Searched refs:CHECKSITE (Results 1 – 11 of 11) sorted by relevance
/dports/biology/bbmap/bbmap/current/stream/ |
H A D | SiteScore.java | 251 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()
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H A D | Read.java | 3727 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
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/dports/biology/bbmap/bbmap/current/align2/ |
H A D | AbstractMapThread.java | 999 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()
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H A D | TranslateColorspaceRead.java | 235 assert(Read.CHECKSITE(ss, bases, id)); in realign_new() 652 assert(Read.CHECKSITE(ss, bases, id)); in realign_new()
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H A D | MultiStateAligner9XFlat.java | 1929 assert(Read.CHECKSITE(ss, read, -1));
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H A D | MultiStateAligner9Flat.java | 2009 assert(Read.CHECKSITE(ss, read, -1));
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H A D | MultiStateAligner9PacBio.java | 2009 assert(Read.CHECKSITE(ss, read, -1));
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/dports/biology/bbmap/bbmap/current/aligner/ |
H A D | MultiStateAligner9PacBioAdapter.java | 1111 assert(Read.CHECKSITE(ss, read, -1));
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H A D | MultiStateAligner9PacBioAdapter2.java | 1294 assert(Read.CHECKSITE(ss, read, -1));
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H A D | MultiStateAligner9PacBioAdapter3.java | 1117 assert(Read.CHECKSITE(ss, read, -1)); in scoreNoIndels()
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H A D | MultiStateAligner9PacBioAdapter_WithBarriers.java | 2096 assert(Read.CHECKSITE(ss, read, -1));
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