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

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

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  2. Remove gaps when tiling.

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

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

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  2. Open BGZF files in binary mode.

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    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.

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  2. Documented new options.

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  3. Improved informational logging.

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  4. Allow setting compression level.

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  5. Shut down execution on error.

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  6. Added Executor for parallel tasks in maf_bgzip.

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

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

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    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.
  9. Refactored Access to use #with_index.

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    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.

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  2. Set Kyoto Cabinet options on index file.

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    Enable linear mode, small mode, and periodic defragmentation.
  3. Improved logging for maf_bgzip.

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

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