public void VcfLineToAllelesTests_SomaticForcedGTExample_PICS_1168()
{
//some example crummy input
var inputLines = new List <string>()
{
"chr4\t56236582\t1ai\tA\tC\t.\t.\t.\t.\t.\r",
"chr4\t56236583\t1aii\tA\tAA\t.\t.\t.\t.\t.",
"chr18\t9888034\t6b\tA\t.\t.\t.\t.\t.\t.blah",
"chr21\t46644966\t6b\tA\t.\t.\t.\t.\tboo\too",
"chr21\t33694232\t6b\tA\t.\t.\t.\t.\t.\t.",
"chr21\t33694239\t6c\tT\t<del>\t.\t.\t.\t.\t.",
"chr8\t1817367\t6d\tC\tA\t.\t.\t.\t.\t.",
"chr1\t109465143\tPICS827\tCTGCCATACAGCTTCAACAACAACTT\tATGCCATACAGCTTCAACAACAA\t.\t.\t.\t.\t.",
};
var outputAlleles = new List <CalledAllele>()
{
};
foreach (var line in inputLines)
{
//make sure nothing throws
var outputAllelesForLine = AlleleReader.VcfLineToAlleles(line, true);
//make sure we only ever read 1 allele per line, since this is somatic input
Assert.Equal(1, outputAllelesForLine.Count());
outputAlleles.Add(outputAllelesForLine[0]);
}
//sanity check results
var allele1 = outputAlleles[0];
var allele2 = outputAlleles[7];
Assert.Equal("chr4", allele1.Chromosome);
Assert.Equal(56236582, allele1.ReferencePosition);
Assert.Equal("A", allele1.ReferenceAllele);
Assert.Equal("C", allele1.AlternateAllele);
Assert.Equal("chr1", allele2.Chromosome);
Assert.Equal(109465143, allele2.ReferencePosition);
Assert.Equal("CTGCCATACAGCTTCAACAACAACTT", allele2.ReferenceAllele);
Assert.Equal("ATGCCATACAGCTTCAACAACAA", allele2.AlternateAllele);
}
public void CloseColocatedGroupVariantTests()
{
List <string> resultStrings = new List <string>();
string incomingHangingVariantLine = null;
string outgoingHangingVariantLine = null;
Dictionary <string, List <CalledAllele> > ColocatedAlleles = new Dictionary <string, List <CalledAllele> >();
var vr = new AlleleReader(ColocatedVcfTestFile);
var nextClosedLines = vr.CloseColocatedLines(incomingHangingVariantLine, out outgoingHangingVariantLine);
var nextClosedGroup = AlleleReader.VcfLinesToAlleles(nextClosedLines);
var outgoingHangingVariants = AlleleReader.VcfLineToAlleles(outgoingHangingVariantLine);
//the algorithm should have grouped the first two, and left the last one hanging.
//chr1 223906728.G. 100 PASS DP = 532 GT: GQ: AD: DP: VF: NL: SB 0 / 0:100:532:532:0.00:20:-100.0000
//chr1 223906728.G A 100 PASS DP = 532 GT: GQ: AD: DP: VF: NL: SB 0 / 1:100:276,256:532:0.48:20:-100.0000
//chr1 223906729.G. 100 PASS DP = 532 GT: GQ: AD: DP: VF: NL: SB 0 / 0:100:532:532:0.00:20:-100.0000
Assert.Equal(2, nextClosedGroup.Count);
Assert.Equal(1, outgoingHangingVariants.Count);
Assert.Equal(nextClosedGroup[0].Chromosome, "chr1");
Assert.Equal(nextClosedGroup[0].ReferenceAllele, "G");
Assert.Equal(nextClosedGroup[0].AlternateAllele, ".");
Assert.Equal(nextClosedGroup[0].ReferencePosition, 223906728);
Assert.Equal(nextClosedGroup[1].Chromosome, "chr1");
Assert.Equal(nextClosedGroup[1].ReferenceAllele, "G");
Assert.Equal(nextClosedGroup[1].AlternateAllele, "A");
Assert.Equal(nextClosedGroup[1].ReferencePosition, 223906728);
Assert.Equal(outgoingHangingVariants[0].Chromosome, "chr1");
Assert.Equal(outgoingHangingVariants[0].ReferenceAllele, "G");
Assert.Equal(outgoingHangingVariants[0].AlternateAllele, ".");
Assert.Equal(outgoingHangingVariants[0].ReferencePosition, 223906729);
ColocatedAlleles.Add(nextClosedGroup[0].Chromosome + "_" + nextClosedGroup[0].ReferencePosition, nextClosedGroup);
//now read the rest of the file
while (true)
{
incomingHangingVariantLine = outgoingHangingVariantLine;
if (incomingHangingVariantLine == null)
{
break;
}
var nextGroupLines = vr.CloseColocatedLines(incomingHangingVariantLine, out outgoingHangingVariantLine);
var nextGroup = AlleleReader.VcfLinesToAlleles(nextGroupLines);
ColocatedAlleles.Add(nextGroup[0].Chromosome + "_" + nextGroup[0].ReferencePosition, nextGroup);
