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- Jul 23, 2008
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cvs2git authored
merge'. Sprout from master 2008-07-23 13:25:47 UTC Andreas Kusalananda Kähäri <ak4@sanger.ac.uk> 'Add clear_cache() method to enable slightly cleaner emptying of feature' 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/analysis_description/analysis.descriptions 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/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/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/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/meta_coord/update_meta_coord.pl misc-scripts/meta_levels.pl misc-scripts/probe_mapping/compare_mappings.pl misc-scripts/probe_mapping/probe2transcript.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/convert120_130.pl misc-scripts/surgery/convert_6_main.pl misc-scripts/surgery/convert_7a_main.pl 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_mapping/XrefMapper/BasicMapper.pm misc-scripts/xref_mapping/XrefMapper/CoordinateMapper.pm misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateBasic.pm misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateBest1.pm misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateGappedBest1.pm misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateGappedBest1_agam.pm misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateGappedBest_90_perc_id.pm misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateUngappedBest1.pm misc-scripts/xref_mapping/XrefMapper/Methods/LocalExonerateGappedBest1.pm misc-scripts/xref_mapping/XrefMapper/Methods/PBSExonerateGappedBest1.pm misc-scripts/xref_mapping/XrefMapper/VBCoordinateMapper.pm misc-scripts/xref_mapping/XrefMapper/aedes_aegypti.pm misc-scripts/xref_mapping/XrefMapper/anopheles_gambiae.pm misc-scripts/xref_mapping/XrefMapper/caenorhabditis_elegans.pm misc-scripts/xref_mapping/XrefMapper/canis_familiaris.pm misc-scripts/xref_mapping/XrefMapper/ciona_intestinalis.pm misc-scripts/xref_mapping/XrefMapper/danio_rerio.pm misc-scripts/xref_mapping/XrefMapper/db.pm misc-scripts/xref_mapping/XrefMapper/drosophila_melanogaster.pm misc-scripts/xref_mapping/XrefMapper/fugu_rubripes.pm misc-scripts/xref_mapping/XrefMapper/homo_sapiens.pm misc-scripts/xref_mapping/XrefMapper/macaca_mulatta.pm misc-scripts/xref_mapping/XrefMapper/monodelphis_domestica.pm misc-scripts/xref_mapping/XrefMapper/mus_musculus.pm misc-scripts/xref_mapping/XrefMapper/ornithorhynchus_anatinus.pm misc-scripts/xref_mapping/XrefMapper/rattus_norvegicus.pm misc-scripts/xref_mapping/XrefMapper/tetraodon_nigroviridis.pm misc-scripts/xref_mapping/XrefMapper/xenopus_tropicalis.pm misc-scripts/xref_mapping/XrefParser/AedesGenBankParser.pm misc-scripts/xref_mapping/XrefParser/AgilentParser.pm misc-scripts/xref_mapping/XrefParser/AnophelesSymbolParser.pm misc-scripts/xref_mapping/XrefParser/BaseParser.pm misc-scripts/xref_mapping/XrefParser/CCDSParser.pm misc-scripts/xref_mapping/XrefParser/CeleraParser.pm misc-scripts/xref_mapping/XrefParser/CeleraProteinParser.pm misc-scripts/xref_mapping/XrefParser/CeleraTranscriptParser.pm misc-scripts/xref_mapping/XrefParser/CodelinkParser.pm misc-scripts/xref_mapping/XrefParser/CoordinateParser.pm misc-scripts/xref_mapping/XrefParser/DatabaseParser.pm misc-scripts/xref_mapping/XrefParser/DirectParser.pm misc-scripts/xref_mapping/XrefParser/EntrezGeneParser.pm