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ed macro

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chhylp123
2022-09-14 15:38:55 -04:00
parent 2300dc63bb
commit 69d0e18fe5
3 changed files with 234 additions and 225 deletions
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Correct.cpp
+6 -3
View File
@@ -3657,16 +3657,19 @@ char *qstr, char *tstr, char *tstr1, Correct_dumy* dumy, uint32_t rev, uint32_t
// fprintf(stderr, "[qstr] %.*s\n", (int32_t)ql, q_string);
// }
// assert(dbg_e <= (int32_t)error);
// bit_extz_t exz; ///ed_band_cal_global_128bit(t_string+r_ts, t_end+1-r_ts, q_string, ql, thres, &exz);
// bit_extz_t exz;
// ed_band_cal_extension_128bit(t_string+r_ts, t_end+1-r_ts, q_string, ql, thres, &exz);
// assert(exz.err <= (int32_t)error);
// ed_band_cal_global_128bit(t_string+r_ts, t_end+1-r_ts, q_string, ql, thres, &exz);
// assert(exz.err <= (int32_t)error);
// if(exz.err > (int32_t)error && ql == 1) {
// fprintf(stderr, "[M::%s::] error::%u, ed_extension::%d, ql::%ld, thres::%ld\n",
// __func__, error, exz.err, ql, thres);
// fprintf(stderr, "[tstr] %.*s\n", t_end+1-r_ts, t_string+r_ts);
// fprintf(stderr, "[qstr] %.*s\n", (int32_t)ql, q_string);
// }
// assert(exz.err <= (int32_t)error);
// assert(ed_band_cal_global(t_string+r_ts, t_end+1-r_ts, q_string, ql, thres) ==
// ed_band_cal_global_128bit(t_string+r_ts, t_end+1-r_ts, q_string, ql, thres));
Levenshtein_distance.h
+224 -218
View File
@@ -612,6 +612,11 @@ typedef struct {
// asg16_v cigar; w64_trace_t path;
} bit_extz_t;
#define init_base_ed(ez, thre, pn, tn) {\
(ez).thre = (thre), (ez).err = INT32_MAX, (ez).pl = pn, (ez).tl = tn;\
(ez).done_cigar = (ez).done_path = (ez).cigar_n = (ez).path_n = 0;\
}
#define w128_bit(x, b) ((x).a[((b)>>bitw)]|=(((w_sig)1)<<((b)&bitz)))
#define w128_get_bit(x, b) (((x).a[((b)>>bitw)]>>((b)&bitz))&((w_sig)1))
@@ -650,7 +655,9 @@ typedef struct {
else (x).a[1] = (((w_sig)1)<<((l)-bitwbit))-1;\
} while (0) \
#define ed_core_w128(Peq, VP, VN, X, D0, HN, HP) { \
#define ed_core_w128b(Peq, VP, VN, X, D0, HN, HP) { \
/**X = Peq[seq_nt4_table[(uint8_t)tstr[i]]] | VN;**/\
c = seq_nt4_table[(uint8_t)tstr[i]]; w128_or(X, Peq[c], VN);\
/**D0 = ((VP + (X&VP)) ^ VP) | X;**/\
@@ -672,228 +679,227 @@ typedef struct {
w128_or(VP, X, HP);\
w128_self_not(VP);\
w128_self_or(VP, HN);\
}
}
#define ed_core_w128_reshift(Peq) {\
#define ed_core(sf, Peq, VP, VN, X, D0, HN, HP) { \
/**X = Peq[seq_nt4_table[(uint8_t)tstr[i]]] | VN;**/\
c = seq_nt4_table[(uint8_t)tstr[i]]; ##sf##or(X, Peq[c], VN);\
/**D0 = ((VP + (X&VP)) ^ VP) | X;**/\
##sf##and(D0, X, VP);\
##sf##self_add(D0, VP);\
##sf##self_xor(D0, VP);\
##sf##self_or(D0, X);\
/**HN = VP&D0;**/\
##sf##and(HN, VP, D0);\
