private static void CheckSimpleCombinations(
CalledAllele VarA, CalledAllele VarB, ConsensusBuilder cb,
Genotype ExpectedGT, string ExpectedAlt,
VariantComparisonCase ComparisonCase)
{
var AandB = cb.CombineVariants(VarA, VarB, ComparisonCase);
var BandA = cb.CombineVariants(VarB, VarA, ComparisonCase);
var AandNull = cb.CombineVariants(VarA, null, VariantComparisonCase.CanNotCombine);
var NullAndB = cb.CombineVariants(null, VarB, VariantComparisonCase.CanNotCombine);
int ExpectedAlleleCount = VarA.AlleleSupport + VarB.AlleleSupport;
if (ComparisonCase == VariantComparisonCase.OneReferenceOneAlternate)
{
//for this test, we presume we are calling alternate.
ExpectedAlleleCount = (VarA.Type == AlleleCategory.Snv) ? VarA.AlleleSupport : VarB.AlleleSupport;
}
//check alt-and-nocalls
Assert.Equal(ExpectedGT, AandB.Genotype);
Assert.Equal(VarA.ReferenceAllele, AandB.ReferenceAllele);
Assert.Equal(ExpectedAlt, AandB.AlternateAllele);
Assert.Equal(VarA.TotalCoverage + VarB.TotalCoverage, AandB.TotalCoverage);
Assert.Equal(ExpectedAlleleCount, AandB.AlleleSupport);
Assert.Equal(ExpectedGT, BandA.Genotype);
Assert.Equal(VarA.ReferenceAllele, BandA.ReferenceAllele);
Assert.Equal(ExpectedAlt, BandA.AlternateAllele);
Assert.Equal(VarA.TotalCoverage + VarB.TotalCoverage, BandA.TotalCoverage);
Assert.Equal(ExpectedAlleleCount, BandA.AlleleSupport);
Assert.Equal(ConsensusBuilder.DoDefensiveGenotyping(VarA), AandNull.Genotype);
Assert.Equal(VarA.ReferenceAllele, AandNull.ReferenceAllele);
Assert.Equal(VarA.AlternateAllele, AandNull.AlternateAllele);
Assert.Equal(VarA.TotalCoverage, AandNull.TotalCoverage);
Assert.Equal(VarA.AlleleSupport, AandNull.AlleleSupport);
Assert.Equal(ConsensusBuilder.DoDefensiveGenotyping(VarB), NullAndB.Genotype);
Assert.Equal(VarB.ReferenceAllele, NullAndB.ReferenceAllele);
Assert.Equal(VarB.AlternateAllele, NullAndB.AlternateAllele);
Assert.Equal(VarB.TotalCoverage, NullAndB.TotalCoverage);
Assert.Equal(VarB.AlleleSupport, NullAndB.AlleleSupport);
}
public void VennVcf_CombineTwoPoolVariants_Qscore_DiffentNL_Test()
{
//chr3 41266161 . A G 30 PASS DP=3067 GT:GQ:AD:VF:NL:SB 0/1:30:3005,54:0.0176:35:-100.0000
CalledAllele VarA = new CalledAllele()
{
Chromosome = "chr3",
ReferencePosition = 41266161,
TotalCoverage = 3067,
Genotype = Pisces.Domain.Types.Genotype.HeterozygousAltRef,
VariantQscore = 30,
GenotypeQscore = 30,
AlleleSupport = 54,
ReferenceSupport = 3005,
NoiseLevelApplied = 35,
StrandBiasResults = new Pisces.Domain.Models.BiasResults()
{
GATKBiasScore = -100.0000
},
ReferenceAllele = "A",
AlternateAllele = "G",
Type = Pisces.Domain.Types.AlleleCategory.Snv
};
///chr3 41266161 . A . 75 PASS DP=3795 GT:GQ:AD:VF:NL:SB 0/0:75:3780:0.0040:2:-100.0000
CalledAllele VarB = new CalledAllele()
{
Chromosome = "chr3",
ReferencePosition = 41266161,
TotalCoverage = 3795,
Genotype = Pisces.Domain.Types.Genotype.HomozygousRef,
VariantQscore = 75,
GenotypeQscore = 75,
AlleleSupport = 3780,
ReferenceSupport = 3780,
NoiseLevelApplied = 2,
StrandBiasResults = new Pisces.Domain.Models.BiasResults()
{
GATKBiasScore = -100.0000
},
ReferenceAllele = "A",
AlternateAllele = ".",
