CatFinder GENEral

#include <stdio.h>
#include <string>
#include <algorithm>

int main()
{
  long count = 0;
  long update = 0;
  FILE * fp = fopen("hg19.fa", "rt");

  std::string ongoing = "";
  std::string start = "";
  std::string newLine = "";

  // Each line
  while (!feof(fp))
  {
    char line[151];
    fgets(line, 150, fp);
    newLine = line;
    newLine.erase(std::remove(newLine.begin(), newLine.end(), '\n'), newLine.end());
    ongoing += newLine;

    // Check the first 3 chars until we only have 2 left
    while (ongoing.length() > 2)
    {
      start = ongoing.substr(0, 3);
      std::transform(ongoing.begin(), ongoing.end(), ongoing.begin(), ::tolower);
      if (start == "cat")
      {
        // Take off 3 chars and continue
        count++;
        update++;
        ongoing = ongoing.substr(3, ongoing.length()-3);
      } else
      {
        // Take off 1 char and continue
        ongoing = ongoing.substr(1, ongoing.length()-1);
      }
    }

    // Keep updating every 100 finds so we know it is still going
    if (update >= 1000)
    {
      printf("Count: %d\n", count);
      update = 0;
    }
  }
  fclose(fp);

    printf("Final count: %d\n", count);
    return 0;
}