- for (i = 0; i < right - left; ++i)
- r[i] = (cns[i] && (double)(cns[i]&0xffff) / ((cns[i]&0xffff)+(cns[i]>>16&0xffff)) < 0.7)? 15 : ref0[i];
-// for (i = 0; i < right - left; ++i) fputc("=ACMGRSVTWYHKDBN"[(int)r[i]], stderr); fputc('\n', stderr);
+ for (i = 0; i < right - left; ++i) r[i] = ref0[i];
+ max = max2 = 0; max_i = max2_i = -1;
+ for (i = 0; i < right - left; ++i) {
+ if (cns[i]>>16 >= max>>16) max2 = max, max2_i = max_i, max = cns[i], max_i = i;
+ else if (cns[i]>>16 >= max2>>16) max2 = cns[i], max2_i = i;
+ }
+ if ((double)(max&0xffff) / ((max&0xffff) + (max>>16)) >= 0.7) max_i = -1;
+ if ((double)(max2&0xffff) / ((max2&0xffff) + (max2>>16)) >= 0.7) max2_i = -1;
+ if (max_i >= 0) r[max_i] = 15;
+ if (max2_i >= 0) r[max2_i] = 15;
+ //for (i = 0; i < right - left; ++i) fputc("=ACMGRSVTWYHKDBN"[(int)r[i]], stderr); fputc('\n', stderr);