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初始化bsw文件

This commit is contained in:
zzh 2023-08-15 22:19:39 +08:00
parent ede75a66fa
commit 2a14c17c68
6 changed files with 603 additions and 83 deletions
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2
.gitignore vendored
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@ -1,4 +1,6 @@
*.[oa] *.[oa]
*.txt
*.fa
sw_perf sw_perf
sw_perf_discrete sw_perf_discrete
test test

4
Makefile
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@ -1,6 +1,6 @@
CC= gcc CC= gcc
#CFLAGS= -g -Wall -Wno-unused-function CFLAGS= -g -Wall -Wno-unused-function -mavx2
CFLAGS= -Wall -Wno-unused-function -O2 -mavx2 #CFLAGS= -Wall -Wno-unused-function -O2 -mavx2
DFLAGS= -DSHOW_PERF DFLAGS= -DSHOW_PERF
OBJS= ksw_normal.o ksw_avx2.o ksw_cuda.o ksw_avx2_u8.o OBJS= ksw_normal.o ksw_avx2.o ksw_cuda.o ksw_avx2_u8.o
PROG= sw_perf PROG= sw_perf

425
bsw_avx2.c 100644
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@ -0,0 +1,425 @@
#include <stdlib.h>
#include <stdint.h>
#include <assert.h>
#include <emmintrin.h>
#include <stdio.h>
#include <immintrin.h>
#include <emmintrin.h>
#ifdef __GNUC__
#define LIKELY(x) __builtin_expect((x), 1)
#define UNLIKELY(x) __builtin_expect((x), 0)
#else
#define LIKELY(x) (x)
#define UNLIKELY(x) (x)
#endif
#undef MAX
#undef MIN
#define MAX(x, y) ((x) > (y) ? (x) : (y))
#define MIN(x, y) ((x) < (y) ? (x) : (y))
#define SIMD_WIDTH 16
static const uint16_t h_vec_int_mask[SIMD_WIDTH][SIMD_WIDTH] = {
{0xffff, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{0xffff, 0xffff, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{0xffff, 0xffff, 0xffff, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{0xffff, 0xffff, 0xffff, 0xffff, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0, 0, 0, 0, 0, 0, 0, 0},
{0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0, 0, 0, 0, 0, 0, 0},
{0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0, 0, 0, 0, 0, 0},
{0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0, 0, 0, 0, 0},
{0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0, 0, 0, 0},
{0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0, 0, 0},
{0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0, 0},
{0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0},
{0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff}};
// const int permute_mask = _MM_SHUFFLE(0, 1, 2, 3);
#define permute_mask _MM_SHUFFLE(0, 1, 2, 3)
// 初始化变量
#define SIMD_INIT \
int oe_del = o_del + e_del, oe_ins = o_ins + e_ins; \
__m256i zero_vec; \
__m256i max_vec; \
__m256i oe_del_vec; \
__m256i oe_ins_vec; \
__m256i e_del_vec; \
__m256i e_ins_vec; \
__m256i h_vec_mask[SIMD_WIDTH]; \
zero_vec = _mm256_setzero_si256(); \
oe_del_vec = _mm256_set1_epi16(-oe_del); \
oe_ins_vec = _mm256_set1_epi16(-oe_ins); \
e_del_vec = _mm256_set1_epi16(-e_del); \
e_ins_vec = _mm256_set1_epi16(-e_ins); \
__m256i match_sc_vec = _mm256_set1_epi16(a); \
__m256i mis_sc_vec = _mm256_set1_epi16(-b); \
__m256i amb_sc_vec = _mm256_set1_epi16(-1); \
__m256i amb_vec = _mm256_set1_epi16(4); \
for (i = 0; i < SIMD_WIDTH; ++i) \
h_vec_mask[i] = _mm256_loadu_si256((__m256i *)(&h_vec_int_mask[i]));
/*
* e 表示当前ref的碱基被删除
* f 表示当前seq的碱基插入
* m 表示当前碱基匹配（可以相等，也可以不想等）
* h 表示最大值
*/
// load向量化数据
#define SIMD_LOAD \
__m256i m1 = _mm256_loadu_si256((__m256i *)(&mA1[j])); \
__m256i e1 = _mm256_loadu_si256((__m256i *)(&eA1[j])); \
__m256i m1j1 = _mm256_loadu_si256((__m256i *)(&mA1[j - 1])); \
__m256i f1j1 = _mm256_loadu_si256((__m256i *)(&fA1[j - 1])); \
__m256i h0j1 = _mm256_loadu_si256((__m256i *)(&hA0[j - 1])); \
__m256i qs_vec = _mm256_loadu_si256((__m256i *)(&seq[j - 1])); \
__m256i ts_vec = _mm256_loadu_si256((__m256i *)(&ref[i]));
// 比对ref和seq的序列，计算罚分
#define SIMD_CMP_SEQ \
ts_vec = _mm256_permute4x64_epi64(ts_vec, permute_mask); \
ts_vec = _mm256_shufflelo_epi16(ts_vec, permute_mask); \
ts_vec = _mm256_shufflehi_epi16(ts_vec, permute_mask); \
