private static bool CheckIfUsed(List <CalledAllele> usedAlleles, CalledAllele originalCall)
{
foreach (var allele in usedAlleles)
{
if (originalCall.IsSameAllele(allele))
{
return(true);
}
}
return(false);
}
public static void CheckVariantsMatch(CalledAllele baseline, CalledAllele test)
{
Assert.True(test.IsSameAllele(baseline));
Assert.Equal(baseline.Genotype, test.Genotype);
}
public static VariantComparisonCase GetComparisonCase(CalledAllele VariantA, CalledAllele VariantB)
{
//if we have two or more different alternates, it should have already have been split up, upstream,
//into two or more entries to be processed ie, (alt, null) and (alt' ,nul).
//So if we have a (VariantB == null) or (VariantA == null) situation, we know its TwoDifferentAlternates;
if ((VariantB == null) || (VariantA == null))
{
return(VariantComparisonCase.CanNotCombine);
}
//sanity checking - these input should never be allowed.
if (VariantA.Chromosome != VariantB.Chromosome)
{
throw new InvalidDataException("Check input variants to var compare algs.");
}
if (VariantA.ReferencePosition != VariantB.ReferencePosition)
{
throw new InvalidDataException("Check input variants to var compare algs.");
}
//now several reasonable cases remain. we are only accepting the following cases as "possible to combine"
//
// . + . -> . (treat as twos refs)
// ref + . -> ref (treat as twos refs)
// alt + . -> alt (treat as one ref, one alt)
// Ref + ref -> ref
// alt + alt -> alt (0/1 or 1/1)
// ref + alt -> alt (filtered)
//this case below, is not allowed.
// alt + alt' -> alt/alt' (filtered -> should not come into this algorithm)
// intead this will go through the algorithm twice, as one (alt + null) and another (null + alt')
//the no-calls GT will be preverved by the CombineGT algorthm.
bool RefA = (VariantA.Type == Pisces.Domain.Types.AlleleCategory.Reference);
bool RefB = (VariantB.Type == Pisces.Domain.Types.AlleleCategory.Reference);
if (RefA && RefB)
{
return(VariantComparisonCase.AgreedOnReference);
}
if ((RefA && !RefB) || (!RefA && RefB))
{
return(VariantComparisonCase.OneReferenceOneAlternate);
}
if (VariantA.IsSameAllele(VariantB))
{
return(VariantComparisonCase.AgreedOnAlternate);
}
else
{
//we could have different variants *or* different references (ie, in the case of a deletion)
// (this should not happen - these should never be submitted for comparison to this alg.)
throw new InvalidDataException("Check input variants to var compare algs.");
}
}