public BasicStitcher(int minBaseCallQuality, bool nifyDisagreements = true, bool useSoftclippedBases = true, bool debug = false,
bool nifyUnstitchablePairs = false, bool allowRescuedInsertionBaseDisagreement = false, bool ignoreProbeSoftclips = true, int maxReadLength = 1024)
{
_nifyUnstitchablePairs = nifyUnstitchablePairs;
_ignoreProbeSoftclips = ignoreProbeSoftclips;
_useSoftclippedBases = useSoftclippedBases;
_debug = debug;
_statusCounter = new ReadStatusCounter();
_cigarReconciler = new CigarReconciler(_statusCounter, _useSoftclippedBases, _debug, _ignoreProbeSoftclips, maxReadLength);
_readMerger = new ReadMerger(minBaseCallQuality, allowRescuedInsertionBaseDisagreement, _useSoftclippedBases,
nifyDisagreements, _statusCounter, _debug, _ignoreProbeSoftclips);
}
public BasicStitcher(int minBaseCallQuality, bool nifyDisagreements = true, bool useSoftclippedBases = true, bool debug = false,
bool nifyUnstitchablePairs = false, bool allowRescuedInsertionBaseDisagreement = false, bool ignoreProbeSoftclips = true, int maxReadLength = 1024,
bool ignoreReadsAboveMaxLength = false, uint minMapQuality = 1, bool dontStitchHomopolymerBridge = true, int thresholdNumDisagreeingBases = int.MaxValue)
{
_nifyUnstitchablePairs = nifyUnstitchablePairs;
_ignoreProbeSoftclips = ignoreProbeSoftclips;
_useSoftclippedBases = useSoftclippedBases;
_debug = debug;
_minMapQuality = minMapQuality;
_dontStitchHomopolymerBridge = dontStitchHomopolymerBridge;
_statusCounter = new ReadStatusCounter();
_cigarReconciler = new CigarReconciler(_statusCounter, _useSoftclippedBases, _debug, _ignoreProbeSoftclips, maxReadLength, minBaseCallQuality, ignoreReadsAboveMaxStitchedLength: ignoreReadsAboveMaxLength, nifyDisagreements: nifyDisagreements);
_readMerger = new ReadMerger(minBaseCallQuality, allowRescuedInsertionBaseDisagreement, _useSoftclippedBases,
nifyDisagreements, _statusCounter, _debug, _ignoreProbeSoftclips);
_thresholdNumDisagreeingBases = thresholdNumDisagreeingBases;
}