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));
}