Type = Pisces.Domain.Types.AlleleCategory.Reference
};
//old answer
//chr3 41266161 . A . 100.00 PASS DP=6862;cosmic=COSM1423020,COSM1423021;EVS=0|69.0|6503;phastCons GT:GQ:AD:VF:NL:SB:PB:GQX 0/0:100:6785:0.0079:35:-100:-100.0000:100
SampleAggregationParameters SampleAggregationOptions = new SampleAggregationParameters();
SampleAggregationOptions.ProbePoolBiasThreshold = 0.5f;
SampleAggregationOptions.HowToCombineQScore = SampleAggregationParameters.CombineQScoreMethod.CombinePoolsAndReCalculate;
_basicOptions.BamFilterParams.MinimumBaseCallQuality = 20;
_basicOptions.VariantCallingParams.MinimumFrequency = 0.01f;
_basicOptions.VariantCallingParams.MinimumFrequencyFilter = 0.03f;
_basicOptions.SampleAggregationParameters = SampleAggregationOptions;
string consensusOut = Path.Combine(_TestDataPath, "ConsensusOut.vcf");
VariantComparisonCase ComparisonCase = VennProcessor.GetComparisonCase(VarA, VarB);
ConsensusBuilder consensusBuilder = new ConsensusBuilder(consensusOut, _basicOptions);
AggregateAllele consensus = consensusBuilder.CombineVariants(VarA, VarB, ComparisonCase);
Console.WriteLine(consensus.ToString());
double expectedNoiseLevel = MathOperations.PtoQ(
(MathOperations.QtoP(35) + MathOperations.QtoP(2)) / (2.0)); // 5
//GT:GQ:AD:VF:NL:SB:PB:GQX 0/0:100:6785:0.0079:35:-100:-100.0000:100
Assert.NotNull(consensus);
Assert.Equal(consensus.VariantQscore, 100);
Assert.Equal(consensus.ReferenceAllele, "A");
Assert.Equal(consensus.AlternateAllele, ".");
Assert.Equal(consensus.Genotype, Pisces.Domain.Types.Genotype.HomozygousRef);
Assert.Equal(consensus.TotalCoverage, 6862);
Assert.Equal(consensus.ReferenceSupport, 6785);
Assert.Equal(consensus.AlleleSupport, 6785);
Assert.Equal(consensus.GenotypeQscore, 100);
Assert.Equal(consensus.Frequency, 0.98877877f);
Assert.Equal(consensus.NoiseLevelApplied, ((int)expectedNoiseLevel));
Assert.Equal(consensus.NoiseLevelApplied, 5);
Assert.Equal(consensus.StrandBiasResults.GATKBiasScore, -100);
Assert.Equal(consensus.PoolBiasResults.GATKBiasScore, -100.0000);
//now check, we take the min NL score if we are taking the min Q score.
// (in this case of combined alt+ref -> ref, the q score will still need to be recalculated.
//just with the MIN NL.
SampleAggregationOptions.HowToCombineQScore = SampleAggregationParameters.CombineQScoreMethod.TakeMin;
ComparisonCase = VennProcessor.GetComparisonCase(VarA, VarB);
consensus = consensusBuilder.CombineVariants(VarA, VarB, ComparisonCase);
Assert.Equal(consensus.NoiseLevelApplied, 2);
Assert.Equal(consensus.VariantQscore, 100);
//ok, now sanity check we dont barf if either input is null:
ComparisonCase = VennProcessor.GetComparisonCase(VarA, null);
consensus = consensusBuilder.CombineVariants(VarA, null, ComparisonCase);
Assert.Equal(consensus.NoiseLevelApplied, 35);
Assert.Equal(consensus.VariantQscore, 100);
ComparisonCase = VennProcessor.GetComparisonCase(null, VarB);
consensus = consensusBuilder.CombineVariants(null, VarB, ComparisonCase);
Assert.Equal(consensus.NoiseLevelApplied, 2);
Assert.Equal(consensus.VariantQscore, 100);
//ok, lets check this again, for the PoolQScores option.
