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3067771783b6c74adb1d93ffdec7588080fe2bcd
hifiasm/Levenshtein_distance.h
chhylp123 e8b18560a5 0.20.0-r631
2024-10-09 17:09:10 -04:00

5043 lines
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#ifndef __LEVENSHTEIN__
#define __LEVENSHTEIN__
#define __STDC_LIMIT_MACROS
#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;
}
}
}
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 = w-1; k >= 0; k--) fprintf(stderr, "%llu", (z>>k)&(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;
}
#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);
}
}
inline uint32_t pop_trace(asg16_v *res, uint32_t i, uint16_t *c, uint32_t *len)
{
(*c) = (res->a[i]>>14); (*len) = (res->a[i]&(0x3fff));
for (i++; (i < res->n) && ((*c) == (res->a[i]>>14)); i++) {
(*len) += (res->a[i]&(0x3fff));
}
return i;
}
inline int32_t pop_trace_back(asg16_v *res, int32_t i, uint16_t *c, uint32_t *len)
{
(*c) = (res->a[i]>>14); (*len) = (res->a[i]&(0x3fff));
for (i--; (i >= 0) && ((*c) == (res->a[i]>>14)); i--) {
(*len) += (res->a[i]&(0x3fff));
}
return i;
}
///compact functions
#define pop_trac_bpc(in, rc, rb, rl) do { \
(rc) = ((in)>>14);\
if((rc) == 1 || (rc) == 2) {(rb) = (((in)>>12)&3); (rl) = ((in)&(0xfff));}\
else {(rl) = ((in)&(0x3fff));}\
} while (0)
inline void push_trace_bp(asg16_v *res, uint16_t c, uint16_t b, uint32_t len, uint32_t is_append)
{
uint16_t p, c0, b0, len0, mm;
if((is_append) && (res->n)) {
b0 = b;
pop_trac_bpc(res->a[res->n-1], c0, b0, len0);
if((c == c0) && (b == b0)) {
res->n--; len += len0;
}
}
mm = (0x3fff); c0 = c; c <<= 14;
if(c0 == 1 || c0 == 2) {
mm = (0xfff); c += ((b&3) << 12);
}
while (len >= mm) {
p = (c + mm); kv_push(uint16_t, *res, p); len -= mm;
}
// fprintf(stderr, "[M::%s] c::%u, len::%u\n", __func__, c, len);
if(len) {
p = (c + len); kv_push(uint16_t, *res, p);
}
}
inline uint32_t pop_trace_bp(asg16_v *res, uint32_t i, uint16_t *c, uint16_t *b, uint32_t *len)
{
(*c) = (res->a[i]>>14);
if((*c) == 1 || (*c) == 2) {
(*b) = ((res->a[i]>>12)&3);
(*len) = (res->a[i]&(0xfff));
} else {
(*b) = (uint16_t)-1;
(*len) = (res->a[i]&(0x3fff));
}
uint32_t sl; uint16_t sb;
for (i++; (i < res->n) && ((*c) == (res->a[i]>>14)); i++) {
if((*c) == 1 || (*c) == 2) {
sb = ((res->a[i]>>12)&3); sl = (res->a[i]&(0xfff));
} else {
sb = (uint16_t)-1; sl = (res->a[i]&(0x3fff));
}
if((*b) != sb) break;
(*len) += sl;
}
return i;
}
inline int64_t pop_trace_bp_rev(asg16_v *res, int64_t i, uint16_t *c, uint16_t *b, uint32_t *len)
{
(*c) = (res->a[i]>>14);
if((*c) == 1 || (*c) == 2) {
(*b) = ((res->a[i]>>12)&3);
(*len) = (res->a[i]&(0xfff));
} else {
(*b) = (uint16_t)-1;
(*len) = (res->a[i]&(0x3fff));
}
uint32_t sl; uint16_t sb;
for (i--; (i >= 0) && ((*c) == (res->a[i]>>14)); i--) {
if((*c) == 1 || (*c) == 2) {
sb = ((res->a[i]>>12)&3); sl = (res->a[i]&(0xfff));
} else {
sb = (uint16_t)-1; sl = (res->a[i]&(0x3fff));
}
if((*b) != sb) break;
(*len) += sl;
}
return i;
}
///full functions
#define pop_trac_bpc_f(in, rc, rbq, rbt, rl) do { \
(rc) = ((in)>>14);\
if((rc) == 2 || (rc) == 3) {(rbt) = (((in)>>12)&3); (rl) = ((in)&(0xfff));}\
else if((rc) == 1) {(rbt) = (((in)>>12)&3); (rbq) = (((in)>>10)&3); (rl) = ((in)&(0x3ff));}\
else {(rl) = ((in)&(0x3fff));}\
} while (0)
inline void push_trace_bp_f(asg16_v *res, uint16_t c, uint16_t bq, uint16_t bt, uint32_t len, uint32_t is_append)
{
uint16_t p, c0 = c, bq0, bt0, len0, mm;
if(c == 3) {
bt = bq; bq = (uint16_t)-1;
}
if((is_append) && (res->n)) {
bq0 = bq; bt0 = bt;
pop_trac_bpc_f(res->a[res->n-1], c0, bq0, bt0, len0);
if((c == c0) && (bq == bq0) && (bt == bt0)) {
res->n--; len += len0;
}
}
c0 = c; c <<= 14;
if(c0 == 2 || c0 == 3) {
mm = (0xfff); c += ((bt&3) << 12);
} else if(c0 == 1) {
mm = (0x3ff); c += ((bt&3) << 12); c += ((bq&3) << 10);
} else {
mm = (0x3fff);
}
while (len >= mm) {
p = (c + mm); kv_push(uint16_t, *res, p); len -= mm;
}
// fprintf(stderr, "[M::%s] c::%u, len::%u\n", __func__, c, len);
if(len) {
p = (c + len); kv_push(uint16_t, *res, p);
}
}
inline uint32_t pop_trace_bp_f(asg16_v *res, uint32_t i, uint16_t *c, uint16_t *bq, uint16_t *bt, uint32_t *len)
{
(*c) = (res->a[i]>>14); (*bq) = (*bt) = (uint16_t)-1;
if((*c) == 2 || (*c) == 3) {
(*bt) = ((res->a[i]>>12)&3);
(*len) = (res->a[i]&(0xfff));
} else if((*c) == 1) {
(*bt) = ((res->a[i]>>12)&3);
(*bq) = ((res->a[i]>>10)&3);
(*len) = (res->a[i]&(0x3ff));
} else {
(*len) = (res->a[i]&(0x3fff));
}
uint32_t sl; uint16_t sbq, sbt;
for (i++; (i < res->n) && ((*c) == (res->a[i]>>14)); i++) {
sbq = sbt = (uint16_t)-1;
if((*c) == 2 || (*c) == 3) {
sbt = ((res->a[i]>>12)&3);
sl = (res->a[i]&(0xfff));
} else if((*c) == 1) {
sbt = ((res->a[i]>>12)&3);
sbq = ((res->a[i]>>10)&3);
sl = (res->a[i]&(0x3ff));
} else {
sl = (res->a[i]&(0x3fff));
}
if((*bq) != sbq || (*bt) != sbt) break;
(*len) += sl;
}
if((*c) == 3) {
(*bq) = (*bt); (*bt) = (uint16_t)-1;
}
return i;
}
inline int64_t pop_trace_bp_rev_f(asg16_v *res, int64_t i, uint16_t *c, uint16_t *bq, uint16_t *bt, uint32_t *len)
{
(*c) = (res->a[i]>>14); (*bq) = (*bt) = (uint16_t)-1;
if((*c) == 2 || (*c) == 3) {
(*bt) = ((res->a[i]>>12)&3);
(*len) = (res->a[i]&(0xfff));
} else if((*c) == 1) {
(*bt) = ((res->a[i]>>12)&3);
(*bq) = ((res->a[i]>>10)&3);
(*len) = (res->a[i]&(0x3ff));
} else {
(*len) = (res->a[i]&(0x3fff));
}
uint32_t sl; uint16_t sbq, sbt;
for (i--; (i >= 0) && ((*c) == (res->a[i]>>14)); i--) {
sbq = sbt = (uint16_t)-1;
if((*c) == 2 || (*c) == 3) {
sbt = ((res->a[i]>>12)&3);
sl = (res->a[i]&(0xfff));
} else if((*c) == 1) {
sbt = ((res->a[i]>>12)&3);
sbq = ((res->a[i]>>10)&3);
sl = (res->a[i]&(0x3ff));
} else {
sl = (res->a[i]&(0x3fff));
}
if((*bq) != sbq || (*bt) != sbt) break;
(*len) += sl;
}
if((*c) == 3) {
(*bq) = (*bt); (*bt) = (uint16_t)-1;
}
return i;
}
///511 -> 16 64-bits
// #define MAX_E 511
// #define MAX_L 2500
///511 -> 32 64-bits
#define MAX_CNS_E 1023
#define MAX_CNS_L 3072
#define FORCE_CNS_L 256
#define MAX_SIN_E 2047
#define MAX_SIN_L 10000
#define FORCE_SIN_L 512
typedef uint64_t w_sig;
#define bitw (6)
#define bitwbit (64)
#define bitz (63)
// typedef uint32_t w_sig;
// #define bitw (5)
// #define bitwbit (32)
// #define bitz (31)
// typedef uint16_t w_sig;
// #define bitw (4)
// #define bitwbit (16)
// #define bitz (15)
// typedef uint8_t w_sig;
// #define bitw (3)
// #define bitwbit (8)
// #define bitz (7)
typedef struct {w_sig *a;} w128_t;
typedef struct {size_t n, m; w_sig *a;} w64_trace_t;
typedef struct {
int32_t done_cigar, cigar_n, done_path, path_n;
int32_t ps, pe, pl, ts, te, tl;
int32_t thre, err, nword, mword;
uint32_t m, mm_thres; w_sig *a;
w128_t Peq[5], mm, VP, VN, X, D0, HN, HP;
asg16_v cigar; w64_trace_t path;
} bit_extz_t;
#define is_align(exz) ((exz).err<=(exz).thre)
#define clear_align(exz) ((exz).err=INT32_MAX)
inline uint32_t cigar_check(char *pstr, char *tstr, bit_extz_t *ez)
{
int32_t pi = ez->ps, ti = ez->ts, err = 0; uint32_t ci = 0, cl, k; uint16_t c;
while (ci < ez->cigar.n) {
ci = pop_trace(&(ez->cigar), ci, &c, &cl);
// fprintf(stderr, "# %u = %u\n", c, cl);
if(c == 0) {
for (k=0;(k<cl)&&(pstr[pi]==tstr[ti]);k++,pi++,ti++);
if(k!=cl) {
fprintf(stderr, "ERROR-d-0, pi::%d, ti::%d\n", pi, ti);
return 0;
}
} else {
err += cl;
if(c == 1) {
for (k=0;(k<cl)&&(pstr[pi]!=tstr[ti]);k++,pi++,ti++);
if(k!=cl) {
fprintf(stderr, "ERROR-d-1, pi::%d, ti::%d\n", pi, ti);
return 0;
}
} else if(c == 2) {///more p
pi+=cl;
} else if(c == 3) {
ti+=cl;
}
}
}
if(err != ez->err) {
fprintf(stderr, "ERROR-err\n");
return 0;
}
return 1;
}
inline int32_t dbg_ext_err(int32_t i, int32_t thre, int32_t err, int32_t pe, w128_t *VP, w128_t *VN)
{
int32_t poff = i-thre, tmp_e = INT32_MAX, k, bd, k_bd;
if((poff) + (thre<<1) >= (pe)) {
tmp_e = err;
for ((k) = 0; (poff) < (pe); (poff)++) {
bd = (k>>bitw); k_bd = (k&bitz);
(tmp_e) += ((VP->a[bd]>>k_bd)&((w_sig)1));
(tmp_e) -= ((VN->a[bd]>>k_bd)&((w_sig)1));
(k)++;
}
}
return tmp_e;
}
inline void print_bits(w_sig *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 = sw - 1, k = w-1; m >= 0 && k >= 0; m--) {
for (ks = k%s; ks >= 0 && k >= 0; ks--, k--) fprintf(stderr, "%llu", (az[m]>>ks)&(1ULL));
}
fprintf(stderr, "\n");
}
#define prt_bit_extz_t(ez, w) do { \
print_bits((ez).Peq[0].a, w, "Peq[0]");\
print_bits((ez).Peq[1].a, w, "Peq[1]");\
print_bits((ez).Peq[2].a, w, "Peq[2]");\
print_bits((ez).Peq[3].a, w, "Peq[3]");\
print_bits((ez).Peq[4].a, w, "Peq[4]");\
print_bits((ez).VP.a, w, "VP");\
print_bits((ez).VN.a, w, "VN");\
print_bits((ez).X.a, w, "X");\
print_bits((ez).D0.a, w, "D0");\
print_bits((ez).HN.a, w, "HN");\
print_bits((ez).HP.a, w, "HP");\
} while (0)
#define resize_bit_extz_t(ex, thres) do { \
if(((int32_t)(thres)) > ((int32_t)(ex).mm_thres)) {\
(ex).mm_thres = (((thres)<<1)+1);\
(ex).mm_thres = (((ex).mm_thres>>bitw)+(!!((ex).mm_thres&bitz)))*12;\
if((ex).mm_thres > (ex).m) {\
(ex).a = (w_sig *)realloc((ex).a, (ex).mm_thres * sizeof(*((ex).a)));\
(ex).mm_thres/=12; (ex).m=0;\
(ex).Peq[0].a = (ex).a; (ex).m+=(ex).mm_thres;\
(ex).Peq[1].a = (ex).a+(ex).m; (ex).m+=(ex).mm_thres;\
(ex).Peq[2].a = (ex).a+(ex).m; (ex).m+=(ex).mm_thres;\
(ex).Peq[3].a = (ex).a+(ex).m; (ex).m+=(ex).mm_thres;\
(ex).Peq[4].a = (ex).a+(ex).m; (ex).m+=(ex).mm_thres;\
(ex).mm.a = (ex).a+(ex).m; (ex).m+=(ex).mm_thres;\
(ex).VP.a = (ex).a+(ex).m; (ex).m+=(ex).mm_thres;\
(ex).VN.a = (ex).a+(ex).m; (ex).m+=(ex).mm_thres;\
(ex).X.a = (ex).a+(ex).m; (ex).m+=(ex).mm_thres;\
(ex).D0.a = (ex).a+(ex).m; (ex).m+=(ex).mm_thres;\
(ex).HN.a = (ex).a+(ex).m; (ex).m+=(ex).mm_thres;\
(ex).HP.a = (ex).a+(ex).m; (ex).m+=(ex).mm_thres;\
(ex).mword = (ex).mm_thres;\
}\
(ex).mm_thres = (thres);\
}\
} while (0)
inline void init_bit_extz_t(bit_extz_t *ex, uint64_t thres) {
memset(ex, 0, sizeof((*ex)));
///(bitwbit<<2) >= (((thres)<<1)+1);->at least 4 cells for each w128_t
if(((uint64_t)thres)<(((((uint64_t)bitwbit)<<2)-1)>>1)) thres=(((bitwbit<<2)-1)>>1);
resize_bit_extz_t((*ex), (thres));
}
inline void destroy_bit_extz_t(bit_extz_t *ex) {
free((*ex).a); free((*ex).path.a); free((*ex).cigar.a);
}
inline void gen_trace(bit_extz_t *ez, int32_t ptrim, int32_t reverse)///ptrim = thre for global and extension; = 0 for semi
{
if(ez->err > ez->thre) return;
ez->cigar.n = 0;
int32_t V, H, D, min, cur, tn = (ez->te+1-ez->ts), pn = tn + (ez->thre<<1), bd = (ez->thre<<1)+1;
int32_t bs = ez->path.n/tn, bbs = bs/5, poff = ez->pe, sft = bd - (pn - ez->pe - ptrim);
int32_t i = tn, low = bd-1, wi, wm, d = 0, pd = -1, pdn = 0; cur = ez->err;
w_sig *D0, *VP, *VN, *HP, *HN;
// fprintf(stderr, "\n[M::%s::] bs::%d, bbs::%d, cur::%d, poff::%d, sft::%d\n", __func__, bs, bbs, cur, poff, sft);
while (i > 0 && cur > 0) {
D0 = ez->path.a + ((i-1)*bs); VP = D0 + bbs; VN = VP + bbs; HP = VN + bbs; HN = HP + bbs;
wi = (sft>>bitw); wm = sft&bitz;
D = cur - ((~(D0[wi]>>wm))&(1ULL)); d = 0; min = D;
H = V = INT32_MAX;
if(sft!=low) {
H = cur + ((HN[wi]>> wm)&(1ULL)) - ((HP[wi]>> wm)&(1ULL));
if ((H+1) == cur && H <= min) {//prefer indels
min = H; d = 3;
}
}
if(sft!=0) {
wi = ((sft-1)>>bitw); wm = (sft-1)&bitz;
V = cur + ((VN[wi]>> wm)&(1ULL)) - ((VP[wi]>> wm)&(1ULL));
if ((V+1) == cur && V <= min) {//prefer indels
min = V; d = 2;
}
}
// fprintf(stderr, "[M::%s::] cur::%d, D::%d, V::%d, H::%d, poff::%d, toff::%d, d::%d\n", __func__, cur, D, V, H, poff, i, d);
if(d == 0) {
if(D != cur) d = 1;
i--; poff--;
} else if(d == 2) {//more pstr
sft--; poff--;
} else if(d == 3) {///more tstr
i--; sft++;
}
if(d == pd) {
pdn++;
} else {
if(pdn > 0) push_trace(&(ez->cigar), pd, pdn);
pd = d; pdn = 1;
}
cur = min;
}
if (i > 0) {
d = 0; poff -= i;
if(d == pd) {
pdn += i;
} else {
if(pdn > 0) push_trace(&(ez->cigar), pd, pdn);
pd = d; pdn = i;
}
}
poff++;
// fprintf(stderr, "[M::%s::] poff::%d, ez->ps::%d\n", __func__, poff, ez->ps);
if(ez->ps < 0 || ez->ps >= ez->pl) {//ps is unavailable
ez->ps = poff;
} else if(poff > ez->ps){
d = 2; i = poff - ez->ps;
if(d == pd) {
pdn += i;
} else {
if(pdn > 0) push_trace(&(ez->cigar), pd, pdn);
pd = d; pdn = i;
}
}
if(pdn > 0) push_trace(&(ez->cigar), pd, pdn);
if(reverse) {
uint16_t t; pdn = ez->cigar.n>>1;
for (i = 0; i < pdn; i++) {
t = ez->cigar.a[i];
ez->cigar.a[i] = ez->cigar.a[ez->cigar.n-i-1];
ez->cigar.a[ez->cigar.n-i-1] = 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 w_bit(x, b) ((x).a[((b)>>bitw)]|=(((w_sig)1)<<((b)&bitz)))
#define w_get_bit(x, b) (((x).a[((b)>>bitw)]>>((b)&bitz))&((w_sig)1))
/***********************2 words***********************/
#define w_128_clear(x) ((x).a[0]=(x).a[1]=0)
#define w_128_word (2)
#define w_128_self_not(x) ((x).a[0]=~(x).a[0], \
(x).a[1]=~(x).a[1])
#define w_128_self_or(x, y) ((x).a[0]|=(y).a[0], \
(x).a[1]|=(y).a[1])
#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])
#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])
