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hifiasm/Levenshtein_distance.h
Heng Li 03c8899a34 fixed clang warnings
2019-12-26 09:40:35 -05:00

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#ifndef __LEVENSHTEIN__
#define __LEVENSHTEIN__
#include <stdint.h>
#include "emmintrin.h"
#include "nmmintrin.h"
#include "smmintrin.h"
#include <immintrin.h>
#include <string.h>
#include <stdlib.h>
#include <stdio.h>
typedef uint64_t Word;
typedef uint32_t Word_32;
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 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;
}
}
}
/**
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;
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;
}
#endif
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