__m256i match_mask_vec = _mm256_cmpeq_epi16(qs_vec, ts_vec); \
__m256i mis_score_vec = _mm256_andnot_si256(match_mask_vec, mis_sc_vec); \
__m256i score_vec = _mm256_and_si256(match_sc_vec, match_mask_vec); \
score_vec = _mm256_or_si256(score_vec, mis_score_vec); \
__m256i q_amb_mask_vec = _mm256_cmpeq_epi16(qs_vec, amb_vec); \
__m256i t_amb_mask_vec = _mm256_cmpeq_epi16(ts_vec, amb_vec); \
__m256i amb_mask_vec = _mm256_or_si256(q_amb_mask_vec, t_amb_mask_vec); \
score_vec = _mm256_andnot_si256(amb_mask_vec, score_vec); \
__m256i amb_score_vec = _mm256_and_si256(amb_mask_vec, amb_sc_vec); \
score_vec = _mm256_or_si256(score_vec, amb_score_vec);
// 向量化计算h, e, f, m
#define SIMD_COMPUTE \
__m256i en_vec0 = _mm256_add_epi16(m1, oe_del_vec); \
__m256i en_vec1 = _mm256_add_epi16(e1, e_del_vec); \
__m256i en_vec = _mm256_max_epi16(en_vec0, en_vec1); \
__m256i fn_vec0 = _mm256_add_epi16(m1j1, oe_ins_vec); \
__m256i fn_vec1 = _mm256_add_epi16(f1j1, e_ins_vec); \
__m256i fn_vec = _mm256_max_epi16(fn_vec0, fn_vec1); \
__m256i mn_vec0 = _mm256_add_epi16(h0j1, score_vec); \
__m256i mn_mask = _mm256_cmpgt_epi16(h0j1, zero_vec); \
__m256i mn_vec = _mm256_and_si256(mn_vec0, mn_mask); \
__m256i hn_vec0 = _mm256_max_epi16(en_vec, fn_vec); \
__m256i hn_vec = _mm256_max_epi16(hn_vec0, mn_vec); \
en_vec = _mm256_max_epi16(en_vec, zero_vec); \
fn_vec = _mm256_max_epi16(fn_vec, zero_vec); \
mn_vec = _mm256_max_epi16(mn_vec, zero_vec); \
hn_vec = _mm256_max_epi16(hn_vec, zero_vec);
// 存储向量化结果
#define SIMD_STORE \
max_vec = _mm256_max_epi16(max_vec, hn_vec); \
_mm256_storeu_si256((__m256i *)&eA2[j], en_vec); \
_mm256_storeu_si256((__m256i *)&fA2[j], fn_vec); \
_mm256_storeu_si256((__m256i *)&mA2[j], mn_vec); \
_mm256_storeu_si256((__m256i *)&hA2[j], hn_vec);
// 去除多余的部分
#define SIMD_REMOVE_EXTRA \
en_vec = _mm256_and_si256(en_vec, h_vec_mask[end - j]); \
fn_vec = _mm256_and_si256(fn_vec, h_vec_mask[end - j]); \
mn_vec = _mm256_and_si256(mn_vec, h_vec_mask[end - j]); \
hn_vec = _mm256_and_si256(hn_vec, h_vec_mask[end - j]);
// 找最大值和位置
#define SIMD_FIND_MAX \
max_vec = _mm256_max_epu16(max_vec, _mm256_alignr_epi8(max_vec, max_vec, 2)); \
max_vec = _mm256_max_epu16(max_vec, _mm256_alignr_epi8(max_vec, max_vec, 4)); \
max_vec = _mm256_max_epu16(max_vec, _mm256_alignr_epi8(max_vec, max_vec, 6)); \
max_vec = _mm256_max_epu16(max_vec, _mm256_alignr_epi8(max_vec, max_vec, 8)); \
max_vec = _mm256_max_epu16(max_vec, _mm256_permute2x128_si256(max_vec, max_vec, 0x01)); \
int16_t *maxVal = (int16_t *)&max_vec; \
m = maxVal[0]; \
if (m > 0) \
{ \
for (j = beg, i = iend; j <= end; j += SIMD_WIDTH, i -= SIMD_WIDTH) \
{ \
__m256i h2_vec = _mm256_loadu_si256((__m256i *)(&hA2[j])); \
__m256i vcmp = _mm256_cmpeq_epi16(h2_vec, max_vec); \
uint32_t mask = _mm256_movemask_epi8(vcmp); \
if (mask > 0) \
{ \
int pos = SIMD_WIDTH - 1 - ((__builtin_clz(mask)) >> 1); \
mj = j - 1 + pos; \
mi = i - 1 - pos; \
} \
} \
}
// 每轮迭代后，交换数组
#define SWAP_DATA_POINTER \
int16_t *tmp = hA0; \
hA0 = hA1; \
hA1 = hA2; \
hA2 = tmp; \
tmp = eA1; \
eA1 = eA2; \
eA2 = tmp; \
tmp = fA1; \
fA1 = fA2; \
fA2 = tmp; \
tmp = mA1; \
mA1 = mA2; \
mA2 = tmp;
int bsw_avx2(int qlen, // query length 待匹配段碱基的query长度
const uint8_t *query, // read碱基序列
int tlen, // target length reference的长度
const uint8_t *target, // reference序列
int is_left, // 是不是向左扩展
int m, // 碱基种类 (5)
const int8_t *mat, // 每个位置的query和target的匹配得分 m*m
int o_del, // deletion 错配开始的惩罚系数
int e_del, // deletion extension的惩罚系数
int o_ins, // insertion 错配开始的惩罚系数
int e_ins, // insertion extension的惩罚系数SIMD_BTYES
int a, // 碱基match时的分数
int b, // 碱基mismatch时的惩罚分数（正数）
int w, // 提前剪枝系数，w =100 匹配位置和beg的最大距离
int end_bonus, // 如果query比对到了最后一个字符，额外奖励分值
int zdrop, // 没匹配上的太多（max-(m+ins or del score)），退出后续匹配
int h0, // 该seed的初始得分（完全匹配query的碱基数）
int *_qle, // 匹配得到全局最大得分的碱基在query的位置
int *_tle, // 匹配得到全局最大得分的碱基在reference的位置
int *_gtle, // query全部匹配上的target的长度
int *_gscore, // query的端到端匹配得分