misc-scripts/xref_mapping/XrefParser/FastaParser.pm misc-scripts/xref_mapping/XrefParser/FlybaseParser.pm misc-scripts/xref_mapping/XrefParser/Flybase_dmel_GFFv3_Parser.pm misc-scripts/xref_mapping/XrefParser/GOParser.pm misc-scripts/xref_mapping/XrefParser/HGNCParser.pm misc-scripts/xref_mapping/XrefParser/HGNC_CCDSParser.pm misc-scripts/xref_mapping/XrefParser/HGNC_ENSGParser.pm misc-scripts/xref_mapping/XrefParser/IPIParser.pm misc-scripts/xref_mapping/XrefParser/IlluminaParser.pm misc-scripts/xref_mapping/XrefParser/InterproGoParser.pm misc-scripts/xref_mapping/XrefParser/InterproParser.pm misc-scripts/xref_mapping/XrefParser/JGI_Parser.pm misc-scripts/xref_mapping/XrefParser/JGI_ProteinParser.pm misc-scripts/xref_mapping/XrefParser/MGDParser.pm misc-scripts/xref_mapping/XrefParser/MIMParser.pm misc-scripts/xref_mapping/XrefParser/OTTTParser.pm misc-scripts/xref_mapping/XrefParser/RGDParser.pm misc-scripts/xref_mapping/XrefParser/RefSeqGPFFParser.pm misc-scripts/xref_mapping/XrefParser/RefSeqParser.pm misc-scripts/xref_mapping/XrefParser/RefSeq_CCDSParser.pm misc-scripts/xref_mapping/XrefParser/SGDParser.pm misc-scripts/xref_mapping/XrefParser/SegmentParser.pm misc-scripts/xref_mapping/XrefParser/UCSCParser.pm misc-scripts/xref_mapping/XrefParser/UniGeneParser.pm misc-scripts/xref_mapping/XrefParser/UniProtParser.pm misc-scripts/xref_mapping/XrefParser/UniProtParser_descriptions_only.pm misc-scripts/xref_mapping/XrefParser/UniProtVarSplicParser.pm misc-scripts/xref_mapping/XrefParser/VbDirectParser.pm misc-scripts/xref_mapping/XrefParser/VbGFF3Parser.pm misc-scripts/xref_mapping/XrefParser/VegaParser.pm misc-scripts/xref_mapping/XrefParser/Vega_TranParser.pm misc-scripts/xref_mapping/XrefParser/WilsonAffyParser.pm misc-scripts/xref_mapping/XrefParser/WormPepParser.pm misc-scripts/xref_mapping/XrefParser/WormbaseDatabaseStableIDParser.pm misc-scripts/xref_mapping/XrefParser/XenopusJamboreeParser.pm misc-scripts/xref_mapping/XrefParser/ZFINParser.pm misc-scripts/xref_mapping/XrefParser/ncRNAParser.pm misc-scripts/xref_mapping/compare_mapping.pl misc-scripts/xref_mapping/compare_xrefs_by_source.pl misc-scripts/xref_mapping/convert_xrefs_to_all_translations.pl misc-scripts/xref_mapping/ensembl_xrefs.pdf misc-scripts/xref_mapping/ensembl_xrefs.sxw misc-scripts/xref_mapping/gen_perc_file.pl misc-scripts/xref_mapping/generate_csv_graph_file.pl misc-scripts/xref_mapping/parsing_information.txt misc-scripts/xref_mapping/sql/table.sql misc-scripts/xref_mapping/test_mapping_files.pl misc-scripts/xref_mapping/test_xref_mapper.pl misc-scripts/xref_mapping/xref_config.ini misc-scripts/xref_mapping/xref_config2sql.pl misc-scripts/xref_mapping/xref_mapper.input misc-scripts/xref_mapping/xref_mapper.pl misc-scripts/xref_mapping/xref_parser.pl misc-scripts/xref_mapping/xrefs_overview.txt 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_37.conf misc-scripts/xref_projection/release_38.conf misc-scripts/xref_projection/release_47.ini misc-scripts/xref_projection/release_48.ini misc-scripts/xref_projection/submit_projections.pl modules/t/MultiTestDB.conf.example modules/t/MultiTestDB.t modules/t/README modules/t/TestUtils.pm modules/t/affy.t modules/t/affyAdaptors.t modules/t/analysis.t modules/t/archiveStableId.t modules/t/argument.t modules/t/assemblyException.t modules/t/assemblyExceptionFeature.t modules/t/assemblyMapper.t modules/t/attribute.t