Subject 1: EXC_BAD_ACCESS (code = 1, address = 0x0) standard C memory problem

Question

I am writing code to compare two input files in standard C using the Xcode IDE. I keep getting this error: Thread 1: EXC_BAD_ACCESS (code = 1, address = 0x0). I read about it and believe that this is a memory problem, but no matter what I try, I cannot fix it (I also tried to make the structures dynamically using malloc, and indicated that the code is below). This is strange because it writes all the data and then spits out this error at the end. The file format looks something like this: start (int) .. stop (int) id (+ or -) now some things that I don’t need for the rest of the line I just tested this in a file with only + id, so the aspect “- "is not part of the problem. In any case, I was pretty tired and looked at it for several hours, so please forgive me if this does not make sense,I will update it after several hours of sleep.

typedef struct
{
  int start;
  int stop;
  char *strandID;
} location;

int main(int argc, const char * argv[])
{
  if (argc != 4)
  {
    fprintf(stderr,
        "Usage is ./a.out windowfile.txt genefile.txt outputFileName");
    exit(-1);
  }

  //const vars
  const char *windowInput = argv[1];
  const char *geneInput = argv[2];
  const char *outputfile = argv[3];

  const int windowHeader = 9;
  const int geneHeader = 3;

  //get size of structures -- I have debugged and these work correctly, returning the size of my structure
  const int posWsize = getSize(windowInput, "+", windowHeader);
  const int negWsize = getSize(windowInput, "-", windowHeader);
  const int posGsize = getSize(geneInput, "+", geneHeader);
  const int negGsize = getSize(geneInput, "-", geneHeader);

  //declare structs
  location posWindow[posWsize];
  location negWindow[negWsize];
  location posGene[posGsize];
  location negGene[negGsize];

  //extract data here
  getLocations(posWindow, negWindow, windowInput, windowHeader);
  return 0;
}

void getLocations(location *posL, location *negL, const char *input,
    const int header)
{
  FILE *fileptr = NULL;
  fileptr = fopen(input, "r"); //open file

  if (fileptr == NULL)
  { //check for errors while opening
    fprintf(stderr, "Error reading %s\n", input);
    exit(-1);
  }

  char tmpLoc[20];
  char tmpID[2];
  int eofVar = 0;
  int lineCount = 0;

  while (lineCount < header)
  { //skip header and get to data
    eofVar = fgetc(fileptr);
    if (eofVar == '\n')
      lineCount++;
  }

  int pCount = 0;
  int nCount = 0;

  while (eofVar != EOF)
  {
    fscanf(fileptr, "%s %s", tmpLoc, tmpID); //scan in first two strings
    if (!strcmp(tmpID, "+"))
    { //if + strand
      char *locTok = NULL;
      locTok = strtok(tmpLoc, ".."); //tok and get values
      posL[pCount].start = atoi(locTok);
      locTok = strtok(NULL, "..");
      posL[pCount].stop = atoi(locTok); //ERROR IS SHOWN HERE

      posL[pCount].strandID = tmpID;
      printf("start=%d\tstop=%d\tID=%s\tindex=%d\n", posL[pCount].start,
          posL[pCount].stop, posL[pCount].strandID, pCount);
      pCount++;
    }
    else if (!strcmp(tmpID, "-"))
    { //if - strand
      char *locTok = NULL;
      locTok = strtok(tmpLoc, ".."); //tok and get values
      negL[nCount].start = atoi(locTok);
      locTok = strtok(NULL, "..");
      negL[nCount].stop = atoi(locTok);

      negL[nCount].strandID = tmpID;
      nCount++;
    }

    while ((eofVar = fgetc(fileptr)) != '\n')
    {
      if (eofVar == EOF)
        break;
    }
  }

  fclose(fileptr);
}

//dynamic way...same issue -- just replace this with the above if statement and use the create location function
if (!strcmp(tmpID, "+"))
{ //if + strand
  int locStart;
  int locStop;

  locStart = atoi(strtok(tmpLoc, ".."));//tok and get values
  locStop = atoi(strtok(NULL, ".."));

  posL[pCount] = *createlocation(locStart, locStop, tmpID);

  pCount++;
}

location *createlocation(int start, int stop, char *strandID)
{
  location *tmp = NULL;
  tmp = (location *) malloc(sizeof(location) * 1);

  tmp->start = start;
  tmp->stop = stop;
  tmp->strandID = (char *) malloc(sizeof(char) * 2);
  strcpy(tmp->strandID, strandID);

  return tmp;
}

Answer 1

strtok.

locTok = strtok(NULL, "..");
posL[pCount].stop = atoi(locTok); //ERROR IS SHOWN HERE

strtok NULL ,

, .

, , 0x0, - NULL.

, atoi -NULL .

Answer 2

. .