/**HP = VN | ~(VP | D0);**/\
##sf##or(HP, VP, D0);\
##sf##self_not(HP);\
##sf##self_or(HP, VN);\
/**X = D0 >> 1;**/\
X = D0; ##sf##self_rsft_1(X);\
/**VN = X&HP;**/\
##sf##and(VN, X, HP);\
/**VP = HN | ~(X | HP);**/\
##sf##or(VP, X, HP);\
##sf##self_not(VP);\
##sf##self_or(VP, HN);\
}
#define HA_ED_INIT(sf)\
inline void ed_band_cal_global_##sf##bit(char *pstr, int32_t pn, char *tstr, int32_t tn, int32_t thre, bit_extz_t *ez)\
{\
init_base_ed(*ez, thre, pn, tn); ez->ps = ez->ts = 0;\
if((pn > tn + thre) || (tn > pn + thre)) return;\
/**if((pn < thre + 1) || (tn < thre + 1)) return;**/\
int32_t i, err, tn0 = tn - 1, cut = thre+(thre<<1), bd = thre+1, i_bd = thre; uint8_t c;\
w##sf##_clear(ez->Peq[0]); w##sf##_clear(ez->Peq[1]); w##sf##_clear(ez->Peq[2]); w##sf##_clear(ez->Peq[3]); w##sf##_clear(ez->Peq[4]);\
\
w##sf##_clear(ez->mm); w##sf##_bit(ez->mm, thre); /**mm = (((Word)1)<<thre)**/\
for (i = 0; i < bd && i < pn; i++) {\
w##sf##_self_or(ez->Peq[seq_nt4_table[(uint8_t)pstr[i]]], ez->mm); w##sf##_self_lsft_1(ez->mm);\
/** Peq[seq_nt4_table[(uint8_t)pstr[i]]] |= mm; mm <<= 1;**/\
}\
w##sf##_clear(ez->Peq[4]);\
err = thre;\
w##sf##_set_bit_lsub(ez->VN, thre); /**VN = (((Word)1)<<(thre))-1;**/\
w##sf##_set_bit_lsub(ez->VP, (thre<<1)+1); /**VP = (((Word)1)<<((thre<<1)+1))-1;**/\
w##sf##_self_xor(ez->VP, ez->VN); /**VP ^= VN;**/\
\
/** print_bits(VP.a, (thre<<1)+1, "-VP");**/\
/**should make Peq[4] = 0 if N is always an error**/\
i = 0; \
/**for the incoming char/last char**/\
w##sf##_clear(ez->mm); w##sf##_bit(ez->mm, (thre<<1)); /**mm = ((Word)1 << (thre<<1));**/\
while (i < tn0) {\
ed_core_w##sf##b(ez->Peq, ez->VP, ez->VN, ez->X, ez->D0, ez->HN, ez->HP);\
if (!(ez->D0.a[0]&(1ULL))) {\
++err; if (err>cut) return;\
}\
/** Peq[0] >>= 1; Peq[1] >>= 1; Peq[2] >>= 1; Peq[3] >>= 1;**/\
w128_self_rsft_1(Peq[0]); w128_self_rsft_1(Peq[1]);\
w128_self_rsft_1(Peq[2]); w128_self_rsft_1(Peq[3]);\
}
#define init_base_ed(ez, thre, pn, tn) {\
(ez).thre = (thre), (ez).err = INT32_MAX, (ez).pl = pn, (ez).tl = tn;\
(ez).done_cigar = (ez).done_path = (ez).cigar_n = (ez).path_n = 0;\
}
#define tst_band_err(p_off, t_off, p_end, dif, ez, k) {\
if((p_off) + (((ez).thre)<<1) >= (p_end)) { \
for ((k) = 0; (p_off) < (p_end); (p_off)++) {\
(dif) += w128_get_bit((ez).VP, (k));\
(dif) -= w128_get_bit((ez).VN, (k));\
(k)++;}\
if((dif) <= (ez).thre && (dif) < (ez).err) {\
(ez).err = dif; (ez).pe = p_off; (ez).te = t_off;}\
w##sf##_self_rsft_1(ez->Peq[0]); w##sf##_self_rsft_1(ez->Peq[1]);\
w##sf##_self_rsft_1(ez->Peq[2]); w##sf##_self_rsft_1(ez->Peq[3]);\
++i; ++i_bd;\
if(i_bd < pn) {\
c = seq_nt4_table[(uint8_t)pstr[i_bd]];\
/**if(c < 4) Peq[c] |= mm;**/\
if(c < 4) w##sf##_self_or(ez->Peq[c], ez->mm);\
}\
}\