int *_max_off) // 取得最大得分时在query和reference上位置差的 最大值
{
int16_t *mA, *hA, *eA, *fA, *mA1, *mA2, *hA0, *hA1, *eA1, *fA1, *hA2, *eA2, *fA2; // hA0保存上上个col的H，其他的保存上个H E F M
int16_t *seq, *ref;
uint8_t *mem;
int16_t *qtmem, *vmem;
int seq_size = qlen + SIMD_WIDTH, ref_size = tlen + SIMD_WIDTH;
int i, iStart, D, j, k, beg, end, max, max_i, max_j, max_ins, max_del, max_ie, gscore, max_off;
int Dloop = tlen + qlen; // 循环跳出条件
int span, beg1, end1; // 边界条件计算
int col_size = qlen + 2 + SIMD_WIDTH;
int val_mem_size = (col_size * 9 * 2 + 31) >> 5 << 5; // 32字节的整数倍
int mem_size = (seq_size + ref_size) * 2 + val_mem_size;
SIMD_INIT; // 初始化simd用的数据
assert(h0 > 0);
// allocate memory
mem = malloc(mem_size);
qtmem = (int16_t *)&mem[0];
seq = &qtmem[0];
ref = &qtmem[seq_size];
if (is_left)
{
for (i = 0; i < qlen; ++i)
seq[i] = query[qlen - 1 - i];
for (i = 0; i < tlen; ++i)
ref[i + SIMD_WIDTH] = target[tlen - 1 - i];
}
else
{
for (i = 0; i < qlen; ++i)
seq[i] = query[i];
for (i = 0; i < tlen; ++i)
ref[i + SIMD_WIDTH] = target[i];
}
vmem = &ref[ref_size];
for (i = 0; i < (val_mem_size >> 1); i += SIMD_WIDTH)
{
_mm256_storeu_si256((__m256i *)&vmem[i], zero_vec);
}
hA = &vmem[0];
mA = &vmem[col_size * 3];
eA = &vmem[col_size * 5];
fA = &vmem[col_size * 7];
hA0 = &hA[0];
hA1 = &hA[col_size];
hA2 = &hA1[col_size];
mA1 = &mA[0];
mA2 = &mA[col_size];
eA1 = &eA[0];
eA2 = &eA[col_size];
fA1 = &fA[0];
fA2 = &fA[col_size];
// adjust $w if it is too large
k = m * m;
// get the max score
for (i = 0, max = 0; i < k; ++i)
max = max > mat[i] ? max : mat[i];
max_ins = (int)((double)(qlen * max + end_bonus - o_ins) / e_ins + 1.);
max_ins = max_ins > 1 ? max_ins : 1;
w = w < max_ins ? w : max_ins;
max_del = (int)((double)(qlen * max + end_bonus - o_del) / e_del + 1.);
max_del = max_del > 1 ? max_del : 1;
w = w < max_del ? w : max_del; // TODO: is this necessary?
if (tlen < qlen)
w = MIN(tlen - 1, w);
// DP loop
max = h0, max_i = max_j = -1;
max_ie = -1, gscore = -1;
;
max_off = 0;
beg = 1;
end = qlen;
// init h0
hA0[0] = h0; // 左上角
if (qlen == 0 || tlen == 0)
Dloop = 0; // 防止意外情况
if (w >= qlen)
{
max_ie = 0;
gscore = 0;
}
int m_last = 0;
int iend;
for (D = 1; LIKELY(D < Dloop); ++D)
{
// 边界条件一定要注意！ tlen 大于，等于，小于 qlen时的情况
if (D > tlen)
{
span = MIN(Dloop - D, w);
beg1 = MAX(D - tlen + 1, ((D - w) / 2) + 1);
}
else
{
span = MIN(D - 1, w);
beg1 = MAX(1, ((D - w) / 2) + 1);
}
end1 = MIN(qlen, beg1 + span);
if (beg < beg1)
beg = beg1;
if (end > end1)
end = end1;
if (beg > end)
break; // 不用计算了，直接跳出，否则hA2没有被赋值，里边是上一轮hA0的值，会出bug
iend = D - (beg - 1); // ref开始计算的位置，倒序
span = end - beg;
iStart = iend - span - 1; // 0开始的ref索引位置
// 每一轮需要记录的数据
int m = 0, mj = -1, mi = -1;
max_vec = zero_vec;
// 要处理边界
// 左边界 处理f (insert)
if (iStart == 0)
{
hA1[end] = MAX(0, h0 - (o_ins + e_ins * end));
}
// 上边界
if (beg == 1)
{
hA1[0] = MAX(0, h0 - (o_del + e_del * iend));
}
else
{
hA1[beg - 1] = 0;
eA1[beg - 1] = 0;
}
for (j = beg, i = iend; j <= end + 1 - SIMD_WIDTH; j += SIMD_WIDTH, i -= SIMD_WIDTH)
{
// 取数据
SIMD_LOAD;
// 比对seq，计算罚分
SIMD_CMP_SEQ;
// 计算
SIMD_COMPUTE;
// 存储结果
SIMD_STORE;
}
// 剩下的计算单元
if (j <= end)
{
// 取数据
SIMD_LOAD;
// 比对seq，计算罚分
SIMD_CMP_SEQ;
// 计算
SIMD_COMPUTE;
// 去除多余计算的部分
SIMD_REMOVE_EXTRA;
// 存储结果
SIMD_STORE;
}
SIMD_FIND_MAX;
// 注意最后跳出循环j的值
j = end + 1;
if (j == qlen + 1)
{
max_ie = gscore > hA2[qlen] ? max_ie : iStart;
gscore = gscore > hA2[qlen] ? gscore : hA2[qlen];
}
// if (m == 0 && m_last == 0)
// break; // 一定要注意，斜对角遍历和按列遍历的不同点
if (m > max)
{
max = m, max_i = mi, max_j = mj;
max_off = max_off > abs(mj - mi) ? max_off : abs(mj - mi);
}
else if (zdrop > 0)
{
if (mi - max_i > mj - max_j)
{
if (max - m - ((mi - max_i) - (mj - max_j)) * e_del > zdrop)
break;
}
else
{
if (max - m - ((mj - max_j) - (mi - max_i)) * e_ins > zdrop)
break;
}
}
// 调整计算的边界
for (j = beg; LIKELY(j <= end); ++j)
{
int has_val = hA1[j - 1] | hA2[j];
if (has_val)
break;
}
beg = j;
for (j = end + 1; LIKELY(j >= beg); --j)
{
int has_val = hA1[j - 1] | hA2[j];