//sanity check we dont barf if either input is null:
SampleAggregationOptions.HowToCombineQScore = SampleAggregationParameters.CombineQScoreMethod.CombinePoolsAndReCalculate;
ComparisonCase = VennProcessor.GetComparisonCase(VarA, null);
consensus = consensusBuilder.CombineVariants(VarA, null, ComparisonCase);
Assert.Equal(consensus.NoiseLevelApplied, 35);
Assert.Equal(consensus.VariantQscore, 100);//low freq variant -> nocall. note, qscore would be 41 if NL = 20.
ComparisonCase = VennProcessor.GetComparisonCase(null, VarB);
consensus = consensusBuilder.CombineVariants(null, VarB, ComparisonCase);
Assert.Equal(consensus.NoiseLevelApplied, 2);
Assert.Equal(consensus.VariantQscore, 100); //sold ref
}
public void VennVcf_CombineTwoPoolVariants_Qscore_Test()
{
//Var A, kdot-43_S3.genome.vcf
//chr3 41266161 . A G 30 PASS DP=3067 GT:GQ:AD:VF:NL:SB 0/1:30:3005,54:0.0176:35:-100.0000
CalledAllele VarA = new CalledAllele();
VarA.Chromosome = "chr3";
VarA.ReferencePosition = 41266161;
VarA.TotalCoverage = 3067;
VarA.Genotype = Pisces.Domain.Types.Genotype.HeterozygousAltRef;
VarA.GenotypeQscore = 30;
VarA.AlleleSupport = 54;
VarA.ReferenceSupport = 3005;
// "VF", "0.0176"
VarA.NoiseLevelApplied = 35;
VarA.StrandBiasResults = new Pisces.Domain.Models.BiasResults()
{
GATKBiasScore = -100
};
VarA.ReferenceAllele = "A";
VarA.AlternateAllele = "G";
VarA.Filters = new List <Pisces.Domain.Types.FilterType>();
VarA.VariantQscore = 30;
VarA.Type = Pisces.Domain.Types.AlleleCategory.Snv;
//Var B, kdot-43_S4.genome.vcf
//chr3 41266161 . A . 75 PASS DP=3795 GT:GQ:AD:VF:NL:SB 0/0:75:3780:0.0040:35:-100.0000
CalledAllele VarB = new CalledAllele();
VarB.Chromosome = "chr3";
VarB.ReferencePosition = 41266161;
VarB.TotalCoverage = 3795;
VarB.Genotype = Pisces.Domain.Types.Genotype.HomozygousRef;
VarB.GenotypeQscore = 75;
VarB.AlleleSupport = 3780;
VarB.ReferenceSupport = 3780;
// "VF", "0.0040"
VarB.NoiseLevelApplied = 35;
VarB.StrandBiasResults = new Pisces.Domain.Models.BiasResults()
{
GATKBiasScore = -100
};
VarB.ReferenceAllele = "A";
VarB.AlternateAllele = ".";
VarB.Filters = new List <Pisces.Domain.Types.FilterType>();
VarB.VariantQscore = 75;
VarB.Type = Pisces.Domain.Types.AlleleCategory.Reference;
//old answer
//chr3 41266161 . A . 100.00 PASS DP=6862;cosmic=COSM1423020,COSM1423021;EVS=0|69.0|6503;phastCons GT:GQ:AD:VF:NL:SB:PB:GQX 0/0:100:6785:0.0079:35:-100:-100.0000:100
VennVcfOptions parameters = new VennVcfOptions();
parameters.VariantCallingParams.MinimumFrequencyFilter = 0.03f;
parameters.VariantCallingParams.MinimumFrequency = 0.01f;
parameters.BamFilterParams.MinimumBaseCallQuality = 20;
parameters.SampleAggregationParameters.ProbePoolBiasThreshold = 0.5f;
parameters.SampleAggregationParameters.HowToCombineQScore = SampleAggregationParameters.CombineQScoreMethod.TakeMin;
VariantComparisonCase ComparisonCase = VennProcessor.GetComparisonCase(VarA, VarB);
ConsensusBuilder consensusBuilder = new ConsensusBuilder("", parameters);
AggregateAllele consensus = consensusBuilder.CombineVariants(VarA, VarB, ComparisonCase);
