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  1. 15 Apr, 2009 1 commit
    • cvs2git's avatar
      This commit was manufactured by cvs2svn to create tag 'mergepoint-vega-46 · c09efab8
      cvs2git authored
      -dev-head-1'.
      
      Sprout from master 2008-02-14 08:57:57 UTC Glenn Proctor <gp1@sanger.ac.uk> 'Fix job naming.'
      Cherrypick from master 2009-04-15 12:17:55 UTC Kerstin Howe <kj2@sanger.ac.uk> 'added FOS ends for zebrafish':
          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/canonical_transcripts/set_canonical_transcripts.pl
          misc-scripts/db-space.pl
          misc-scripts/ebi_search_dump/ebi_search_dump.pl
          misc-scripts/id_mapping/synteny_rescore.pl
          misc-scripts/id_mapping/utils/compare_scores.pl
          misc-scripts/misc_feature/misc_set.descriptions
          misc-scripts/misc_feature/update_misc_set_descripitons.pl
          misc-scripts/translation_attribs.pl
          misc-scripts/translation_attribs_wrapper.pl
          misc-scripts/update_mapping_set.pl
          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/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/XrefLoader.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_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/XrefParser/DBASSParser.pm
          misc-scripts/xref_mapping/XrefParser/HGNC_ENSTParser.pm
          misc-scripts/xref_mapping/XrefParser/HGNC_curated_transcriptParser.pm
          misc-scripts/xref_mapping/XrefParser/HPAParser.pm
          misc-scripts/xref_mapping/XrefParser/IlluminaWGParser.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/MGI_curated_transcriptParser.pm
          misc-scripts/xref_mapping/XrefParser/Vega_TranParser.pm
          misc-scripts/xref_mapping/XrefParser/ncRNA_DBParser.pm
          misc-scripts/xref_mapping/xref_tracker.pl
          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/DBSQL/GOTermAdaptor.pm
          modules/Bio/EnsEMBL/DBSQL/OntologyDBAdaptor.pm
          modules/Bio/EnsEMBL/DBSQL/OntologyTermAdaptor.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/StableIdGenerator/AedesAegypti.pm
          modules/Bio/EnsEMBL/IdMapping/StableIdGenerator/EnsemblGeneric.pm
          modules/Bio/EnsEMBL/OntologyTerm.pm
          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/seq_region_mapping.sql
          modules/t/test-genome-DBs/homo_sapiens/core/seq_region_mapping.txt
          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/patch_50_51_e.sql
          sql/patch_50_51_f.sql
          sql/patch_50_51_g.sql
          sql/patch_50_51_h.sql
          sql/patch_50_51_i.sql
          sql/patch_51_52_a.sql
          sql/patch_51_52_b.sql
          sql/patch_51_52_c.sql
          sql/patch_51_52_d.sql
          sql/patch_52_53_a.sql
          sql/patch_52_53_b.sql
          sql/patch_52_53_c.sql
          sql/patch_52_53_d.sql
          sql/patch_53_54_a.sql
          sql/patch_53_54_b.sql
          sql/patch_53_54_c.sql
      Delete:
          misc-scripts/protein_match/process_pmach.pl
          modules/Bio/EnsEMBL/Collection/DnaAlignFeature.pm
          modules/Bio/EnsEMBL/Collection/ProteinAlignFeature.pm
          modules/Bio/EnsEMBL/DBSQL/Clone.pm
      c09efab8
  2. 14 Feb, 2008 3 commits
  3. 12 Feb, 2008 4 commits
    • Nathan Johnson's avatar
      added promiscuous probeset log · 8725e0b0
      Nathan Johnson authored
      8725e0b0
    • Nathan Johnson's avatar
      1993748a
    • Nathan Johnson's avatar
      just some tidyup · c0930f9c
      Nathan Johnson authored
      c0930f9c
    • Nathan Johnson's avatar
      #Implemented strand check and unmapped object for anti-sense mapping · 80aa6f99
      Nathan Johnson authored
      #Changed transcript_probeset_count cache to use dbID instead of complete name
      #Renamed check_names_match to validate_arrays and extended to perform probeset warning, external_db name guess and returns cache, user array param validation and association check
      #Merged delete_unampped objects into delete_existing_xrefs due to dependency. Now throws if arrays param set until force_delete specified, deletes using IN list
      #cache_arrays_per_probeset now uses arrays param to reduce size of cache
      #removed unmapped_object dbID = 2000>
      #Change all probe specific unmapped object to reeflect the individual probe rather than the probeset
      #Updated logs
      #Updated docs
      #Added control of promiscuous probesets and unmapped objects
      80aa6f99
  4. 11 Feb, 2008 1 commit
  5. 07 Feb, 2008 3 commits
  6. 06 Feb, 2008 1 commit
  7. 05 Feb, 2008 1 commit
  8. 01 Feb, 2008 1 commit
  9. 31 Jan, 2008 1 commit
  10. 29 Jan, 2008 12 commits
  11. 28 Jan, 2008 12 commits