}
//check that everything loaded correctly
Assert.Equal(28, ColocatedAlleles.Keys.Count);
//example ref site with one allele
//chr1 223906730 . G . 100 PASS DP=532 GT:GQ:AD:DP:VF:NL:SB 0/0:100:532:532:0.00:20:-100.0000
var ex1 = ColocatedAlleles["chr1_223906730"];
Assert.Equal(ex1.Count, 1);
Assert.Equal(ex1[0].Chromosome, "chr1");
Assert.Equal(ex1[0].ReferenceAllele, "G");
Assert.Equal(ex1[0].AlternateAllele, ".");
Assert.Equal(ex1[0].ReferencePosition, 223906730);
//example mulit allelic site as one vcf line
//chr1 223906731 . C A,T 100 PASS DP=532 GT:GQ:AD:DP:VF:NL:SB 1/2:100:254,254:532:0.95:20:-100.0000
var ex2 = ColocatedAlleles["chr1_223906731"];
Assert.Equal(ex2.Count, 2);
Assert.Equal(ex2[0].Chromosome, "chr1");
Assert.Equal(ex2[0].ReferenceAllele, "C");
Assert.Equal(ex2[0].AlternateAllele, "A");
Assert.Equal(ex2[0].ReferencePosition, 223906731);
Assert.Equal(ex2[1].Chromosome, "chr1");
Assert.Equal(ex2[1].ReferenceAllele, "C");
Assert.Equal(ex2[1].AlternateAllele, "T");
Assert.Equal(ex2[1].ReferencePosition, 223906731);
//example multi allelic site as multiple vcf lines
//chr1 223906746.G. 100 PASS DP = 532 GT: GQ: AD: DP: VF: NL: SB 0 / 0:100:532:532:0.00:20:-100.0000
//chr1 223906746.G A 100 PASS DP = 532 GT: GQ: AD: DP: VF: NL: SB 0 / 1:100:276,256:532:0.48:20:-100.0000
//chr1 223906746.G AC 100 PASS DP = 532 GT: GQ: AD: DP: VF: NL: SB 0 / 1:100:276,256:532:0.48:20:-100.0000
//chr1 223906746.GG AT 100 PASS DP = 532 GT: GQ: AD: DP: VF: NL: SB 0 / 1:100:276,256:532:0.48:20:-100.0000
var ex3 = ColocatedAlleles["chr1_223906746"];
Assert.Equal(ex3.Count, 4);
Assert.Equal(ex3[0].Chromosome, "chr1");
Assert.Equal(ex3[0].ReferenceAllele, "G");
Assert.Equal(ex3[0].AlternateAllele, ".");
Assert.Equal(ex3[0].ReferencePosition, 223906746);
Assert.Equal(ex3[1].Chromosome, "chr1");
Assert.Equal(ex3[1].ReferenceAllele, "G");
Assert.Equal(ex3[1].AlternateAllele, "A");
Assert.Equal(ex3[1].ReferencePosition, 223906746);
Assert.Equal(ex3[2].Chromosome, "chr1");
Assert.Equal(ex3[2].ReferenceAllele, "G");
Assert.Equal(ex3[2].AlternateAllele, "AC");
Assert.Equal(ex3[2].ReferencePosition, 223906746);
Assert.Equal(ex3[3].Chromosome, "chr1");
Assert.Equal(ex3[3].ReferenceAllele, "GG");
Assert.Equal(ex3[3].AlternateAllele, "AT");
Assert.Equal(ex3[3].ReferencePosition, 223906746);
//check the last vcf lines
//chrY 87003973 . T . 100 PASS DP=532 GT:GQ:AD:DP:VF:NL:SB 0/0:100:276:532:0.48:20:-100.0000
//chrY 87003973.ATCTC A 100 PASS DP = 532 GT: GQ: AD: DP: VF: NL: SB 0 / 1:100:276,256:532:0.48:20:-100.0000
var ex4 = ColocatedAlleles["chrY_87003973"];
Assert.Equal(ex4.Count, 2);
Assert.Equal(ex4[0].Chromosome, "chrY");
Assert.Equal(ex4[0].ReferenceAllele, "T");
Assert.Equal(ex4[0].AlternateAllele, ".");
Assert.Equal(ex4[0].ReferencePosition, 87003973);
Assert.Equal(ex4[1].Chromosome, "chrY");
Assert.Equal(ex4[1].ReferenceAllele, "ATCTC");
Assert.Equal(ex4[1].AlternateAllele, "A");
Assert.Equal(ex4[1].ReferencePosition, 87003973);
}
public void VcfLineToAllelesTests_ThreeIndelExample()
{
//chr2 19946216.ATGTGTG ATG,ATGTG,A 0 PASS metal = platinum; cgi =.; bwa_freebayes = HD:0,LOOHD: 0; bwa_platypus =.; bwa_gatk3 = HD:2,LOOHD: 2; cortex =.; isaac2 = HD:1,LOOHD: 1; dist2closest = 192 GT 1 | 2
string platypusLine = "chr2\t19946216\t.\tATGTGTG\tATG,ATGTG,A\t0\tPASS\tmetal=platinum;cgi=.;bwa_freebayes=HD:0,LOOHD: 0;bwa_platypus =.;bwa_gatk3=HD:2,LOOHD:2;cortex=.;isaac2=HD:1,LOOHD:1;dist2closest=192\tGT\t1|2";
var varCalls = AlleleReader.VcfLineToAlleles(platypusLine, true);
var testvar0 = varCalls[0];
var testvar1 = varCalls[1];
var testvar2 = varCalls[2];
Assert.Equal(3, varCalls.Count);
Assert.Equal("chr2", testvar0.Chromosome);
