public PairHandler(Dictionary <int, string> refIdMapping, IAlignmentStitcher stitcher, bool filterUnstitchablePairs, ReadStatusCounter statusCounter)
{
_refIdMapping = refIdMapping;
_stitcher = stitcher;
_filterUnstitchablePairs = filterUnstitchablePairs;
_statusCounter = statusCounter;
_stitcher.SetStatusCounter(_statusCounter);
}
public PairHandler(Dictionary <int, string> refIdMapping, IAlignmentStitcher stitcher, ReadStatusCounter statusCounter, bool filterUnstitchablePairs = false, bool tryStitch = true)
{
_refIdMapping = refIdMapping;
_stitcher = stitcher;
_filterUnstitchablePairs = filterUnstitchablePairs;
_masterStatusCounter = statusCounter;
_statusCounter = new ReadStatusCounter();
_stitcher.SetStatusCounter(_statusCounter);
_tryStitch = tryStitch;
}