#define w_128_self_xor(x, y) ((x).a[0]^=(y).a[0], \
(x).a[1]^=(y).a[1])
#define w_128_self_lsft_1(x) ((x).a[1] = ((x).a[1]<<1)|((x).a[0]>>bitz), \
(x).a[0] <<= 1)
#define w_128_self_rsft_1(x) ((x).a[0] = ((x).a[0]>>1)|((x).a[1]<<bitz), \
(x).a[1] >>= 1)
#define w_128_rsft_1(x, y) ((x).a[0] = ((y).a[0]>>1)|((y).a[1]<<bitz), \
(x).a[1] = (y).a[1]>>1)
#define w_128_self_add(x, y, c) ((x).a[0]+=(y).a[0], \
(x).a[1]+=(y).a[1]+((x).a[0]<(y).a[0]))
#define w_128_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 w_128_copy(x, y) ((x).a[0]=(y).a[0], (x).a[1]=(y).a[1])
/***********************3 words***********************/
#define w_192_clear(x) ((x).a[0]=(x).a[1]=(x).a[2]=0)
#define w_192_word (3)
#define w_192_self_not(x) ((x).a[0]=~(x).a[0],\
(x).a[1]=~(x).a[1],\
(x).a[2]=~(x).a[2])
#define w_192_self_or(x, y) ((x).a[0]|=(y).a[0],\
(x).a[1]|=(y).a[1],\
(x).a[2]|=(y).a[2])
#define w_192_or(r, x, y) ((r).a[0]=(x).a[0]|(y).a[0],\
(r).a[1] = (x).a[1]|(y).a[1],\
(r).a[2] = (x).a[2]|(y).a[2])
#define w_192_and(r, x, y) ((r).a[0] = (x).a[0]&(y).a[0], \
(r).a[1] = (x).a[1]&(y).a[1], \
(r).a[2] = (x).a[2]&(y).a[2])
#define w_192_self_xor(x, y) ((x).a[0]^=(y).a[0], \
(x).a[1]^=(y).a[1], \
(x).a[2]^=(y).a[2])
#define w_192_self_lsft_1(x) ((x).a[2] = ((x).a[2]<<1)|((x).a[1]>>bitz), \
(x).a[1] = ((x).a[1]<<1)|((x).a[0]>>bitz), \
(x).a[0] <<= 1)
#define w_192_self_rsft_1(x) ((x).a[0] = ((x).a[0]>>1)|((x).a[1]<<bitz), \
(x).a[1] = ((x).a[1]>>1)|((x).a[2]<<bitz), \
(x).a[2] >>= 1)
#define w_192_rsft_1(x, y) ((x).a[0] = ((y).a[0]>>1)|((y).a[1]<<bitz), \
(x).a[1] = ((y).a[1]>>1)|((y).a[2]<<bitz), \
(x).a[2] = (y).a[2]>>1)
#define w_192_self_add(x, y, c) ((x).a[0]+=(y).a[0], c=((x).a[0]<(y).a[0]),\
(x).a[1]+=c, c=((x).a[1]<c), (x).a[1]+=(y).a[1], c|=((x).a[1]<(y).a[1]),\
(x).a[2]+=c, (x).a[2]+=(y).a[2])
#define w_192_set_bit_lsub(x, l) do { \
(x).a[0] = (x).a[1] = (x).a[2] = 0; \
if((l)>>bitw) memset((x).a, -1, sizeof(*((x).a))*((l)>>bitw));\
if((l)&bitz) (x).a[(l)>>bitw] = (((w_sig)1)<<((l)&bitz))-1; \
} while (0) \
#define w_192_copy(x, y) ((x).a[0]=(y).a[0], (x).a[1]=(y).a[1], (x).a[2]=(y).a[2])
/***********************4 words***********************/
#define w_256_clear(x) ((x).a[0]=(x).a[1]=(x).a[2]=(x).a[3]=0)
#define w_256_word (4)
#define w_256_self_not(x) ((x).a[0]=~(x).a[0],\
(x).a[1]=~(x).a[1],\
(x).a[2]=~(x).a[2],\
(x).a[3]=~(x).a[3])
#define w_256_self_or(x, y) ((x).a[0]|=(y).a[0],\
(x).a[1]|=(y).a[1],\
(x).a[2]|=(y).a[2],\
(x).a[3]|=(y).a[3])
#define w_256_or(r, x, y) ((r).a[0]=(x).a[0]|(y).a[0],\
(r).a[1] = (x).a[1]|(y).a[1],\
(r).a[2] = (x).a[2]|(y).a[2],\
(r).a[3] = (x).a[3]|(y).a[3])
#define w_256_and(r, x, y) ((r).a[0] = (x).a[0]&(y).a[0], \
(r).a[1] = (x).a[1]&(y).a[1], \
(r).a[2] = (x).a[2]&(y).a[2], \
(r).a[3] = (x).a[3]&(y).a[3])
#define w_256_self_xor(x, y) ((x).a[0]^=(y).a[0], \
(x).a[1]^=(y).a[1], \
(x).a[2]^=(y).a[2],\
(x).a[3]^=(y).a[3])
#define w_256_self_lsft_1(x) ((x).a[3] = ((x).a[3]<<1)|((x).a[2]>>bitz), \
(x).a[2] = ((x).a[2]<<1)|((x).a[1]>>bitz), \
(x).a[1] = ((x).a[1]<<1)|((x).a[0]>>bitz), \
(x).a[0] <<= 1)
#define w_256_self_rsft_1(x) ((x).a[0] = ((x).a[0]>>1)|((x).a[1]<<bitz), \
(x).a[1] = ((x).a[1]>>1)|((x).a[2]<<bitz), \
(x).a[2] = ((x).a[2]>>1)|((x).a[3]<<bitz), \
(x).a[3] >>= 1)
#define w_256_rsft_1(x, y) ((x).a[0] = ((y).a[0]>>1)|((y).a[1]<<bitz), \
(x).a[1] = ((y).a[1]>>1)|((y).a[2]<<bitz), \
(x).a[2] = ((y).a[2]>>1)|((y).a[3]<<bitz), \
(x).a[3] = (y).a[3]>>1)
#define w_256_self_add(x, y, c) ((x).a[0]+=(y).a[0], c=((x).a[0]<(y).a[0]),\
(x).a[1]+=c, c=((x).a[1]<c), (x).a[1]+=(y).a[1], c|=((x).a[1]<(y).a[1]),\
(x).a[2]+=c, c=((x).a[2]<c), (x).a[2]+=(y).a[2], c|=((x).a[2]<(y).a[2]),\
(x).a[3]+=c, (x).a[3]+=(y).a[3])
#define w_256_set_bit_lsub(x, l) do { \
(x).a[0] = (x).a[1] = (x).a[2] = (x).a[3] = 0; \
if((l)>>bitw) memset((x).a, -1, sizeof(*((x).a))*((l)>>bitw));\
if((l)&bitz) (x).a[(l)>>bitw] = (((w_sig)1)<<((l)&bitz))-1; \
} while (0)
#define w_256_copy(x, y) ((x).a[0]=(y).a[0], (x).a[1]=(y).a[1], (x).a[2]=(y).a[2], (x).a[3]=(y).a[3])
#define cmp_Word(des, src, dd, ws) {\
for ((dd)=0;(dd)<64;dd+=bitwbit){\
if((((des)>>dd)&((w_sig)-1))!=(src).a[dd>>bitw]) break;\
}\
if((dd)<64) {\
print_bit((des), (ws), "des");\
print_bits((src).a, (ws), "src");\
exit(0);\
}\
}
#define dump_Word(des, src, dd, ws) {\
for ((dd)=bitwbit,(des)=((Word)(src).a[0]);(dd)<64;dd+=bitwbit) {\
(des) |= ((Word)(src).a[dd>>bitw])<<dd;\
}\
cmp_Word((des), (src), (dd), (ws));\
}
#define prt_address(Peq, VP, VN, X, D0, HN, HP) {\
fprintf(stderr, "Peq[0].a::%p, Peq[1].a::%p, Peq[2].a::%p, Peq[3].a::%p, Peq[4].a::%p, VP.a::%p, VN.a::%p, X.a::%p, D0.a::%p, HN.a::%p, HP.a::%p\n",\
Peq[0].a, Peq[1].a, Peq[2].a, Peq[3].a, Peq[4].a, VP.a, VN.a, X.a, D0.a, HN.a, HP.a);\
}
#define prt_vector(Peq, VP, VN, X, D0, HN, HP, ws) {\
print_bit((Peq)[0], (ws), "Peq[0]");\
print_bit((Peq)[1], (ws), "Peq[1]");\
print_bit((Peq)[2], (ws), "Peq[2]");\
print_bit((Peq)[3], (ws), "Peq[3]");\
print_bit((Peq)[4], (ws), "Peq[4]");\
print_bit((VP), (ws), "VP");\
print_bit((VN), (ws), "VN");\
print_bit((X), (ws), "X");\
print_bit((D0), (ws), "D0");\
print_bit((HN), (ws), "HN");\
print_bit((HP), (ws), "HP");\
}
#define ed_core_debug(sf, Peq, VP, VN, X, D0, HN, HP, z, c, ws) { \
Word Peq_d[5], VP_d, VN_d, X_d, D0_d, HN_d, HP_d, dd;\
dump_Word(Peq_d[0], Peq[0], dd, ws);\
dump_Word(Peq_d[1], Peq[1], dd, ws);\
dump_Word(Peq_d[2], Peq[2], dd, ws);\
dump_Word(Peq_d[3], Peq[3], dd, ws);\
dump_Word(Peq_d[4], Peq[4], dd, ws);\
dump_Word(VP_d, VP, dd, ws);\
dump_Word(VN_d, VN, dd, ws);\
dump_Word(X_d, X, dd, ws);\
dump_Word(D0_d, D0, dd, ws);\
dump_Word(HN_d, HN, dd, ws);\
dump_Word(HP_d, HP, dd, ws);\
/**X = Peq[seq_nt4_table[(uint8_t)tstr[i]]] | VN;**/\
prt_address(Peq, VP, VN, X, D0, HN, HP);\
(c) = seq_nt4_table[(z)];\
print_bit(Peq_d[(c)], 64, "raw-Peq[]");print_bits(Peq[(c)].a, 64, "bit-Peq[]");\
print_bit(VN_d, 64, "raw-VN");print_bits((VN).a, 64, "bit-VN");\
w##sf##or((X), (Peq)[(c)], (VN));\
print_bits((X).a, 64, "+bit-X");\
X_d = Peq_d[(c)]|VN_d; fprintf(stderr, "X=Peq[]|VN\n"); \
print_bit(X_d, 64, "raw-X");print_bits((X).a, 64, "-bit-X");\
cmp_Word(X_d, (X), dd, ws);\
/**D0 = ((VP + (X&VP)) ^ VP) | X;**/\
w##sf##and((D0), (X), (VP));\
prt_address(Peq, VP, VN, X, D0, HN, HP);\
D0_d = X_d&VP_d; fprintf(stderr, "D0=X&VP\n"); cmp_Word(D0_d, (D0), dd, ws);\
w##sf##self_add((D0), (VP), (c));\
prt_address(Peq, VP, VN, X, D0, HN, HP);\
D0_d += VP_d; fprintf(stderr, "D0+=VP\n"); cmp_Word(D0_d, (D0), dd, ws);\
w##sf##self_xor((D0), (VP));\
prt_address(Peq, VP, VN, X, D0, HN, HP);\
D0_d ^= VP_d; fprintf(stderr, "D0^=VP\n"); cmp_Word(D0_d, (D0), dd, ws);\
/**print_bit(D0_d, (ws), "raw-D0"); print_bit(X_d, (ws), "raw-X");**/\
/**print_bits((D0).a, (ws), "bit-D0"); print_bits((X).a, (ws), "bit-X");**/\
w##sf##self_or((D0), (X));\
prt_address(Peq, VP, VN, X, D0, HN, HP);\
D0_d |= X_d; fprintf(stderr, "D0|=X\n"); cmp_Word(D0_d, (D0), dd, ws);\
/**HN = VP&D0;**/\
w##sf##and((HN), (VP), (D0));\
prt_address(Peq, VP, VN, X, D0, HN, HP);\
HN_d = VP_d&D0_d; fprintf(stderr, "HN=VP&D0\n"); cmp_Word(HN_d, (HN), dd, ws);\
/**HP = VN | ~(VP | D0);**/\
w##sf##or((HP), (VP), (D0));\
prt_address(Peq, VP, VN, X, D0, HN, HP);\
HP_d = VP_d|D0_d; fprintf(stderr, "HP=VP|D0\n"); cmp_Word(HP_d, (HP), dd, ws);\
w##sf##self_not((HP));\
prt_address(Peq, VP, VN, X, D0, HN, HP);\
HP_d = ~HP_d; fprintf(stderr, "HP~=HP\n"); cmp_Word(HP_d, (HP), dd, ws);\
w##sf##self_or((HP), (VN));\
prt_address(Peq, VP, VN, X, D0, HN, HP);\
HP_d |= VN_d; fprintf(stderr, "HP|=VN\n"); cmp_Word(HP_d, (HP), dd, ws);\
/**X = D0 >> 1;**/\
w##sf##copy((X), (D0));\
prt_address(Peq, VP, VN, X, D0, HN, HP);\
X_d = D0_d; fprintf(stderr, "X=D0\n"); cmp_Word(X_d, (X), dd, ws);\
w##sf##self_rsft_1((X)); \
prt_address(Peq, VP, VN, X, D0, HN, HP);\
X_d >>= 1; fprintf(stderr, "X>>=1\n"); cmp_Word(X_d, (X), dd, ws);\
/**VN = X&HP;**/\
w##sf##and((VN), (X), (HP));\
prt_address(Peq, VP, VN, X, D0, HN, HP);\
VN_d = X_d&HP_d; fprintf(stderr, "VN=X&HP\n"); cmp_Word(VN_d, (VN), dd, ws);\
/**VP = HN | ~(X | HP);**/\
w##sf##or((VP), (X), (HP));\
prt_address(Peq, VP, VN, X, D0, HN, HP);\
VP_d = X_d|HP_d; fprintf(stderr, "VP=X|HP\n"); cmp_Word(VP_d, (VP), dd, ws);\
w##sf##self_not((VP));\
prt_address(Peq, VP, VN, X, D0, HN, HP);\
VP_d = ~VP_d; fprintf(stderr, "VP=~VP\n"); cmp_Word(VP_d, (VP), dd, ws);\
w##sf##self_or((VP), (HN));\
prt_address(Peq, VP, VN, X, D0, HN, HP);\
VP_d |= HN_d; fprintf(stderr, "VP|=HN\n"); cmp_Word(VP_d, (VP), dd, ws);\
}
#define ed_core(sf, Peq, VP, VN, X, D0, HN, HP, z, c) { \
/**X = Peq[seq_nt4_table[(uint8_t)tstr[i]]] | VN;**/\
(c) = seq_nt4_table[(z)];\
w##sf##or((X), (Peq)[(c)], (VN));\
/**D0 = ((VP + (X&VP)) ^ VP) | X;**/\
w##sf##and((D0), (X), (VP));\
w##sf##self_add((D0), (VP), (c));\
w##sf##self_xor((D0), (VP));\
w##sf##self_or((D0), (X));\
/**HN = VP&D0;**/\
w##sf##and((HN), (VP), (D0));\
/**HP = VN | ~(VP | D0);**/\
w##sf##or((HP), (VP), (D0));\
w##sf##self_not((HP));\
w##sf##self_or((HP), (VN));\
/**X = D0 >> 1;**/\
/**w##sf##copy((X), (D0));w##sf##self_rsft_1((X));**/\
w##sf##rsft_1((X), (D0));\
/**VN = X&HP;**/\
w##sf##and((VN), (X), (HP));\
/**VP = HN | ~(X | HP);**/\
w##sf##or((VP), (X), (HP));\
w##sf##self_not((VP));\
w##sf##self_or((VP), (HN));\
}
#define ed_init_core(i, bd, i_bd, S, Peq) { \
for ((i) = 0; (i) < (bd); (i)++) {\
w_bit((Peq)[seq_nt4_table[(uint8_t)(S)[(i)]]], (i_bd));i_bd++;\
}\
}
#define HA_ED_INIT(sf)\
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;\
if((pn > tn + thre) || (tn > pn + thre)) return;\
int32_t i, err, tn0 = tn - 1, cut = thre+(thre<<1), bd, i_bd, Peq_i; w_sig c, Peq_m;\
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]);\
\
bd = thre+1; bd = ((bd<=pn)?bd:pn); i_bd = thre;\
ed_init_core(i, bd, i_bd, pstr, ez->Peq);\
bd = thre+1, i_bd = thre;\
\
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**/\
Peq_i = (((thre<<1))>>bitw); Peq_m = (((w_sig)1)<<(((thre<<1))&bitz));\
while (i < tn0) {\
ed_core(_##sf##_, ez->Peq, ez->VP, ez->VN, ez->X, ez->D0, ez->HN, ez->HP, (uint8_t)tstr[i], c);\
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; c = 4;\
if(i_bd < pn) c = seq_nt4_table[(uint8_t)pstr[i_bd]];\
if(c < 4) ez->Peq[c].a[Peq_i]|=Peq_m;\
}\
ed_core(_##sf##_, ez->Peq, ez->VP, ez->VN, ez->X, ez->D0, ez->HN, ez->HP, (uint8_t)tstr[i], c);\
if (!(ez->D0.a[0]&(1ULL))) {\
++err; if (err>cut) return;\
}\
\
int32_t site = tn - 1 - thre;/**up bound**/\
for (cut = pn - 1, i = 0; site < cut; site++, i++) {\
bd = (i>>bitw); i_bd = (i&bitz);\
err += (((*ez).VP.a[bd]>>i_bd)&((w_sig)1));\
err -= (((*ez).VN.a[bd]>>i_bd)&((w_sig)1));\
}\
\
if (site == cut && err <= thre) {\
ez->err = err; \
ez->pe = pn-1; ez->te = tn-1;\
}\
return;\
}\
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;\
int32_t bd, i, err = 0, i_bd, cut = thre+(thre<<1), tn0 = tn - 1, Peq_i; w_sig c, Peq_m;\
if((pn > tn + cut) || (tn > pn + cut)) return;\
\
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->VP);\
w_##sf##_clear(ez->VN);\
\
bd = (thre<<1)+1; bd = ((bd<=pn)?bd:pn); i_bd = 0;\
ed_init_core(i, bd, i_bd, pstr, ez->Peq);\
bd = (thre<<1)+1, i_bd = (thre<<1);\
\
w_##sf##_clear(ez->Peq[4]);\
i = 0;\
/**for the incoming char/last char; mm = ((Word)1 << (thre<<1))**/\
Peq_i = (((thre<<1))>>bitw); Peq_m = (((w_sig)1)<<(((thre<<1))&bitz));\
while (i < tn0) {\
ed_core(_##sf##_, ez->Peq, ez->VP, ez->VN, ez->X, ez->D0, ez->HN, ez->HP, (uint8_t)tstr[i], c);\
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; c = 4;\
if(i_bd < pn) c = seq_nt4_table[(uint8_t)pstr[i_bd]];\
if(c < 4) ez->Peq[c].a[Peq_i]|=Peq_m;\
}\
ed_core(_##sf##_, ez->Peq, ez->VP, ez->VN, ez->X, ez->D0, ez->HN, ez->HP, (uint8_t)tstr[i], c);\
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) {\
bd = (i>>bitw); i_bd = (i&bitz);\
err += (((*ez).VP.a[bd]>>i_bd)&((w_sig)1));\
err -= (((*ez).VN.a[bd]>>i_bd)&((w_sig)1));\
++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##_0_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; ez->pe = ez->te = -1;\
if(pn > tn + thre) pn = tn + thre;\
else if(tn > pn + thre) tn = pn + thre;\
int32_t i, err, tn0 = tn - 1, cut = thre+(thre<<1), bd, i_bd, k_bd, Peq_i; w_sig c, Peq_m;\
int32_t poff, pe = pn-1, tmp_e = INT32_MAX, 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]);\
\
bd = thre+1; bd = ((bd<=pn)?bd:pn); i_bd = thre;\
ed_init_core(i, bd, i_bd, pstr, ez->Peq);\
bd = thre+1, i_bd = thre;\
\
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; mm = ((Word)1 << (thre<<1))**/\
Peq_i = (((thre<<1))>>bitw); Peq_m = (((w_sig)1)<<(((thre<<1))&bitz));\
while (i < tn0) {\
ed_core(_##sf##_, ez->Peq, ez->VP, ez->VN, ez->X, ez->D0, ez->HN, ez->HP, (uint8_t)tstr[i], c);\
if (!(ez->D0.a[0]&(1ULL))) {\
++err; if (err>cut) return;\
}\
\
{\
poff = i-thre; k = i+thre-pe;/**poff:[i-thre, i+thre]**/\
if(k >= 0) {\
