xxay/hifiasm
1
0
Fork 0
mirror of https://github.com/chhylp123/hifiasm.git synced 2026-10-11 03:10:56 +08:00
Code Issues Packages Projects Releases Wiki Activity

inner define

Browse Source
This commit is contained in:
chhylp123
2022-09-14 21:10:31 -04:00
parent 69d0e18fe5
commit 54b733ef2f
2 changed files with 85 additions and 105 deletions
Download Patch File Download Diff File Expand all files Collapse all files
Correct.cpp
+9 -5
View File
@@ -3657,12 +3657,16 @@ char *qstr, char *tstr, char *tstr1, Correct_dumy* dumy, uint32_t rev, uint32_t
// fprintf(stderr, "[qstr] %.*s\n", (int32_t)ql, q_string); // fprintf(stderr, "[qstr] %.*s\n", (int32_t)ql, q_string);
// } // }
// assert(dbg_e <= (int32_t)error); // assert(dbg_e <= (int32_t)error);
// bit_extz_t exz; bit_extz_t exz;
// ed_band_cal_extension_128bit(t_string+r_ts, t_end+1-r_ts, q_string, ql, thres, &exz); ed_band_cal_extension_128_w(t_string+r_ts, t_end+1-r_ts, q_string, ql, thres, &exz);
// assert(exz.err <= (int32_t)error); assert(exz.err <= (int32_t)error);
ed_band_cal_global_128_w(t_string+r_ts, t_end+1-r_ts, q_string, ql, thres, &exz);
assert(exz.err <= (int32_t)error);
ed_band_cal_semi_128_w(t_string, aln_l, 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) { // if(exz.err > (int32_t)error && ql == 1) {
// fprintf(stderr, "[M::%s::] error::%u, ed_extension::%d, ql::%ld, thres::%ld\n", // fprintf(stderr, "[M::%s::] error::%u, ed_extension::%d, ql::%ld, thres::%ld\n",
// __func__, error, exz.err, ql, thres); // __func__, error, exz.err, ql, thres);
Levenshtein_distance.h
+76 -100
View File
@@ -617,39 +617,39 @@ typedef struct {
(ez).done_cigar = (ez).done_path = (ez).cigar_n = (ez).path_n = 0;\ (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 w_128_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)) #define w_128_get_bit(x, b) (((x).a[((b)>>bitw)]>>((b)&bitz))&((w_sig)1))
#define w128_clear(x) ((x).a[0]=(x).a[1]=0) #define w_128_clear(x) ((x).a[0]=(x).a[1]=0)
#define w128_self_not(x) ((x).a[0]=~(x).a[0], \ #define w_128_self_not(x) ((x).a[0]=~(x).a[0], \
(x).a[1]=~(x).a[1]) (x).a[1]=~(x).a[1])
#define w128_self_or(x, y) ((x).a[0]|=(y).a[0], \ #define w_128_self_or(x, y) ((x).a[0]|=(y).a[0], \
(x).a[1]|=(y).a[1]) (x).a[1]|=(y).a[1])
#define w128_or(r, x, y) ((r).a[0] = (x).a[0]|(y).a[0], \ #define w_128_or(r, x, y) ((r).a[0] = (x).a[0]|(y).a[0], \
(r).a[1] = (x).a[1]|(y).a[1]) (r).a[1] = (x).a[1]|(y).a[1])
#define w128_and(r, x, y) ((r).a[0] = (x).a[0]&(y).a[0], \ #define w_128_and(r, x, y) ((r).a[0] = (x).a[0]&(y).a[0], \
(r).a[1] = (x).a[1]&(y).a[1]) (r).a[1] = (x).a[1]&(y).a[1])
#define w128_self_xor(x, y) ((x).a[0]^=(y).a[0], \ #define w_128_self_xor(x, y) ((x).a[0]^=(y).a[0], \
(x).a[1]^=(y).a[1]) (x).a[1]^=(y).a[1])
