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

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

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

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

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

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

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

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

    csw committed Aug 8, 2012
  2. Documented new options.

    csw committed Aug 8, 2012
  3. Allow setting compression level.

    csw committed Aug 8, 2012
  4. Shut down execution on error.

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

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

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

    csw committed Aug 8, 2012
    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.
  8. Refactored Access to use #with_index.

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

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

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

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

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

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