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);
}