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;
 }

Thread 1: EXC_BAD_ACCESS (code=1, address=0x0)