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Searched refs:setPerfectFlag (Results 1 – 8 of 8) sorted by relevance

/dports/biology/bbmap/bbmap/current/align2/
H A DBBMapThread5.java498 if(SLOW_ALIGN || USE_AFFINE_SCORE){r.setPerfectFlag(maxSwScore);} in processRead()
1087 r.setPerfectFlag(maxSwScore1); in processReadPair()
1088 r2.setPerfectFlag(maxSwScore2); in processReadPair()
H A DBBMapThreadPacBio.java499 if(SLOW_ALIGN || USE_AFFINE_SCORE){r.setPerfectFlag(maxSwScore);} in processRead()
1092 r.setPerfectFlag(maxSwScore1); in processReadPair()
1093 r2.setPerfectFlag(maxSwScore2); in processReadPair()
H A DBBMapThread.java506 if(SLOW_ALIGN || USE_AFFINE_SCORE){r.setPerfectFlag(maxSwScore);} in processRead()
1155 r.setPerfectFlag(maxSwScore1); in processReadPair()
1156 r2.setPerfectFlag(maxSwScore2); in processReadPair()
H A DBBMapThreadAcc.java550 if(SLOW_ALIGN || USE_AFFINE_SCORE){r.setPerfectFlag(maxSwScore);} in processRead()
1188 r.setPerfectFlag(maxSwScore1); in processReadPair()
1189 r2.setPerfectFlag(maxSwScore2); in processReadPair()
H A DBBMapThreadPacBioSkimmer.java857 if(SLOW_ALIGN || USE_AFFINE_SCORE){r.setPerfectFlag(maxSwScore);} in processRead()
1480 r.setPerfectFlag(maxSwScore1); in processReadPair()
1481 r2.setPerfectFlag(maxSwScore2); in processReadPair()
H A DAbstractMapThread.java1062 ss.setPerfectFlag(maxSwScore, bases); in genMatchStringForSite()
/dports/biology/bbmap/bbmap/current/stream/
H A DSiteScore.java233 public boolean setPerfectFlag(int maxScore, byte[] bases){ in setPerfectFlag() method in SiteScore
H A DRead.java3066 public boolean setPerfectFlag(int maxScore){ in setPerfectFlag() method in Read