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hifiasm/Levenshtein_distance.h
T
Haoyu Cheng 1892b4d2db prefilter
2019-07-08 01:06:36 -04:00

589 lines
13 KiB
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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;
/**
pattern是长的那个，是y
p_length是长的那个的长度, p_length实际没用
text是短的那个，是x
t_length是短的那个的长度
errthold是阈值
return_err是编辑距离
返回值是结束位置
**/
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['A'] = (Word)0;
Peq['T'] = (Word)0;
Peq['G'] = (Word)0;
Peq['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[pattern[i]] = Peq[pattern[i]] | tmp_Peq_1;
tmp_Peq_1 = tmp_Peq_1 << 1;
}
///Peq['T'] = Peq['T'] | Peq['C'];
Peq_A = Peq['A'];
Peq_C = Peq['C'];
Peq_T = Peq['T'];
Peq_G = Peq['G'];
memset(Peq, 0, sizeof(Word)* 256);
Peq['A'] = Peq_A;
Peq['C'] = Peq_C;
Peq['T'] = Peq_T;
Peq['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)
{
///pattern[0]ÔÚPeq[2k], ¶øpattern[2k]ÔÚPeq[0]
X = Peq[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;
///¼´Ê¹È«²¿µÝ¼õ£¬Ò²¾Í¼õ2k
if ((err - last_high)>errthold)
{
///fprintf(stderr, "0 ######, i: %u\n", i);
return -1;
}
}
Peq['A'] = Peq['A'] >> 1;
Peq['C'] = Peq['C'] >> 1;
Peq['G'] = Peq['G'] >> 1;
Peq['T'] = Peq['T'] >> 1;
++i;
++i_bd;
Peq[pattern[i_bd]] = Peq[pattern[i_bd]] | Mask;
///Peq['T'] = Peq['T'] | Peq['C'];
}
X = Peq[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;
if ((err <= errthold) && (err<=*return_err))
{
*return_err = err;
return_site = site;
}
int i_last = i;
i = 0;
while (i<errthold)
{
err = err + ((VP >> i)&(Word)1);
err = err - ((VN >> i)&(Word)1);
++i;
if ((err <= errthold) && (err <= *return_err))
{
*return_err = err;
return_site = site + i;
}
}
unsigned int ungap_err;
ungap_err = err;
while (i<last_high)
{
err = err + ((VP >> i)&(Word)1);
err = err - ((VN >> i)&(Word)1);
++i;
if ((err <= errthold) && (err<=*return_err))
{
*return_err = err;
return_site = site + i;
}
}
if ((ungap_err <= errthold) && (ungap_err == *return_err))
{
return_site = site + errthold;
}
return return_site;
}
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['A'], 0, sizeof(Word_32)* 4);
memset(Peq['C'], 0, sizeof(Word_32)* 4);
memset(Peq['G'], 0, sizeof(Word_32)* 4);
memset(Peq['T'], 0, sizeof(Word_32)* 4);
for (i = 0; i<band_length; i++)
{
Peq[pattern1[i]][0] = Peq[pattern1[i]][0] | tmp_Peq_1;
Peq[pattern2[i]][1] = Peq[pattern2[i]][1] | tmp_Peq_1;
Peq[pattern3[i]][2] = Peq[pattern3[i]][2] | tmp_Peq_1;
Peq[pattern4[i]][3] = Peq[pattern4[i]][3] | tmp_Peq_1;
tmp_Peq_1 = tmp_Peq_1 << 1;
}
Peq_SSE['A'] = _mm_set_epi32(Peq['A'][3], Peq['A'][2], Peq['A'][1], Peq['A'][0]);
Peq_SSE['C'] = _mm_set_epi32(Peq['C'][3], Peq['C'][2], Peq['C'][1], Peq['C'][0]);
Peq_SSE['G'] = _mm_set_epi32(Peq['G'][3], Peq['G'][2], Peq['G'][1], Peq['G'][0]);
Peq_SSE['T'] = _mm_set_epi32(Peq['T'][3], Peq['T'][2], Peq['T'][1], Peq['T'][0]);
///Peq_SSE['T'] = _mm_or_si128(Peq_SSE['T'], Peq_SSE['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[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['A'] = _mm_srli_epi32(Peq_SSE['A'], 1);
Peq_SSE['T'] = _mm_srli_epi32(Peq_SSE['T'], 1);
Peq_SSE['G'] = _mm_srli_epi32(Peq_SSE['G'], 1);
Peq_SSE['C'] = _mm_srli_epi32(Peq_SSE['C'], 1);
++i;
++i_bd;
Peq_SSE[pattern1[i_bd]] = _mm_or_si128(Mask1, Peq_SSE[pattern1[i_bd]]);
Peq_SSE[pattern2[i_bd]] = _mm_or_si128(Mask2, Peq_SSE[pattern2[i_bd]]);