// #define w128_self_lsft_l(x, l) ((x).a[1] = ((x).a[1]<<(l))|((x).a[0]>>(bitwbit-(l))), (x).a[0] <<= (l)) // #define w128_self_lsft_l(x, l) ((x).a[1] = ((x).a[1]<<(l))|((x).a[0]>>(bitwbit-(l))), (x).a[0] <<= (l))
#define w128_self_lsft_1(x) ((x).a[1] = ((x).a[1]<<1)|((x).a[0]>>bitz), \ #define w_128_self_lsft_1(x) ((x).a[1] = ((x).a[1]<<1)|((x).a[0]>>bitz), \
(x).a[0] <<= 1) (x).a[0] <<= 1)
#define w128_self_rsft_1(x) ((x).a[0] = ((x).a[0]>>1)|((x).a[1]<<bitz), \ #define w_128_self_rsft_1(x) ((x).a[0] = ((x).a[0]>>1)|((x).a[1]<<bitz), \
(x).a[1] >>= 1) (x).a[1] >>= 1)
#define w128_self_add(x, y) ((x).a[0]+=(y).a[0], \ #define w_128_self_add(x, y) ((x).a[0]+=(y).a[0], \
(x).a[1]+=(y).a[1]+((x).a[0]<(y).a[0])) (x).a[1]+=(y).a[1]+((x).a[0]<(y).a[0]))
#define w128_set_bit_lsub(x, l) do { \ #define w_128_set_bit_lsub(x, l) do { \
(x).a[0] = (w_sig)-1, (x).a[1] = 0; \ (x).a[0] = (w_sig)-1, (x).a[1] = 0; \
if((l) <= bitwbit) (x).a[0] = (((w_sig)1)<<(l))-1; \ if((l) <= bitwbit) (x).a[0] = (((w_sig)1)<<(l))-1; \
else (x).a[1] = (((w_sig)1)<<((l)-bitwbit))-1;\ else (x).a[1] = (((w_sig)1)<<((l)-bitwbit))-1;\
@@ -657,96 +657,72 @@ typedef struct {
#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;**/\
w128_and(D0, X, VP);\
w128_self_add(D0, VP);\
w128_self_xor(D0, VP);\
w128_self_or(D0, X);\
/**HN = VP&D0;**/\
w128_and(HN, VP, D0);\
/**HP = VN | ~(VP | D0);**/\
w128_or(HP, VP, D0);\
w128_self_not(HP);\
w128_self_or(HP, VN);\
/**X = D0 >> 1;**/\
X = D0; w128_self_rsft_1(X);\
/**VN = X&HP;**/\
w128_and(VN, X, HP);\
/**VP = HN | ~(X | HP);**/\
w128_or(VP, X, HP);\
w128_self_not(VP);\
w128_self_or(VP, HN);\
}
#define ed_core(sf, Peq, VP, VN, X, D0, HN, HP) { \ #define ed_core(sf, Peq, VP, VN, X, D0, HN, HP) { \
/**X = Peq[seq_nt4_table[(uint8_t)tstr[i]]] | VN;**/\ /**X = Peq[seq_nt4_table[(uint8_t)tstr[i]]] | VN;**/\
c = seq_nt4_table[(uint8_t)tstr[i]]; ##sf##or(X, Peq[c], VN);\ c = seq_nt4_table[(uint8_t)tstr[i]]; w##sf##or(X, Peq[c], VN);\
/**D0 = ((VP + (X&VP)) ^ VP) | X;**/\ /**D0 = ((VP + (X&VP)) ^ VP) | X;**/\
##sf##and(D0, X, VP);\ w##sf##and(D0, X, VP);\
##sf##self_add(D0, VP);\ w##sf##self_add(D0, VP);\
##sf##self_xor(D0, VP);\ w##sf##self_xor(D0, VP);\
##sf##self_or(D0, X);\ w##sf##self_or(D0, X);\
/**HN = VP&D0;**/\ /**HN = VP&D0;**/\
##sf##and(HN, VP, D0);\ w##sf##and(HN, VP, D0);\
/**HP = VN | ~(VP | D0);**/\ /**HP = VN | ~(VP | D0);**/\
##sf##or(HP, VP, D0);\ w##sf##or(HP, VP, D0);\
##sf##self_not(HP);\ w##sf##self_not(HP);\
##sf##self_or(HP, VN);\ w##sf##self_or(HP, VN);\
/**X = D0 >> 1;**/\ /**X = D0 >> 1;**/\
X = D0; ##sf##self_rsft_1(X);\ X = D0; w##sf##self_rsft_1(X);\
/**VN = X&HP;**/\ /**VN = X&HP;**/\
##sf##and(VN, X, HP);\ w##sf##and(VN, X, HP);\
/**VP = HN | ~(X | HP);**/\ /**VP = HN | ~(X | HP);**/\
##sf##or(VP, X, HP);\ w##sf##or(VP, X, HP);\
##sf##self_not(VP);\ w##sf##self_not(VP);\
##sf##self_or(VP, HN);\ w##sf##self_or(VP, HN);\