if(tmp_e == INT32_MAX) {\
tmp_e = err;\
for ((k) = 0; (poff) < (pe); (poff)++, (k)++) {\
bd = (k>>bitw); k_bd = (k&bitz);\
(tmp_e) += (((*ez).VP.a[bd]>>k_bd)&((w_sig)1));\
(tmp_e) -= (((*ez).VN.a[bd]>>k_bd)&((w_sig)1));\
}\
} else {\
k = (thre<<1) - k;\
if(k >= 0) {\
bd = (k>>bitw); k_bd = (k&bitz);\
(tmp_e) += (((*ez).HP.a[bd]>>k_bd)&((w_sig)1));\
(tmp_e) -= (((*ez).HN.a[bd]>>k_bd)&((w_sig)1));\
}\
}\
if((tmp_e) <= (*ez).thre && (tmp_e) < (*ez).err) {\
(*ez).err = tmp_e; (*ez).pe = pe; (*ez).te = i;\
}\
}\
/**if(dbg_ext_err(i, thre, err, pe, &((*ez).VP), &((*ez).VN))!=tmp_e)**/\
}\
\
/** 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; c = 4;\
if(i_bd < pn) c = seq_nt4_table[(uint8_t)pstr[i_bd]];\
if(c < 4) ez->Peq[c].a[Peq_i]|=Peq_m;\
}\
ed_core(_##sf##_, ez->Peq, ez->VP, ez->VN, ez->X, ez->D0, ez->HN, ez->HP, (uint8_t)tstr[i], c);\
if (!(ez->D0.a[0]&(1ULL))) {\
++err; if (err>cut) return;\
}\
\
int32_t site = tn - 1 - thre;/**up bound; site:[tn - 1 - thre, tn - 1 + thre]**/\
for (cut = pn - 1, i = 0; site < cut; i++) {\
bd = (i>>bitw); i_bd = (i&bitz);\
err += (((*ez).VP.a[bd]>>i_bd)&((w_sig)1));\
err -= (((*ez).VN.a[bd]>>i_bd)&((w_sig)1));\
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;\
}\
/**require:: (pn >= tn - thre && pn <= tn + thre)**/\
inline void ed_band_cal_extension_##sf##_1_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 = INT32_MAX; ez->pe = pn-1; ez->te = tn-1;\
if(pn > tn + thre) pn = tn + thre;\
else if(tn > pn + thre) tn = pn + thre;\
int32_t i, err, tn0 = tn - 1, cut = thre+(thre<<1), bd, i_bd, k_bd, Peq_i; w_sig c, Peq_m;\
int32_t poff, pe = pn-1, tmp_e = INT32_MAX, k, pidx = ez->pe, tidx = ez->te;\
\
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]);\
\
bd = thre+1; bd = ((bd<=pn)?bd:pn); i_bd = thre;\
for (i = 0; i < bd; i++, i_bd++) {\
w_bit((ez->Peq)[seq_nt4_table[(uint8_t)(pstr)[pidx-i]]], (i_bd));\
}\
bd = thre+1, i_bd = thre;\
\
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; mm = ((Word)1 << (thre<<1))**/\
Peq_i = (((thre<<1))>>bitw); Peq_m = (((w_sig)1)<<(((thre<<1))&bitz));\
while (i < tn0) {\
ed_core(_##sf##_, ez->Peq, ez->VP, ez->VN, ez->X, ez->D0, ez->HN, ez->HP, (uint8_t)tstr[tidx-i], c);\
if (!(ez->D0.a[0]&(1ULL))) {\
++err; if (err>cut) return;\
}\
\
{\
poff = i-thre; k = i+thre-pe;/**poff:[i-thre, i+thre]**/\
if(k >= 0) {\
if(tmp_e == INT32_MAX) {\
tmp_e = err;\
for ((k) = 0; (poff) < (pe); (poff)++, (k)++) {\
bd = (k>>bitw); k_bd = (k&bitz);\
(tmp_e) += (((*ez).VP.a[bd]>>k_bd)&((w_sig)1));\
(tmp_e) -= (((*ez).VN.a[bd]>>k_bd)&((w_sig)1));\
}\
} else {\
k = (thre<<1) - k;\
if(k >= 0) {\
bd = (k>>bitw); k_bd = (k&bitz);\
(tmp_e) += (((*ez).HP.a[bd]>>k_bd)&((w_sig)1));\
(tmp_e) -= (((*ez).HN.a[bd]>>k_bd)&((w_sig)1));\
}\
}\
if((tmp_e) <= (*ez).thre && (tmp_e) < (*ez).err) {\
(*ez).err = tmp_e; (*ez).ps = pidx - pe; (*ez).ts = tidx-i;\
}\
}\
/**if(dbg_ext_err(i, thre, err, pe, &((*ez).VP), &((*ez).VN))!=tmp_e)**/\
}\
\
/** 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; c = 4;\
if(i_bd < pn) c = seq_nt4_table[(uint8_t)pstr[pidx-i_bd]];\
if(c < 4) ez->Peq[c].a[Peq_i]|=Peq_m;\
}\
ed_core(_##sf##_, ez->Peq, ez->VP, ez->VN, ez->X, ez->D0, ez->HN, ez->HP, (uint8_t)tstr[tidx-i], c);\
if (!(ez->D0.a[0]&(1ULL))) {\
++err; if (err>cut) return;\
}\
\
int32_t site = tn - 1 - thre;/**up bound; site:[tn - 1 - thre, tn - 1 + thre]**/\
for (cut = pn - 1, i = 0; site < cut; i++) {\
bd = (i>>bitw); i_bd = (i&bitz);\
err += (((*ez).VP.a[bd]>>i_bd)&((w_sig)1));\
err -= (((*ez).VN.a[bd]>>i_bd)&((w_sig)1));\
site++;\
if(err <= thre && err < ez->err) {\
ez->err = err; ez->ps = pidx-site; ez->ts = tidx+1-tn;\
}\
}\
if(err <= thre && err < ez->err) {\
ez->err = err; ez->ps = pidx-site; ez->ts = tidx+1-tn;\
}\
return;\
}\
inline void ed_band_cal_global_##sf##_w_trace(char *pstr, int32_t pn, char *tstr, int32_t tn, int32_t thre, bit_extz_t *ez)\
{\
ez->cigar.n = 0; ez->nword = w_##sf##_word;\
if(ez->err > thre) {\
init_base_ed(*ez, thre, pn, tn); ez->ps = ez->ts = 0;\
} else if(ez->err == 0) {\
push_trace(&(ez->cigar), 0, ez->te+1-ez->ts); return;\
}\
if((pn > tn + thre) || (tn > pn + thre)) return;\
int32_t i, err, tn0 = tn - 1, cut = thre+(thre<<1), bd, i_bd, ws, Peq_i; w_sig c, Peq_m;\
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]);\
\
bd = thre+1; bd = ((bd<=pn)?bd:pn); i_bd = thre;\
ed_init_core(i, bd, i_bd, pstr, ez->Peq);\
bd = thre+1, i_bd = thre;\
\
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; ws = sizeof(*(ez->a))*(ez->nword);\
ez->path.n=(ez->nword*tn*5);\
kv_resize(w_sig, ez->path, ez->path.n); ez->path.n=0;\
\
/**for the incoming char/last char**/\
Peq_i = (((thre<<1))>>bitw); Peq_m = (((w_sig)1)<<(((thre<<1))&bitz));\
while (i < tn0) {\
ed_core(_##sf##_, ez->Peq, ez->VP, ez->VN, ez->X, ez->D0, ez->HN, ez->HP, (uint8_t)tstr[i], c);\
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; c = 4;\
if(i_bd < pn) c = seq_nt4_table[(uint8_t)pstr[i_bd]];\
if(c < 4) ez->Peq[c].a[Peq_i]|=Peq_m;\
\
memcpy(ez->path.a+ez->path.n, ez->D0.a, ws); ez->path.n += ez->nword;\
memcpy(ez->path.a+ez->path.n, ez->VP.a, ws); ez->path.n += ez->nword;\
memcpy(ez->path.a+ez->path.n, ez->VN.a, ws); ez->path.n += ez->nword;\
memcpy(ez->path.a+ez->path.n, ez->HP.a, ws); ez->path.n += ez->nword;\
memcpy(ez->path.a+ez->path.n, ez->HN.a, ws); ez->path.n += ez->nword;\
}\
ed_core(_##sf##_, ez->Peq, ez->VP, ez->VN, ez->X, ez->D0, ez->HN, ez->HP, (uint8_t)tstr[i], c);\
if (!(ez->D0.a[0]&(1ULL))) {\
++err; if (err>cut) return;\
}\
memcpy(ez->path.a+ez->path.n, ez->D0.a, ws); ez->path.n += ez->nword;\
memcpy(ez->path.a+ez->path.n, ez->VP.a, ws); ez->path.n += ez->nword;\
memcpy(ez->path.a+ez->path.n, ez->VN.a, ws); ez->path.n += ez->nword;\
memcpy(ez->path.a+ez->path.n, ez->HP.a, ws); ez->path.n += ez->nword;\
memcpy(ez->path.a+ez->path.n, ez->HN.a, ws); ez->path.n += ez->nword;\
\
int32_t site = tn - 1 - thre;/**up bound**/\
if(ez->err > thre) {\
for (cut = pn - 1, i = 0; site < cut; site++, i++) {\
bd = (i>>bitw); i_bd = (i&bitz);\
err += (((*ez).VP.a[bd]>>i_bd)&((w_sig)1));\
err -= (((*ez).VN.a[bd]>>i_bd)&((w_sig)1));\
}\
\
if (site == cut && err <= thre) {\
ez->err = err; \
ez->pe = pn-1; ez->te = tn-1;\
}\
}\
gen_trace(ez, thre, 1);\
return;\
}\
inline void ed_band_cal_semi_##sf##_w_trace(char *pstr, int32_t pn, char *tstr, int32_t tn, int32_t thre, bit_extz_t *ez)\
{\
ez->cigar.n = 0; ez->nword = w_##sf##_word;\
if(ez->err > thre) {\
init_base_ed(*ez, thre, pn, tn); ez->ps = ez->pe = -1; ez->ts = 0; ez->te = tn-1;\
} else if(ez->err == 0) {\
push_trace(&(ez->cigar), 0, ez->te+1-ez->ts);\
ez->ps = ez->pe - (ez->te-ez->ts);\
return;\
}\
int32_t bd, i, err = 0, i_bd, cut = thre+(thre<<1), tn0 = tn - 1, Peq_i, ws; w_sig c, Peq_m;\
if((pn > tn + cut) || (tn > pn + cut)) return;\
\
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->VP);\
w_##sf##_clear(ez->VN);\
\
bd = (thre<<1)+1; bd = ((bd<=pn)?bd:pn); i_bd = 0;\
ed_init_core(i, bd, i_bd, pstr, ez->Peq);\
bd = (thre<<1)+1, i_bd = (thre<<1);\
\
w_##sf##_clear(ez->Peq[4]);\
i = 0; ws = sizeof(*(ez->a))*(ez->nword);\
ez->path.n=(ez->nword*tn*5);\
kv_resize(w_sig, ez->path, ez->path.n); ez->path.n=0;\
/**for the incoming char/last char; mm = ((Word)1 << (thre<<1))**/\
Peq_i = (((thre<<1))>>bitw); Peq_m = (((w_sig)1)<<(((thre<<1))&bitz));\
while (i < tn0) {\
ed_core(_##sf##_, ez->Peq, ez->VP, ez->VN, ez->X, ez->D0, ez->HN, ez->HP, (uint8_t)tstr[i], c);\
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; c = 4;\
if(i_bd < pn) c = seq_nt4_table[(uint8_t)pstr[i_bd]];\
if(c < 4) ez->Peq[c].a[Peq_i]|=Peq_m;\
\
memcpy(ez->path.a+ez->path.n, ez->D0.a, ws); ez->path.n += ez->nword;\
memcpy(ez->path.a+ez->path.n, ez->VP.a, ws); ez->path.n += ez->nword;\
memcpy(ez->path.a+ez->path.n, ez->VN.a, ws); ez->path.n += ez->nword;\
memcpy(ez->path.a+ez->path.n, ez->HP.a, ws); ez->path.n += ez->nword;\
memcpy(ez->path.a+ez->path.n, ez->HN.a, ws); ez->path.n += ez->nword;\
}\
ed_core(_##sf##_, ez->Peq, ez->VP, ez->VN, ez->X, ez->D0, ez->HN, ez->HP, (uint8_t)tstr[i], c);\
if (!(ez->D0.a[0]&(1ULL))) {\
++err; if (err>cut) return;\
}\
memcpy(ez->path.a+ez->path.n, ez->D0.a, ws); ez->path.n += ez->nword;\
memcpy(ez->path.a+ez->path.n, ez->VP.a, ws); ez->path.n += ez->nword;\
memcpy(ez->path.a+ez->path.n, ez->VN.a, ws); ez->path.n += ez->nword;\
memcpy(ez->path.a+ez->path.n, ez->HP.a, ws); ez->path.n += ez->nword;\
memcpy(ez->path.a+ez->path.n, ez->HN.a, ws); ez->path.n += ez->nword;\
\
int32_t site = tn - 1;/**up bound**/\
/**in most cases, ai = (thre<<1)**/\
int32_t ai = pn - tn, uge = INT32_MAX;\
if(ez->err > thre) {\
if ((err <= thre) && (err <= ez->err)) {\
ez->err = err; ez->pe = site;\
}\
\
i = 0;\
while (i < ai) {\
bd = (i>>bitw); i_bd = (i&bitz);\
err += (((*ez).VP.a[bd]>>i_bd)&((w_sig)1));\
err -= (((*ez).VN.a[bd]>>i_bd)&((w_sig)1));\
++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;\
}\
gen_trace(ez, 0, 1);\
}\
inline void ed_band_cal_extension_##sf##_0_w_trace(char *pstr, int32_t pn, char *tstr, int32_t tn, int32_t thre, bit_extz_t *ez)\
{\
int32_t done = 1;\
ez->cigar.n = 0; ez->nword = w_##sf##_word;\
if(ez->err > thre) {\
init_base_ed(*ez, thre, pn, tn); ez->ps = ez->ts = 0; ez->pe = ez->te = -1;\
if(pn > tn + thre) pn = tn + thre;\
else if(tn > pn + thre) tn = pn + thre;\
done = 0;\
} else if(ez->err == 0) {\
push_trace(&(ez->cigar), 0, ez->te+1-ez->ts); return;\
} else {\
pn = ez->pe + 1 - ez->ps; tn = ez->te + 1 - ez->ts;\
}\
int32_t i, err, tn0 = tn - 1, cut = thre+(thre<<1), bd, i_bd, k_bd, Peq_i, ws; w_sig c, Peq_m;\
int32_t poff, pe = pn-1, tmp_e = INT32_MAX, 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]);\
\
bd = thre+1; bd = ((bd<=pn)?bd:pn); i_bd = thre;\
ed_init_core(i, bd, i_bd, pstr, ez->Peq);\
bd = thre+1, i_bd = thre;\
\
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; ws = sizeof(*(ez->a))*(ez->nword);\
ez->path.n=(ez->nword*tn*5);\
kv_resize(w_sig, ez->path, ez->path.n); ez->path.n=0;\
/**for the incoming char/last char; mm = ((Word)1 << (thre<<1))**/\
Peq_i = (((thre<<1))>>bitw); Peq_m = (((w_sig)1)<<(((thre<<1))&bitz));\
while (i < tn0) {\
ed_core(_##sf##_, ez->Peq, ez->VP, ez->VN, ez->X, ez->D0, ez->HN, ez->HP, (uint8_t)tstr[i], c);\
if (!(ez->D0.a[0]&(1ULL))) {\
++err; if (err>cut) return;\
}\
\
if(!done) {\
poff = i-thre; k = i+thre-pe;/**poff:[i-thre, i+thre]**/\
if(k >= 0) {\
if(tmp_e == INT32_MAX) {\
tmp_e = err;\
for ((k) = 0; (poff) < (pe); (poff)++, (k)++) {\
bd = (k>>bitw); k_bd = (k&bitz);\
(tmp_e) += (((*ez).VP.a[bd]>>k_bd)&((w_sig)1));\
(tmp_e) -= (((*ez).VN.a[bd]>>k_bd)&((w_sig)1));\
}\
} else {\
k = (thre<<1) - k;\
if(k >= 0) {\
bd = (k>>bitw); k_bd = (k&bitz);\
(tmp_e) += (((*ez).HP.a[bd]>>k_bd)&((w_sig)1));\
(tmp_e) -= (((*ez).HN.a[bd]>>k_bd)&((w_sig)1));\
}\
}\
if((tmp_e) <= (*ez).thre && (tmp_e) < (*ez).err) {\
(*ez).err = tmp_e; (*ez).pe = pe; (*ez).te = i;\
}\
}\
/**if(dbg_ext_err(i, thre, err, pe, &((*ez).VP), &((*ez).VN))!=tmp_e)**/\
}\
\
/** 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; c = 4;\
if(i_bd < pn) c = seq_nt4_table[(uint8_t)pstr[i_bd]];\
if(c < 4) ez->Peq[c].a[Peq_i]|=Peq_m;\
\
memcpy(ez->path.a+ez->path.n, ez->D0.a, ws); ez->path.n += ez->nword;\
memcpy(ez->path.a+ez->path.n, ez->VP.a, ws); ez->path.n += ez->nword;\
memcpy(ez->path.a+ez->path.n, ez->VN.a, ws); ez->path.n += ez->nword;\
memcpy(ez->path.a+ez->path.n, ez->HP.a, ws); ez->path.n += ez->nword;\
memcpy(ez->path.a+ez->path.n, ez->HN.a, ws); ez->path.n += ez->nword;\
}\
ed_core(_##sf##_, ez->Peq, ez->VP, ez->VN, ez->X, ez->D0, ez->HN, ez->HP, (uint8_t)tstr[i], c);\
if (!(ez->D0.a[0]&(1ULL))) {\
++err; if (err>cut) return;\
}\
memcpy(ez->path.a+ez->path.n, ez->D0.a, ws); ez->path.n += ez->nword;\
memcpy(ez->path.a+ez->path.n, ez->VP.a, ws); ez->path.n += ez->nword;\
memcpy(ez->path.a+ez->path.n, ez->VN.a, ws); ez->path.n += ez->nword;\
memcpy(ez->path.a+ez->path.n, ez->HP.a, ws); ez->path.n += ez->nword;\
memcpy(ez->path.a+ez->path.n, ez->HN.a, ws); ez->path.n += ez->nword;\
\
int32_t site = tn - 1 - thre;/**up bound; site:[tn - 1 - thre, tn - 1 + thre]**/\
if(!done) {\
for (cut = pn - 1, i = 0; site < cut; i++) {\
bd = (i>>bitw); i_bd = (i&bitz);\
err += (((*ez).VP.a[bd]>>i_bd)&((w_sig)1));\
err -= (((*ez).VN.a[bd]>>i_bd)&((w_sig)1));\
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;\
}\
}\
\
if((ez->te-ez->ts+1) != tn) {\
ez->path.n /= tn; ez->path.n *= (ez->te+1-ez->ts);\
}\
gen_trace(ez, thre, 1);\
return;\
}\
inline void ed_band_cal_extension_##sf##_1_w_trace(char *pstr, int32_t pn, char *tstr, int32_t tn, int32_t thre, bit_extz_t *ez)\
{\
int32_t done = 1;\
ez->cigar.n = 0; ez->nword = w_##sf##_word;\
if(ez->err > thre) {\
init_base_ed(*ez, thre, pn, tn); ez->ps = ez->ts = INT32_MAX; ez->pe = pn-1; ez->te = tn-1;\
if(pn > tn + thre) pn = tn + thre;\
