml2html.xsl
          docs/schema_description/xml2wiki.xsl
          docs/tutorial/ensembl_tutorial.pdf
          docs/tutorial/ensembl_tutorial.sxw
          docs/tutorial/ensembl_tutorial.txt
          misc-scripts/CopyDBoverServer.pl
          misc-scripts/CreateFile4CopyDBoverServer.pl
          misc-scripts/README.schema_patching
          misc-scripts/add_species_aliases.pl
          misc-scripts/alternative_splicing/README.txt
          misc-scripts/alternative_splicing/load_alt_slice_gff.pl
          misc-scripts/analysis_description/analysis.descriptions
          misc-scripts/analysis_description/apply_rules.pl
          misc-scripts/analysis_description/chech_web_data_column.pl
          misc-scripts/analysis_description/load_analysis_descriptions.pl
          misc-scripts/anopheles_scripts/check_bad_regions.pl
          misc-scripts/anopheles_scripts/check_stops.pl
          misc-scripts/anopheles_scripts/dump_genbank_45.pl
          misc-scripts/anopheles_scripts/dump_genebank.pl
          misc-scripts/anopheles_scripts/dump_genebank_38.pl
          misc-scripts/anopheles_scripts/format_bacs.pl
          misc-scripts/anopheles_scripts/format_blat.pl
          misc-scripts/anopheles_scripts/format_matepairs.pl
          misc-scripts/anopheles_scripts/get_est_supporting_evidences.pl
          misc-scripts/anopheles_scripts/get_freqs.pl
          misc-scripts/anopheles_scripts/get_good_matepairs.pl
          misc-scripts/anopheles_scripts/get_transposon_repeats.pl
          misc-scripts/anopheles_scripts/load_karyotype.pl
          misc-scripts/anopheles_scripts/location_check_for_dump.pl
          misc-scripts/anopheles_scripts/produce_snap_training_set.pl
          misc-scripts/anopheles_scripts/protein_annotation_from_embl.pl
          misc-scripts/anopheles_scripts/remove_proteins_from_db.pl
          misc-scripts/anopheles_scripts/split_fasta_in_subslices_anopheles.pl
          misc-scripts/assembly/AssemblyMapper/BlastzAligner.pm
          misc-scripts/assembly/EXAMPLE.use_mapping.pl
          misc-scripts/assembly/README
          misc-scripts/assembly/align_by_clone_identity.pl
          misc-scripts/assembly/align_nonident_regions.pl
          misc-scripts/assembly/align_nonident_regions_wrapper.pl
          misc-scripts/assembly/blastz_matrix.txt
          misc-scripts/assembly/check_mapping.pl
          misc-scripts/assembly/cleanup_tmp_tables.sql
          misc-scripts/assembly/compare_assemblies.pl
          misc-scripts/assembly/find_overlaps.pl
          misc-scripts/assembly/fix_overlaps.pl
          misc-scripts/assembly/load_alternative_assembly.pl
          misc-scripts/assembly/mapping_stats.pl
          misc-scripts/attribute_types/attrib_type.txt
          misc-scripts/attribute_types/upload_attributes.pl
          misc-scripts/canonical_transcripts/set_canonical_transcripts.pl
          misc-scripts/chain/axt2assembly.pl
          misc-scripts/chain/chain2assembly.pl
          misc-scripts/chimp/Deletion.pm
          misc-scripts/chimp/Gene.pm
          misc-scripts/chimp/Insertion.pm
          misc-scripts/chimp/InterimExon.pm
          misc-scripts/chimp/InterimTranscript.pm
          misc-scripts/chimp/Length.pm
