| /dports/biology/bwa/bwa-0.7.17/ |
| H A D | bwt.c | 42 void bwt_gen_cnt_table(bwt_t *bwt) in bwt_gen_cnt_table()
62 void bwt_cal_sa(bwt_t *bwt, int intv) in bwt_cal_sa()
86 bwtint_t bwt_sa(const bwt_t *bwt, bwtint_t k) in bwt_sa()
107 bwtint_t bwt_occ(const bwt_t *bwt, bwtint_t k, ubyte_t c) in bwt_occ()
165 #define __occ_aux4(bwt, b) \ argument
169 void bwt_occ4(const bwt_t *bwt, bwtint_t k, bwtint_t cnt[4]) in bwt_occ4()
385 void bwt_dump_bwt(const char *fn, const bwt_t *bwt) in bwt_dump_bwt()
396 void bwt_dump_sa(const char *fn, const bwt_t *bwt) in bwt_dump_sa()
421 void bwt_restore_sa(const char *fn, bwt_t *bwt) in bwt_restore_sa()
445 bwt_t *bwt; in bwt_restore_bwt() local
[all …]
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| H A D | bwtindex.c | 67 bwt_t *bwt; in bwt_pac2bwt() local
131 bwt_t *bwt; in bwa_pac2bwt() local
151 void bwt_bwtupdate_core(bwt_t *bwt) in bwt_bwtupdate_core()
177 bwt_t *bwt; in bwa_bwtupdate() local
191 bwt_t *bwt; in bwa_bwt2sa() local
284 bwt_t *bwt; in bwa_idx_build() local
292 bwt_t *bwt; in bwa_idx_build() local
311 bwt_t *bwt; in bwa_idx_build() local
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| H A D | bwt_lite.c | 59 uint32_t bwtl_occ(const bwtl_t *bwt, uint32_t k, uint8_t c) in bwtl_occ()
72 void bwtl_occ4(const bwtl_t *bwt, uint32_t k, uint32_t cnt[4]) in bwtl_occ4()
87 void bwtl_2occ4(const bwtl_t *bwt, uint32_t k, uint32_t l, uint32_t cntk[4], uint32_t cntl[4]) in bwtl_2occ4()
92 void bwtl_destroy(bwtl_t *bwt) in bwtl_destroy()
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| H A D | bwtaln.c | 57 int bwt_cal_width(const bwt_t *bwt, int len, const ubyte_t *str, bwt_width_t *width) in bwt_cal_width()
83 void bwa_cal_sa_reg_gap(int tid, bwt_t *const bwt, int n_seqs, bwa_seq_t *seqs, const gap_opt_t *op… in bwa_cal_sa_reg_gap()
131 bwt_t *bwt; member
166 bwt_t *bwt; in bwa_aln_core() local
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| H A D | bwamem_extra.c | 12 const bwt_t *bwt; member
22 smem_i *smem_itr_init(const bwt_t *bwt) in smem_itr_init()
76 mem_alnreg_v mem_align1(const mem_opt_t *opt, const bwt_t *bwt, const bntseq_t *bns, const uint8_t … in mem_align1()
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| H A D | bwt.h | 51 uint32_t *bwt; // BWT member
80 #define bwt_set_intv(bwt, c, ik) ((ik).x[0] = (bwt)->L2[(int)(c)]+1, (ik).x[2] = (bwt)->L2[(int)(c)… argument
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| H A D | maxk.c | 17 bwt_t *bwt; in KSEQ_DECLARE() local
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| H A D | bwt_gen.c | 87 BWT *bwt; member
325 BWT *bwt; in BWTCreate() local
503 static void BWTIncBuildPackedBwt(const bgint_t *relativeRank, unsigned int* __restrict bwt, const b… in BWTIncBuildPackedBwt()
535 static inline bgint_t BWTOccValueExplicit(const BWT *bwt, const bgint_t occIndexExplicit, in BWTOccValueExplicit()
618 bgint_t BWTOccValue(const BWT *bwt, bgint_t index, const unsigned int character) in BWTOccValue()
642 static bgint_t BWTIncGetAbsoluteRank(BWT *bwt, bgint_t* __restrict absoluteRank, bgint_t* __restric… in BWTIncGetAbsoluteRank()
1063 void BWTClearTrailingBwtCode(BWT *bwt) in BWTClearTrailingBwtCode()
1087 void BWTGenerateOccValueFromBwt(const unsigned int* bwt, unsigned int* __restrict occValue, in BWTGenerateOccValueFromBwt()
1566 void BWTSaveBwtCodeAndOcc(const BWT *bwt, const char *bwtFileName, const char *occValueFileName) in BWTSaveBwtCodeAndOcc()
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| H A D | bwt_lite.h | 9 uint32_t *bwt, *occ, *sa, L2[5]; member
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| H A D | bwase.c | 112 bwtint_t bwa_sa2pos(const bntseq_t *bns, const bwt_t *bwt, bwtint_t sapos, int ref_len, int *strand) in bwa_sa2pos()
131 void bwa_cal_pac_pos_core(const bntseq_t *bns, const bwt_t *bwt, bwa_seq_t *seq, const int max_mm, … in bwa_cal_pac_pos_core()
148 bwt_t *bwt; in bwa_cal_pac_pos() local
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| /dports/emulators/mess/mame-mame0226/3rdparty/bimg/3rdparty/nvtt/bc7/ |
| H A D | avpcl_utils.cpp | 126 float rwt, gwt, bwt; in metric4() local
153 float rwt, gwt, bwt; in metric3() local
189 float rwt, gwt, bwt, awt; in metric1() local
252 float rwt, gwt, bwt; in metric4premult() local
283 float rwt, gwt, bwt; in metric3premult_alphaout() local
