- for (i = 0; i < 16; ++i) {
- if (tmp[i] < 0) continue;
- if (tmp[i] < min) {
- min3 = min2; min2 = min; min = tmp[i]; min_g2 = min_g; min_g = i;
- } else if (tmp[i] < min2) {
- min3 = min2; min2 = tmp[i]; min_g2 = i;
- } else if (tmp[i] < min3) min3 = tmp[i];
- }
- x = min_g >= 0? (1U<<(min_g>>2&3) | 1U<<(min_g&3)) << 28 : 0xf << 28;
- x |= min_g2 >= 0? (1U<<(min_g2>>2&3) | 1U<<(min_g2&3)) << 24 : 0xf << 24;
- x |= (uint32_t)g->max_mapQ << 16;
- x |= min2 < 10000? (min2 - min < 256? min2 - min : 255) << 8 : 0xff << 8;
- x |= min2 < 10000 && min3 < 10000? (min3 - min2 < 256? min3 - min2 : 255) : 0xff;
+ for (i = 1; i < 10; ++i) // insertion sort
+ for (j = i; j > 0 && p[j] < p[j-1]; --j)
+ k = p[j], p[j] = p[j-1], p[j-1] = k;
+ x = (1u<<(p[0]&3) | 1u<<(p[0]>>2&3)) << 28; // the best genotype
+ x |= (uint32_t)g->max_mapQ << 16; // rms mapQ
+ x |= ((p[1]>>4) - (p[0]>>4) < 256? (p[1]>>4) - (p[0]>>4) : 255) << 8; // consensus Q
+ for (k = 0; k < 10; ++k)
+ if ((p[k]&0xf) == (ref4<<2|ref4)) break;
+ if (k == 10) k = 9;
+ x |= (p[k]>>4) - (p[0]>>4) < 256? (p[k]>>4) - (p[0]>>4) : 255; // snp Q