          misc-scripts/chimp/README
          misc-scripts/chimp/StatLogger.pm
          misc-scripts/chimp/StatMsg.pm
          misc-scripts/chimp/Transcript.pm
          misc-scripts/chimp/Utils.pm
          misc-scripts/chimp/chimp_chr_ctg_assembly.pl
          misc-scripts/chimp/get_stats.pl
          misc-scripts/chimp/human2chimp.pl
          misc-scripts/chimp/lift_assembly.pl
          misc-scripts/chimp/run_hum2chimp.sh
          misc-scripts/constitutive_exon.pl
          misc-scripts/db-space.pl
          misc-scripts/db/cleanup_tmp_tables.pl
          misc-scripts/db/multidb_sql.pl
          misc-scripts/density_feature/DensityCalc.sh
          misc-scripts/density_feature/densities_multi_db.pl
          misc-scripts/density_feature/density_feature_fetch.pl
          misc-scripts/density_feature/gene_density_calc.pl
          misc-scripts/density_feature/glovar_snp_density.pl
          misc-scripts/density_feature/logicname_density_calc.pl
          misc-scripts/density_feature/percent_gc_calc.pl
          misc-scripts/density_feature/repeat_coverage_calc.pl
          misc-scripts/density_feature/seq_region_stats.pl
          misc-scripts/density_feature/variation_density.pl
          misc-scripts/ebi_search_dump/count_entries.sh
          misc-scripts/ebi_search_dump/dump_44.sh
          misc-scripts/ebi_search_dump/dump_ebi.pl
          misc-scripts/ebi_search_dump/ebi_search_dump.pl
          misc-scripts/external_db/README
          misc-scripts/external_db/convert_external_dbs.pl
          misc-scripts/external_db/external_dbs.txt
          misc-scripts/external_db/load_additional_human_affy_xrefs.pl
          misc-scripts/external_db/load_additional_human_gkb_xrefs.pl
          misc-scripts/external_db/update_external_dbs.pl
          misc-scripts/frameshift_transcript_attribs.pl
          misc-scripts/gene_gc.pl
          misc-scripts/generate_stable_ids.pl
          misc-scripts/golden_path/check_sum.pl
          misc-scripts/golden_path/fin_agp2ensembl
          misc-scripts/golden_path/get_contig.pl
          misc-scripts/golden_path/gp_contig_mismatch.pl
          misc-scripts/golden_path/gp_incons_test.pl
          misc-scripts/golden_path/gp_parse.pl
          misc-scripts/golden_path/makeunique.pl
          misc-scripts/golden_path/ncbi2ensembl
          misc-scripts/golden_path/nt_crossmatch.pl
          misc-scripts/golden_path/pfetch2ensembl
          misc-scripts/golden_path/rat_agp2ensembl
          misc-scripts/id_mapping/README
          misc-scripts/id_mapping/default.conf
          misc-scripts/id_mapping/dump_by_seq_region.pl
          misc-scripts/id_mapping/dump_cache.pl
          misc-scripts/id_mapping/fake_stable_id_mapping.pl
          misc-scripts/id_mapping/id_mapping.pl
          misc-scripts/id_mapping/myRun.ksh
          misc-scripts/id_mapping/run.pl
          misc-scripts/id_mapping/synteny_rescore.pl
          misc-scripts/id_mapping/utils/batch_id_history.pl
          misc-scripts/id_mapping/utils/compare_results.pl
          misc-scripts/id_mapping/utils/compare_scores.pl
          misc-scripts/id_mapping/utils/dump_scores.pl
          misc-scripts/id_mapping/utils/id_mapping_clean.sql
          misc-scripts/id_mapping/utils/manage_id_mapping_tables.pl