Peq_SSE[pattern3[i_bd]] = _mm_or_si128(Mask3, Peq_SSE[pattern3[i_bd]]);
Peq_SSE[pattern4[i_bd]] = _mm_or_si128(Mask4, Peq_SSE[pattern4[i_bd]]);
///Peq_SSE['T'] = _mm_or_si128(Peq_SSE['T'], Peq_SSE['C']);
}
///X = Peq[text[i]] | VN;
X = _mm_or_si128(Peq_SSE[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 <= errthold) && (err1 <= return_sites_error[0]))
{
return_sites[0] = site;
return_sites_error[0] = err1;
}
if ((err2 <= errthold) && (err2 <= return_sites_error[1]))
{
return_sites[1] = site;
return_sites_error[1] = err2;
}
if ((err3 <= errthold) && (err3 <= return_sites_error[2]))
{
return_sites[2] = site;
return_sites_error[2] = err3;
}
if ((err4 <= errthold) && (err4 <= return_sites_error[3]))
{
return_sites[3] = site;
return_sites_error[3] = err4;
}
i = 0;
while (i<errthold)
{
///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 <= errthold) && (err1 <= return_sites_error[0]))
{
return_sites[0] = site + i;
return_sites_error[0] = err1;
}
if ((err2 <= errthold) && (err2 <= return_sites_error[1]))
{
return_sites[1] = site + i;
return_sites_error[1] = err2;
}
if ((err3 <= errthold) && (err3 <= return_sites_error[2]))
{
return_sites[2] = site + i;
return_sites_error[2] = err3;
}
if ((err4 <= errthold) && (err4 <= return_sites_error[3]))
{
return_sites[3] = site + i;
return_sites_error[3] = err4;
}
}
unsigned int ungap_err1;
unsigned int ungap_err2;
unsigned int ungap_err3;
unsigned int ungap_err4;
ungap_err1 = err1;
ungap_err2 = err2;
ungap_err3 = err3;
ungap_err4 = err4;
while (i<last_high)
{
///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 <= errthold) && (err1 <= return_sites_error[0]))
{
return_sites[0] = site + i;
return_sites_error[0] = err1;
}
if ((err2 <= errthold) && (err2 <= return_sites_error[1]))
{
return_sites[1] = site + i;
return_sites_error[1] = err2;
}
if ((err3 <= errthold) && (err3 <= return_sites_error[2]))
{
return_sites[2] = site + i;
return_sites_error[2] = err3;
}
if ((err4 <= errthold) && (err4 <= return_sites_error[3]))
{
return_sites[3] = site + i;
return_sites_error[3] = err4;
}
}
if ((ungap_err1 <= errthold) && ungap_err1 == return_sites_error[0])
{
return_sites[0] = site + errthold;
}
if ((ungap_err2 <= errthold) && ungap_err2 == return_sites_error[1])
{
return_sites[1] = site + errthold;
}
if ((ungap_err3 <= errthold) && ungap_err3 == return_sites_error[2])
{
return_sites[2] = site + errthold;
}
if ((ungap_err4 <= errthold) && ungap_err4 == return_sites_error[3])
{
return_sites[3] = site + errthold;
}
return 1;
}
void output_bit_myers(Word x, int length);
void prase_vertical(Word VP, Word VN, int length, int matrix[1000][1000], int i);
void prase_D0(Word D0, int length, int matrix[1000][1000], int i);
void prase_H(Word HP, Word HN, int length, int matrix[1000][1000], int i);
int Reserve_Banded_BPM_debug(char *pattern, int p_length, char *text, int t_length, unsigned short errthold,
unsigned int* return_err, int matrix[1000][1000]);
int Reserve_Banded_BPM_new(char *pattern,int p_length,char *text,int t_length,unsigned short errthold,
unsigned short band_down,unsigned short band_below,unsigned short band_length,int* return_err, int thread_id);
int BS_Reserve_Banded_BPM
(char *pattern, int p_length, char *text, int t_length, unsigned short errthold, unsigned int* return_err);
#endif
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