100 lines
4.3 KiB
C
100 lines
4.3 KiB
C
/*********************************************************************************************
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Description: sw extend functions in bwa-mem
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Copyright : All right reserved by NCIC.ICT
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Author : Zhang Zhonghai
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Date : 2024/04/08
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***********************************************************************************************/
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#include <stdio.h>
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#include <stdlib.h>
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#include "byte_alloc.h"
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#include "utils.h"
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#include "profiling.h"
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#include "extend.h"
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#include "debug.h"
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#define EXTEND_PERFORMANCE_TEST(kernel_id, func, sp, ep) \
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do \
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{ \
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PROF_START(extend); \
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int i, score; \
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for (i = sp; i < ep; ++i) \
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{ \
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score = func( \
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&bmem, \
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kv_A(kv_A(i_arr, i), 0), kv_A(q_arr, i).a, \
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kv_A(kv_A(i_arr, i), 1), kv_A(t_arr, i).a, \
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5, mat, 6, 1, 6, 1, 100, 5, 100, \
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/*kv_A(kv_A(i_arr, i), 2)*/10, \
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&qle, &tle, >le, &gscore, &max_off[0]); \
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score_total[kernel_id] += score; \
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} \
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PROF_END(gprof[kernel_prof_idx[kernel_id]], extend); \
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} while (0)
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/******
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* 输入说明：三个文件，query.fa, target.fa, info.txt
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* query.fa: 每一行代表一个query序列，由ACGTN组成
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* target.fa: 每一行代表一个reference（target）序列，由ACGTN组成
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* info.txt: 每一行由三个数字组成，分别代表query序列长度，target序列长度，以及初始分数h0
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*/
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int main_extend(int argc, char *argv[])
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{
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if (argc < 3) {
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fprintf(stderr, "Need 3 files: query, target, info.\n");
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return -1;
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}
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const char *qf_path = argv[0];
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const char *tf_path = argv[1];
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const char *if_path = argv[2];
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FILE *qfp = fopen(qf_path, "r");
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FILE *tfp = fopen(tf_path, "r");
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FILE *ifp = fopen(if_path, "r");
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buf_t read_buf = {0};
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seq_v q_arr = {0};
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seq_v t_arr = {0};
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qti_v i_arr = {0};
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uint64_t score_total[EXTEND_FUNC_NUM] = {0};
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const int kmax_row = 3000000;
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int query_read_row = read_seq(&q_arr, &read_buf, kmax_row, qfp);
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int target_read_row = read_seq(&t_arr, &read_buf, kmax_row, tfp);
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int info_read_row = read_qt_info(&i_arr, &read_buf, kmax_row, 3, ifp);
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// fprintf(stderr, "read row: %d\t%d\t%d\n", query_read_row, target_read_row, info_read_row);
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int8_t mat[25] = {1, -4, -4, -4, -1,
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-4, 1, -4, -4, -1,
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-4, -4, 1, -4, -1,
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-4, -4, -4, 1, -1,
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-1, -1, -1, -1, -1};
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int kernel_prof_idx[] = {G_EXT_SCALAR, G_EXT_AVX2_I16, G_EXT_AVX2_U8, G_EXT_AVX2_I16_SP};
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byte_mem_t bmem = {0};
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byte_mem_init_alloc(&bmem, 1024 * 1024);
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int max_off[2], qle, tle, gtle, gscore;
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int excute_lines = MIN(MIN(query_read_row, target_read_row), info_read_row);
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//open_qti_files();
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//open_debug_files();
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fprintf(stderr, "excute nums: %d\n", excute_lines);
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EXTEND_PERFORMANCE_TEST(0, extend_scalar, 0, excute_lines);
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EXTEND_PERFORMANCE_TEST(1, extend_avx2_i16, 0, excute_lines);
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EXTEND_PERFORMANCE_TEST(2, extend_avx2_u8, 0, excute_lines);
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EXTEND_PERFORMANCE_TEST(3, extend_avx2_i16_sp, 0, excute_lines);
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int i = 0; for(; i<ARRAY_SIZE(kernel_prof_idx); ++i) { gdata[kernel_prof_idx[i]] = score_total[i]; }
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#ifdef SHOW_PERF
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fprintf(stderr, "[extend scalar ] time: %9.6lf s; score: %ld\n", gprof[G_EXT_SCALAR] / TIME_DIVIDE_BY, gdata[G_EXT_SCALAR]);
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fprintf(stderr, "[extend avx i16] time: %9.6lf s; score: %ld\n", gprof[G_EXT_AVX2_I16] / TIME_DIVIDE_BY, gdata[G_EXT_AVX2_I16]);
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fprintf(stderr, "[extend avx u8 ] time: %9.6lf s; score: %ld\n", gprof[G_EXT_AVX2_U8] / TIME_DIVIDE_BY, gdata[G_EXT_AVX2_U8]);
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fprintf(stderr, "[extend avx sp ] time: %9.6lf s; score: %ld\n", gprof[G_EXT_AVX2_I16_SP] / TIME_DIVIDE_BY, gdata[G_EXT_AVX2_I16_SP]);
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#endif
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// close_files();
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fclose(qfp);
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fclose(tfp);
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fclose(ifp);
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return 0;
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} |