else if(tn > pn + thre) tn = pn + thre;\
done = 0;\
} else if(ez->err == 0) {\
push_trace(&(ez->cigar), 0, ez->te+1-ez->ts); return;\
} else {\
pn = ez->pe + 1 - ez->ps; tn = ez->te + 1 - ez->ts;\
}\
int32_t i, err, tn0 = tn - 1, cut = thre+(thre<<1), bd, i_bd, k_bd, Peq_i, ws; w_sig c, Peq_m;\
int32_t poff, pe = pn-1, tmp_e = INT32_MAX, k, pidx = ez->pe, tidx = ez->te;\
\
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]);\
\
bd = thre+1; bd = ((bd<=pn)?bd:pn); i_bd = thre;\
for (i = 0; i < bd; i++, i_bd++) {\
w_bit((ez->Peq)[seq_nt4_table[(uint8_t)(pstr)[pidx-i]]], (i_bd));\
}\
bd = thre+1, i_bd = thre;\
\
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; ws = sizeof(*(ez->a))*(ez->nword);\
ez->path.n=(ez->nword*tn*5);\
kv_resize(w_sig, ez->path, ez->path.n); ez->path.n=0;\
/**for the incoming char/last char; mm = ((Word)1 << (thre<<1))**/\
Peq_i = (((thre<<1))>>bitw); Peq_m = (((w_sig)1)<<(((thre<<1))&bitz));\
while (i < tn0) {\
ed_core(_##sf##_, ez->Peq, ez->VP, ez->VN, ez->X, ez->D0, ez->HN, ez->HP, (uint8_t)tstr[tidx-i], c);\
if (!(ez->D0.a[0]&(1ULL))) {\
++err; if (err>cut) return;\
}\
\
if(!done) {\
poff = i-thre; k = i+thre-pe;/**poff:[i-thre, i+thre]**/\
if(k >= 0) {\
if(tmp_e == INT32_MAX) {\
tmp_e = err;\
for ((k) = 0; (poff) < (pe); (poff)++, (k)++) {\
bd = (k>>bitw); k_bd = (k&bitz);\
(tmp_e) += (((*ez).VP.a[bd]>>k_bd)&((w_sig)1));\
(tmp_e) -= (((*ez).VN.a[bd]>>k_bd)&((w_sig)1));\
}\
} else {\
k = (thre<<1) - k;\
if(k >= 0) {\
bd = (k>>bitw); k_bd = (k&bitz);\
(tmp_e) += (((*ez).HP.a[bd]>>k_bd)&((w_sig)1));\
(tmp_e) -= (((*ez).HN.a[bd]>>k_bd)&((w_sig)1));\
}\
}\
if((tmp_e) <= (*ez).thre && (tmp_e) < (*ez).err) {\
(*ez).err = tmp_e; (*ez).ps = pidx - pe; (*ez).ts = tidx-i;\
}\
}\
/**if(dbg_ext_err(i, thre, err, pe, &((*ez).VP), &((*ez).VN))!=tmp_e)**/\
}\
\
/** 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; c = 4;\
if(i_bd < pn) c = seq_nt4_table[(uint8_t)pstr[pidx-i_bd]];\
if(c < 4) ez->Peq[c].a[Peq_i]|=Peq_m;\
\
memcpy(ez->path.a+ez->path.n, ez->D0.a, ws); ez->path.n += ez->nword;\
memcpy(ez->path.a+ez->path.n, ez->VP.a, ws); ez->path.n += ez->nword;\
memcpy(ez->path.a+ez->path.n, ez->VN.a, ws); ez->path.n += ez->nword;\
memcpy(ez->path.a+ez->path.n, ez->HP.a, ws); ez->path.n += ez->nword;\
memcpy(ez->path.a+ez->path.n, ez->HN.a, ws); ez->path.n += ez->nword;\
}\
ed_core(_##sf##_, ez->Peq, ez->VP, ez->VN, ez->X, ez->D0, ez->HN, ez->HP, (uint8_t)tstr[tidx-i], c);\
if (!(ez->D0.a[0]&(1ULL))) {\
++err; if (err>cut) return;\
}\
memcpy(ez->path.a+ez->path.n, ez->D0.a, ws); ez->path.n += ez->nword;\
memcpy(ez->path.a+ez->path.n, ez->VP.a, ws); ez->path.n += ez->nword;\
memcpy(ez->path.a+ez->path.n, ez->VN.a, ws); ez->path.n += ez->nword;\
memcpy(ez->path.a+ez->path.n, ez->HP.a, ws); ez->path.n += ez->nword;\
memcpy(ez->path.a+ez->path.n, ez->HN.a, ws); ez->path.n += ez->nword;\
\
int32_t site = tn - 1 - thre;/**up bound; site:[tn - 1 - thre, tn - 1 + thre]**/\
if(!done) {\
for (cut = pn - 1, i = 0; site < cut; i++) {\
bd = (i>>bitw); i_bd = (i&bitz);\
err += (((*ez).VP.a[bd]>>i_bd)&((w_sig)1));\
err -= (((*ez).VN.a[bd]>>i_bd)&((w_sig)1));\
site++;\
if(err <= thre && err < ez->err) {\
ez->err = err; ez->ps = pidx-site; ez->ts = tidx+1-tn;\
}\
}\
if(err <= thre && err < ez->err) {\
ez->err = err; ez->ps = pidx-site; ez->ts = tidx+1-tn;\
}\
}\
\
if((ez->te-ez->ts+1) != tn) {\
ez->path.n /= tn; ez->path.n *= (ez->te+1-ez->ts);\
}\
\
poff = ez->ps; ez->ps = pidx - ez->pe; ez->pe = pidx - poff;\
gen_trace(ez, thre, 0);\
poff = ez->ps; ez->ps = pidx - ez->pe; ez->pe = pidx - poff;\
return;\
}\
inline void ed_band_cal_semi_##sf##_w_absent_diag(char *pstr, int32_t pn, char *tstr, int32_t tn, int32_t thre, int32_t abs_diag, bit_extz_t *ez)\
{\
init_base_ed(*ez, thre, pn, tn); ez->ps = ez->pe = -1; ez->ts = 0; ez->te = tn-1;\
int32_t bd, i, err = abs_diag, i_bd, cut = thre+(thre<<1), tn0 = tn - 1, Peq_i; w_sig c, Peq_m;\
if((pn > tn + cut) || (tn > pn + cut)) return;\
\
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->VP);\
w_##sf##_set_bit_lsub(ez->VN, abs_diag);\
\
bd = ((thre<<1)+1)-abs_diag; bd = ((bd<=pn)?bd:pn); i_bd = abs_diag; \
ed_init_core(i, bd, i_bd, pstr, ez->Peq);\
i_bd = (thre<<1)-abs_diag;\
\
w_##sf##_clear(ez->Peq[4]);\
i = 0;\
/**for the incoming char/last char; mm = ((Word)1 << (thre<<1))**/\
Peq_i = (((thre<<1))>>bitw); Peq_m = (((w_sig)1)<<(((thre<<1))&bitz));\
while (i < tn0) {\
ed_core(_##sf##_, ez->Peq, ez->VP, ez->VN, ez->X, ez->D0, ez->HN, ez->HP, (uint8_t)tstr[i], c);\
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; c = 4;\
if(i_bd < pn) c = seq_nt4_table[(uint8_t)pstr[i_bd]];\
if(c < 4) ez->Peq[c].a[Peq_i]|=Peq_m;\
}\
ed_core(_##sf##_, ez->Peq, ez->VP, ez->VN, ez->X, ez->D0, ez->HN, ez->HP, (uint8_t)tstr[i], c);\
if (!(ez->D0.a[0]&(1ULL))) {\
++err; if (err>cut) return;\
}\
\
int32_t site = tn - 1 - abs_diag;/**up bound**/\
/**in most cases, ai = (thre<<1)**/\
int32_t ai = pn - tn + abs_diag, uge = INT32_MAX; i = 0;\
for (i = 0; site < 0 && i < ai; i++, site++) {\
bd = (i>>bitw); i_bd = (i&bitz);\
err += (((*ez).VP.a[bd]>>i_bd)&((w_sig)1));\
err -= (((*ez).VN.a[bd]>>i_bd)&((w_sig)1));\
}\
if ((err <= thre) && (err <= ez->err)) {\
ez->err = err; ez->pe = site;\
}\
\
site -= i;\
while (i < ai) {\
bd = (i>>bitw); i_bd = (i&bitz);\
err += (((*ez).VP.a[bd]>>i_bd)&((w_sig)1));\
err -= (((*ez).VN.a[bd]>>i_bd)&((w_sig)1));\
++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;\
}\
inline void ed_band_cal_semi_##sf##_w_absent_diag_trace(char *pstr, int32_t pn, char *tstr, int32_t tn, int32_t thre, int32_t abs_diag, bit_extz_t *ez)\
{\
ez->cigar.n = 0; ez->nword = w_##sf##_word;\
if(ez->err > thre) {\
init_base_ed(*ez, thre, pn, tn); ez->ps = ez->pe = -1; ez->ts = 0; ez->te = tn-1;\
} else if(ez->err == 0) {\
push_trace(&(ez->cigar), 0, ez->te+1-ez->ts);\
ez->ps = ez->pe - (ez->te-ez->ts);\
return;\
}\
int32_t bd, i, err = abs_diag, i_bd, cut = thre+(thre<<1), tn0 = tn - 1, Peq_i, ws; w_sig c, Peq_m;\
if((pn > tn + cut) || (tn > pn + cut)) return;\
\
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->VP);\
w_##sf##_set_bit_lsub(ez->VN, abs_diag);\
\
bd = ((thre<<1)+1)-abs_diag; bd = ((bd<=pn)?bd:pn); i_bd = abs_diag;\
ed_init_core(i, bd, i_bd, pstr, ez->Peq);\
i_bd = (thre<<1)-abs_diag;\
\
w_##sf##_clear(ez->Peq[4]);\
i = 0; ws = sizeof(*(ez->a))*(ez->nword);\
ez->path.n=(ez->nword*tn*5);\
kv_resize(w_sig, ez->path, ez->path.n); ez->path.n=0;\
/**for the incoming char/last char; mm = ((Word)1 << (thre<<1))**/\
Peq_i = (((thre<<1))>>bitw); Peq_m = (((w_sig)1)<<(((thre<<1))&bitz));\
while (i < tn0) {\
ed_core(_##sf##_, ez->Peq, ez->VP, ez->VN, ez->X, ez->D0, ez->HN, ez->HP, (uint8_t)tstr[i], c);\
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; c = 4;\
if(i_bd < pn) c = seq_nt4_table[(uint8_t)pstr[i_bd]];\
if(c < 4) ez->Peq[c].a[Peq_i]|=Peq_m;\
\
memcpy(ez->path.a+ez->path.n, ez->D0.a, ws); ez->path.n += ez->nword;\
memcpy(ez->path.a+ez->path.n, ez->VP.a, ws); ez->path.n += ez->nword;\
memcpy(ez->path.a+ez->path.n, ez->VN.a, ws); ez->path.n += ez->nword;\
memcpy(ez->path.a+ez->path.n, ez->HP.a, ws); ez->path.n += ez->nword;\
memcpy(ez->path.a+ez->path.n, ez->HN.a, ws); ez->path.n += ez->nword;\
}\
ed_core(_##sf##_, ez->Peq, ez->VP, ez->VN, ez->X, ez->D0, ez->HN, ez->HP, (uint8_t)tstr[i], c);\
if (!(ez->D0.a[0]&(1ULL))) {\
++err; if (err>cut) return;\
}\
memcpy(ez->path.a+ez->path.n, ez->D0.a, ws); ez->path.n += ez->nword;\
memcpy(ez->path.a+ez->path.n, ez->VP.a, ws); ez->path.n += ez->nword;\
memcpy(ez->path.a+ez->path.n, ez->VN.a, ws); ez->path.n += ez->nword;\
memcpy(ez->path.a+ez->path.n, ez->HP.a, ws); ez->path.n += ez->nword;\
memcpy(ez->path.a+ez->path.n, ez->HN.a, ws); ez->path.n += ez->nword;\
\
int32_t site = tn - 1 - abs_diag;/**up bound**/\
/**in most cases, ai = (thre<<1)**/\
int32_t ai = pn - tn + abs_diag, uge = INT32_MAX; i = 0;\
if(ez->err > thre) {\
for (i = 0; site < 0 && i < ai; i++, site++) {\
bd = (i>>bitw); i_bd = (i&bitz);\
err += (((*ez).VP.a[bd]>>i_bd)&((w_sig)1));\
err -= (((*ez).VN.a[bd]>>i_bd)&((w_sig)1));\
}\
if ((err <= thre) && (err <= ez->err)) {\
ez->err = err; ez->pe = site;\
}\
\
site -= i;\
while (i < ai) {\
bd = (i>>bitw); i_bd = (i&bitz);\
err += (((*ez).VP.a[bd]>>i_bd)&((w_sig)1));\
err -= (((*ez).VN.a[bd]>>i_bd)&((w_sig)1));\
++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;\
}\
gen_trace(ez, abs_diag, 1);\
}\
HA_ED_INIT(128)
HA_ED_INIT(192)
HA_ED_INIT(256)
#define w_infi_clear(x, nw) (memset((x).a, 0, sizeof(*((x).a))*(nw)))
#define w_infi_set_bit_lsub(x, l, nw) do { \
w_infi_clear(x, nw);\
if((l)>>bitw) memset((x).a, -1, sizeof(*((x).a))*((l)>>bitw));\
if((l)&bitz) (x).a[(l)>>bitw] = (((w_sig)1)<<((l)&bitz))-1; \
} while (0)
#define w_infi_self_xor(x, y, nw, w_z) {\
for((w_z)=0; (w_z)<(nw); (w_z)++) (x).a[w_z]^=(y).a[w_z];}
#define w_self_add_sin(x, y, w_z, ad) {\
(x).a[(w_z)]+=(ad), (ad)=((x).a[(w_z)]<(ad)), (x).a[(w_z)]+=(y).a[(w_z)], (ad)|=((x).a[(w_z)]<(y).a[(w_z)]);}
#define ed_infi_core(Peq, VP, VN, X, D0, HN, HP, z, c, ad, w_z, nw) {\
(c) = seq_nt4_table[(z)];\
for((w_z)=(ad)=0; (w_z)<(nw); (w_z)++){\
/**X = Peq[seq_nt4_table[(uint8_t)tstr[i]]] | VN;**/\
(X).a[(w_z)]=(Peq)[(c)].a[(w_z)]|(VN).a[(w_z)];\
/**D0 = ((VP + (X&VP)) ^ VP) | X;**/\
(D0).a[(w_z)]=(X).a[(w_z)]&(VP).a[(w_z)];\
w_self_add_sin((D0), (VP), (w_z), (ad));\
(D0).a[(w_z)]^=(VP).a[(w_z)];\
(D0).a[(w_z)]|=(X).a[(w_z)];\
/**HN = VP&D0;**/\
(HN).a[(w_z)]=(VP).a[(w_z)]&(D0).a[(w_z)];\
/**HP = VN | ~(VP | D0);**/\
(HP).a[(w_z)]=~((VP).a[(w_z)]|(D0).a[(w_z)]);\
(HP).a[(w_z)]|=(VN).a[(w_z)];\
}\
for((w_z)=(nw)-1,(ad)=0; (w_z)>=0; (w_z)--){\
/**X = D0 >> 1;**/\
(X).a[(w_z)]=((D0).a[(w_z)]>>1)|(ad),(ad)=(D0).a[(w_z)]<<bitz;\
/**VN = X&HP;**/\
(VN).a[(w_z)]=(X).a[(w_z)]&(HP).a[(w_z)];\
/**VP = HN | ~(X | HP);**/\
(VP).a[(w_z)]=~((X).a[(w_z)]|(HP).a[(w_z)]);\
(VP).a[(w_z)]|=(HN).a[(w_z)];\
}\
}
#define ed_infi_post_Peq(Peq, w_z, w_z1, nw) {\
/** Peq[0] >>= 1; Peq[1] >>= 1; Peq[2] >>= 1; Peq[3] >>= 1;**/\
for((w_z)=0, (w_z1)=1; (w_z1)<(nw); (w_z)++,(w_z1)++){\
Peq[0].a[(w_z)]=(Peq[0].a[(w_z)]>>1)|(Peq[0].a[(w_z1)]<<bitz);\
Peq[1].a[(w_z)]=(Peq[1].a[(w_z)]>>1)|(Peq[1].a[(w_z1)]<<bitz);\
Peq[2].a[(w_z)]=(Peq[2].a[(w_z)]>>1)|(Peq[2].a[(w_z1)]<<bitz);\
Peq[3].a[(w_z)]=(Peq[3].a[(w_z)]>>1)|(Peq[3].a[(w_z1)]<<bitz);\
}\
(w_z)=(nw)-1;\
Peq[0].a[(w_z)]>>=1;\
Peq[1].a[(w_z)]>>=1;\
Peq[2].a[(w_z)]>>=1;\
Peq[3].a[(w_z)]>>=1;\
}
inline void ed_band_cal_global_infi_w(char *pstr, int32_t pn, char *tstr, int32_t tn, int32_t thre, int32_t *nword, bit_extz_t *ez)
{
init_base_ed(*ez, thre, pn, tn); ez->ps = ez->ts = 0;
if((pn > tn + thre) || (tn > pn + thre)) return;
int32_t i, err, tn0 = tn - 1, cut = thre+(thre<<1), bd, i_bd, wz, wz1, Peq_i; w_sig c, ad, Peq_m;
if(nword) {
ez->nword = (*nword);
} else {
bd = (((thre)<<1)+1); ez->nword = ((bd>>bitw)+(!!(bd&bitz)));
}
resize_bit_extz_t((*ez), (thre));
wz = sizeof(*(ez->a))*(ez->nword);
memset((ez->Peq[0]).a, 0, wz);
memset((ez->Peq[1]).a, 0, wz);
memset((ez->Peq[2]).a, 0, wz);
memset((ez->Peq[3]).a, 0, wz);
memset((ez->Peq[4]).a, 0, wz);
bd = thre+1; bd = ((bd<=pn)?bd:pn); i_bd = thre;
ed_init_core(i, bd, i_bd, pstr, ez->Peq);
bd = thre+1, i_bd = thre;
memset((ez->Peq[4]).a, 0, wz);
err = thre;
w_infi_set_bit_lsub(ez->VN, thre, ez->nword); /**VN = (((Word)1)<<(thre))-1;**/
w_infi_set_bit_lsub(ez->VP, (thre<<1)+1, ez->nword); /**VP = (((Word)1)<<((thre<<1)+1))-1;**/
w_infi_self_xor(ez->VP, ez->VN, ez->nword, wz) /**VP ^= VN;**/
i = 0;
/**for the incoming char/last char; mm = ((Word)1 << (thre<<1))**/
Peq_i = (((thre<<1))>>bitw); Peq_m = (((w_sig)1)<<(((thre<<1))&bitz));
while (i < tn0) {
// fprintf(stderr, "\ni::%d\n", i);
// prt_bit_extz_t((*ez), (((thre<<1))+1));
ed_infi_core(ez->Peq, ez->VP, ez->VN, ez->X, ez->D0, ez->HN, ez->HP, (uint8_t)tstr[i], c, ad, wz, ez->nword);
if (!(ez->D0.a[0]&(1ULL))) {
++err; if (err>cut) return;
}
ed_infi_post_Peq(ez->Peq, wz, wz1, ez->nword);
++i; ++i_bd; c = 4;
if(i_bd < pn) c = seq_nt4_table[(uint8_t)pstr[i_bd]];
if(c < 4) ez->Peq[c].a[Peq_i]|=Peq_m;
// fprintf(stderr, "c::%u\n", c);
// print_bits(ez->Peq[c].a, (((thre<<1))+1), "Peq[c]");
}
ed_infi_core(ez->Peq, ez->VP, ez->VN, ez->X, ez->D0, ez->HN, ez->HP, (uint8_t)tstr[i], c, ad, wz, ez->nword);
if (!(ez->D0.a[0]&(1ULL))) {
++err; if (err>cut) return;
}
int32_t site = tn - 1 - thre;/**up bound**/
for (cut = pn - 1, i = 0; site < cut; site++, i++) {
bd = (i>>bitw); i_bd = (i&bitz);
err += (((*ez).VP.a[bd]>>i_bd)&((w_sig)1));
err -= (((*ez).VN.a[bd]>>i_bd)&((w_sig)1));
}
if (site == cut && err <= thre) {
ez->err = err;
ez->pe = pn-1; ez->te = tn-1;
}
return;
}
inline void ed_band_cal_semi_infi_w(char *pstr, int32_t pn, char *tstr, int32_t tn, int32_t thre, int32_t *nword, bit_extz_t *ez)
{
