protected override void ProgramExecution()
{
AdjustOptions(ref _options);
try
{
var factory = new Factory(_options);
var variantPhaser = new VariantPhaser(factory);
variantPhaser.Execute(_options.NumThreads);
}
catch (Exception ex)
{
var wrappedException = new Exception("Unable to process: " + ex.Message, ex);
Logger.WriteExceptionToLog(wrappedException);
throw wrappedException;
}
}
public void GetPhasingProbabilities()
{
var variantSites = new List <VariantSite>
{
new VariantSite(1),
new VariantSite(2),
new VariantSite(45)
};
var clusters = new SetOfClusters(new ClusteringParameters());
// There should be a PhasingResult for each variant in variantSites
var phasingProbabilities = VariantPhaser.GetPhasingProbabilities(variantSites, clusters);
Assert.Equal(variantSites.Count, phasingProbabilities.Count);
Assert.Equal(variantSites.Select(x => x), phasingProbabilities.Keys.ToList());
}
private void ExecuteNeighborhoodThreadingTest(int numberOfThreads, int expectedNumberOfThreads)
{
var bamFilePath = Path.Combine(TestPaths.LocalTestDataDirectory, "MNV-25-var216_S216.bam");
var vcfFilePath = Path.Combine(TestPaths.LocalTestDataDirectory, "MNV-25-var216_S216.vcf");
var outFolder = Path.Combine(TestPaths.LocalScratchDirectory, "Out");
var options = new ScyllaApplicationOptions
{
BamPath = bamFilePath,
VcfPath = vcfFilePath,
OutputDirectory = outFolder
};
options.SetIODirectories("Scylla");
var logFile = Path.Combine(options.LogFolder, options.LogFileNameBase);
if (File.Exists(logFile))
{
File.Delete(logFile);
}
var factory = new MockFactoryWithDefaults(options);
factory.MockVcfWriter = new Mock <IVcfFileWriter <CalledAllele> >();
factory.MockVcfWriter.Setup(s => s.Write(It.IsAny <IEnumerable <CalledAllele> >(), It.IsAny <IRegionMapper>())).Callback(() =>
{
Thread.Sleep(500);
});
var neighborhoods = GetNeighborhoods(expectedNumberOfThreads);
factory.MockNeighborhoodBuilder = new Mock <INeighborhoodBuilder>();
factory.MockNeighborhoodBuilder.Setup(s => s.GetBatchOfNeighborhoods(0))
.Returns(neighborhoods);
factory.MockVeadSource = MockVeadSource();
factory.MockVariantSource = new Mock <IVcfVariantSource>();
factory.MockVariantSource.Setup(s => s.GetVariants()).Returns(new List <VcfVariant>()
{
new VcfVariant()
{
ReferenceName = "chr1",
ReferencePosition = 123,
VariantAlleles = new[] { "A" },
GenotypeTagOrder = new[] { "GT", "GQ", "AD", "VF", "NL", "SB", "NC" },
InfoTagOrder = new[] { "DP" },
Genotypes = new List <Dictionary <string, string> >()
{
new Dictionary <string, string>()
{
{ "GT", "0/1" },
{ "GQ", "100" },
{ "AD", "6830,156" },
{ "VF", "0.05" },
{ "NL", "20" },
{ "SB", "-20" },
{ "NC", "0.01" }
}
},
InfoFields = new Dictionary <string, string>()
{
{ "DP", "1000" }
},
ReferenceAllele = "C"
},
new VcfVariant()
{
ReferenceName = "chr2",
ReferencePosition = 123,
VariantAlleles = new[] { "A" },
GenotypeTagOrder = new[] { "GT", "GQ", "AD", "VF", "NL", "SB", "NC" },
InfoTagOrder = new[] { "DP" },
Genotypes = new List <Dictionary <string, string> >()
{
new Dictionary <string, string>()
{
{ "GT", "0/1" },
{ "GQ", "100" },
{ "AD", "6830,156" },
{ "VF", "0.05" },
{ "NL", "20" },
