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hifiasm/Levenshtein_distance.h
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chhylp123 5da05f308f extend ed alignment
2022-09-13 17:29:27 -04:00

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#ifndef __LEVENSHTEIN__
#define __LEVENSHTEIN__
#include <stdint.h>
#include "emmintrin.h"
#include "nmmintrin.h"
#include "smmintrin.h"
#include <immintrin.h>
#include <string.h>
#include <stdlib.h>
#include <stdio.h>
#include "kvec.h"
extern const unsigned char seq_nt4_table[256];
typedef uint64_t Word;
typedef uint32_t Word_32;
typedef struct {size_t n, m; uint16_t *a; } asg16_v;
inline void get_error(int t_length, int errthold, int init_err, Word VP, Word VN,
unsigned int* return_err, int* back_site)
{
(*return_err) = (unsigned int)-1;
int site = t_length - 1;
int return_site = -1;
///in most cases, p_length should be t_length + 2 * errthold
///int available_i = p_length - t_length;
int available_i = 2 * errthold;
if ((init_err <= errthold) && ((unsigned int)init_err <= (*return_err)))
{
(*return_err) = init_err;
return_site = site;
}
int i = 0;
unsigned int ungap_error = (unsigned int)-1;
while (i < available_i)
{
init_err = init_err + ((VP >> i)&(Word)1);
init_err = init_err - ((VN >> i)&(Word)1);
++i;
if ((init_err <= errthold) && ((unsigned int)init_err <= *return_err))
{
*return_err = init_err;
return_site = site + i;
}
/****************************may have bugs********************************/
if(i == errthold)
{
ungap_error = init_err;
}
/****************************may have bugs********************************/
}
/****************************may have bugs********************************/
if((ungap_error<=(unsigned int)errthold) && (ungap_error == (*return_err)))
{
return_site = site + errthold;
}
/****************************may have bugs********************************/
(*back_site) = return_site;
}
inline int Reserve_Banded_BPM_Extension
(char *pattern, int p_length, char *text, int t_length, unsigned short errthold,
unsigned int* return_err, int* return_p_end, int* return_t_end)
{
(*return_err) = (unsigned int)-1;
(*return_p_end) = -1;
(*return_t_end) = -1;
Word Peq[256];
unsigned int line_error = (unsigned int)-1;
int return_site;
int band_length = (errthold << 1) + 1;
int i = 0;
Word tmp_Peq_1 = (Word)1;
Peq[(uint8_t)'A'] = (Word)0;
Peq[(uint8_t)'T'] = (Word)0;
Peq[(uint8_t)'G'] = (Word)0;
Peq[(uint8_t)'C'] = (Word)0;
Word Peq_A;
Word Peq_T;
Word Peq_C;
Word Peq_G;
///band_length = 2k + 1
for (i = 0; i<band_length; i++)
{
Peq[(uint8_t)pattern[i]] = Peq[(uint8_t)pattern[i]] | tmp_Peq_1;
tmp_Peq_1 = tmp_Peq_1 << 1;
}
Peq_A = Peq[(uint8_t)'A'];
Peq_C = Peq[(uint8_t)'C'];
Peq_T = Peq[(uint8_t)'T'];
Peq_G = Peq[(uint8_t)'G'];
memset(Peq, 0, sizeof(Word)* 256);
Peq[(uint8_t)'A'] = Peq_A;
Peq[(uint8_t)'C'] = Peq_C;
Peq[(uint8_t)'T'] = Peq_T;
Peq[(uint8_t)'G'] = Peq_G;
Word Mask = ((Word)1 << (errthold << 1));
Word VP = 0;
Word VN = 0;
Word X = 0;
Word D0 = 0;
Word HN = 0;
Word HP = 0;
i = 0;
int err = 0;
Word err_mask = (Word)1;
int i_bd = (errthold << 1);
int last_high = (errthold << 1);
int t_length_1 = t_length - 1;
while (i<t_length_1)
{
X = Peq[(uint8_t)text[i]] | VN;
D0 = ((VP + (X&VP)) ^ VP) | X;
HN = VP&D0;
HP = VN | ~(VP | D0);
X = D0 >> 1;
VN = X&HP;
VP = HN | ~(X | HP);
if (!(D0&err_mask))
{
++err;
if ((err - last_high)>errthold)
{
return (*return_t_end);
}
}
get_error(i + 1, errthold, err, VP, VN, &line_error, &return_site);
if(line_error != (unsigned int)-1)
{
(*return_t_end) = i;
(*return_p_end) = return_site;
(*return_err) = line_error;
}
Peq[(uint8_t)'A'] = Peq[(uint8_t)'A'] >> 1;
Peq[(uint8_t)'C'] = Peq[(uint8_t)'C'] >> 1;
Peq[(uint8_t)'G'] = Peq[(uint8_t)'G'] >> 1;
Peq[(uint8_t)'T'] = Peq[(uint8_t)'T'] >> 1;
++i;
++i_bd;
Peq[(uint8_t)pattern[i_bd]] = Peq[(uint8_t)pattern[i_bd]] | Mask;
}
X = Peq[(uint8_t)text[i]] | VN;
D0 = ((VP + (X&VP)) ^ VP) | X;
HN = VP&D0;
HP = VN | ~(VP | D0);
X = D0 >> 1;
VN = X&HP;
VP = HN | ~(X | HP);
if (!(D0&err_mask))
{
++err;
if ((err - last_high)>errthold)
{
return (*return_t_end);
}
}
///i = t_length - 1
get_error(i + 1, errthold, err, VP, VN, &line_error, &return_site);
if(line_error != (unsigned int)-1)
{
(*return_t_end) = i;
(*return_p_end) = return_site;
(*return_err) = line_error;
}
return (*return_t_end);
}
inline int Reserve_Banded_BPM_Extension_REV
(char *pattern, int p_length, char *text, int t_length, unsigned short errthold,
unsigned int* return_err, int* return_p_end, int* return_t_end)
{
(*return_err) = (unsigned int)-1;
(*return_p_end) = -1;
(*return_t_end) = -1;
Word Peq[256];
unsigned int line_error = (unsigned int)-1;
int return_site;
int band_length = (errthold << 1) + 1;
int i = 0;
Word tmp_Peq_1 = (Word)1;
Peq[(uint8_t)'A'] = (Word)0;
Peq[(uint8_t)'T'] = (Word)0;
Peq[(uint8_t)'G'] = (Word)0;
Peq[(uint8_t)'C'] = (Word)0;
Word Peq_A;
Word Peq_T;
Word Peq_C;
Word Peq_G;
///band_length = 2k + 1
for (i = 0; i<band_length; i++)
{
Peq[(uint8_t)pattern[p_length-i-1]] = Peq[(uint8_t)pattern[p_length-i-1]] | tmp_Peq_1;
tmp_Peq_1 = tmp_Peq_1 << 1;
}
Peq_A = Peq[(uint8_t)'A'];
Peq_C = Peq[(uint8_t)'C'];
Peq_T = Peq[(uint8_t)'T'];
Peq_G = Peq[(uint8_t)'G'];
memset(Peq, 0, sizeof(Word)* 256);
Peq[(uint8_t)'A'] = Peq_A;
Peq[(uint8_t)'C'] = Peq_C;
Peq[(uint8_t)'T'] = Peq_T;
Peq[(uint8_t)'G'] = Peq_G;
Word Mask = ((Word)1 << (errthold << 1));
Word VP = 0;
Word VN = 0;
Word X = 0;
Word D0 = 0;
Word HN = 0;
Word HP = 0;
i = 0;
int err = 0;
Word err_mask = (Word)1;
int i_bd = (errthold << 1);
int last_high = (errthold << 1);
int t_length_1 = t_length - 1;
while (i<t_length_1)
{