} }
#define HA_ED_INIT(sf)\ #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)\ inline void ed_band_cal_global_##sf##_w(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;\ init_base_ed(*ez, thre, pn, tn); ez->ps = ez->ts = 0;\
if((pn > tn + thre) || (tn > pn + thre)) return;\ if((pn > tn + thre) || (tn > pn + thre)) return;\
/**if((pn < thre + 1) || (tn < thre + 1)) 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 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->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)**/\ w_##sf##_clear(ez->mm); w_##sf##_bit(ez->mm, thre); /**mm = (((Word)1)<<thre)**/\
for (i = 0; i < bd && i < pn; i++) {\ for (i = 0, bd = ((bd<=pn)?bd:pn); 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);\ 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;**/\ /** Peq[seq_nt4_table[(uint8_t)pstr[i]]] |= mm; mm <<= 1;**/\
}\ }\
w##sf##_clear(ez->Peq[4]);\ w_##sf##_clear(ez->Peq[4]);\
err = thre;\ err = thre;\
w##sf##_set_bit_lsub(ez->VN, thre); /**VN = (((Word)1)<<(thre))-1;**/\ 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##_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;**/\ w_##sf##_self_xor(ez->VP, ez->VN); /**VP ^= VN;**/\
\ \
/** print_bits(VP.a, (thre<<1)+1, "-VP");**/\ /** print_bits(VP.a, (thre<<1)+1, "-VP");**/\
/**should make Peq[4] = 0 if N is always an error**/\ /**should make Peq[4] = 0 if N is always an error**/\
i = 0; \ i = 0; \
/**for the incoming char/last char**/\ /**for the incoming char/last char**/\
w##sf##_clear(ez->mm); w##sf##_bit(ez->mm, (thre<<1)); /**mm = ((Word)1 << (thre<<1));**/\ w_##sf##_clear(ez->mm); w_##sf##_bit(ez->mm, (thre<<1)); /**mm = ((Word)1 << (thre<<1));**/\
while (i < tn0) {\ while (i < tn0) {\
ed_core_w##sf##b(ez->Peq, ez->VP, ez->VN, ez->X, ez->D0, ez->HN, ez->HP);\ ed_core(_##sf##_, ez->Peq, ez->VP, ez->VN, ez->X, ez->D0, ez->HN, ez->HP);\
if (!(ez->D0.a[0]&(1ULL))) {\ if (!(ez->D0.a[0]&(1ULL))) {\
++err; if (err>cut) return;\ ++err; if (err>cut) return;\
}\ }\
/** Peq[0] >>= 1; Peq[1] >>= 1; Peq[2] >>= 1; Peq[3] >>= 1;**/\ /** 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[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]);\ w_##sf##_self_rsft_1(ez->Peq[2]); w_##sf##_self_rsft_1(ez->Peq[3]);\
++i; ++i_bd;\ ++i; ++i_bd;\
if(i_bd < pn) {\ if(i_bd < pn) {\
c = seq_nt4_table[(uint8_t)pstr[i_bd]];\ c = seq_nt4_table[(uint8_t)pstr[i_bd]];\
/**if(c < 4) Peq[c] |= mm;**/\ /**if(c < 4) Peq[c] |= mm;**/\
if(c < 4) w##sf##_self_or(ez->Peq[c], ez->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);\ ed_core(_##sf##_, ez->Peq, ez->VP, ez->VN, ez->X, ez->D0, ez->HN, ez->HP);\
if (!(ez->D0.a[0]&(1ULL))) {\ if (!(ez->D0.a[0]&(1ULL))) {\
++err; if (err>cut) return;\ ++err; if (err>cut) return;\
}\ }\
@@ -754,9 +730,9 @@ inline void ed_band_cal_global_##sf##bit(char *pstr, int32_t pn, char *tstr, int