//GT:GQ:AD:VF:NL:SB:PB:GQX 0/0:100:6785:0.0079:35:-100:-100.0000:100
Assert.NotNull(consensus);
Assert.Equal(consensus.VariantQscore, 100);
Assert.Equal(consensus.GenotypeQscore, 100);
Assert.Equal(consensus.ReferenceAllele, "A");
Assert.Equal(consensus.AlternateAllele, ".");
Assert.Equal(consensus.Genotype, Pisces.Domain.Types.Genotype.HomozygousRef);
Assert.Equal(consensus.GenotypeQscore, 100);
Assert.Equal(consensus.AlleleSupport, 6785);
Assert.Equal(consensus.ReferenceSupport, 6785);
Assert.Equal(consensus.TotalCoverage, 6862);
Assert.Equal(consensus.Frequency, 0.98877, 4);
Assert.Equal(consensus.NoiseLevelApplied, 35);
Assert.Equal(consensus.StrandBiasResults.GATKBiasScore, -100);
Assert.Equal(consensus.PoolBiasResults.GATKBiasScore, -100);
}
public void VennVcf_CombineTwoPoolVariants_RulesAthroughD_Tests()
{
var outDir = TestPaths.LocalScratchDirectory;
var VcfPathRoot = _TestDataPath;
string OutputPath = Path.Combine(outDir, "outEandF.vcf");
if (File.Exists(OutputPath))
{
File.Delete(OutputPath);
}
VennVcfOptions parameters = new VennVcfOptions();
parameters.VariantCallingParams.MinimumFrequencyFilter = 0.03f;
parameters.VariantCallingParams.MinimumFrequency = 0.01f;
parameters.ConsensusFileName = OutputPath;
string VcfPath_PoolA = Path.Combine(VcfPathRoot, "09H-03403-MT1-1_S7.genome.vcf");
var PoolAVariants = (AlleleReader.GetAllVariantsInFile(VcfPath_PoolA)).ToList();
string VcfPath_PoolB = Path.Combine(VcfPathRoot, "09H-03403-MT1-1_S8.genome.vcf");
var PoolBVariants = (AlleleReader.GetAllVariantsInFile(VcfPath_PoolB)).ToList();
CalledAllele VariantA = PoolAVariants[0];
CalledAllele VariantB = PoolBVariants[0];
List <CalledAllele[]> pairs = VennProcessor.SelectPairs(
new List <CalledAllele>()
{
VariantA
},
new List <CalledAllele>
{
VariantB
});
VariantComparisonCase ComparisonCase = VennProcessor.GetComparisonCase(pairs[0][0], pairs[0][1]);
ConsensusBuilder consensusBuilder = new ConsensusBuilder("", parameters);
CalledAllele Consensus = consensusBuilder.CombineVariants(
VariantA, VariantB, ComparisonCase);
//Rule "A" test
//A if combined VF<1% and less than 2.6% in each pool, call REF
//(note, we were Alt in one pool and ref in another)
Assert.Equal(VariantA.Genotype, Pisces.Domain.Types.Genotype.HomozygousRef);
Assert.Equal(VariantA.Frequency, 0.9979, 4);
Assert.Equal(VariantA.VariantQscore, 100);
Assert.Equal(VariantA.Filters, new List <Pisces.Domain.Types.FilterType> {
});
Assert.Equal(VariantB.Genotype, Pisces.Domain.Types.Genotype.HeterozygousAltRef);
Assert.Equal(VariantB.Frequency, 0.0173, 4);
Assert.Equal(VariantB.VariantQscore, 100);
Assert.Equal(VariantB.Filters, new List <Pisces.Domain.Types.FilterType> {
});
Assert.Equal(ComparisonCase, VariantComparisonCase.OneReferenceOneAlternate);
Assert.Equal(Consensus.Genotype, Pisces.Domain.Types.Genotype.HomozygousRef);
Assert.Equal(Consensus.Frequency, 0.9907, 4);
Assert.Equal(Consensus.VariantQscore, 100);
Assert.Equal(Consensus.Filters, new List <Pisces.Domain.Types.FilterType> {
}); //<-low VF tag will NOT added by post-processing b/c is ref call
