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Commits on Jan 20, 2012
  1. update README

    James Casbon authored
  2. version bump

    James Casbon authored
  3. add FILTERS.md

    James Casbon authored
  4. add TODOs

    James Casbon authored
  5. vcf filter now inserts into meta, applies ok

    James Casbon authored
  6. argparse for python < 2.7

    James Casbon authored
  7. add vcf_filter.py script

    James Casbon authored
  8. add filter lines, but writer needs improvement

    James Casbon authored
  9. initial work on an extensible VCF filter

    James Casbon authored
  10. typo in HISTORY

    James Casbon authored
  11. writer now correctly writes metadata

    James Casbon authored
  12. git ignore

    James Casbon authored
Commits on Jan 19, 2012
  1. Remove ordereddict for performance, replace with genotype method for

    James Casbon authored
    lookup of genotypes
Commits on Jan 18, 2012
  1. speed optimisations, drop properties for direct access

    James Casbon authored
  2. test for 1kg files, allow QUAL=.

    James Casbon authored
Commits on Jan 17, 2012
  1. REST syntax fix

    James Casbon authored
  2. Support fetching from tabix files, fixes #7

    James Casbon authored
  3. support opening via filename and gzipped data

    James Casbon authored
Commits on Jan 16, 2012
  1. change vcf.VCFReader to vcf.Reader (docs)

    James Casbon authored
  2. change vcf.VCFReader to vcf.Reader

    James Casbon authored
  3. include VCFWriter class and test cases

    James Casbon authored
  4. update README.rst, add HISTORY, fix doctests

    James Casbon authored
  5. run doctest, fixes #5

    James Casbon authored
  6. remove redundant code now using ordereddict

    James Casbon authored
  7. use ordered dict for samples, fixes #2

    James Casbon authored
  8. include really basic tests

    James Casbon authored
  9. @martijnvermaat

    Tolerate negative Number values in INFO and FORMAT fields

    martijnvermaat authored James Casbon committed
    Negative values for the Number entry in INFO and FORMAT fields are not allowed
    by the VCF spec, but we see them in practice (samtools uses -1 in the PL
    format). We silently convert them to None or '.'.
Commits on Jan 12, 2012
  1. add meta to setup.py, note about fork to README

    James Casbon authored
  2. Merge remote-tracking branch 'upstream/master'

    James Casbon authored
Commits on Dec 18, 2011
  1. @jdoughertyii

    adding a license

    jdoughertyii authored
Commits on Nov 2, 2011
  1. convienience methods for changing a record

    James Casbon authored
Commits on Oct 30, 2011
  1. vcf_melt for turning wide tsv into long tsv

    James Casbon authored
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