if (has_val)
break;
else
hA0[j - 1] = 0;
}
end = j + 1 <= qlen ? j + 1 : qlen;
// beg = 0;
// end = qlen; // uncomment this line for debugging
m_last = m;
// swap m, h, e, f
SWAP_DATA_POINTER;
}
free(mem);
if (_qle)
*_qle = max_j + 1;
if (_tle)
*_tle = max_i + 1;
if (_gtle)
*_gtle = max_ie + 1;
if (_gscore)
*_gscore = gscore;
if (_max_off)
*_max_off = max_off;
return max;
}

14
ksw_avx2.c
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@ -194,13 +194,6 @@ int ksw_avx2(int qlen, // query length 待匹配段碱基的query
int *_gscore, // query的端到端匹配得分 int *_gscore, // query的端到端匹配得分
int *_max_off) // 取得最大得分时在query和reference上位置差的 最大值 int *_max_off) // 取得最大得分时在query和reference上位置差的 最大值
{ {
// ksw_extend2_origin
// return ksw_extend2_origin(qlen, query, tlen, target, is_left, m, mat, o_del, e_del, o_ins, e_ins, w, end_bonus, zdrop, h0, _qle, _tle, _gtle, _gscore, _max_off);
// fprintf(stderr, "qlen: %d, tlen: %d\n", qlen, tlen);
// if (qlen * a + h0 < 255)
// return ksw_extend2_avx2_u8(qlen, query, tlen, target, is_left, m, mat, o_del, e_del, o_ins, e_ins, a, b, w, end_bonus, zdrop, h0, _qle, _tle, _gtle, _gscore, _max_off);
int16_t *mA, *hA, *eA, *fA, *mA1, *mA2, *hA0, *hA1, *eA1, *fA1, *hA2, *eA2, *fA2; // hA0保存上上个col的H，其他的保存上个H E F M int16_t *mA, *hA, *eA, *fA, *mA1, *mA2, *hA0, *hA1, *eA1, *fA1, *hA2, *eA2, *fA2; // hA0保存上上个col的H，其他的保存上个H E F M
int16_t *seq, *ref; int16_t *seq, *ref;
uint8_t *mem; uint8_t *mem;
@ -375,8 +368,8 @@ int ksw_avx2(int qlen, // query length 待匹配段碱基的query
max_ie = gscore > hA2[qlen] ? max_ie : iStart; max_ie = gscore > hA2[qlen] ? max_ie : iStart;
gscore = gscore > hA2[qlen] ? gscore : hA2[qlen]; gscore = gscore > hA2[qlen] ? gscore : hA2[qlen];
} }
if (m == 0 && m_last == 0) // if (m == 0 && m_last == 0)
break; // 一定要注意，斜对角遍历和按列遍历的不同点 // break; // 一定要注意，斜对角遍历和按列遍历的不同点
if (m > max) if (m > max)
{ {
max = m, max_i = mi, max_j = mj; max = m, max_i = mi, max_j = mj;
@ -413,7 +406,8 @@ int ksw_avx2(int qlen, // query length 待匹配段碱基的query
hA0[j - 1] = 0; hA0[j - 1] = 0;
} }
end = j + 1 <= qlen ? j + 1 : qlen; end = j + 1 <= qlen ? j + 1 : qlen;
// beg = 0;
// end = qlen; // uncomment this line for debugging
m_last = m; m_last = m;
// swap m, h, e, f // swap m, h, e, f
SWAP_DATA_POINTER; SWAP_DATA_POINTER;

76
ksw_normal.c
View File

@ -28,68 +28,69 @@ int ksw_normal(int qlen, const uint8_t *query, int tlen, const uint8_t *target,
{ {
const int8_t *p = &mat[k * m]; const int8_t *p = &mat[k * m];
for (j = 0; j < qlen; ++j) for (j = 0; j < qlen; ++j)
qp[i++] = p[query[j]]; qp[i++] = p[query[j]]; // 对于qp数组，第0到qlen个元素，表示和A比对的分值，第qlen到2*qlen，表示和C比对的分值，以此类推
} }
// fill the first row // fill the first row
// 初始化第一行分值
eh[0].h = h0; eh[0].h = h0;
eh[1].h = h0 > oe_ins ? h0 - oe_ins : 0; eh[1].h = h0 > oe_ins ? h0 - oe_ins : 0;
for (j = 2; j <= qlen && eh[j - 1].h > e_ins; ++j) for (j = 2; j <= qlen && eh[j - 1].h > e_ins; ++j)
eh[j].h = eh[j - 1].h - e_ins; eh[j].h = eh[j - 1].h - e_ins;
// adjust $w if it is too large // adjust $w if it is too large
k = m * m; k = m * m; // 字符矩阵
for (i = 0, max = 0; i < k; ++i) // get the max score for (i = 0, max = 0; i < k; ++i) // get the max score
max = max > mat[i] ? max : mat[i]; max = max > mat[i] ? max : mat[i];
max_ins = (int)((double)(qlen * max + end_bonus - o_ins) / e_ins + 1.); max_ins = (int)((double)(qlen * max + end_bonus - o_ins) / e_ins + 1.); // 最大可插入的长度？
max_ins = max_ins > 1 ? max_ins : 1; max_ins = max_ins > 1 ? max_ins : 1;
w = w < max_ins ? w : max_ins; w = w < max_ins ? w : max_ins;
max_del = (int)((double)(qlen * max + end_bonus - o_del) / e_del + 1.); max_del = (int)((double)(qlen * max + end_bonus - o_del) / e_del + 1.);
max_del = max_del > 1 ? max_del : 1; max_del = max_del > 1 ? max_del : 1;
w = w < max_del ? w : max_del; // TODO: is this necessary? w = w < max_del ? w : max_del; // TODO: is this necessary? 上述几行代码都是为了看看能否缩小窗口，减小计算
// DP loop // DP loop
max = h0, max_i = max_j = -1; max = h0, max_i = max_j = -1;
