public ValidationParser(PileupProcessorOptions options, MpileupResult result) { _options = options; _parser = options.GetPileupItemParser(false); _rdFilter = new PileupItemReadDepthFilter(options.MinimumReadDepth, options.MinimumBaseQuality); _normalTest = new PileupItemNormalTest(options.MaximumPercentageOfMinorAlleleInNormal); _tumorTest = new PileupItemTumorTest(options.MinimumReadsOfMinorAlleleInTumor, options.MinimumPercentageOfMinorAlleleInTumor); _result = result; }
public void TestAccept() { //only sample2 will be used to do the test var f = new FisherExactTestResult(); f.Sample1.Failed = 0; f.Sample1.Succeed = 0; f.Sample2.Failed = 3; f.Sample2.Succeed = 30; var t = new PileupItemTumorTest(1, 0.1); Assert.IsFalse(t.Accept(f)); //test minimum percentage f.Sample2.Failed = 4; Assert.IsTrue(t.Accept(f)); //test minimum reads t = new PileupItemTumorTest(5, 0.1); Assert.IsFalse(t.Accept(f)); }