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Commits on Dec 7, 2012
  1. README fix again

    committed Dec 7, 2012
  2. README fix

    committed Dec 7, 2012
  3. Update README.rdoc

    committed Dec 7, 2012
Commits on Dec 1, 2012
Commits on Nov 5, 2012
  1. Version bump to 0.1.0

    Ben J. Woodcroft committed Nov 5, 2012
Commits on Aug 31, 2012
  1. Fix bug where bin/gag was not correctly passing along the sequence co…

    …ntexts to PileupIterator
    Ben J. Woodcroft committed Aug 31, 2012
  2. more cmdline options and requirements, documentation

    Ben J. Woodcroft committed Aug 31, 2012
Commits on May 18, 2012
  1. more doco

    Ben J. Woodcroft committed May 18, 2012
  2. Add reference to Loman et. al. 2012

    Ben J. Woodcroft committed May 18, 2012
Commits on May 17, 2012
  1. Rakefile_update

    Ben J. Woodcroft committed May 17, 2012
  2. fix tests so they are proper pileup format - tabs not spaces

    Ben J. Woodcroft committed May 17, 2012
  3. Version bump to 0.0.1

    Ben J. Woodcroft committed May 17, 2012
  4. finished adding support for a whitelisted set of possible GAG errors …

    …and abandoning the XYX filter
    Ben J. Woodcroft committed May 17, 2012
Commits on May 16, 2012
  1. started integrating more specific cases for fixing GAG errors, breaki…

    …ng things
    Ben J Woodcroft committed May 16, 2012
  2. modified README to be more specific and helpful

    Ben J Woodcroft committed May 16, 2012
Commits on May 9, 2012
  1. update doco

    Ben J. Woodcroft committed May 9, 2012
Commits on Apr 10, 2012
  1. allow double-checking of gag errors by comparison with open reading f…

    …rames
    Ben J. Woodcroft committed Apr 10, 2012
Commits on Apr 4, 2012
  1. gitignores, properly indent bin/gag, change how bin/gag arguments are…

    … handled internally
    Ben J. Woodcroft committed Apr 4, 2012
  2. various fixes, particularly don't accept gagging reads that have mism…

    …atches in the X of the XYX
    Ben J. Woodcroft committed Apr 4, 2012
Commits on Apr 2, 2012
  1. point to the no_debug pileup_iterator

    Ben J Woodcroft committed Apr 2, 2012
  2. remove debug comments

    Ben J Woodcroft committed Apr 2, 2012
  3. stderr not stdout by default

    Ben J Woodcroft committed Apr 2, 2012
  4. default to stderr not stdout for logging, fix warning message when so…

    …me gags have no sequences to fix
    Ben J Woodcroft committed Apr 2, 2012
  5. remove dependence on Bio::Faster, test for sequences that have commen…

    …ts and sequences that are devoid of gag errors
    Ben J Woodcroft committed Apr 2, 2012
  6. initial commit

    Ben J Woodcroft committed Apr 2, 2012
  7. Version bump to 0.0.0

    Ben J Woodcroft committed Apr 2, 2012
  8. Initial commit to bio-gag.

    Ben J Woodcroft committed Apr 2, 2012