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Searched refs:GAPCOST (Results 1 – 11 of 11) sorted by relevance

/dports/biology/bbmap/bbmap/jni/
H A DMultiStateAligner11tsJNI.c19 #define GAPCOST max(1,GAPLEN/64) macro
61 #define POINTS_GAP (0-GAPCOST) //default -10
/dports/biology/bbmap/bbmap/current/align2/
H A DMSA.java706 static final int GAPCOST=Shared.GAPCOST; field in MSA
H A DMultiStateAligner11tsJNI.java1480 public static final int POINTS_GAP=0-GAPCOST;
H A DMultiStateAligner11ts.java2462 public static final int POINTS_GAP=0-GAPCOST;
H A DMultiStateAligner9XFlat.java2263 public static final int POINTS_GAP=0-GAPCOST;
H A DMultiStateAligner9ts.java2327 public static final int POINTS_GAP=0-GAPCOST;
H A DMultiStateAligner9Flat.java2372 public static final int POINTS_GAP=0-GAPCOST;
H A DMultiStateAligner9PacBio.java2372 public static final int POINTS_GAP=0-GAPCOST;
H A DMultiStateAligner10ts.java3500 public static final int POINTS_GAP=0-GAPCOST;
/dports/biology/bbmap/bbmap/current/shared/
H A DShared.java124 public static final int GAPCOST=Tools.max(1, GAPLEN/64); field in Shared
/dports/biology/bbmap/bbmap/current/aligner/
H A DMultiStateAligner9PacBioAdapter_WithBarriers.java2453 public static final int GAPCOST=Shared.GAPCOST*2;
2543 public static final int POINTS_GAP=0-GAPCOST;