Assert.Equal(19946216, testvar0.ReferencePosition);
Assert.Equal("ATGTG", testvar0.ReferenceAllele);
Assert.Equal("A", testvar0.AlternateAllele);
Assert.Equal(Genotype.HeterozygousAlt1Alt2, testvar0.Genotype);
Assert.Equal(0, testvar0.GenotypeQscore);
Assert.Equal(0, testvar0.VariantQscore);
Assert.Equal(AlleleCategory.Deletion, testvar0.Type);
Assert.Equal(0, testvar0.Filters.Count);
Assert.Equal(0, testvar0.TotalCoverage);
Assert.Equal(0, testvar0.AlleleSupport);
Assert.Equal(0, testvar0.ReferenceSupport);
Assert.Equal(0, testvar0.Frequency, 4);
Assert.Equal(0, testvar0.NoiseLevelApplied);
Assert.Equal(-100, testvar0.StrandBiasResults.GATKBiasScore);
Assert.Equal(0, testvar0.FractionNoCalls);
Assert.Equal(8, testvar0.ReadCollapsedCountsMut.Length);
Assert.Equal(8, testvar0.ReadCollapsedCountTotal.Length);
Assert.Equal("chr2", testvar1.Chromosome);
Assert.Equal(19946216, testvar1.ReferencePosition);
Assert.Equal("ATG", testvar1.ReferenceAllele);
Assert.Equal("A", testvar1.AlternateAllele);
Assert.Equal(Genotype.HeterozygousAlt1Alt2, testvar1.Genotype);
Assert.Equal(0, testvar1.GenotypeQscore);
Assert.Equal(0, testvar1.VariantQscore);
Assert.Equal(AlleleCategory.Deletion, testvar1.Type);
Assert.Equal(0, testvar1.Filters.Count);
Assert.Equal(0, testvar1.TotalCoverage);
Assert.Equal(0, testvar1.AlleleSupport);
Assert.Equal(0, testvar1.ReferenceSupport);
Assert.Equal(0, testvar1.Frequency, 4);
Assert.Equal(0, testvar1.NoiseLevelApplied);
Assert.Equal(-100, testvar1.StrandBiasResults.GATKBiasScore);
Assert.Equal(0, testvar1.FractionNoCalls);
Assert.Equal(8, testvar1.ReadCollapsedCountsMut.Length);
Assert.Equal(8, testvar1.ReadCollapsedCountTotal.Length);
Assert.Equal("chr2", testvar2.Chromosome);
Assert.Equal(19946216, testvar2.ReferencePosition);
Assert.Equal("ATGTGTG", testvar2.ReferenceAllele);
Assert.Equal("A", testvar2.AlternateAllele);
Assert.Equal(Genotype.HeterozygousAlt1Alt2, testvar1.Genotype);
Assert.Equal(0, testvar2.GenotypeQscore);
Assert.Equal(0, testvar2.VariantQscore);
Assert.Equal(AlleleCategory.Deletion, testvar2.Type);
Assert.Equal(0, testvar2.Filters.Count);
Assert.Equal(0, testvar2.TotalCoverage);
Assert.Equal(0, testvar2.AlleleSupport);
Assert.Equal(0, testvar2.ReferenceSupport);
Assert.Equal(0, testvar2.Frequency, 4);
Assert.Equal(0, testvar2.NoiseLevelApplied);
Assert.Equal(-100, testvar2.StrandBiasResults.GATKBiasScore);
Assert.Equal(0, testvar2.FractionNoCalls);
Assert.Equal(8, testvar2.ReadCollapsedCountsMut.Length);
Assert.Equal(8, testvar2.ReadCollapsedCountTotal.Length);
}
public void VcfLineToAllelesTests()
{
//Basic line parsing, starting with simple variants, and ending with more complex examples.
//Make sure everythign is read back properly.
string line1 = "chr4\t7\t.\tC\tA\t3\tPASS\tDP=5394\tGT:GQ:AD:DP:VF:NL:SB:NC\t1/1:10:7,2387:5394:0.4425:23:0.0000:0.0000";
var varCalls = AlleleReader.VcfLineToAlleles(line1);
var testvar = varCalls[0];
Assert.Equal(1, varCalls.Count);
Assert.Equal("chr4", testvar.Chromosome);
Assert.Equal(7, testvar.ReferencePosition);
Assert.Equal("C", testvar.ReferenceAllele);
Assert.Equal("A", testvar.AlternateAllele);
Assert.Equal(Genotype.HomozygousAlt, testvar.Genotype);
Assert.Equal(10, testvar.GenotypeQscore);
Assert.Equal(3, testvar.VariantQscore);
Assert.Equal(AlleleCategory.Snv, testvar.Type);
Assert.Equal(0, testvar.Filters.Count);
Assert.Equal(5394, testvar.TotalCoverage);
Assert.Equal(2387, testvar.AlleleSupport);
Assert.Equal(7, testvar.ReferenceSupport);
Assert.Equal(0.4425, testvar.Frequency, 4);
Assert.Equal(23, testvar.NoiseLevelApplied);
Assert.Equal(0, testvar.StrandBiasResults.GATKBiasScore);
Assert.Equal(0, testvar.FractionNoCalls);
Assert.Equal(8, testvar.ReadCollapsedCountsMut.Length);
