1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
|
#include "pysam.h"
#include <stdlib.h>
#include <stdint.h>
#include "bcf.h"
#define MAX_GENO 359
int8_t seq_bitcnt[] = { 4, 1, 1, 2, 1, 2, 2, 3, 1, 2, 2, 3, 2, 3, 3, 4 };
char *seq_nt16rev = "XACMGRSVTWYHKDBN";
uint32_t *bcf_trio_prep(int is_x, int is_son)
{
int i, j, k, n, map[10];
uint32_t *ret;
ret = calloc(MAX_GENO, 4);
for (i = 0, k = 0; i < 4; ++i)
for (j = i; j < 4; ++j)
map[k++] = 1<<i|1<<j;
for (i = 0, n = 1; i < 10; ++i) { // father
if (is_x && seq_bitcnt[map[i]] != 1) continue;
if (is_x && is_son) {
for (j = 0; j < 10; ++j) // mother
for (k = 0; k < 10; ++k) // child
if (seq_bitcnt[map[k]] == 1 && (map[j]&map[k]))
ret[n++] = j<<16 | i<<8 | k;
} else {
for (j = 0; j < 10; ++j) // mother
for (k = 0; k < 10; ++k) // child
if ((map[i]&map[k]) && (map[j]&map[k]) && ((map[i]|map[j])&map[k]) == map[k])
ret[n++] = j<<16 | i<<8 | k;
}
}
ret[0] = n - 1;
return ret;
}
int bcf_trio_call(const uint32_t *prep, const bcf1_t *b, int *llr, int64_t *gt)
{
int i, j, k;
const bcf_ginfo_t *PL;
uint8_t *gl10;
int map[10];
if (b->n_smpl != 3) return -1; // not a trio
for (i = 0; i < b->n_gi; ++i)
if (b->gi[i].fmt == bcf_str2int("PL", 2)) break;
if (i == b->n_gi) return -1; // no PL
gl10 = alloca(10 * b->n_smpl);
if (bcf_gl10(b, gl10) < 0) {
if (bcf_gl10_indel(b, gl10) < 0) return -1;
}
PL = b->gi + i;
for (i = 0, k = 0; i < 4; ++i)
for (j = i; j < 4; ++j)
map[k++] = seq_nt16rev[1<<i|1<<j];
for (j = 0; j < 3; ++j) // check if ref hom is the most probable in all members
if (((uint8_t*)PL->data)[j * PL->len] != 0) break;
if (j < 3) { // we need to go through the complex procedure
uint8_t *g[3];
int minc = 1<<30, minc_j = -1, minf = 0, gtf = 0, gtc = 0;
g[0] = gl10;
g[1] = gl10 + 10;
g[2] = gl10 + 20;
for (j = 1; j <= (int)prep[0]; ++j) { // compute LK with constraint
int sum = g[0][prep[j]&0xff] + g[1][prep[j]>>8&0xff] + g[2][prep[j]>>16&0xff];
if (sum < minc) minc = sum, minc_j = j;
}
gtc |= map[prep[minc_j]&0xff]; gtc |= map[prep[minc_j]>>8&0xff]<<8; gtc |= map[prep[minc_j]>>16]<<16;
for (j = 0; j < 3; ++j) { // compute LK without constraint
int min = 1<<30, min_k = -1;
for (k = 0; k < 10; ++k)
if (g[j][k] < min) min = g[j][k], min_k = k;
gtf |= map[min_k]<<(j*8);
minf += min;
}
*llr = minc - minf; *gt = (int64_t)gtc<<32 | gtf;
} else *llr = 0, *gt = -1;
return 0;
}
int bcf_pair_call(const bcf1_t *b)
{
int i, j, k;
const bcf_ginfo_t *PL;
if (b->n_smpl != 2) return -1; // not a pair
for (i = 0; i < b->n_gi; ++i)
if (b->gi[i].fmt == bcf_str2int("PL", 2)) break;
if (i == b->n_gi) return -1; // no PL
PL = b->gi + i;
for (j = 0; j < 2; ++j) // check if ref hom is the most probable in all members
if (((uint8_t*)PL->data)[j * PL->len] != 0) break;
if (j < 2) { // we need to go through the complex procedure
uint8_t *g[2];
int minc = 1<<30, minf = 0;
g[0] = PL->data;
g[1] = (uint8_t*)PL->data + PL->len;
for (j = 0; j < PL->len; ++j) // compute LK with constraint
minc = minc < g[0][j] + g[1][j]? minc : g[0][j] + g[1][j];
for (j = 0; j < 2; ++j) { // compute LK without constraint
int min = 1<<30;
for (k = 0; k < PL->len; ++k)
min = min < g[j][k]? min : g[j][k];
minf += min;
}
return minc - minf;
} else return 0;
}
int bcf_min_diff(const bcf1_t *b)
{
int i, min = 1<<30;
const bcf_ginfo_t *PL;
for (i = 0; i < b->n_gi; ++i)
if (b->gi[i].fmt == bcf_str2int("PL", 2)) break;
if (i == b->n_gi) return -1; // no PL
PL = b->gi + i;
for (i = 0; i < b->n_smpl; ++i) {
int m1, m2, j;
const uint8_t *p = (uint8_t*)PL->data;
m1 = m2 = 1<<30;
for (j = 0; j < PL->len; ++j) {
if ((int)p[j] < m1) m2 = m1, m1 = p[j];
else if ((int)p[j] < m2) m2 = p[j];
}
min = min < m2 - m1? min : m2 - m1;
}
return min;
}
|
