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将sw动态开辟内存改成静态数组

This commit is contained in:
zzh 2023-08-22 11:25:34 +08:00
parent 3f06d433e7
commit b58cc1f574
4 changed files with 17 additions and 13 deletions
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8
bsw_avx2.c
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@ -196,6 +196,8 @@ static const uint16_t h_vec_int_mask[SIMD_WIDTH][SIMD_WIDTH] = {
mA1 = mA2; \ mA1 = mA2; \
mA2 = tmp; mA2 = tmp;
uint8_t mem[102400];
int bsw_avx2(int qlen, // query length 待匹配段碱基的query长度 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 const uint8_t *query, // read碱基序列
int tlen, // target length reference的长度 int tlen, // target length reference的长度
@ -221,7 +223,7 @@ int bsw_avx2(int qlen, // query length 待匹配段碱基的query
{ {
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;
int16_t *qtmem, *vmem; int16_t *qtmem, *vmem;
int seq_size = qlen + SIMD_WIDTH, ref_size = tlen + SIMD_WIDTH; 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 i, iStart, D, j, k, beg, end, max, max_i, max_j, max_ins, max_del, max_ie, gscore, max_off;
@ -237,7 +239,7 @@ int bsw_avx2(int qlen, // query length 待匹配段碱基的query
assert(h0 > 0); assert(h0 > 0);
// allocate memory // allocate memory
mem = malloc(mem_size); // mem = malloc(mem_size);
qtmem = (int16_t *)&mem[0]; qtmem = (int16_t *)&mem[0];
seq = &qtmem[0]; seq = &qtmem[0];
ref = &qtmem[seq_size]; ref = &qtmem[seq_size];
@ -534,7 +536,7 @@ int bsw_avx2(int qlen, // query length 待匹配段碱基的query
// } // }
// } // }
free(mem); // free(mem);
if (_qle) if (_qle)
*_qle = max_j + 1; *_qle = max_j + 1;
if (_tle) if (_tle)

8
ksw_avx2_u8.c
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@ -213,6 +213,8 @@ static const uint8_t reverse_mask[SIMD_WIDTH] = {7, 6, 5, 4, 3, 2, 1, 0, 15, 14,
mA1 = mA2; \ mA1 = mA2; \
mA2 = tmp; mA2 = tmp;
uint8_t mem1[102400];
int ksw_avx2_u8(int qlen, // query length 待匹配段碱基的query长度 int ksw_avx2_u8(int qlen, // query length 待匹配段碱基的query长度
const uint8_t *query, // read碱基序列 const uint8_t *query, // read碱基序列
int tlen, // target length reference的长度 int tlen, // target length reference的长度
@ -247,7 +249,7 @@ int ksw_avx2_u8(int qlen, // query length 待匹配段碱基的que
#endif #endif
uint8_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 uint8_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
uint8_t *seq, *ref; uint8_t *seq, *ref;
uint8_t *mem, *qtmem, *vmem; uint8_t *mem = &mem1[0], *qtmem, *vmem;
int seq_size = qlen + SIMD_WIDTH, ref_size = tlen + SIMD_WIDTH; 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 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 Dloop = tlen + qlen; // 循环跳出条件
@ -261,7 +263,7 @@ int ksw_avx2_u8(int qlen, // query length 待匹配段碱基的que
assert(h0 > 0); assert(h0 > 0);
// allocate memory // allocate memory
mem = malloc(mem_size); // mem = malloc(mem_size);
qtmem = &mem[0]; qtmem = &mem[0];
seq = (uint8_t *)&qtmem[0]; seq = (uint8_t *)&qtmem[0];
ref = (uint8_t *)&qtmem[seq_size]; ref = (uint8_t *)&qtmem[seq_size];
@ -488,7 +490,7 @@ int ksw_avx2_u8(int qlen, // query length 待匹配段碱基的que
#endif #endif
} }
free(mem); // free(mem);
if (_qle) if (_qle)
*_qle = max_j + 1; *_qle = max_j + 1;
if (_tle) if (_tle)

2
ksw_normal.c
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@ -18,7 +18,7 @@ typedef struct
int ksw_normal(int qlen, const uint8_t *query, int tlen, const uint8_t *target, int m, const int8_t *mat, int o_del, int e_del, int o_ins, int e_ins, int w, int end_bonus, int zdrop, int h0, int *_qle, int *_tle, int *_gtle, int *_gscore, int *_max_off) int ksw_normal(int qlen, const uint8_t *query, int tlen, const uint8_t *target, int m, const int8_t *mat, int o_del, int e_del, int o_ins, int e_ins, int w, int end_bonus, int zdrop, int h0, int *_qle, int *_tle, int *_gtle, int *_gscore, int *_max_off)
{ {
return h0; // return h0;
eh_t *eh; // score array eh_t *eh; // score array
int8_t *qp; // query profile int8_t *qp; // query profile
int i, j, k, oe_del = o_del + e_del, oe_ins = o_ins + e_ins, beg, end, max, max_i, max_j, max_ins, max_del, max_ie, gscore, max_off; int i, j, k, oe_del = o_del + e_del, oe_ins = o_ins + e_ins, beg, end, max, max_i, max_j, max_ins, max_del, max_ie, gscore, max_off;

12
main.c
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@ -130,12 +130,12 @@ int main(int argc, char *argv[])
// const char *qf_path = "/home/zzh/data/sw/q_m.fa"; // const char *qf_path = "/home/zzh/data/sw/q_m.fa";
// const char *tf_path = "/home/zzh/data/sw/t_m.fa"; // const char *tf_path = "/home/zzh/data/sw/t_m.fa";
// const char *if_path = "/home/zzh/data/sw/i_m.txt"; // const char *if_path = "/home/zzh/data/sw/i_m.txt";
const char *qf_path = "/home/zzh/data/sw/q_l.fa"; // const char *qf_path = "/home/zzh/data/sw/q_l.fa";
const char *tf_path = "/home/zzh/data/sw/t_l.fa"; // const char *tf_path = "/home/zzh/data/sw/t_l.fa";
const char *if_path = "/home/zzh/data/sw/i_l.txt"; // const char *if_path = "/home/zzh/data/sw/i_l.txt";
// const char *qf_path = "/public/home/zzh/data/sw/query.fa"; const char *qf_path = "/home/zzh/data/sw/query.fa";
// const char *tf_path = "/public/home/zzh/data/sw/target.fa"; const char *tf_path = "/home/zzh/data/sw/target.fa";
// const char *if_path = "/public/home/zzh/data/sw/info.txt"; const char *if_path = "/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");