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));
}