Assert.Equal(8, testvar.ReadCollapsedCountTotal.Length);
string line2 = "chr4\t8\t.\tC\t.\t0\tLowDP\tDP=0\tGT:GQ:AD:DP:VF:NL:SB:NC\t./.:0:0:0:0.0000:23:0.0000:0.0000";
varCalls = AlleleReader.VcfLineToAlleles(line2);
testvar = varCalls[0];
Assert.Equal(1, varCalls.Count);
Assert.Equal("chr4", testvar.Chromosome);
Assert.Equal(8, testvar.ReferencePosition);
Assert.Equal("C", testvar.ReferenceAllele);
Assert.Equal(".", testvar.AlternateAllele);
Assert.Equal(Genotype.RefLikeNoCall, testvar.Genotype);
Assert.Equal(0, testvar.GenotypeQscore);
Assert.Equal(0, testvar.VariantQscore);
Assert.Equal(AlleleCategory.Reference, testvar.Type);
Assert.Equal(1, testvar.Filters.Count);
Assert.Equal(FilterType.LowDepth, testvar.Filters[0]);
Assert.Equal(0, testvar.TotalCoverage);
Assert.Equal(0, testvar.AlleleSupport);
Assert.Equal(0, testvar.ReferenceSupport);
Assert.Equal(0.0, testvar.Frequency, 4);
Assert.Equal(23, testvar.NoiseLevelApplied);
Assert.Equal(0, testvar.StrandBiasResults.GATKBiasScore);
Assert.Equal(0, testvar.FractionNoCalls);
Assert.Equal(8, testvar.ReadCollapsedCountsMut.Length);
Assert.Equal(8, testvar.ReadCollapsedCountTotal.Length);
string line3 = "chr4\t10\t.\tAA\tGA,G\t0\tPASS\tDP=5394\tGT:GQ:AD:DP:VF:NL:SB:NC\t1/2:0:2387,2000:5394:0.8133:23:0.0000:0.0000";
varCalls = AlleleReader.VcfLineToAlleles(line3);
var testvar0 = varCalls[0];
var testvar1 = varCalls[1];
Assert.Equal(2, varCalls.Count);
Assert.Equal("chr4", testvar0.Chromosome);
Assert.Equal(10, testvar0.ReferencePosition);
Assert.Equal("AA", testvar0.ReferenceAllele);
Assert.Equal("GA", testvar0.AlternateAllele);
Assert.Equal(Genotype.HeterozygousAlt1Alt2, testvar0.Genotype);
Assert.Equal(0, testvar0.GenotypeQscore);
Assert.Equal(0, testvar0.VariantQscore);
Assert.Equal(AlleleCategory.Mnv, testvar0.Type);
Assert.Equal(0, testvar0.Filters.Count);
Assert.Equal(5394, testvar0.TotalCoverage);
Assert.Equal(2387, testvar0.AlleleSupport);
Assert.Equal(5394 - 2387 - 2000, testvar0.ReferenceSupport);
Assert.Equal(2387.0 / 5394.0, testvar0.Frequency, 4);
Assert.Equal(23, testvar0.NoiseLevelApplied);
Assert.Equal(0, testvar0.StrandBiasResults.GATKBiasScore);
Assert.Equal(0, testvar0.FractionNoCalls);
Assert.Equal(8, testvar0.ReadCollapsedCountsMut.Length);
Assert.Equal(8, testvar0.ReadCollapsedCountTotal.Length);
Assert.Equal("chr4", testvar1.Chromosome);
Assert.Equal(10, testvar1.ReferencePosition);
Assert.Equal("AA", testvar1.ReferenceAllele);
Assert.Equal("G", testvar1.AlternateAllele);
Assert.Equal(Genotype.HeterozygousAlt1Alt2, testvar1.Genotype);
Assert.Equal(0, testvar1.GenotypeQscore);
Assert.Equal(0, testvar1.VariantQscore);
Assert.Equal(AlleleCategory.Deletion, testvar1.Type);
Assert.Equal(0, testvar1.Filters.Count);
Assert.Equal(5394, testvar1.TotalCoverage);
Assert.Equal(2000, testvar1.AlleleSupport);
Assert.Equal(5394 - 2387 - 2000, testvar1.ReferenceSupport);
Assert.Equal(2000.0 / 5394.0, testvar1.Frequency, 4);
Assert.Equal(23, testvar1.NoiseLevelApplied);
Assert.Equal(0, testvar1.StrandBiasResults.GATKBiasScore);
Assert.Equal(0, testvar1.FractionNoCalls);
Assert.Equal(8, testvar1.ReadCollapsedCountsMut.Length);
Assert.Equal(8, testvar1.ReadCollapsedCountTotal.Length);
string line4 = "chr2\t87003972\t.\tTTATCTC\tT\t100\tPASS\tDP=532\tGT:GQ:AD:DP:VF:NL:SB\t0/1:100:276,256:532:0.48:20:-100.0000";
varCalls = AlleleReader.VcfLineToAlleles(line4);
testvar = varCalls[0];
Assert.Equal(1, varCalls.Count);
Assert.Equal("chr2", testvar.Chromosome);
Assert.Equal(87003972, testvar.ReferencePosition);
Assert.Equal("TTATCTC", testvar.ReferenceAllele);
Assert.Equal("T", testvar.AlternateAllele);
Assert.Equal(Genotype.HeterozygousAltRef, testvar.Genotype);
