コード例 #1
0
ファイル: BasicStitcher.cs プロジェクト: snashraf/Pisces
 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);
 }
コード例 #2
0
 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;
 }