max_ie = -1, gscore = -1; max_ie = -1, gscore = -1;
max_off = 0; max_off = 0;
beg = 0, end = qlen; beg = 0, end = qlen;
for (i = 0; LIKELY(i < tlen); ++i) for (i = 0; LIKELY(i < tlen); ++i) // 对target逐个字符进行遍历
{ {
int t, f = 0, h1, m = 0, mj = -1; int t, f = 0, h1, m = 0, mj = -1;
int8_t *q = &qp[target[i] * qlen]; int8_t *q = &qp[target[i] * qlen]; // 对于target第i个字符，query中每个字符的分值，只有匹配和不匹配
// apply the band and the constraint (if provided) // apply the band and the constraint (if provided)
if (beg < i - w) // if (beg < i - w) // 检查开始点是否可以缩小一些
beg = i - w; // beg = i - w;
if (end > i + w + 1) // if (end > i + w + 1) // 检查终点是否可以缩小，使得整体的遍历范围缩小
end = i + w + 1; // end = i + w + 1;
if (end > qlen) // if (end > qlen) // 终点不超过query长度
end = qlen; // end = qlen;
// compute the first column // compute the first column
if (beg == 0) if (beg == 0)
{ {
h1 = h0 - (o_del + e_del * (i + 1)); h1 = h0 - (o_del + e_del * (i + 1)); // 只消耗了target序列，query从第一个字符开始匹配第i个target字符
if (h1 < 0) if (h1 < 0)
h1 = 0; h1 = 0;
} }
else else
h1 = 0; h1 = 0;
for (j = beg; LIKELY(j < end); ++j) for (j = beg; LIKELY(j < end); ++j) // 遍历query字符序列
{ {
// At the beginning of the loop: eh[j] = { H(i-1,j-1), E(i,j) }, f = F(i,j) and h1 = H(i,j-1) // At the beginning of the loop: eh[j] = { H(i-1,j-1), E(i,j) }, f = F(i,j) and h1 = H(i,j-1)
// Similar to SSE2-SW, cells are computed in the following order: // Similar to SSE2-SW, cells are computed in the following order:
// H(i,j) = max{H(i-1,j-1)+S(i,j), E(i,j), F(i,j)} // H(i,j) = max{H(i-1,j-1)+S(i,j), E(i,j), F(i,j)}
// E(i+1,j) = max{H(i,j)-gapo, E(i,j)} - gape // E(i+1,j) = max{H(i,j)-gapo, E(i,j)} - gape // E表示delete，只消耗target
// F(i,j+1) = max{H(i,j)-gapo, F(i,j)} - gape // F(i,j+1) = max{H(i,j)-gapo, F(i,j)} - gape // F表示insert，只消耗query
eh_t *p = &eh[j]; eh_t *p = &eh[j];
int h, M = p->h, e = p->e; // get H(i-1,j-1) and E(i-1,j) int h, M = p->h, e = p->e; // get H(i-1,j-1) and E(i-1,j) // 获取上一轮h值和e值
p->h = h1; // set H(i,j-1) for the next row p->h = h1; // set H(i,j-1) for the next row // h1是上一轮计算的结果
M = M ? M + q[j] : 0; // separating H and M to disallow a cigar like "100M3I3D20M" M = M ? M + q[j] : 0; // separating H and M to disallow a cigar like "100M3I3D20M" // M大于0则当前两个字符进行匹配，无论是否相等，将分值加到M上，此时M可能变为负数
h = M > e ? M : e; // e and f are guaranteed to be non-negative, so h>=0 even if M<0 h = M > e ? M : e; // e and f are guaranteed to be non-negative, so h>=0 even if M<0 // e和f保证是非负的，所以h肯定非负，即使M可能是负数，因为h取e,f和M的最大值
h = h > f ? h : f; h = h > f ? h : f;
h1 = h; // save H(i,j) to h1 for the next column h1 = h; // save H(i,j) to h1 for the next column // 用h1来保存当前表格（i,j)对应的分值，用来下次计算
mj = m > h ? mj : j; // record the position where max score is achieved mj = m > h ? mj : j; // record the position where max score is achieved // 记录取得最大值时query的字符位置
m = m > h ? m : h; // m is stored at eh[mj+1] m = m > h ? m : h; // m is stored at eh[mj+1] 因为eh[mj+1]->h表示的是H(i, mj)，及上一轮记录的h
t = M - oe_del; t = M - oe_del; // 用来计算delete，假设当前字符(i,j)匹配（无论match还是mismatch），target下一个字符串被空消耗（delete)的分值F(i+1, j)
t = t > 0 ? t : 0; t = t > 0 ? t : 0;
e -= e_del; e -= e_del; // 假设当前query字符
e = e > t ? e : t; // computed E(i+1,j) e = e > t ? e : t; // computed E(i+1,j) // t表示(i,j)强行匹配，(i+1, j)是delete的分数，此前e表示(i+1,j)继续delete的分数
p->e = e; // save E(i+1,j) for the next row p->e = e; // save E(i+1,j) for the next row
t = M - oe_ins; t = M - oe_ins;
t = t > 0 ? t : 0; t = t > 0 ? t : 0;
@ -98,28 +99,28 @@ int ksw_normal(int qlen, const uint8_t *query, int tlen, const uint8_t *target,
} }
eh[end].h = h1; eh[end].h = h1;
eh[end].e = 0; eh[end].e = 0;
if (j == qlen) if (j == qlen) // 此轮遍历到了query的最后一个字符
{ {
max_ie = gscore > h1 ? max_ie : i; max_ie = gscore > h1 ? max_ie : i; // max_ie表示取得全局最大分值时，target字符串的位置
gscore = gscore > h1 ? gscore : h1; gscore = gscore > h1 ? gscore : h1;
} }
if (m == 0) // if (m == 0) // 遍历完query之后，当前轮次的最大分值为0，则跳出循环
break; // break;
