https://github.com/sanger-pathogens/gubbins
Tip revision: 7a929bdc443eac319a8e396640ad3189df858426 authored by andrewjpage on 24 September 2014, 08:22:03 UTC
Update README.md
Update README.md
Tip revision: 7a929bd
helper_methods.c
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <sys/stat.h>
#include <fcntl.h>
#include <unistd.h>
#include <errno.h>
#include "helper_methods.h"
int compare_files(char expected_output_filename[],char actual_output_filename[] )
{
FILE *expected_output_fh;
FILE *actual_output_fh;
char *expected_buffer;
char *actual_buffer;
long numbytes;
expected_output_fh = fopen(expected_output_filename, "r");
actual_output_fh = fopen(actual_output_filename, "r");
fseek(expected_output_fh, 0L, SEEK_END);
numbytes = ftell(expected_output_fh);
fseek(expected_output_fh, 0L, SEEK_SET);
expected_buffer = (char*)calloc(numbytes, sizeof(char));
fread(expected_buffer, sizeof(char), numbytes, expected_output_fh);
fclose(expected_output_fh);
fseek(actual_output_fh, 0L, SEEK_END);
numbytes = ftell(actual_output_fh);
fseek(actual_output_fh, 0L, SEEK_SET);
actual_buffer = (char*)calloc(numbytes, sizeof(char));
fread(actual_buffer, sizeof(char), numbytes, actual_output_fh);
fclose(actual_output_fh);
if(strcmp(expected_buffer,actual_buffer) == 0)
{
free(expected_buffer);
free(actual_buffer);
return 1;
}
free(expected_buffer);
free(actual_buffer);
return 0;
}
int number_of_recombinations_in_file(char * fileName)
{
FILE *file = fopen(fileName, "r");
int ch, prev = '\n', lines = 0;
while ( (ch = fgetc(file)) != EOF )
{
if ( ch == '\n' )
{
++lines;
}
prev = ch;
}
fclose(file);
if ( prev != '\n' )
{
++lines;
}
return (int) lines/5;
}
int file_exists(char * fileName)
{
struct stat buf;
int i = stat ( fileName, &buf );
if ( i == 0 )
{
return 1;
}
return 0;
}
int cp(const char *to, const char *from)
{
int fd_to, fd_from;
char buf[4096];
ssize_t nread;
int saved_errno;
fd_from = open(from, O_RDONLY);
if (fd_from < 0)
return -1;
fd_to = open(to, O_WRONLY | O_CREAT | O_EXCL, 0666);
if (fd_to < 0)
goto out_error;
while (nread = read(fd_from, buf, sizeof buf), nread > 0)
{
char *out_ptr = buf;
ssize_t nwritten;
do {
nwritten = write(fd_to, out_ptr, nread);
if (nwritten >= 0)
{
nread -= nwritten;
out_ptr += nwritten;
}
else if (errno != EINTR)
{
goto out_error;
}
} while (nread > 0);
}
if (nread == 0)
{
if (close(fd_to) < 0)
{
fd_to = -1;
goto out_error;
}
close(fd_from);
/* Success! */
return 0;
}
out_error:
saved_errno = errno;
close(fd_from);
if (fd_to >= 0)
close(fd_to);
errno = saved_errno;
return -1;
}