init_base_ed(*ez, thre, pn, tn); ez->ps = ez->pe = -1; ez->ts = 0; ez->te = tn-1;
int32_t bd, i, err = 0, i_bd, cut = thre+(thre<<1), tn0 = tn - 1, wz, wz1, Peq_i; w_sig c, ad, Peq_m;
if((pn > tn + cut) || (tn > pn + cut)) return;
if(nword) {
ez->nword = (*nword);
} else {
bd = (((thre)<<1)+1); ez->nword = ((bd>>bitw)+(!!(bd&bitz)));
}
resize_bit_extz_t((*ez), (thre));
wz = sizeof(*(ez->a))*(ez->nword);
memset((ez->Peq[0]).a, 0, wz);
memset((ez->Peq[1]).a, 0, wz);
memset((ez->Peq[2]).a, 0, wz);
memset((ez->Peq[3]).a, 0, wz);
memset((ez->Peq[4]).a, 0, wz);
memset((ez->VP).a, 0, wz);
memset((ez->VN).a, 0, wz);
bd = (thre<<1)+1; bd = ((bd<=pn)?bd:pn); i_bd = 0;
ed_init_core(i, bd, i_bd, pstr, ez->Peq);
bd = (thre<<1)+1, i_bd = (thre<<1);
memset((ez->Peq[4]).a, 0, wz);
i = 0;
/**for the incoming char/last char; mm = ((Word)1 << (thre<<1))**/
Peq_i = (((thre<<1))>>bitw); Peq_m = (((w_sig)1)<<(((thre<<1))&bitz));
while (i < tn0) {
ed_infi_core(ez->Peq, ez->VP, ez->VN, ez->X, ez->D0, ez->HN, ez->HP, (uint8_t)tstr[i], c, ad, wz, ez->nword);
if (!(ez->D0.a[0]&(1ULL))) {
++err; if (err>cut) return;
}
ed_infi_post_Peq(ez->Peq, wz, wz1, ez->nword);
++i; ++i_bd; c = 4;
if(i_bd < pn) c = seq_nt4_table[(uint8_t)pstr[i_bd]];
if(c < 4) ez->Peq[c].a[Peq_i]|=Peq_m;
}
ed_infi_core(ez->Peq, ez->VP, ez->VN, ez->X, ez->D0, ez->HN, ez->HP, (uint8_t)tstr[i], c, ad, wz, ez->nword);
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) {
bd = (i>>bitw); i_bd = (i&bitz);
err += (((*ez).VP.a[bd]>>i_bd)&((w_sig)1));
err -= (((*ez).VN.a[bd]>>i_bd)&((w_sig)1));
++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;
}
inline void ed_band_cal_extension_infi_0_w(char *pstr, int32_t pn, char *tstr, int32_t tn, int32_t thre, int32_t *nword, bit_extz_t *ez)
{
init_base_ed(*ez, thre, pn, tn); ez->ps = ez->ts = 0; ez->pe = ez->te = -1;
if(pn > tn + thre) pn = tn + thre;
else if(tn > pn + thre) tn = pn + thre;
int32_t i, err, tn0 = tn - 1, cut = thre+(thre<<1), bd, i_bd, k_bd, wz, wz1, Peq_i; w_sig c, ad, Peq_m;
int32_t poff, pe = pn-1, tmp_e = INT32_MAX, k;
if(nword) {
ez->nword = (*nword);
} else {
bd = (((thre)<<1)+1); ez->nword = ((bd>>bitw)+(!!(bd&bitz)));
}
resize_bit_extz_t((*ez), (thre));
wz = sizeof(*(ez->a))*(ez->nword);
memset((ez->Peq[0]).a, 0, wz);
memset((ez->Peq[1]).a, 0, wz);
memset((ez->Peq[2]).a, 0, wz);
memset((ez->Peq[3]).a, 0, wz);
memset((ez->Peq[4]).a, 0, wz);
bd = thre+1; bd = ((bd<=pn)?bd:pn); i_bd = thre;
ed_init_core(i, bd, i_bd, pstr, ez->Peq);
bd = thre+1, i_bd = thre;
memset((ez->Peq[4]).a, 0, wz);
err = thre;
w_infi_set_bit_lsub(ez->VN, thre, ez->nword); /**VN = (((Word)1)<<(thre))-1;**/
w_infi_set_bit_lsub(ez->VP, (thre<<1)+1, ez->nword); /**VP = (((Word)1)<<((thre<<1)+1))-1;**/
w_infi_self_xor(ez->VP, ez->VN, ez->nword, wz) /**VP ^= VN;**/
i = 0;
/**for the incoming char/last char; mm = ((Word)1 << (thre<<1))**/
Peq_i = (((thre<<1))>>bitw); Peq_m = (((w_sig)1)<<(((thre<<1))&bitz));
//for debug
// memset((ez->X).a, 0, sizeof(*(ez->a))*(ez->nword));
// memset((ez->D0).a, 0, sizeof(*(ez->a))*(ez->nword));
// memset((ez->HN).a, 0, sizeof(*(ez->a))*(ez->nword));
// memset((ez->HP).a, 0, sizeof(*(ez->a))*(ez->nword));
while (i < tn0) {
// fprintf(stderr, "i::%d\n", i);
// prt_bit_extz_t((*ez), ((thre<<1)+1));
ed_infi_core(ez->Peq, ez->VP, ez->VN, ez->X, ez->D0, ez->HN, ez->HP, (uint8_t)tstr[i], c, ad, wz, ez->nword);
if (!(ez->D0.a[0]&(1ULL))) {
++err; if (err>cut) return;
}
{
poff = i-thre; k = i+thre-pe;/**poff:[i-thre, i+thre]**/
if(k >= 0) {
if(tmp_e == INT32_MAX) {
tmp_e = err;
for ((k) = 0; (poff) < (pe); (poff)++, (k)++) {
bd = (k>>bitw); k_bd = (k&bitz);
(tmp_e) += (((*ez).VP.a[bd]>>k_bd)&((w_sig)1));
(tmp_e) -= (((*ez).VN.a[bd]>>k_bd)&((w_sig)1));
}
} else {
k = (thre<<1) - k;
if(k >= 0) {
bd = (k>>bitw); k_bd = (k&bitz);
(tmp_e) += (((*ez).HP.a[bd]>>k_bd)&((w_sig)1));
(tmp_e) -= (((*ez).HN.a[bd]>>k_bd)&((w_sig)1));
}
}
if((tmp_e) <= (*ez).thre && (tmp_e) < (*ez).err) {
(*ez).err = tmp_e; (*ez).pe = pe; (*ez).te = i;
}
}
// if(dbg_ext_err(i, thre, err, pe, &((*ez).VP), &((*ez).VN))!=tmp_e) {
// fprintf(stderr, "i::%d, tmp_e::%d, dbg_ext_err::%d\n", i, tmp_e, dbg_ext_err(i, thre, err, pe, &((*ez).VP), &((*ez).VN)));
// }
}
ed_infi_post_Peq(ez->Peq, wz, wz1, ez->nword);
++i; ++i_bd; c = 4;
if(i_bd < pn) c = seq_nt4_table[(uint8_t)pstr[i_bd]];
if(c < 4) ez->Peq[c].a[Peq_i]|=Peq_m;
}
ed_infi_core(ez->Peq, ez->VP, ez->VN, ez->X, ez->D0, ez->HN, ez->HP, (uint8_t)tstr[i], c, ad, wz, ez->nword);
if (!(ez->D0.a[0]&(1ULL))) {
++err; if (err>cut) return;
}
int32_t site = tn - 1 - thre;/**up bound; site:[tn - 1 - thre, tn - 1 + thre]**/
for (cut = pn - 1, i = 0; site < cut; i++) {
bd = (i>>bitw); i_bd = (i&bitz);
err += (((*ez).VP.a[bd]>>i_bd)&((w_sig)1));
err -= (((*ez).VN.a[bd]>>i_bd)&((w_sig)1));
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_extension_infi_1_w(char *pstr, int32_t pn, char *tstr, int32_t tn, int32_t thre, int32_t *nword, bit_extz_t *ez)
{
init_base_ed(*ez, thre, pn, tn); ez->ps = ez->ts = INT32_MAX; ez->pe = pn-1; ez->te = tn-1;
if(pn > tn + thre) pn = tn + thre;
else if(tn > pn + thre) tn = pn + thre;
int32_t i, err, tn0 = tn - 1, cut = thre+(thre<<1), bd, i_bd, k_bd, wz, wz1, Peq_i;
int32_t poff, pe = pn-1, tmp_e = INT32_MAX, k, pidx = ez->pe, tidx = ez->te; w_sig c, ad, Peq_m;
if(nword) {
ez->nword = (*nword);
} else {
bd = (((thre)<<1)+1); ez->nword = ((bd>>bitw)+(!!(bd&bitz)));
}
resize_bit_extz_t((*ez), (thre));
wz = sizeof(*(ez->a))*(ez->nword);
memset((ez->Peq[0]).a, 0, wz);
memset((ez->Peq[1]).a, 0, wz);
memset((ez->Peq[2]).a, 0, wz);
memset((ez->Peq[3]).a, 0, wz);
memset((ez->Peq[4]).a, 0, wz);
bd = thre+1; bd = ((bd<=pn)?bd:pn); i_bd = thre;
for (i = 0; i < bd; i++, i_bd++) {
w_bit((ez->Peq)[seq_nt4_table[(uint8_t)(pstr)[pidx-i]]], (i_bd));
}
bd = thre+1, i_bd = thre;
memset((ez->Peq[4]).a, 0, wz);
err = thre;
w_infi_set_bit_lsub(ez->VN, thre, ez->nword); /**VN = (((Word)1)<<(thre))-1;**/
w_infi_set_bit_lsub(ez->VP, (thre<<1)+1, ez->nword); /**VP = (((Word)1)<<((thre<<1)+1))-1;**/
w_infi_self_xor(ez->VP, ez->VN, ez->nword, wz) /**VP ^= VN;**/
i = 0;
/**for the incoming char/last char; mm = ((Word)1 << (thre<<1))**/
Peq_i = (((thre<<1))>>bitw); Peq_m = (((w_sig)1)<<(((thre<<1))&bitz));
while (i < tn0) {
ed_infi_core(ez->Peq, ez->VP, ez->VN, ez->X, ez->D0, ez->HN, ez->HP, (uint8_t)tstr[tidx-i], c, ad, wz, ez->nword);
if (!(ez->D0.a[0]&(1ULL))) {
++err; if (err>cut) return;
}
{
poff = i-thre; k = i+thre-pe;/**poff:[i-thre, i+thre]**/
if(k >= 0) {
if(tmp_e == INT32_MAX) {
tmp_e = err;
for ((k) = 0; (poff) < (pe); (poff)++, (k)++) {
bd = (k>>bitw); k_bd = (k&bitz);
(tmp_e) += (((*ez).VP.a[bd]>>k_bd)&((w_sig)1));
(tmp_e) -= (((*ez).VN.a[bd]>>k_bd)&((w_sig)1));
}
} else {
k = (thre<<1) - k;
if(k >= 0) {
bd = (k>>bitw); k_bd = (k&bitz);
(tmp_e) += (((*ez).HP.a[bd]>>k_bd)&((w_sig)1));
(tmp_e) -= (((*ez).HN.a[bd]>>k_bd)&((w_sig)1));
}
}
if((tmp_e) <= (*ez).thre && (tmp_e) < (*ez).err) {
(*ez).err = tmp_e; (*ez).ps = pidx - pe; (*ez).ts = tidx-i;
}
}
}
// if(dbg_ext_err(i, thre, err, pe, &((*ez).VP), &((*ez).VN))!=tmp_e) {
// fprintf(stderr, "i::%d, tmp_e::%d, dbg_ext_err::%d\n", i, tmp_e, dbg_ext_err(i, thre, err, pe, &((*ez).VP), &((*ez).VN)));
// }
ed_infi_post_Peq(ez->Peq, wz, wz1, ez->nword);
++i; ++i_bd; c = 4;
if(i_bd < pn) c = seq_nt4_table[(uint8_t)pstr[pidx-i_bd]];
if(c < 4) ez->Peq[c].a[Peq_i]|=Peq_m;
}
ed_infi_core(ez->Peq, ez->VP, ez->VN, ez->X, ez->D0, ez->HN, ez->HP, (uint8_t)tstr[tidx-i], c, ad, wz, ez->nword);
if (!(ez->D0.a[0]&(1ULL))) {
++err; if (err>cut) return;
}
int32_t site = tn - 1 - thre;/**up bound; site:[tn - 1 - thre, tn - 1 + thre]**/
for (cut = pn - 1, i = 0; site < cut; i++) {
bd = (i>>bitw); i_bd = (i&bitz);
err += (((*ez).VP.a[bd]>>i_bd)&((w_sig)1));
err -= (((*ez).VN.a[bd]>>i_bd)&((w_sig)1));
site++;
if(err <= thre && err < ez->err) {
ez->err = err; ez->ps = pidx-site; ez->ts = tidx+1-tn;
}
}
if(err <= thre && err < ez->err) {
ez->err = err; ez->ps = pidx-site; ez->ts = tidx+1-tn;
}
return;
}
inline void ed_band_cal_global_infi_w_trace(char *pstr, int32_t pn, char *tstr, int32_t tn, int32_t thre, int32_t *nword, bit_extz_t *ez)
{
ez->cigar.n = 0;//diff
if(ez->err > thre) {//diff
init_base_ed(*ez, thre, pn, tn); ez->ps = ez->ts = 0;
} else if(ez->err == 0) {//diff
push_trace(&(ez->cigar), 0, ez->te+1-ez->ts); return;//diff
}
if((pn > tn + thre) || (tn > pn + thre)) return;
int32_t i, err, tn0 = tn - 1, cut = thre+(thre<<1), bd, i_bd, wz, wz1, Peq_i, ws; w_sig c, ad, Peq_m;
if(nword) {
ez->nword = (*nword);
} else {
bd = (((thre)<<1)+1); ez->nword = ((bd>>bitw)+(!!(bd&bitz)));
}
resize_bit_extz_t((*ez), (thre));
wz = ws = sizeof(*(ez->a))*(ez->nword);//diff
memset((ez->Peq[0]).a, 0, wz);
memset((ez->Peq[1]).a, 0, wz);
memset((ez->Peq[2]).a, 0, wz);
memset((ez->Peq[3]).a, 0, wz);
memset((ez->Peq[4]).a, 0, wz);
bd = thre+1; bd = ((bd<=pn)?bd:pn); i_bd = thre;
ed_init_core(i, bd, i_bd, pstr, ez->Peq);
bd = thre+1, i_bd = thre;
memset((ez->Peq[4]).a, 0, wz);
err = thre;
w_infi_set_bit_lsub(ez->VN, thre, ez->nword); /**VN = (((Word)1)<<(thre))-1;**/
w_infi_set_bit_lsub(ez->VP, (thre<<1)+1, ez->nword); /**VP = (((Word)1)<<((thre<<1)+1))-1;**/
w_infi_self_xor(ez->VP, ez->VN, ez->nword, wz) /**VP ^= VN;**/
ez->path.n=(ez->nword*tn*5);//diff
kv_resize(w_sig, ez->path, ez->path.n); ez->path.n=0;//diff
i = 0;
/**for the incoming char/last char; mm = ((Word)1 << (thre<<1))**/
Peq_i = (((thre<<1))>>bitw); Peq_m = (((w_sig)1)<<(((thre<<1))&bitz));
while (i < tn0) {
// fprintf(stderr, "\ni::%d\n", i);
// prt_bit_extz_t((*ez), (((thre<<1))+1));
ed_infi_core(ez->Peq, ez->VP, ez->VN, ez->X, ez->D0, ez->HN, ez->HP, (uint8_t)tstr[i], c, ad, wz, ez->nword);
if (!(ez->D0.a[0]&(1ULL))) {
++err; if (err>cut) return;
}
ed_infi_post_Peq(ez->Peq, wz, wz1, ez->nword);
++i; ++i_bd; c = 4;
if(i_bd < pn) c = seq_nt4_table[(uint8_t)pstr[i_bd]];
if(c < 4) ez->Peq[c].a[Peq_i]|=Peq_m;
// fprintf(stderr, "c::%u\n", c);
// print_bits(ez->Peq[c].a, (((thre<<1))+1), "Peq[c]");
memcpy(ez->path.a+ez->path.n, ez->D0.a, ws); ez->path.n += ez->nword;//diff
memcpy(ez->path.a+ez->path.n, ez->VP.a, ws); ez->path.n += ez->nword;//diff
memcpy(ez->path.a+ez->path.n, ez->VN.a, ws); ez->path.n += ez->nword;//diff
memcpy(ez->path.a+ez->path.n, ez->HP.a, ws); ez->path.n += ez->nword;//diff
memcpy(ez->path.a+ez->path.n, ez->HN.a, ws); ez->path.n += ez->nword;//diff
}
ed_infi_core(ez->Peq, ez->VP, ez->VN, ez->X, ez->D0, ez->HN, ez->HP, (uint8_t)tstr[i], c, ad, wz, ez->nword);
if (!(ez->D0.a[0]&(1ULL))) {
++err; if (err>cut) return;
}
memcpy(ez->path.a+ez->path.n, ez->D0.a, ws); ez->path.n += ez->nword;//diff
memcpy(ez->path.a+ez->path.n, ez->VP.a, ws); ez->path.n += ez->nword;//diff
memcpy(ez->path.a+ez->path.n, ez->VN.a, ws); ez->path.n += ez->nword;//diff
memcpy(ez->path.a+ez->path.n, ez->HP.a, ws); ez->path.n += ez->nword;//diff
memcpy(ez->path.a+ez->path.n, ez->HN.a, ws); ez->path.n += ez->nword;//diff
int32_t site = tn - 1 - thre;/**up bound**/
if(ez->err > thre) {//diff
for (cut = pn - 1, i = 0; site < cut; site++, i++) {
bd = (i>>bitw); i_bd = (i&bitz);
err += (((*ez).VP.a[bd]>>i_bd)&((w_sig)1));
err -= (((*ez).VN.a[bd]>>i_bd)&((w_sig)1));
}
if (site == cut && err <= thre) {
ez->err = err;
ez->pe = pn-1; ez->te = tn-1;
}
}
gen_trace(ez, thre, 1);//diff
return;
}
inline void ed_band_cal_semi_infi_w_trace(char *pstr, int32_t pn, char *tstr, int32_t tn, int32_t thre, int32_t *nword, bit_extz_t *ez)
{
ez->cigar.n = 0;//diff
if(ez->err > thre) {//diff
init_base_ed(*ez, thre, pn, tn); ez->ps = ez->pe = -1; ez->ts = 0; ez->te = tn-1;
} else if(ez->err == 0) {//diff
push_trace(&(ez->cigar), 0, ez->te+1-ez->ts); //diff
ez->ps = ez->pe - (ez->te-ez->ts);//diff
return;//diff
}
int32_t bd, i, err = 0, i_bd, cut = thre+(thre<<1), tn0 = tn - 1, wz, wz1, ws, Peq_i; w_sig c, ad, Peq_m;
if((pn > tn + cut) || (tn > pn + cut)) return;
if(nword) {
ez->nword = (*nword);
} else {
bd = (((thre)<<1)+1); ez->nword = ((bd>>bitw)+(!!(bd&bitz)));
}
resize_bit_extz_t((*ez), (thre));
wz = ws = sizeof(*(ez->a))*(ez->nword);//diff
memset((ez->Peq[0]).a, 0, wz);
memset((ez->Peq[1]).a, 0, wz);
memset((ez->Peq[2]).a, 0, wz);
memset((ez->Peq[3]).a, 0, wz);
memset((ez->Peq[4]).a, 0, wz);
memset((ez->VP).a, 0, wz);
memset((ez->VN).a, 0, wz);
bd = (thre<<1)+1; bd = ((bd<=pn)?bd:pn); i_bd = 0;
ed_init_core(i, bd, i_bd, pstr, ez->Peq);
bd = (thre<<1)+1, i_bd = (thre<<1);
memset((ez->Peq[4]).a, 0, wz);
ez->path.n=(ez->nword*tn*5);//diff
kv_resize(w_sig, ez->path, ez->path.n); ez->path.n=0;//diff
i = 0;
/**for the incoming char/last char; mm = ((Word)1 << (thre<<1))**/
Peq_i = (((thre<<1))>>bitw); Peq_m = (((w_sig)1)<<(((thre<<1))&bitz));
while (i < tn0) {
ed_infi_core(ez->Peq, ez->VP, ez->VN, ez->X, ez->D0, ez->HN, ez->HP, (uint8_t)tstr[i], c, ad, wz, ez->nword);
if (!(ez->D0.a[0]&(1ULL))) {