if (m > max) if (m > max) // 当前轮最大分值大于之前的最大分值
{ {
max = m, max_i = i, max_j = mj; max = m, max_i = i, max_j = mj; // 更新取得最大值的target和query的位置
max_off = max_off > abs(mj - i) ? max_off : abs(mj - i); max_off = max_off > abs(mj - i) ? max_off : abs(mj - i); // 取得最大分值时，query和target对应字符串坐标的差值
} }
else if (zdrop > 0) else if (0) //(zdrop > 0) // 当前轮匹配之后取得的最大分值没有大于之前的最大值，而且zdrop值大于0
{ {
if (i - max_i > mj - max_j) if (i - max_i > mj - max_j)
{ {
if (max - m - ((i - max_i) - (mj - max_j)) * e_del > zdrop) if (max - m - ((i - max_i) - (mj - max_j)) * e_del > zdrop) // 之前最大分值 -（从取得最大值的点出发，当前的delete总长度对应的分值 + 当前轮取得的最大值） > zdrop
break; break;
} }
else else
{ {
if (max - m - ((mj - max_j) - (i - max_i)) * e_ins > zdrop) if (max - m - ((mj - max_j) - (i - max_i)) * e_ins > zdrop) // 同上，不过这次是insert，可能是说明有很多mismatch
break; break;
} }
} }
@ -130,7 +131,8 @@ int ksw_normal(int qlen, const uint8_t *query, int tlen, const uint8_t *target,
for (j = end; LIKELY(j >= beg) && eh[j].h == 0 && eh[j].e == 0; --j) for (j = end; LIKELY(j >= beg) && eh[j].h == 0 && eh[j].e == 0; --j)
; ;
end = j + 2 < qlen ? j + 2 : qlen; end = j + 2 < qlen ? j + 2 : qlen;
// beg = 0; end = qlen; // uncomment this line for debugging beg = 0;
end = qlen; // uncomment this line for debugging
} }
free(eh); free(eh);
free(qp); free(qp);

165
main.c
View File

@ -36,6 +36,32 @@ extern int ksw_avx2(int qlen, const uint8_t *query, int tlen, const uint8_t *tar
extern int ksw_avx2_u8(int qlen, const uint8_t *query, int tlen, const uint8_t *target, int is_left, int m, const int8_t *mat, int o_del, int e_del, extern int ksw_avx2_u8(int qlen, const uint8_t *query, int tlen, const uint8_t *target, int is_left, int m, const int8_t *mat, int o_del, int e_del,
int o_ins, int e_ins, int a, int b, int w, int end_bonus, int zdrop, int h0, int *_qle, int *_tle, int *_gtle, int *_gscore, int *_max_off); int o_ins, int e_ins, int a, int b, int w, int end_bonus, int zdrop, int h0, int *_qle, int *_tle, int *_gtle, int *_gscore, int *_max_off);
unsigned char nst_nt4_table[256] = {
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5 /*'-'*/, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4};
char t_2bit2char[5] = {'A', 'C', 'G', 'T'};
// 将碱基字符转成2位编码
void convert_char_to_2bit(char *str)
{
int i;
for (i = 0; i < strlen(str); ++i)
str[i] = nst_nt4_table[str[i]];
}
/* /*
* 包含一个参数，用来区分调用那个sw算法 * 包含一个参数，用来区分调用那个sw算法
* 参数为 normal/avx2/cuda * 参数为 normal/avx2/cuda
@ -82,6 +108,12 @@ int main(int argc, char *argv[])
int *info_buf = (int *)malloc(SEQ_BUF_SIZE); int *info_buf = (int *)malloc(SEQ_BUF_SIZE);
int **info_arr = (int **)malloc(SEQ_BUF_SIZE); int **info_arr = (int **)malloc(SEQ_BUF_SIZE);
FILE *query_f = 0, *target_f = 0, *info_f = 0; FILE *query_f = 0, *target_f = 0, *info_f = 0;
// const char *qf_path = "q.fa";
// const char *tf_path = "t.fa";
// const char *if_path = "i.txt";
const char *qf_path = "bug_q.fa";
const char *tf_path = "bug_t.fa";
const char *if_path = "bug_i.txt";
// const char *qf_path = "/public/home/zzh/data/sw/q_s.fa"; // const char *qf_path = "/public/home/zzh/data/sw/q_s.fa";
// const char *tf_path = "/public/home/zzh/data/sw/t_s.fa"; // const char *tf_path = "/public/home/zzh/data/sw/t_s.fa";
// const char *if_path = "/public/home/zzh/data/sw/i_s.txt"; // const char *if_path = "/public/home/zzh/data/sw/i_s.txt";
@ -91,13 +123,18 @@ int main(int argc, char *argv[])
// const char *qf_path = "/public/home/zzh/data/sw/q_l.fa"; // const char *qf_path = "/public/home/zzh/data/sw/q_l.fa";
// const char *tf_path = "/public/home/zzh/data/sw/t_l.fa"; // const char *tf_path = "/public/home/zzh/data/sw/t_l.fa";
// const char *if_path = "/public/home/zzh/data/sw/i_l.txt"; // const char *if_path = "/public/home/zzh/data/sw/i_l.txt";
const char *qf_path = "/public/home/zzh/data/sw/query.fa"; // const char *qf_path = "/public/home/zzh/data/sw/query.fa";
const char *tf_path = "/public/home/zzh/data/sw/target.fa"; // const char *tf_path = "/public/home/zzh/data/sw/target.fa";
