/dports/biology/bwa/bwa-0.7.17/ |
H A D | bwt.c | 57 x = bwt->L2[x] + bwt_occ(bwt, k, x); in bwt_invPsi() 71 if (bwt->sa) free(bwt->sa); in bwt_cal_sa() 73 bwt->n_sa = (bwt->seq_len + intv) / intv; in bwt_cal_sa() 95 return sa + bwt->sa[k/bwt->sa_intv]; in bwt_sa() 112 if (k == bwt->seq_len) return bwt->L2[c+1] - bwt->L2[c]; in bwt_occ() 391 err_fwrite(bwt->bwt, 4, bwt->bwt_size, fp); in bwt_dump_bwt() 435 bwt->n_sa = (bwt->seq_len + bwt->sa_intv) / bwt->sa_intv; in bwt_restore_sa() 452 bwt->bwt = (uint32_t*)calloc(bwt->bwt_size, 4); in bwt_restore_bwt() 456 fread_fix(fp, bwt->bwt_size<<2, bwt->bwt); in bwt_restore_bwt() 457 bwt->seq_len = bwt->L2[4]; in bwt_restore_bwt() [all …]
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H A D | bwtindex.c | 67 bwt_t *bwt; in bwt_pac2bwt() local 75 bwt->bwt_size = (bwt->seq_len + 15) >> 4; in bwt_pac2bwt() 89 for (i = 2; i <= 4; ++i) bwt->L2[i] += bwt->L2[i-1]; in bwt_pac2bwt() 94 bwt->primary = is_bwt(buf, bwt->seq_len); in bwt_pac2bwt() 122 bwt->bwt = (uint32_t*)calloc(bwt->bwt_size, 4); in bwt_pac2bwt() 124 bwt->bwt[i>>4] |= buf[i] << ((15 - (i&15)) << 1); in bwt_pac2bwt() 126 return bwt; in bwt_pac2bwt() 131 bwt_t *bwt; in bwa_pac2bwt() local 172 free(bwt->bwt); bwt->bwt = buf; in bwt_bwtupdate_core() 177 bwt_t *bwt; in bwa_bwtupdate() local [all …]
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H A D | bwt_lite.c | 62 if (k == bwt->seq_len) return bwt->L2[c+1] - bwt->L2[c]; in bwtl_occ() 65 n = bwt->occ[k/16<<2|c]; in bwtl_occ() 66 b = bwt->bwt[k/16] & ~((1U<<((15-(k&15))<<1)) - 1); in bwtl_occ() 67 n += (bwt->cnt_table[b&0xff] + bwt->cnt_table[b>>8&0xff] in bwtl_occ() 68 + bwt->cnt_table[b>>16&0xff] + bwt->cnt_table[b>>24]) >> (c<<3) & 0xff; in bwtl_occ() 81 b = bwt->bwt[k>>4] & ~((1U<<((~k&15)<<1)) - 1); in bwtl_occ4() 82 x = bwt->cnt_table[b&0xff] + bwt->cnt_table[b>>8&0xff] in bwtl_occ4() 83 + bwt->cnt_table[b>>16&0xff] + bwt->cnt_table[b>>24]; in bwtl_occ4() 94 if (bwt) { in bwtl_destroy() 95 free(bwt->occ); free(bwt->bwt); free(bwt->sa); in bwtl_destroy() [all …]
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H A D | bwt.h | 51 uint32_t *bwt; // BWT member 73 #define bwt_occ_intv(b, k) ((b)->bwt + ((k)>>7<<4)) 80 …ine bwt_set_intv(bwt, c, ik) ((ik).x[0] = (bwt)->L2[(int)(c)]+1, (ik).x[2] = (bwt)->L2[(int)(c)+1]… argument 86 void bwt_dump_bwt(const char *fn, const bwt_t *bwt); 87 void bwt_dump_sa(const char *fn, const bwt_t *bwt); 90 void bwt_restore_sa(const char *fn, bwt_t *bwt); 92 void bwt_destroy(bwt_t *bwt); 96 void bwt_cal_sa(bwt_t *bwt, int intv); 98 void bwt_bwtupdate_core(bwt_t *bwt); 102 bwtint_t bwt_sa(const bwt_t *bwt, bwtint_t k); [all …]
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H A D | bwt_gen.c | 87 BWT *bwt; member 325 BWT *bwt; in BWTCreate() local 329 bwt->textLength = 0; in BWTCreate() 349 bwt->occValue = NULL; in BWTCreate() 351 return bwt; in BWTCreate() 671 saIndex = bwt->cumulativeFreq[c] + BWTOccValue(bwt, saIndex, c) + 1; in BWTIncGetAbsoluteRank() 1205 c = bwt[bwtIndex]; in BWTGenerateOccValueFromBwt() 1238 c = bwt[bwtIndex]; in BWTGenerateOccValueFromBwt() 1419 BWTGenerateOccValueFromBwt(bwtInc->bwt->bwtCode, bwtInc->bwt->occValue, bwtInc->bwt->occValueMajor, in BWTIncConstruct() 1420 bwtInc->bwt->textLength, bwtInc->bwt->decodeTable); in BWTIncConstruct() [all …]