{ "SB", "-20" },
{ "NC", "0.01" }
}
},
InfoFields = new Dictionary <string, string>()
{
{ "DP", "1000" }
},
ReferenceAllele = "T"
}
});
Logger.OpenLog(options.LogFolder, options.LogFileNameBase, true);
var processor = new VariantPhaser(factory);
processor.Execute(numberOfThreads);
Logger.CloseLog();
var threadsSpawnedBeforeFirstCompleted = 0;
using (var reader = new StreamReader(new FileStream(logFile, FileMode.Open)))
{
string line;
while ((line = reader.ReadLine()) != null)
{
if (string.IsNullOrEmpty(line))
{
continue;
}
if (line.Contains("Completed processing"))
{
break;
}
if (line.Contains("Processing Neighborhood"))
{
threadsSpawnedBeforeFirstCompleted++;
}
}
}
Assert.Equal(expectedNumberOfThreads, threadsSpawnedBeforeFirstCompleted);
}
private void ExecuteNeighborhoodThreadingTest(int numberOfThreads, int expectedNumberOfThreads)
{
var bamFilePath = Path.Combine(TestPaths.LocalTestDataDirectory, "MNV-25-var216_S216.bam");
var vcfFilePath = Path.Combine(TestPaths.LocalTestDataDirectory, "MNV-25-var216_S216.vcf");
var outFolder = Path.Combine(TestPaths.LocalScratchDirectory, "Out");
var options = new ScyllaApplicationOptions
{
BamPath = bamFilePath,
VcfPath = vcfFilePath,
OutputDirectory = outFolder
};
options.SetIODirectories("Scylla");
var logFile = Path.Combine(options.LogFolder, options.LogFileNameBase);
if (File.Exists(logFile))
{
File.Delete(logFile);
}
var factory = new MockFactoryWithDefaults(options);
factory.MockVcfWriter = new Mock <IVcfFileWriter <CalledAllele> >();
factory.MockVcfWriter.Setup(s => s.Write(It.IsAny <IEnumerable <CalledAllele> >(), It.IsAny <IRegionMapper>())).Callback(() =>
{
Thread.Sleep(500);
});
var neighborhoods = GetNeighborhoods(expectedNumberOfThreads);
factory.MockNeighborhoodBuilder = new Mock <INeighborhoodBuilder>();
var numRaw = 0;
factory.MockNeighborhoodBuilder.Setup(s => s.GetBatchOfCallableNeighborhoods(0, out numRaw))
.Returns(neighborhoods);
factory.MockVeadSource = MockVeadSource();
factory.MockVariantSource = new Mock <IAlleleSource>();
factory.MockVariantSource.Setup(s => s.GetVariants()).Returns(new List <CalledAllele>()
{
new CalledAllele()
{
Chromosome = "chr1",
ReferencePosition = 123,
AlternateAllele = "A",
ReferenceAllele = "C",
Genotype = Pisces.Domain.Types.Genotype.HeterozygousAltRef,
TotalCoverage = 10000
},
new CalledAllele()
{
Chromosome = "chr2",
ReferencePosition = 123,
AlternateAllele = "A",
ReferenceAllele = "T",
Genotype = Pisces.Domain.Types.Genotype.HeterozygousAltRef,
TotalCoverage = 10000
}
});
Logger.OpenLog(options.LogFolder, options.LogFileNameBase, true);
var processor = new VariantPhaser(factory);
processor.Execute(numberOfThreads);
Logger.CloseLog();
var threadsSpawnedBeforeFirstCompleted = 0;
using (var reader = new StreamReader(new FileStream(logFile, FileMode.Open)))
{
string line;
while ((line = reader.ReadLine()) != null)
{
if (string.IsNullOrEmpty(line))
{
continue;
}
if (line.Contains("Completed processing"))
{
break;
}
if (line.Contains("Processing Neighborhood"))
{
threadsSpawnedBeforeFirstCompleted++;
}
}
}
Assert.Equal(expectedNumberOfThreads, threadsSpawnedBeforeFirstCompleted);
}