Assert.Equal(100, testvar.GenotypeQscore);
Assert.Equal(100, testvar.VariantQscore);
Assert.Equal(AlleleCategory.Deletion, testvar.Type);
Assert.Equal(0, testvar.Filters.Count);
Assert.Equal(532, testvar.TotalCoverage);
Assert.Equal(256, testvar.AlleleSupport);
Assert.Equal(276, testvar.ReferenceSupport);
Assert.Equal(256.0 / 532.0, testvar.Frequency, 4);
Assert.Equal(20, testvar.NoiseLevelApplied);
Assert.Equal(-100, testvar.StrandBiasResults.GATKBiasScore);
Assert.Equal(0, testvar.FractionNoCalls);
Assert.Equal(8, testvar.ReadCollapsedCountsMut.Length);
Assert.Equal(8, testvar.ReadCollapsedCountTotal.Length);
string line5 = "chr2\t87003973\t.\tT\t.\t100\tPASS\tDP=532\tGT:GQ:AD:DP:VF:NL:SB\t0/0:100:276:532:0.48:20:-100.0000";
varCalls = AlleleReader.VcfLineToAlleles(line5);
testvar = varCalls[0];
Assert.Equal(1, varCalls.Count);
Assert.Equal("chr2", testvar.Chromosome);
Assert.Equal(87003973, testvar.ReferencePosition);
Assert.Equal("T", testvar.ReferenceAllele);
Assert.Equal(".", testvar.AlternateAllele);
Assert.Equal(Genotype.HomozygousRef, testvar.Genotype);
Assert.Equal(100, testvar.GenotypeQscore);
Assert.Equal(100, testvar.VariantQscore);
Assert.Equal(AlleleCategory.Reference, testvar.Type);
Assert.Equal(0, testvar.Filters.Count);
Assert.Equal(532, testvar.TotalCoverage);
Assert.Equal(276, testvar.AlleleSupport);
Assert.Equal(276, testvar.ReferenceSupport);
Assert.Equal(276.0 / 532.0, testvar.Frequency, 4);
Assert.Equal(20, testvar.NoiseLevelApplied);
Assert.Equal(-100, testvar.StrandBiasResults.GATKBiasScore);
Assert.Equal(0, testvar.FractionNoCalls);
Assert.Equal(8, testvar.ReadCollapsedCountsMut.Length);
Assert.Equal(8, testvar.ReadCollapsedCountTotal.Length);
string line6 = "chr2\t87003974\t.\tATCTC\tA\t100\tPASS\tDP=532\tGT:GQ:AD:DP:VF:NL:SB\t0/1:100:276,256:532:0.48:20:-100.0000";
varCalls = AlleleReader.VcfLineToAlleles(line6);
testvar = varCalls[0];
Assert.Equal(1, varCalls.Count);
Assert.Equal("chr2", testvar.Chromosome);
Assert.Equal(87003974, testvar.ReferencePosition);
Assert.Equal("ATCTC", testvar.ReferenceAllele);
Assert.Equal("A", testvar.AlternateAllele);
Assert.Equal(Genotype.HeterozygousAltRef, testvar.Genotype);
Assert.Equal(100, testvar.GenotypeQscore);
Assert.Equal(100, testvar.VariantQscore);
Assert.Equal(AlleleCategory.Deletion, testvar.Type);
Assert.Equal(0, testvar.Filters.Count);
Assert.Equal(532, testvar.TotalCoverage);
Assert.Equal(256, testvar.AlleleSupport);
Assert.Equal(276, testvar.ReferenceSupport);
Assert.Equal(256.0 / 532.0, testvar.Frequency, 4);
Assert.Equal(20, testvar.NoiseLevelApplied);
Assert.Equal(-100, testvar.StrandBiasResults.GATKBiasScore);
Assert.Equal(0.0, testvar.FractionNoCalls);
Assert.Equal(8, testvar.ReadCollapsedCountsMut.Length);
Assert.Equal(8, testvar.ReadCollapsedCountTotal.Length);
string line7 = "chrY\t2655675\t.\tG\t.\t100\tPASS\tDP=532\tGT:GQ:AD:DP:VF:NL:SB\t0:100:532:532:0.00:20:-4.0000";
varCalls = AlleleReader.VcfLineToAlleles(line7);
testvar = varCalls[0];
Assert.Equal(1, varCalls.Count);
Assert.Equal("chrY", testvar.Chromosome);
Assert.Equal(2655675, testvar.ReferencePosition);
Assert.Equal("G", testvar.ReferenceAllele);
Assert.Equal(".", testvar.AlternateAllele);
Assert.Equal(Genotype.HemizygousRef, testvar.Genotype);
Assert.Equal(100, testvar.GenotypeQscore);
Assert.Equal(100, testvar.VariantQscore);
Assert.Equal(AlleleCategory.Reference, testvar.Type);
Assert.Equal(0, testvar.Filters.Count);
Assert.Equal(532, testvar.TotalCoverage);
Assert.Equal(532, testvar.AlleleSupport);
Assert.Equal(532, testvar.ReferenceSupport);
Assert.Equal(1.0, testvar.Frequency, 4); //note the VF in the CLASS is allele freq, and in this case the allele is ref. BUT when we write to VF, its 1-Freq for ref-calls..
