public void GetOriginalVcfIndexes()
{
var originalVar1 = new Pisces.Domain.Models.Alleles.CalledAllele()
{
ReferencePosition = 1
};
var originalVar10 = new Pisces.Domain.Models.Alleles.CalledAllele()
{
ReferencePosition = 10
};
var nbhd = new VcfNeighborhood(new VariantCallingParameters(), 0, "chr1", new VariantSite(123)
{
OriginalAlleleFromVcf = originalVar1
}
, new VariantSite(123)
{
OriginalAlleleFromVcf = originalVar10
}, "T");
var originalVcfIndexes = nbhd.GetOriginalVcfVariants();
Assert.Equal(2, originalVcfIndexes.Count);
Assert.Equal(1, originalVcfIndexes[0].ReferencePosition);
Assert.Equal(10, originalVcfIndexes[1].ReferencePosition);
}
public CalledAllele(CalledAllele originalAllele)
{
Chromosome = originalAllele.Chromosome;
ReferencePosition = originalAllele.ReferencePosition;
ReferenceAllele = originalAllele.ReferenceAllele;
AlternateAllele = originalAllele.AlternateAllele;
Genotype = originalAllele.Genotype;
GenotypeQscore = originalAllele.GenotypeQscore;
VariantQscore = originalAllele.VariantQscore;
NumNoCalls = originalAllele.NumNoCalls;
NoiseLevelApplied = originalAllele.NoiseLevelApplied;
TotalCoverage = originalAllele.TotalCoverage;
AlleleSupport = originalAllele.AlleleSupport;
WellAnchoredSupport = originalAllele.WellAnchoredSupport;
ReferenceSupport = originalAllele.ReferenceSupport;
Type = originalAllele.Type;
SupportByDirection = new int[Constants.NumDirectionTypes];
WellAnchoredSupportByDirection = new int[Constants.NumDirectionTypes];
EstimatedCoverageByDirection = new int[Constants.NumDirectionTypes];
ReadCollapsedCountsMut = new int[Constants.NumReadCollapsedTypes];
ReadCollapsedCountTotal = new int[Constants.NumReadCollapsedTypes];
StrandBiasResults = BiasResults.DeepCopy(originalAllele.StrandBiasResults);
UnanchoredCoverageWeight = originalAllele.UnanchoredCoverageWeight;
ConfidentCoverageStart = originalAllele.ConfidentCoverageStart;
ConfidentCoverageEnd = originalAllele.ConfidentCoverageEnd;
SuspiciousCoverageStart = originalAllele.SuspiciousCoverageStart;
SuspiciousCoverageEnd = originalAllele.SuspiciousCoverageEnd;
Filters = new List <FilterType>();
foreach (var filter in originalAllele.Filters)
{
Filters.Add(filter);
}
for (int i = 0; i < Constants.NumDirectionTypes; i++)
{
SupportByDirection[i] = originalAllele.SupportByDirection[i];
WellAnchoredSupportByDirection[i] = originalAllele.WellAnchoredSupportByDirection[i];
EstimatedCoverageByDirection[i] = originalAllele.EstimatedCoverageByDirection[i];
}
for (int i = 0; i < Constants.NumReadCollapsedTypes; i++)
{
ReadCollapsedCountsMut[i] = originalAllele.ReadCollapsedCountsMut[i];
ReadCollapsedCountTotal[i] = originalAllele.ReadCollapsedCountTotal[i];
}
}
public static CalledAllele DeepCopy(CalledAllele originalAllele)
{
if (originalAllele == null)
{
return(null);
}
var allele = new CalledAllele
{
Chromosome = originalAllele.Chromosome,
Coordinate = originalAllele.Coordinate,
Reference = originalAllele.Reference,
Alternate = originalAllele.Alternate,
Genotype = originalAllele.Genotype,
GenotypeQscore = originalAllele.GenotypeQscore,
VariantQscore = originalAllele.VariantQscore,
FractionNoCalls = originalAllele.FractionNoCalls,
NoiseLevelApplied = originalAllele.NoiseLevelApplied,
TotalCoverage = originalAllele.TotalCoverage,
AlleleSupport = originalAllele.AlleleSupport,
ReferenceSupport = originalAllele.ReferenceSupport,
Type = originalAllele.Type,
SupportByDirection = new int[Constants.NumDirectionTypes],
EstimatedCoverageByDirection = new int[Constants.NumDirectionTypes],
ReadCollapsedCounts = new int[Constants.NumReadCollapsedTypes],
StrandBiasResults = StrandBiasResults.DeepCopy(originalAllele.StrandBiasResults),
Filters = new List <FilterType>()
};
foreach (var filter in originalAllele.Filters)
{
allele.Filters.Add(filter);
}
for (int i = 0; i < Constants.NumDirectionTypes; i++)
{
allele.SupportByDirection[i] = originalAllele.SupportByDirection[i];
allele.EstimatedCoverageByDirection[i] = originalAllele.EstimatedCoverageByDirection[i];
allele.ReadCollapsedCounts[i] = originalAllele.ReadCollapsedCounts[i];
}
return(allele);
}
public AggregateAllele(CalledAllele originalAllele, List <CalledAllele> componentAlleles) : base(originalAllele)
{
ComponentAlleles = componentAlleles;
}
public bool IsCoLocatedAllele(CalledAllele otherAllele)
{
return((otherAllele.Chromosome == Chromosome) &&
(otherAllele.ReferencePosition == ReferencePosition));
}
