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Levenshtein_Cal.h
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/*
Authors:
Haoyu Cheng
*/
#ifndef __LEVENSHTEIN_
#define __LEVENSHTEIN_
#include "Auxiliary.h"
#include <iostream>
#include "emmintrin.h"
#include "nmmintrin.h"
#include "smmintrin.h"
#include <immintrin.h>
#include "ksw.h"
///int each_length;
typedef uint64_t Word;
typedef uint16_t Small_Word;
typedef uint32_t Word_32;
///Word D0_arry_64[2000];
///Word HP_arry_64[2000];
///int Route_Size_Whole[2000];
///char Route_Char_Whole[2000];
///char err_match[2000];
inline void dec_bit(Word input)
{
unsigned int bit_2[64];
int i = 0;
for (i = 0; i < 64; i++)
{
Word tmp = (Word)((Word)input&(Word)1);
input = input >> 1;
if (tmp == (Word)0)
{
bit_2[i] = 0;
}
else
{
bit_2[i] = 1;
}
}
for (i = 63; i >= 0; i--)
{
fprintf(stderr, "%u", bit_2[i]);
}
fprintf(stderr, "\n");
}
int Calcu_Cigar_MD(int Peq_i, 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 err, int match_site, char* cigar, char* MD_Z, int thread_id);
int Brief_2_Banded_BPM_Non_SSE(char *pattern1,char *pattern2,int p_length,char *text,int t_length,
int* return_sites,int* return_sites_error,unsigned short errthold,unsigned short band_down,unsigned short band_below,unsigned short band_length, int thread_id);
int Brief_Reserve_Banded_BPM_4_high_SSE(char *pattern1,char *pattern2,char *pattern3,char *pattern4,int p_length,char *text,int t_length,
int* return_sites,int* return_sites_error,unsigned short errthold,unsigned short band_down,unsigned short band_below,unsigned short band_length, int thread_id);
int Brief_Reserve_Banded_BPM_3_high_SSE(char *pattern1,char *pattern2,char *pattern3,int p_length,char *text,int t_length,
int* return_sites,int* return_sites_error,unsigned short errthold,unsigned short band_down,unsigned short band_below,unsigned short band_length, int thread_id);
int Start_location_Brief_Reserve_Banded_BPM_4_high_SSE(char *pattern1,char *pattern2,char *pattern3,char *pattern4,int p_length,char *text,int t_length,
int* return_sites,int* return_sites_error,unsigned short errthold,unsigned short band_down,unsigned short band_below,unsigned short band_length, int thread_id);
int Start_location_Brief_Reserve_Banded_BPM_3_high_SSE(char *pattern1,char *pattern2,char *pattern3,int p_length,char *text,int t_length,
int* return_sites,int* return_sites_error,unsigned short errthold,unsigned short band_down,unsigned short band_below,unsigned short band_length, int thread_id);
int Start_location_Reserve_Banded_BPM_high(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 Start_location_Calcu_Cigar_MD(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 pre_err, char* cigar,char* MD_Z,int thread_id,int return_site);
int Start_location_Brief_Reserve_Banded_BPM_8_SSE(char *pattern1,char *pattern2,char *pattern3,char *pattern4,char *pattern5,char *pattern6,char *pattern7,char *pattern8,int p_length,char *text,int t_length,
int* return_sites,int* return_sites_error,unsigned short errthold,unsigned short band_down,unsigned short band_below,unsigned short band_length, int thread_id);
int Brief_Reserve_Banded_BPM_8_SSE(char *pattern1,char *pattern2,char *pattern3,char *pattern4,char *pattern5,char *pattern6,char *pattern7,char *pattern8,int p_length,char *text,int t_length,
int* return_sites,int* return_sites_error,unsigned short errthold,unsigned short band_down,unsigned short band_below,unsigned short band_length, int thread_id);
int Brief_Reserve_Banded_BPM_7_SSE(char *pattern1,char *pattern2,char *pattern3,char *pattern4,char *pattern5,char *pattern6,char *pattern7,int p_length,char *text,int t_length,
