Question

This code generates a random 16-character string using only A,C,T,G. It then checks whether this sequence is in the hash (unordered_map), and if not, inserts it and points to a dummy placeholder.

In its current form, it hangs at datact=16384 when the ‘for i loop’ requires 20000 iterations, despite the fact that there are 4^16 strings with ACTG.

But.. if the string length is changed to 8, 9, 10, 11.. to 15, or 17, 18.. it correctly iterates to 20000. Why does unordered_map refuse to hash new sequences, but only when those sequences are 16 characters long?

#include <string>
#include <vector>
#include <unordered_map>
#include <stdio.h>
#include <stdlib.h>
#include <time.h>
#include <iostream>

using namespace std;


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

    srand ( time(NULL) );

    const int buffersize=10000;
    int currentsize=buffersize;

    int datact=0;

    vector <unsigned int> ctarr(buffersize);

    vector <char> nuc(4);
    nuc[0]='A';
    nuc[1]='C';
    nuc[2]='T';
    nuc[3]='G';

    unordered_map <string,unsigned int*> location;

    unsigned int sct;
    sct=1;

    for (int i=0;i<20000; i++)
    {
        do
        {
            funnelstring="";
            for (int i=0; i<16; i++)
            {   // generate random 16 nucleotide sequence
                funnelstring+=nuc[(rand() % 4)];
            }
        } while (location.find(funnelstring) != location.end()); //asks whether this key has been assigned

        ctarr[datact]=sct;
        location[funnelstring]=&ctarr[datact]; //assign current key to point to data count
        datact++;
        cout << datact << endl;

        if (datact>=currentsize)
        {
            ctarr.resize(currentsize+buffersize);
            currentsize+=buffersize;
        }
    }

    return 0;
}

Answer 1

As @us2012 said, the problem is your PRNG, and the poor randomness in the lower order bits. Here’s a relevant quote:

In Numerical Recipes in C: The Art of Scientific Computing (William H. Press, Brian P. Flannery, Saul A. Teukolsky, William T. Vetterling; New York: Cambridge University Press, 1992 (2nd ed., p. 277)), the following comments are made:

"If you want to generate a random integer between 1 and 10, you should always do it by using high-order bits, as in

j = 1 + (int) (10.0 * (rand() / (RAND_MAX + 1.0)));

and never by anything resembling

j = 1 + (rand() % 10);

(which uses lower-order bits)."

Also, as others have pointed out, you can also use a better, more modern RNG.