Assert.Equal(20, testvar.NoiseLevelApplied);
Assert.Equal(-4.0, testvar.StrandBiasResults.GATKBiasScore);
Assert.Equal(0, testvar.FractionNoCalls);
Assert.Equal(8, testvar.ReadCollapsedCountsMut.Length);
Assert.Equal(8, testvar.ReadCollapsedCountTotal.Length);
string line8 = "phix\t2\t.\tA\tC\t0\tq30;SB;LowVariantFreq;ForcedReport\tDP=248\tGT:GQ:AD:DP:VF:NL:SB\t0/1:0:246,0:248:0.00000:0:0.0000";
varCalls = AlleleReader.VcfLineToAlleles(line8);
testvar = varCalls[0];
Assert.Equal(1, varCalls.Count);
Assert.Equal("phix", testvar.Chromosome);
Assert.Equal(2, testvar.ReferencePosition);
Assert.Equal("A", testvar.ReferenceAllele);
Assert.Equal("C", testvar.AlternateAllele);
Assert.Equal(Genotype.HeterozygousAltRef, testvar.Genotype);
Assert.Equal(0, testvar.GenotypeQscore);
Assert.Equal(0, testvar.VariantQscore);
Assert.Equal(AlleleCategory.Snv, testvar.Type);
Assert.Equal(4, testvar.Filters.Count);
Assert.Equal(FilterType.LowVariantQscore, testvar.Filters[0]);
Assert.Equal(FilterType.StrandBias, testvar.Filters[1]);
Assert.Equal(FilterType.LowVariantFrequency, testvar.Filters[2]);
Assert.Equal(FilterType.ForcedReport, testvar.Filters[3]);
Assert.Equal(248, testvar.TotalCoverage);
Assert.Equal(0, testvar.AlleleSupport);
Assert.Equal(246, testvar.ReferenceSupport);
Assert.Equal(0.0, testvar.Frequency, 4);
Assert.Equal(0, testvar.NoiseLevelApplied);
Assert.Equal(0, testvar.StrandBiasResults.GATKBiasScore);
Assert.Equal(0, testvar.FractionNoCalls);
Assert.Equal(8, testvar.ReadCollapsedCountsMut.Length);
Assert.Equal(8, testvar.ReadCollapsedCountTotal.Length);
string line9 = "phix\t2\t.\tA\tG\t35\tPASS\tDP=248\tGT:GQ:AD:DP:VF:NL:SB\t0/1:35:246,2:248:0.00806:40:-23.1080";
varCalls = AlleleReader.VcfLineToAlleles(line9);
testvar = varCalls[0];
Assert.Equal(1, varCalls.Count);
Assert.Equal("phix", testvar.Chromosome);
Assert.Equal(2, testvar.ReferencePosition);
Assert.Equal("A", testvar.ReferenceAllele);
Assert.Equal("G", testvar.AlternateAllele);
Assert.Equal(Genotype.HeterozygousAltRef, testvar.Genotype);
Assert.Equal(35, testvar.GenotypeQscore);
Assert.Equal(35, testvar.VariantQscore);
Assert.Equal(AlleleCategory.Snv, testvar.Type);
Assert.Equal(0, testvar.Filters.Count);
Assert.Equal(248, testvar.TotalCoverage);
Assert.Equal(2, testvar.AlleleSupport);
Assert.Equal(246, testvar.ReferenceSupport);
Assert.Equal(2.0 / 248.0, testvar.Frequency, 4);
Assert.Equal(40, testvar.NoiseLevelApplied);
Assert.Equal(-23.1080, testvar.StrandBiasResults.GATKBiasScore, 4);
Assert.Equal(0, testvar.FractionNoCalls);
Assert.Equal(8, testvar.ReadCollapsedCountsMut.Length);
Assert.Equal(8, testvar.ReadCollapsedCountTotal.Length);
string line10 = "phix\t2\t.\tAGTTT\tGGTTG\t16\tq30;ForcedReport\tDP=248\tGT:GQ:AD:DP:VF:NL:SB\t0/1:0:247,1:248:0.00403:40:-16.9682";
varCalls = AlleleReader.VcfLineToAlleles(line10);
testvar = varCalls[0];
Assert.Equal(1, varCalls.Count);
Assert.Equal("phix", testvar.Chromosome);
Assert.Equal(2, testvar.ReferencePosition);
Assert.Equal("AGTTT", testvar.ReferenceAllele);
Assert.Equal("GGTTG", testvar.AlternateAllele);
Assert.Equal(Genotype.HeterozygousAltRef, testvar.Genotype);
Assert.Equal(0, testvar.GenotypeQscore);
Assert.Equal(16, testvar.VariantQscore);
Assert.Equal(AlleleCategory.Mnv, testvar.Type);
Assert.Equal(2, testvar.Filters.Count);
Assert.Equal(FilterType.LowVariantQscore, testvar.Filters[0]);
Assert.Equal(FilterType.ForcedReport, testvar.Filters[1]);
Assert.Equal(248, testvar.TotalCoverage);
Assert.Equal(1, testvar.AlleleSupport);
Assert.Equal(247, testvar.ReferenceSupport);
Assert.Equal(1.0 / 248.0, testvar.Frequency, 4);
Assert.Equal(40, testvar.NoiseLevelApplied);
Assert.Equal(-16.9682, testvar.StrandBiasResults.GATKBiasScore, 4);
Assert.Equal(0, testvar.FractionNoCalls);
Assert.Equal(8, testvar.ReadCollapsedCountsMut.Length);
Assert.Equal(8, testvar.ReadCollapsedCountTotal.Length);
Assert.Equal(0, testvar.ReadCollapsedCountsMut[0]);
Assert.Equal(0, testvar.ReadCollapsedCountsMut[7]);
Assert.Equal(0, testvar.ReadCollapsedCountTotal[0]);
Assert.Equal(0, testvar.ReadCollapsedCountTotal[7]);
string line11 = "chr1\t9770596\t.\tC\tA\t63\tPASS\tDP=6\tGT:GQ:AD:DP:VF:NL:SB:US\t./.:0:2,4:6:0.667:20:-33.5565:1,0,2,0,1,0,1,0,3,0,2,0";
