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); }