/// <summary>
/// returns the total depth given different sources of information
/// </summary>
public static int?GetTotalDepth(int?infoDepth, IntermediateSampleFields intermediateSampleFields)
{
// use TAR & TIR
if (intermediateSampleFields.TAR != null && intermediateSampleFields.TIR != null)
{
return(GetTotalDepthUsingTarTir(intermediateSampleFields));
}
// use base counts
if (intermediateSampleFields.TotalAlleleCount != null)
{
return(GetTotalDepthUsingAlleleCounts(intermediateSampleFields));
}
// use DPI
if (intermediateSampleFields.FormatIndices.DPI != null)
{
return(GetTotalDepthUsingDpi(intermediateSampleFields));
}
// use DP
if (intermediateSampleFields.FormatIndices.DP != null)
{
return(GetTotalDepthUsingDp(intermediateSampleFields));
}
// use NR
if (intermediateSampleFields.NR != null && intermediateSampleFields.AltAlleles.Length == 1)
{
return(intermediateSampleFields.NR);
}
// use INFO DP (Pisces)
return(infoDepth);
}
/// <summary>
/// returns the genotype quality given different sources of information
/// </summary>
public static int?GetGenotypeQuality(IntermediateSampleFields intermediateSampleFields)
{
var hasGqx = intermediateSampleFields.FormatIndices.GQX != null;
var hasGq = intermediateSampleFields.FormatIndices.GQ != null;
if (!hasGqx && !hasGq)
{
return(null);
}
var gqIndex = hasGqx ? intermediateSampleFields.FormatIndices.GQX.Value : intermediateSampleFields.FormatIndices.GQ.Value;
if (intermediateSampleFields.SampleColumns.Length <= gqIndex)
{
return(null);
}
var gq = intermediateSampleFields.SampleColumns[gqIndex];
if (int.TryParse(gq, out int num))
{
return(num);
}
return(null);
}
public void GetInteger_ReturnNull()
{
var observedResult = IntermediateSampleFields.GetInteger("test");
Assert.Null(observedResult);
observedResult = IntermediateSampleFields.GetInteger(null);
Assert.Null(observedResult);
}
public void GetBool_ReturnFalse()
{
var observedResult = IntermediateSampleFields.GetBool("bob", "test");
Assert.False(observedResult);
observedResult = IntermediateSampleFields.GetBool(null, "test");
Assert.False(observedResult);
}
/// <summary>
/// returns the genotype flag
/// </summary>
public static string GetGenotype(IntermediateSampleFields intermediateSampleFields)
{
if (intermediateSampleFields.FormatIndices.GT == null)
{
return(null);
}
var genotype = intermediateSampleFields.SampleColumns[intermediateSampleFields.FormatIndices.GT.Value];
return(genotype == "." ? null : genotype);
}
/// <summary>
/// returns the failed filter flag
/// </summary>
public static bool GetFailedFilter(IntermediateSampleFields intermediateSampleFields)
{
if (intermediateSampleFields.FormatIndices.FT == null)
{
return(false);
}
var filterValue = intermediateSampleFields.SampleColumns[intermediateSampleFields.FormatIndices.FT.Value];
return(filterValue != "PASS" && filterValue != ".");
}
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);
}
/// <summary>
/// returns the total depth using DP
/// </summary>
private static int?GetTotalDepthUsingDp(IntermediateSampleFields intermediateSampleFields)
{
if (intermediateSampleFields.FormatIndices.DP == null || intermediateSampleFields.SampleColumns.Length <= intermediateSampleFields.FormatIndices.DP.Value)
{
return(null);
}
var depth = intermediateSampleFields.SampleColumns[intermediateSampleFields.FormatIndices.DP.Value];
if (int.TryParse(depth, out int num))
{
return(num);
}
return(null);
}
public static int[] GetPairEndReadCounts(IntermediateSampleFields intermediateSampleFields)
{
if (intermediateSampleFields.FormatIndices.PR == null)
{
return(null);
}
var readCounts = intermediateSampleFields.SampleColumns[intermediateSampleFields.FormatIndices.PR.Value].Split(',');
var pairEndReadCounts = new int[readCounts.Length];
for (int i = 0; i < pairEndReadCounts.Length; i++)
{
if (!int.TryParse(readCounts[i], out var num))
{
return(null);
}
pairEndReadCounts[i] = num;
}
return(pairEndReadCounts);
}
public static int[] GetSplitReadCounts(IntermediateSampleFields intermediateSampleFields)
{
if (intermediateSampleFields.FormatIndices.SR == null)
{
return(null);
}
var splitReadCounts = intermediateSampleFields.SampleColumns[intermediateSampleFields.FormatIndices.SR.Value].Split(',');
var splitReads = new int[splitReadCounts.Length];
for (int i = 0; i < splitReads.Length; i++)
{
if (!int.TryParse(splitReadCounts[i], out var num))
{
return(null);
}
splitReads[i] = num;
}
return(splitReads);
}
public void GetBool_ReturnTrue()
{
var observedResult = IntermediateSampleFields.GetBool("test", "test");
Assert.True(observedResult);
}
public void GetInteger_ReturnInteger()
{
var observedResult = IntermediateSampleFields.GetInteger("1234");
Assert.Equal(1234, observedResult);
}
public void GetFloat_ReturnFloat()
{
var observedResult = IntermediateSampleFields.GetFloat("1.23");
Assert.Equal(1.23f, observedResult);
}
/// <summary>
/// returns the total depth using tier 1 allele counts
/// </summary>
private static int?GetTotalDepthUsingAlleleCounts(IntermediateSampleFields intermediateSampleFields)
{
return(intermediateSampleFields.TotalAlleleCount);
}
/// <summary>
/// returns the total depth using TAR & TIR
/// </summary>
private static int?GetTotalDepthUsingTarTir(IntermediateSampleFields intermediateSampleFields)
{
return(intermediateSampleFields.TAR + intermediateSampleFields.TIR);
}
