From b58cc1f5749fd87e9a89048a686809dc57b56e77 Mon Sep 17 00:00:00 2001 From: zzh Date: Tue, 22 Aug 2023 11:25:34 +0800 Subject: [PATCH] =?UTF-8?q?=E5=B0=86sw=E5=8A=A8=E6=80=81=E5=BC=80=E8=BE=9F?= =?UTF-8?q?=E5=86=85=E5=AD=98=E6=94=B9=E6=88=90=E9=9D=99=E6=80=81=E6=95=B0?= =?UTF-8?q?=E7=BB=84?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- bsw_avx2.c | 8 +++++--- ksw_avx2_u8.c | 8 +++++--- ksw_normal.c | 2 +- main.c | 12 ++++++------ 4 files changed, 17 insertions(+), 13 deletions(-) diff --git a/bsw_avx2.c b/bsw_avx2.c index 44fad1e..2caaa36 100644 --- a/bsw_avx2.c +++ b/bsw_avx2.c @@ -196,6 +196,8 @@ static const uint16_t h_vec_int_mask[SIMD_WIDTH][SIMD_WIDTH] = { mA1 = mA2; \ mA2 = tmp; +uint8_t mem[102400]; + 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 @@ -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 *seq, *ref; - uint8_t *mem; + // 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; @@ -237,7 +239,7 @@ int bsw_avx2(int qlen, // query length 待匹配段碱基的query assert(h0 > 0); // allocate memory - mem = malloc(mem_size); + // mem = malloc(mem_size); qtmem = (int16_t *)&mem[0]; seq = &qtmem[0]; 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) *_qle = max_j + 1; if (_tle) diff --git a/ksw_avx2_u8.c b/ksw_avx2_u8.c index 3627b10..d2c1744 100644 --- a/ksw_avx2_u8.c +++ b/ksw_avx2_u8.c @@ -213,6 +213,8 @@ static const uint8_t reverse_mask[SIMD_WIDTH] = {7, 6, 5, 4, 3, 2, 1, 0, 15, 14, mA1 = mA2; \ mA2 = tmp; +uint8_t mem1[102400]; + 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 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 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 *mem, *qtmem, *vmem; + uint8_t *mem = &mem1[0], *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 @@ -261,7 +263,7 @@ int ksw_avx2_u8(int qlen, // query length 待匹配段碱基的que assert(h0 > 0); // allocate memory - mem = malloc(mem_size); + // mem = malloc(mem_size); qtmem = &mem[0]; seq = (uint8_t *)&qtmem[0]; 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 } - free(mem); + // free(mem); if (_qle) *_qle = max_j + 1; if (_tle) diff --git a/ksw_normal.c b/ksw_normal.c index 3193012..52a2a0c 100644 --- a/ksw_normal.c +++ b/ksw_normal.c @@ -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) { - return h0; + // return h0; eh_t *eh; // score array 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; diff --git a/main.c b/main.c index 80c9a74..bc5f2a6 100644 --- a/main.c +++ b/main.c @@ -130,12 +130,12 @@ int main(int argc, char *argv[]) // const char *qf_path = "/home/zzh/data/sw/q_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 *qf_path = "/home/zzh/data/sw/q_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 *qf_path = "/public/home/zzh/data/sw/query.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 *qf_path = "/home/zzh/data/sw/q_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 *qf_path = "/home/zzh/data/sw/query.fa"; + const char *tf_path = "/home/zzh/data/sw/target.fa"; + const char *if_path = "/home/zzh/data/sw/info.txt"; query_f = fopen(qf_path, "r"); target_f = fopen(tf_path, "r"); info_f = fopen(if_path, "r");