X = Peq[(uint8_t)text[t_length-i-1]] | VN;
D0 = ((VP + (X&VP)) ^ VP) | X;
HN = VP&D0;
HP = VN | ~(VP | D0);
X = D0 >> 1;
VN = X&HP;
VP = HN | ~(X | HP);
if (!(D0&err_mask))
{
++err;
if ((err - last_high)>errthold)
{
return (*return_t_end);
}
}
get_error(i + 1, errthold, err, VP, VN, &line_error, &return_site);
if(line_error != (unsigned int)-1)
{
(*return_t_end) = t_length-i-1;
(*return_p_end) = p_length-return_site-1;
(*return_err) = line_error;
}
Peq[(uint8_t)'A'] = Peq[(uint8_t)'A'] >> 1;
Peq[(uint8_t)'C'] = Peq[(uint8_t)'C'] >> 1;
Peq[(uint8_t)'G'] = Peq[(uint8_t)'G'] >> 1;
Peq[(uint8_t)'T'] = Peq[(uint8_t)'T'] >> 1;
++i;
++i_bd;
Peq[(uint8_t)pattern[p_length-i_bd-1]] = Peq[(uint8_t)pattern[p_length-i_bd-1]] | Mask;
}
X = Peq[(uint8_t)text[t_length-i-1]] | VN;
D0 = ((VP + (X&VP)) ^ VP) | X;
HN = VP&D0;
HP = VN | ~(VP | D0);
X = D0 >> 1;
VN = X&HP;
VP = HN | ~(X | HP);
if (!(D0&err_mask))
{
++err;
if ((err - last_high)>errthold)
{
return (*return_t_end);
}
}
///i = t_length - 1
get_error(i + 1, errthold, err, VP, VN, &line_error, &return_site);
if(line_error != (unsigned int)-1)
{
(*return_t_end) = t_length-i-1;
(*return_p_end) = p_length-return_site-1;
(*return_err) = line_error;
}
return (*return_t_end);
}
inline void reverse_string(char* str, int strLen)
{
int i, Len;
char k;
Len = strLen / 2;
for (i = 0; i < Len; i++)
{
k = str[i];
str[i] = str[strLen - i - 1];
str[strLen - i - 1] = k;
}
}
inline int alignment_extension(char *pattern, int p_length, char *text, int t_length,
unsigned short errthold, int direction, unsigned int* return_err, int* return_p_end,
int* return_t_end, int* return_aligned_t_len)
{
(*return_aligned_t_len) = 0;
if(direction == 0)
{
Reserve_Banded_BPM_Extension(pattern, p_length, text, t_length, errthold, return_err,
return_p_end, return_t_end);
if((*return_p_end) != -1 && (*return_t_end) != -1)
{
(*return_aligned_t_len) = (*return_t_end) + 1;
return 1;
}
else
{
return -1;
}
}
else
{
reverse_string(pattern, p_length);
reverse_string(text, t_length);
Reserve_Banded_BPM_Extension(pattern, p_length, text, t_length, errthold, return_err,
return_p_end, return_t_end);
reverse_string(pattern, p_length);
reverse_string(text, t_length);
if((*return_p_end) != -1 && (*return_t_end) != -1)
{
(*return_aligned_t_len) = (*return_t_end) + 1;
(*return_p_end) = p_length - (*return_p_end);
(*return_t_end) = t_length - (*return_t_end);
return 1;
}
else
{
return -1;
}
}
}
///p_length might be samller than t_length + 2 * errthold
/// pattern is longer than text
inline int32_t ed_band_cal_semi(char *pstr, int32_t pn, char *tstr, int32_t tn, int32_t thre, int32_t *re_err)
{
(*re_err) = INT32_MAX;
Word Peq[5] = {0}, mm = (Word)1, VP = 0, VN = 0, X = 0, D0 = 0, HN = 0, HP = 0;
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;
for (i = 0; i < bd; i++) {
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;
i = 0; mm = ((Word)1 << (thre<<1));///for the incoming char/last char
while (i < tn0) {
X = Peq[seq_nt4_table[(uint8_t)tstr[i]]] | VN;
D0 = ((VP + (X&VP)) ^ VP) | X;
HN = VP&D0;
HP = VN | ~(VP | D0);
X = D0 >> 1;
VN = X&HP;
VP = HN | ~(X | HP);
if (!(D0&(1ULL))) {
++err;
if (err>cut) return -1;
}
Peq[0] >>= 1; Peq[1] >>= 1; Peq[2] >>= 1; Peq[3] >>= 1; ///Peq[4] >>= 1;
++i; ++i_bd;
Peq[seq_nt4_table[(uint8_t)pstr[i_bd]]] |= mm; Peq[4] = 0;
}
X = Peq[seq_nt4_table[(uint8_t)tstr[i]]] | VN;
D0 = ((VP + (X&VP)) ^ VP) | X;
HN = VP&D0;
HP = VN | ~(VP | D0);
X = D0 >> 1;
VN = X&HP;
VP = HN | ~(X | HP);
if (!(D0&(1ULL))) {
++err;
if (err>cut) return -1;
}
int32_t site = tn - 1, end = -1;///up bound
///in most cases, ai = (thre<<1)
int32_t ai = pn - tn, uge = INT32_MAX;
if ((err <= thre) && (err<=(*re_err))) {
*re_err = err; end = site;
}
i = 0;
while (i < ai) {
err += ((VP >> i)&(1ULL)); err -= ((VN >> i)&(1ULL)); ++i;
if ((err <= thre) && (err <= (*re_err))) {
*re_err = err; end = site + i;
}
if(i == thre) uge = err;
}
if((uge<=thre) && (uge == (*re_err))) end = site + thre;
return end;
}
inline void print_bit(Word z, int64_t w, const char *cmd)
{
int64_t k;//, w = (sizeof(Word)<<3);
fprintf(stderr, "%s\t", cmd);
for (k = 0; k < w; k++) fprintf(stderr, "%llu", (z>>k)&(1ULL));
fprintf(stderr, "\n");
}
inline void print_bits(Word *az, int64_t w, const char *cmd)
{
int64_t k, m, s = (sizeof(*az)<<3), sw = (w/s) + (!!(w%s)), ks;
fprintf(stderr, "%s\t", cmd);
for (m = k = 0; m < sw && k < w; m++) {
for (ks = 0; ks < s && k < w; ks++, k++) fprintf(stderr, "%llu", (az[m]>>ks)&(1ULL));
}
fprintf(stderr, "\n");
}
inline int32_t ed_band_cal_global(char *pstr, int32_t pn, char *tstr, int32_t tn, int32_t thre)
{
if((pn > tn + thre) || (tn > pn + thre)) return INT32_MAX;
if((pn < thre + 1) || (tn < thre + 1)) return INT32_MAX;
Word Peq[5] = {0}, mm, VP = 0, VN = 0, X = 0, D0 = 0, HN = 0, HP = 0;
int32_t i, err, tn0 = tn - 1, cut = thre+(thre<<1), bd = thre+1, i_bd = thre;
// fprintf(stderr, "\n[M::%s::]\n", __func__);
for (i = 0, mm = (((Word)1)<<thre); i < bd; i++) {
Peq[seq_nt4_table[(uint8_t)pstr[i]]] |= mm; mm <<= 1;
}
Peq[4] = 0;
err = thre;
VN = (((Word)1)<<(thre))-1;
VP = (((Word)1)<<((thre<<1)+1))-1; VP ^= VN;
// print_bit(Peq[0], (thre<<1)+1, "Peq[A]");
// print_bit(Peq[1], (thre<<1)+1, "Peq[C]");
// print_bit(Peq[2], (thre<<1)+1, "Peq[G]");
// print_bit(Peq[3], (thre<<1)+1, "Peq[T]");
// print_bit(Peq[4], (thre<<1)+1);
// print_bit(VN, (thre<<1)+1, "VN");
// print_bit(VP, (thre<<1)+1, "VP");
///should make Peq[4] = 0 if N is always an error
i = 0; mm = ((Word)1 << (thre<<1));///for the incoming char/last char
while (i < tn0) {
X = Peq[seq_nt4_table[(uint8_t)tstr[i]]] | VN;
D0 = ((VP + (X&VP)) ^ VP) | X;