modules/t/attributeAdaptor.t modules/t/canonicalDBAdaptor.t modules/t/chainedAssemblyMapper.t modules/t/compressedSequenceAdaptor.t modules/t/coordSystem.t modules/t/coordSystemAdaptor.t modules/t/dbConnection.t modules/t/dbEntries.t modules/t/densityFeature.t modules/t/densityFeatureAdaptor.t modules/t/densityType.t modules/t/densityTypeAdaptor.t modules/t/ditag.t modules/t/ditagAdaptor.t modules/t/ditagFeature.t modules/t/ditagFeatureAdaptor.t modules/t/dnaAlignFeatureAdaptor.t modules/t/dnaDnaAlignFeature.t modules/t/dnaPepAlignFeature.t modules/t/easyargv.t modules/t/exception.t modules/t/exon.t modules/t/externalFeatureAdaptor.t modules/t/feature.t modules/t/featurePair.t modules/t/gene.t modules/t/geneview.t modules/t/info_testdb.pl modules/t/intron.t modules/t/karyotypeBand.t modules/t/karyotypeBandAdaptor.t modules/t/mapLocation.t modules/t/mapper.t modules/t/marker.t modules/t/markerAdaptor.t modules/t/markerFeature.t modules/t/markerFeatureAdaptor.t modules/t/markerSynonym.t modules/t/metaContainer.t modules/t/metaCoordContainer.t modules/t/miscFeature.t modules/t/miscFeatureAdaptor.t modules/t/miscSet.t modules/t/miscSetAdaptor.t modules/t/oligo.t modules/t/oligoAdaptors.t modules/t/predictionTranscript.t modules/t/proteinAlignFeatureAdaptor.t modules/t/proteinFeature.t modules/t/proteinFeatureAdaptor.t modules/t/qtl.t modules/t/rangeRegistry.t modules/t/repeatConsensus.t modules/t/repeatConsensusAdaptor.t modules/t/repeatFeature.t modules/t/repeatFeatureAdaptor.t modules/t/repeatMaskedSlice.t modules/t/seqDumper.t modules/t/seqEdit.t modules/t/sequenceAdaptor.t modules/t/simpleFeature.t modules/t/slice.t modules/t/sliceAdaptor.t modules/t/test-genome-DBs/homo_sapiens/core/alt_allele.sql modules/t/test-genome-DBs/homo_sapiens/core/alt_allele.txt modules/t/test-genome-DBs/homo_sapiens/core/analysis.sql modules/t/test-genome-DBs/homo_sapiens/core/analysis.txt modules/t/test-genome-DBs/homo_sapiens/core/analysis_description.sql modules/t/test-genome-DBs/homo_sapiens/core/analysis_description.txt modules/t/test-genome-DBs/homo_sapiens/core/assembly.sql modules/t/test-genome-DBs/homo_sapiens/core/assembly.txt modules/t/test-genome-DBs/homo_sapiens/core/assembly_exception.sql modules/t/test-genome-DBs/homo_sapiens/core/assembly_exception.txt modules/t/test-genome-DBs/homo_sapiens/core/attrib_type.sql modules/t/test-genome-DBs/homo_sapiens/core/attrib_type.txt modules/t/test-genome-DBs/homo_sapiens/core/coord_system.sql modules/t/test-genome-DBs/homo_sapiens/core/coord_system.txt modules/t/test-genome-DBs/homo_sapiens/core/density_feature.sql modules/t/test-genome-DBs/homo_sapiens/core/density_feature.txt modules/t/test-genome-DBs/homo_sapiens/core/density_type.sql modules/t/test-genome-DBs/homo_sapiens/core/density_type.txt modules/t/test-genome-DBs/homo_sapiens/core/ditag.sql modules/t/test-genome-DBs/homo_sapiens/core/ditag.txt modules/t/test-genome-DBs/homo_sapiens/core/ditag_feature.sql modules/t/test-genome-DBs/homo_sapiens/core/ditag_feature.txt modules/t/test-genome-DBs/homo_sapiens/core/dna.sql modules/t/test-genome-DBs/homo_sapiens/core/dna.txt modules/t/test-genome-DBs/homo_sapiens/core/dna_align_feature.sql modules/t/test-genome-DBs/homo_sapiens/core/dna_align_feature.txt modules/t/test-genome-DBs/homo_sapiens/core/dnac.sql modules/t/test-genome-DBs/homo_sapiens/core/dnac.txt modules/t/test-genome-DBs/homo_sapiens/core/exon.sql