private void ExecuteParsingTest(string arguments, bool shouldPass, Action <ApplicationOptions> assertions = null)
{
var options = ApplicationOptions.ParseCommandLine(arguments.Split(' '));
if (shouldPass)
{
if (assertions != null)
{
assertions(options);
}
}
else
{
Assert.Null(options);
}
}
public void PrintAndSaveApplicationLegacyOptions()
{
ApplicationOptions.PrintUsageInfo();
var bamFolder = UnitTestPaths.TestDataDirectory;
var applicationOptionsFile = Path.Combine(UnitTestPaths.TestDataDirectory, "SomaticVariantCallerOptions.used.xml");
if (File.Exists(applicationOptionsFile))
{
File.Delete(applicationOptionsFile);
}
var commandLine1 = string.Format("-minvq 40 -minbq 40 -BAMFolder {0} -t 1000 -g {1} -vqfilter 40", bamFolder, _existingGenome);
var options1 = ApplicationOptions.ParseCommandLine(commandLine1.Split(' '));
options1.Save(applicationOptionsFile);
Assert.True(File.Exists(applicationOptionsFile));
}
public void PrintAndSaveApplicationOptions()
{
ApplicationOptions.PrintUsageInfo();
var bamFolder = UnitTestPaths.TestDataDirectory;
var applicationOptionsFile = Path.Combine(UnitTestPaths.TestDataDirectory, "SomaticVariantCallerOptions.used.xml");
if (File.Exists(applicationOptionsFile))
{
File.Delete(applicationOptionsFile);
}
var commandLine1 = string.Format("-MinVariantQScore 40 -MinBaseCallQuality 40 -BAMFolder {0} -MaxNumThreads 1000 -GenomePaths {1} -VariantQualityFilter 40", bamFolder, _existingGenome);
var options1 = ApplicationOptions.ParseCommandLine(commandLine1.Split(' '));
options1.Save(applicationOptionsFile);
Assert.True(File.Exists(applicationOptionsFile));
}
public void MaxNumberThreads()
{
string bamFolder = UnitTestPaths.TestDataDirectory;
var commandLine1 = string.Format("-minvq 40 -minbq 40 -BAMFolder {0} -t 1000 -g {1} -vqfilter 40", bamFolder, _existingGenome);
var options1 = ApplicationOptions.ParseCommandLine(commandLine1.Split(' '));
Assert.Equal(Environment.ProcessorCount, options1.MaxNumThreads);
var commandLine2 = string.Format("-minvq 40 -minbq 40 -BAMFolder {0} -g {1} -vqfilter 40", bamFolder, _existingGenome);
var options2 = ApplicationOptions.ParseCommandLine(commandLine2.Split(' '));
Assert.Equal(Environment.ProcessorCount, options2.MaxNumThreads);
var commandLine3 = string.Format("-minvq 40 -minbq 40 -BAMFolder {0} -g {1} -vqfilter 40 -t 1", bamFolder, _existingGenome);
var options3 = ApplicationOptions.ParseCommandLine(commandLine3.Split(' '));
Assert.Equal(1, options3.MaxNumThreads);
}