int* return_sites,int* return_sites_error,unsigned short errthold,unsigned short band_down,unsigned short band_below,unsigned short band_length, int thread_id);
int Start_location_Brief_Reserve_Banded_BPM_7_SSE(char *pattern1,char *pattern2,char *pattern3,char *pattern4,char *pattern5,char *pattern6,char *pattern7,int p_length,char *text,int t_length,
int* return_sites,int* return_sites_error,unsigned short errthold,unsigned short band_down,unsigned short band_below,unsigned short band_length, int thread_id);
int Brief_Reserve_Banded_BPM_6_SSE(char *pattern1,char *pattern2,char *pattern3,char *pattern4,char *pattern5,char *pattern6,int p_length,char *text,int t_length,
int* return_sites,int* return_sites_error,unsigned short errthold,unsigned short band_down,unsigned short band_below,unsigned short band_length, int thread_id);
int Start_location_Brief_Reserve_Banded_BPM_6_SSE(char *pattern1,char *pattern2,char *pattern3,char *pattern4,char *pattern5,char *pattern6,int p_length,char *text,int t_length,
int* return_sites,int* return_sites_error,unsigned short errthold,unsigned short band_down,unsigned short band_below,unsigned short band_length, int thread_id);
int Brief_Reserve_Banded_BPM_5_SSE(char *pattern1,char *pattern2,char *pattern3,char *pattern4,char *pattern5,int p_length,char *text,int t_length,
int* return_sites,int* return_sites_error,unsigned short errthold,unsigned short band_down,unsigned short band_below,unsigned short band_length, int thread_id);
int Start_location_Brief_Reserve_Banded_BPM_5_SSE(char *pattern1,char *pattern2,char *pattern3,char *pattern4,char *pattern5,int p_length,char *text,int t_length,
int* return_sites,int* return_sites_error,unsigned short errthold,unsigned short band_down,unsigned short band_below,unsigned short band_length, int thread_id);
int Reserve_Banded_BPM(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 Start_location_Reserve_Banded_BPM(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);
/**************************************************�����ȶ�***************************************************************************************************/
///�������ʵ�ʾͼ���pattern�����п�����N
inline int BS_Reserve_Banded_BPM_back
(char *pattern, int p_length, char *text, int t_length, unsigned short errthold, unsigned int* return_err)
{
(*return_err) = (unsigned int)-1;
///������Ǹ���ҪԤ����������
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
///���ǰ�pattern��ǰ2k + 1���ַ�Ԥ����
///pattern[0]��ӦPeq[0]
///pattern[2k]��ӦPeq[2k]
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]��Peq[2k], ��pattern[2k]��Peq[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);
///���б�Խ��߷���ƥ����D0��1
///�����ƥ����D0��0
///�����˼����������������Խ����ϵ�б�Խ��߷���������,��ִ���ڲ�����
///
if (!(D0&err_mask))
{
++err;
///��ʹȫ���ݼ���Ҳ�ͼ�2k
if ((err - last_high)>errthold)
return -1;
}
///pattern[0]��Peq[2k], ��pattern[2k]��Peq[0]
//����ʵ�����ǰ�pattern[0]�Ƶ���
Peq['A'] = Peq['A'] >> 1;
Peq['C'] = Peq['C'] >> 1;
Peq['G'] = Peq['G'] >> 1;
Peq['T'] = Peq['T'] >> 1;
++i;
++i_bd;
///���ǰ��µ�pattern[2k]�ӽ���, ��ò���Ǽӵ�Peq[2k]����
Peq[pattern[i_bd]] = Peq[pattern[i_bd]] | Mask;
Peq['T'] = Peq['T'] | Peq['C'];
}
///fprintf(stderr, "sucess(1)\n");
///���ѭ���ó�����Ϊ�˷�ֹ�ڴ�й¶
///��ʵҲ����ѭ��������һ������
///��ȫ����pattern����һλ
///��������Ҳ�ã����Լ��ټ��㿪��
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
///��ʱ���siteò���������������Խ��ߵ�λ��
///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;
}
/**************************************************�����ȶ�***************************************************************************************************/
///�������ʵ�ʾͼ���pattern�����п�����N
inline int BS_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;