++err; if (err>cut) return;
}
ed_infi_post_Peq(ez->Peq, wz, wz1, ez->nword);
++i; ++i_bd; c = 4;
if(i_bd < pn) c = seq_nt4_table[(uint8_t)pstr[i_bd]];
if(c < 4) ez->Peq[c].a[Peq_i]|=Peq_m;
memcpy(ez->path.a+ez->path.n, ez->D0.a, ws); ez->path.n += ez->nword;//diff
memcpy(ez->path.a+ez->path.n, ez->VP.a, ws); ez->path.n += ez->nword;//diff
memcpy(ez->path.a+ez->path.n, ez->VN.a, ws); ez->path.n += ez->nword;//diff
memcpy(ez->path.a+ez->path.n, ez->HP.a, ws); ez->path.n += ez->nword;//diff
memcpy(ez->path.a+ez->path.n, ez->HN.a, ws); ez->path.n += ez->nword;//diff
}
ed_infi_core(ez->Peq, ez->VP, ez->VN, ez->X, ez->D0, ez->HN, ez->HP, (uint8_t)tstr[i], c, ad, wz, ez->nword);
if (!(ez->D0.a[0]&(1ULL))) {
++err; if (err>cut) return;
}
memcpy(ez->path.a+ez->path.n, ez->D0.a, ws); ez->path.n += ez->nword;//diff
memcpy(ez->path.a+ez->path.n, ez->VP.a, ws); ez->path.n += ez->nword;//diff
memcpy(ez->path.a+ez->path.n, ez->VN.a, ws); ez->path.n += ez->nword;//diff
memcpy(ez->path.a+ez->path.n, ez->HP.a, ws); ez->path.n += ez->nword;//diff
memcpy(ez->path.a+ez->path.n, ez->HN.a, ws); ez->path.n += ez->nword;//diff
int32_t site = tn - 1;/**up bound**/
/**in most cases, ai = (thre<<1)**/
int32_t ai = pn - tn, uge = INT32_MAX;
if(ez->err > thre) {//diff
if ((err <= thre) && (err <= ez->err)) {
ez->err = err; ez->pe = site;
}
i = 0;
while (i < ai) {
bd = (i>>bitw); i_bd = (i&bitz);
err += (((*ez).VP.a[bd]>>i_bd)&((w_sig)1));
err -= (((*ez).VN.a[bd]>>i_bd)&((w_sig)1));
++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;
}
gen_trace(ez, 0, 1);//diff
}
inline void ed_band_cal_extension_infi_0_w_trace(char *pstr, int32_t pn, char *tstr, int32_t tn, int32_t thre, int32_t *nword, bit_extz_t *ez)
{
int32_t done = 1;//diff
ez->cigar.n = 0; //diff
if(ez->err > thre) {//diff
init_base_ed(*ez, thre, pn, tn); ez->ps = ez->ts = 0; ez->pe = ez->te = -1;
if(pn > tn + thre) pn = tn + thre;
else if(tn > pn + thre) tn = pn + thre;
done = 0;//diff
} else if(ez->err == 0) {//diff
push_trace(&(ez->cigar), 0, ez->te+1-ez->ts); return;//diff
} else {
pn = ez->pe + 1 - ez->ps; tn = ez->te + 1 - ez->ts; //diff
}
int32_t i, err, tn0 = tn - 1, cut = thre+(thre<<1), bd, i_bd, k_bd, wz, wz1, ws, Peq_i; w_sig c, ad, Peq_m;
int32_t poff, pe = pn-1, tmp_e = INT32_MAX, k;
if(nword) {
ez->nword = (*nword);
} else {
bd = (((thre)<<1)+1); ez->nword = ((bd>>bitw)+(!!(bd&bitz)));
}
resize_bit_extz_t((*ez), (thre));
wz = ws = sizeof(*(ez->a))*(ez->nword);//diff
memset((ez->Peq[0]).a, 0, wz);
memset((ez->Peq[1]).a, 0, wz);
memset((ez->Peq[2]).a, 0, wz);
memset((ez->Peq[3]).a, 0, wz);
memset((ez->Peq[4]).a, 0, wz);
bd = thre+1; bd = ((bd<=pn)?bd:pn); i_bd = thre;
ed_init_core(i, bd, i_bd, pstr, ez->Peq);
bd = thre+1, i_bd = thre;
memset((ez->Peq[4]).a, 0, wz);
err = thre;
w_infi_set_bit_lsub(ez->VN, thre, ez->nword); /**VN = (((Word)1)<<(thre))-1;**/
w_infi_set_bit_lsub(ez->VP, (thre<<1)+1, ez->nword); /**VP = (((Word)1)<<((thre<<1)+1))-1;**/
w_infi_self_xor(ez->VP, ez->VN, ez->nword, wz) /**VP ^= VN;**/
ez->path.n=(ez->nword*tn*5);//diff
kv_resize(w_sig, ez->path, ez->path.n); ez->path.n=0;//diff
i = 0;
/**for the incoming char/last char; mm = ((Word)1 << (thre<<1))**/
Peq_i = (((thre<<1))>>bitw); Peq_m = (((w_sig)1)<<(((thre<<1))&bitz));
//for debug
// memset((ez->X).a, 0, sizeof(*(ez->a))*(ez->nword));
// memset((ez->D0).a, 0, sizeof(*(ez->a))*(ez->nword));
// memset((ez->HN).a, 0, sizeof(*(ez->a))*(ez->nword));
// memset((ez->HP).a, 0, sizeof(*(ez->a))*(ez->nword));
while (i < tn0) {
// fprintf(stderr, "i::%d\n", i);
// prt_bit_extz_t((*ez), ((thre<<1)+1));
ed_infi_core(ez->Peq, ez->VP, ez->VN, ez->X, ez->D0, ez->HN, ez->HP, (uint8_t)tstr[i], c, ad, wz, ez->nword);
if (!(ez->D0.a[0]&(1ULL))) {
++err; if (err>cut) return;
}
if(!done) {//diff
poff = i-thre; k = i+thre-pe;/**poff:[i-thre, i+thre]**/
if(k >= 0) {
if(tmp_e == INT32_MAX) {
tmp_e = err;
for ((k) = 0; (poff) < (pe); (poff)++, (k)++) {
bd = (k>>bitw); k_bd = (k&bitz);
(tmp_e) += (((*ez).VP.a[bd]>>k_bd)&((w_sig)1));
(tmp_e) -= (((*ez).VN.a[bd]>>k_bd)&((w_sig)1));
}
} else {
k = (thre<<1) - k;
if(k >= 0) {
bd = (k>>bitw); k_bd = (k&bitz);
(tmp_e) += (((*ez).HP.a[bd]>>k_bd)&((w_sig)1));
(tmp_e) -= (((*ez).HN.a[bd]>>k_bd)&((w_sig)1));
}
}
if((tmp_e) <= (*ez).thre && (tmp_e) < (*ez).err) {
(*ez).err = tmp_e; (*ez).pe = pe; (*ez).te = i;
}
}
// if(dbg_ext_err(i, thre, err, pe, &((*ez).VP), &((*ez).VN))!=tmp_e) {
// fprintf(stderr, "i::%d, tmp_e::%d, dbg_ext_err::%d\n", i, tmp_e, dbg_ext_err(i, thre, err, pe, &((*ez).VP), &((*ez).VN)));
// }
}
ed_infi_post_Peq(ez->Peq, wz, wz1, ez->nword);
++i; ++i_bd; c = 4;
if(i_bd < pn) c = seq_nt4_table[(uint8_t)pstr[i_bd]];
if(c < 4) ez->Peq[c].a[Peq_i]|=Peq_m;
memcpy(ez->path.a+ez->path.n, ez->D0.a, ws); ez->path.n += ez->nword;//diff
memcpy(ez->path.a+ez->path.n, ez->VP.a, ws); ez->path.n += ez->nword;//diff
memcpy(ez->path.a+ez->path.n, ez->VN.a, ws); ez->path.n += ez->nword;//diff
memcpy(ez->path.a+ez->path.n, ez->HP.a, ws); ez->path.n += ez->nword;//diff
memcpy(ez->path.a+ez->path.n, ez->HN.a, ws); ez->path.n += ez->nword;//diff
}
ed_infi_core(ez->Peq, ez->VP, ez->VN, ez->X, ez->D0, ez->HN, ez->HP, (uint8_t)tstr[i], c, ad, wz, ez->nword);
if (!(ez->D0.a[0]&(1ULL))) {
++err; if (err>cut) return;
}
memcpy(ez->path.a+ez->path.n, ez->D0.a, ws); ez->path.n += ez->nword;//diff
memcpy(ez->path.a+ez->path.n, ez->VP.a, ws); ez->path.n += ez->nword;//diff
memcpy(ez->path.a+ez->path.n, ez->VN.a, ws); ez->path.n += ez->nword;//diff
memcpy(ez->path.a+ez->path.n, ez->HP.a, ws); ez->path.n += ez->nword;//diff
memcpy(ez->path.a+ez->path.n, ez->HN.a, ws); ez->path.n += ez->nword;//diff
int32_t site = tn - 1 - thre;/**up bound; site:[tn - 1 - thre, tn - 1 + thre]**/
if(!done) {//diff
for (cut = pn - 1, i = 0; site < cut; i++) {
bd = (i>>bitw); i_bd = (i&bitz);
err += (((*ez).VP.a[bd]>>i_bd)&((w_sig)1));
err -= (((*ez).VN.a[bd]>>i_bd)&((w_sig)1));
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;
}
}
if((ez->te-ez->ts+1) != tn) {//diff
ez->path.n /= tn; ez->path.n *= (ez->te+1-ez->ts);//diff
}//diff
gen_trace(ez, thre, 1);//diff
return;
}
inline void ed_band_cal_extension_infi_1_w_trace(char *pstr, int32_t pn, char *tstr, int32_t tn, int32_t thre, int32_t *nword, bit_extz_t *ez)
{
int32_t done = 1;//diff
ez->cigar.n = 0;//diff
if(ez->err > thre) {//diff
init_base_ed(*ez, thre, pn, tn); ez->ps = ez->ts = INT32_MAX; ez->pe = pn-1; ez->te = tn-1;
if(pn > tn + thre) pn = tn + thre;
else if(tn > pn + thre) tn = pn + thre;
done = 0;//diff
} else if(ez->err == 0) {//diff
push_trace(&(ez->cigar), 0, ez->te+1-ez->ts); return;//diff
} else {
pn = ez->pe + 1 - ez->ps; tn = ez->te + 1 - ez->ts; //diff
}
int32_t i, err, tn0 = tn - 1, cut = thre+(thre<<1), bd, i_bd, k_bd, wz, wz1, ws, Peq_i;
int32_t poff, pe = pn-1, tmp_e = INT32_MAX, k, pidx = ez->pe, tidx = ez->te; w_sig c, ad, Peq_m;
if(nword) {
ez->nword = (*nword);
} else {
bd = (((thre)<<1)+1); ez->nword = ((bd>>bitw)+(!!(bd&bitz)));
}
resize_bit_extz_t((*ez), (thre));
wz = ws = sizeof(*(ez->a))*(ez->nword);//diff
memset((ez->Peq[0]).a, 0, wz);
memset((ez->Peq[1]).a, 0, wz);
memset((ez->Peq[2]).a, 0, wz);
memset((ez->Peq[3]).a, 0, wz);
memset((ez->Peq[4]).a, 0, wz);
bd = thre+1; bd = ((bd<=pn)?bd:pn); i_bd = thre;
for (i = 0; i < bd; i++, i_bd++) {
w_bit((ez->Peq)[seq_nt4_table[(uint8_t)(pstr)[pidx-i]]], (i_bd));
}
bd = thre+1, i_bd = thre;
memset((ez->Peq[4]).a, 0, wz);
err = thre;
w_infi_set_bit_lsub(ez->VN, thre, ez->nword); /**VN = (((Word)1)<<(thre))-1;**/
w_infi_set_bit_lsub(ez->VP, (thre<<1)+1, ez->nword); /**VP = (((Word)1)<<((thre<<1)+1))-1;**/
w_infi_self_xor(ez->VP, ez->VN, ez->nword, wz) /**VP ^= VN;**/
ez->path.n=(ez->nword*tn*5);//diff
kv_resize(w_sig, ez->path, ez->path.n); ez->path.n=0;//diff
i = 0;
/**for the incoming char/last char; mm = ((Word)1 << (thre<<1))**/
Peq_i = (((thre<<1))>>bitw); Peq_m = (((w_sig)1)<<(((thre<<1))&bitz));
while (i < tn0) {
ed_infi_core(ez->Peq, ez->VP, ez->VN, ez->X, ez->D0, ez->HN, ez->HP, (uint8_t)tstr[tidx-i], c, ad, wz, ez->nword);
if (!(ez->D0.a[0]&(1ULL))) {
++err; if (err>cut) return;
}
if(!done) {//diff
poff = i-thre; k = i+thre-pe;/**poff:[i-thre, i+thre]**/
if(k >= 0) {
if(tmp_e == INT32_MAX) {
tmp_e = err;
for ((k) = 0; (poff) < (pe); (poff)++, (k)++) {
bd = (k>>bitw); k_bd = (k&bitz);
(tmp_e) += (((*ez).VP.a[bd]>>k_bd)&((w_sig)1));
(tmp_e) -= (((*ez).VN.a[bd]>>k_bd)&((w_sig)1));
}
} else {
k = (thre<<1) - k;
if(k >= 0) {
bd = (k>>bitw); k_bd = (k&bitz);
(tmp_e) += (((*ez).HP.a[bd]>>k_bd)&((w_sig)1));
(tmp_e) -= (((*ez).HN.a[bd]>>k_bd)&((w_sig)1));
}
}
if((tmp_e) <= (*ez).thre && (tmp_e) < (*ez).err) {
(*ez).err = tmp_e; (*ez).ps = pidx - pe; (*ez).ts = tidx-i;
}
}
}
// if(dbg_ext_err(i, thre, err, pe, &((*ez).VP), &((*ez).VN))!=tmp_e) {
// fprintf(stderr, "i::%d, tmp_e::%d, dbg_ext_err::%d\n", i, tmp_e, dbg_ext_err(i, thre, err, pe, &((*ez).VP), &((*ez).VN)));
// }
ed_infi_post_Peq(ez->Peq, wz, wz1, ez->nword);
++i; ++i_bd; c = 4;
if(i_bd < pn) c = seq_nt4_table[(uint8_t)pstr[pidx-i_bd]];
if(c < 4) ez->Peq[c].a[Peq_i]|=Peq_m;
memcpy(ez->path.a+ez->path.n, ez->D0.a, ws); ez->path.n += ez->nword;//diff
memcpy(ez->path.a+ez->path.n, ez->VP.a, ws); ez->path.n += ez->nword;//diff
memcpy(ez->path.a+ez->path.n, ez->VN.a, ws); ez->path.n += ez->nword;//diff
memcpy(ez->path.a+ez->path.n, ez->HP.a, ws); ez->path.n += ez->nword;//diff
memcpy(ez->path.a+ez->path.n, ez->HN.a, ws); ez->path.n += ez->nword;//diff
}
ed_infi_core(ez->Peq, ez->VP, ez->VN, ez->X, ez->D0, ez->HN, ez->HP, (uint8_t)tstr[tidx-i], c, ad, wz, ez->nword);
if (!(ez->D0.a[0]&(1ULL))) {
++err; if (err>cut) return;
}
memcpy(ez->path.a+ez->path.n, ez->D0.a, ws); ez->path.n += ez->nword;//diff
memcpy(ez->path.a+ez->path.n, ez->VP.a, ws); ez->path.n += ez->nword;//diff
memcpy(ez->path.a+ez->path.n, ez->VN.a, ws); ez->path.n += ez->nword;//diff
memcpy(ez->path.a+ez->path.n, ez->HP.a, ws); ez->path.n += ez->nword;//diff
memcpy(ez->path.a+ez->path.n, ez->HN.a, ws); ez->path.n += ez->nword;//diff
int32_t site = tn - 1 - thre;/**up bound; site:[tn - 1 - thre, tn - 1 + thre]**/
if(!done) {//diff
for (cut = pn - 1, i = 0; site < cut; i++) {
bd = (i>>bitw); i_bd = (i&bitz);
err += (((*ez).VP.a[bd]>>i_bd)&((w_sig)1));
err -= (((*ez).VN.a[bd]>>i_bd)&((w_sig)1));
site++;
if(err <= thre && err < ez->err) {
ez->err = err; ez->ps = pidx-site; ez->ts = tidx+1-tn;
}
}
if(err <= thre && err < ez->err) {
ez->err = err; ez->ps = pidx-site; ez->ts = tidx+1-tn;
}
}
if((ez->te-ez->ts+1) != tn) {//diff
ez->path.n /= tn; ez->path.n *= (ez->te+1-ez->ts);//diff
}//diff
poff = ez->ps; ez->ps = pidx - ez->pe; ez->pe = pidx - poff;//diff
gen_trace(ez, thre, 0);//diff
poff = ez->ps; ez->ps = pidx - ez->pe; ez->pe = pidx - poff;//diff
return;
}
inline void ed_band_cal_semi_infi_w_absent_diag(char *pstr, int32_t pn, char *tstr, int32_t tn, int32_t thre, int32_t abs_diag, int32_t *nword, bit_extz_t *ez)
{
init_base_ed(*ez, thre, pn, tn); ez->ps = ez->pe = -1; ez->ts = 0; ez->te = tn-1;
int32_t bd, i, err = abs_diag, i_bd, cut = thre+(thre<<1), tn0 = tn - 1, wz, wz1, Peq_i; w_sig c, ad, Peq_m;
if((pn > tn + cut) || (tn > pn + cut)) return;
if(nword) {
ez->nword = (*nword);
} else {
bd = (((thre)<<1)+1); ez->nword = ((bd>>bitw)+(!!(bd&bitz)));
}
resize_bit_extz_t((*ez), (thre));
wz = sizeof(*(ez->a))*(ez->nword);
memset((ez->Peq[0]).a, 0, wz);
memset((ez->Peq[1]).a, 0, wz);
memset((ez->Peq[2]).a, 0, wz);
memset((ez->Peq[3]).a, 0, wz);
memset((ez->Peq[4]).a, 0, wz);
memset((ez->VP).a, 0, wz);
w_infi_set_bit_lsub(ez->VN, abs_diag, ez->nword); /**VN = (((Word)1)<<(abs_diag))-1; ;**/
bd = ((thre<<1)+1)-abs_diag; bd = ((bd<=pn)?bd:pn); i_bd = abs_diag;
ed_init_core(i, bd, i_bd, pstr, ez->Peq);
i_bd = (thre<<1)-abs_diag;
memset((ez->Peq[4]).a, 0, wz);
i = 0;
/**for the incoming char/last char; mm = ((Word)1 << (thre<<1))**/
Peq_i = (((thre<<1))>>bitw); Peq_m = (((w_sig)1)<<(((thre<<1))&bitz));
while (i < tn0) {
ed_infi_core(ez->Peq, ez->VP, ez->VN, ez->X, ez->D0, ez->HN, ez->HP, (uint8_t)tstr[i], c, ad, wz, ez->nword);
if (!(ez->D0.a[0]&(1ULL))) {
++err; if (err>cut) return;
}
ed_infi_post_Peq(ez->Peq, wz, wz1, ez->nword);
++i; ++i_bd; c = 4;
if(i_bd < pn) c = seq_nt4_table[(uint8_t)pstr[i_bd]];
if(c < 4) ez->Peq[c].a[Peq_i]|=Peq_m;
}
ed_infi_core(ez->Peq, ez->VP, ez->VN, ez->X, ez->D0, ez->HN, ez->HP, (uint8_t)tstr[i], c, ad, wz, ez->nword);
if (!(ez->D0.a[0]&(1ULL))) {
++err; if (err>cut) return;
}
int32_t site = tn - 1 - abs_diag;/**up bound**/
/**in most cases, ai = (thre<<1)**/
int32_t ai = pn - tn + abs_diag, uge = INT32_MAX; i = 0;
for (i = 0; site < 0 && i < ai; i++, site++) {
bd = (i>>bitw); i_bd = (i&bitz);
err += (((*ez).VP.a[bd]>>i_bd)&((w_sig)1));
err -= (((*ez).VN.a[bd]>>i_bd)&((w_sig)1));
}
if ((err <= thre) && (err <= ez->err)) {