int32_t site = tn - 1 - thre;/**up bound**/\ int32_t site = tn - 1 - thre;/**up bound**/\
for (cut = pn - 1; site < cut; site++) {\ for (cut = pn - 1; site < cut; site++) {\
/**err += ((VP >> i)&(1ULL));**/\ /**err += ((VP >> i)&(1ULL));**/\
err += ez->VP.a[0]&(1ULL); w##sf##_self_rsft_1(ez->VP); \ err += ez->VP.a[0]&(1ULL); w_##sf##_self_rsft_1(ez->VP); \
/**err -= ((VN >> i)&(1ULL));**/\ /**err -= ((VN >> i)&(1ULL));**/\
err -= ez->VN.a[0]&(1ULL); w##sf##_self_rsft_1(ez->VN); \ err -= ez->VN.a[0]&(1ULL); w_##sf##_self_rsft_1(ez->VN); \
}\ }\
\ \
if (site == cut && err <= thre) {\ if (site == cut && err <= thre) {\
@@ -765,39 +741,39 @@ inline void ed_band_cal_global_##sf##bit(char *pstr, int32_t pn, char *tstr, int
}\ }\
return;\ 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)\ inline void ed_band_cal_semi_##sf##_w(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;\ 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->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]);\ 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 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;\ int32_t cut = thre+last_high; uint8_t c;\
\ \
for (i = 0; i < bd; i++) {\ 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);\ 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;**/\ /** Peq[seq_nt4_table[(uint8_t)pstr[i]]] |= mm; mm <<= 1;**/\
}\ }\
/**should make Peq[4] = 0 if N is always an error**/\ /**should make Peq[4] = 0 if N is always an error**/\
/** Peq[4] = 0;**/\ /** Peq[4] = 0;**/\
w##sf##_clear(ez->Peq[4]);\ w_##sf##_clear(ez->Peq[4]);\
/**mm = ((Word)1 << (thre<<1));///for the incoming char/last char**/\ /**mm = ((Word)1 << (thre<<1));///for the incoming char/last char**/\
w##sf##_clear(ez->mm); w##sf##_bit(ez->mm, (thre<<1));\ w_##sf##_clear(ez->mm); w_##sf##_bit(ez->mm, (thre<<1));\
\ \
i = 0;\ i = 0;\
while (i < tn0) {\ while (i < tn0) {\
ed_core_w##sf##b(ez->Peq, ez->VP, ez->VN, ez->X, ez->D0, ez->HN, ez->HP);\ ed_core(_##sf##_, ez->Peq, ez->VP, ez->VN, ez->X, ez->D0, ez->HN, ez->HP);\
if (!(ez->D0.a[0]&(1ULL))) {\ if (!(ez->D0.a[0]&(1ULL))) {\
++err; if (err>cut) return;\ ++err; if (err>cut) return;\
}\ }\
/** Peq[0] >>= 1; Peq[1] >>= 1; Peq[2] >>= 1; Peq[3] >>= 1;**/\ /** 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[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]);\ w_##sf##_self_rsft_1(ez->Peq[2]); w_##sf##_self_rsft_1(ez->Peq[3]);\
++i; ++i_bd; \ ++i; ++i_bd; \
/** Peq[seq_nt4_table[(uint8_t)pstr[i_bd]]] |= mm; Peq[4] = 0;**/\ /** Peq[seq_nt4_table[(uint8_t)pstr[i_bd]]] |= mm; Peq[4] = 0;**/\
c = seq_nt4_table[(uint8_t)pstr[i_bd]]; \ c = seq_nt4_table[(uint8_t)pstr[i_bd]]; \
if(c < 4) w##sf##_self_or(ez->Peq[c], ez->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);\ ed_core(_##sf##_, ez->Peq, ez->VP, ez->VN, ez->X, ez->D0, ez->HN, ez->HP);\
