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 TestCommandLineGeneration()
{
var jobManager = new Mock <IJobManager>();
List <IJob> jobs = null;
jobManager.Setup(x => x.Process(It.IsAny <List <IJob> >()))
.Callback <List <IJob> >(x => jobs = x);
List <ChrReference> chrRef = new List <ChrReference>()
{
new ChrReference()
{
Name = "chr19", Sequence = "AAA"
},
new ChrReference()
{
Name = "chrX", Sequence = "AAA"
},
};
var genome = new MockGenome(chrRef);
var files = new[] { @"C:\foo\foo.bam", @"C:\foo\bar.bam" };
var processor = new MyProcessor(genome, jobManager.Object, files,
new[] { "-bamFoLder", @"C:\foo", "-maxNumThreads", "5", "-outFOLDER", @"C:\blee" },
@"C:\blee", "");
processor.Execute(0);
// should be 1 job for each file x each chromosome
Assert.NotNull(jobs);
var realJobs = jobs.Cast <ExternalProcessJob>().ToArray();
Assert.Equal(4, realJobs.Length);
Assert.Equal(0, realJobs.Count(x => x.CommandLineArguments.Contains("outFOLDER")));
Assert.Equal(0, realJobs.Count(x => x.CommandLineArguments.Contains("bamFoLder")));
Assert.Equal(2, realJobs.Count(x => x.CommandLineArguments.Contains(@"-OutFolder C:\blee\chr19")));
Assert.Equal(2, realJobs.Count(x => x.CommandLineArguments.Contains(@"-OutFolder C:\blee\chrX")));
Assert.Equal(2, realJobs.Count(x => x.CommandLineArguments.Contains(@"-bampaths C:\foo\foo.bam")));
Assert.Equal(2, realJobs.Count(x => x.CommandLineArguments.Contains(@"-bampaths C:\foo\bar.bam")));
Assert.Equal(2, realJobs.Count(x => x.CommandLineArguments.Contains("-chrfilter chr19")));
Assert.Equal(2, realJobs.Count(x => x.CommandLineArguments.Contains("-chrfilter chrX")));
Assert.Equal(4, realJobs.Count(x => x.CommandLineArguments.Contains("-InsideSubProcess true")));
Assert.Equal(4, realJobs.Count(x => x.CommandLineArguments.Contains("-MaxNumThreads 1")));
}
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)));
}
}
}
public void Execute(
string bamFilePath,
string vcfFilePath,
string intervalPath,
List <CalledAllele> 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,
PiscesApplicationOptions applicationOptions = null,
bool collapse = true)
{
if (doCheckReferences)
{
vcfFilePath = Path.ChangeExtension(vcfFilePath, "genome.vcf");
}
if (applicationOptions == null)
{
applicationOptions = new PiscesApplicationOptions
{
BAMPaths = new[] { bamFilePath },
IntervalPaths = string.IsNullOrEmpty(intervalPath) ? null : new[] { intervalPath },
GenomePaths = new[] { GenomeDirectory },
OutputBiasFiles = true,
DebugMode = doLog,
CallMNVs = callMnvs,
MaxGapBetweenMNV = 10,
MaxSizeMNV = 15,
Collapse = collapse,
BamFilterParameters = new BamFilterParameters()
{
MinimumBaseCallQuality = 20
},
VariantCallingParameters = new VariantCallingParameters(),
VcfWritingParameters = new VcfWritingParameters()
{
OutputGvcfFile = doCheckReferences,
},
CommandLineArguments = new string[] { "some", "cmds" }
};
}
applicationOptions.OutputDirectory = OutputDirectory;
var factory = GetFactory(applicationOptions);
IGenome genome;
if (fakeReferences == null)
{
genome = factory.GetReferenceGenome(GenomeDirectory);
}
else
{
genome = new MockGenome(fakeReferences, GenomeDirectory);
}
if (threadByChr)
{
var processor = new GenomeProcessor(factory, genome, false);
processor.Execute(1);
}
else
{
var processor = new GenomeProcessor(factory, genome);
processor.Execute(1);
}
var alleles = AlleleReader.GetAllVariantsInFile(vcfFilePath);
var variantCalls = alleles.Where(a => !a.IsRefType).ToList();
if (doCheckVariants)
{
if (doCountsOnly > 0)
{
Assert.Equal(variantCalls.Count(), doCountsOnly);
}
else
{
CheckVariants(variantCalls, expectedVariants);
}
}
if (doCheckReferences)
{
var referenceAlleles = alleles.Where(a => a.IsRefType).ToList();
// make sure no reference calls at variant positions
Assert.Equal(referenceAlleles.Count(),
alleles.Count(a => !variantCalls.Select(v => v.ReferencePosition).Contains(a.ReferencePosition)));
}
}
public void Pisces_LowDepthTest()
{
List <ChrReference> chrRef = new List <ChrReference>()
{
new ChrReference()
{
Name = "chr19",
Sequence = "TTGTCAGTGCGCTTTTCCCAACACCACCTGCTCCGACCACCACCAGTTTGTACTCAGTCATTTCACACCAGCAAGAACCTGTTGGAAACCAGTAATCAGGGTTAATTGGCGGCGAAAAAAAAAAAAAAAAAAAAAAAAAA"
}
};
var options = new PiscesApplicationOptions()
{
BAMPaths = new[] { _bamSmallS1 },
GenomePaths = new[] { _genomeChr19 },
//IntervalPaths = new[] { _intervalsChr17Chr19 },
DebugMode = true,
CallMNVs = true,
UseMNVReallocation = false,
MaxSizeMNV = 100,
OutputDirectory = TestPaths.LocalTestDataDirectory,
BamFilterParameters = new Domain.Options.BamFilterParameters()
{
MinimumBaseCallQuality = 20
},
VariantCallingParameters = new Domain.Options.VariantCallingParameters()
{
MinimumVariantQScore = 20,
MinimumCoverage = 1000,
},
VcfWritingParameters = new Domain.Options.VcfWritingParameters()
{
OutputGvcfFile = true,
}
};
var vcfFilePath = Path.ChangeExtension(options.BAMPaths[0], "genome.vcf");
var factory = new Factory(options);
IGenome genomeRef;
genomeRef = new MockGenome(chrRef, _genomeChr19);
var bp = new GenomeProcessor(factory, genomeRef);
bp.Execute(1);
var coverage1000results = AlleleReader.GetAllVariantsInFile(vcfFilePath);
options = new PiscesApplicationOptions()
{
BAMPaths = new[] { _bamSmallS1 },
GenomePaths = new[] { _genomeChr19 },
// IntervalPaths = new[] { _intervalsChr17Chr19 },
DebugMode = true,
CallMNVs = true,
UseMNVReallocation = false,
OutputDirectory = TestPaths.LocalTestDataDirectory,
VcfWritingParameters = new Domain.Options.VcfWritingParameters()
{
OutputGvcfFile = false,
}
};
factory = new Factory(options);
bp = new GenomeProcessor(factory, genomeRef);
bp.Execute(1);
var coverage10results = AlleleReader.GetAllVariantsInFile(vcfFilePath);
}
