#include <stdio.h>
#include <stdlib.h>
#include <sys/time.h>

#include "util.h"

// base转成2bit值
int bval(char b)
{
    if (b == 'A')
        return 0;
    if (b == 'C')
        return 1;
    if (b == 'G')
        return 2;
    if (b == 'T')
        return 3;
    return 4;
}

// 互补碱基值
int cbval(char b)
{
    return 3 - bval(b);
}

double realtime(void)
{
    struct timeval tp;
    struct timezone tzp;
    gettimeofday(&tp, &tzp);
    return tp.tv_sec + tp.tv_usec * 1e-6;
}

// 打印故障信息，并终止程序
void _err_fatal_simple_core(const char *func, const char *msg)
{
    fprintf(stderr, "[%s] %s Abort!\n", func, msg);
    abort();
}

// 读取数据
bwtint_t fread_fix(FILE *fp, bwtint_t size, void *a)
{                                  /* Mac/Darwin has a bug when reading data longer than 2GB. This function fixes this issue by reading data in small chunks */
    const int bufsize = 0x1000000; // 16M block
    bwtint_t offset = 0;
    while (size)
    {
        int x = bufsize < size ? bufsize : size;
        if ((x = fread((uint8_t *)a + offset, 1, x, fp)) == 0)
            break;
        size -= x;
        offset += x;
    }
    return offset;
}