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Jun 27, 2012

  1. Bump version to 0.5.0

    James Casbon authored
  2. enable travis on py3.2 fixes #56

    James Casbon authored
  3. Merge pull request #59 from msabramo/py32

    Python 3.2 compatibility tweaks
    James Casbon authored
  4. Merge pull request #58 from lennax/lenna

    For pair formatting, check that a flag is true
    James Casbon authored

Jun 26, 2012

  1. Marc Abramowitz

    Python 3 compatibility

    msabramo authored
  2. Lenna Peterson

    Check that flag is true.

    lennax authored
  3. Marc Abramowitz

    vcf/__init__.py: Use absolute imports for better Python 3 compatibility

    msabramo authored
  4. fix syntax error from PR

    James Casbon authored
  5. Merge pull request #54 from msabramo/tox

    Add support for tox (http://tox.testrun.org/)
    James Casbon authored
  6. Merge pull request #55 from cmclean/master

    Modifications to have Writer output match Reader input
    James Casbon authored
  7. use first line of filter docstring in FILTER meta, update README

    James Casbon authored
  8. add filters from @libor-m

    James Casbon authored
  9. add doctests for breakends, fix str for breakends and add to tests

    James Casbon authored
  10. disable python 3 travis, for the moment, HISTORY, better docs

    James Casbon authored
  11. Merge branch 'master' of github.com:jamescasbon/PyVCF

    James Casbon authored
  12. Merge pull request #22 from martijnvermaat/trim-variant

    Trim variant
    James Casbon authored

Jun 25, 2012

  1. Cory McLean

    Modify Writer to output FILTER field properly for multiple filters:

      * Writes as ";"-delimited string rather than the Python list representation
      * Writes non-existent or "PASS" filters as "PASS" rather than "."
    
    Modify Writer to output INFO field properly:
      * Writes Flag outputs just as present, not using the X=Y format
      * E.g. the DB flag to indicate presence in dbSNP will be written as "DB", rather than as "DB=True"
    
    Modify Writer to allow different line terminator to be used:
      * Default remains "\r\n" for backward compatibility
    cmclean authored
  2. Marc Abramowitz

    Add .tox to .gitignore

    msabramo authored
  3. Marc Abramowitz

    Add tox.ini for tox (http://tox.testrun.org/)

    msabramo authored
  4. LICENCSE update

    James Casbon authored
  5. store multiple metadata values with the same key, closes #52

    James Casbon authored
  6. repr for SV

    James Casbon authored
  7. Add error bias filter

    James Casbon authored
  8. Merge pull request #53 from lennax/lenna

    Fix writing of Number=A and G INFO/FORMAT fields
    James Casbon authored
  9. reenable doctests, PEP8 enhancements

    James Casbon authored

Jun 21, 2012

  1. Lenna Peterson

    Fix ALT writing ('.' for None).

    lennax authored

Jun 20, 2012

  1. Lenna Peterson

    Removing _map; in header only Number can be None

    lennax authored
  2. Lenna Peterson

    Refactor metadata writing: fix incorrect Number.

    lennax authored
  3. Lenna Peterson

    More extensible conversion of header field counts.

    lennax authored

Jun 18, 2012

  1. ignore noseids

    James Casbon authored
  2. Merge pull request #51 from lennax/lenna

    Make metadata RE reluctant (stop on first = not last)
    James Casbon authored

Jun 16, 2012

  1. Lenna Peterson

    Make metadata RE reluctant (stop on first =)

    lennax authored

Jun 15, 2012

  1. Merge pull request #48 from dzerbino/altClasses

    Alt classes
    James Casbon authored
  2. remove print left in

    James Casbon authored
  3. #49 allow malformed INFO string fields

    James Casbon authored
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