          misc-scripts/id_mapping/utils/myManager.ksh
          misc-scripts/meta_coord/update_meta_coord.pl
          misc-scripts/meta_levels.pl
          misc-scripts/misc_feature/misc_set.descriptions
          misc-scripts/misc_feature/update_misc_set_descripitons.pl
          misc-scripts/ontology/README
          misc-scripts/ontology/scripts/add_subset_maps.pl
          misc-scripts/ontology/scripts/compute_closure.pl
          misc-scripts/ontology/scripts/demo1.pl
          misc-scripts/ontology/scripts/demo2.pl
          misc-scripts/ontology/scripts/load_OBO_file.pl
          misc-scripts/ontology/sql/table.sql
          misc-scripts/overlapping_regions.pl
          misc-scripts/protein_match/process_pmach.pl
          misc-scripts/qtl/extract_rat_map_ids.pl
          misc-scripts/qtl/qtl_feature_calculation.pl
          misc-scripts/qtl/rat_qtl_import.pl
          misc-scripts/qtl/run_rat_import.pl
          misc-scripts/regulatory_regions/RegulatoryFeatureParser/BaseParser.pm
          misc-scripts/regulatory_regions/RegulatoryFeatureParser/cisred.pm
          misc-scripts/regulatory_regions/RegulatoryFeatureParser/enhancer.pm
          misc-scripts/regulatory_regions/RegulatoryFeatureParser/miranda.pm
          misc-scripts/regulatory_regions/gene_coverage.pl
          misc-scripts/regulatory_regions/load_regulatory.pl
          misc-scripts/regulatory_regions/parse_cisred.pl
          misc-scripts/repeats/repeat-libraries.pl
          misc-scripts/repeats/repeat-types.pl
          misc-scripts/repeats/repeats.txt
          misc-scripts/repeats/shrink_trfs.pl
          misc-scripts/repeats/vega_repeat_libraries.pl
          misc-scripts/schema_patch.pl
          misc-scripts/search_dbs.pl
          misc-scripts/surgery/SchemaConverter.pm
          misc-scripts/surgery/SeqStoreConverter/AnophelesGambiae.pm
          misc-scripts/surgery/SeqStoreConverter/ApisMellifera.pm
          misc-scripts/surgery/SeqStoreConverter/BasicConverter.pm
          misc-scripts/surgery/SeqStoreConverter/CaenorhabditisBriggsae.pm
          misc-scripts/surgery/SeqStoreConverter/CaenorhabditisElegans.pm
          misc-scripts/surgery/SeqStoreConverter/CanisFamiliaris.pm
          misc-scripts/surgery/SeqStoreConverter/DanioRerio.pm
          misc-scripts/surgery/SeqStoreConverter/DrosophilaMelanogaster.pm
          misc-scripts/surgery/SeqStoreConverter/FuguRubripes.pm
          misc-scripts/surgery/SeqStoreConverter/GallusGallus.pm
          misc-scripts/surgery/SeqStoreConverter/HomoSapiens.pm
          misc-scripts/surgery/SeqStoreConverter/MusMusculus.pm
          misc-scripts/surgery/SeqStoreConverter/PanTroglodytes.pm
          misc-scripts/surgery/SeqStoreConverter/RattusNorvegicus.pm
          misc-scripts/surgery/SeqStoreConverter/vega/CanisFamiliaris.pm
          misc-scripts/surgery/SeqStoreConverter/vega/DanioRerio.pm
          misc-scripts/surgery/SeqStoreConverter/vega/HomoSapiens.pm
          misc-scripts/surgery/SeqStoreConverter/vega/MusMusculus.pm
          misc-scripts/surgery/SeqStoreConverter/vega/VBasicConverter.pm
          misc-scripts/surgery/convert_seqstore.pl
          misc-scripts/surgery/converter.input
