public void ExtractSample_EmptySampleColumn_ReturnEmptySample()
{
var formatIndices = new FormatIndices();
var sample = SampleFieldExtractor.ExtractSample(null, formatIndices, GetSimplePositionUsingAlleleNum(1), null);
Assert.True(sample.IsEmpty);
}
public void ExtractSample_EmptySampleColumn_ReturnEmptySample()
{
var formatIndices = new FormatIndices();
var sample = SampleFieldExtractor.ExtractSample(null, formatIndices, 1);
Assert.True(sample.IsEmpty);
}
public void ExtractSample_DotInSampleColumn_ReturnEmptySample()
{
var formatIndices = new FormatIndices();
var sample = SampleFieldExtractor.ExtractSample(".", formatIndices, 1, false);
Assert.True(sample.IsEmpty);
}
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 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 = new FormatIndices();
formatIndicies.Set(formatColumn);
Assert.Equal(0, formatIndicies.AU);
Assert.Equal(7, formatIndicies.CU);
Assert.Equal(1, formatIndicies.GU);
Assert.Equal(8, formatIndicies.TU);
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(17, formatIndicies.DST);
Assert.Equal(25, formatIndicies.AQ);
Assert.Equal(26, formatIndicies.LQ);
formatIndicies.Set(null);
Assert.Null(formatIndicies.TIR);
Assert.Null(formatIndicies.AU);
formatIndicies.Set("TEMP:DPI:BOB");
Assert.Equal(1, formatIndicies.DPI);
Assert.Null(formatIndicies.AU);
}
public void ExtractSample_DragenCNV_MCN_LOH(string formatField, string sampleField)
{
var formatIndices = new FormatIndices();
formatIndices.Set(formatField);
var sample = SampleFieldExtractor.ExtractSample(sampleField, formatIndices, GetSimplePositionUsingAlleleNum(1), null);
Assert.True(sample.IsLossOfHeterozygosity);
}
public void ExtractSample_ExpansionHunter()
{
var formatIndices = new FormatIndices();
formatIndices.Set("GT:SO:REPCN:REPCI:ADSP:ADFL:ADIR:LC");
var sample = SampleFieldExtractor.ExtractSample("1/1:SPANNING/SPANNING:15/15:15-15/15-15:22/22:23/23:0/0:38.270270", formatIndices, GetSimplePositionUsingAlleleNum(1), null);
Assert.Equal("1/1", sample.Genotype);
Assert.Equal(new[] { 15, 15 }, sample.RepeatUnitCounts);
}
public void ExtractSample_DragenCNV_AsExpected()
{
var formatIndices = new FormatIndices();
formatIndices.Set("GT:CN:MCN");
var sample = SampleFieldExtractor.ExtractSample("0|1:3:1", formatIndices, GetSimplePositionUsingAlleleNum(1), null);
Assert.Equal("0|1", sample.Genotype);
Assert.Equal(3, sample.CopyNumber);
Assert.Equal(1, sample.MinorHaplotypeCopyNumber);
}
public void ExtractSample_DragenSomatic_AsExpected()
{
var formatIndices = new FormatIndices();
formatIndices.Set("GT:SQ:AD:AF:F1R2:F2R1:DP:SB:MB:PS");
var sample = SampleFieldExtractor.ExtractSample("0|1:3.96:33,8:0.195:13,6:20,2:41:17,16,4,4:13,20,4,4:534234", formatIndices, GetSimplePositionUsingAlleleNum(1), null);
Assert.Equal("0|1", sample.Genotype);
Assert.Equal(3.96, sample.SomaticQuality);
Assert.Equal(new[] { 33, 8 }, sample.AlleleDepths);
Assert.Equal(41, sample.TotalDepth);
Assert.Equal(new[] { 8 / 41.0 }, sample.VariantFrequencies);
}
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 ToSamples_SMN1_CNV()
{
// GT:AD:DST:RPL:LC
// 0/1:30,20:-:35.8981:45.810811
// GT:SM:CN:BC:QS:FT:DN
// ./1:1.24763:3:4:5:cnvLength:.