modules/t/test-genome-DBs/homo_sapiens/core/exon.txt modules/t/test-genome-DBs/homo_sapiens/core/exon_stable_id.sql modules/t/test-genome-DBs/homo_sapiens/core/exon_stable_id.txt modules/t/test-genome-DBs/homo_sapiens/core/exon_transcript.sql modules/t/test-genome-DBs/homo_sapiens/core/exon_transcript.txt modules/t/test-genome-DBs/homo_sapiens/core/external_db.sql modules/t/test-genome-DBs/homo_sapiens/core/external_db.txt modules/t/test-genome-DBs/homo_sapiens/core/external_synonym.sql modules/t/test-genome-DBs/homo_sapiens/core/external_synonym.txt modules/t/test-genome-DBs/homo_sapiens/core/gene.sql modules/t/test-genome-DBs/homo_sapiens/core/gene.txt modules/t/test-genome-DBs/homo_sapiens/core/gene_archive.sql modules/t/test-genome-DBs/homo_sapiens/core/gene_archive.txt modules/t/test-genome-DBs/homo_sapiens/core/gene_attrib.sql modules/t/test-genome-DBs/homo_sapiens/core/gene_attrib.txt modules/t/test-genome-DBs/homo_sapiens/core/gene_stable_id.sql modules/t/test-genome-DBs/homo_sapiens/core/gene_stable_id.txt modules/t/test-genome-DBs/homo_sapiens/core/go_xref.sql modules/t/test-genome-DBs/homo_sapiens/core/go_xref.txt modules/t/test-genome-DBs/homo_sapiens/core/identity_xref.sql modules/t/test-genome-DBs/homo_sapiens/core/identity_xref.txt modules/t/test-genome-DBs/homo_sapiens/core/interpro.sql modules/t/test-genome-DBs/homo_sapiens/core/interpro.txt modules/t/test-genome-DBs/homo_sapiens/core/karyotype.sql modules/t/test-genome-DBs/homo_sapiens/core/karyotype.txt modules/t/test-genome-DBs/homo_sapiens/core/map.sql modules/t/test-genome-DBs/homo_sapiens/core/map.txt modules/t/test-genome-DBs/homo_sapiens/core/mapping_session.sql modules/t/test-genome-DBs/homo_sapiens/core/mapping_session.txt modules/t/test-genome-DBs/homo_sapiens/core/mapping_set.sql modules/t/test-genome-DBs/homo_sapiens/core/mapping_set.txt modules/t/test-genome-DBs/homo_sapiens/core/marker.sql modules/t/test-genome-DBs/homo_sapiens/core/marker.txt modules/t/test-genome-DBs/homo_sapiens/core/marker_feature.sql modules/t/test-genome-DBs/homo_sapiens/core/marker_feature.txt modules/t/test-genome-DBs/homo_sapiens/core/marker_map_location.sql modules/t/test-genome-DBs/homo_sapiens/core/marker_map_location.txt modules/t/test-genome-DBs/homo_sapiens/core/marker_synonym.sql modules/t/test-genome-DBs/homo_sapiens/core/marker_synonym.txt modules/t/test-genome-DBs/homo_sapiens/core/meta.sql modules/t/test-genome-DBs/homo_sapiens/core/meta.txt modules/t/test-genome-DBs/homo_sapiens/core/meta_coord.sql modules/t/test-genome-DBs/homo_sapiens/core/meta_coord.txt modules/t/test-genome-DBs/homo_sapiens/core/misc_attrib.sql modules/t/test-genome-DBs/homo_sapiens/core/misc_attrib.txt modules/t/test-genome-DBs/homo_sapiens/core/misc_feature.sql modules/t/test-genome-DBs/homo_sapiens/core/misc_feature.txt modules/t/test-genome-DBs/homo_sapiens/core/misc_feature_misc_set.sql modules/t/test-genome-DBs/homo_sapiens/core/misc_feature_misc_set.txt modules/t/test-genome-DBs/homo_sapiens/core/misc_set.sql modules/t/test-genome-DBs/homo_sapiens/core/misc_set.txt modules/t/test-genome-DBs/homo_sapiens/core/object_xref.sql modules/t/test-genome-DBs/homo_sapiens/core/object_xref.txt modules/t/test-genome-DBs/homo_sapiens/core/oligo_array.sql modules/t/test-genome-DBs/homo_sapiens/core/oligo_array.txt modules/t/test-genome-DBs/homo_sapiens/core/oligo_feature.sql modules/t/test-genome-DBs/homo_sapiens/core/oligo_feature.txt