          misc-scripts/surgery/create_fixsql.pl
          misc-scripts/surgery/dump_seq_in_region
          misc-scripts/surgery/fuller_test_genome_9_chr20.pl
          misc-scripts/surgery/push_align_features.pl
          misc-scripts/surgery/set_nonredundant_attribs.pl
          misc-scripts/surgery/shortintrons2frameshifts.pl
          misc-scripts/surgery/table_column_munge
          misc-scripts/transfer_karyotype.pl
          misc-scripts/translation_attribs.pl
          misc-scripts/translation_attribs_wrapper.pl
          misc-scripts/unmapped_reason/unmapped_reason.txt
          misc-scripts/unmapped_reason/update_unmapped_reasons.pl
          misc-scripts/update_mapping_set.pl
          misc-scripts/utilities/dna_compress.pl
          misc-scripts/utilities/parse_embl.pl
          misc-scripts/utilities/show_method_status.pl
          misc-scripts/utilities/split_fasta.pl
          misc-scripts/web_stats.sh
          misc-scripts/xref_projection/README
          misc-scripts/xref_projection/README_projection.txt
          misc-scripts/xref_projection/project_display_xrefs.pl
          misc-scripts/xref_projection/projection_db.sql
          misc-scripts/xref_projection/release_48.ini
          misc-scripts/xref_projection/submit_projections.pl
          modules/Bio/EnsEMBL/AlignStrainSlice.pm
          modules/Bio/EnsEMBL/Analysis.pm
          modules/Bio/EnsEMBL/Analysis/PairAlign.pm
          modules/Bio/EnsEMBL/Analysis/Programs.pm
          modules/Bio/EnsEMBL/ArchiveStableId.pm
          modules/Bio/EnsEMBL/AssemblyExceptionFeature.pm
          modules/Bio/EnsEMBL/AssemblyMapper.pm
          modules/Bio/EnsEMBL/Attribute.pm
          modules/Bio/EnsEMBL/BaseAlignFeature.pm
          modules/Bio/EnsEMBL/ChainedAssemblyMapper.pm
          modules/Bio/EnsEMBL/Collection.pm
          modules/Bio/EnsEMBL/Collection/Exon.pm
          modules/Bio/EnsEMBL/Collection/Gene.pm
          modules/Bio/EnsEMBL/Collection/RepeatFeature.pm
          modules/Bio/EnsEMBL/Collection/Transcript.pm
          modules/Bio/EnsEMBL/CoordSystem.pm
          modules/Bio/EnsEMBL/DB/ExternalFeatureFactoryI.pm
          modules/Bio/EnsEMBL/DBEntry.pm
          modules/Bio/EnsEMBL/DBLoader.pm
          modules/Bio/EnsEMBL/DBSQL/AnalysisAdaptor.pm
          modules/Bio/EnsEMBL/DBSQL/ArchiveStableIdAdaptor.pm
          modules/Bio/EnsEMBL/DBSQL/AssemblyExceptionFeatureAdaptor.pm
          modules/Bio/EnsEMBL/DBSQL/AssemblyMapperAdaptor.pm
          modules/Bio/EnsEMBL/DBSQL/AssemblySliceAdaptor.pm
          modules/Bio/EnsEMBL/DBSQL/AttributeAdaptor.pm
          modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm
          modules/Bio/EnsEMBL/DBSQL/BaseAlignFeatureAdaptor.pm
          modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm
          modules/Bio/EnsEMBL/DBSQL/BaseMetaContainer.pm
          modules/Bio/EnsEMBL/DBSQL/CompressedSequenceAdaptor.pm
          modules/Bio/EnsEMBL/DBSQL/CoordSystemAdaptor.pm
          modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm
          modules/Bio/EnsEMBL/DBSQL/DBConnection.pm
          modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
          modules/Bio/EnsEMBL/DBSQL/DensityFeatureAdaptor.pm