const char *if_path = "/public/home/zzh/data/sw/info.txt"; // const char *if_path = "/public/home/zzh/data/sw/info.txt";
query_f = fopen(qf_path, "r"); query_f = fopen(qf_path, "r");
target_f = fopen(tf_path, "r"); target_f = fopen(tf_path, "r");
info_f = fopen(if_path, "r"); info_f = fopen(if_path, "r");
// 将每次比对的得分等信息写入文件，进行debug
FILE *normal_out_f = fopen("normal_out.txt", "w");
FILE *avx2_out_f = fopen("avx2_out.txt", "w");
FILE *avx2_u8_out_f = fopen("avx2_u8_out.txt", "w");
// 每次读取一定量的数据，然后执行，直到处理完所有数据 // 每次读取一定量的数据，然后执行，直到处理完所有数据
int total_line_num = 0; // 目前处理的总的数据行数 int total_line_num = 0; // 目前处理的总的数据行数
int block_line_num = 0; // 当前循环包含的数据行数 int block_line_num = 0; // 当前循环包含的数据行数
@ -119,6 +156,7 @@ int main(int argc, char *argv[])
} }
int score_normal = 0, score_avx2 = 0, score_avx2_u8 = 0; int score_normal = 0, score_avx2 = 0, score_avx2_u8 = 0;
int score_normal_total = 0, score_avx2_total = 0, score_avx2_u8_total = 0;
while (!feof(target_f)) while (!feof(target_f))
{ {
@ -129,8 +167,14 @@ int main(int argc, char *argv[])
{ {
if (fgets(read_buf, READ_BUF_SIZE, target_f) == NULL) if (fgets(read_buf, READ_BUF_SIZE, target_f) == NULL)
break; break;
const int line_size = strlen(read_buf); int line_size = strlen(read_buf);
assert(line_size < READ_BUF_SIZE); assert(line_size < READ_BUF_SIZE);
if (read_buf[line_size - 1] == '\n')
{
read_buf[line_size - 1] = '\0';
line_size--;
}
convert_char_to_2bit(read_buf);
++block_line_num; ++block_line_num;
++total_line_num; ++total_line_num;
strncpy(target_arr + cur_read_size, read_buf, line_size); strncpy(target_arr + cur_read_size, read_buf, line_size);
@ -144,8 +188,14 @@ int main(int argc, char *argv[])
{ {
if (fgets(read_buf, READ_BUF_SIZE, query_f) == NULL) if (fgets(read_buf, READ_BUF_SIZE, query_f) == NULL)
break; break;
const int line_size = strlen(read_buf); int line_size = strlen(read_buf);
assert(line_size < READ_BUF_SIZE); assert(line_size < READ_BUF_SIZE);
if (read_buf[line_size - 1] == '\n')
{
read_buf[line_size - 1] = '\0';
line_size--;
}
convert_char_to_2bit(read_buf);
strncpy(query_arr + cur_read_size, read_buf, line_size); strncpy(query_arr + cur_read_size, read_buf, line_size);
cur_read_size += line_size; cur_read_size += line_size;
} }
@ -174,7 +224,7 @@ int main(int argc, char *argv[])
#ifdef SHOW_PERF #ifdef SHOW_PERF
int64_t start_time = get_mseconds(); int64_t start_time = get_mseconds();
#endif #endif
score_normal += ksw_normal( score_normal = ksw_normal(
info_arr[i][0], info_arr[i][0],
(uint8_t *)query_arr + cur_query_pos, (uint8_t *)query_arr + cur_query_pos,
info_arr[i][1], info_arr[i][1],
@ -185,21 +235,14 @@ int main(int argc, char *argv[])
#ifdef SHOW_PERF #ifdef SHOW_PERF
time_sw_normal += get_mseconds() - start_time; time_sw_normal += get_mseconds() - start_time;
#endif #endif
// 更新query和target位置信息 score_normal_total += score_normal;
cur_query_pos += info_arr[i][0]; // fprintf(normal_out_f, "%d %d\n", info_arr[i][2], score_normal);
cur_target_pos += info_arr[i][1]; fprintf(normal_out_f, "%d %d %d %d %d %d %d\n", info_arr[i][2], score_normal, qle, tle, gtle, gscore, max_off[0]);
// fprintf(stderr, "%d %d %d %d %d %d %d\n", score_normal, qle, tle, gtle, gscore, max_off[0], max_off[1]);
}
// avx2 sw
cur_query_pos = 0;
cur_target_pos = 0;
for (i = 0; i < block_line_num; ++i)
{
#ifdef SHOW_PERF #ifdef SHOW_PERF
int64_t start_time = get_mseconds(); start_time = get_mseconds();
#endif #endif
score_avx2 += ksw_avx2( score_avx2 = ksw_avx2(
info_arr[i][0], info_arr[i][0],
(uint8_t *)query_arr + cur_query_pos, (uint8_t *)query_arr + cur_query_pos,
info_arr[i][1], info_arr[i][1],
@ -212,21 +255,13 @@ int main(int argc, char *argv[])
#ifdef SHOW_PERF #ifdef SHOW_PERF
time_sw_avx2 += get_mseconds() - start_time; time_sw_avx2 += get_mseconds() - start_time;
#endif #endif
// 更新query和target位置信息 score_avx2_total += score_avx2;