varCalls = AlleleReader.VcfLineToAlleles(line11);
testvar = varCalls[0];
Assert.Equal(1, varCalls.Count);
Assert.Equal("chr1", testvar.Chromosome);
Assert.Equal(9770596, testvar.ReferencePosition);
Assert.Equal("C", testvar.ReferenceAllele);
Assert.Equal("A", testvar.AlternateAllele);
Assert.Equal(Genotype.AltLikeNoCall, testvar.Genotype);
Assert.Equal(0, testvar.GenotypeQscore);
Assert.Equal(63, testvar.VariantQscore);
Assert.Equal(AlleleCategory.Snv, testvar.Type);
Assert.Equal(0, testvar.Filters.Count);
Assert.Equal(6, testvar.TotalCoverage);
Assert.Equal(4, testvar.AlleleSupport);
Assert.Equal(2, testvar.ReferenceSupport);
Assert.Equal(4.0 / 6.0, testvar.Frequency, 4);
Assert.Equal(20, testvar.NoiseLevelApplied);
Assert.Equal(-33.5565, testvar.StrandBiasResults.GATKBiasScore, 4);
Assert.Equal(0, testvar.FractionNoCalls);
Assert.Equal(8, testvar.ReadCollapsedCountsMut.Length);
Assert.Equal(8, testvar.ReadCollapsedCountTotal.Length);
Assert.Equal(1, testvar.ReadCollapsedCountsMut[0]);
Assert.Equal(2, testvar.ReadCollapsedCountsMut[4]);
Assert.Equal(0, testvar.ReadCollapsedCountsMut[7]);
Assert.Equal(1, testvar.ReadCollapsedCountTotal[0]);
Assert.Equal(3, testvar.ReadCollapsedCountTotal[4]);
Assert.Equal(0, testvar.ReadCollapsedCountTotal[7]);
string line12 = "chr1\t9770597\t.\tA\t.\t100\tPASS\tDP=6\tGT:GQ:AD:DP:VF:NL:SB:US\t./.:0:6:6:0.000:20:-53.5655:0,0,0,0,0,0,1,0,3,0,2,0";
varCalls = AlleleReader.VcfLineToAlleles(line12);
testvar = varCalls[0];
Assert.Equal(1, varCalls.Count);
Assert.Equal("chr1", testvar.Chromosome);
Assert.Equal(9770597, testvar.ReferencePosition);
Assert.Equal("A", testvar.ReferenceAllele);
Assert.Equal(".", testvar.AlternateAllele);
Assert.Equal(Genotype.RefLikeNoCall, testvar.Genotype);
Assert.Equal(0, testvar.GenotypeQscore);
Assert.Equal(100, testvar.VariantQscore);
Assert.Equal(AlleleCategory.Reference, testvar.Type);
Assert.Equal(0, testvar.Filters.Count);
Assert.Equal(6, testvar.TotalCoverage);
Assert.Equal(6, testvar.AlleleSupport);
Assert.Equal(6, testvar.ReferenceSupport);
Assert.Equal(1.0, testvar.Frequency, 4);
Assert.Equal(20, testvar.NoiseLevelApplied);
Assert.Equal(-53.5655, testvar.StrandBiasResults.GATKBiasScore, 4);
Assert.Equal(0, testvar.FractionNoCalls);
Assert.Equal(8, testvar.ReadCollapsedCountsMut.Length);
Assert.Equal(8, testvar.ReadCollapsedCountTotal.Length);
Assert.Equal(8, testvar.ReadCollapsedCountTotal.Length);
Assert.Equal(0, testvar.ReadCollapsedCountsMut[0]);
Assert.Equal(0, testvar.ReadCollapsedCountsMut[4]);
Assert.Equal(0, testvar.ReadCollapsedCountsMut[7]);
Assert.Equal(1, testvar.ReadCollapsedCountTotal[0]);
Assert.Equal(3, testvar.ReadCollapsedCountTotal[4]);
Assert.Equal(0, testvar.ReadCollapsedCountTotal[7]);
string line13 = "chr4\t169663548\t.\tT\tG,TCGGCAGCGTCAGATGTGTATAAGAGACAG\t66\tPASS\tDP=13\tGT:GQ:AD:DP:VF:NL:SB:NC:US\t1/2:6:5,7:13:0.923:20:-100.0000:0.0000:0,0,0,0,0,0,0,1,0,0,0,2";
varCalls = AlleleReader.VcfLineToAlleles(line13);
Assert.Equal(2, varCalls.Count);
testvar0 = varCalls[0];
testvar1 = varCalls[1];
Assert.Equal("chr4", testvar0.Chromosome);
Assert.Equal(169663548, testvar0.ReferencePosition);
Assert.Equal("T", testvar0.ReferenceAllele);
Assert.Equal("G", testvar0.AlternateAllele);
Assert.Equal(Genotype.HeterozygousAlt1Alt2, testvar0.Genotype);
Assert.Equal(6, testvar0.GenotypeQscore);
Assert.Equal(66, testvar0.VariantQscore);
Assert.Equal(AlleleCategory.Snv, testvar0.Type);
Assert.Equal(0, testvar0.Filters.Count);
Assert.Equal(13, testvar0.TotalCoverage);
Assert.Equal(5, testvar0.AlleleSupport);
Assert.Equal(1, testvar0.ReferenceSupport);
Assert.Equal(5.0 / 13.0, testvar0.Frequency, 4);
Assert.Equal(20, testvar0.NoiseLevelApplied);
Assert.Equal(-100, testvar0.StrandBiasResults.GATKBiasScore);
Assert.Equal(0, testvar0.FractionNoCalls);
Assert.Equal(8, testvar0.ReadCollapsedCountsMut.Length);
Assert.Equal(8, testvar0.ReadCollapsedCountTotal.Length);
Assert.Equal(0, testvar.ReadCollapsedCountsMut[0]);
Assert.Equal(0, testvar.ReadCollapsedCountsMut[4]);
Assert.Equal(0, testvar.ReadCollapsedCountsMut[7]);
Assert.Equal(1, testvar.ReadCollapsedCountTotal[0]);