HN = VP&D0;
HP = VN | ~(VP | D0);
X = D0 >> 1;
VN = X&HP;
VP = HN | ~(X | HP);
// fprintf(stderr, "\n[M::%s::i->%d]\n", __func__, i);
// print_bit(VN, (thre<<1)+1, "VN");
// print_bit(VP, (thre<<1)+1, "VP");
// print_bit(HN, (thre<<1)+1, "HN");
// print_bit(HP, (thre<<1)+1, "HP");
// print_bit(D0, (thre<<1)+1, "D0");
if (!(D0&(1ULL))) {
++err;
if (err>cut) return INT32_MAX;
}
// fprintf(stderr, "[M::%s::i->%d] err->%d\n", __func__, i, err);
Peq[0] >>= 1; Peq[1] >>= 1; Peq[2] >>= 1; Peq[3] >>= 1; ///Peq[4] >>= 1;
++i; ++i_bd;
if(i_bd < pn) {
Peq[seq_nt4_table[(uint8_t)pstr[i_bd]]] |= mm; Peq[4] = 0;
}
// if(i < pn) Peq[seq_nt4_table[(uint8_t)pstr[i]]] |= mm;
}
X = Peq[seq_nt4_table[(uint8_t)tstr[i]]] | VN;
D0 = ((VP + (X&VP)) ^ VP) | X;
HN = VP&D0;
HP = VN | ~(VP | D0);
X = D0 >> 1;
VN = X&HP;
VP = HN | ~(X | HP);
// fprintf(stderr, "\n[M::%s::i->%d]\n", __func__, i);
// print_bit(VN, (thre<<1)+1, "VN");
// print_bit(VP, (thre<<1)+1, "VP");
// print_bit(HN, (thre<<1)+1, "HN");
// print_bit(HP, (thre<<1)+1, "HP");
// print_bit(D0, (thre<<1)+1, "D0");
if (!(D0&(1ULL))) {
++err;
if (err>cut) return INT32_MAX;
}
// fprintf(stderr, "[M::%s::i->%d] err->%d\n", __func__, i, err);
int32_t site = tn - 1 - thre;///up bound
for (cut = pn - 1, i = 0; site < cut; site++, i++) {
// fprintf(stderr, "+[M::%s::site->%d] err->%d\n", __func__, site, err);
err += ((VP >> i)&(1ULL)); err -= ((VN >> i)&(1ULL));
// fprintf(stderr, "-[M::%s::site->%d] err->%d\n", __func__, site, err);
}
if (site == cut && err <= thre) return err;
return INT32_MAX;
}
typedef uint64_t w_sig;
typedef struct {w_sig a[2];} w128_t;
#define bitw (6)
#define bitwbit (64)
#define bitz (63)
// typedef uint32_t w_sig;
// typedef struct {w_sig a[2];} w128_t;
// #define bitw (5)
// #define bitwbit (32)
// #define bitz (31)
#define w128_bit(x, b) ((x).a[((b)>>bitw)]|=(((w_sig)1)<<((b)&bitz)))
#define w128_clear(x) ((x).a[0]=(x).a[1]=0)
#define w128_self_not(x) ((x).a[0]=~(x).a[0], \
(x).a[1]=~(x).a[1])
#define w128_self_or(x, y) ((x).a[0]|=(y).a[0], \
(x).a[1]|=(y).a[1])
#define w128_or(r, x, y) ((r).a[0] = (x).a[0]|(y).a[0], \
(r).a[1] = (x).a[1]|(y).a[1])
#define w128_and(r, x, y) ((r).a[0] = (x).a[0]&(y).a[0], \
(r).a[1] = (x).a[1]&(y).a[1])
#define w128_self_xor(x, y) ((x).a[0]^=(y).a[0], \
(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_1(x) ((x).a[1] = ((x).a[1]<<1)|((x).a[0]>>bitz), \
(x).a[0] <<= 1)
#define w128_self_rsft_1(x) ((x).a[0] = ((x).a[0]>>1)|((x).a[1]<<bitz), \
(x).a[1] >>= 1)
#define w128_self_add(x, y) ((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 { \
(x).a[0] = (w_sig)-1, (x).a[1] = 0; \
if((l) <= bitwbit) (x).a[0] = (((w_sig)1)<<(l))-1; \
else (x).a[1] = (((w_sig)1)<<((l)-bitwbit))-1;\
} while (0) \
#define ed_core_w128(RE) { \
/**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);\
/**if (!(D0&(1ULL)))**/\
if (!(D0.a[0]&(1ULL))) {\
++err;\
if (err>cut) return RE;\
}\
/** 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]);\
}
inline int32_t ed_band_cal_global_128bit(char *pstr, int32_t pn, char *tstr, int32_t tn, int32_t thre)
{
if((pn > tn + thre) || (tn > pn + thre)) return INT32_MAX;
if((pn < thre + 1) || (tn < thre + 1)) return INT32_MAX;
w128_t Peq[5], mm, VP, VN, X, D0, HN, HP; uint8_t c;
int32_t i, err, tn0 = tn - 1, cut = thre+(thre<<1), bd = thre+1, i_bd = thre;
w128_clear(Peq[0]); w128_clear(Peq[1]); w128_clear(Peq[2]); w128_clear(Peq[3]); w128_clear(Peq[4]);
w128_clear(mm); w128_bit(mm, thre); ///mm = (((Word)1)<<thre)
for (i = 0; i < bd; i++) {
w128_self_or(Peq[seq_nt4_table[(uint8_t)pstr[i]]], mm); w128_self_lsft_1(mm);
// Peq[seq_nt4_table[(uint8_t)pstr[i]]] |= mm; mm <<= 1;
}
w128_clear(Peq[4]);
err = thre;
w128_set_bit_lsub(VN, thre); ///VN = (((Word)1)<<(thre))-1;
w128_set_bit_lsub(VP, (thre<<1)+1); ///VP = (((Word)1)<<((thre<<1)+1))-1;
w128_self_xor(VP, 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(mm); w128_bit(mm, (thre<<1)); ///mm = ((Word)1 << (thre<<1));
//VP + ((Peq|VN)&VP)
while (i < tn0) {
///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);
//if (!(D0&(1ULL)))
if (!(D0.a[0]&(1ULL))) {
++err;
if (err>cut) return INT32_MAX;
}
// fprintf(stderr, "[M::%s::i->%d] err->%d\n", __func__, i, err);
// 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]);
++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(Peq[c], mm);
}
}
// 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);
// if (!(D0&(1ULL))) {
if (!(D0.a[0]&(1ULL))) {
++err;
if (err>cut) return INT32_MAX;
}
// fprintf(stderr, "[M::%s::i->%d] err->%d\n", __func__, i, err);
int32_t site = tn - 1 - thre;///up bound
for (cut = pn - 1, i = 0; site < cut; site++, i++) {
// err += ((VP >> i)&(1ULL));
err += VP.a[0]&(1ULL); w128_self_rsft_1(VP);
// err -= ((VN >> i)&(1ULL));
err -= VN.a[0]&(1ULL); w128_self_rsft_1(VN);
}
if (site == cut && err <= thre) return err;
return INT32_MAX;
}
inline int32_t ed_band_cal_semi_128bit(char *pstr, int32_t pn, char *tstr, int32_t tn, int32_t thre, int32_t *re_err)
{
(*re_err) = INT32_MAX;
w128_t Peq[5], mm, VP, VN, X, D0, HN, HP;
//Peq[5] = {0}, mm = (Word)1, VP = 0, VN = 0, X, D0, HN, HP;
w128_clear(VP); w128_clear(VN); w128_clear(mm); w128_bit(mm, 0);
w128_clear(Peq[0]); w128_clear(Peq[1]); w128_clear(Peq[2]); w128_clear(Peq[3]); w128_clear(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(Peq[seq_nt4_table[(uint8_t)pstr[i]]], mm); w128_self_lsft_1(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(Peq[4]);
//mm = ((Word)1 << (thre<<1));///for the incoming char/last char
w128_clear(mm); w128_bit(mm, (thre<<1));
i = 0;
while (i < tn0) {
