public Factory(HygeaOptions options) : base(options)
{
_options = options;
UpdateWorkRequests();
UpdateKnownPriors();
}
public void ExecuteTest(string inputBamFile, string outputBamFile, int expectedNumRealignedReads, int maxShift = 250)
{
if (File.Exists(outputBamFile))
{
File.Delete(outputBamFile);
}
var options = new HygeaOptions();
options.SkipAndRemoveDuplicates = false; //(old default/simple behavior for regression testing basic execution)
options.MaxRealignShift = maxShift;
var factory = new Factory(options);
var chrRef = GetGenomeSnippet();
var writer = new RemapBamWriter(inputBamFile, outputBamFile);
writer.Initialize();
var realigner = (ChrRealigner)factory.CreateRealigner(chrRef, inputBamFile, writer);
realigner.Execute();
writer.FinishAll();
Assert.True(File.Exists(outputBamFile));
Assert.Equal(expectedNumRealignedReads, realigner.TotalRealignedReads);
}
public void PopulateBAMPaths()
{
//Happy Path
var options_1 = new HygeaOptions()
{
BAMPaths = new string[] { TestPaths.LocalTestDataDirectory },
GenomePaths = new[] { _existingGenome },
};
Assert.NotNull(options_1.BAMPaths);
Assert.True(options_1.BAMPaths.Length > 0);
//no bam files found
var options_3 = new HygeaOptions()
{
BAMPaths = new string[] { TestPaths.LocalTestDataDirectory },
GenomePaths = new[] { _existingGenome },
};
var appOptions = new HygeaOptionParser()
{
Options = options_3
};
appOptions.ValidateOptions();
Assert.IsType <ArgumentException>(appOptions.ParsingResult.Exception);
}
private HygeaOptions GetBasicOptions()
{
var basicOptions = new HygeaOptions()
{
BAMPaths = new[] { _existingBamPath },
GenomePaths = new[] { _existingGenome }
};
basicOptions.SetIODirectories("Hygea");
return(basicOptions);
}
public void OpenLogTest()
{
var outDir = Path.Combine(TestPaths.LocalScratchDirectory, "HygeaTestsOutDir");
var options = new HygeaOptions();
options.OutputDirectory = outDir;
Logger.OpenLog(options.OutputDirectory, "testLog.txt", true);
Logger.CloseLog();
Assert.True(Directory.Exists(outDir));
Assert.True(File.Exists(Path.Combine(options.OutputDirectory, "testLog.txt")));
//cleanup and redirect logging
var SafeLogDir = TestPaths.LocalScratchDirectory;
Logger.OpenLog(SafeLogDir, "DefaultLog.txt", true);
Logger.CloseLog();
Directory.Delete(outDir, true);
}
public void GetLogFolder()
{
var options = GetBasicOptions();
Assert.Equal(Path.Combine(Path.GetDirectoryName(_existingBamPath), "HygeaLogs"), options.LogFolder);
// when multiple bam paths, use first bam file
options = new HygeaOptions();
var nonExistingBam = Path.Combine(TestPaths.LocalScratchDirectory, "nonexistant.bam");
options.BAMPaths = new[] { nonExistingBam, _existingBamPath };
options.SetIODirectories("Hygea");
Assert.Equal(Path.Combine(Path.GetDirectoryName(nonExistingBam), "HygeaLogs"), options.LogFolder);
// use output folder if provided
options = new HygeaOptions();
options.BAMPaths = new[] { _existingBamPath };
options.OutputDirectory = @"C:\SomeOutput";
options.SetIODirectories("Hygea");
Assert.Equal(Path.Combine(options.OutputDirectory, "HygeaLogs"), options.LogFolder);
}
public void ReadGenome()
{
Directory.CreateDirectory(_outputFolder);
var options_1 = new HygeaOptions()
{
BAMPaths = BamProcessorParsingUtils.UpdateBamPathsWithBamsFromFolder(_existingBamFolder),
GenomePaths = new[] { _existingGenome },
OutputDirectory = _outputFolder
};
var factory = new Factory(options_1);
Assert.Equal(factory.GetOutputFile(_existingBamPath), _outputFilePath);
// Run the genome processor using the filter for chr19, it will run through the IndelRealigner path as usual.
var genome = new Genome(_existingGenome, new List <string>()
{
"chr19"
});
var gp1 = new GenomeProcessor(factory, genome, "chr19");
gp1.Execute(1);
var outputFilePath = Path.Combine(_outputFolder, Path.GetFileName(_existingBamPath));
Assert.True(File.Exists(outputFilePath));
Assert.NotEqual(new FileInfo(outputFilePath).Length, new FileInfo(_existingBamPath).Length);
File.Delete(outputFilePath);
// Run the genome processor using the filter for chr18 to follow the path in GenomeProcessor.Process
// for chromosomes outside the filter.
var gp2 = new GenomeProcessor(factory, genome, "chr18");
gp2.Execute(1);
Assert.True(File.Exists(outputFilePath));
Assert.NotEqual(new FileInfo(outputFilePath).Length, new FileInfo(_existingBamPath).Length);
}
public MockFactoryWithDefaults(HygeaOptions options) : base(options)
{
}
