/// <summary>
/// sometimes we get variant sites like this, below in the original vcf.
/// And in truth, the insertion should come after the C>T.
/// So, we reorder. Keeping this list ordered makes downstream calculations easier.
/// chr7 140453136 . A . 100 PASS
/// chr7 140453137 . C CGTA 52 PASS
/// chr7 140453137 . C T 58
/// </summary>
public void OrderVariantSitesByFirstTrueStartPosition()
{
var indexes = VcfVariantSites.Select(vs => vs.OriginalAlleleFromVcf).ToList();
VcfVariantSites.Sort();
for (int i = 0; i < VcfVariantSites.Count; i++)
{
VcfVariantSites[i].OriginalAlleleFromVcf = indexes[i];
}
}
public List <CalledAllele> GetOriginalVcfVariants()
{
return(VcfVariantSites.Select(vs => vs.OriginalAlleleFromVcf).ToList());
}
public bool LastPositionIsNotMatch(VariantSite variantSite)
{
return(VcfVariantSites.Last().VcfReferencePosition != variantSite.VcfReferencePosition);
}