          modules/Bio/EnsEMBL/DBSQL/DensityTypeAdaptor.pm
          modules/Bio/EnsEMBL/DBSQL/DnaAlignFeatureAdaptor.pm
          modules/Bio/EnsEMBL/DBSQL/ExonAdaptor.pm
          modules/Bio/EnsEMBL/DBSQL/GOTermAdaptor.pm
          modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
          modules/Bio/EnsEMBL/DBSQL/KaryotypeBandAdaptor.pm
          modules/Bio/EnsEMBL/DBSQL/MergedAdaptor.pm
          modules/Bio/EnsEMBL/DBSQL/MetaContainer.pm
          modules/Bio/EnsEMBL/DBSQL/MetaCoordContainer.pm
          modules/Bio/EnsEMBL/DBSQL/MiscFeatureAdaptor.pm
          modules/Bio/EnsEMBL/DBSQL/MiscSetAdaptor.pm
          modules/Bio/EnsEMBL/DBSQL/OntologyDBAdaptor.pm
          modules/Bio/EnsEMBL/DBSQL/OntologyTermAdaptor.pm
          modules/Bio/EnsEMBL/DBSQL/PredictionExonAdaptor.pm
          modules/Bio/EnsEMBL/DBSQL/PredictionTranscriptAdaptor.pm
          modules/Bio/EnsEMBL/DBSQL/ProteinAlignFeatureAdaptor.pm
          modules/Bio/EnsEMBL/DBSQL/ProteinFeatureAdaptor.pm
          modules/Bio/EnsEMBL/DBSQL/ProxySNPAdaptor.pm
          modules/Bio/EnsEMBL/DBSQL/RepeatConsensusAdaptor.pm
          modules/Bio/EnsEMBL/DBSQL/RepeatFeatureAdaptor.pm
          modules/Bio/EnsEMBL/DBSQL/SOTermAdaptor.pm
          modules/Bio/EnsEMBL/DBSQL/SequenceAdaptor.pm
          modules/Bio/EnsEMBL/DBSQL/SimpleFeatureAdaptor.pm
          modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
          modules/Bio/EnsEMBL/DBSQL/SplicingEventAdaptor.pm
          modules/Bio/EnsEMBL/DBSQL/SplicingEventFeatureAdaptor.pm
          modules/Bio/EnsEMBL/DBSQL/SplicingTranscriptPairAdaptor.pm
          modules/Bio/EnsEMBL/DBSQL/StatementHandle.pm
          modules/Bio/EnsEMBL/DBSQL/SupportingFeatureAdaptor.pm
          modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
          modules/Bio/EnsEMBL/DBSQL/TranscriptSupportingFeatureAdaptor.pm
          modules/Bio/EnsEMBL/DBSQL/TranslationAdaptor.pm
          modules/Bio/EnsEMBL/DBSQL/UnconventionalTranscriptAssociationAdaptor.pm
          modules/Bio/EnsEMBL/DBSQL/UnmappedObjectAdaptor.pm
          modules/Bio/EnsEMBL/DensityFeature.pm
          modules/Bio/EnsEMBL/DensityFeatureSet.pm
          modules/Bio/EnsEMBL/DensityPlot/BinValue.pm
          modules/Bio/EnsEMBL/DensityPlot/BinValueSet.pm
          modules/Bio/EnsEMBL/DensityType.pm
          modules/Bio/EnsEMBL/DnaDnaAlignFeature.pm
          modules/Bio/EnsEMBL/DnaPepAlignFeature.pm
          modules/Bio/EnsEMBL/Exon.pm
          modules/Bio/EnsEMBL/External/BlastAdaptor.pm
          modules/Bio/EnsEMBL/External/ExternalFeatureAdaptor.pm
          modules/Bio/EnsEMBL/Feature.pm
          modules/Bio/EnsEMBL/FeaturePair.pm
          modules/Bio/EnsEMBL/Gene.pm
          modules/Bio/EnsEMBL/GoXref.pm
          modules/Bio/EnsEMBL/IdMapping/Archiver.pm
          modules/Bio/EnsEMBL/IdMapping/BaseObject.pm
          modules/Bio/EnsEMBL/IdMapping/Cache.pm
          modules/Bio/EnsEMBL/IdMapping/Entry.pm
          modules/Bio/EnsEMBL/IdMapping/ExonScoreBuilder.pm
          modules/Bio/EnsEMBL/IdMapping/GeneScoreBuilder.pm
          modules/Bio/EnsEMBL/IdMapping/InternalIdMapper.pm
          modules/Bio/EnsEMBL/IdMapping/InternalIdMapper/BaseMapper.pm