//B if combined VF<1% and more than 2.6% in one pool, call NO CALL
VariantA = PoolAVariants[1];
VariantB = PoolBVariants[1];
ComparisonCase = VennProcessor.GetComparisonCase(VariantA, VariantB);
Consensus = consensusBuilder.CombineVariants(
VariantA, VariantB, ComparisonCase);
Assert.Equal(VariantA.Genotype, Pisces.Domain.Types.Genotype.HeterozygousAltRef);
Assert.Equal(VariantA.Frequency, 0.0776, 4);
Assert.Equal(VariantA.VariantQscore, 100);
Assert.Equal(VariantA.Filters, new List <Pisces.Domain.Types.FilterType> {
});
Assert.Equal(VariantB.Genotype, Pisces.Domain.Types.Genotype.HomozygousRef);
Assert.Equal(VariantB.Frequency, 0.9989, 4);
Assert.Equal(VariantB.VariantQscore, 100);
Assert.Equal(VariantB.Filters, new List <Pisces.Domain.Types.FilterType> {
});
Assert.Equal(ComparisonCase, VariantComparisonCase.OneReferenceOneAlternate);
Assert.Equal(Consensus.Genotype, Pisces.Domain.Types.Genotype.AltLikeNoCall);
Assert.Equal(Consensus.Frequency, 0.0070, 4);
Assert.Equal(Consensus.VariantQscore, 0);
Assert.Equal(Consensus.Filters, new List <Pisces.Domain.Types.FilterType>
{
Pisces.Domain.Types.FilterType.PoolBias
}); //<-low VF tag will also get added by post-processing
//Rule "Ca" test
//C-a if combined 1%<VF<2.6%
// and more than 2.6% in one pool and less than 1% in the other, call NO CALL w/PB
VariantA = PoolAVariants[2];
VariantB = PoolBVariants[2];
ComparisonCase = VennProcessor.GetComparisonCase(VariantA, VariantB);
Consensus = consensusBuilder.CombineVariants(
VariantA, VariantB, ComparisonCase);
Assert.Equal(VariantA.Genotype, Pisces.Domain.Types.Genotype.HeterozygousAltRef);
Assert.Equal(VariantA.Frequency, 0.0367, 4);
Assert.Equal(VariantA.VariantQscore, 100);
Assert.Equal(VariantA.Filters, new List <Pisces.Domain.Types.FilterType> {
});
Assert.Equal(VariantB.Genotype, Pisces.Domain.Types.Genotype.HomozygousRef);
Assert.Equal(VariantB.Frequency, 0.9976, 4);
Assert.Equal(VariantB.VariantQscore, 100);
Assert.Equal(VariantB.Filters, new List <Pisces.Domain.Types.FilterType> {
});
Assert.Equal(ComparisonCase, VariantComparisonCase.OneReferenceOneAlternate);
Assert.Equal(Consensus.Genotype, Pisces.Domain.Types.Genotype.AltLikeNoCall);
Assert.Equal(Consensus.Frequency, 0.0117, 4);
Assert.Equal(Consensus.VariantQscore, 23);
Assert.Equal(Consensus.Filters, new List <Pisces.Domain.Types.FilterType> {
Pisces.Domain.Types.FilterType.PoolBias
});
//Rule "Cb" test
//C-a if combined 1%<VF<2.6%
// and more than 2.6% in one pool and between 1% and 2.6% in the other, call NO CALL w/ no PB
VariantA = PoolAVariants[3];
VariantB = PoolBVariants[3];
ComparisonCase = VennProcessor.GetComparisonCase(VariantA, VariantB);
Consensus = consensusBuilder.CombineVariants(
VariantA, VariantB, ComparisonCase);
Assert.Equal(VariantA.Genotype, Pisces.Domain.Types.Genotype.HeterozygousAltRef);
Assert.Equal(VariantA.Frequency, 0.01725, 4);
Assert.Equal(VariantA.VariantQscore, 100);
Assert.Equal(VariantA.Filters, new List <Pisces.Domain.Types.FilterType> {
});
Assert.Equal(VariantB.Genotype, Pisces.Domain.Types.Genotype.HeterozygousAltRef);
Assert.Equal(VariantB.Frequency, 0.03667, 4);
