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Commits on Aug 21, 2012
  1. Documented new features.

    committed Aug 21, 2012
Commits on Aug 18, 2012
  1. Added debugging code.

    committed Aug 18, 2012
  2. Remove gaps when tiling.

    committed Aug 18, 2012
  3. Apparent no-op change for non_fill.

    committed Aug 18, 2012
Commits on Aug 15, 2012
  1. Added support for a comma-separated list with --species.

    For Galaxy support.
    committed Aug 15, 2012
Commits on Aug 13, 2012
Commits on Aug 9, 2012
  1. Added :upcase parser option.

    committed Aug 9, 2012
  2. Correctly indicate default log destination as stderr.

    Was stdout.
    committed Aug 9, 2012
  3. Open BGZF files in binary mode.

    Works around a possible bug in JRuby 1.7.0.preview2, and seems to
    improve performance a bit anyway.
    committed Aug 9, 2012
Commits on Aug 8, 2012
  1. Updated build date.

    committed Aug 8, 2012
  2. Documented new options.

    committed Aug 8, 2012
  3. Improved informational logging.

    committed Aug 8, 2012
  4. Allow setting compression level.

    committed Aug 8, 2012
  5. Shut down execution on error.

    committed Aug 8, 2012
  6. Added Executor for parallel tasks in maf_bgzip.

    Specifically, this lets a separate thread handle indexing under JRuby.
    committed Aug 8, 2012
  7. Added JobRunner tool for running parallel tasks.

    Uses threads on JRuby and fork() on MRI.
    committed Aug 8, 2012
  8. Only open indexes as needed in Access. Closes #109.

    Previously Access would hold all the KyotoIndex objects (and
    corresponding Kyoto Cabinet DB instances) open. This could lead to
    problematic memory consumption with a large set of indexes.
    committed Aug 8, 2012
  9. Refactored Access to use #with_index.

    This is preparatory for not holding all indexes open. It required
    returning Arrays instead of Enumerables when no block is given.
    committed Aug 8, 2012
Commits on Aug 7, 2012
  1. Track total struct size.

    committed Aug 7, 2012
  2. Set Kyoto Cabinet options on index file.

    Enable linear mode, small mode, and periodic defragmentation.
    committed Aug 7, 2012
  3. Validate index version. Closes #105.

    committed Aug 7, 2012
  4. Improved logging for maf_bgzip.

    committed Aug 7, 2012
Commits on Aug 6, 2012
  1. Added --one-based option. Treats all intervals as 1-based.

    Needed because some tools like Ensembl output BED files using 1-based
    intervals, even though this is against the standard.
    
    Closes #107.
    committed Aug 6, 2012