//Function usage:

(checkMTM(pair1.reflinks, j, pair1.genlinks[j][k])

//with pair1 being of type:

typedef struct
{
    int reflinks[200][50];
    int genlinks[200][50];
    int reftokensind;
    int gentokensind;
} alignment_t;

//and checkMTM declared as

int checkMTM(int** links, int referral, int referer)

//compiler says:

warning: passing argument 1 of ‘checkMTM’ from incompatible pointer type