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Searched refs:gfmBw (Results 1 – 5 of 5) sorted by relevance

/dports/biology/hisat2/hisat2-2.2.1/
H A Daligner_seed2.h2526 gfmBw, // mirror index in go()
2612 gfmBw, // mirror index in advance()
2656 gfmBw, in advance()
2847 gfmBw, in init()
2875 gfmBw, in init()
2947 gfmBw, in init()
2975 gfmBw, in init()
3510 gfmBw, // mirror index in bounce()
3710 gfmBw, // mirror index in followBestOutgoing()
3754 tloc.initFromRow(topb, gfmBw.gh(), gfmBw.gfm()); in nextLocsBi()
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H A Daligner_sw_driver.h339 const GFM<index_t>* gfmBw, // BWT'
388 const GFM<index_t>* gfmBw, // BWT'
488 const GFM<index_t>* gfmBw, // BWT'
853 bool bwContains = gfmBw != NULL && gfmBw->contains(tmp_rdseq_); in extend()
925 if(lim > 0 && gfmBw != NULL) { in extend()
926 const GFM<index_t> *gfm = gfmBw; in extend()
998 bool bwContains = gfmBw != NULL && gfmBw->contains(tmp_rdseq_); in extend()
1017 const GFM<index_t>* gfmBw, // BWT in prioritizeSATups() argument
1102 gfmBw, in prioritizeSATups()
1384 gfmBw, // BWT' in extendSeeds()
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H A Daligner_driver.h202 const GFM<index_t>& gfmBw,
H A Daligner_seed.cpp509 GFM gfmBw( in main() local
H A Dgfm.h1239 GFM<index_t> *gfmBw = new GFM<index_t>( in fromStrings() local
1262 return make_pair(gfmFw, gfmBw); in fromStrings()