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

    Allow partially-called genotypes to be considered called
    martijnvermaat committed on GitHub Feb 15, 2017
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
  1. handle empty string as none

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

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

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

    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.
    sambrightman committed with martijnvermaat Jan 26, 2017
  3. Merge branch 'pr-228'

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

    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
    rwness committed with martijnvermaat Mar 9, 2016
Commits on Oct 21, 2016
  1. Merge pull request #253 from adamnovak/patch-1

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

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

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

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

    Redmar committed Aug 22, 2016
Commits on Aug 14, 2016
  1. Merge pull request #248 from Redmar-van-den-Berg/is_filt

    Is filt
    martijnvermaat committed on GitHub Aug 14, 2016
Commits on Aug 13, 2016
  1. Minor code cleanup

    Redmar committed Aug 13, 2016
Commits on Aug 11, 2016
  1. Merge pull request #247 from Redmar-van-den-Berg/issue246

    Issue246
    martijnvermaat committed on GitHub Aug 11, 2016
Commits on Aug 1, 2016
  1. Implemented is_filt for _Call and _Record

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

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

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

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

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

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

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