if (!(ez->D0.a[0]&(1ULL))) {\ if (!(ez->D0.a[0]&(1ULL))) {\
++err; if (err>cut) return;\ ++err; if (err>cut) return;\
}\ }\
@@ -812,9 +788,9 @@ inline void ed_band_cal_semi_##sf##bit(char *pstr, int32_t pn, char *tstr, int32
\ \
while (i < ai) {\ while (i < ai) {\
/** err += ((VP >> i)&(1ULL)); **/\ /** err += ((VP >> i)&(1ULL)); **/\
err += ez->VP.a[0]&(1ULL); w##sf##_self_rsft_1(ez->VP); \ err += ez->VP.a[0]&(1ULL); w_##sf##_self_rsft_1(ez->VP); \
/** err -= ((VN >> i)&(1ULL)); **/\ /** err -= ((VN >> i)&(1ULL)); **/\
err -= ez->VN.a[0]&(1ULL); w##sf##_self_rsft_1(ez->VN); \ err -= ez->VN.a[0]&(1ULL); w_##sf##_self_rsft_1(ez->VN); \
++i;\ ++i;\
if ((err <= thre) && (err <= ez->err)) {\ if ((err <= thre) && (err <= ez->err)) {\
ez->err = err; ez->pe = site + i;\ ez->err = err; ez->pe = site + i;\
@@ -825,33 +801,33 @@ inline void ed_band_cal_semi_##sf##bit(char *pstr, int32_t pn, char *tstr, int32
if((uge <= thre) && (uge == ez->err)) ez->pe = site + thre;\ if((uge <= thre) && (uge == ez->err)) ez->pe = site + thre;\
}\ }\
/**require:: (pn >= tn - thre && pn <= tn + 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)\ inline void ed_band_cal_extension_##sf##_w(char *pstr, int32_t pn, char *tstr, int32_t tn, int32_t thre, bit_extz_t *ez)\
{\ {\
if(pn > tn + thre) pn = tn + thre;\ if(pn > tn + thre) pn = tn + thre;\
else if(tn > pn + thre) tn = pn + 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;\ 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 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;\ 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->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)**/\ w_##sf##_clear(ez->mm); w_##sf##_bit(ez->mm, thre); /**mm = (((Word)1)<<thre)**/\
for (i = 0; i < bd && i < pn; i++) {\ for (i = 0, bd = ((bd<=pn)?bd:pn); 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);\ 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;**/\ /**Peq[seq_nt4_table[(uint8_t)pstr[i]]] |= mm; mm <<= 1;**/\
}\ }\
w##sf##_clear(ez->Peq[4]);\ w_##sf##_clear(ez->Peq[4]);\
err = thre;\ err = thre;\
w##sf##_set_bit_lsub(ez->VN, thre); /**VN = (((Word)1)<<(thre))-1; **/\ 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##_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;**/\ w_##sf##_self_xor(ez->VP, ez->VN); /**VP ^= VN;**/\
\ \
/** print_bits(ez->VP.a, (thre<<1)+1, "-VP");**/\ /** print_bits(ez->VP.a, (thre<<1)+1, "-VP");**/\
/**should make Peq[4] = 0 if N is always an error**/\ /**should make Peq[4] = 0 if N is always an error**/\
i = 0; \ i = 0; \
/**for the incoming char/last char**/\ /**for the incoming char/last char**/\
w##sf##_clear(ez->mm); w##sf##_bit(ez->mm, (thre<<1)); /**mm = ((Word)1 << (thre<<1));**/\ w_##sf##_clear(ez->mm); w_##sf##_bit(ez->mm, (thre<<1)); /**mm = ((Word)1 << (thre<<1));**/\