ed_core_w##sf##b(ez->Peq, ez->VP, ez->VN, ez->X, ez->D0, ez->HN, ez->HP);\
if (!(ez->D0.a[0]&(1ULL))) {\
++err; if (err>cut) return;\
}\
\
int32_t site = tn - 1 - thre;/**up bound**/\
for (cut = pn - 1; site < cut; site++) {\
/**err += ((VP >> i)&(1ULL));**/\
err += ez->VP.a[0]&(1ULL); w##sf##_self_rsft_1(ez->VP); \
/**err -= ((VN >> i)&(1ULL));**/\
err -= ez->VN.a[0]&(1ULL); w##sf##_self_rsft_1(ez->VN); \
}\
\
if (site == cut && err <= thre) {\
ez->err = err; \
ez->pe = pn-1; ez->te = tn-1;\
}\
return;\
}\
inline void ed_band_cal_semi_##sf##bit(char *pstr, int32_t pn, char *tstr, int32_t tn, int32_t thre, bit_extz_t *ez)\
{\
init_base_ed(*ez, thre, pn, tn); ez->ps = ez->pe = -1; ez->ts = 0; ez->te = tn-1;\
w##sf##_clear(ez->VP); w##sf##_clear(ez->VN); w##sf##_clear(ez->mm); w##sf##_bit(ez->mm, 0);\
w##sf##_clear(ez->Peq[0]); w##sf##_clear(ez->Peq[1]); w##sf##_clear(ez->Peq[2]); w##sf##_clear(ez->Peq[3]); w##sf##_clear(ez->Peq[4]);\
int32_t bd = (thre<<1)+1, i, err = 0, i_bd = (thre<<1), last_high = (thre<<1), tn0 = tn - 1;\
int32_t cut = thre+last_high; uint8_t c;\
\
for (i = 0; i < bd; i++) {\
w##sf##_self_or(ez->Peq[seq_nt4_table[(uint8_t)pstr[i]]], ez->mm); w##sf##_self_lsft_1(ez->mm);\
/** Peq[seq_nt4_table[(uint8_t)pstr[i]]] |= mm; mm <<= 1;**/\
}\
/**should make Peq[4] = 0 if N is always an error**/\
/** Peq[4] = 0;**/\
w##sf##_clear(ez->Peq[4]);\
/**mm = ((Word)1 << (thre<<1));///for the incoming char/last char**/\
w##sf##_clear(ez->mm); w##sf##_bit(ez->mm, (thre<<1));\
\
i = 0;\
while (i < tn0) {\
ed_core_w##sf##b(ez->Peq, ez->VP, ez->VN, ez->X, ez->D0, ez->HN, ez->HP);\
if (!(ez->D0.a[0]&(1ULL))) {\
++err; if (err>cut) return;\
}\
/** Peq[0] >>= 1; Peq[1] >>= 1; Peq[2] >>= 1; Peq[3] >>= 1;**/\
w##sf##_self_rsft_1(ez->Peq[0]); w##sf##_self_rsft_1(ez->Peq[1]);\
w##sf##_self_rsft_1(ez->Peq[2]); w##sf##_self_rsft_1(ez->Peq[3]);\
++i; ++i_bd; \
/** Peq[seq_nt4_table[(uint8_t)pstr[i_bd]]] |= mm; Peq[4] = 0;**/\
c = seq_nt4_table[(uint8_t)pstr[i_bd]]; \
if(c < 4) w##sf##_self_or(ez->Peq[c], ez->mm);\
}\
ed_core_w##sf##b(ez->Peq, ez->VP, ez->VN, ez->X, ez->D0, ez->HN, ez->HP);\
if (!(ez->D0.a[0]&(1ULL))) {\
++err; if (err>cut) return;\
}\
\
int32_t site = tn - 1;/**up bound**/\
/**in most cases, ai = (thre<<1)**/\
int32_t ai = pn - tn, uge = INT32_MAX;\
if ((err <= thre) && (err <= ez->err)) {\
ez->err = err; ez->pe = site;\
}\
i = 0;\
\
while (i < ai) {\
/** err += ((VP >> i)&(1ULL)); **/\
err += ez->VP.a[0]&(1ULL); w##sf##_self_rsft_1(ez->VP); \
/** err -= ((VN >> i)&(1ULL)); **/\
err -= ez->VN.a[0]&(1ULL); w##sf##_self_rsft_1(ez->VN); \
++i;\
if ((err <= thre) && (err <= ez->err)) {\
ez->err = err; ez->pe = site + i;\
}\
if(i == thre) uge = err;\
}\
\
