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Here are some improvements that are planned for future releases.
Updated Apr 23, 2010 by aaronqui...@gmail.com
  1. Continued integration of native BAM support.
  2. Native support for "gzipped" BED and GFF files.
  3. New tool: annotateBed. Will allow one to compare one BED file to many others in a single command.
  4. Reduced memory consumption and increased speed.
  5. Potential "drawing" tools for overlaps, etc.
  6. Multi-threading for processing BAM files.

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