public void FormatIndicesTest()
{
const string formatColumn = "AU:GU:TAR:FT:GQ:DP:VF:CU:TU:TIR:GT:GQX:BOB:DPI:NV:NR";
var formatIndicies = FormatIndices.Extract(formatColumn);
Assert.Equal(0, formatIndicies.AU);
Assert.Equal(7, formatIndicies.CU);
Assert.Equal(1, formatIndicies.GU);
Assert.Equal(8, formatIndicies.TU);
Assert.Equal(15, formatIndicies.NR);
Assert.Equal(2, formatIndicies.TAR);
Assert.Equal(9, formatIndicies.TIR);
Assert.Equal(3, formatIndicies.FT);
Assert.Equal(10, formatIndicies.GT);
Assert.Equal(4, formatIndicies.GQ);
Assert.Equal(11, formatIndicies.GQX);
Assert.Equal(5, formatIndicies.DP);
Assert.Equal(6, formatIndicies.VF);
Assert.Equal(13, formatIndicies.DPI);
Assert.Equal(14, formatIndicies.NV);
Assert.Null(FormatIndices.Extract(null));
formatIndicies = FormatIndices.Extract("TEMP:DPI:BOB");
Assert.Equal(1, formatIndicies.DPI);
Assert.Null(formatIndicies.AU);
}
public void IntermediateSampleFields_AlleleCounts()
{
const string vcfLine = "chr1\t5592503\t.\tC\tT\t900.00\tPASS\t.\tGT:AU:CU:GU:TU:DP:DPF:AD\t1/1:10,11:20,21:30,31:40,41:70:3:0,70";
var cols = vcfLine.Split('\t');
var formatIndices = FormatIndices.Extract(cols[VcfCommon.FormatIndex]);
var sampleCols = cols[VcfCommon.GenotypeIndex].Split(':');
var sampleFields = new IntermediateSampleFields(cols, formatIndices, sampleCols);
Assert.Equal(10, sampleFields.ACount);
Assert.Equal(20, sampleFields.CCount);
Assert.Equal(30, sampleFields.GCount);
Assert.Equal(40, sampleFields.TCount);
}
public void FormatIndicesTest()
{
const string formatColumn = "AU:GU:TAR:FT:GQ:DP:VF:CU:TU:TIR:GT:GQX:BOB:DPI:NV:NR:CHC:DST:PCH:DCS:DID:PLG:PCN:MAD:SCH:AQ:LQ";
var formatIndicies = FormatIndices.Extract(formatColumn);
Assert.Equal(0, formatIndicies.AU);
Assert.Equal(7, formatIndicies.CU);
Assert.Equal(1, formatIndicies.GU);
Assert.Equal(8, formatIndicies.TU);
Assert.Equal(15, formatIndicies.NR);
Assert.Equal(2, formatIndicies.TAR);
Assert.Equal(9, formatIndicies.TIR);
Assert.Equal(3, formatIndicies.FT);
Assert.Equal(10, formatIndicies.GT);
Assert.Equal(4, formatIndicies.GQ);
Assert.Equal(11, formatIndicies.GQX);
Assert.Equal(5, formatIndicies.DP);
Assert.Equal(6, formatIndicies.VF);
Assert.Equal(13, formatIndicies.DPI);
Assert.Equal(14, formatIndicies.NV);
Assert.Equal(16, formatIndicies.CHC);
Assert.Equal(17, formatIndicies.DST);
Assert.Equal(18, formatIndicies.PCH);
Assert.Equal(19, formatIndicies.DCS);
Assert.Equal(20, formatIndicies.DID);
Assert.Equal(21, formatIndicies.PLG);
Assert.Equal(22, formatIndicies.PCN);
Assert.Equal(23, formatIndicies.MAD);
Assert.Equal(24, formatIndicies.SCH);
Assert.Equal(25, formatIndicies.AQ);
Assert.Equal(26, formatIndicies.LQ);
Assert.Null(FormatIndices.Extract(null));
formatIndicies = FormatIndices.Extract("TEMP:DPI:BOB");
Assert.Equal(1, formatIndicies.DPI);
Assert.Null(formatIndicies.AU);
}