modules/t/test-genome-DBs/homo_sapiens/core/oligo_probe.sql modules/t/test-genome-DBs/homo_sapiens/core/oligo_probe.txt modules/t/test-genome-DBs/homo_sapiens/core/peptide_archive.sql modules/t/test-genome-DBs/homo_sapiens/core/peptide_archive.txt modules/t/test-genome-DBs/homo_sapiens/core/prediction_exon.sql modules/t/test-genome-DBs/homo_sapiens/core/prediction_exon.txt modules/t/test-genome-DBs/homo_sapiens/core/prediction_transcript.sql modules/t/test-genome-DBs/homo_sapiens/core/prediction_transcript.txt modules/t/test-genome-DBs/homo_sapiens/core/protein_align_feature.sql modules/t/test-genome-DBs/homo_sapiens/core/protein_align_feature.txt modules/t/test-genome-DBs/homo_sapiens/core/protein_feature.sql modules/t/test-genome-DBs/homo_sapiens/core/protein_feature.txt modules/t/test-genome-DBs/homo_sapiens/core/qtl.sql modules/t/test-genome-DBs/homo_sapiens/core/qtl.txt modules/t/test-genome-DBs/homo_sapiens/core/qtl_feature.sql modules/t/test-genome-DBs/homo_sapiens/core/qtl_feature.txt modules/t/test-genome-DBs/homo_sapiens/core/qtl_synonym.sql modules/t/test-genome-DBs/homo_sapiens/core/qtl_synonym.txt modules/t/test-genome-DBs/homo_sapiens/core/repeat_consensus.sql modules/t/test-genome-DBs/homo_sapiens/core/repeat_consensus.txt modules/t/test-genome-DBs/homo_sapiens/core/repeat_feature.sql modules/t/test-genome-DBs/homo_sapiens/core/repeat_feature.txt modules/t/test-genome-DBs/homo_sapiens/core/seq_region.sql modules/t/test-genome-DBs/homo_sapiens/core/seq_region.txt modules/t/test-genome-DBs/homo_sapiens/core/seq_region_attrib.sql modules/t/test-genome-DBs/homo_sapiens/core/seq_region_attrib.txt modules/t/test-genome-DBs/homo_sapiens/core/seq_region_mapping.sql modules/t/test-genome-DBs/homo_sapiens/core/seq_region_mapping.txt modules/t/test-genome-DBs/homo_sapiens/core/simple_feature.sql modules/t/test-genome-DBs/homo_sapiens/core/simple_feature.txt modules/t/test-genome-DBs/homo_sapiens/core/stable_id_event.sql modules/t/test-genome-DBs/homo_sapiens/core/stable_id_event.txt modules/t/test-genome-DBs/homo_sapiens/core/supporting_feature.sql modules/t/test-genome-DBs/homo_sapiens/core/supporting_feature.txt modules/t/test-genome-DBs/homo_sapiens/core/transcript.sql modules/t/test-genome-DBs/homo_sapiens/core/transcript.txt modules/t/test-genome-DBs/homo_sapiens/core/transcript_attrib.sql modules/t/test-genome-DBs/homo_sapiens/core/transcript_attrib.txt modules/t/test-genome-DBs/homo_sapiens/core/transcript_stable_id.sql modules/t/test-genome-DBs/homo_sapiens/core/transcript_stable_id.txt modules/t/test-genome-DBs/homo_sapiens/core/transcript_supporting_feature.sql modules/t/test-genome-DBs/homo_sapiens/core/transcript_supporting_feature.txt modules/t/test-genome-DBs/homo_sapiens/core/translation.sql modules/t/test-genome-DBs/homo_sapiens/core/translation.txt modules/t/test-genome-DBs/homo_sapiens/core/translation_attrib.sql modules/t/test-genome-DBs/homo_sapiens/core/translation_attrib.txt modules/t/test-genome-DBs/homo_sapiens/core/translation_stable_id.sql modules/t/test-genome-DBs/homo_sapiens/core/translation_stable_id.txt modules/t/test-genome-DBs/homo_sapiens/core/unconventional_transcript_association.sql modules/t/test-genome-DBs/homo_sapiens/core/unconventional_transcript_association.txt modules/t/test-genome-DBs/homo_sapiens/core/unmapped_object.sql modules/t/test-genome-DBs/homo_sapiens/core/unmapped_object.txt