Assert.Equal(VariantB.VariantQscore, 100);
Assert.Equal(VariantB.Filters, new List <Pisces.Domain.Types.FilterType> {
});
Assert.Equal(ComparisonCase, VariantComparisonCase.AgreedOnAlternate);
Assert.Equal(Consensus.Genotype, Pisces.Domain.Types.Genotype.AltLikeNoCall);
Assert.Equal(Consensus.Frequency, 0.02347, 4);
Assert.Equal(Consensus.VariantQscore, 100);
Assert.Equal(Consensus.Filters, new List <Pisces.Domain.Types.FilterType> {
}); //<-low VF tag will also get added by post-processing
//Rule "D" test
//D if combined VF>=2.6% call VARIANT (PB if only present in one pool, using 1% as the cutoff)
VariantA = PoolAVariants[4];
VariantB = PoolBVariants[4];
ComparisonCase = VennProcessor.GetComparisonCase(VariantA, VariantB);
Consensus = consensusBuilder.CombineVariants(
VariantA, VariantB, ComparisonCase);
Assert.Equal(VariantA.Genotype, Pisces.Domain.Types.Genotype.HeterozygousAltRef);
Assert.Equal(VariantA.Frequency, 0.2509, 4);
Assert.Equal(VariantA.VariantQscore, 100);
Assert.Equal(VariantA.Filters, new List <Pisces.Domain.Types.FilterType> {
});
Assert.Equal(VariantB.Genotype, Pisces.Domain.Types.Genotype.HeterozygousAltRef);
Assert.Equal(VariantB.Frequency, 0.0367, 4);
Assert.Equal(VariantB.VariantQscore, 100);
Assert.Equal(VariantB.Filters, new List <Pisces.Domain.Types.FilterType> {
});
Assert.Equal(ComparisonCase, VariantComparisonCase.AgreedOnAlternate);
Assert.Equal(Consensus.Genotype, Pisces.Domain.Types.Genotype.HeterozygousAltRef);
Assert.Equal(Consensus.Frequency, 0.1716, 4);
Assert.Equal(Consensus.VariantQscore, 100);
Assert.Equal(Consensus.Filters, new List <Pisces.Domain.Types.FilterType> {
}); //<-low VF tag will also get set by post processor
}
//check consensus builder works on GT "1" and "0" .
//and in combination with 0/1, etc.
public void CombineHaploidCalls()
{
var options = new VennVcfOptions();
options.Validate();//set defaults
var hemiAltA = new CalledAllele();
hemiAltA.Chromosome = "chr1";
hemiAltA.ReferencePosition = 1;
hemiAltA.ReferenceAllele = "A";
hemiAltA.AlternateAllele = "T";
hemiAltA.Type = AlleleCategory.Snv;
hemiAltA.TotalCoverage = 100;
hemiAltA.AlleleSupport = 25;
hemiAltA.Genotype = Genotype.HemizygousAlt;
var hemiAltB = new CalledAllele();
hemiAltB.Chromosome = "chr1";
hemiAltB.ReferencePosition = 1;
hemiAltB.ReferenceAllele = "A";
hemiAltB.AlternateAllele = "T";
hemiAltB.Type = AlleleCategory.Snv;
hemiAltB.TotalCoverage = 100;
hemiAltB.AlleleSupport = 25;
hemiAltB.Genotype = Genotype.HemizygousAlt;
var hemiRefA = new CalledAllele();
hemiRefA.Chromosome = "chr1";
hemiRefA.ReferencePosition = 1;
hemiRefA.ReferenceAllele = "A";
hemiRefA.AlternateAllele = ".";
hemiRefA.Type = AlleleCategory.Reference;
hemiRefA.TotalCoverage = 100;
hemiRefA.AlleleSupport = 25;
hemiRefA.ReferenceSupport = 25;
hemiRefA.Genotype = Genotype.HemizygousRef;
var hemiRefB = new CalledAllele();
hemiRefB.Chromosome = "chr1";
hemiRefB.ReferencePosition = 1;
hemiRefB.ReferenceAllele = "A";
hemiRefB.AlternateAllele = ".";
hemiRefB.Type = AlleleCategory.Reference;
hemiRefB.TotalCoverage = 100;
hemiRefB.AlleleSupport = 25;
