This commit was manufactured by cvs2svn to create tag 'before-
release-59-tag'. Sprout from master 2010-07-23 09:05:23 UTC Andreas Kusalananda Kähäri <ak4@sanger.ac.uk> 'Only submit sequence dumping jobs if there are jobs to submit.' 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/AltSplicingToolkit/AUTHORS misc-scripts/alternative_splicing/AltSplicingToolkit/BUGS misc-scripts/alternative_splicing/AltSplicingToolkit/COPYING misc-scripts/alternative_splicing/AltSplicingToolkit/ChangeLog misc-scripts/alternative_splicing/AltSplicingToolkit/INSTALL misc-scripts/alternative_splicing/AltSplicingToolkit/INSTALL.configure misc-scripts/alternative_splicing/AltSplicingToolkit/Makefile.am misc-scripts/alternative_splicing/AltSplicingToolkit/Makefile.in misc-scripts/alternative_splicing/AltSplicingToolkit/NEWS misc-scripts/alternative_splicing/AltSplicingToolkit/README misc-scripts/alternative_splicing/AltSplicingToolkit/THANKS misc-scripts/alternative_splicing/AltSplicingToolkit/aclocal.m4 misc-scripts/alternative_splicing/AltSplicingToolkit/configure.ac misc-scripts/alternative_splicing/AltSplicingToolkit/depcomp misc-scripts/alternative_splicing/AltSplicingToolkit/release_notes.txt misc-scripts/alternative_splicing/AltSplicingToolkit/src/Constants.h misc-scripts/alternative_splicing/AltSplicingToolkit/src/Main.cpp misc-scripts/alternative_splicing/AltSplicingToolkit/src/Makefile.am misc-scripts/alternative_splicing/AltSplicingToolkit/src/Makefile.in misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/Coordinates.cpp misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/Coordinates.h misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/ExonChunk.cpp misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/ExonChunk.h misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/Feature.cpp misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/Feature.h misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/Gene.cpp misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/Gene.h misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/GeneFeature.cpp misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/GeneFeature.h misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/RegionChunk.cpp misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/RegionChunk.h misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/SplicingEvent.cpp misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/SplicingEvent.h misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/SplicingEventContainer.cpp misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/SplicingEventContainer.h misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/SplicingEventMatrix.cpp misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/SplicingEventMatrix.h misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/SplicingGraph.cpp misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/SplicingGraph.h misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/SplicingVertex.cpp misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/SplicingVertex.h misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/Transcript.cpp misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/Transcript.h misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/TranscriptFeature.cpp misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/TranscriptFeature.h misc-scripts/alternative_splicing/AltSplicingToolkit/src/gff/BioMartGffHandler.cpp misc-scripts/alternative_splicing/AltSplicingToolkit/src/gff/BioMartGffHandler.h misc-scripts/alternative_splicing/AltSplicingToolkit/src/gff/GffEventModel.cpp misc-scripts/alternative_splicing/AltSplicingToolkit/src/gff/GffEventModel.h misc-scripts/alternative_splicing/AltSplicingToolkit/src/gff/GffParser.cpp misc-scripts/alternative_splicing/AltSplicingToolkit/src/gff/GffParser.h misc-scripts/alternative_splicing/AltSplicingToolkit/src/gff/GffSimpleHandler.cpp misc-scripts/alternative_splicing/AltSplicingToolkit/src/gff/GffSimpleHandler.h misc-scripts/alternative_splicing/AltSplicingToolkit/src/gff/SplicingEventGffGenerator.cpp misc-scripts/alternative_splicing/AltSplicingToolkit/src/gff/SplicingEventGffGenerator.h misc-scripts/alternative_splicing/AltSplicingToolkit/src/util/Logger.cpp misc-scripts/alternative_splicing/AltSplicingToolkit/src/util/Logger.h misc-scripts/alternative_splicing/AltSplicingToolkit/src/util/StringUtil.cpp misc-scripts/alternative_splicing/AltSplicingToolkit/src/util/StringUtil.h misc-scripts/alternative_splicing/Fetch_gff.pl misc-scripts/alternative_splicing/README.txt misc-scripts/alternative_splicing/load_alt_splice_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/assembly_patches/README.TXT misc-scripts/assembly_patches/assembly_patch_load.