Help! Heap Corruption

[casybay]

Hi all,

I am trying to read two .txt files, save them to two 1D arrays and record their length. Then I define two 2D arrays and allocate memory to them for further use. After these, I free all these memories. But I get errors when I debug:

Windows has triggered a breakpoint in aa.exe.

This may be due to a corruption of the heap, and indicates a bug in aa.exe or any of the DLLs it has loaded.

The output window may have more diagnostic information

The break point locates in close.c--_free_osfhnd(fh );

Here is my code, could you please check and let me know where the problem is?

long getFileSize(char *fileName){
  long res = 0; 
  FILE *pFile;
  
  if(fopen(fileName,"r+")==NULL){
    printf("Cannot open file.\n");
	res = 0;
  }else{
	pFile = fopen (fileName,"r+");
	fseek (pFile,0,SEEK_END);
	res = ftell(pFile);
	fclose (pFile);
  }
  return res;
}

char* getSequence(char*fileName,long size){
  char *res;
  res=(char*)malloc(size*sizeof(char));

  FILE *pFile;
  pFile = fopen(fileName,"r+");
  fgets(res,size-1,pFile);
  fclose (pFile);
  return res;
  free(res);
}

void free2DArray(int **arr, int size)
{	
	for(int i=0 ; i<size; ++i)
		free(arr[i]); 

	free (arr); 
}
int main() { 
  
  //read sequences from files
  char targetFile[] = "target.txt";
  char queryFile[] = "query.txt";
  long targetSize = getFileSize(targetFile)+1;
  long querySize = getFileSize(queryFile)+1;
  printf("targetSize is %d and querySize is %d\n",targetSize,querySize);
  
  if(targetSize==0 || querySize==0){
    printf("File error!\n");
	exit(1);
  }
  char *targetSeq,*querySeq;
  targetSeq = (char*)malloc(targetSize*sizeof(char));
  querySeq = (char*)malloc(querySize*sizeof(char));
  
  targetSeq = getSequence(targetFile,targetSize);
  querySeq = getSequence(queryFile,querySize);
 
  /* first we reserve memory for all the variables we will use */
  int i,j,......;
  int maxAlign = targetSize+querySize;
  int **distance,**trace;
  distance = (int**)malloc(querySize*sizeof(int*));
  trace = (int**)malloc(querySize*sizeof(int*));
  for(i=0;i<targetSize;i++){
     *(distance+i) = (int*)malloc(targetSize*sizeof(int));
	 *(trace+i) = (int*)malloc(targetSize*sizeof(int));
  } 
	free(targetSeq);
	free(querySeq);
	free2DArray(distance,targetSize);
	free2DArray(trace,targetSize);
	return 0;
}

Thanks a bunch!!

[weaknessforcats]

Why are you going to all that trouble. You already have the data in a array.

[code=c]
char arr[100];

char (*arr1)[5] = (char(*)[5])arr;

[/code]

arr1 is now a [20][5] array of char.

You might read this article: http://www.thescripts.com/forum/thread772412.html.

[casybay]

Why are you going to all that trouble. You already have the data in a array.

[code=c]
char arr[100];

char (*arr1)[5] = (char(*)[5])arr;

[/code]

arr1 is now a [20][5] array of char.

You might read this article: http://www.thescripts.com/forum/thread772412.html.

Because I am assigning dynamic arrays, which lengths are determined by the length of the text files, these could be changed.

[casybay]

Because I am assigning dynamic arrays, which lengths are determined by the length of the text files, these could be changed.

This is even weird, cause even though I get errors, but it still runs. But when the row number of 2D array is greater or equal to the column number, the program will crash. How come?