// ./.:1.17879:2:4:8:cnvLength:.
// ./1:1.26335:3:4:6:cnvLength:Inherited
var formatIndices = new FormatIndices();
string[] cols =
{
"chr1",
"125068769",
"DRAGEN:GAIN:125068770-125075279",
"N",
"<DUP>",
".",
"SampleFT",
"SVTYPE=CNV;END=125075279;REFLEN=6510",
"GT:AD:DST:RPL:LC:SM:CN:BC:QS:FT:DN",
"0/1:30,20:-:35.8981:45.810811",
"./1:.:.:.:.:1.24763:3:4:5:cnvLength:.",
"./.:.:.:.:.:1.17879:2:4:8:cnvLength:.",
"./1:.:.:.:.:1.26335:3:4:6:cnvLength:Inherited"
};
ISample[] samples = cols.ToSamples(formatIndices, GetSimplePositionUsingAlleleNum(1), null);
Assert.Equal(4, samples.Length);
Assert.Equal("0/1", samples[0].Genotype);
Assert.Equal(new[] { 30, 20 }, samples[0].AlleleDepths);
Assert.Equal(new[] { "-" }, samples[0].DiseaseAffectedStatuses);
Assert.Equal("./1", samples[1].Genotype);
Assert.Equal(3, samples[1].CopyNumber);
Assert.True(samples[1].FailedFilter);
Assert.Equal("./.", samples[2].Genotype);
Assert.Equal(2, samples[2].CopyNumber);
Assert.True(samples[2].FailedFilter);
Assert.Equal("./1", samples[3].Genotype);
Assert.Equal(3, samples[3].CopyNumber);
Assert.True(samples[3].FailedFilter);
}
public void ExtractSample_PEPE()
{
var formatIndices = new FormatIndices();
formatIndices.Set("GT:GQ:AD:DP:VF:NL:SB:NC:US:AQ:LQ");
var sample = SampleFieldExtractor.ExtractSample("0/1:5:338,1:339:0.00295:30:-7.3191:0.0314:0,0,0,1,0,0,17,1,129,21,148,22:3.366:0.000", formatIndices, GetSimplePositionUsingAlleleNum(1), null);
Assert.Equal("0/1", sample.Genotype);
Assert.Equal(5, sample.GenotypeQuality);
Assert.Equal(new[] { 338, 1 }, sample.AlleleDepths);
Assert.Equal(339, sample.TotalDepth);
Assert.Equal(new[] { 0.00295 }, sample.VariantFrequencies);
Assert.Equal(3.366f, sample.ArtifactAdjustedQualityScore);
Assert.Equal(0.000f, sample.LikelihoodRatioQualityScore);
}
public void ExtractSample_MitoHeteroplasmy_AsExpected()
{
var provider = new MitoHeteroplasmyProvider();
provider.Add(1, "C", new[] { 0.123, 0.200, 0.301 }, new[] { 1, 2, 4 });
provider.Add(1, "G", new[] { 0.101, 0.201 }, new[] { 1, 2 });
var simplePosition = new SimplePosition(ChromosomeUtilities.ChrM, 1, "A", new[] { "C", "T" });
var formatIndices = new FormatIndices();
formatIndices.Set("GT:SQ:AD:AF:F1R2:F2R1:DP:SB:MB:PS");
var sample = SampleFieldExtractor.ExtractSample("1|2:3.96:0,15,85:0.195:13,6:20,2:100:17,16,4,4:13,20,4,4:534234", formatIndices, simplePosition, provider);
Assert.Equal(new[] { 15 / 100.0, 85 / 100.0 }, sample.VariantFrequencies);
Assert.Equal(new[] { "14.29", "null" }, sample.HeteroplasmyPercentile);
}
public void ToSamples_TooFewVcfColumns_ReturnNull()
{
var formatIndices = new FormatIndices();
string[] cols =
{
"chr1",
"125068769",
"DRAGEN:GAIN:125068770-125075279",
"N",
"<DUP>",
".",
"SampleFT",
"SVTYPE=CNV;END=125075279;REFLEN=6510"
};
ISample[] samples = cols.ToSamples(formatIndices, GetSimplePositionUsingAlleleNum(1), null);
Assert.Null(samples);
}
// ReSharper restore InconsistentNaming
// ReSharper disable once SuggestBaseTypeForParameter