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H A D | Makefile | 53 bwamem_extra.o: bwa.h bntseq.h bwt.h bwamem.h kstring.h malloc_wrap.h 60 bwaseqio.o: bwtaln.h bwt.h utils.h bamlite.h malloc_wrap.h kseq.h 61 bwashm.o: bwa.h bntseq.h bwt.h 62 bwt.o: utils.h bwt.h kvec.h malloc_wrap.h 66 bwtgap.o: bwtgap.h bwt.h bwtaln.h malloc_wrap.h 67 bwtindex.o: bntseq.h bwa.h bwt.h utils.h rle.h rope.h malloc_wrap.h 68 bwtsw2_aux.o: bntseq.h bwt_lite.h utils.h bwtsw2.h bwt.h kstring.h 73 bwtsw2_main.o: bwt.h bwtsw2.h bntseq.h bwt_lite.h utils.h bwa.h 74 bwtsw2_pair.o: utils.h bwt.h bntseq.h bwtsw2.h bwt_lite.h kstring.h 76 example.o: bwamem.h bwt.h bntseq.h bwa.h kseq.h malloc_wrap.h [all …]
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H A D | bwt_lite.h | 9 uint32_t *bwt, *occ, *sa, L2[5]; member 13 #define bwtl_B0(b, k) ((b)->bwt[(k)>>4]>>((~(k)&0xf)<<1)&3) 20 uint32_t bwtl_occ(const bwtl_t *bwt, uint32_t k, uint8_t c); 21 void bwtl_occ4(const bwtl_t *bwt, uint32_t k, uint32_t cnt[4]); 22 void bwtl_2occ4(const bwtl_t *bwt, uint32_t k, uint32_t l, uint32_t cntk[4], uint32_t cntl[4]); 23 void bwtl_destroy(bwtl_t *bwt);
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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 73 #define bwt_occ_intv(b, k) ((b)->bwt + ((k)>>7<<4)) 80 …ine bwt_set_intv(bwt, c, ik) ((ik).x[0] = (bwt)->L2[(int)(c)]+1, (ik).x[2] = (bwt)->L2[(int)(c)+1]… argument 86 void bwt_dump_bwt(const char *fn, const bwt_t *bwt); 87 void bwt_dump_sa(const char *fn, const bwt_t *bwt); 90 void bwt_restore_sa(const char *fn, bwt_t *bwt); 92 void bwt_destroy(bwt_t *bwt); 96 void bwt_cal_sa(bwt_t *bwt, int intv); 98 void bwt_bwtupdate_core(bwt_t *bwt); 102 bwtint_t bwt_sa(const bwt_t *bwt, bwtint_t k); [all …]
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/dports/sysutils/helmfile/vault-f6547fa8e820/vendor/github.com/dsnet/compress/bzip2/ |
H A D | bwt.go | 41 bwt.buf = append(append(bwt.buf[:0], buf...), buf...) 42 if cap(bwt.sa) < 2*n { 43 bwt.sa = make([]int, 2*n) 45 t := bwt.buf[:2*n] 46 sa := bwt.sa[:2*n] 89 if cap(bwt.perm) < len(buf) { 90 bwt.perm = make([]uint32, len(buf)) 92 perm := bwt.perm[:len(buf)] 100 if cap(bwt.buf) < len(buf) { 101 bwt.buf = make([]byte, len(buf)) [all …]
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/dports/sysutils/istio/istio-1.6.7/vendor/github.com/dsnet/compress/bzip2/ |
H A D | bwt.go | 41 bwt.buf = append(append(bwt.buf[:0], buf...), buf...) 42 if cap(bwt.sa) < 2*n { 43 bwt.sa = make([]int, 2*n) 45 t := bwt.buf[:2*n] 46 sa := bwt.sa[:2*n] 89 if cap(bwt.perm) < len(buf) { 90 bwt.perm = make([]uint32, len(buf)) 92 perm := bwt.perm[:len(buf)] 100 if cap(bwt.buf) < len(buf) { 101 bwt.buf = make([]byte, len(buf)) [all …]
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/dports/www/gitea/gitea-1.16.5/vendor/github.com/dsnet/compress/bzip2/ |
H A D | bwt.go | 41 bwt.buf = append(append(bwt.buf[:0], buf...), buf...) 42 if cap(bwt.sa) < 2*n { 43 bwt.sa = make([]int, 2*n) 45 t := bwt.buf[:2*n] 46 sa := bwt.sa[:2*n] 89 if cap(bwt.perm) < len(buf) { 90 bwt.perm = make([]uint32, len(buf)) 92 perm := bwt.perm[:len(buf)] 100 if cap(bwt.buf) < len(buf) { 101 bwt.buf = make([]byte, len(buf)) [all …]
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/dports/misc/concourse/vault-bdd38fca2cff/vendor/github.com/dsnet/compress/bzip2/ |
