1. 16 Dec, 2019 2 commits
  2. 09 Dec, 2019 1 commit
  3. 04 Dec, 2019 1 commit
  4. 03 Dec, 2019 1 commit
  5. 02 Dec, 2019 1 commit
  6. 26 Nov, 2019 1 commit
  7. 25 Nov, 2019 5 commits
  8. 19 Nov, 2019 1 commit
  9. 12 Nov, 2019 2 commits
  10. 04 Nov, 2019 1 commit
    • rrvandenberg's avatar
      Add test cases for missing ALT in call vcf · 955802ec
      rrvandenberg authored
      When a vcf file contains calls for all specified positions, the ALT field will
      be empty if there is only a reference call in that position. This commits adds
      tests for this case.
      955802ec
  11. 25 Oct, 2019 3 commits
    • rrvandenberg's avatar
      Fixed bug with partial no calls · 0ab4c701
      rrvandenberg authored
      To fix this, we had to rewrite the logic used when comparing variants.
      As a side effect, 'allele_no_call' is now only counted for partial calls
      when they occur in the call set. The test case
      test_partial_positive_no_call was updated to reflect this change.
      
      Also fixed an error where the known and called variants were switched
      when they were being passed to parse_variants.
      0ab4c701
    • rrvandenberg's avatar
      bbb226bc
    • rrvandenberg's avatar
      Add test cases where the ALT and REF differ · b63f7cb0
      rrvandenberg authored
      The actual genotypes are the same between gatk.vcf and
      gatk_ref_alt_changed.vcf, but the REF, ALT and corresponding genotype
      calls differ. This is to test if the conversion of genotype call
      (e.g. 1/3) to the actual genotype (e.g. A/T) is working as intended.
      b63f7cb0
  12. 24 Oct, 2019 7 commits
  13. 23 Oct, 2019 1 commit
    • rrvandenberg's avatar
      Compare allele genotypes directly · fb075df9
      rrvandenberg authored
      Previously we used cyvcf2 gt_types, which indicate whether a site is
      hom_ref, heterozygous, hom_alt or unknown. A limitation of this approach
      is that it only makes sense when the two vcf files have the same REF and
      ALT alleles for a given position.
      
      If this was not the case, vtools would silently skip the variant.
      However, even when the ALT alleles are different between two vcf files,
      the actual genotypes can still be compared. This was implemented in this
      commit, which also fixes issue #8.
      fb075df9
  14. 22 Oct, 2019 8 commits
  15. 27 Aug, 2019 4 commits
  16. 26 Aug, 2019 1 commit