public void AddAndGetCollapsedCount_NonCollapsedBAM(ReadCollapsedType type) { int minQuality = 20; // non collapsed BAM (no reco @PG line in BAM header) var stateManager = new RegionStateManager(false, minQuality, expectStitchedReads: true); var readpair = ReadTestHelper.CreateProperReadPair("test", 6, type, pos: 10, matePos: 15); stateManager.AddAlleleCounts(readpair.Item1); stateManager.AddAlleleCounts(readpair.Item2); Assert.Equal(0, stateManager.GetCollapsedReadCount(10, type)); Assert.Equal(0, stateManager.GetCollapsedReadCount(11, type)); Assert.Equal(0, stateManager.GetCollapsedReadCount(12, type)); Assert.Equal(0, stateManager.GetCollapsedReadCount(13, type)); Assert.Equal(0, stateManager.GetCollapsedReadCount(14, type)); Assert.Equal(0, stateManager.GetCollapsedReadCount(15, type)); // overlapping Assert.Equal(0, stateManager.GetCollapsedReadCount(16, type)); Assert.Equal(0, stateManager.GetCollapsedReadCount(17, type)); Assert.Equal(0, stateManager.GetCollapsedReadCount(18, type)); Assert.Equal(0, stateManager.GetCollapsedReadCount(19, type)); Assert.Equal(0, stateManager.GetCollapsedReadCount(20, type)); Assert.Equal(0, stateManager.GetCollapsedReadCount(9, type)); }