H A D | bwt.go | 41 bwt.buf = append(append(bwt.buf[:0], buf...), buf...) 42 if cap(bwt.sa) < 2*n { 43 bwt.sa = make([]int, 2*n) 45 t := bwt.buf[:2*n] 46 sa := bwt.sa[:2*n] 89 if cap(bwt.perm) < len(buf) { 90 bwt.perm = make([]uint32, len(buf)) 92 perm := bwt.perm[:len(buf)] 100 if cap(bwt.buf) < len(buf) { 101 bwt.buf = make([]byte, len(buf)) [all …]
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/dports/misc/concourse/concourse-6.7.2/vendor/github.com/hashicorp/vault/vendor/github.com/dsnet/compress/bzip2/ |
H A D | bwt.go | 41 bwt.buf = append(append(bwt.buf[:0], buf...), buf...) 42 if cap(bwt.sa) < 2*n { 43 bwt.sa = make([]int, 2*n) 45 t := bwt.buf[:2*n] 46 sa := bwt.sa[:2*n] 89 if cap(bwt.perm) < len(buf) { 90 bwt.perm = make([]uint32, len(buf)) 92 perm := bwt.perm[:len(buf)] 100 if cap(bwt.buf) < len(buf) { 101 bwt.buf = make([]byte, len(buf)) [all …]
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/dports/net/bosh-bootloader/bosh-bootloader-7.2.12/vendor/github.com/dsnet/compress/bzip2/ |
H A D | bwt.go | 41 bwt.buf = append(append(bwt.buf[:0], buf...), buf...) 42 if cap(bwt.sa) < 2*n { 43 bwt.sa = make([]int, 2*n) 45 t := bwt.buf[:2*n] 46 sa := bwt.sa[:2*n] 89 if cap(bwt.perm) < len(buf) { 90 bwt.perm = make([]uint32, len(buf)) 92 perm := bwt.perm[:len(buf)] 100 if cap(bwt.buf) < len(buf) { 101 bwt.buf = make([]byte, len(buf)) [all …]
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/dports/security/vault/vault-1.8.2/vendor/github.com/dsnet/compress/bzip2/ |
H A D | bwt.go | 41 bwt.buf = append(append(bwt.buf[:0], buf...), buf...) 42 if cap(bwt.sa) < 2*n { 43 bwt.sa = make([]int, 2*n) 45 t := bwt.buf[:2*n] 46 sa := bwt.sa[:2*n] 89 if cap(bwt.perm) < len(buf) { 90 bwt.perm = make([]uint32, len(buf)) 92 perm := bwt.perm[:len(buf)] 100 if cap(bwt.buf) < len(buf) { 101 bwt.buf = make([]byte, len(buf)) [all …]
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/dports/net/ooni-mini/probe-engine-0.23.0/vendor/github.com/dsnet/compress/bzip2/ |
H A D | bwt.go | 41 bwt.buf = append(append(bwt.buf[:0], buf...), buf...) 42 if cap(bwt.sa) < 2*n { 43 bwt.sa = make([]int, 2*n) 45 t := bwt.buf[:2*n] 46 sa := bwt.sa[:2*n] 89 if cap(bwt.perm) < len(buf) { 90 bwt.perm = make([]uint32, len(buf)) 92 perm := bwt.perm[:len(buf)] 100 if cap(bwt.buf) < len(buf) { 101 bwt.buf = make([]byte, len(buf)) [all …]
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/dports/net/ooni-probe-cli/probe-cli-3.10.1/vendor/github.com/dsnet/compress/bzip2/ |
H A D | bwt.go | 41 bwt.buf = append(append(bwt.buf[:0], buf...), buf...) 42 if cap(bwt.sa) < 2*n { 43 bwt.sa = make([]int, 2*n) 45 t := bwt.buf[:2*n] 46 sa := bwt.sa[:2*n] 89 if cap(bwt.perm) < len(buf) { 90 bwt.perm = make([]uint32, len(buf)) 92 perm := bwt.perm[:len(buf)] 100 if cap(bwt.buf) < len(buf) { 101 bwt.buf = make([]byte, len(buf)) [all …]
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/dports/www/mattermost-server/mattermost-server-6.0.2/vendor/github.com/dsnet/compress/bzip2/ |
H A D | bwt.go | 41 bwt.buf = append(append(bwt.buf[:0], buf...), buf...) 42 if cap(bwt.sa) < 2*n { 43 bwt.sa = make([]int, 2*n) 45 t := bwt.buf[:2*n] 46 sa := bwt.sa[:2*n] 89 if cap(bwt.perm) < len(buf) { 90 bwt.perm = make([]uint32, len(buf)) 92 perm := bwt.perm[:len(buf)] 100 if cap(bwt.buf) < len(buf) { 101 bwt.buf = make([]byte, len(buf)) [all …]
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/dports/security/obfs4proxy-tor/obfs4proxy-0.0.11/vendor/github.com/dsnet/compress/bzip2/ |
