/// <summary>
/// Writes the variant
/// </summary>
public void WriteVariant(VcfVariant variant)
{
// sanity check
if (!IsOpen)
{
throw new ApplicationException("ERROR: An attempt was made to write a variant to an unopened file.");
}
_writer.WriteLine(variant.ToString());
}
public void VennVcf_CombineTwoPoolVariants_MergeRefCalls()
{
//this is from an issue where there were multiple co-located variants in one pool,
//and just ref in the other, at chr15 92604460. The consensus answer should be
// a single ref call (and not multiple ref calls!).
var outDir = TestPaths.LocalScratchDirectory;
var vcfPathRoot = _TestDataPath;
string VcfPath_PoolA = Path.Combine(vcfPathRoot, "C64-Ct-4_S17.genome.vcf");
string VcfPath_PoolB = Path.Combine(vcfPathRoot, "C64-Ct-4_S18.genome.vcf");
string VcfPath_Consensus = Path.Combine(vcfPathRoot, "ExpectedConsensus2.vcf");
string OutputPath = Path.Combine(outDir, "Consensus2.vcf");
if (File.Exists(OutputPath))
{
File.Delete(OutputPath);
}
VennVcfOptions parameters = new VennVcfOptions();
parameters.VariantCallingParams.MinimumFrequencyFilter = 0.03f;
parameters.InputFiles = new string[] { VcfPath_PoolA, VcfPath_PoolB };
parameters.OutputDirectory = outDir; //Path.Combine(outDir, "RefMergeOut.vcf");
parameters.ConsensusFileName = OutputPath;
VennProcessor venn = new VennProcessor(parameters.InputFiles, parameters);
venn.DoPairwiseVenn(false);
Assert.Equal(File.Exists(OutputPath), true);
List <VcfVariant> CombinedVariants = VcfReader.GetAllVariantsInFile(OutputPath);
List <VcfVariant> ExpectedVariants = VcfReader.GetAllVariantsInFile(VcfPath_Consensus);
Assert.Equal(ExpectedVariants.Count, CombinedVariants.Count);
int NumVariantsAtPos92604460 = 0;
for (int i = 0; i < ExpectedVariants.Count; i++)
{
VcfVariant EVariant = ExpectedVariants[i];
VcfVariant Variant = CombinedVariants[i];
if ((Variant.ReferencePosition == 92604460) &&
(Variant.ReferenceName == "chr15"))
{
NumVariantsAtPos92604460++;
}
Assert.Equal(EVariant.ToString(), Variant.ToString());
}
Assert.Equal(NumVariantsAtPos92604460, 1);
}
public void VennVcf_FxnlTest()
{
var outDir = TestPaths.LocalScratchDirectory;
var VcfPathRoot = _TestDataPath;
string VcfA = Path.Combine(VcfPathRoot, "control_S15.vcf");
string VcfB = Path.Combine(VcfPathRoot, "control_S18.vcf");
string OutputPath = Path.Combine(outDir, "Consensus.vcf");
string ExpectedPath = Path.Combine(VcfPathRoot, "ExpectedConsensus.vcf");
VennVcfOptions parameters = new VennVcfOptions();
parameters.VariantCallingParams.MinimumFrequencyFilter = 0.03f;
parameters.VariantCallingParams.MinimumFrequency = 0.01f;
parameters.ConsensusFileName = Path.Combine(outDir, "Consensus.vcf");
parameters.OutputDirectory = outDir;
parameters.DebugMode = true;
VennProcessor Venn = new VennProcessor(new string[] { VcfA, VcfB }, parameters);
Venn.DoPairwiseVenn(false);
Assert.True(File.Exists(OutputPath));
using (VcfReader ReaderE = new VcfReader(ExpectedPath))
{
using (VcfReader ReaderO = new VcfReader(OutputPath))
{
VcfVariant ExpectedVariant = new VcfVariant();
VcfVariant OutputVariant = new VcfVariant();
while (true)
{
bool ExpectedVariantExists = ReaderE.GetNextVariant(ExpectedVariant);
bool OutputVariantExists = ReaderO.GetNextVariant(OutputVariant);
Assert.Equal(ExpectedVariantExists, OutputVariantExists);
if (!ExpectedVariantExists || !OutputVariantExists)
{
break;
}
Assert.Equal(ExpectedVariant.ToString(), OutputVariant.ToString());
}
}
}
}
