+ // To prevent long stretches of N's to be mistaken for indels (sometimes thousands of bases),
+ // check the number of N's in the sequence. TODO: this may not be the best place and the best way of doing it
+ int nN=0; for (i=0; i<max_rd_len && ref[i]; i++) if ( ref[i]=='N' ) nN++;
+ if ( nN*2>i ) return -1;
+