H A D | bwt.go | 41 bwt.buf = append(append(bwt.buf[:0], buf...), buf...) 42 if cap(bwt.sa) < 2*n { 43 bwt.sa = make([]int, 2*n) 45 t := bwt.buf[:2*n] 46 sa := bwt.sa[:2*n] 89 if cap(bwt.perm) < len(buf) { 90 bwt.perm = make([]uint32, len(buf)) 92 perm := bwt.perm[:len(buf)] 100 if cap(bwt.buf) < len(buf) { 101 bwt.buf = make([]byte, len(buf)) [all …]
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/dports/sysutils/jest/jest-f76bc46/vendor/github.com/dsnet/compress/bzip2/ |
H A D | bwt.go | 41 bwt.buf = append(append(bwt.buf[:0], buf...), buf...) 42 if cap(bwt.sa) < 2*n { 43 bwt.sa = make([]int, 2*n) 45 t := bwt.buf[:2*n] 46 sa := bwt.sa[:2*n] 89 if cap(bwt.perm) < len(buf) { 90 bwt.perm = make([]uint32, len(buf)) 92 perm := bwt.perm[:len(buf)] 100 if cap(bwt.buf) < len(buf) { 101 bwt.buf = make([]byte, len(buf)) [all …]
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/dports/devel/bit/bit-1.1.2/vendor/github.com/dsnet/compress/bzip2/ |
H A D | bwt.go | 41 bwt.buf = append(append(bwt.buf[:0], buf...), buf...) 42 if cap(bwt.sa) < 2*n { 43 bwt.sa = make([]int, 2*n) 45 t := bwt.buf[:2*n] 46 sa := bwt.sa[:2*n] 89 if cap(bwt.perm) < len(buf) { 90 bwt.perm = make([]uint32, len(buf)) 92 perm := bwt.perm[:len(buf)] 100 if cap(bwt.buf) < len(buf) { 101 bwt.buf = make([]byte, len(buf)) [all …]
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/dports/sysutils/sensu-go/sensu-go-5.11.1/vendor/github.com/dsnet/compress/bzip2/ |
H A D | bwt.go | 41 bwt.buf = append(append(bwt.buf[:0], buf...), buf...) 42 if cap(bwt.sa) < 2*n { 43 bwt.sa = make([]int, 2*n) 45 t := bwt.buf[:2*n] 46 sa := bwt.sa[:2*n] 89 if cap(bwt.perm) < len(buf) { 90 bwt.perm = make([]uint32, len(buf)) 92 perm := bwt.perm[:len(buf)] 100 if cap(bwt.buf) < len(buf) { 101 bwt.buf = make([]byte, len(buf)) [all …]
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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 139 err.z *= bwt; in metric4() 153 float rwt, gwt, bwt; in metric3() local 176 err.z *= bwt; in metric3() 189 float rwt, gwt, bwt, awt; in metric1() local 252 float rwt, gwt, bwt; in metric4premult() local 265 err.z *= bwt; in metric4premult() 283 float rwt, gwt, bwt; in metric3premult_alphaout() local 296 err.z *= bwt; in metric3premult_alphaout() 338 float rwt, gwt, bwt; in metric3premult_alphain() local [all …]
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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 139 err.z *= bwt; in metric4() 153 float rwt, gwt, bwt; in metric3() local 176 err.z *= bwt; in metric3() 189 float rwt, gwt, bwt, awt; in metric1() local 252 float rwt, gwt, bwt; in metric4premult() local 265 err.z *= bwt; in metric4premult() 283 float rwt, gwt, bwt; in metric3premult_alphaout() local 296 err.z *= bwt; in metric3premult_alphaout() 338 float rwt, gwt, bwt; in metric3premult_alphain() local [all …]
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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 196 symbolicBitVector(const bwt w, const unsigned v); 201 bwt getWidth(void) const; 204 static symbolicBitVector<isSigned> one(const bwt &w); 205 static symbolicBitVector<isSigned> zero(const bwt &w); 206 static symbolicBitVector<isSigned> allOnes(const bwt &w); 211 static symbolicBitVector<isSigned> maxValue(const bwt &w); 267 symbolicBitVector<isSigned> extend(bwt extension) const; 269 symbolicBitVector<isSigned> resize(bwt newSize) const; [all …]
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