338 float rwt, gwt, bwt; in metric3premult_alphain() local
364 float rwt, gwt, bwt, awt; in metric1premult() local
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| /dports/emulators/mame/mame-mame0226/3rdparty/bimg/3rdparty/nvtt/bc7/ |
| H A D | avpcl_utils.cpp | 126 float rwt, gwt, bwt; in metric4() local
153 float rwt, gwt, bwt; in metric3() local
189 float rwt, gwt, bwt, awt; in metric1() local
252 float rwt, gwt, bwt; in metric4premult() local
283 float rwt, gwt, bwt; in metric3premult_alphaout() local
338 float rwt, gwt, bwt; in metric3premult_alphain() local
364 float rwt, gwt, bwt, awt; in metric1premult() local
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| /dports/math/cvc4/CVC4-1.7/src/theory/fp/ |
| H A D | fp_converter.h | 77 typedef unsigned bwt; typedef
101 typedef traits::bwt bwt; typedef
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| /dports/devel/R-cran-gbm/gbm/demo/ |
| H A D | printExamples.R | 21 bwt <- birthwt globalVar
22 bwt <- bwt[ sample( 1:nrow( bwt ) ),] globalVar
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| /dports/math/cvc4/CVC4-1.7/src/util/ |
| H A D | floatingpoint.h.in | 135 typedef unsigned bwt; typedef
156 typedef traits::bwt bwt; typedef
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| /dports/misc/thrill/thrill-12c5b59bca66df93b66628b3829027bd0f110dd9/examples/suffix_sorting/ |
| H A D | wavelet_tree3.cpp | 54 std::string bwt = "aaaaaaaaaaabbbbaaaaaaaccccdddaacacaffatttttttttttyyyyaaaaa"; in main() local
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| /dports/biology/seqan1/seqan-1.3.1/seqan/index/ |
| H A D | index_shims.h | 459 TBWT &bwt, in createBWTableExt()
493 inline void _createBWTableWrapper(TBWT &bwt, TText const &s, TSA const &sa, TTextRandom_ const) in _createBWTableWrapper()
501 inline void _createBWTableWrapper(TBWT &bwt, TText const &s, TSA const &sa, True const) in _createBWTableWrapper()
508 inline void createBWTable(TBWT &bwt, TText const &s, TSA const &sa) in createBWTable()
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| /dports/biology/freebayes/freebayes-1.3.5/contrib/SeqLib/bwa/ |
| H A D | bwt.h | 51 uint32_t *bwt; // BWT member
80 #define bwt_set_intv(bwt, c, ik) ((ik).x[0] = (bwt)->L2[(int)(c)]+1, (ik).x[2] = (bwt)->L2[(int)(c)… argument
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| H A D | bwa.h | 16 bwt_t *bwt; // FM-index member
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/index/ |
| H A D | index_shims.h | 494 TBWT &bwt, in createBWTableExt()
529 …inline void _createBWTableWrapper(TBWT &bwt, TText const &s, TSA const &sa, TTextRandom_ co… in _createBWTableWrapper()
536 inline void _createBWTableWrapper(TBWT &bwt, TText const &s, TSA const &sa, True const) in _createBWTableWrapper()
542 inline void createBWTable(TBWT &bwt, TText const &s, TSA const &sa) in createBWTable()
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| /dports/biology/seqan/seqan-library-2.4.0/include/seqan/index/ |
| H A D | index_shims.h | 494 TBWT &bwt, in createBWTableExt()
529 …inline void _createBWTableWrapper(TBWT &bwt, TText const &s, TSA const &sa, TTextRandom_ co… in _createBWTableWrapper()
536 inline void _createBWTableWrapper(TBWT &bwt, TText const &s, TSA const &sa, True const) in _createBWTableWrapper()
542 inline void createBWTable(TBWT &bwt, TText const &s, TSA const &sa) in createBWTable()
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| /dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/index/ |
| H A D | index_shims.h | 510 TBWT &bwt, in createBWTableExt()
546 …inline void _createBWTableWrapper(TBWT &bwt, TText const &s, TSA const &sa, TTextRandom_ co… in _createBWTableWrapper()
554 inline void _createBWTableWrapper(TBWT &bwt, TText const &s, TSA const &sa, True const) in _createBWTableWrapper()
561 inline void createBWTable(TBWT &bwt, TText const &s, TSA const &sa) in createBWTable()
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| /dports/math/R/R-4.1.2/src/library/stats/tests/ |
| H A D | simulate.R | 54 bwt <- with(birthwt, { globalVar
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| /dports/math/libRmath/R-4.1.1/src/library/stats/tests/ |
| H A D | simulate.R | 54 bwt <- with(birthwt, { globalVar
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| /dports/security/libsectok/libsectok-20030619/palm/ |
| H A D | sectok.h | 66 int t, etu, cwt, bwt, n; member
|