// 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);
// if (!(D0&(1ULL))) {
if (!(D0.a[0]&(1ULL))) {
++err;
if (err>cut) return -1;
}
// 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]);
++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(Peq[c], mm);
}
// 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);
// if (!(D0&(1ULL))) {
if (!(D0.a[0]&(1ULL))) {
++err;
if (err>cut) return -1;
}
int32_t site = tn - 1, end = -1;///up bound
///in most cases, ai = (thre<<1)
int32_t ai = pn - tn, uge = INT32_MAX;
if ((err <= thre) && (err<=(*re_err))) {
*re_err = err; end = site;
}
i = 0;
while (i < ai) {
// err += ((VP >> i)&(1ULL));
err += VP.a[0]&(1ULL); w128_self_rsft_1(VP);
// err -= ((VN >> i)&(1ULL));
err -= VN.a[0]&(1ULL); w128_self_rsft_1(VN);
++i;
if ((err <= thre) && (err <= (*re_err))) {
*re_err = err; end = site + i;
}
if(i == thre) uge = err;
}
if((uge<=thre) && (uge == (*re_err))) end = site + thre;
return end;
}
/**
pattern is the longer one, while text is the shorter one
**/
inline int Reserve_Banded_BPM
(char *pattern, int p_length, char *text, int t_length, unsigned short errthold, unsigned int* return_err)
{
(*return_err) = (unsigned int)-1;
// int32_t rerr, rsite = ed_band_cal_semi_128bit(pattern, p_length, text, t_length, errthold, &rerr);
// if(rsite >= 0) (*return_err) = rerr;
// return rsite;
Word Peq[256];
int band_length = (errthold << 1) + 1;
int i = 0;
Word tmp_Peq_1 = (Word)1;
Peq[(uint8_t)'A'] = (Word)0;
Peq[(uint8_t)'T'] = (Word)0;
Peq[(uint8_t)'G'] = (Word)0;
Peq[(uint8_t)'C'] = (Word)0;
Word Peq_A;
Word Peq_T;
Word Peq_C;
Word Peq_G;
///band_length = 2k + 1
for (i = 0; i<band_length; i++)
{
Peq[(uint8_t)pattern[i]] = Peq[(uint8_t)pattern[i]] | tmp_Peq_1;
tmp_Peq_1 = tmp_Peq_1 << 1;
}
///Peq[(uint8_t)'T'] = Peq[(uint8_t)'T'] | Peq[(uint8_t)'C'];
Peq_A = Peq[(uint8_t)'A'];
Peq_C = Peq[(uint8_t)'C'];
Peq_T = Peq[(uint8_t)'T'];
Peq_G = Peq[(uint8_t)'G'];
memset(Peq, 0, sizeof(Word)* 256);
Peq[(uint8_t)'A'] = Peq_A;
Peq[(uint8_t)'C'] = Peq_C;
Peq[(uint8_t)'T'] = Peq_T;
Peq[(uint8_t)'G'] = Peq_G;
Word Mask = ((Word)1 << (errthold << 1));
Word VP = 0;
Word VN = 0;
Word X = 0;
Word D0 = 0;
Word HN = 0;
Word HP = 0;
i = 0;
int err = 0;
Word err_mask = (Word)1;
///band_down = 2k
///i_bd = 2k
///int i_bd = i + band_down;
int i_bd = (errthold << 1);
int last_high = (errthold << 1);
/// t_length_1 = SEQ_LENGTH - 1
int t_length_1 = t_length - 1;
//while(i<t_length)
while (i<t_length_1)
{
X = Peq[(uint8_t)text[i]] | VN;
D0 = ((VP + (X&VP)) ^ VP) | X;
HN = VP&D0;
HP = VN | ~(VP | D0);
X = D0 >> 1;
VN = X&HP;
VP = HN | ~(X | HP);
if (!(D0&err_mask))
{
++err;
if ((err - last_high)>(int)errthold)
{
return -1;
}
}
Peq[(uint8_t)'A'] = Peq[(uint8_t)'A'] >> 1;
Peq[(uint8_t)'C'] = Peq[(uint8_t)'C'] >> 1;
Peq[(uint8_t)'G'] = Peq[(uint8_t)'G'] >> 1;
Peq[(uint8_t)'T'] = Peq[(uint8_t)'T'] >> 1;
++i;
++i_bd;
Peq[(uint8_t)pattern[i_bd]] = Peq[(uint8_t)pattern[i_bd]] | Mask;
}
X = Peq[(uint8_t)text[i]] | VN;
D0 = ((VP + (X&VP)) ^ VP) | X;
HN = VP&D0;
HP = VN | ~(VP | D0);
X = D0 >> 1;
VN = X&HP;
VP = HN | ~(X | HP);
if (!(D0&err_mask))
{
++err;
if ((err - last_high)>errthold)
return -1;
}
////fprintf(stderr, "sucess(2)\n");
/// last_high = 2k
/// site = (SEQ_LENGTH + 2k) - 2k -1
/// site = SEQ_LENGTH - 1
///int site = p_length - last_high - 1;
int site = t_length - 1;
int return_site = -1;
///in most cases, p_lengthshould be t_length + 2 * errthold
int available_i = p_length - t_length;
if ((err <= errthold) && ((unsigned int)err<=*return_err))
{
*return_err = err;
return_site = site;
}
i = 0;
/****************************may have bugs********************************/
unsigned int ungap_error = (unsigned int)-1;
/****************************may have bugs********************************/
while (i < available_i)
{
err = err + ((VP >> i)&(Word)1);
err = err - ((VN >> i)&(Word)1);
++i;
if ((err <= (int)errthold) && ((unsigned int)err <= *return_err))
{
*return_err = err;
return_site = site + i;
}
/****************************may have bugs********************************/
if(i == (int)errthold)
{
ungap_error = err;
}
/****************************may have bugs********************************/
}
/****************************may have bugs********************************/
if((ungap_error<=errthold) && (ungap_error == (*return_err)))
{
return_site = site + errthold;
}
/****************************may have bugs********************************/
return return_site;
}
inline int try_cigar(char *pattern, int p_length,
char *text, int t_length, int end_site, char* path,
int error,
int* return_start_site,
int* return_path_length)
{
int i = 0;
int tmp_err = 0;
///start pos of y
int start_site = end_site - t_length + 1;
if (start_site >= 0)
{
for (i = 0; i < t_length; i++)
{
///path[i] = 0;
///path is saved backwards
path[t_length - i - 1] = 0;
if (text[i] != pattern[i + start_site])
{
path[t_length - i - 1] = 1;
tmp_err++;
if (tmp_err > error)
{
return 0;
}
}
}
if (tmp_err == error)
{
(*return_path_length) = t_length;
(*return_start_site) = start_site;
return 6;
}
}
return 0;
}
///p_length might be samller than t_length + 2 * errthold
inline int Reserve_Banded_BPM_PATH
(char *pattern, int p_length, char *text, int t_length, unsigned short errthold,
unsigned int* return_err, int* return_start_site, int* return_path_length, Word* matrix_bit, char* path,
int old_error, int old_end_site)
{
if (old_error != -1 && old_end_site != -1)
{
if (old_error == 0)
{
(*return_err) = old_error;
(*return_start_site) = old_end_site - t_length + 1;
return old_end_site;
}
if (try_cigar(pattern, p_length, text, t_length, old_end_site, path,
