// tests two bams in different folders
// expectations:
// - if outputfolder is not specified, logs are in directory of first bam
// - if outputfolder specified, logs are in output folder
// - vcf files have header and both chromosomes, output is where normally expected
private void ExecuteTest(int numberOfThreads, string outputFolder = null)
{
var sourcePath = Path.Combine(TestPaths.LocalTestDataDirectory, "Chr17Chr19.bam");
var otherTestDirectory = Path.Combine(TestPaths.LocalScratchDirectory, "MultiProcessIn");
var bamFilePath1 = Stage(sourcePath, "In1", otherTestDirectory + "1");
var bamFilePath2 = Stage(sourcePath, "In2", otherTestDirectory + "2");
var genomePath = Path.Combine(TestPaths.SharedGenomesDirectory, "chr17chr19");
var options = new PiscesApplicationOptions
{
BAMPaths = new[] { bamFilePath1, bamFilePath2 },
GenomePaths = new[] { genomePath },
OutputDirectory = outputFolder,
CommandLineArguments = string.Format("-B {0},{1} -g {2}{3} -gVCF false", bamFilePath1, bamFilePath2, genomePath, string.IsNullOrEmpty(outputFolder) ? string.Empty : " -OutFolder " + outputFolder).Split(' '),
VcfWritingParameters = new VcfWritingParameters()
{
OutputGvcfFile = true
}
};
options.SetIODirectories("Pisces");
var factory = new Factory(options);
foreach (var workRequest in factory.WorkRequests)
{
if (File.Exists(workRequest.OutputFilePath))
{
File.Delete(workRequest.OutputFilePath);
}
}
Logger.OpenLog(options.LogFolder, options.LogFileName, true);
var processor = new GenomeProcessor(factory, factory.GetReferenceGenome(options.GenomePaths[0]), false, true);
processor.Execute(numberOfThreads);
Logger.CloseLog();
foreach (var workRequest in factory.WorkRequests)
{
using (var reader = new VcfReader(workRequest.OutputFilePath))
{
Assert.True(reader.HeaderLines.Any());
var variants = reader.GetVariants().ToList();
Assert.Equal(251, variants.Count());
Assert.Equal("chr17", variants.First().ReferenceName);
Assert.Equal("chr19", variants.Last().ReferenceName);
}
}
Assert.True(Directory.GetFiles(options.LogFolder, options.LogFileNameBase).Any());
}
private PiscesApplicationOptions GetBasicOptions()
{
var options = new PiscesApplicationOptions()
{
BAMPaths = new[] { _existingBamPath },
GenomePaths = new[] { _existingGenome }
};
options.SetIODirectories("Pisces");
return(options);
}
public void CheckLogFolderTest()
{
var bamFilePath = Path.Combine(TestPaths.SharedBamDirectory, "Chr17Chr19.bam");
var genomePath = Path.Combine(TestPaths.SharedGenomesDirectory, "chr17chr19");
var outDir = Path.Combine(TestPaths.LocalScratchDirectory, "PiscesApplicationsOptionsTests");
var defaultLogFolder = "PiscesLogs";
//check when an out folder is specified
var options = new PiscesApplicationOptions
{
BAMPaths = new[] { bamFilePath },
GenomePaths = new[] { genomePath },
VcfWritingParameters = new VcfWritingParameters()
{
OutputGvcfFile = false
},
OutputDirectory = outDir
};
options.SetIODirectories("Pisces");
Assert.Equal(Path.Combine(outDir, defaultLogFolder), options.LogFolder);
//check when a bam is specified w/no out folder
options = new PiscesApplicationOptions
{
BAMPaths = new[] { bamFilePath },
GenomePaths = new[] { genomePath },
VcfWritingParameters = new VcfWritingParameters()
{
OutputGvcfFile = false
},
};
options.SetIODirectories("Pisces");
Assert.Equal(Path.Combine(TestPaths.SharedBamDirectory, defaultLogFolder), options.LogFolder);
//check when a bam parent folder does not exist
options = new PiscesApplicationOptions
{
BAMPaths = new[] { "mybam.bam" },
GenomePaths = new[] { genomePath },
VcfWritingParameters = new VcfWritingParameters()
{
OutputGvcfFile = false
},
};
options.SetIODirectories("Pisces");
Assert.Equal(defaultLogFolder, options.LogFolder);
}
private void ExecuteChromosomeThreadingTest(int numberOfThreads, int expectedNumberOfThreads, string outDir)
{
var bamFilePath = Path.Combine(TestPaths.LocalTestDataDirectory, "Chr17Chr19.bam");
var vcfFilePath = Path.Combine(outDir, "Chr17Chr19.vcf");
var genomePath = Path.Combine(TestPaths.SharedGenomesDirectory, "chr17chr19");
var options = new PiscesApplicationOptions
{
BAMPaths = new[] { bamFilePath },
GenomePaths = new[] { genomePath },
VcfWritingParameters = new VcfWritingParameters()
{
OutputGvcfFile = false
},
OutputDirectory = outDir
};
options.SetIODirectories("Pisces");
var logFile = Path.Combine(options.LogFolder, options.LogFileName);
if (File.Exists(logFile))
{
File.Delete(logFile);
}
Logger.OpenLog(options.LogFolder, options.LogFileName);
var factory = new MockFactoryWithDefaults(options);
factory.MockSomaticVariantCaller = new Mock <ISmallVariantCaller>();
factory.MockSomaticVariantCaller.Setup(s => s.Execute()).Callback(() =>
{
Thread.Sleep(500);
});
var processor = new GenomeProcessor(factory, factory.GetReferenceGenome(genomePath), false);
processor.Execute(numberOfThreads);
Assert.False(File.Exists(vcfFilePath + "_chr17"));
Assert.False(File.Exists(vcfFilePath + "_chr19"));
Assert.True(File.Exists(vcfFilePath));
Logger.CloseLog();
//var threadsSpawnedBeforeFirstCompleted = 0;
/* dont worry about logging
* using (var reader = new StreamReader(new FileStream(logFile, FileMode.Open, FileAccess.Read)))
* {
* 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);
}