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cvs2git authored
-dev-head'. Sprout from master 2009-04-20 12:53:38 UTC Susan Fairley <sf7@sanger.ac.uk> 'Remaining part of db_display_name added for Tgut_symbol.' Cherrypick from master 2010-02-04 11:06:22 UTC Andreas Kusalananda Kähäri <ak4@sanger.ac.uk> 'Remove unimplemented methods from synopsis.': 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_slice_gff.pl misc-scripts/assembly/cleanup_tmp_tables.sql misc-scripts/constitutive_exon.pl misc-scripts/id_mapping/myRun.ksh misc-scripts/id_mapping/utils/myManager.ksh 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/xref_mapping/FAQ.txt misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateGappedBest1_culex.pm misc-scripts/xref_mapping/XrefMapper/culex_pipiens.pm misc-scripts/xref_mapping/XrefMapper/ixodes_scapularis.pm misc-scripts/xref_mapping/XrefParser/AedesCAPParser.pm misc-scripts/xref_mapping/XrefParser/FantomParser.pm misc-scripts/xref_mapping/XrefParser/GOSlimParser.pm misc-scripts/xref_mapping/XrefParser/IxodesCAPParser.pm misc-scripts/xref_mapping/XrefParser/Mim2GeneParser.pm misc-scripts/xref_mapping/XrefParser/UniProtDirectParser.pm misc-scripts/xref_mapping/XrefParser/VBCommunitySymbolParser.pm misc-scripts/xref_mapping/xrefs_detailed_docs.txt modules/Bio/EnsEMBL/DBSQL/SOTermAdaptor.pm modules/Bio/EnsEMBL/DBSQL/SplicingEventAdaptor.pm modules/Bio/EnsEMBL/DBSQL/SplicingEventFeatureAdaptor.pm modules/Bio/EnsEMBL/DBSQL/SplicingTranscriptPairAdaptor.pm modules/Bio/EnsEMBL/IdMapping/StableIdGenerator/AnophelesGambiae.pm modules/Bio/EnsEMBL/LRGSlice.pm modules/Bio/EnsEMBL/SplicingEvent.pm modules/Bio/EnsEMBL/SplicingEventFeature.pm modules/Bio/EnsEMBL/SplicingTranscriptPair.pm sql/patch_54_55_a.sql sql/patch_54_55_b.sql sql/patch_54_55_c.sql sql/patch_54_55_d.sql sql/patch_54_55_e.sql sql/patch_54_55_f.sql sql/patch_54_55_g.sql sql/patch_54_55_h.sql sql/patch_55_56_a.sql sql/patch_55_56_b.sql sql/patch_55_56_c.sql sql/patch_55_56_d.sql sql/patch_56_57_a.sql sql/patch_56_57_b.sql sql/patch_56_57_c.sql sql/patch_56_57_d.sql sql/patch_56_57_e.sql sql/patch_56_57_f.sql Delete: misc-scripts/protein_match/process_pmach.pl
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