old_error, return_start_site, return_path_length))
{
(*return_err) = old_error;
return old_end_site;
}
}
(*return_err) = (unsigned int)-1;
Word Peq[256];
int band_length = (errthold << 1) + 1;
int i = 0;
Word tmp_Peq_1 = (Word)1;
Peq[(uint8_t)'A'] = (Word)0;
Peq[(uint8_t)'T'] = (Word)0;
Peq[(uint8_t)'G'] = (Word)0;
Peq[(uint8_t)'C'] = (Word)0;
Word Peq_A;
Word Peq_T;
Word Peq_C;
Word Peq_G;
///band_length = 2k + 1
for (i = 0; i<band_length; i++)
{
Peq[(uint8_t)pattern[i]] = Peq[(uint8_t)pattern[i]] | tmp_Peq_1;
tmp_Peq_1 = tmp_Peq_1 << 1;
}
///Peq[(uint8_t)'T'] = Peq[(uint8_t)'T'] | Peq[(uint8_t)'C'];
Peq_A = Peq[(uint8_t)'A'];
Peq_C = Peq[(uint8_t)'C'];
Peq_T = Peq[(uint8_t)'T'];
Peq_G = Peq[(uint8_t)'G'];
memset(Peq, 0, sizeof(Word)* 256);
Peq[(uint8_t)'A'] = Peq_A;
Peq[(uint8_t)'C'] = Peq_C;
Peq[(uint8_t)'T'] = Peq_T;
Peq[(uint8_t)'G'] = Peq_G;
Word Mask = ((Word)1 << (errthold << 1));
Word VP = 0;
Word VN = 0;
Word X = 0;
Word D0 = 0;
Word HN = 0;
Word HP = 0;
i = 0;
Word column_start;
int err = 0;
Word err_mask = (Word)1;
///band_down = 2k
///i_bd = 2k
///int i_bd = i + band_down;
int i_bd = (errthold << 1);
int last_high = (errthold << 1);
/// t_length_1 = SEQ_LENGTH - 1
int t_length_1 = t_length - 1;
//while(i<t_length)
while (i<t_length_1)
{
///pattern[0]ÔÚPeq[2k], ¶øpattern[2k]ÔÚPeq[0]
X = Peq[(uint8_t)text[i]] | VN;
D0 = ((VP + (X&VP)) ^ VP) | X;
HN = VP&D0;
HP = VN | ~(VP | D0);
X = D0 >> 1;
VN = X&HP;
VP = HN | ~(X | HP);
if (!(D0&err_mask))
{
++err;
if ((err - last_high)>(int)errthold)
{
return -1;
}
}
Peq[(uint8_t)'A'] = Peq[(uint8_t)'A'] >> 1;
Peq[(uint8_t)'C'] = Peq[(uint8_t)'C'] >> 1;
Peq[(uint8_t)'G'] = Peq[(uint8_t)'G'] >> 1;
Peq[(uint8_t)'T'] = Peq[(uint8_t)'T'] >> 1;
++i;
++i_bd;
Peq[(uint8_t)pattern[i_bd]] = Peq[(uint8_t)pattern[i_bd]] | Mask;
///Peq[(uint8_t)'T'] = Peq[(uint8_t)'T'] | Peq[(uint8_t)'C'];
column_start = i << 3;
matrix_bit[column_start] = D0;
matrix_bit[column_start + 1] = VP;
matrix_bit[column_start + 2] = VN;
matrix_bit[column_start + 3] = HP;
matrix_bit[column_start + 4] = HN;
}
X = Peq[(uint8_t)text[i]] | VN;
D0 = ((VP + (X&VP)) ^ VP) | X;
HN = VP&D0;
HP = VN | ~(VP | D0);
X = D0 >> 1;
VN = X&HP;
VP = HN | ~(X | HP);
if (!(D0&err_mask))
{
++err;
if ((err - last_high)>(int)errthold)
return -1;
}
column_start = (i + 1) << 3;
matrix_bit[column_start] = D0;
matrix_bit[column_start + 1] = VP;
matrix_bit[column_start + 2] = VN;
matrix_bit[column_start + 3] = HP;
matrix_bit[column_start + 4] = HN;
////fprintf(stderr, "sucess(2)\n");
/// last_high = 2k
/// site = (SEQ_LENGTH + 2k) - 2k -1
/// site = SEQ_LENGTH - 1
///int site = p_length - last_high - 1;
int site = t_length - 1;
int return_site = -1;
/****************************may have bugs********************************/
unsigned int ungap_error = (unsigned int)-1;
/****************************may have bugs********************************/
///in most cases, p_length should be t_length + 2 * errthold
int available_i = p_length - t_length;
if ((err <= (int)errthold) && ((unsigned int)err<=*return_err))
{
*return_err = err;
return_site = site;
}
i = 0;
while (i < available_i)
{
err = err + ((VP >> i)&(Word)1);
err = err - ((VN >> i)&(Word)1);
++i;
if ((err <= (int)errthold) && ((unsigned int)err <= *return_err))
{
*return_err = err;
return_site = site + i;
}
/****************************may have bugs********************************/
if(i == (int)errthold)
{
ungap_error = err;
}
/****************************may have bugs********************************/
}
if ((*return_err) == (unsigned int)-1)
{
return return_site;
}
/****************************may have bugs********************************/
if((ungap_error<=errthold) && (ungap_error == (*return_err)))
{
return_site = site + errthold;
}
/****************************may have bugs********************************/
///need to correct p_length here, since p_length might be smaller than t_length + 2* err_threashlod
p_length = t_length + 2 * errthold;
///end_site is always correct
int end_site = return_site;
int start_site = end_site;
int back_track_site = band_length - (p_length - end_site);
Word v_value, h_value, delta_value, min_value, current_value;
///Word direction; ///0 is match, 1 is mismatch, 2 is up, 3 is left
Word direction = 0; ///0 is match, 1 is mismatch, 2 is up, 3 is left
i = t_length;
int path_length = 0;
current_value = *return_err;
int low_bound = band_length - 1;
while (i>0)
{
if (current_value == 0)
{
break;
}
column_start = i << 3;
delta_value = current_value -
((~(matrix_bit[column_start] >> back_track_site))&err_mask);
if (back_track_site == 0)
{
///HP
h_value = current_value - ((matrix_bit[column_start + 3] >> back_track_site)&err_mask);
//HN
h_value = h_value + ((matrix_bit[column_start + 4] >> back_track_site)&err_mask);
min_value = delta_value;
direction = 0;
if (h_value < min_value)
{
min_value = h_value;
direction = 3;
}
}
else if (back_track_site == low_bound)
{
v_value = current_value - ((matrix_bit[column_start + 1] >> (back_track_site - 1))&err_mask);
v_value = v_value + ((matrix_bit[column_start + 2] >> (back_track_site - 1))&err_mask);
min_value = delta_value;
direction = 0;
if (v_value < min_value)
{
min_value = v_value;
direction = 2;
}
}
else
{
h_value = current_value - ((matrix_bit[column_start + 3] >> back_track_site)&(Word)1);
h_value = h_value + ((matrix_bit[column_start + 4] >> back_track_site)&(Word)1);
v_value = current_value - ((matrix_bit[column_start + 1] >> (back_track_site - 1))&err_mask);
v_value = v_value + ((matrix_bit[column_start + 2] >> (back_track_site - 1))&err_mask);
min_value = delta_value;
direction = 0;
