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Commits on Feb 15, 2017
  1. Merge pull request #266 from sambrightman/called-definition

    martijnvermaat committed Feb 15, 2017
    Allow partially-called genotypes to be considered called
Commits on Feb 14, 2017
Commits on Feb 5, 2017
Commits on Feb 2, 2017
  1. CR comments

    ericman93 committed Feb 2, 2017
Commits on Feb 1, 2017
Commits on Jan 29, 2017
  1. Merge pull request #263 from sambrightman/travis

    martijnvermaat committed Jan 29, 2017
    Fix Travis tests
Commits on Jan 28, 2017
Commits on Jan 26, 2017
  1. Merge pull request #259 from sambrightman/singleton-list

    martijnvermaat committed Jan 26, 2017
    Always use a list for list-type fields
  2. Always use a list for list-type fields

    sambrightman authored and martijnvermaat committed Jan 26, 2017
    Singleton lists - e.g. Number=A with a single allele - are now parsed
    into lists instead of being treated as single values. This is more
    consistent with the meaning of the field definition and thus easier
    for client code.
    
    Fixes #254.
  3. Merge branch 'pr-228'

    martijnvermaat committed Jan 26, 2017
    Closes #228
  4. Correct indel definition

    rwness authored and martijnvermaat committed Mar 9, 2016
    1. Corrected RECORD.is_indel to not call reference sites as indels
    2. Corrected RECORD.is_deletion to not call reference sites as deletions
    3. Added deletion site to vcf/test/example-4.0.vcf
    4. Added deletion site to vcf/test/walk_left.vcf
    5. Corrected tests to account for site 1230237 not being an indel or
    deletion
    5. Added tests for new site 1231234 which is an actual deletion
Commits on Oct 21, 2016
  1. Merge pull request #253 from adamnovak/patch-1

    martijnvermaat committed Oct 21, 2016
    Fix docstring spelling
Commits on Oct 19, 2016
  1. Fix docstring spelling

    adamnovak committed Oct 19, 2016
Commits on Sep 6, 2016
  1. Merge pull request #250 from Redmar-van-den-Berg/write_FT

    martijnvermaat committed Sep 6, 2016
    Added support for writing FT annotations
Commits on Sep 5, 2016
  1. Removed code duplication

    Redmar
    Redmar committed Sep 5, 2016
Commits on Aug 22, 2016
  1. Added support for writing FT annotations

    Redmar
    Redmar committed Aug 22, 2016
Commits on Aug 14, 2016
Commits on Aug 13, 2016
  1. Minor code cleanup

    Redmar
    Redmar committed Aug 13, 2016
Commits on Aug 11, 2016
Commits on Aug 1, 2016
  1. Implemented is_filt for _Call and _Record

    Redmar
    Redmar committed Aug 1, 2016
Commits on Jul 31, 2016
  1. Added FT as a special case when parsing format

    trijntje trijntje
    trijntje authored and trijntje committed Jul 31, 2016
  2. Added example file and 2 testcases

    trijntje trijntje
    trijntje authored and trijntje committed Jul 31, 2016
  3. Moved code into Reader._parse_filter so it can be reused for FT

    trijntje trijntje
    trijntje authored and trijntje committed Jul 31, 2016
Commits on Jul 21, 2016
  1. Merge pull request #244 from bow/fix-issue243

    martijnvermaat committed Jul 21, 2016
    Fixes for GitHub issue #243
  2. Fixes for GitHub issue #243

    bow committed Jul 21, 2016
Commits on Jul 3, 2016
  1. Merge pull request #238 from rwness/patch-2

    martijnvermaat committed Jul 3, 2016
    Typo in ALT header line error message in parser.py
Commits on Jun 29, 2016
  1. Update parser.py

    rwness committed Jun 29, 2016
    I think this was a typo and gives a misleading error message
Commits on Jun 15, 2016
  1. Merge pull request #235 from jsmedmar/master

    martijnvermaat committed Jun 15, 2016
    allows info_pattern to match empty values. Fixes #234