if((uge <= thre) && (uge == ez->err)) ez->pe = site + thre;\
}\
/**require:: (pn >= tn - thre && pn <= tn + thre)**/\
inline void ed_band_cal_extension_##sf##bit(char *pstr, int32_t pn, char *tstr, int32_t tn, int32_t thre, bit_extz_t *ez)\
{\
if(pn > tn + thre) pn = tn + thre;\
else if(tn > pn + thre) tn = pn + thre;\
init_base_ed(*ez, thre, pn, tn); ez->ps = ez->ts = 0; ez->pe = ez->te = -1;\
int32_t i, err, tn0 = tn - 1, cut = thre+(thre<<1), bd = thre+1, i_bd = thre; uint8_t c;\
int32_t poff, pe = pn-1, tmp_e, k;\
w##sf##_clear(ez->Peq[0]); w##sf##_clear(ez->Peq[1]); w##sf##_clear(ez->Peq[2]); w##sf##_clear(ez->Peq[3]); w##sf##_clear(ez->Peq[4]);\
\
w##sf##_clear(ez->mm); w##sf##_bit(ez->mm, thre); /**mm = (((Word)1)<<thre)**/\
for (i = 0; i < bd && i < pn; i++) {\
w##sf##_self_or(ez->Peq[seq_nt4_table[(uint8_t)pstr[i]]], ez->mm); w##sf##_self_lsft_1(ez->mm);\
/**Peq[seq_nt4_table[(uint8_t)pstr[i]]] |= mm; mm <<= 1;**/\
}\
w##sf##_clear(ez->Peq[4]);\
err = thre;\
w##sf##_set_bit_lsub(ez->VN, thre); /**VN = (((Word)1)<<(thre))-1; **/\
w##sf##_set_bit_lsub(ez->VP, (thre<<1)+1); /**VP = (((Word)1)<<((thre<<1)+1))-1;**/\
w##sf##_self_xor(ez->VP, ez->VN); /**VP ^= VN;**/\
\
/** print_bits(ez->VP.a, (thre<<1)+1, "-VP");**/\
/**should make Peq[4] = 0 if N is always an error**/\
i = 0; \
/**for the incoming char/last char**/\
w##sf##_clear(ez->mm); w##sf##_bit(ez->mm, (thre<<1)); /**mm = ((Word)1 << (thre<<1));**/\
while (i < tn0) {\
ed_core_w##sf##b(ez->Peq, ez->VP, ez->VN, ez->X, ez->D0, ez->HN, ez->HP);\
if (!(ez->D0.a[0]&(1ULL))) {\
++err; if (err>cut) return;\
}\
\
{\
poff = i-thre; tmp_e = err; /**poff:[i-thre, i+thre]**/\
if((poff) + (((*ez).thre)<<1) >= (pe)) { \
for ((k) = 0; (poff) < (pe); (poff)++) {\
(tmp_e) += w##sf##_get_bit((*ez).VP, (k));\
(tmp_e) -= w##sf##_get_bit((*ez).VN, (k));\
(k)++;}\
if((tmp_e) <= (*ez).thre && (tmp_e) < (*ez).err) {\
(*ez).err = tmp_e; (*ez).pe = poff; (*ez).te = i;}\
}\
}\
\
/** Peq[0] >>= 1; Peq[1] >>= 1; Peq[2] >>= 1; Peq[3] >>= 1;**/\
w##sf##_self_rsft_1(ez->Peq[0]); w##sf##_self_rsft_1(ez->Peq[1]);\
w##sf##_self_rsft_1(ez->Peq[2]); w##sf##_self_rsft_1(ez->Peq[3]);\
++i; ++i_bd;\
if(i_bd < pn) {\
c = seq_nt4_table[(uint8_t)pstr[i_bd]]; \
if(c < 4) w##sf##_self_or(ez->Peq[c], ez->mm);\
}\
}\
ed_core_w##sf##b(ez->Peq, ez->VP, ez->VN, ez->X, ez->D0, ez->HN, ez->HP);\
if (!(ez->D0.a[0]&(1ULL))) {\
++err; if (err>cut) return;\
}\
/**i = tn - 1**/\
int32_t site = tn - 1 - thre;/**up bound; site:[tn - 1 - thre, tn - 1 + thre]**/\
for (cut = pn - 1; site < cut; ) {\
/** err += ((VP >> i)&(1ULL)); **/\
err += ez->VP.a[0]&(1ULL); w##sf##_self_rsft_1(ez->VP); \
/** err -= ((VN >> i)&(1ULL));**/\
err -= ez->VN.a[0]&(1ULL); w##sf##_self_rsft_1(ez->VN); \