if (v_value < min_value)
{
min_value = v_value;
direction = 2;
}
if (h_value < min_value)
{
min_value = h_value;
direction = 3;
}
}
if (direction == 0)
{
if (delta_value != current_value)
{
direction = 1;
}
i--;
start_site--;
}
if (direction == 2)///ru guo xiang shang yi dong, bing bu huan lie
{
back_track_site--;
start_site--;
}
else if (direction == 3)///ru guo xiang zuo yi dong
{
i--;
back_track_site++;
}
path[path_length++] = direction;
current_value = min_value;
}
if (i > 0)
{
memset(path + path_length, 0, i);
start_site = start_site - i;
direction = 0;
path_length = path_length + i;
}
if (direction != 3)
{
start_site++;
}
(*return_start_site) = start_site;
(*return_path_length) = path_length;
return return_site;
}
////four patterns have the same p_length
inline int Reserve_Banded_BPM_4_SSE_only(char *pattern1, char *pattern2, char *pattern3, char *pattern4, int p_length, char *text, int t_length,
int* return_sites, unsigned int* return_sites_error, unsigned short errthold, __m128i* Peq_SSE)
{
memset(return_sites, -1, sizeof(int)* 4);
memset(return_sites_error, -1, sizeof(unsigned int)* 4);
Word_32 Peq[256][4];
int band_length = (errthold << 1) + 1;
int i;
Word_32 tmp_Peq_1 = 1;
memset(Peq[(uint8_t)'A'], 0, sizeof(Word_32)* 4);
memset(Peq[(uint8_t)'C'], 0, sizeof(Word_32)* 4);
memset(Peq[(uint8_t)'G'], 0, sizeof(Word_32)* 4);
memset(Peq[(uint8_t)'T'], 0, sizeof(Word_32)* 4);
for (i = 0; i<band_length; i++)
{
Peq[(uint8_t)pattern1[i]][0] = Peq[(uint8_t)pattern1[i]][0] | tmp_Peq_1;
Peq[(uint8_t)pattern2[i]][1] = Peq[(uint8_t)pattern2[i]][1] | tmp_Peq_1;
Peq[(uint8_t)pattern3[i]][2] = Peq[(uint8_t)pattern3[i]][2] | tmp_Peq_1;
Peq[(uint8_t)pattern4[i]][3] = Peq[(uint8_t)pattern4[i]][3] | tmp_Peq_1;
tmp_Peq_1 = tmp_Peq_1 << 1;
}
Peq_SSE[(uint8_t)'A'] = _mm_set_epi32(Peq[(uint8_t)'A'][3], Peq[(uint8_t)'A'][2], Peq[(uint8_t)'A'][1], Peq[(uint8_t)'A'][0]);
Peq_SSE[(uint8_t)'C'] = _mm_set_epi32(Peq[(uint8_t)'C'][3], Peq[(uint8_t)'C'][2], Peq[(uint8_t)'C'][1], Peq[(uint8_t)'C'][0]);
Peq_SSE[(uint8_t)'G'] = _mm_set_epi32(Peq[(uint8_t)'G'][3], Peq[(uint8_t)'G'][2], Peq[(uint8_t)'G'][1], Peq[(uint8_t)'G'][0]);
Peq_SSE[(uint8_t)'T'] = _mm_set_epi32(Peq[(uint8_t)'T'][3], Peq[(uint8_t)'T'][2], Peq[(uint8_t)'T'][1], Peq[(uint8_t)'T'][0]);
///Peq_SSE[(uint8_t)'T'] = _mm_or_si128(Peq_SSE[(uint8_t)'T'], Peq_SSE[(uint8_t)'C']);
Word_32 Mask = ((Word_32)1 << (errthold << 1));
__m128i Mask1 = _mm_set_epi32(0, 0, 0, Mask);
__m128i Mask2 = _mm_set_epi32(0, 0, Mask, 0);
__m128i Mask3 = _mm_set_epi32(0, Mask, 0, 0);
__m128i Mask4 = _mm_set_epi32(Mask, 0, 0, 0);
__m128i VP = _mm_setzero_si128();
__m128i VN = _mm_setzero_si128();
__m128i X = _mm_setzero_si128();
__m128i D0 = _mm_setzero_si128();
__m128i HN = _mm_setzero_si128();
__m128i HP = _mm_setzero_si128();
__m128i tmp_process;
__m128i tmp_process1;
__m128i Err_4 = _mm_setzero_si128();
__m128i err_mask = _mm_set_epi32(1, 1, 1, 1);
///for_not li quan shi 1
__m128i for_not = _mm_set1_epi32(-1);
__m128i err_arry;
__m128i cmp_result;
int i_bd = (errthold << 1);
int last_high = (errthold << 1);
int t_length_1 = t_length - 1;
int err1;
int err2;
int err3;
int err4;
__m128i pre_end = _mm_set_epi32
(last_high + errthold, last_high + errthold, last_high + errthold, last_high + errthold);
i = 0;
while (i<t_length_1)
{
///X = Peq[text[i]] | VN;
X = _mm_or_si128(Peq_SSE[(uint8_t)text[i]], VN);
/*************D0 = ((VP + (X&VP)) ^ VP) | X*********************/
///X&VP
tmp_process1 = _mm_and_si128(X, VP);
///(VP + (X&VP))
tmp_process = _mm_add_epi32(tmp_process1, VP);
///((VP + (X&VP)) ^ VP)
tmp_process = _mm_xor_si128(tmp_process, VP);
///((VP + (X&VP)) ^ VP) | X
D0 = _mm_or_si128(tmp_process, X);
/*************D0 = ((VP + (X&VP)) ^ VP) | X*********************/
///HN = VP&D0;
HN = _mm_and_si128(D0, VP);
///HP = VN | ~(VP | D0);
tmp_process = _mm_or_si128(D0, VP);
tmp_process = _mm_andnot_si128(tmp_process, for_not);
HP = _mm_or_si128(tmp_process, VN);
///X = D0 >> 1;
X = _mm_srli_epi32(D0, 1);
///VN = X&HP;
VN = _mm_and_si128(X, HP);
///VP = HN | ~(X | HP);
tmp_process = _mm_or_si128(X, HP);
tmp_process = _mm_andnot_si128(tmp_process, for_not);
VP = _mm_or_si128(HN, tmp_process);
///D0&err_mask
err_arry = _mm_and_si128(D0, err_mask);
Err_4 = _mm_add_epi32(Err_4, err_mask);
Err_4 = _mm_sub_epi32(Err_4, err_arry);
/**************** */
///shi ji shang zhe ge zhi hen xiao d
cmp_result = _mm_cmpgt_epi32(Err_4, pre_end);
///jian zhi
if (_mm_extract_epi32(cmp_result, 0) && _mm_extract_epi32(cmp_result, 1)
&& _mm_extract_epi32(cmp_result, 2) && _mm_extract_epi32(cmp_result, 3))
return 1;
/**************** */
Peq_SSE[(uint8_t)'A'] = _mm_srli_epi32(Peq_SSE[(uint8_t)'A'], 1);
Peq_SSE[(uint8_t)'T'] = _mm_srli_epi32(Peq_SSE[(uint8_t)'T'], 1);
Peq_SSE[(uint8_t)'G'] = _mm_srli_epi32(Peq_SSE[(uint8_t)'G'], 1);
Peq_SSE[(uint8_t)'C'] = _mm_srli_epi32(Peq_SSE[(uint8_t)'C'], 1);
++i;
++i_bd;
Peq_SSE[(uint8_t)pattern1[i_bd]] = _mm_or_si128(Mask1, Peq_SSE[(uint8_t)pattern1[i_bd]]);
Peq_SSE[(uint8_t)pattern2[i_bd]] = _mm_or_si128(Mask2, Peq_SSE[(uint8_t)pattern2[i_bd]]);
Peq_SSE[(uint8_t)pattern3[i_bd]] = _mm_or_si128(Mask3, Peq_SSE[(uint8_t)pattern3[i_bd]]);
Peq_SSE[(uint8_t)pattern4[i_bd]] = _mm_or_si128(Mask4, Peq_SSE[(uint8_t)pattern4[i_bd]]);
///Peq_SSE[(uint8_t)'T'] = _mm_or_si128(Peq_SSE[(uint8_t)'T'], Peq_SSE[(uint8_t)'C']);
}
///X = Peq[text[i]] | VN;
X = _mm_or_si128(Peq_SSE[(uint8_t)text[i]], VN);
/*************D0 = ((VP + (X&VP)) ^ VP) | X*********************/
///X&VP
tmp_process1 = _mm_and_si128(X, VP);
///(VP + (X&VP))
tmp_process = _mm_add_epi32(tmp_process1, VP);
///((VP + (X&VP)) ^ VP)