hemiRefB.ReferenceSupport = 25;
hemiRefB.Genotype = Genotype.HemizygousRef;
var hemiNoCallA = new CalledAllele();
hemiNoCallA.Chromosome = "chr1";
hemiNoCallA.ReferencePosition = 1;
hemiNoCallA.ReferenceAllele = "A";
hemiNoCallA.AlternateAllele = ".";
hemiNoCallA.Type = AlleleCategory.Reference;
hemiNoCallA.TotalCoverage = 100;
hemiNoCallA.AlleleSupport = 25;
hemiNoCallA.ReferenceSupport = 25;
hemiNoCallA.Genotype = Genotype.HemizygousNoCall;
var hemiNoCallB = new CalledAllele();
hemiNoCallB.Chromosome = "chr1";
hemiNoCallB.ReferencePosition = 1;
hemiNoCallB.ReferenceAllele = "A";
hemiNoCallB.AlternateAllele = ".";
hemiNoCallB.Type = AlleleCategory.Reference;
hemiNoCallB.TotalCoverage = 100;
hemiNoCallB.AlleleSupport = 25;
hemiNoCallB.ReferenceSupport = 25;
hemiNoCallB.Genotype = Genotype.HemizygousNoCall;
var NormalAltA = new CalledAllele();
NormalAltA.Chromosome = "chr1";
NormalAltA.ReferencePosition = 1;
NormalAltA.ReferenceAllele = "A";
NormalAltA.AlternateAllele = "T";
NormalAltA.Type = AlleleCategory.Snv;
NormalAltA.TotalCoverage = 100;
NormalAltA.AlleleSupport = 25;
NormalAltA.Genotype = Genotype.HeterozygousAltRef;
var NormalRefA = new CalledAllele();
NormalRefA.Chromosome = "chr1";
NormalRefA.ReferencePosition = 1;
NormalRefA.ReferenceAllele = "A";
NormalRefA.AlternateAllele = ".";
NormalRefA.Type = AlleleCategory.Reference;
NormalRefA.TotalCoverage = 300;
NormalRefA.AlleleSupport = 50;
NormalRefA.ReferenceSupport = 50;
NormalRefA.Genotype = Genotype.HomozygousRef;
var cb = new ConsensusBuilder("cbHaploid.vcf", options);
CheckSimpleCombinations(hemiAltA, hemiAltB, cb, Genotype.HomozygousAlt, hemiAltA.AlternateAllele, VariantComparisonCase.AgreedOnAlternate);//<- default untill we update consensus code with 1/. etc.
CheckSimpleCombinations(hemiRefA, hemiRefB, cb, Genotype.HomozygousRef, hemiRefA.AlternateAllele, VariantComparisonCase.AgreedOnReference);
CheckSimpleCombinations(hemiNoCallA, hemiNoCallB, cb, Genotype.RefLikeNoCall, hemiNoCallA.AlternateAllele, VariantComparisonCase.AgreedOnReference);
CheckSimpleCombinations(hemiAltA, NormalAltA, cb, Genotype.HeterozygousAltRef, NormalAltA.AlternateAllele, VariantComparisonCase.AgreedOnAlternate);//<- default untill we update consensus code with 1/. etc.
CheckSimpleCombinations(hemiRefA, NormalAltA, cb, Genotype.HeterozygousAltRef, NormalAltA.AlternateAllele, VariantComparisonCase.OneReferenceOneAlternate);
CheckSimpleCombinations(hemiNoCallA, NormalAltA, cb, Genotype.HeterozygousAltRef, NormalAltA.AlternateAllele, VariantComparisonCase.OneReferenceOneAlternate);
CheckSimpleCombinations(hemiAltA, NormalRefA, cb, Genotype.HeterozygousAltRef, hemiAltA.AlternateAllele, VariantComparisonCase.OneReferenceOneAlternate);//<- default untill we update consensus code with 1/. etc.
CheckSimpleCombinations(hemiRefA, NormalRefA, cb, Genotype.HomozygousRef, NormalRefA.AlternateAllele, VariantComparisonCase.AgreedOnReference);
CheckSimpleCombinations(hemiNoCallA, NormalRefA, cb, Genotype.HomozygousRef, NormalRefA.AlternateAllele, VariantComparisonCase.AgreedOnReference);
}