public void CallSomaticVariants_LowDepthTest()
{
List <ChrReference> chrRef = new List <ChrReference>()
{
new ChrReference()
{
Name = "chr19",
Sequence = "TTGTCAGTGCGCTTTTCCCAACACCACCTGCTCCGACCACCACCAGTTTGTACTCAGTCATTTCACACCAGCAAGAACCTGTTGGAAACCAGTAATCAGGGTTAATTGGCGGCGAAAAAAAAAAAAAAAAAAAAAAAAAA"
}
};
var options = new ApplicationOptions()
{
BAMPaths = new[] { _bamSmallS1 },
GenomePaths = new[] { _genomeChr19 },
//IntervalPaths = new[] { _intervalsChr17Chr19 },
DebugMode = true,
CallMNVs = true,
UseMNVReallocation = false,
MaxSizeMNV = 100,
OutputgVCFFiles = true,
MinimumCoverage = 1000,
OutputFolder = UnitTestPaths.TestDataDirectory
};
var vcfFilePath = Path.ChangeExtension(options.BAMPaths[0], "genome.vcf");
var factory = new Factory(options);
IGenome genomeRef;
genomeRef = new MockGenome(chrRef);
var bp = new BamProcessor(factory, genomeRef);
bp.Execute(1);
List <VcfVariant> coverage1000results = VcfReader.GetAllVariantsInFile(vcfFilePath);
options = new ApplicationOptions()
{
BAMPaths = new[] { _bamSmallS1 },
GenomePaths = new[] { _genomeChr19 },
// IntervalPaths = new[] { _intervalsChr17Chr19 },
DebugMode = true,
CallMNVs = true,
UseMNVReallocation = false,
OutputgVCFFiles = true,
OutputFolder = UnitTestPaths.TestDataDirectory
};
factory = new Factory(options);
bp = new BamProcessor(factory, genomeRef);
bp.Execute(1);
List <VcfVariant> coverage10results = VcfReader.GetAllVariantsInFile(vcfFilePath);
// Assert.NotEqual(coverage1000results.Count, coverage10results.Count);
// Assert.Equal(coverage1000results.Count, 84);
// Assert.Equal(coverage10results.Count, 100);
}
public void Execute()
{
var factory = new Factory(_options);
if (!_options.ThreadByChr)
{
var distinctGenomeDirectories = _options.GenomePaths.Distinct();
foreach (var genomeDirectory in distinctGenomeDirectories)
{
var genome = factory.GetReferenceGenome(genomeDirectory);
var genomeProcessor = new GenomeProcessor(factory, genome);
genomeProcessor.Execute(_options.MaxNumThreads);
}
}
else
{
var workRequest = factory.WorkRequests.First();
var genome = factory.GetReferenceGenome(workRequest.GenomeDirectory);
var bamProcessor = new BamProcessor(factory, genome);
bamProcessor.Execute(_options.MaxNumThreads);
}
}
public void Execute(
string bamFilePath,
string vcfFilePath,
string intervalPath,
List <BaseCalledAllele> expectedVariants,
List <ChrReference> fakeReferences = null,
bool doCheckVariants = true,
bool doCheckReferences = false,
int expectedNumCoveredPositions = 0,
bool threadByChr = false,
int doCountsOnly = 0,
bool doLog = false,
bool callMnvs = true,
ApplicationOptions applicationOptions = null)
{
if (doCheckReferences)
{
vcfFilePath = Path.ChangeExtension(vcfFilePath, "genome.vcf");
}
if (applicationOptions == null)
{
applicationOptions = new ApplicationOptions
{
BAMPaths = new[] { bamFilePath },
IntervalPaths = string.IsNullOrEmpty(intervalPath) ? null : new[] { intervalPath },
GenomePaths = new[] { GenomeDirectory },
OutputgVCFFiles = doCheckReferences,
OutputBiasFiles = true,
DebugMode = doLog,
MinimumBaseCallQuality = 20,
CallMNVs = callMnvs
};
}
Logger.TryOpenLog(applicationOptions.LogFolder, ApplicationOptions.LogFileName);
var factory = GetFactory(applicationOptions);
IGenome genome;
if (fakeReferences == null)
{
genome = factory.GetReferenceGenome(GenomeDirectory);
}
else
{
genome = new MockGenome(fakeReferences, GenomeDirectory);
}
if (threadByChr)
{
var processor = new BamProcessor(factory, genome);
processor.Execute(1);
}
else
{
var processor = new GenomeProcessor(factory, genome);
processor.Execute(1);
}
Logger.TryCloseLog();
using (var reader = new VcfReader(vcfFilePath))
{
var alleles = reader.GetVariants().ToList();
var variantCalls = alleles.Where(a => a.VariantAlleles[0] != ".").ToList();
if (doCheckVariants)
{
if (doCountsOnly > 0)
{
Assert.Equal(variantCalls.Count(), doCountsOnly);
}
else
{
CheckVariants(variantCalls, expectedVariants);
}
}
if (doCheckReferences)
{
var referenceAlleles = alleles.Where(a => a.VariantAlleles[0] == ".").ToList();
// make sure no reference calls at variant positions
Assert.Equal(referenceAlleles.Count(), alleles.Count(a => !variantCalls.Select(v => v.ReferencePosition).Contains(a.ReferencePosition)));
}
}
}
private void ExecuteChromosomeThreadingTest(int numberOfThreads, int expectedNumberOfThreads)
{
var bamFilePath = Path.Combine(UnitTestPaths.TestDataDirectory, "var123var35.bam");
var vcfFilePath = Path.Combine(UnitTestPaths.TestDataDirectory, "var123var35.vcf");
var genomePath = Path.Combine(UnitTestPaths.TestGenomesDirectory, "chr17chr19");
var options = new ApplicationOptions
{
BAMPaths = new[] { bamFilePath },
GenomePaths = new[] { genomePath },
};
var logFile = Path.Combine(options.LogFolder, ApplicationOptions.LogFileName);
if (File.Exists(logFile))
{
File.Delete(logFile);
}
Logger.TryOpenLog(options.LogFolder, ApplicationOptions.LogFileName);
var factory = new MockFactoryWithDefaults(options);
factory.MockSomaticVariantCaller = new Mock <ISomaticVariantCaller>();
factory.MockSomaticVariantCaller.Setup(s => s.Execute()).Callback(() =>
{
Thread.Sleep(500);
});
var processor = new BamProcessor(factory, factory.GetReferenceGenome(genomePath));
processor.Execute(numberOfThreads);
Assert.False(File.Exists(vcfFilePath + "_chr17"));
Assert.False(File.Exists(vcfFilePath + "_chr19"));
Assert.True(File.Exists(vcfFilePath));
Logger.TryCloseLog();
var threadsSpawnedBeforeFirstCompleted = 0;
using (var reader = new StreamReader(logFile))
{
string line;
while ((line = reader.ReadLine()) != null)
{
if (string.IsNullOrEmpty(line))
{
continue;
}
if (line.Contains("Completed processing chr"))
{
break;
}
if (line.Contains("Start processing chr"))
{
threadsSpawnedBeforeFirstCompleted++;
}
}
}
Assert.Equal(expectedNumberOfThreads, threadsSpawnedBeforeFirstCompleted);
}