public IntermediateSampleFields(string[] vcfColumns, FormatIndices formatIndices, string[] sampleCols)
{
VcfRefAllele = vcfColumns[VcfCommon.RefIndex];
AltAlleles = vcfColumns[VcfCommon.AltIndex].OptimizedSplit(',');
FormatIndices = formatIndices;
SampleColumns = sampleCols;
(TAR, TIR) = GetLinkedIntegers(GetFirstValue(GetString(formatIndices.TAR, sampleCols)), GetFirstValue(GetString(formatIndices.TIR, sampleCols)));
MajorChromosomeCount = GetInteger(GetString(formatIndices.MCC, sampleCols));
DST = GetStrings(GetString(formatIndices.DST, sampleCols));
AQ = GetFloat(GetString(formatIndices.AQ, sampleCols));
LQ = GetFloat(GetString(formatIndices.LQ, sampleCols));
VF = GetDouble(GetString(formatIndices.VF, sampleCols));
CopyNumber = GetCopyNumber(GetString(formatIndices.CN, sampleCols), vcfColumns[VcfCommon.AltIndex].Contains("STR"));
(ACount, CCount, GCount, TCount, TotalAlleleCount) = GetAlleleCounts(
GetString(formatIndices.AU, sampleCols), GetString(formatIndices.CU, sampleCols),
GetString(formatIndices.GU, sampleCols), GetString(formatIndices.TU, sampleCols));
}
public void FormatIndicesTest()
{
const string formatColumn = "AD:AQ:BOB:CN:DN:DP:DST:FT:GQ:GT:LQ:PR:SR:VF";
var formatIndices = new FormatIndices();
formatIndices.Set(formatColumn);
Assert.Equal(0, formatIndices.AD);
Assert.Equal(1, formatIndices.AQ);
Assert.Equal(3, formatIndices.CN);
Assert.Equal(4, formatIndices.DN);
Assert.Equal(5, formatIndices.DP);
Assert.Equal(6, formatIndices.DST);
Assert.Equal(7, formatIndices.FT);
Assert.Equal(8, formatIndices.GQ);
Assert.Equal(9, formatIndices.GT);
Assert.Equal(10, formatIndices.LQ);
Assert.Equal(11, formatIndices.PR);
Assert.Equal(12, formatIndices.SR);
Assert.Equal(13, formatIndices.VF);
formatIndices.Set(null);
Assert.False(formatIndices.AD.HasValue);
Assert.False(formatIndices.AQ.HasValue);
Assert.False(formatIndices.CN.HasValue);
Assert.False(formatIndices.DN.HasValue);
Assert.False(formatIndices.DP.HasValue);
Assert.False(formatIndices.DST.HasValue);
Assert.False(formatIndices.FT.HasValue);
Assert.False(formatIndices.GQ.HasValue);
Assert.False(formatIndices.GT.HasValue);
Assert.False(formatIndices.LQ.HasValue);
Assert.False(formatIndices.PR.HasValue);
Assert.False(formatIndices.SR.HasValue);
Assert.False(formatIndices.VF.HasValue);
formatIndices.Set("TEMP:DP:BOB");
Assert.Equal(1, formatIndices.DP);
}
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);
}
/// <summary>
/// extracts the index from each genotype format field
/// </summary>
internal static FormatIndices Extract(string formatColumn)
{
// sanity check: make sure we have a format column
if (formatColumn == null)
{
return(null);
}
var formatIndices = new FormatIndices();
var formatCols = formatColumn.Split(':');
for (var index = 0; index < formatCols.Length; index++)
{
// ReSharper disable once SwitchStatementMissingSomeCases
switch (formatCols[index])
{
case "AU":
formatIndices.AU = index;
break;
case "CU":
formatIndices.CU = index;
break;
case "GU":
formatIndices.GU = index;
break;
case "TU":