          modules/Bio/EnsEMBL/IdMapping/InternalIdMapper/EnsemblExonGeneric.pm
          modules/Bio/EnsEMBL/IdMapping/InternalIdMapper/EnsemblGeneGeneric.pm
          modules/Bio/EnsEMBL/IdMapping/InternalIdMapper/EnsemblTranscriptGeneric.pm
          modules/Bio/EnsEMBL/IdMapping/MappingList.pm
          modules/Bio/EnsEMBL/IdMapping/ResultAnalyser.pm
          modules/Bio/EnsEMBL/IdMapping/ScoreBuilder.pm
          modules/Bio/EnsEMBL/IdMapping/ScoredMappingMatrix.pm
          modules/Bio/EnsEMBL/IdMapping/Serialisable.pm
          modules/Bio/EnsEMBL/IdMapping/StableIdGenerator/AedesAegypti.pm
          modules/Bio/EnsEMBL/IdMapping/StableIdGenerator/AnophelesGambiae.pm
          modules/Bio/EnsEMBL/IdMapping/StableIdGenerator/EnsemblGeneric.pm
          modules/Bio/EnsEMBL/IdMapping/StableIdMapper.pm
          modules/Bio/EnsEMBL/IdMapping/SyntenyFramework.pm
          modules/Bio/EnsEMBL/IdMapping/SyntenyRegion.pm
          modules/Bio/EnsEMBL/IdMapping/TinyExon.pm
          modules/Bio/EnsEMBL/IdMapping/TinyFeature.pm
          modules/Bio/EnsEMBL/IdMapping/TinyGene.pm
          modules/Bio/EnsEMBL/IdMapping/TinyTranscript.pm
          modules/Bio/EnsEMBL/IdMapping/TinyTranslation.pm
          modules/Bio/EnsEMBL/IdMapping/TranscriptScoreBuilder.pm
          modules/Bio/EnsEMBL/IdentityXref.pm
          modules/Bio/EnsEMBL/IndividualSlice.pm
          modules/Bio/EnsEMBL/IndividualSliceFactory.pm
          modules/Bio/EnsEMBL/Intron.pm
          modules/Bio/EnsEMBL/KaryotypeBand.pm
          modules/Bio/EnsEMBL/Lite/DBAdaptor.pm
          modules/Bio/EnsEMBL/Lite/SNPAdaptor.pm
          modules/Bio/EnsEMBL/Map/DBSQL/DitagAdaptor.pm
          modules/Bio/EnsEMBL/Map/DBSQL/DitagFeatureAdaptor.pm
          modules/Bio/EnsEMBL/Map/DBSQL/MarkerAdaptor.pm
          modules/Bio/EnsEMBL/Map/DBSQL/MarkerFeatureAdaptor.pm
          modules/Bio/EnsEMBL/Map/DBSQL/QtlAdaptor.pm
          modules/Bio/EnsEMBL/Map/DBSQL/QtlFeatureAdaptor.pm
          modules/Bio/EnsEMBL/Map/Ditag.pm
          modules/Bio/EnsEMBL/Map/DitagFeature.pm
          modules/Bio/EnsEMBL/Map/MapLocation.pm
          modules/Bio/EnsEMBL/Map/Marker.pm
          modules/Bio/EnsEMBL/Map/MarkerFeature.pm
          modules/Bio/EnsEMBL/Map/MarkerSynonym.pm
          modules/Bio/EnsEMBL/Map/Qtl.pm
          modules/Bio/EnsEMBL/Map/QtlFeature.pm
          modules/Bio/EnsEMBL/MappedSlice.pm
          modules/Bio/EnsEMBL/MappedSliceContainer.pm
          modules/Bio/EnsEMBL/Mapper.pm
          modules/Bio/EnsEMBL/Mapper/Coordinate.pm
          modules/Bio/EnsEMBL/Mapper/Gap.pm
          modules/Bio/EnsEMBL/Mapper/IndelCoordinate.pm
          modules/Bio/EnsEMBL/Mapper/IndelPair.pm
          modules/Bio/EnsEMBL/Mapper/Pair.pm
          modules/Bio/EnsEMBL/Mapper/RangeRegistry.pm
          modules/Bio/EnsEMBL/Mapper/Unit.pm
          modules/Bio/EnsEMBL/MiscFeature.pm
          modules/Bio/EnsEMBL/MiscSet.pm
          modules/Bio/EnsEMBL/OntologyTerm.pm
          modules/Bio/EnsEMBL/PepDnaAlignFeature.pm
          modules/Bio/EnsEMBL/PredictionExon.pm
          modules/Bio/EnsEMBL/PredictionTranscript.pm
          modules/Bio/EnsEMBL/ProjectionSegment.pm
          modules/Bio/EnsEMBL/ProteinFeature.pm
          modules/Bio/EnsEMBL/Registry.pm