site++;\
if(err <= thre && err < ez->err) {\
ez->err = err; ez->pe = site; ez->te = tn-1;\
}\
}\
if(err <= thre && err < ez->err) {\
ez->err = err; ez->pe = site; ez->te = tn-1;\
}\
return;\
}
inline void ed_band_cal_global_128bit(char *pstr, int32_t pn, char *tstr, int32_t tn, int32_t thre, bit_extz_t *ez)
{
init_base_ed(*ez, thre, pn, tn); ez->ps = ez->ts = 0;
if((pn > tn + thre) || (tn > pn + thre)) return;
// if((pn < thre + 1) || (tn < thre + 1)) return;
int32_t i, err, tn0 = tn - 1, cut = thre+(thre<<1), bd = thre+1, i_bd = thre; uint8_t c;
w128_clear(ez->Peq[0]); w128_clear(ez->Peq[1]); w128_clear(ez->Peq[2]); w128_clear(ez->Peq[3]); w128_clear(ez->Peq[4]);
w128_clear(ez->mm); w128_bit(ez->mm, thre); ///mm = (((Word)1)<<thre)
for (i = 0; i < bd && i < pn; i++) {
w128_self_or(ez->Peq[seq_nt4_table[(uint8_t)pstr[i]]], ez->mm); w128_self_lsft_1(ez->mm);
// Peq[seq_nt4_table[(uint8_t)pstr[i]]] |= mm; mm <<= 1;
}
w128_clear(ez->Peq[4]);
err = thre;
w128_set_bit_lsub(ez->VN, thre); ///VN = (((Word)1)<<(thre))-1;
w128_set_bit_lsub(ez->VP, (thre<<1)+1); ///VP = (((Word)1)<<((thre<<1)+1))-1;
w128_self_xor(ez->VP, ez->VN); ///VP ^= VN;
// print_bits(Peq[0].a, (thre<<1)+1, "-Peq[A]");
// print_bits(Peq[1].a, (thre<<1)+1, "-Peq[C]");
// print_bits(Peq[2].a, (thre<<1)+1, "-Peq[G]");
// print_bits(Peq[3].a, (thre<<1)+1, "-Peq[T]");
// print_bits(VN.a, (thre<<1)+1, "-VN");
// print_bits(VP.a, (thre<<1)+1, "-VP");
///should make Peq[4] = 0 if N is always an error
i = 0;
///for the incoming char/last char
w128_clear(ez->mm); w128_bit(ez->mm, (thre<<1)); ///mm = ((Word)1 << (thre<<1));
//VP + ((Peq|VN)&VP)
while (i < tn0) {
ed_core_w128(ez->Peq, ez->VP, ez->VN, ez->X, ez->D0, ez->HN, ez->HP);
if (!(ez->D0.a[0]&(1ULL))) {
++err; if (err>cut) return;
}
ed_core_w128_reshift(ez->Peq);
++i; ++i_bd;
if(i_bd < pn) {
c = seq_nt4_table[(uint8_t)pstr[i_bd]];
///if(c < 4) Peq[c] |= mm;
if(c < 4) w128_self_or(ez->Peq[c], ez->mm);
}
}
ed_core_w128(ez->Peq, ez->VP, ez->VN, ez->X, ez->D0, ez->HN, ez->HP);
if (!(ez->D0.a[0]&(1ULL))) {
++err; if (err>cut) return;
}
int32_t site = tn - 1 - thre;///up bound
for (cut = pn - 1; site < cut; site++) {
// err += ((VP >> i)&(1ULL));
err += ez->VP.a[0]&(1ULL); w128_self_rsft_1(ez->VP);
// err -= ((VN >> i)&(1ULL));
err -= ez->VN.a[0]&(1ULL); w128_self_rsft_1(ez->VN);
}
if (site == cut && err <= thre) {
ez->err = err;
ez->pe = pn-1; ez->te = tn-1;
}
return;
}
inline void ed_band_cal_semi_128bit(char *pstr, int32_t pn, char *tstr, int32_t tn, int32_t thre, bit_extz_t *ez)
{
// (*re_err) = INT32_MAX;
init_base_ed(*ez, thre, pn, tn); ez->ps = ez->pe = -1; ez->ts = 0; ez->te = tn-1;
w128_clear(ez->VP); w128_clear(ez->VN); w128_clear(ez->mm); w128_bit(ez->mm, 0);
