9423dc741a1da8ffbee5d9b7ae6a49d00d3ed151,deepvariant/vcf_stats.py,,_get_variant_type,#Any#,66

Before Change

def _get_variant_type(variant):
  Returns the type of variant as a string.
  if variant_utils.is_biallelic(variant):
    if variant_utils.is_snp(variant):
      return "SNP"
    elif variant_utils.is_insertion(variant.reference_bases,
                                    variant.alternate_bases[0]):
      return "Insertion"
    elif variant_utils.is_deletion(variant.reference_bases,
                                   variant.alternate_bases[0]):
      return "Deletion"

  return "Other"


def _tstv(variant, vtype):

After Change

    insertion = all(
        variant_utils.is_insertion(variant.reference_bases, alt)
        for alt in variant.alternate_bases)
    deletion = all(
        variant_utils.is_deletion(variant.reference_bases, alt)
        for alt in variant.alternate_bases)

    if biallelic:
      if snp:
        return BIALLELIC_SNP

Instances