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

/dports/biology/bbmap/bbmap/current/stream/
H A DSiteScore.java251 assert(Read.CHECKSITE(this, bases, 0)) : new String(bases)+"\n"+this+"\n"; //123 in setPerfect()
272 assert(Read.CHECKSITE(this, bases, 0)); //123 in setPerfect()
288 assert(Read.CHECKSITE(this, bases, 0)); //123 in setPerfect()
296 assert(Read.CHECKSITE(this, bases, 0)); //123 in setPerfect()
H A DRead.java3727 public static final boolean CHECKSITE(SiteScore ss, byte[] basesP, byte[] basesM, long id){ in CHECKSITE() method in Read
3728 return CHECKSITE(ss, ss.plus() ? basesP : basesM, id); in CHECKSITE()
3732 public static final boolean CHECKSITE(SiteScore ss, byte[] bases, long id){ in CHECKSITE() method in Read
/dports/biology/bbmap/bbmap/current/align2/
H A DAbstractMapThread.java999 assert(Read.CHECKSITE(ss, bases, id)); in genMatchStringForSite()
1031 assert(Read.CHECKSITE(ss, bases, id)); in genMatchStringForSite()
1046 assert(Read.CHECKSITE(ss, bases, id)); in genMatchStringForSite()
1054 assert(Read.CHECKSITE(ss, bases, id)); in genMatchStringForSite()
1069 assert(Read.CHECKSITE(ss, bases, id)); in genMatchStringForSite()
1094 assert(Read.CHECKSITE(ss, bases, id)); in genMatchStringForSite()
H A DTranslateColorspaceRead.java235 assert(Read.CHECKSITE(ss, bases, id)); in realign_new()
652 assert(Read.CHECKSITE(ss, bases, id)); in realign_new()
H A DMultiStateAligner9XFlat.java1929 assert(Read.CHECKSITE(ss, read, -1));
H A DMultiStateAligner9Flat.java2009 assert(Read.CHECKSITE(ss, read, -1));
H A DMultiStateAligner9PacBio.java2009 assert(Read.CHECKSITE(ss, read, -1));
/dports/biology/bbmap/bbmap/current/aligner/
H A DMultiStateAligner9PacBioAdapter.java1111 assert(Read.CHECKSITE(ss, read, -1));
H A DMultiStateAligner9PacBioAdapter2.java1294 assert(Read.CHECKSITE(ss, read, -1));
H A DMultiStateAligner9PacBioAdapter3.java1117 assert(Read.CHECKSITE(ss, read, -1)); in scoreNoIndels()
H A DMultiStateAligner9PacBioAdapter_WithBarriers.java2096 assert(Read.CHECKSITE(ss, read, -1));