          modules/Bio/EnsEMBL/RepeatConsensus.pm
          modules/Bio/EnsEMBL/RepeatFeature.pm
          modules/Bio/EnsEMBL/RepeatMaskedSlice.pm
          modules/Bio/EnsEMBL/Root.pm
          modules/Bio/EnsEMBL/SNP.pm
          modules/Bio/EnsEMBL/SeqEdit.pm
          modules/Bio/EnsEMBL/SeqFeature.pm
          modules/Bio/EnsEMBL/SeqFeatureI.pm
          modules/Bio/EnsEMBL/SimpleFeature.pm
          modules/Bio/EnsEMBL/Slice.pm
          modules/Bio/EnsEMBL/SplicingEvent.pm
          modules/Bio/EnsEMBL/SplicingEventFeature.pm
          modules/Bio/EnsEMBL/SplicingTranscriptPair.pm
          modules/Bio/EnsEMBL/StableIdEvent.pm
          modules/Bio/EnsEMBL/StableIdHistoryTree.pm
          modules/Bio/EnsEMBL/Storable.pm
          modules/Bio/EnsEMBL/StrainSlice.pm
          modules/Bio/EnsEMBL/TopLevelAssemblyMapper.pm
          modules/Bio/EnsEMBL/Transcript.pm
          modules/Bio/EnsEMBL/TranscriptFactory.pm
          modules/Bio/EnsEMBL/TranscriptMapper.pm
          modules/Bio/EnsEMBL/Translation.pm
          modules/Bio/EnsEMBL/UnconventionalTranscriptAssociation.pm
          modules/Bio/EnsEMBL/UnmappedObject.pm
          modules/Bio/EnsEMBL/Upstream.pm
          modules/Bio/EnsEMBL/Utils/Argument.pm
          modules/Bio/EnsEMBL/Utils/AssemblyProjector.pm
          modules/Bio/EnsEMBL/Utils/BitString.pm
          modules/Bio/EnsEMBL/Utils/Cache.pm
          modules/Bio/EnsEMBL/Utils/CigarString.pm
          modules/Bio/EnsEMBL/Utils/ConfParser.pm
          modules/Bio/EnsEMBL/Utils/ConfigRegistry.pm
          modules/Bio/EnsEMBL/Utils/ConversionSupport.pm
          modules/Bio/EnsEMBL/Utils/Converter.pm
          modules/Bio/EnsEMBL/Utils/Converter/bio_ens.pm
          modules/Bio/EnsEMBL/Utils/Converter/bio_ens_analysis.pm
          modules/Bio/EnsEMBL/Utils/Converter/bio_ens_exon.pm
          modules/Bio/EnsEMBL/Utils/Converter/bio_ens_featurePair.pm
          modules/Bio/EnsEMBL/Utils/Converter/bio_ens_gene.pm
          modules/Bio/EnsEMBL/Utils/Converter/bio_ens_hit.pm
          modules/Bio/EnsEMBL/Utils/Converter/bio_ens_hsp.pm
          modules/Bio/EnsEMBL/Utils/Converter/bio_ens_predictionExon.pm
          modules/Bio/EnsEMBL/Utils/Converter/bio_ens_predictionGene.pm
          modules/Bio/EnsEMBL/Utils/Converter/bio_ens_seqFeature.pm
          modules/Bio/EnsEMBL/Utils/Converter/bio_ens_transcript.pm
          modules/Bio/EnsEMBL/Utils/Converter/ens_bio.pm
          modules/Bio/EnsEMBL/Utils/Converter/ens_bio_featurePair.pm
          modules/Bio/EnsEMBL/Utils/Converter/ens_bio_seqFeature.pm
          modules/Bio/EnsEMBL/Utils/EasyArgv.pm
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      e4d8dcbb
    • Ian Longden's avatar
      update staging databases etc · adf5748a
      Ian Longden authored
      adf5748a
    • Ian Longden's avatar
      set ignore correctly dependong on the mode · 3b363ab2
      Ian Longden authored
      3b363ab2
    • Ian Longden's avatar
      baab5fc7
    • Ian Longden's avatar
    • Ian Longden's avatar
  2. 30 Oct, 2009 2 commits
  3. 29 Oct, 2009 3 commits
  4. 28 Oct, 2009 8 commits
  5. 27 Oct, 2009 9 commits
  6. 23 Oct, 2009 1 commit
  7. 21 Oct, 2009 1 commit
  8. 20 Oct, 2009 5 commits