public Variant(Interval parent, VariantContext variant, Chromosome chromosome)
: base(parent, variant.Chr, "", "+", variant.Start, variant.End, null)
{
Chromosome = chromosome;
VariantContext = variant;
ReferenceAllele = variant.Reference;
ReferenceAlleleString = variant.Reference.BaseString;
Genotype = variant.Genotypes.First(); // assumes just one sample
GenotypeType = Genotype.Type;
ReadDepth = Genotype.DP;
FirstAlleleDepth = Genotype.AD == null ? -1 : Genotype.AD[0];
SecondAlleleDepth = Genotype.AD == null ? -1 : Genotype.AD[1];
FirstAllele = Genotype.GetAllele(0);
FirstAlleleString = FirstAllele.BaseString;
SecondAllele = Genotype.GetAllele(1);
SecondAlleleString = SecondAllele.BaseString;
CalculateType();
if (variant.Attributes.TryGetValue("ANN", out object snpEffAnnotationObj))
{
if (snpEffAnnotationObj as string[] != null)
{
SnpEffAnnotations = (snpEffAnnotationObj as string[]).Select(x => new SnpEffAnnotation(this, x)).ToList();
}
if (snpEffAnnotationObj as string != null)
{
SnpEffAnnotations = new List <SnpEffAnnotation> {
new SnpEffAnnotation(this, snpEffAnnotationObj as string)
};
}
}
}