formatIndices.TU = index;
break;
case "TAR":
formatIndices.TAR = index;
break;
case "TIR":
formatIndices.TIR = index;
break;
case "FT":
formatIndices.FT = index;
break;
case "GT":
formatIndices.GT = index;
break;
case "GQ":
formatIndices.GQ = index;
break;
case "GQX":
formatIndices.GQX = index;
break;
case "DP":
formatIndices.DP = index;
break;
case "DPI":
formatIndices.DPI = index;
break;
case "AD":
formatIndices.AD = index;
break;
case "VF":
formatIndices.VF = index;
break;
case "MCC":
formatIndices.MCC = index;
break;
case "CN":
formatIndices.CN = index;
break;
case "CI":
formatIndices.CI = index;
break;
case "NR":
formatIndices.NR = index;
break;
case "NV":
formatIndices.NV = index;
break;
case "DQ":
formatIndices.DQ = index;
break;
case "PR":
formatIndices.PR = index;
break;
case "SR":
formatIndices.SR = index;
break;
case "MAD":
formatIndices.MAD = index;
break;
case "SCH":
formatIndices.SCH = index;
break;
case "PLG":
formatIndices.PLG = index;
break;
case "PCN":
formatIndices.PCN = index;
break;
case "DCS":
formatIndices.DCS = index;
break;
case "DID":
formatIndices.DID = index;
break;
case "DST":
formatIndices.DST = index;
break;
case "PCH":
formatIndices.PCH = index;
break;
case "CHC":
formatIndices.CHC = index;
break;
case "AQ":
formatIndices.AQ = index;
break;
case "LQ":
formatIndices.LQ = index;
break;
}
}
return(formatIndices);
}
internal LegacySampleFieldExtractor(string[] vcfColumns, FormatIndices formatIndices)
{
_vcfColumns = vcfColumns;
_infoDepth = GetInfoDepth(vcfColumns[VcfCommon.InfoIndex]);
_formatIndices = formatIndices;
}
// ReSharper restore InconsistentNaming
#endregion
/// <summary>
/// extracts the index from each genotype format field
/// </summary>
internal static FormatIndices Extract(string formatColumn)
{
// sanity check: make sure we have a format column
if (formatColumn == null)
{
return(null);
}
var formatIndices = new FormatIndices();
var formatCols = formatColumn.Split(':');
for (var index = 0; index < formatCols.Length; index++)
{
switch (formatCols[index])
{
case "AU":
formatIndices.AU = index;
break;
case "CU":
formatIndices.CU = index;
break;
case "GU":
formatIndices.GU = index;
break;
case "TU":
formatIndices.TU = index;
break;
case "TAR":
formatIndices.TAR = index;
break;
case "TIR":
formatIndices.TIR = index;
break;
case "FT":
formatIndices.FT = index;
break;
case "GT":
formatIndices.GT = index;
break;
case "GQ":
formatIndices.GQ = index;
break;
case "GQX":
formatIndices.GQX = index;
break;
case "DP":
formatIndices.DP = index;
break;
case "DPI":
formatIndices.DPI = index;
break;
case "AD":
formatIndices.AD = index;
break;
case "VF":
formatIndices.VF = index;
break;
case "MCC":
formatIndices.MCC = index;
break;
case "CN":
formatIndices.CN = index;
break;
case "NR":
formatIndices.NR = index;
break;
case "NV":
formatIndices.NV = index;
break;
case "DQ":
formatIndices.DQ = index;
break;
case "PR":
formatIndices.PR = index;
break;
case "SR":
formatIndices.SR = index;
break;
}
}
return(formatIndices);
}