modules/t/test-genome-DBs/homo_sapiens/core/unmapped_reason.sql modules/t/test-genome-DBs/homo_sapiens/core/unmapped_reason.txt modules/t/test-genome-DBs/homo_sapiens/core/xref.sql modules/t/test-genome-DBs/homo_sapiens/core/xref.txt modules/t/topLevelAssemblyMapper.t modules/t/transcript.t modules/t/translation.t modules/t/unconventionalTranscriptAssociation.t modules/t/unconventionalTranscriptAssociationAdaptor.t modules/t/unmappedObject.t modules/t/unmappedObjectAdaptor.t sql/README sql/foreign_keys.sql sql/patch_21_22.sql sql/patch_23_24.sql sql/patch_24_25.sql sql/patch_25_26.sql sql/patch_26_27.sql sql/patch_27_28.sql sql/patch_28_29.sql sql/patch_29_30.sql sql/patch_30_31.sql sql/patch_31_32.sql sql/patch_32_33.sql sql/patch_33_34.sql sql/patch_34_35.sql sql/patch_35_36.sql sql/patch_36_37.sql sql/patch_37_38.sql sql/patch_38_39_a.sql sql/patch_38_39_b.sql sql/patch_38_39_c.sql sql/patch_38_39_d.sql sql/patch_38_39_e.sql sql/patch_39_40_a.sql sql/patch_39_40_b.sql sql/patch_39_40_c.sql sql/patch_39_40_d.sql sql/patch_39_40_e.sql sql/patch_39_40_f.sql sql/patch_39_40_g.sql sql/patch_39_40_h.sql sql/patch_39_40_i.sql sql/patch_39_40_j.sql sql/patch_40_41_a.sql sql/patch_40_41_b.sql sql/patch_40_41_c.sql sql/patch_40_41_d.sql sql/patch_40_41_e.sql sql/patch_40_41_f.sql sql/patch_41_42_a.sql sql/patch_41_42_b.sql sql/patch_41_42_c.sql sql/patch_41_42_d.sql sql/patch_41_42_e.sql sql/patch_41_42_f.sql sql/patch_41_42_g.sql sql/patch_42_43_a.sql sql/patch_42_43_b.sql sql/patch_42_43_c.sql sql/patch_42_43_d.sql sql/patch_42_43_e.sql sql/patch_42_43_f.sql sql/patch_43_44_a.sql sql/patch_43_44_b.sql sql/patch_43_44_c.sql sql/patch_43_44_d.sql sql/patch_43_44_e.sql sql/patch_43_44_f.sql sql/patch_44_45_a.sql sql/patch_44_45_b.sql sql/patch_44_45_c.sql sql/patch_45_46_a.sql sql/patch_45_46_b.sql sql/patch_45_46_c.sql sql/patch_45_46_d.sql sql/patch_45_46_e.sql sql/patch_45_46_f.sql sql/patch_45_46_g.sql sql/patch_46_47_a.sql sql/patch_46_47_b.sql sql/patch_46_47_c.sql sql/patch_47_48_a.sql sql/patch_48_49_a.sql sql/patch_48_49_b.sql sql/patch_48_49_c.sql sql/patch_48_49_d.sql sql/patch_48_49_e.sql sql/patch_49_50_a.sql sql/patch_49_50_b.sql sql/patch_49_50_c.sql sql/patch_49_50_d.sql sql/patch_49_50_e.sql sql/patch_50_51_a.sql sql/patch_50_51_b.sql sql/patch_50_51_c.sql sql/patch_50_51_d.sql sql/populate_meta_coord.pl sql/table.sql sql/transfer_misc_affy.pl sql/vega_latest_schema.sql sql/vega_specific_tables.sql
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Andreas Kusalananda Kähäri authored
cache than "$adaptor->{'_slice_feature_cache'} = ();" in user code.
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- Jul 22, 2008
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Daniel Rios authored
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Daniel Rios authored
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Daniel Rios authored
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Daniel Rios authored
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Daniel Rios authored
tested 2 new methods: to get db_name for an external_db_id and fetch db_entries for a source (db_name)
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- Jul 21, 2008
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Daniel Rios authored
added use of method bind_param_generic_fetch to allow binding parameters when using the generic fetch method