Assert.Equal(3, testvar.ReadCollapsedCountTotal[4]);
Assert.Equal(0, testvar.ReadCollapsedCountTotal[7]);
Assert.Equal("chr4", testvar1.Chromosome);
Assert.Equal(169663548, testvar1.ReferencePosition);
Assert.Equal("T", testvar1.ReferenceAllele);
Assert.Equal("TCGGCAGCGTCAGATGTGTATAAGAGACAG", testvar1.AlternateAllele);
Assert.Equal(Genotype.HeterozygousAlt1Alt2, testvar1.Genotype);
Assert.Equal(6, testvar1.GenotypeQscore);
Assert.Equal(66, testvar1.VariantQscore);
Assert.Equal(AlleleCategory.Insertion, testvar1.Type);
Assert.Equal(0, testvar1.Filters.Count);
Assert.Equal(13, testvar1.TotalCoverage);
Assert.Equal(7, testvar1.AlleleSupport);
Assert.Equal(1, testvar1.ReferenceSupport);
Assert.Equal(7.0 / 13.0, testvar1.Frequency, 4);
Assert.Equal(20, testvar1.NoiseLevelApplied);
Assert.Equal(-100, testvar1.StrandBiasResults.GATKBiasScore);
Assert.Equal(0, testvar1.FractionNoCalls);
Assert.Equal(8, testvar1.ReadCollapsedCountsMut.Length);
Assert.Equal(8, testvar1.ReadCollapsedCountTotal.Length);
Assert.Equal(0, testvar.ReadCollapsedCountsMut[0]);
Assert.Equal(0, testvar.ReadCollapsedCountsMut[4]);
Assert.Equal(0, testvar.ReadCollapsedCountsMut[7]);
Assert.Equal(1, testvar.ReadCollapsedCountTotal[0]);
Assert.Equal(3, testvar.ReadCollapsedCountTotal[4]);
Assert.Equal(0, testvar.ReadCollapsedCountTotal[7]);
string line14 = "chr4\t169663549\t.\tA\t.\t100\tPASS\tDP=21\tGT:GQ:AD:DP:VF:NL:SB:NC:US\t0/0:42:21:21:0.000:20:-100.0000:0.0100:0,0,0,0,0,0,0,1,0,0,0,2";
varCalls = AlleleReader.VcfLineToAlleles(line14);
testvar = varCalls[0];
Assert.Equal(1, varCalls.Count);
Assert.Equal("chr4", testvar.Chromosome);
Assert.Equal(169663549, testvar.ReferencePosition);
Assert.Equal("A", testvar.ReferenceAllele);
Assert.Equal(".", testvar.AlternateAllele);
Assert.Equal(Genotype.HomozygousRef, testvar.Genotype);
Assert.Equal(42, testvar.GenotypeQscore);
Assert.Equal(100, testvar.VariantQscore);
Assert.Equal(AlleleCategory.Reference, testvar.Type);
Assert.Equal(0, testvar.Filters.Count);
Assert.Equal(21, testvar.TotalCoverage);
Assert.Equal(21, testvar.AlleleSupport);
Assert.Equal(21, testvar.ReferenceSupport);
Assert.Equal(1.0, testvar.Frequency, 4);
Assert.Equal(20, testvar.NoiseLevelApplied);
Assert.Equal(-100.0000, testvar.StrandBiasResults.GATKBiasScore);
Assert.Equal(0.0100, testvar.FractionNoCalls, 4);
Assert.Equal(8, testvar.ReadCollapsedCountsMut.Length);
Assert.Equal(8, testvar.ReadCollapsedCountTotal.Length);
Assert.Equal(0, testvar.ReadCollapsedCountsMut[0]);
Assert.Equal(0, testvar.ReadCollapsedCountsMut[4]);
Assert.Equal(0, testvar.ReadCollapsedCountsMut[7]);
Assert.Equal(0, testvar.ReadCollapsedCountTotal[0]);
Assert.Equal(0, testvar.ReadCollapsedCountTotal[4]);
Assert.Equal(2, testvar.ReadCollapsedCountTotal[7]);
string line15 = "phix\t3\t.\tG\t.\t100\tPASS\tDP=248\tGT:GQ:AD:DP:VF:NL:SB\t0/.:100:247:248:0.00403:40:-100.0000";
varCalls = AlleleReader.VcfLineToAlleles(line15);
testvar = varCalls[0];
Assert.Equal(1, varCalls.Count);
Assert.Equal("phix", testvar.Chromosome);
Assert.Equal(3, testvar.ReferencePosition);
Assert.Equal("G", testvar.ReferenceAllele);
Assert.Equal(".", testvar.AlternateAllele);
Assert.Equal(Genotype.RefAndNoCall, testvar.Genotype);
Assert.Equal(100, testvar.GenotypeQscore);
Assert.Equal(100, testvar.VariantQscore);
Assert.Equal(AlleleCategory.Reference, testvar.Type);
Assert.Equal(0, testvar.Filters.Count);
Assert.Equal(248, testvar.TotalCoverage);
Assert.Equal(247, testvar.AlleleSupport);
Assert.Equal(247, testvar.ReferenceSupport);
Assert.Equal(247.0 / 248.0, testvar.Frequency, 4);
Assert.Equal(40, testvar.NoiseLevelApplied);
Assert.Equal(-100.0000, testvar.StrandBiasResults.GATKBiasScore);
Assert.Equal(0, testvar.FractionNoCalls);
Assert.Equal(8, testvar.ReadCollapsedCountsMut.Length);
Assert.Equal(8, testvar.ReadCollapsedCountTotal.Length);
Assert.Equal(0, testvar.ReadCollapsedCountsMut[0]);
Assert.Equal(0, testvar.ReadCollapsedCountsMut[4]);
Assert.Equal(0, testvar.ReadCollapsedCountsMut[7]);
Assert.Equal(0, testvar.ReadCollapsedCountTotal[0]);
Assert.Equal(0, testvar.ReadCollapsedCountTotal[4]);
Assert.Equal(0, testvar.ReadCollapsedCountTotal[7]);
}