w128_clear(ez->Peq[0]); w128_clear(ez->Peq[1]); w128_clear(ez->Peq[2]); w128_clear(ez->Peq[3]); w128_clear(ez->Peq[4]);
int32_t bd = (thre<<1)+1, i, err = 0, i_bd = (thre<<1), last_high = (thre<<1), tn0 = tn - 1;
int32_t cut = thre+last_high; uint8_t c;
for (i = 0; i < bd; i++) {
w128_self_or(ez->Peq[seq_nt4_table[(uint8_t)pstr[i]]], ez->mm); w128_self_lsft_1(ez->mm);
// Peq[seq_nt4_table[(uint8_t)pstr[i]]] |= mm; mm <<= 1;
}
///should make Peq[4] = 0 if N is always an error
// Peq[4] = 0;
w128_clear(ez->Peq[4]);
//mm = ((Word)1 << (thre<<1));///for the incoming char/last char
w128_clear(ez->mm); w128_bit(ez->mm, (thre<<1));
i = 0;
while (i < tn0) {
ed_core_w128(ez->Peq, ez->VP, ez->VN, ez->X, ez->D0, ez->HN, ez->HP);
if (!(ez->D0.a[0]&(1ULL))) {
++err; if (err>cut) return;
}
ed_core_w128_reshift(ez->Peq);
++i; ++i_bd;
// Peq[seq_nt4_table[(uint8_t)pstr[i_bd]]] |= mm; Peq[4] = 0;
c = seq_nt4_table[(uint8_t)pstr[i_bd]];
if(c < 4) w128_self_or(ez->Peq[c], ez->mm);
}
ed_core_w128(ez->Peq, ez->VP, ez->VN, ez->X, ez->D0, ez->HN, ez->HP);
if (!(ez->D0.a[0]&(1ULL))) {
++err; if (err>cut) return;
}
int32_t site = tn - 1;///up bound
///in most cases, ai = (thre<<1)
int32_t ai = pn - tn, uge = INT32_MAX;
if ((err <= thre) && (err <= ez->err)) {
ez->err = err; ez->pe = site;
}
i = 0;
while (i < ai) {
// err += ((VP >> i)&(1ULL));
err += ez->VP.a[0]&(1ULL); w128_self_rsft_1(ez->VP);
// err -= ((VN >> i)&(1ULL));
err -= ez->VN.a[0]&(1ULL); w128_self_rsft_1(ez->VN);
++i;
if ((err <= thre) && (err <= ez->err)) {
ez->err = err; ez->pe = site + i;
}
if(i == thre) uge = err;
}
if((uge <= thre) && (uge == ez->err)) ez->pe = site + thre;
}
///require:: (pn >= tn - thre && pn <= tn + thre)
inline void ed_band_cal_extension_128bit(char *pstr, int32_t pn, char *tstr, int32_t tn, int32_t thre, bit_extz_t *ez)
{
// fprintf(stderr, "\n[M::%s::] pn::%d, tn::%d, thre::%d\n", __func__, pn, tn, thre);
if(pn > tn + thre) pn = tn + thre;
else if(tn > pn + thre) tn = pn + thre;
// fprintf(stderr, "[M::%s::] pn::%d, tn::%d, thre::%d\n", __func__, pn, tn, thre);
init_base_ed(*ez, thre, pn, tn); ez->ps = ez->ts = 0; ez->pe = ez->te = -1;
// if((pn > tn + thre) || (tn > pn + thre)) return;
// if((pn < thre + 1) || (tn < thre + 1)) return;
int32_t i, err, tn0 = tn - 1, cut = thre+(thre<<1), bd = thre+1, i_bd = thre; uint8_t c;
int32_t poff, pe = pn-1, tmp_e, k;
w128_clear(ez->Peq[0]); w128_clear(ez->Peq[1]); w128_clear(ez->Peq[2]); w128_clear(ez->Peq[3]); w128_clear(ez->Peq[4]);
w128_clear(ez->mm); w128_bit(ez->mm, thre); ///mm = (((Word)1)<<thre)
for (i = 0; i < bd && i < pn; i++) {
w128_self_or(ez->Peq[seq_nt4_table[(uint8_t)pstr[i]]], ez->mm); w128_self_lsft_1(ez->mm);
// Peq[seq_nt4_table[(uint8_t)pstr[i]]] |= mm; mm <<= 1;