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/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/mouse_knockouts/add_ikmc_as_simple_features.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/variation/nonsense_transcript_attribs.pl misc-scripts/web_stats.sh misc-scripts/xref_mapping/FAQ.txt misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm misc-scripts/xref_mapping/XrefMapper/CoordinateMapper.pm misc-scripts/xref_mapping/XrefMapper/CoreInfo.pm misc-scripts/xref_mapping/XrefMapper/DisplayXrefs.pm misc-scripts/xref_mapping/XrefMapper/Interpro.pm misc-scripts/xref_mapping/XrefMapper/LoadMapper.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/ExonerateGappedBest1_culex.pm misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateGappedBest_100_perc_id.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/ProcessMappings.pm misc-scripts/xref_mapping/XrefMapper/ProcessPaired.pm misc-scripts/xref_mapping/XrefMapper/ProcessPrioritys.pm misc-scripts/xref_mapping/XrefMapper/SubmitMapper.pm misc-scripts/xref_mapping/XrefMapper/TestMappings.pm misc-scripts/xref_mapping/XrefMapper/VBCoordinateMapper.pm misc-scripts/xref_mapping/XrefMapper/XrefLoader.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/culex_pipiens.pm misc-scripts/xref_mapping/XrefMapper/danio_rerio.pm misc-scripts/xref_mapping/XrefMapper/db.pm misc-scripts/xref_mapping/XrefMapper/drosophila_ananassae.pm misc-scripts/xref_mapping/XrefMapper/drosophila_erecta.pm misc-scripts/xref_mapping/XrefMapper/drosophila_grimshawi.pm misc-scripts/xref_mapping/XrefMapper/drosophila_melanogaster.pm misc-scripts/xref_mapping/XrefMapper/drosophila_mojavensis.pm misc-scripts/xref_mapping/XrefMapper/drosophila_persimilis.pm misc-scripts/xref_mapping/XrefMapper/drosophila_pseudoobscura.pm misc-scripts/xref_mapping/XrefMapper/drosophila_sechellia.pm misc-scripts/xref_mapping/XrefMapper/drosophila_simulans.pm misc-scripts/xref_mapping/XrefMapper/drosophila_virilis.pm misc-scripts/xref_mapping/XrefMapper/drosophila_willistoni.pm misc-scripts/xref_mapping/XrefMapper/drosophila_yakuba.pm misc-scripts/xref_mapping/XrefMapper/fugu_rubripes.pm misc-scripts/xref_mapping/XrefMapper/homo_sapiens.pm misc-scripts/xref_mapping/XrefMapper/ixodes_scapularis.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/saccharomyces_cerevisiae.pm misc-scripts/xref_mapping/XrefMapper/tetraodon_nigroviridis.pm misc-scripts/xref_mapping/XrefMapper/xenopus_tropicalis.pm misc-scripts/xref_mapping/XrefParser/AedesCAPParser.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/DBASSParser.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/FantomParser.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/GOSlimParser.pm misc-scripts/xref_mapping/XrefParser/HGNCParser.pm misc-scripts/xref_mapping/XrefParser/HGNC_CCDSParser.pm misc-scripts/xref_mapping/XrefParser/HGNC_ENSTParser.pm misc-scripts/xref_mapping/XrefParser/HPAParser.pm misc-scripts/xref_mapping/XrefParser/IPIParser.pm misc-scripts/xref_mapping/XrefParser/IlluminaParser.pm misc-scripts/xref_mapping/XrefParser/IlluminaWGParser.pm misc-scripts/xref_mapping/XrefParser/InterproGoParser.pm misc-scripts/xref_mapping/XrefParser/InterproParser.pm misc-scripts/xref_mapping/XrefParser/IxodesCAPParser.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/MGI_CCDS_Parser.pm misc-scripts/xref_mapping/XrefParser/MGI_Desc_Parser.pm misc-scripts/xref_mapping/XrefParser/MGI_Vega_Parser.pm misc-scripts/xref_mapping/XrefParser/MIMParser.pm misc-scripts/xref_mapping/XrefParser/Mim2GeneParser.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/UniProtDirectParser.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/VBCommunitySymbolParser.pm misc-scripts/xref_mapping/XrefParser/VbDirectParser.pm misc-scripts/xref_mapping/XrefParser/VbGFF3Parser.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/curated_transcriptParser.pm misc-scripts/xref_mapping/XrefParser/ncRNAParser.pm misc-scripts/xref_mapping/XrefParser/ncRNA_DBParser.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/core_vega_link_check.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/xref_tracker.pl misc-scripts/xref_mapping/xrefs_detailed_docs.txt misc-scripts/xref_mapping/xrefs_overview.txt misc-scripts/xref_projection/README 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 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