ez->err = err; ez->pe = site;
}
site -= i;
while (i < ai) {
bd = (i>>bitw); i_bd = (i&bitz);
err += (((*ez).VP.a[bd]>>i_bd)&((w_sig)1));
err -= (((*ez).VN.a[bd]>>i_bd)&((w_sig)1));
++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;
}
inline void ed_band_cal_semi_infi_w_absent_diag_trace(char *pstr, int32_t pn, char *tstr, int32_t tn, int32_t thre, int32_t abs_diag, int32_t *nword, bit_extz_t *ez)
{
ez->cigar.n = 0;//diff
if(ez->err > thre) {//diff
init_base_ed(*ez, thre, pn, tn); ez->ps = ez->pe = -1; ez->ts = 0; ez->te = tn-1;
} else if(ez->err == 0) {//diff
push_trace(&(ez->cigar), 0, ez->te+1-ez->ts); //diff
ez->ps = ez->pe - (ez->te-ez->ts);//diff
return;//diff
}
int32_t bd, i, err = abs_diag, i_bd, cut = thre+(thre<<1), tn0 = tn - 1, wz, wz1, ws, Peq_i; w_sig c, ad, Peq_m;
if((pn > tn + cut) || (tn > pn + cut)) return;
if(nword) {
ez->nword = (*nword);
} else {
bd = (((thre)<<1)+1); ez->nword = ((bd>>bitw)+(!!(bd&bitz)));
}
resize_bit_extz_t((*ez), (thre));
wz = ws = sizeof(*(ez->a))*(ez->nword);//diff
memset((ez->Peq[0]).a, 0, wz);
memset((ez->Peq[1]).a, 0, wz);
memset((ez->Peq[2]).a, 0, wz);
memset((ez->Peq[3]).a, 0, wz);
memset((ez->Peq[4]).a, 0, wz);
memset((ez->VP).a, 0, wz);
w_infi_set_bit_lsub(ez->VN, abs_diag, ez->nword); /**VN = (((Word)1)<<(abs_diag))-1; ;**/
bd = ((thre<<1)+1)-abs_diag; bd = ((bd<=pn)?bd:pn); i_bd = abs_diag;
ed_init_core(i, bd, i_bd, pstr, ez->Peq);
i_bd = (thre<<1)-abs_diag;
memset((ez->Peq[4]).a, 0, wz);
ez->path.n=(ez->nword*tn*5);//diff
kv_resize(w_sig, ez->path, ez->path.n); ez->path.n=0;//diff
i = 0;
/**for the incoming char/last char; mm = ((Word)1 << (thre<<1))**/
Peq_i = (((thre<<1))>>bitw); Peq_m = (((w_sig)1)<<(((thre<<1))&bitz));
while (i < tn0) {
ed_infi_core(ez->Peq, ez->VP, ez->VN, ez->X, ez->D0, ez->HN, ez->HP, (uint8_t)tstr[i], c, ad, wz, ez->nword);
if (!(ez->D0.a[0]&(1ULL))) {
++err; if (err>cut) return;
}
ed_infi_post_Peq(ez->Peq, wz, wz1, ez->nword);
++i; ++i_bd; c = 4;
if(i_bd < pn) c = seq_nt4_table[(uint8_t)pstr[i_bd]];
if(c < 4) ez->Peq[c].a[Peq_i]|=Peq_m;
memcpy(ez->path.a+ez->path.n, ez->D0.a, ws); ez->path.n += ez->nword;//diff
memcpy(ez->path.a+ez->path.n, ez->VP.a, ws); ez->path.n += ez->nword;//diff
memcpy(ez->path.a+ez->path.n, ez->VN.a, ws); ez->path.n += ez->nword;//diff
memcpy(ez->path.a+ez->path.n, ez->HP.a, ws); ez->path.n += ez->nword;//diff
memcpy(ez->path.a+ez->path.n, ez->HN.a, ws); ez->path.n += ez->nword;//diff
}
ed_infi_core(ez->Peq, ez->VP, ez->VN, ez->X, ez->D0, ez->HN, ez->HP, (uint8_t)tstr[i], c, ad, wz, ez->nword);
if (!(ez->D0.a[0]&(1ULL))) {
++err; if (err>cut) return;
}
memcpy(ez->path.a+ez->path.n, ez->D0.a, ws); ez->path.n += ez->nword;//diff
memcpy(ez->path.a+ez->path.n, ez->VP.a, ws); ez->path.n += ez->nword;//diff
memcpy(ez->path.a+ez->path.n, ez->VN.a, ws); ez->path.n += ez->nword;//diff
memcpy(ez->path.a+ez->path.n, ez->HP.a, ws); ez->path.n += ez->nword;//diff
memcpy(ez->path.a+ez->path.n, ez->HN.a, ws); ez->path.n += ez->nword;//diff
int32_t site = tn - 1 - abs_diag;/**up bound**/
/**in most cases, ai = (thre<<1)**/
int32_t ai = pn - tn + abs_diag, uge = INT32_MAX; i = 0;
if(ez->err > thre) {//diff
for (i = 0; site < 0 && i < ai; i++, site++) {
bd = (i>>bitw); i_bd = (i&bitz);
err += (((*ez).VP.a[bd]>>i_bd)&((w_sig)1));
err -= (((*ez).VN.a[bd]>>i_bd)&((w_sig)1));
}
if ((err <= thre) && (err <= ez->err)) {
ez->err = err; ez->pe = site;
}
site -= i;
while (i < ai) {
bd = (i>>bitw); i_bd = (i&bitz);
err += (((*ez).VP.a[bd]>>i_bd)&((w_sig)1));
err -= (((*ez).VN.a[bd]>>i_bd)&((w_sig)1));
++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;
}
gen_trace(ez, abs_diag, 1);//diff
}
#define ed_core_64(Peq, VP, VN, X, D0, HN, HP, z) { \
/**X = Peq[seq_nt4_table[(uint8_t)tstr[i]]] | VN;**/\
(X) = (Peq)[(seq_nt4_table[(z)])]|(VN);\
(D0) = (((VP) + ((X)&(VP))) ^ (VP)) | (X);\
(HN) = (VP)&(D0);\
(HP) = (VN) | ~((VP) | (D0));\
(X) = (D0) >> 1;\
(VN) = (X)&(HP);\
(VP) = (HN) | ~((X) | (HP));\
}
inline void ed_band_cal_global_64_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;
if((pn > tn + thre) || (tn > pn + thre)) return;
int32_t i, err, tn0 = tn - 1, cut = thre+(thre<<1), bd, i_bd;
Word c, Peq[5] = {0}, VP, VN, X, D0, HN, HP, mm;
bd = thre+1; bd = ((bd<=pn)?bd:pn); i_bd = thre;
for (i = 0, mm = (((Word)1)<<i_bd); i < bd; i++) {
Peq[seq_nt4_table[(uint8_t)pstr[i]]] |= mm; mm <<= 1;
}
bd = thre+1, i_bd = thre; Peq[4] = 0; err = thre;
VN = (((Word)1)<<(thre))-1; VP = (((Word)1)<<((thre<<1)+1))-1; VP ^= VN;
i = 0; mm = ((Word)1 << (thre<<1));///for the incoming char/last char
while (i < tn0) {
// fprintf(stderr, "\ni::%d\n", i);
// prt_vector(Peq, VP, VN, X, D0, HN, HP, (((thre<<1))+1));
ed_core_64(Peq, VP, VN, X, D0, HN, HP, (uint8_t)tstr[i]);
if (!(D0&(1ULL))) {
++err; if (err>cut) return;
}
Peq[0] >>= 1; Peq[1] >>= 1; Peq[2] >>= 1; Peq[3] >>= 1;
++i; ++i_bd;
if(i_bd < pn) {
c = seq_nt4_table[(uint8_t)pstr[i_bd]];
if(c < 4) Peq[c] |= mm;
// fprintf(stderr, "c::%lu\n", c);
// print_bit(Peq[c], (((thre<<1))+1), "Peq[c]");
}
}
ed_core_64(Peq, VP, VN, X, D0, HN, HP, (uint8_t)tstr[i]);
if (!(D0&(1ULL))) {
++err; if (err>cut) return;
}
int32_t site = tn - 1 - thre;/**up bound**/\
for (cut = pn - 1; site < cut; site++) {
err += VP&(1ULL); VP >>= 1; err -= VN&(1ULL); VN >>= 1;
}
if (site == cut && err <= thre) {
ez->err = err;
ez->pe = pn-1; ez->te = tn-1;
}
return;
}
inline void ed_band_cal_semi_64_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;
Word c, Peq[5] = {0}, VP = 0, VN = 0, X, D0, HN, HP, mm;
int32_t bd, i, err = 0, i_bd, last_high = (thre<<1), tn0 = tn - 1, cut = thre+last_high;
if((pn > tn + cut) || (tn > pn + cut)) return;
bd = (thre<<1)+1; bd = ((bd<=pn)?bd:pn);
for (i = 0, mm = 1; i < bd; i++) {
Peq[seq_nt4_table[(uint8_t)pstr[i]]] |= mm; mm <<= 1;
}
bd = (thre<<1)+1, i_bd = (thre<<1);
i = 0; Peq[4] = 0; mm = ((Word)1 << (thre<<1));///for the incoming char/last char**
while (i < tn0) {
ed_core_64(Peq, VP, VN, X, D0, HN, HP, (uint8_t)tstr[i]);
if (!(D0&(1ULL))) {
++err; if (err>cut) return;
}
Peq[0] >>= 1; Peq[1] >>= 1; Peq[2] >>= 1; Peq[3] >>= 1;
++i; ++i_bd; c = 4;
if(i_bd < pn) c = seq_nt4_table[(uint8_t)pstr[i_bd]];
if(c < 4) Peq[c] |= mm;
}
ed_core_64(Peq, VP, VN, X, D0, HN, HP, (uint8_t)tstr[i]);
if (!(D0&(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 -= ((VN >> i)&(1ULL)); ++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;
}
inline void ed_band_cal_extension_64_0_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; ez->pe = ez->te = -1;
if(pn > tn + thre) pn = tn + thre;
else if(tn > pn + thre) tn = pn + thre;
int32_t i, err, tn0 = tn - 1, cut = thre+(thre<<1), bd, i_bd, poff, pe = pn-1, tmp_e = INT32_MAX, k;
Word c, Peq[5] = {0}, VP, VN, X, D0, HN, HP, mm;
bd = thre+1; bd = ((bd<=pn)?bd:pn); i_bd = thre;
for (i = 0, mm = (((Word)1)<<i_bd); i < bd; i++) {
Peq[seq_nt4_table[(uint8_t)pstr[i]]] |= mm; mm <<= 1;
}
bd = thre+1, i_bd = thre; Peq[4] = 0; err = thre;
VN = (((Word)1)<<(thre))-1; VP = (((Word)1)<<((thre<<1)+1))-1; VP ^= VN;
i = 0; mm = ((Word)1 << (thre<<1));
// X = D0 = HN = HP = mm = 0;//for debug
while (i < tn0) {
// fprintf(stderr, "i::%d\n", i);
// prt_vector(Peq, VP, VN, X, D0, HN, HP, ((thre<<1)+1));
ed_core_64(Peq, VP, VN, X, D0, HN, HP, (uint8_t)tstr[i]);
if (!(D0&(1ULL))) {
++err; if (err>cut) return;
}
{
poff = i-thre; k = i+thre-pe;/**poff:[i-thre, i+thre]**/
if(k >= 0) {
if(tmp_e == INT32_MAX) {
tmp_e = err;
for (k = 0; poff < pe; poff++, (k)++) {
tmp_e += ((VP>>k)&(1ULL)); tmp_e -= ((VN>>k)&(1ULL));
}
} else {
k = (thre<<1) - k;
if(k >= 0) {
tmp_e += ((HP>>k)&(1ULL)); tmp_e -= ((HN>>k)&(1ULL));
}
}
if(tmp_e <= (*ez).thre && tmp_e < (*ez).err) {
(*ez).err = tmp_e; (*ez).pe = pe; (*ez).te = i;
}
}
}
// fprintf(stderr, "i::%d, tmp_e::%d, err::%d\n", i, tmp_e, err);
Peq[0] >>= 1; Peq[1] >>= 1; Peq[2] >>= 1; Peq[3] >>= 1;
++i; ++i_bd;
if(i_bd < pn) {
c = seq_nt4_table[(uint8_t)pstr[i_bd]];
if(c < 4) Peq[c] |= mm;
}
}
ed_core_64(Peq, VP, VN, X, D0, HN, HP, (uint8_t)tstr[i]);
if (!(D0&(1ULL))) {
++err; if (err>cut) return;
}
int32_t site = tn - 1 - thre;/**up bound; site:[tn - 1 - thre, tn - 1 + thre]**/\
for (cut = pn - 1; site < cut; ) {
err += VP&(1ULL); VP >>= 1; err -= VN&(1ULL); VN >>= 1;
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_extension_64_1_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 = INT32_MAX; ez->pe = pn-1; ez->te = tn-1;
if(pn > tn + thre) pn = tn + thre;
else if(tn > pn + thre) tn = pn + thre;
int32_t i, err, tn0 = tn - 1, cut = thre+(thre<<1), bd, i_bd;
int32_t poff, pe = pn-1, tmp_e = INT32_MAX, k, pidx = ez->pe, tidx = ez->te;
Word c, Peq[5] = {0}, VP, VN, X, D0, HN, HP, mm;
bd = thre+1; bd = ((bd<=pn)?bd:pn); i_bd = thre;
for (i = 0, mm = (((Word)1)<<i_bd); i < bd; i++) {
Peq[seq_nt4_table[(uint8_t)pstr[pidx-i]]] |= mm; mm <<= 1;
}
bd = thre+1, i_bd = thre; Peq[4] = 0; err = thre;
VN = (((Word)1)<<(thre))-1; VP = (((Word)1)<<((thre<<1)+1))-1; VP ^= VN;
i = 0; mm = ((Word)1 << (thre<<1));
// X = D0 = HN = HP = mm = 0;//for debug
while (i < tn0) {
// fprintf(stderr, "i::%d\n", i);
// prt_vector(Peq, VP, VN, X, D0, HN, HP, ((thre<<1)+1));
ed_core_64(Peq, VP, VN, X, D0, HN, HP, (uint8_t)tstr[tidx-i]);
if (!(D0&(1ULL))) {
++err; if (err>cut) return;
}
{
poff = i-thre; k = i+thre-pe;/**poff:[i-thre, i+thre]**/
if(k >= 0) {
if(tmp_e == INT32_MAX) {
tmp_e = err;
for (k = 0; poff < pe; poff++, (k)++) {
tmp_e += ((VP>>k)&(1ULL)); tmp_e -= ((VN>>k)&(1ULL));
}
} else {
k = (thre<<1) - k;
if(k >= 0) {
tmp_e += ((HP>>k)&(1ULL)); tmp_e -= ((HN>>k)&(1ULL));
}
}
if(tmp_e <= (*ez).thre && tmp_e < (*ez).err) {
(*ez).err = tmp_e; (*ez).ps = pidx - pe; (*ez).ts = tidx-i;
}
}
}
// fprintf(stderr, "i::%d, tmp_e::%d, err::%d\n", i, tmp_e, err);
Peq[0] >>= 1; Peq[1] >>= 1; Peq[2] >>= 1; Peq[3] >>= 1;
++i; ++i_bd;
if(i_bd < pn) {
c = seq_nt4_table[(uint8_t)pstr[pidx-i_bd]];
if(c < 4) Peq[c] |= mm;
}
}
ed_core_64(Peq, VP, VN, X, D0, HN, HP, (uint8_t)tstr[tidx-i]);
if (!(D0&(1ULL))) {
++err; if (err>cut) return;
}
int32_t site = tn - 1 - thre;/**up bound; site:[tn - 1 - thre, tn - 1 + thre]**/\
for (cut = pn - 1; site < cut; ) {
err += VP&(1ULL); VP >>= 1; err -= VN&(1ULL); VN >>= 1;
site++;
if(err <= thre && err < ez->err) {
ez->err = err; ez->ps = pidx-site; ez->ts = tidx+1-tn;
}
}
if(err <= thre && err < ez->err) {
ez->err = err; ez->ps = pidx-site; ez->ts = tidx+1-tn;
}
return;
}
inline void ed_band_cal_global_64_w_trace(char *pstr, int32_t pn, char *tstr, int32_t tn, int32_t thre, bit_extz_t *ez)
{
ez->cigar.n = 0; ez->nword = 1;//diff
if(ez->err > thre) {//diff
init_base_ed(*ez, thre, pn, tn); ez->ps = ez->ts = 0;//diff
} else if(ez->err == 0) {//diff
push_trace(&(ez->cigar), 0, ez->te+1-ez->ts); return;//diff
}
if((pn > tn + thre) || (tn > pn + thre)) return;
int32_t i, err, tn0 = tn - 1, cut = thre+(thre<<1), bd, i_bd;
w_sig c, Peq[5] = {0}, VP, VN, X, D0, HN, HP, mm;
bd = thre+1; bd = ((bd<=pn)?bd:pn); i_bd = thre;
for (i = 0, mm = (((w_sig)1)<<i_bd); i < bd; i++) {
Peq[seq_nt4_table[(uint8_t)pstr[i]]] |= mm; mm <<= 1;
}
bd = thre+1, i_bd = thre; Peq[4] = 0; err = thre;
VN = (((w_sig)1)<<(thre))-1; VP = (((w_sig)1)<<((thre<<1)+1))-1; VP ^= VN;
ez->path.n=(ez->nword*tn*5);//diff
kv_resize(w_sig, ez->path, ez->path.n); ez->path.n=0;//diff
i = 0; mm = ((w_sig)1 << (thre<<1));///for the incoming char/last char
while (i < tn0) {
// fprintf(stderr, "\ni::%d\n", i);
// prt_vector(Peq, VP, VN, X, D0, HN, HP, (((thre<<1))+1));
ed_core_64(Peq, VP, VN, X, D0, HN, HP, (uint8_t)tstr[i]);
if (!(D0&(1ULL))) {
++err; if (err>cut) return;
}
Peq[0] >>= 1; Peq[1] >>= 1; Peq[2] >>= 1; Peq[3] >>= 1;
++i; ++i_bd;
if(i_bd < pn) {
c = seq_nt4_table[(uint8_t)pstr[i_bd]];
if(c < 4) Peq[c] |= mm;
}
ez->path.a[ez->path.n++] = D0;//diff
ez->path.a[ez->path.n++] = VP;//diff
ez->path.a[ez->path.n++] = VN;//diff
ez->path.a[ez->path.n++] = HP;//diff
ez->path.a[ez->path.n++] = HN;//diff
}
ed_core_64(Peq, VP, VN, X, D0, HN, HP, (uint8_t)tstr[i]);
if (!(D0&(1ULL))) {
++err; if (err>cut) return;
}
ez->path.a[ez->path.n++] = D0;//diff
ez->path.a[ez->path.n++] = VP;//diff
ez->path.a[ez->path.n++] = VN;//diff
ez->path.a[ez->path.n++] = HP;//diff
ez->path.a[ez->path.n++] = HN;//diff
int32_t site = tn - 1 - thre;/**up bound**/\
if(ez->err > thre) {//diff
for (cut = pn - 1; site < cut; site++) {
err += VP&(1ULL); VP >>= 1; err -= VN&(1ULL); VN >>= 1;
}
if (site == cut && err <= thre) {
ez->err = err;
ez->pe = pn-1; ez->te = tn-1;
}
}
///should update ez->path.n for extension
gen_trace(ez, thre, 1);//diff
return;
}
inline void ed_band_cal_semi_64_w_trace(char *pstr, int32_t pn, char *tstr, int32_t tn, int32_t thre, bit_extz_t *ez)
{
ez->cigar.n = 0; ez->nword = 1;//diff
if(ez->err > thre) {//diff
init_base_ed(*ez, thre, pn, tn); ez->ps = ez->pe = -1; ez->ts = 0; ez->te = tn-1;//diff