}
w128_clear(ez->Peq[4]);
err = thre;
w128_set_bit_lsub(ez->VN, thre); ///VN = (((Word)1)<<(thre))-1;
w128_set_bit_lsub(ez->VP, (thre<<1)+1); ///VP = (((Word)1)<<((thre<<1)+1))-1;
w128_self_xor(ez->VP, ez->VN); ///VP ^= VN;
// print_bits(ez->Peq[0].a, (thre<<1)+1, "-Peq[A]");
// print_bits(ez->Peq[1].a, (thre<<1)+1, "-Peq[C]");
// print_bits(ez->Peq[2].a, (thre<<1)+1, "-Peq[G]");
// print_bits(ez->Peq[3].a, (thre<<1)+1, "-Peq[T]");
// print_bits(ez->VN.a, (thre<<1)+1, "-VN");
// print_bits(ez->VP.a, (thre<<1)+1, "-VP");
///should make Peq[4] = 0 if N is always an error
i = 0;
///for the incoming char/last char
w128_clear(ez->mm); w128_bit(ez->mm, (thre<<1)); ///mm = ((Word)1 << (thre<<1));
//VP + ((Peq|VN)&VP)
while (i < tn0) {
ed_core_w128(ez->Peq, ez->VP, ez->VN, ez->X, ez->D0, ez->HN, ez->HP);
if (!(ez->D0.a[0]&(1ULL))) {
++err; if (err>cut) return;
}
poff = i-thre; tmp_e = err; //poff:[i-thre, i+thre]
tst_band_err(poff, i, pe, tmp_e, *ez, k);
ed_core_w128_reshift(ez->Peq);
++i; ++i_bd;
if(i_bd < pn) {
c = seq_nt4_table[(uint8_t)pstr[i_bd]];
if(c < 4) w128_self_or(ez->Peq[c], ez->mm);
}
}
ed_core_w128(ez->Peq, ez->VP, ez->VN, ez->X, ez->D0, ez->HN, ez->HP);
if (!(ez->D0.a[0]&(1ULL))) {
++err; if (err>cut) return;
}
///i = tn - 1
int32_t site = tn - 1 - thre;///up bound; site:[tn - 1 - thre, tn - 1 + thre]
for (cut = pn - 1; site < cut; ) {
// err += ((VP >> i)&(1ULL));
err += ez->VP.a[0]&(1ULL); w128_self_rsft_1(ez->VP);
// err -= ((VN >> i)&(1ULL));
err -= ez->VN.a[0]&(1ULL); w128_self_rsft_1(ez->VN);
site++;
if(err <= thre && err < ez->err) {
ez->err = err; ez->pe = site; ez->te = tn-1;
}
}
if(err <= thre && err < ez->err) {
ez->err = err; ez->pe = site; ez->te = tn-1;
}
return;
}
HA_ED_INIT(128)
/**
main.cpp
+4 -4
View File
@@ -12,11 +12,11 @@ int main(int argc, char *argv[])
yak_reset_realtime();
init_opt(&asm_opt);
if (!CommandLine_process(argc, argv, &asm_opt)) return 0;
bit_extz_t exz; ///ed_band_cal_global_128bit(t_string+r_ts, t_end+1-r_ts, q_string, ql, thres, &exz);
ed_band_cal_extension_128bit((char *)"AAGTTTA", 7, (char *)"CCTTTTTT", 8, 4, &exz);
//bit_extz_t exz; ///ed_band_cal_global_128bit(t_string+r_ts, t_end+1-r_ts, q_string, ql, thres, &exz);
// ed_band_cal_extension_128bit((char *)"AAGTTTA", 7, (char *)"CCTTTTTT", 8, 4, &exz);
// ed_band_cal_extension_128bit((char *)"AA", 2, (char *)"ACTTTTTT", 8, 1, &exz);
fprintf(stderr, "ed_extension::%d, pe::%d, te::%d\n", exz.err, exz.pe, exz.te);
exit(1);
// fprintf(stderr, "ed_extension::%d, pe::%d, te::%d\n", exz.err, exz.pe, exz.te);
// exit(1);
// fprintf(stderr, "[M::%s::] ed_global::%d, ed_global_128bit::%d\n", __func__,
// ed_band_cal_global((char *)"ACT", 3, (char *)"AAT", 3, 1),