best way to deal with big array or vector?

[dukevn]

My guess is that code like that should execute at the speed of file I/O.
I know I can copy a 1GB file in about 30 seconds, so 11 minutes sounds like WAY too much.
Could you comment out everything in your code except for I/O and see how long that takes?
Do you mind posting your code and a sample data file?

Here is the final code

#include <map>
#include <vector>
#include <stdio.h>
#include <stdlib.h>
#include <fstream>
#include <iostream>
#include <sstream>
#include <string>
#include <time.h>

using namespace std;

int main( int argc, char *argv[] ) {

  if ( argc == 1 ) {
    fprintf(stderr, "Usage: xytest <input> <output>\n");
    return 1;
  }

  time_t start,end;
  double diff;
  time (&start);
  map<int, int> mapTest;
  ifstream fin(argv[1]);
  string tempLine;
  int x1, x2;
  while ( fin >> tempLine >> x1 >> x2 ) {
    getline(fin,tempLine);
    for ( int i = x1; i <= x2; ++i ) {
      ++mapTest[i];
    }
  }
  fin.close();
  ofstream fout(argv[2]);
  for ( map<int, int>::iterator i = mapTest.begin(), end = mapTest.end(); i != end; ++i ) {
    fout << i->first << '\t' << i->second << '\n';
  }
  fout.close();
  time (&end);
  diff = difftime(end, start);
  printf("Running time: %.2lf\n",diff);
  return 0;
}

Some lines in the input file is like this

a1	35952485	35952517	2	0	-
a1	66611781	66611813	15	0	+
a1	154104890	154104922	10	0	+
a1	224631511	224631543	6	0	-

and there are 25501054 lines similar like that in the file. The size of file is 1141987065.

Let me try your suggestion to see what results are.