bb621f07cb33b6e8ab46c3d7b6d51db7bd8dba68,deepvariant/haplotypes.py,,_nonref_genotype_count,#Any#,487

Before Change

def _nonref_genotype_count(variant):
  Returns the number of non-reference alleles in the called genotype.
  if len(variant.calls) != 1:
    raise ValueError(
        "Expecting only single-sample variant calls: {}".format(variant))
  return sum(g > 0 for g in variant.calls[0].genotype)

After Change

def _nonref_genotype_count(variant):
  Returns the number of non-reference alleles in the called genotype.
  return sum(g > 0 for g in variant_utils.only_call(variant).genotype)

Instances