while (i < tn0) {\ while (i < tn0) {\
ed_core_w##sf##b(ez->Peq, ez->VP, ez->VN, ez->X, ez->D0, ez->HN, ez->HP);\ ed_core(_##sf##_, ez->Peq, ez->VP, ez->VN, ez->X, ez->D0, ez->HN, ez->HP);\
if (!(ez->D0.a[0]&(1ULL))) {\ if (!(ez->D0.a[0]&(1ULL))) {\
++err; if (err>cut) return;\ ++err; if (err>cut) return;\
}\ }\
@@ -860,8 +836,8 @@ inline void ed_band_cal_extension_##sf##bit(char *pstr, int32_t pn, char *tstr,
poff = i-thre; tmp_e = err; /**poff:[i-thre, i+thre]**/\ poff = i-thre; tmp_e = err; /**poff:[i-thre, i+thre]**/\
if((poff) + (((*ez).thre)<<1) >= (pe)) { \ if((poff) + (((*ez).thre)<<1) >= (pe)) { \
for ((k) = 0; (poff) < (pe); (poff)++) {\ for ((k) = 0; (poff) < (pe); (poff)++) {\
(tmp_e) += w##sf##_get_bit((*ez).VP, (k));\ (tmp_e) += w_##sf##_get_bit((*ez).VP, (k));\
(tmp_e) -= w##sf##_get_bit((*ez).VN, (k));\ (tmp_e) -= w_##sf##_get_bit((*ez).VN, (k));\
(k)++;}\ (k)++;}\
if((tmp_e) <= (*ez).thre && (tmp_e) < (*ez).err) {\ if((tmp_e) <= (*ez).thre && (tmp_e) < (*ez).err) {\
(*ez).err = tmp_e; (*ez).pe = poff; (*ez).te = i;}\ (*ez).err = tmp_e; (*ez).pe = poff; (*ez).te = i;}\
@@ -869,15 +845,15 @@ inline void ed_band_cal_extension_##sf##bit(char *pstr, int32_t pn, char *tstr,
}\ }\
\ \
/** Peq[0] >>= 1; Peq[1] >>= 1; Peq[2] >>= 1; Peq[3] >>= 1;**/\ /** 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[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]);\ w_##sf##_self_rsft_1(ez->Peq[2]); w_##sf##_self_rsft_1(ez->Peq[3]);\
++i; ++i_bd;\ ++i; ++i_bd;\
if(i_bd < pn) {\ if(i_bd < pn) {\
c = seq_nt4_table[(uint8_t)pstr[i_bd]]; \ c = seq_nt4_table[(uint8_t)pstr[i_bd]]; \
if(c < 4) w##sf##_self_or(ez->Peq[c], ez->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);\ ed_core(_##sf##_, ez->Peq, ez->VP, ez->VN, ez->X, ez->D0, ez->HN, ez->HP);\
if (!(ez->D0.a[0]&(1ULL))) {\ if (!(ez->D0.a[0]&(1ULL))) {\
++err; if (err>cut) return;\ ++err; if (err>cut) return;\
}\ }\
@@ -885,9 +861,9 @@ inline void ed_band_cal_extension_##sf##bit(char *pstr, int32_t pn, char *tstr,
int32_t site = tn - 1 - thre;/**up bound; site:[tn - 1 - thre, tn - 1 + thre]**/\ int32_t site = tn - 1 - thre;/**up bound; site:[tn - 1 - thre, tn - 1 + thre]**/\
for (cut = pn - 1; site < cut; ) {\ for (cut = pn - 1; site < cut; ) {\
/** err += ((VP >> i)&(1ULL)); **/\ /** err += ((VP >> i)&(1ULL)); **/\
err += ez->VP.a[0]&(1ULL); w##sf##_self_rsft_1(ez->VP); \ err += ez->VP.a[0]&(1ULL); w_##sf##_self_rsft_1(ez->VP); \
/** err -= ((VN >> i)&(1ULL));**/\ /** err -= ((VN >> i)&(1ULL));**/\
err -= ez->VN.a[0]&(1ULL); w##sf##_self_rsft_1(ez->VN); \ err -= ez->VN.a[0]&(1ULL); w_##sf##_self_rsft_1(ez->VN); \
site++;\ site++;\
if(err <= thre && err < ez->err) {\ if(err <= thre && err < ez->err) {\
ez->err = err; ez->pe = site; ez->te = tn-1;\ ez->err = err; ez->pe = site; ez->te = tn-1;\