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  1. 24 May, 2010 4 commits
    • cvs2git's avatar
      This commit was manufactured by cvs2svn to create tag 'before-EG-patch'. · ceb34f0e
      cvs2git authored
      Sprout from master 2010-05-24 12:52:11 UTC Andreas Kusalananda Kähäri <ak4@sanger.ac.uk> 'Punish stable IDs that change biotype harder.'
      Delete:
          LICENSE
          docs/ensembl_changes_spec.txt
          docs/ensembl_das/Homo_sapiens.ini
          docs/ensembl_das/demo.ini
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          misc-scripts/alternative_splicing/AltSplicingToolkit/AUTHORS
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          misc-scripts/alternative_splicing/AltSplicingToolkit/NEWS
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          misc-scripts/alternative_splicing/AltSplicingToolkit/THANKS
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          misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/TranscriptFeature.h
          misc-scripts/alternative_splicing/AltSplicingToolkit/src/gff/BioMartGffHandler.cpp
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          misc-scripts/alternative_splicing/AltSplicingToolkit/src/gff/GffEventModel.cpp
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          modules/t/test-genome-DBs/homo_sapiens/core/xref.sql
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          modules/t/topLevelAssemblyMapper.t
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      ceb34f0e
    • Andreas Kusalananda Kähäri's avatar
    • Andreas Kusalananda Kähäri's avatar
      Small fixes. · 0baafddc
      Andreas Kusalananda Kähäri authored
      0baafddc
    • Andreas Kusalananda Kähäri's avatar
      By default, optimize the tables on the source database server. This is · fa96f28e
      Andreas Kusalananda Kähäri authored
      to flush index data to file before copying.
      
      Add new flag:
      
        --noopt           (Optional)
                          Skip the optimization step.  The database tables are
                          optimized (as with "OPTIMIZE TABLE") to flush the
                          index data onto disk.  This may be a time consuming
                          operation for very large tables.  The --noopt flag
                          disables the optimization.
      fa96f28e
  2. 21 May, 2010 4 commits
  3. 20 May, 2010 1 commit
  4. 19 May, 2010 3 commits
  5. 17 May, 2010 3 commits
  6. 14 May, 2010 1 commit
  7. 12 May, 2010 1 commit
  8. 11 May, 2010 1 commit
  9. 07 May, 2010 1 commit
  10. 06 May, 2010 5 commits
    • Andreas Kusalananda Kähäri's avatar
      Added new 'species' argument to load_registry_from_db(): · 4b3a1051
      Andreas Kusalananda Kähäri authored
      Arg [SPECIES]:  (optional) string
                      By default, all databases that are found on the server
                      and that corresponds to the correct release are probed
                      for aliases etc.  For some people, depending on where
                      they are in the world, this might be a slow operation.
                      With the '-species' argument, one may reduce the startup
                      time by restricting the set of databases that are probed
                      to those of a particular species.
      
                      Note that the latin name of the species is required,
                      e.g., 'homo sapiens', 'gallus gallus', 'callithrix
                      jacchus' etc.  It may be the whole species name, or only
                      the first part of the name, e.g. 'homo', 'gallus', or
                      'callithrix'.  This will be used in matching against the
                      name of the databases.
      4b3a1051
    • Eugene Kulesha's avatar
      another typo · d10f6768
      Eugene Kulesha authored
      d10f6768
    • Eugene Kulesha's avatar
      fixed a typo · cc5830e9
      Eugene Kulesha authored
      cc5830e9
    • Ian Longden's avatar
      LRGSlice fixes · 4a9b9a8d
      Ian Longden authored
      4a9b9a8d
    • Ian Longden's avatar
      fixes for LRGSlices and new methods to find nearest gene to a feature (this... · 5bd6ce87
      Ian Longden authored
      fixes for LRGSlices and new methods to find nearest gene to a feature (this will change greatly as this is a very simple case)
      5bd6ce87
  11. 05 May, 2010 3 commits
  12. 04 May, 2010 4 commits
  13. 23 Apr, 2010 1 commit
  14. 22 Apr, 2010 4 commits
  15. 21 Apr, 2010 1 commit
  16. 20 Apr, 2010 3 commits