tmp_process = _mm_xor_si128(tmp_process, VP);
///((VP + (X&VP)) ^ VP) | X
D0 = _mm_or_si128(tmp_process, X);
/*************D0 = ((VP + (X&VP)) ^ VP) | X*********************/
///HN = VP&D0;
HN = _mm_and_si128(D0, VP);
///HP = VN | ~(VP | D0);
tmp_process = _mm_or_si128(D0, VP);
tmp_process = _mm_andnot_si128(tmp_process, for_not);
HP = _mm_or_si128(tmp_process, VN);
///X = D0 >> 1;
X = _mm_srli_epi32(D0, 1);
///VN = X&HP;
VN = _mm_and_si128(X, HP);
///VP = HN | ~(X | HP);
tmp_process = _mm_or_si128(X, HP);
tmp_process = _mm_andnot_si128(tmp_process, for_not);
VP = _mm_or_si128(HN, tmp_process);
///D0&err_mask
err_arry = _mm_and_si128(D0, err_mask);
Err_4 = _mm_add_epi32(Err_4, err_mask);
Err_4 = _mm_sub_epi32(Err_4, err_arry);
///shi ji shang zhe ge zhi hen xiao d
cmp_result = _mm_cmpgt_epi32(Err_4, pre_end);
///jian zhi
if (_mm_extract_epi32(cmp_result, 0) && _mm_extract_epi32(cmp_result, 1)
&& _mm_extract_epi32(cmp_result, 2) && _mm_extract_epi32(cmp_result, 3))
return 1;
int site = t_length - 1;
err1 = _mm_extract_epi32(Err_4, 0);
err2 = _mm_extract_epi32(Err_4, 1);
err3 = _mm_extract_epi32(Err_4, 2);
err4 = _mm_extract_epi32(Err_4, 3);
if ((err1 <= (int)errthold) && ((unsigned int)err1 <= return_sites_error[0]))
{
return_sites[0] = site;
return_sites_error[0] = err1;
}
if ((err2 <= (int)errthold) && ((unsigned int)err2 <= return_sites_error[1]))
{
return_sites[1] = site;
return_sites_error[1] = err2;
}
if ((err3 <= (int)errthold) && ((unsigned int)err3 <= return_sites_error[2]))
{
return_sites[2] = site;
return_sites_error[2] = err3;
}
if ((err4 <= (int)errthold) && ((unsigned int)err4 <= return_sites_error[3]))
{
return_sites[3] = site;
return_sites_error[3] = err4;
}
i = 0;
/****************************may have bugs********************************/
unsigned int ungap_error1 = (unsigned int)-1;
unsigned int ungap_error2 = (unsigned int)-1;
unsigned int ungap_error3 = (unsigned int)-1;
unsigned int ungap_error4 = (unsigned int)-1;
/****************************may have bugs********************************/
///in most cases, p_length should be t_length + 2 * errthold
int available_i = p_length - t_length;
while (i < available_i)
{
///err = err + ((VP >> i)&(Word_32)1);
tmp_process = _mm_srli_epi32(VP, i);
tmp_process = _mm_and_si128(tmp_process, err_mask);
Err_4 = _mm_add_epi32(Err_4, tmp_process);
///err = err - ((VN >> i)&(Word_32)1);
tmp_process1 = _mm_srli_epi32(VN, i);
tmp_process1 = _mm_and_si128(tmp_process1, err_mask);
Err_4 = _mm_sub_epi32(Err_4, tmp_process1);
++i;
err1 = _mm_extract_epi32(Err_4, 0);
err2 = _mm_extract_epi32(Err_4, 1);
err3 = _mm_extract_epi32(Err_4, 2);
err4 = _mm_extract_epi32(Err_4, 3);
if ((err1 <= (int)errthold) && ((unsigned int)err1 <= return_sites_error[0]))
{
return_sites[0] = site + i;
return_sites_error[0] = err1;
}
if ((err2 <= (int)errthold) && ((unsigned int)err2 <= return_sites_error[1]))
{
return_sites[1] = site + i;
return_sites_error[1] = err2;
}
if ((err3 <= (int)errthold) && ((unsigned int)err3 <= return_sites_error[2]))
{
return_sites[2] = site + i;
return_sites_error[2] = err3;
}
if ((err4 <= (int)errthold) && ((unsigned int)err4 <= return_sites_error[3]))
{
return_sites[3] = site + i;
return_sites_error[3] = err4;
}
/****************************may have bugs********************************/
if(i == (int)errthold)
{
ungap_error1 = err1;
ungap_error2 = err2;
ungap_error3 = err3;
ungap_error4 = err4;
}
/****************************may have bugs********************************/
}
/****************************may have bugs********************************/
if((ungap_error1<=errthold) && (ungap_error1 == return_sites_error[0]))
{
return_sites[0] = site + errthold;
}
if((ungap_error2<=errthold) && (ungap_error2 == return_sites_error[1]))
{
return_sites[1] = site + errthold;
}
if((ungap_error3<=errthold) && (ungap_error3 == return_sites_error[2]))
{
return_sites[2] = site + errthold;
}
if((ungap_error4<=errthold) && (ungap_error4 == return_sites_error[3]))
{
return_sites[3] = site + errthold;
}
/****************************may have bugs********************************/
return 1;
}
#define EAC_M 0
#define MIS_M 1
#define MOR_YP 2
#define MOR_XT 3
inline void push_trace(asg16_v *res, uint16_t c, uint32_t len)
{
uint16_t p; c <<= 14;
while (len >= (0x3fff)) {
p = (c + (0x3fff)); kv_push(uint16_t, *res, p); len -= (0x3fff);
}
if(len) {
p = (c + len); kv_push(uint16_t, *res, p);
}
}
// void move_trace_gap(uint16_t *trace, int32_t trace_n, int32_t trace_i,
// char *pstr, int32_t pi, char *tstr, int32_t ti, int32_t *err)
// {
// uint16_t c = trace[trace_i]>>14, l = (trace[trace_i]<<2)>>2;
// if(c != 3 && c != 2) return;
// trace_i--;
// if(c == 3) pi--;
// else if(c == 2) ti--;
// if()
// }
// void adjust_trace(uint16_t *trace, int32_t *trace_n, int32_t *p_beg, int32_t *p_end, int32_t *err, char *pstr, char *tstr)
// {
// if((*err) == 0) return;
// int32_t i, pi, ti; uint16_t c, l;
// for (i = 0; i < (*trace_n) && (trace[i]>>14) == 1; i++) {
// trace[i] <<= 2; trace[i] >>= 2; trace[i] += (((uint16_t)3)<<14);
// l = (trace[i]<<2)>>2; (*p_beg) += l;
// }
// for (i = (*trace_n) - 1; i >= 0 && (trace[i]>>14) == 1; i--) {
// trace[i] <<= 2; trace[i] >>= 2; trace[i] += (((uint16_t)3)<<14);
// l = (trace[i]<<2)>>2; (*p_end) -= l;
// }
// i = 0; pi = (*p_beg); ti = 0;
// for (i = 0; i < (*trace_n); i++) {
// c = trace[i]>>14; l = (trace[i]<<2)>>2;
// if(c == 0 || c == 1) {
// pi += l; ti += l;
// } else if(c == 2) {
// // move_trace_gap(trace, *trace_n, i, pstr, pi, tstr, ti, err);
// pi += l;
// } else if(c == 3) {
// // move_trace_gap(trace, *trace_n, i, pstr, pi, tstr, ti, err);