///������Ǹ���ҪԤ����������
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
///���ǰ�pattern��ǰ2k + 1���ַ�Ԥ����
///pattern[0]��ӦPeq[0]
///pattern[2k]��ӦPeq[2k]
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]��Peq[2k], ��pattern[2k]��Peq[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);
///���б�Խ��߷���ƥ����D0��1
///�����ƥ����D0��0
///�����˼����������������Խ����ϵ�б�Խ��߷���������,��ִ���ڲ�����
///
if (!(D0&err_mask))
{
++err;
///��ʹȫ���ݼ���Ҳ�ͼ�2k
if ((err - last_high)>errthold)
return -1;
}
///pattern[0]��Peq[2k], ��pattern[2k]��Peq[0]
//����ʵ�����ǰ�pattern[0]�Ƶ���
Peq['A'] = Peq['A'] >> 1;
Peq['C'] = Peq['C'] >> 1;
Peq['G'] = Peq['G'] >> 1;
Peq['T'] = Peq['T'] >> 1;
++i;
++i_bd;
///���ǰ��µ�pattern[2k]�ӽ���, ��ò���Ǽӵ�Peq[2k]����
Peq[pattern[i_bd]] = Peq[pattern[i_bd]] | Mask;
Peq['T'] = Peq['T'] | Peq['C'];
}
///fprintf(stderr, "sucess(1)\n");
///���ѭ���ó�����Ϊ�˷�ֹ�ڴ�й¶
///��ʵҲ����ѭ��������һ������
///��ȫ����pattern����һλ
///��������Ҳ�ã����Լ��ټ��㿪��
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
///��ʱ���siteò���������������Խ��ߵ�λ��
///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;
}
/***************************************************2���ȶ�**************************************************/
inline int BS_Reserve_Banded_BPM_2_SSE_back(char *pattern1, char *pattern2, int p_length, char *text, int t_length,
int* return_sites, unsigned int* return_sites_error, unsigned short errthold)
{
return_sites_error[0] = (unsigned int)-1;
return_sites_error[1] = (unsigned int)-1;
return_sites[0] = -1;
return_sites[1] = -1;
Word Peq[256][2];
int band_length = (errthold << 1) + 1;
__m128i Peq_SSE[256];
int i;
Word tmp_Peq_1 = 1;
Peq['A'][0] = 0;
Peq['A'][1] = 0;
Peq['C'][0] = 0;
Peq['C'][1] = 0;
Peq['G'][0] = 0;
Peq['G'][1] = 0;
Peq['T'][0] = 0;
Peq['T'][1] = 0;
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;
tmp_Peq_1 = tmp_Peq_1 << 1;
}
Peq['T'][0] = Peq['T'][0] | Peq['C'][0];
Peq['T'][1] = Peq['T'][1] | Peq['C'][1];
for (i = 0; i < 256; i++)
{
Peq_SSE[i] = _mm_setzero_si128();
}
Peq_SSE['A'] = _mm_set_epi64x(Peq['A'][1], Peq['A'][0]);
Peq_SSE['C'] = _mm_set_epi64x(Peq['C'][1], Peq['C'][0]);
Peq_SSE['G'] = _mm_set_epi64x(Peq['G'][1], Peq['G'][0]);
Peq_SSE['T'] = _mm_set_epi64x(Peq['T'][1], Peq['T'][0]);
Word Mask = ((Word)1 << (errthold << 1));
__m128i Mask1 = _mm_set_epi64x(0, Mask);
__m128i Mask2 = _mm_set_epi64x(Mask, 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_2 = _mm_set_epi64x(0, 0);
__m128i err_mask = _mm_set_epi64x(1, 1);
///for_not li quan shi 1
__m128i for_not=_mm_set1_epi32(-1);
__m128i err_arry;
__m128i cmp_result;
/**********************************�����Ϊ��ֹ���****************************/
Word a_mask=((Word)-1)>>(64-band_length);
///zui gao wei shi 0, fang zhi yi chu
__m128i add_mask=_mm_set_epi64x(a_mask,a_mask);
/******************************************************************************************/
int i_bd = (errthold << 1);
int last_high = (errthold << 1);
int t_length_1 = t_length - 1;
int err1;
int err2;
__m128i pre_end=_mm_set_epi64x(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);
/*****************************************�����������Ǵ����ֹ���*************************/
tmp_process1 = _mm_and_si128(tmp_process1, add_mask);
VP = _mm_and_si128(VP, add_mask);
/*************************************************************************************/
///(VP + (X&VP))
tmp_process = _mm_add_epi64(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_epi64(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_2 = _mm_add_epi64(Err_2, err_mask);
Err_2 = _mm_sub_epi64(Err_2, err_arry);
///shi ji shang zhe ge zhi hen xiao d
cmp_result = _mm_cmpgt_epi64(Err_2, pre_end);
