예제 #1
0
 public void PrintOptionsTest()
 {
     try
     {
         ApplicationOptions.PrintUsageInfo();
         Assert.True(true);
     }
     catch
     {
         Assert.True(false);
     }
 }
예제 #2
0
        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));
        }
예제 #3
0
        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));
        }