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Searched refs:GAPBUFFER (Results 1 – 10 of 10) sorted by relevance

/dports/biology/bbmap/bbmap/current/shared/
H A DShared.java120 public static final int GAPBUFFER=64; //TODO: Seems to break less than 64, for some reason field in Shared
121 public static final int GAPBUFFER2=2*GAPBUFFER;
/dports/biology/bbmap/bbmap/current/align2/
H A DMSA.java702 static final int GAPBUFFER=Shared.GAPBUFFER; field in MSA
H A DMultiStateAligner11tsJNI.java669 int lim=y+GAPBUFFER+rem;
683 for(int r=z-GAPBUFFER; r<z; r++, gpos++){
H A DMultiStateAligner11ts.java1521 int lim=y+GAPBUFFER+rem;
1535 for(int r=z-GAPBUFFER; r<z; r++, gpos++){
H A DMultiStateAligner9XFlat.java1434 int lim=y+GAPBUFFER+rem;
1448 for(int r=z-GAPBUFFER; r<z; r++, gpos++){
H A DMultiStateAligner9ts.java1405 int lim=y+GAPBUFFER+rem;
1419 for(int r=z-GAPBUFFER; r<z; r++, gpos++){
H A DMultiStateAligner9Flat.java1450 int lim=y+GAPBUFFER+rem;
1464 for(int r=z-GAPBUFFER; r<z; r++, gpos++){
H A DMultiStateAligner9PacBio.java1450 int lim=y+GAPBUFFER+rem;
1464 for(int r=z-GAPBUFFER; r<z; r++, gpos++){
H A DMultiStateAligner10ts.java2374 int lim=y+GAPBUFFER+rem;
2388 for(int r=z-GAPBUFFER; r<z; r++, gpos++){
/dports/biology/bbmap/bbmap/current/aligner/
H A DMultiStateAligner9PacBioAdapter_WithBarriers.java1527 int lim=y+GAPBUFFER+rem;
1541 for(int r=z-GAPBUFFER; r<z; r++, gpos++){
2449 public static final int GAPBUFFER=Shared.GAPBUFFER;