///jian zhi
if (_mm_extract_epi64(cmp_result, 0) && _mm_extract_epi64(cmp_result, 1))
return 1;
Peq_SSE['A'] = _mm_srli_epi64(Peq_SSE['A'], 1);
Peq_SSE['T'] = _mm_srli_epi64(Peq_SSE['T'], 1);
Peq_SSE['G'] = _mm_srli_epi64(Peq_SSE['G'], 1);
Peq_SSE['C'] = _mm_srli_epi64(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['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);
/*****************************************�����������Ǵ����ֹ���*************************/
tmp_process1 = _mm_and_si128(tmp_process1, add_mask);
VP = _mm_and_si128(VP, add_mask);
/*************************************************************************************/
///(VP + (X&VP))
tmp_process = _mm_add_epi64(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_epi64(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_2 = _mm_add_epi64(Err_2, err_mask);
Err_2 = _mm_sub_epi64(Err_2, err_arry);
///shi ji shang zhe ge zhi hen xiao d
cmp_result = _mm_cmpgt_epi64(Err_2, pre_end);
///jian zhi
if (_mm_extract_epi64(cmp_result, 0) && _mm_extract_epi64(cmp_result, 1))
return 1;
int site = t_length - 1;
err1=_mm_extract_epi64(Err_2,0);
err2=_mm_extract_epi64(Err_2,1);
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;
}
i=0;
while (i<errthold)
{
///err = err + ((VP >> i)&(Word)1);
tmp_process = _mm_srli_epi64(VP, i);
tmp_process = _mm_and_si128(tmp_process, err_mask);
Err_2 = _mm_add_epi64(Err_2, tmp_process);
///err = err - ((VN >> i)&(Word)1);
tmp_process1 = _mm_srli_epi64(VN, i);
tmp_process1 = _mm_and_si128(tmp_process1, err_mask);
Err_2 = _mm_sub_epi64(Err_2, tmp_process1);
++i;
err1 = _mm_extract_epi64(Err_2, 0);
err2 = _mm_extract_epi64(Err_2, 1);
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;
}
}
unsigned int ungap_err1;
unsigned int ungap_err2;
ungap_err1 = err1;
ungap_err2 = err2;
while(i<last_high)
{
///err = err + ((VP >> i)&(Word)1);
tmp_process=_mm_srli_epi64(VP,i);
tmp_process=_mm_and_si128(tmp_process,err_mask);
Err_2=_mm_add_epi64(Err_2,tmp_process);
///err = err - ((VN >> i)&(Word)1);
tmp_process1=_mm_srli_epi64(VN,i);
tmp_process1=_mm_and_si128(tmp_process1,err_mask);
Err_2=_mm_sub_epi64(Err_2,tmp_process1);
++i;
err1=_mm_extract_epi64(Err_2,0);
err2=_mm_extract_epi64(Err_2,1);
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 ((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;
}
return 1;
}
/***************************************************2���ȶ�**************************************************/
inline int BS_Reserve_Banded_BPM_2_SSE(char *pattern1, char *pattern2, int p_length, char *text, int t_length,
int* return_sites, unsigned int* return_sites_error, unsigned short errthold)
{
return_sites_error[0] = (unsigned int)-1;
return_sites_error[1] = (unsigned int)-1;
return_sites[0] = -1;
return_sites[1] = -1;
Word Peq[256][2];
int band_length = (errthold << 1) + 1;
__m128i Peq_SSE[256];
int i;
Word tmp_Peq_1 = 1;
Peq['A'][0] = 0;
Peq['A'][1] = 0;
Peq['C'][0] = 0;
Peq['C'][1] = 0;
Peq['G'][0] = 0;
Peq['G'][1] = 0;
Peq['T'][0] = 0;
Peq['T'][1] = 0;
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;
tmp_Peq_1 = tmp_Peq_1 << 1;
}
Peq['T'][0] = Peq['T'][0] | Peq['C'][0];
Peq['T'][1] = Peq['T'][1] | Peq['C'][1];
for (i = 0; i < 256; i++)
{
Peq_SSE[i] = _mm_setzero_si128();
}
Peq_SSE['A'] = _mm_set_epi64x(Peq['A'][1], Peq['A'][0]);
Peq_SSE['C'] = _mm_set_epi64x(Peq['C'][1], Peq['C'][0]);
Peq_SSE['G'] = _mm_set_epi64x(Peq['G'][1], Peq['G'][0]);
Peq_SSE['T'] = _mm_set_epi64x(Peq['T'][1], Peq['T'][0]);
Word Mask = ((Word)1 << (errthold << 1));
__m128i Mask1 = _mm_set_epi64x(0, Mask);
__m128i Mask2 = _mm_set_epi64x(Mask, 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_2 = _mm_set_epi64x(0, 0);