// ti += l;
// }
// }
// }
inline int32_t ungap_trace(char *pstr, int32_t pn, char *tstr, int32_t tn, int32_t know_err, int32_t know_end,
int32_t *r_err, int32_t *r_beg, asg16_v *cigar, int32_t *cigar_l)
{
int32_t cn = cigar->n, pk, tk, e, l;
(*r_err) = (*r_beg) = INT32_MAX; (*cigar_l) = 0;
if(know_err < 0 || know_end < 0) return -1;
if(know_err == 0) {
push_trace(cigar, EAC_M, tn);
(*r_err) = know_err; (*r_beg) = know_end + 1 - tn; (*cigar_l) = cigar->n - cn;
return know_end;
}
pk = know_end+1-tn; tk = 0; e = 0;
for (l = 0; tk < tn; tk++, pk++) {
if(pstr[pk]!=tstr[tk]) {
e++; if(e > know_err) break;
if(tk > l) push_trace(cigar, EAC_M, tk-l);
push_trace(cigar, MIS_M, 1); l = tk + 1;
}
}
if(tk == tn) {
if(tk > l) push_trace(cigar, EAC_M, tk-l);
(*r_err) = know_err; (*r_beg) = know_end + 1 - tn; (*cigar_l) = cigar->n - cn;
return know_end;
}
cigar->n = cn;
return -1;
}
// ///p_length might be samller than t_length + 2 * errthold
inline int32_t ed_band_cal_semi_trace(char *pstr, int32_t pn, char *tstr, int32_t tn, int32_t thre,
int32_t know_err, int32_t know_end, int32_t *r_err, int32_t *r_beg, Word *buf, asg16_v *cigar, int32_t *cigar_l) {
int32_t cn = cigar->n; (*r_err) = (*r_beg) = INT32_MAX; (*cigar_l) = 0;
Word Peq[5] = {0}, mm = (Word)1, VP = 0, VN = 0, X = 0, D0 = 0, HN = 0, HP = 0, i_col, i_col_dux;
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; ///kv_resize(uint16_t, *cigar, cigar->n+(uint32_t)know_err+2);//pre-alloc
if(ungap_trace(pstr, pn, tstr, tn, know_err, know_end, r_err, r_beg, cigar, cigar_l) >= 0) {
return know_end;
}
for (i = 0; i < bd; i++) {
Peq[seq_nt4_table[(uint8_t)pstr[i]]] |= mm; mm <<= 1;
}
Peq[4] = 0;
///should make Peq[4] = 0 if N is always an error
i = i_col = 0; mm = ((Word)1 << (thre<<1));///for the incoming char/last char
while (i < tn0) {
X = Peq[seq_nt4_table[(uint8_t)tstr[i]]] | VN;
D0 = ((VP + (X&VP)) ^ VP) | X;
HN = VP&D0;
HP = VN | ~(VP | D0);
X = D0 >> 1;
VN = X&HP;
VP = HN | ~(X | HP);
if (!(D0&(1ULL))) {
++err;
if (err>cut) return -1;
}
Peq[0] >>= 1; Peq[1] >>= 1; Peq[2] >>= 1; Peq[3] >>= 1; ///Peq[4] >>= 1;
++i; ++i_bd;
Peq[seq_nt4_table[(uint8_t)pstr[i_bd]]] |= mm; Peq[4] = 0;
buf[i_col++] = D0; buf[i_col++] = VP; buf[i_col++] = VN; buf[i_col++] = HP; buf[i_col++] = HN;
}
X = Peq[seq_nt4_table[(uint8_t)tstr[i]]] | VN;
D0 = ((VP + (X&VP)) ^ VP) | X;
HN = VP&D0;
HP = VN | ~(VP | D0);
X = D0 >> 1;
VN = X&HP;
VP = HN | ~(X | HP);
if (!(D0&(1ULL))) {
++err;
if (err>cut) return -1;
}
buf[i_col++] = D0; buf[i_col++] = VP; buf[i_col++] = VN; buf[i_col++] = HP; buf[i_col++] = HN;
i_col_dux = i_col/tn;
int32_t site = tn - 1, end = -1;///up bound
///in most cases, ai = (thre<<1)
int32_t ai = pn - tn, uge = INT32_MAX;
if ((err <= thre) && (err<=(*r_err))) {
*r_err = err; end = site;
}
i = 0;
while (i < ai) {
err += ((VP >> i)&(1ULL)); err -= ((VN >> i)&(1ULL)); ++i;
if ((err <= thre) && (err <= (*r_err))) {
*r_err = err; end = site + i;
}
if(i == thre) uge = err;
}
if((uge<=thre) && (uge == (*r_err))) end = site + thre;
if ((*r_err) > thre) return end;
///need to correct pn here, since pn might be smaller than tn + 2* thre
pn = tn + (thre<<1);
int32_t beg = end, back_track_site = bd - (pn - end);
Word v_value, h_value, delta_value, min_value, current_value;
///Word direction; ///0 is match, 1 is mismatch, 2 is up, 3 is left
Word direction = 0, *ba, pd, pdl; ///0 is match, 1 is mismatch, 2 is up, 3 is left
i = tn; pd = (Word)-1; pdl = 0;
current_value = *r_err;
int32_t low_bound = bd - 1;
while (i > 0) {
if (current_value == 0) break;
ba = buf + ((i*i_col_dux) - i_col_dux);
delta_value = current_value - ((~(ba[0]>>back_track_site))&(1ULL));
if (back_track_site == 0) {
///HP
h_value = current_value - ((ba[3] >> back_track_site)&(1ULL));
//HN
h_value = h_value + ((ba[4] >> back_track_site)&1ULL);
min_value = delta_value; direction = 0;
if (h_value < min_value) {
min_value = h_value;
direction = 3;
}
} else if (back_track_site == low_bound) {
v_value = current_value - ((ba[1]>>(back_track_site-1))&(1ULL));
v_value = v_value + ((ba[2]>>(back_track_site-1))&(1ULL));
min_value = delta_value; direction = 0;
if (v_value < min_value) {
min_value = v_value;
direction = 2;
}
}
else {
h_value = current_value-((ba[3]>>back_track_site)&(1ULL));
h_value = h_value+((ba[4]>>back_track_site)&(1ULL));
v_value = current_value - ((ba[1]>>(back_track_site-1))&(1ULL));
v_value = v_value + ((ba[2]>>(back_track_site-1))&(1ULL));
min_value = delta_value; direction = 0;
if (v_value < min_value) {
min_value = v_value;
direction = 2;
}
if (h_value < min_value) {
min_value = h_value;
direction = 3;
}
}
if (direction == 0) {
if (delta_value != current_value) {
direction = 1;
}
i--; beg--;
}
if (direction == 2) {///ru guo xiang shang yi dong, bing bu huan lie
back_track_site--; beg--;
}
else if (direction == 3) {///ru guo xiang zuo yi dong
i--;
back_track_site++;
}
if(direction != pd) {
if(pdl > 0) push_trace(cigar, pd, pdl);
pd = direction; pdl = 1;
} else {
pdl++;
}
// path[path_length++] = direction;
current_value = min_value;
}
if (i > 0) {
direction = 0; beg -= i;
if(direction != pd) {
if(pdl > 0) push_trace(cigar, pd, pdl);
pd = direction; pdl = i;
} else {
pdl += i;
}
}
if(pdl > 0) push_trace(cigar, pd, pdl);
if (direction != 3) beg++;
uint16_t *trac = cigar->a + cn, tt; int32_t trac_n = cigar->n - cn; ai = trac_n>>1;
for (i = 0; i < ai; i++) {
tt = trac[i]; trac[i] = trac[trac_n-i-1]; trac[trac_n-i-1] = tt;
}
(*cigar_l) = cigar->n - cn;
(*r_beg) = beg; (*cigar_l) = cigar->n - cn;
return end;
}
#endif
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