7 int8_t seq_bitcnt[] = { 4, 1, 1, 2, 1, 2, 2, 3, 1, 2, 2, 3, 2, 3, 3, 4 };
8 char *seq_nt16rev = "XACMGRSVTWYHKDBN";
10 uint32_t *bcf_trio_prep(int is_x, int is_son)
12 int i, j, k, n, map[10];
14 ret = calloc(MAX_GENO, 4);
15 for (i = 0, k = 0; i < 4; ++i)
16 for (j = i; j < 4; ++j)
18 for (i = 0, n = 1; i < 10; ++i) { // father
19 if (is_x && seq_bitcnt[map[i]] != 1) continue;
21 for (j = 0; j < 10; ++j) // mother
22 for (k = 0; k < 10; ++k) // child
23 if (seq_bitcnt[map[k]] == 1 && (map[j]&map[k]))
24 ret[n++] = j<<16 | i<<8 | k;
26 for (j = 0; j < 10; ++j) // mother
27 for (k = 0; k < 10; ++k) // child
28 if ((map[i]&map[k]) && (map[j]&map[k]) && ((map[i]|map[j])&map[k]) == map[k])
29 ret[n++] = j<<16 | i<<8 | k;
37 int bcf_trio_call(const uint32_t *prep, const bcf1_t *b, int *llr, int64_t *gt)
40 const bcf_ginfo_t *PL;
43 if (b->n_smpl != 3) return -1; // not a trio
44 for (i = 0; i < b->n_gi; ++i)
45 if (b->gi[i].fmt == bcf_str2int("PL", 2)) break;
46 if (i == b->n_gi) return -1; // no PL
47 gl10 = alloca(10 * b->n_smpl);
48 if (bcf_gl10(b, gl10) < 0) {
49 if (bcf_gl10_indel(b, gl10) < 0) return -1;
52 for (i = 0, k = 0; i < 4; ++i)
53 for (j = i; j < 4; ++j)
54 map[k++] = seq_nt16rev[1<<i|1<<j];
55 for (j = 0; j < 3; ++j) // check if ref hom is the most probable in all members
56 if (((uint8_t*)PL->data)[j * PL->len] != 0) break;
57 if (j < 3) { // we need to go through the complex procedure
59 int minc = 1<<30, minc_j = -1, minf = 0, gtf = 0, gtc = 0;
63 for (j = 1; j <= (int)prep[0]; ++j) { // compute LK with constraint
64 int sum = g[0][prep[j]&0xff] + g[1][prep[j]>>8&0xff] + g[2][prep[j]>>16&0xff];
65 if (sum < minc) minc = sum, minc_j = j;
67 gtc |= map[prep[minc_j]&0xff]; gtc |= map[prep[minc_j]>>8&0xff]<<8; gtc |= map[prep[minc_j]>>16]<<16;
68 for (j = 0; j < 3; ++j) { // compute LK without constraint
69 int min = 1<<30, min_k = -1;
70 for (k = 0; k < 10; ++k)
71 if (g[j][k] < min) min = g[j][k], min_k = k;
72 gtf |= map[min_k]<<(j*8);
75 *llr = minc - minf; *gt = (int64_t)gtc<<32 | gtf;
76 } else *llr = 0, *gt = -1;
80 int bcf_pair_call(const bcf1_t *b)
83 const bcf_ginfo_t *PL;
84 if (b->n_smpl != 2) return -1; // not a pair
85 for (i = 0; i < b->n_gi; ++i)
86 if (b->gi[i].fmt == bcf_str2int("PL", 2)) break;
87 if (i == b->n_gi) return -1; // no PL
89 for (j = 0; j < 2; ++j) // check if ref hom is the most probable in all members
90 if (((uint8_t*)PL->data)[j * PL->len] != 0) break;
91 if (j < 2) { // we need to go through the complex procedure
93 int minc = 1<<30, minf = 0;
95 g[1] = (uint8_t*)PL->data + PL->len;
96 for (j = 0; j < PL->len; ++j) // compute LK with constraint
97 minc = minc < g[0][j] + g[1][j]? minc : g[0][j] + g[1][j];
98 for (j = 0; j < 2; ++j) { // compute LK without constraint
100 for (k = 0; k < PL->len; ++k)
101 min = min < g[j][k]? min : g[j][k];
108 int bcf_min_diff(const bcf1_t *b)
111 const bcf_ginfo_t *PL;
112 for (i = 0; i < b->n_gi; ++i)
113 if (b->gi[i].fmt == bcf_str2int("PL", 2)) break;
114 if (i == b->n_gi) return -1; // no PL
116 for (i = 0; i < b->n_smpl; ++i) {
118 const uint8_t *p = (uint8_t*)PL->data;
120 for (j = 0; j < PL->len; ++j) {
121 if ((int)p[j] < m1) m2 = m1, m1 = p[j];
122 else if ((int)p[j] < m2) m2 = p[j];
124 min = min < m2 - m1? min : m2 - m1;