cur_query_pos += info_arr[i][0]; // fprintf(avx2_out_f, "%d %d\n", info_arr[i][2], score_avx2);
cur_target_pos += info_arr[i][1]; fprintf(avx2_out_f, "%d %d %d %d %d %d %d\n", info_arr[i][2], score_avx2, qle, tle, gtle, gscore, max_off[0]);
// fprintf(stderr, "%d %d %d %d %d %d %d\n", score_avx2, qle, tle, gtle, gscore, max_off[0], max_off[1]);
}
// avx2 u8 sw
cur_query_pos = 0;
cur_target_pos = 0;
for (i = 0; i < block_line_num; ++i)
{
#ifdef SHOW_PERF #ifdef SHOW_PERF
int64_t start_time = get_mseconds(); start_time = get_mseconds();
#endif #endif
score_avx2_u8 += ksw_avx2_u8( score_avx2_u8 = ksw_avx2_u8(
info_arr[i][0], info_arr[i][0],
(uint8_t *)query_arr + cur_query_pos, (uint8_t *)query_arr + cur_query_pos,
info_arr[i][1], info_arr[i][1],
@ -239,21 +274,77 @@ int main(int argc, char *argv[])
#ifdef SHOW_PERF #ifdef SHOW_PERF
time_sw_avx2_u8 += get_mseconds() - start_time; time_sw_avx2_u8 += get_mseconds() - start_time;
#endif #endif
score_avx2_u8_total += score_avx2_u8;
fprintf(avx2_u8_out_f, "%d %d %d %d %d %d\n", score_avx2_u8, qle, tle, gtle, gscore, max_off[0]);
// 更新query和target位置信息 // 更新query和target位置信息
cur_query_pos += info_arr[i][0]; cur_query_pos += info_arr[i][0];
cur_target_pos += info_arr[i][1]; cur_target_pos += info_arr[i][1];
// fprintf(stderr, "%d %d %d %d %d %d %d\n", score_normal, qle, tle, gtle, gscore, max_off[0], max_off[1]); // fprintf(stderr, "%d %d %d %d %d %d %d\n", score_normal, qle, tle, gtle, gscore, max_off[0], max_off[1]);
} }
/*
// avx2 sw
cur_query_pos = 0;
cur_target_pos = 0;
for (i = 0; i < block_line_num; ++i)
{
#ifdef SHOW_PERF
int64_t start_time = get_mseconds();
#endif
score_avx2 += ksw_avx2(
info_arr[i][0],
(uint8_t *)query_arr + cur_query_pos,
info_arr[i][1],
(uint8_t *)target_arr + cur_target_pos,
0, 5, mat, 6, 1, 6, 1,
1, 4,
100, 5, 100,
info_arr[i][2],
&qle, &tle, &gtle, &gscore, &max_off[0]);
#ifdef SHOW_PERF
time_sw_avx2 += get_mseconds() - start_time;
#endif
// 更新query和target位置信息
cur_query_pos += info_arr[i][0];
cur_target_pos += info_arr[i][1];
// fprintf(stderr, "%d %d %d %d %d %d %d\n", score_avx2, qle, tle, gtle, gscore, max_off[0], max_off[1]);
}
// avx2 u8 sw
cur_query_pos = 0;
cur_target_pos = 0;
for (i = 0; i < block_line_num; ++i)
{
#ifdef SHOW_PERF
int64_t start_time = get_mseconds();
#endif
score_avx2_u8 += ksw_avx2_u8(
info_arr[i][0],
(uint8_t *)query_arr + cur_query_pos,
info_arr[i][1],
(uint8_t *)target_arr + cur_target_pos,
0, 5, mat, 6, 1, 6, 1,
1, 4,
100, 5, 100,
info_arr[i][2],
&qle, &tle, &gtle, &gscore, &max_off[0]);
#ifdef SHOW_PERF
time_sw_avx2_u8 += get_mseconds() - start_time;
#endif
// 更新query和target位置信息
cur_query_pos += info_arr[i][0];
cur_target_pos += info_arr[i][1];
// fprintf(stderr, "%d %d %d %d %d %d %d\n", score_normal, qle, tle, gtle, gscore, max_off[0], max_off[1]);
}
*/
// fprintf(stderr, "%d %d \n", block_line_num, total_line_num); // fprintf(stderr, "%d %d \n", block_line_num, total_line_num);
} }
// fprintf(stderr, "%d \n", score_normal); // fprintf(stderr, "%d \n", score_normal);
#ifdef SHOW_PERF #ifdef SHOW_PERF
fprintf(stderr, "time_sw_normal: %f s; score: %d\n", time_sw_normal / 1000.0, score_normal); fprintf(stderr, "time_sw_normal: %f s; score: %d\n", time_sw_normal / 1000.0, score_normal_total);
fprintf(stderr, "time_sw_avx2: %f s; score: %d\n", time_sw_avx2 / 1000.0, score_avx2); fprintf(stderr, "time_sw_avx2: %f s; score: %d\n", time_sw_avx2 / 1000.0, score_avx2_total);
fprintf(stderr, "time_sw_avx2_u8: %f s; score: %d\n", time_sw_avx2_u8 / 1000.0, score_avx2_u8); fprintf(stderr, "time_sw_avx2_u8: %f s; score: %d\n", time_sw_avx2_u8 / 1000.0, score_avx2_u8_total);
#endif #endif
if (query_f != 0) if (query_f != 0)
@ -262,4 +353,10 @@ int main(int argc, char *argv[])
fclose(target_f); fclose(target_f);
if (info_f != 0) if (info_f != 0)
fclose(info_f); fclose(info_f);
if (avx2_out_f != 0)
fclose(avx2_out_f);
if (avx2_u8_out_f != 0)
fclose(avx2_u8_out_f);
if (normal_out_f != 0)
fclose(normal_out_f);
} }