sw_perf/utils.h

/*********************************************************************************************
    Description: Some useful functions

    Copyright : All right reserved by NCIC.ICT

    Author : Zhang Zhonghai
    Date : 2023/08/25
***********************************************************************************************/
#ifndef __UTILS_H
#define __UTILS_H

#include <stdlib.h>
#include <stdio.h>
#include <stdint.h>
#include "kvec.h"

#undef MAX
#undef MIN
#define MAX(x, y) ((x) > (y) ? (x) : (y))
#define MIN(x, y) ((x) < (y) ? (x) : (y))

#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

#define ARRAY_SIZE(arr) (sizeof(arr) / sizeof((arr)[0]))

#define BUF_SIZE 1048576

typedef kvec_t(uint8_t) seq_t;
typedef kvec_t(seq_t) seq_v;

typedef kvec_t(int) qti_t; // query target info type
typedef kvec_t(qti_t) qti_v;

typedef struct { size_t m; uint8_t *addr; } buf_t;


extern const char *BASE;

extern unsigned char nst_nt4_table[256];

// 将碱基字符(ACGTN)转成int编码(0~4)
void base_char_to_int(char *str);

int read_qt_info(qti_v *qti_arr, buf_t *buf, int row_num_to_read, int info_num, FILE *fp);

int read_seq(seq_v *seq_arr, buf_t *buf, int row_num_to_read, FILE *fp);

void write_query_target_sequence(int qlen, const uint8_t *query, int tlen, const uint8_t *target, int h0, int fnum);

#endif