Searched refs:setPerfectFlag (Results 1 – 8 of 8) sorted by relevance
498 if(SLOW_ALIGN || USE_AFFINE_SCORE){r.setPerfectFlag(maxSwScore);} in processRead()1087 r.setPerfectFlag(maxSwScore1); in processReadPair()1088 r2.setPerfectFlag(maxSwScore2); in processReadPair()
499 if(SLOW_ALIGN || USE_AFFINE_SCORE){r.setPerfectFlag(maxSwScore);} in processRead()1092 r.setPerfectFlag(maxSwScore1); in processReadPair()1093 r2.setPerfectFlag(maxSwScore2); in processReadPair()
506 if(SLOW_ALIGN || USE_AFFINE_SCORE){r.setPerfectFlag(maxSwScore);} in processRead()1155 r.setPerfectFlag(maxSwScore1); in processReadPair()1156 r2.setPerfectFlag(maxSwScore2); in processReadPair()
550 if(SLOW_ALIGN || USE_AFFINE_SCORE){r.setPerfectFlag(maxSwScore);} in processRead()1188 r.setPerfectFlag(maxSwScore1); in processReadPair()1189 r2.setPerfectFlag(maxSwScore2); in processReadPair()
857 if(SLOW_ALIGN || USE_AFFINE_SCORE){r.setPerfectFlag(maxSwScore);} in processRead()1480 r.setPerfectFlag(maxSwScore1); in processReadPair()1481 r2.setPerfectFlag(maxSwScore2); in processReadPair()
1062 ss.setPerfectFlag(maxSwScore, bases); in genMatchStringForSite()
233 public boolean setPerfectFlag(int maxScore, byte[] bases){ in setPerfectFlag() method in SiteScore
3066 public boolean setPerfectFlag(int maxScore){ in setPerfectFlag() method in Read