} else if(ez->err == 0) {//diff
push_trace(&(ez->cigar), 0, ez->te+1-ez->ts); //diff
ez->ps = ez->pe - (ez->te-ez->ts);//diff
return;//diff
}
Word c, Peq[5] = {0}, VP = 0, VN = 0, X, D0, HN, HP, mm;
int32_t bd, i, err = 0, i_bd, last_high = (thre<<1), tn0 = tn - 1, cut = thre+last_high;
if((pn > tn + cut) || (tn > pn + cut)) return;
bd = (thre<<1)+1; bd = ((bd<=pn)?bd:pn);
for (i = 0, mm = 1; i < bd; i++) {
Peq[seq_nt4_table[(uint8_t)pstr[i]]] |= mm; mm <<= 1;
}
bd = (thre<<1)+1, i_bd = (thre<<1);
ez->path.n=(ez->nword*tn*5);//diff
kv_resize(w_sig, ez->path, ez->path.n); ez->path.n=0;//diff
i = 0; Peq[4] = 0; mm = ((Word)1 << (thre<<1));///for the incoming char/last char**
while (i < tn0) {
ed_core_64(Peq, VP, VN, X, D0, HN, HP, (uint8_t)tstr[i]);
if (!(D0&(1ULL))) {
++err; if (err>cut) return;
}
Peq[0] >>= 1; Peq[1] >>= 1; Peq[2] >>= 1; Peq[3] >>= 1;
++i; ++i_bd; c = 4;
if(i_bd < pn) c = seq_nt4_table[(uint8_t)pstr[i_bd]];
if(c < 4) Peq[c] |= mm;
ez->path.a[ez->path.n++] = D0;//diff
ez->path.a[ez->path.n++] = VP;//diff
ez->path.a[ez->path.n++] = VN;//diff
ez->path.a[ez->path.n++] = HP;//diff
ez->path.a[ez->path.n++] = HN;//diff
}
ed_core_64(Peq, VP, VN, X, D0, HN, HP, (uint8_t)tstr[i]);
if (!(D0&(1ULL))) {
++err; if (err>cut) return;
}
ez->path.a[ez->path.n++] = D0;//diff
ez->path.a[ez->path.n++] = VP;//diff
ez->path.a[ez->path.n++] = VN;//diff
ez->path.a[ez->path.n++] = HP;//diff
ez->path.a[ez->path.n++] = HN;//diff
int32_t site = tn - 1;/**up bound**/
/**in most cases, ai = (thre<<1)**/
int32_t ai = pn - tn, uge = INT32_MAX;
if(ez->err > thre) {//diff
if ((err <= thre) && (err <= ez->err)) {
ez->err = err; ez->pe = site;
}
i = 0;
while (i < ai) {
err += ((VP >> i)&(1ULL)); err -= ((VN >> i)&(1ULL)); ++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;
}
///should update ez->path.n for extension
gen_trace(ez, 0, 1);//diff
}
inline void ed_band_cal_extension_64_0_w_trace(char *pstr, int32_t pn, char *tstr, int32_t tn, int32_t thre, bit_extz_t *ez)
{
int32_t done = 1;//diff
ez->cigar.n = 0; ez->nword = 1;//diff
if(ez->err > thre) {//diff
init_base_ed(*ez, thre, pn, tn); ez->ps = ez->ts = 0; ez->pe = ez->te = -1;
if(pn > tn + thre) pn = tn + thre;
else if(tn > pn + thre) tn = pn + thre;
done = 0;//diff
} else if(ez->err == 0) {//diff
push_trace(&(ez->cigar), 0, ez->te+1-ez->ts); return;//diff
} else {
pn = ez->pe + 1 - ez->ps; tn = ez->te + 1 - ez->ts; //diff
}
int32_t i, err, tn0 = tn - 1, cut = thre+(thre<<1), bd, i_bd, poff, pe = pn-1, tmp_e = INT32_MAX, k;
Word c, Peq[5] = {0}, VP, VN, X, D0, HN, HP, mm;
bd = thre+1; bd = ((bd<=pn)?bd:pn); i_bd = thre;
for (i = 0, mm = (((Word)1)<<i_bd); i < bd; i++) {
Peq[seq_nt4_table[(uint8_t)pstr[i]]] |= mm; mm <<= 1;
}
bd = thre+1, i_bd = thre; Peq[4] = 0; err = thre;
VN = (((Word)1)<<(thre))-1; VP = (((Word)1)<<((thre<<1)+1))-1; VP ^= VN;
ez->path.n=(ez->nword*tn*5);//diff
kv_resize(w_sig, ez->path, ez->path.n); ez->path.n=0;//diff
i = 0; mm = ((Word)1 << (thre<<1));
// X = D0 = HN = HP = mm = 0;//for debug
while (i < tn0) {
// fprintf(stderr, "i::%d\n", i);
// prt_vector(Peq, VP, VN, X, D0, HN, HP, ((thre<<1)+1));
ed_core_64(Peq, VP, VN, X, D0, HN, HP, (uint8_t)tstr[i]);
if (!(D0&(1ULL))) {
++err; if (err>cut) return;
}
if(!done) {//diff
poff = i-thre; k = i+thre-pe;/**poff:[i-thre, i+thre]**/
if(k >= 0) {
if(tmp_e == INT32_MAX) {
tmp_e = err;
for (k = 0; poff < pe; poff++, (k)++) {
tmp_e += ((VP>>k)&(1ULL)); tmp_e -= ((VN>>k)&(1ULL));
}
} else {
k = (thre<<1) - k;
if(k >= 0) {
tmp_e += ((HP>>k)&(1ULL)); tmp_e -= ((HN>>k)&(1ULL));
}
}
if(tmp_e <= (*ez).thre && tmp_e < (*ez).err) {
(*ez).err = tmp_e; (*ez).pe = pe; (*ez).te = i;
}
// fprintf(stderr, "i::%d, (*ez).err::%d, (*ez).pe::%d, (*ez).te::%d, thre::%d, err::%d, tmp_e::%d, poff::%d, k::%d, pe::%d\n",
// i, (*ez).err, (*ez).pe, (*ez).te, thre, err, tmp_e, i-thre, i+thre-pe, pe);
}
}
Peq[0] >>= 1; Peq[1] >>= 1; Peq[2] >>= 1; Peq[3] >>= 1;
++i; ++i_bd;
if(i_bd < pn) {
c = seq_nt4_table[(uint8_t)pstr[i_bd]];
if(c < 4) Peq[c] |= mm;
}
// if(((ez->path.n+5)>(ez->nword*tn*5))||((ez->path.n+5)>(ez->path.m))) {
// fprintf(stderr, "[M::%s::] pn::%d, tn::%d\n", __func__, pn, tn);
// }
ez->path.a[ez->path.n++] = D0;//diff
ez->path.a[ez->path.n++] = VP;//diff
ez->path.a[ez->path.n++] = VN;//diff
ez->path.a[ez->path.n++] = HP;//diff
ez->path.a[ez->path.n++] = HN;//diff
}
ed_core_64(Peq, VP, VN, X, D0, HN, HP, (uint8_t)tstr[i]);
if (!(D0&(1ULL))) {
++err; if (err>cut) return;
}
// if(((ez->path.n+5)>(ez->nword*tn*5))||((ez->path.n+5)>(ez->path.m))) {
// fprintf(stderr, "[M::%s::] pn::%d, tn::%d\n", __func__, pn, tn);
// }
ez->path.a[ez->path.n++] = D0;//diff
ez->path.a[ez->path.n++] = VP;//diff
ez->path.a[ez->path.n++] = VN;//diff
ez->path.a[ez->path.n++] = HP;//diff
ez->path.a[ez->path.n++] = HN;//diff
int32_t site = tn - 1 - thre;/**up bound; site:[tn - 1 - thre, tn - 1 + thre]**/
if(!done) {//diff
for (cut = pn - 1; site < cut; ) {
err += VP&(1ULL); VP >>= 1; err -= VN&(1ULL); VN >>= 1;
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;
}
}
if((ez->te-ez->ts+1) != tn) {//diff
ez->path.n /= tn; ez->path.n *= (ez->te+1-ez->ts);//diff
}//diff
gen_trace(ez, thre, 1);//diff
return;
}
inline void ed_band_cal_extension_64_1_w_trace(char *pstr, int32_t pn, char *tstr, int32_t tn, int32_t thre, bit_extz_t *ez)
{
int32_t done = 1;//diff
ez->cigar.n = 0; ez->nword = 1;//diff
if(ez->err > thre) {//diff
init_base_ed(*ez, thre, pn, tn); ez->ps = ez->ts = INT32_MAX; ez->pe = pn-1; ez->te = tn-1;
if(pn > tn + thre) pn = tn + thre;
else if(tn > pn + thre) tn = pn + thre;
done = 0;//diff
} else if(ez->err == 0) {//diff
push_trace(&(ez->cigar), 0, ez->te+1-ez->ts); return;//diff
} else {
pn = ez->pe + 1 - ez->ps; tn = ez->te + 1 - ez->ts; //diff
}
int32_t i, err, tn0 = tn - 1, cut = thre+(thre<<1), bd, i_bd;
int32_t poff, pe = pn-1, tmp_e = INT32_MAX, k, pidx = ez->pe, tidx = ez->te;
Word c, Peq[5] = {0}, VP, VN, X, D0, HN, HP, mm;
bd = thre+1; bd = ((bd<=pn)?bd:pn); i_bd = thre;
for (i = 0, mm = (((Word)1)<<i_bd); i < bd; i++) {
Peq[seq_nt4_table[(uint8_t)pstr[pidx-i]]] |= mm; mm <<= 1;
}
bd = thre+1, i_bd = thre; Peq[4] = 0; err = thre;
VN = (((Word)1)<<(thre))-1; VP = (((Word)1)<<((thre<<1)+1))-1; VP ^= VN;
ez->path.n=(ez->nword*tn*5);//diff
kv_resize(w_sig, ez->path, ez->path.n); ez->path.n=0;//diff
i = 0; mm = ((Word)1 << (thre<<1));
// X = D0 = HN = HP = mm = 0;//for debug
while (i < tn0) {
// fprintf(stderr, "i::%d\n", i);
// prt_vector(Peq, VP, VN, X, D0, HN, HP, ((thre<<1)+1));
ed_core_64(Peq, VP, VN, X, D0, HN, HP, (uint8_t)tstr[tidx-i]);
if (!(D0&(1ULL))) {
++err; if (err>cut) return;
}
if(!done) {//diff
poff = i-thre; k = i+thre-pe;/**poff:[i-thre, i+thre]**/
if(k >= 0) {
if(tmp_e == INT32_MAX) {
tmp_e = err;
for (k = 0; poff < pe; poff++, (k)++) {
tmp_e += ((VP>>k)&(1ULL)); tmp_e -= ((VN>>k)&(1ULL));
}
} else {
k = (thre<<1) - k;
if(k >= 0) {
tmp_e += ((HP>>k)&(1ULL)); tmp_e -= ((HN>>k)&(1ULL));
}
}
if(tmp_e <= (*ez).thre && tmp_e < (*ez).err) {
(*ez).err = tmp_e; (*ez).ps = pidx - pe; (*ez).ts = tidx-i;
}
}
}
// fprintf(stderr, "i::%d, tmp_e::%d, err::%d\n", i, tmp_e, err);
Peq[0] >>= 1; Peq[1] >>= 1; Peq[2] >>= 1; Peq[3] >>= 1;
++i; ++i_bd;
if(i_bd < pn) {
c = seq_nt4_table[(uint8_t)pstr[pidx-i_bd]];
if(c < 4) Peq[c] |= mm;
}
ez->path.a[ez->path.n++] = D0;//diff
ez->path.a[ez->path.n++] = VP;//diff
ez->path.a[ez->path.n++] = VN;//diff
ez->path.a[ez->path.n++] = HP;//diff
ez->path.a[ez->path.n++] = HN;//diff
}
ed_core_64(Peq, VP, VN, X, D0, HN, HP, (uint8_t)tstr[tidx-i]);
if (!(D0&(1ULL))) {
++err; if (err>cut) return;
}
ez->path.a[ez->path.n++] = D0;//diff
ez->path.a[ez->path.n++] = VP;//diff
ez->path.a[ez->path.n++] = VN;//diff
ez->path.a[ez->path.n++] = HP;//diff
ez->path.a[ez->path.n++] = HN;//diff
int32_t site = tn - 1 - thre;/**up bound; site:[tn - 1 - thre, tn - 1 + thre]**/\
if(!done) {//diff
for (cut = pn - 1; site < cut; ) {
err += VP&(1ULL); VP >>= 1; err -= VN&(1ULL); VN >>= 1;
site++;
if(err <= thre && err < ez->err) {
ez->err = err; ez->ps = pidx-site; ez->ts = tidx+1-tn;
}
}
if(err <= thre && err < ez->err) {
ez->err = err; ez->ps = pidx-site; ez->ts = tidx+1-tn;
}
}
if((ez->te-ez->ts+1) != tn) {//diff
ez->path.n /= tn; ez->path.n *= (ez->te+1-ez->ts);//diff
}//diff
poff = ez->ps; ez->ps = pidx - ez->pe; ez->pe = pidx - poff;//diff
gen_trace(ez, thre, 0);//diff
poff = ez->ps; ez->ps = pidx - ez->pe; ez->pe = pidx - poff;//diff
return;
}
inline void ed_band_cal_semi_64_w_absent_diag(char *pstr, int32_t pn, char *tstr, int32_t tn, int32_t thre, int32_t abs_diag, bit_extz_t *ez)
{
init_base_ed(*ez, thre, pn, tn); ez->ps = ez->pe = -1; ez->ts = 0; ez->te = tn-1;
Word c, Peq[5] = {0}, VP = 0, VN, X, D0, HN, HP, mm;
int32_t bd, i, err = abs_diag, i_bd, last_high = (thre<<1), tn0 = tn - 1, cut = thre+last_high;
if((pn > tn + cut) || (tn > pn + cut)) return;
bd = ((thre<<1)+1)-abs_diag; bd = ((bd<=pn)?bd:pn); i_bd = abs_diag;
for (i = 0, mm = (((Word)1)<<i_bd); i < bd; i++) {
Peq[seq_nt4_table[(uint8_t)pstr[i]]] |= mm; mm <<= 1;
}
i_bd = (thre<<1)-abs_diag; VN = (((Word)1)<<(abs_diag))-1;
i = 0; Peq[4] = 0; mm = ((Word)1 << (thre<<1));///for the incoming char/last char**
while (i < tn0) {
ed_core_64(Peq, VP, VN, X, D0, HN, HP, (uint8_t)tstr[i]);
if (!(D0&(1ULL))) {
++err; if (err>cut) return;
}
Peq[0] >>= 1; Peq[1] >>= 1; Peq[2] >>= 1; Peq[3] >>= 1;
++i; ++i_bd; c = 4;
if(i_bd < pn) c = seq_nt4_table[(uint8_t)pstr[i_bd]];
if(c < 4) Peq[c] |= mm;
}
ed_core_64(Peq, VP, VN, X, D0, HN, HP, (uint8_t)tstr[i]);
if (!(D0&(1ULL))) {
++err; if (err>cut) return;
}
int32_t site = tn - 1 - abs_diag;/**up bound**/
/**in most cases, ai = (thre<<1)**/
int32_t ai = pn - tn + abs_diag, uge = INT32_MAX; i = 0;
for (i = 0; site < 0 && i < ai; i++, site++) {
err += ((VP >> i)&(1ULL)); err -= ((VN >> i)&(1ULL));
}
if ((err <= thre) && (err <= ez->err)) {
ez->err = err; ez->pe = site;
}
site -= i;
while (i < ai) {
err += ((VP >> i)&(1ULL)); err -= ((VN >> i)&(1ULL)); ++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;
}
inline void ed_band_cal_semi_64_w_absent_diag_trace(char *pstr, int32_t pn, char *tstr, int32_t tn, int32_t thre, int32_t abs_diag, bit_extz_t *ez)
{
ez->cigar.n = 0; ez->nword = 1;//diff
if(ez->err > thre) {//diff
init_base_ed(*ez, thre, pn, tn); ez->ps = ez->pe = -1; ez->ts = 0; ez->te = tn-1;//diff
} else if(ez->err == 0) {//diff
push_trace(&(ez->cigar), 0, ez->te+1-ez->ts); //diff
ez->ps = ez->pe - (ez->te-ez->ts);//diff
return;//diff
}
Word c, Peq[5] = {0}, VP = 0, VN, X, D0, HN, HP, mm;
int32_t bd, i, err = abs_diag, i_bd, last_high = (thre<<1), tn0 = tn - 1, cut = thre+last_high;
if((pn > tn + cut) || (tn > pn + cut)) return;
bd = ((thre<<1)+1)-abs_diag; bd = ((bd<=pn)?bd:pn); i_bd = abs_diag;
for (i = 0, mm = (((Word)1)<<i_bd); i < bd; i++) {
Peq[seq_nt4_table[(uint8_t)pstr[i]]] |= mm; mm <<= 1;
}
i_bd = (thre<<1)-abs_diag; VN = (((Word)1)<<(abs_diag))-1;
ez->path.n=(ez->nword*tn*5);//diff
kv_resize(w_sig, ez->path, ez->path.n); ez->path.n=0;//diff
i = 0; Peq[4] = 0; mm = ((Word)1 << (thre<<1));///for the incoming char/last char**
while (i < tn0) {
ed_core_64(Peq, VP, VN, X, D0, HN, HP, (uint8_t)tstr[i]);
if (!(D0&(1ULL))) {
++err; if (err>cut) return;
}
Peq[0] >>= 1; Peq[1] >>= 1; Peq[2] >>= 1; Peq[3] >>= 1;
++i; ++i_bd; c = 4;
if(i_bd < pn) c = seq_nt4_table[(uint8_t)pstr[i_bd]];
if(c < 4) Peq[c] |= mm;
ez->path.a[ez->path.n++] = D0;//diff
ez->path.a[ez->path.n++] = VP;//diff
ez->path.a[ez->path.n++] = VN;//diff
ez->path.a[ez->path.n++] = HP;//diff
ez->path.a[ez->path.n++] = HN;//diff
}
ed_core_64(Peq, VP, VN, X, D0, HN, HP, (uint8_t)tstr[i]);
if (!(D0&(1ULL))) {
++err; if (err>cut) return;
}
ez->path.a[ez->path.n++] = D0;//diff
ez->path.a[ez->path.n++] = VP;//diff
ez->path.a[ez->path.n++] = VN;//diff
ez->path.a[ez->path.n++] = HP;//diff
ez->path.a[ez->path.n++] = HN;//diff
int32_t site = tn - 1 - abs_diag;/**up bound**/
/**in most cases, ai = (thre<<1)**/
int32_t ai = pn - tn + abs_diag, uge = INT32_MAX; i = 0;
if(ez->err > thre) {//diff
for (i = 0; site < 0 && i < ai; i++, site++) {
err += ((VP >> i)&(1ULL)); err -= ((VN >> i)&(1ULL));
}
if ((err <= thre) && (err <= ez->err)) {
ez->err = err; ez->pe = site;
}
site -= i;
while (i < ai) {
err += ((VP >> i)&(1ULL)); err -= ((VN >> i)&(1ULL)); ++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;
}
///should update ez->path.n for extension
gen_trace(ez, abs_diag, 1);//diff
}
/**
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;
// bit_extz_t exz; ed_band_cal_semi_128bit(pattern, p_length, text, t_length, errthold, &exz);
// if(exz.err <= exz.thre) (*return_err) = exz.err;
// return exz.pe;
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;
}
// 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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