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- Jul 18, 2008
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Daniel Rios authored
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Andreas Kusalananda Kähäri authored
Correct the name of patch 'c' (meta --> meta_coord). Adjust the insertion of patch identifiers to take into account the species_id column in the meta table (needs explicit NULL).
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Ian Longden authored
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Ian Longden authored
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Ian Longden authored
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Ian Longden authored
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Ian Longden authored
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Daniel Rios authored
added new method: bind_param_generic_fetch to allow binding parameters instead of using parameters within sql
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Andreas Kusalananda Kähäri authored
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Glenn Proctor authored
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Glenn Proctor authored
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Glenn Proctor authored
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Glenn Proctor authored
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Glenn Proctor authored
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Glenn Proctor authored
Incorporated changes from patch_50_51_a.sql (version changes) and patch_50_51_b.sql (protein feature hit_id -> hit_name)
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Glenn Proctor authored
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Glenn Proctor authored
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- Jul 17, 2008
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Yuan Chen authored
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- Jul 16, 2008
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Ian Longden authored
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Ian Longden authored
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Ian Longden authored
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Ian Longden authored
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Ian Longden authored
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Ian Longden authored
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Ian Longden authored
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Ian Longden authored
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Ian Longden authored
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- Jul 15, 2008
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Andreas Kusalananda Kähäri authored
Something went wrong here. This file was removed by Arek 7 years ago...
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Stephen Keenan authored
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- Jul 14, 2008
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Daniel Rios authored
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- Jul 11, 2008
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Susan Fairley authored
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- Jul 10, 2008
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Daniel Rios authored
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