private void CallVariantsWithMockData(string vcfOutputPath, ApplicationOptions options, AmpliconTestFactory atf)
{
var appFactory = new MockFactoryWithDefaults(options);
using (var vcfWriter = appFactory.CreateVcfWriter(vcfOutputPath, new VcfWriterInputContext()))
{
var svc = CreateMockVariantCaller(vcfWriter, options, atf.ChrInfo, atf._MAE);
vcfWriter.WriteHeader();
svc.Execute();
}
Assert.True(File.Exists(vcfOutputPath));
}
public static void CallStrandedVariantsWithMockData(string vcfOutputPath, ApplicationOptions options, AmpliconTestFactory testFactory)
{
var appFactory = new MockFactoryWithDefaults(options);
using (var vcfWriter = appFactory.CreateVcfWriter(vcfOutputPath, new VcfWriterInputContext()))
{
using (var biasWriter = new StrandBiasFileWriter(vcfOutputPath))
{
var svc = CreateMockVariantCaller(vcfWriter, options, testFactory.ChrInfo, testFactory.AlignmentExtractor, biasWriter);
vcfWriter.WriteHeader();
biasWriter.WriteHeader();
svc.Execute();
biasWriter.Dispose();
}
}
Assert.True(File.Exists(vcfOutputPath));
}