56 lines
1.2 KiB
C++
56 lines
1.2 KiB
C++
#include <stdio.h>
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#include <stdlib.h>
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#include <sys/time.h>
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#include "util.h"
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// base转成2bit值
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int bval(char b)
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{
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if (b == 'A')
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return 0;
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if (b == 'C')
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return 1;
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if (b == 'G')
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return 2;
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if (b == 'T')
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return 3;
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return 4;
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}
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// 互补碱基值
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int cbval(char b)
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{
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return 3 - bval(b);
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}
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double realtime(void)
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{
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struct timeval tp;
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struct timezone tzp;
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gettimeofday(&tp, &tzp);
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return tp.tv_sec + tp.tv_usec * 1e-6;
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}
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// 打印故障信息，并终止程序
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void _err_fatal_simple_core(const char *func, const char *msg)
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{
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fprintf(stderr, "[%s] %s Abort!\n", func, msg);
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abort();
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}
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// 读取数据
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bwtint_t fread_fix(FILE *fp, bwtint_t size, void *a)
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{ /* Mac/Darwin has a bug when reading data longer than 2GB. This function fixes this issue by reading data in small chunks */
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const int bufsize = 0x1000000; // 16M block
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bwtint_t offset = 0;
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while (size)
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{
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int x = bufsize < size ? bufsize : size;
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if ((x = fread((uint8_t *)a + offset, 1, x, fp)) == 0)
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break;
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size -= x;
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offset += x;
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}
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return offset;
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} |