5 KHASH_MAP_INIT_STR(str2id, int)
7 void *bcf_build_refhash(bcf_hdr_t *h)
11 hash = kh_init(str2id);
12 for (i = 0; i < h->n_ref; ++i) {
14 k = kh_put(str2id, hash, h->ns[i], &ret); // FIXME: check ret
20 void *bcf_str2id_init()
22 return kh_init(str2id);
25 void bcf_str2id_destroy(void *_hash)
27 khash_t(str2id) *hash = (khash_t(str2id)*)_hash;
28 if (hash) kh_destroy(str2id, hash); // Note that strings are not freed.
31 int bcf_str2id(void *_hash, const char *str)
33 khash_t(str2id) *hash = (khash_t(str2id)*)_hash;
36 k = kh_get(str2id, hash, str);
37 return k == kh_end(hash)? -1 : kh_val(hash, k);
40 int bcf_str2id_add(void *_hash, const char *str)
44 khash_t(str2id) *hash = (khash_t(str2id)*)_hash;
46 k = kh_put(str2id, hash, str, &ret);
47 if (ret == 0) return kh_val(hash, k);
48 kh_val(hash, k) = kh_size(hash) - 1;
49 return kh_val(hash, k);
52 int bcf_shrink_alt(bcf1_t *b, int n)
55 int i, j, k, *z, n_smpl = b->n_smpl;
56 if (b->n_alleles <= n) return -1;
58 for (p = b->alt, k = 1; *p; ++p)
59 if (*p == ',' && ++k == n) break;
61 } else p = b->alt, *p = '\0';
63 memmove(p, b->flt, b->str + b->l_str - b->flt);
64 b->l_str -= b->flt - p;
65 z = alloca(sizeof(int) / 2 * n * (n+1));
66 for (i = k = 0; i < n; ++i)
67 for (j = 0; j < n - i; ++j)
68 z[k++] = i * b->n_alleles + j;
69 for (i = 0; i < b->n_gi; ++i) {
70 bcf_ginfo_t *g = b->gi + i;
71 if (g->fmt == bcf_str2int("PL", 2)) {
72 int l, x = b->n_alleles * (b->n_alleles + 1) / 2;
73 uint8_t *d = (uint8_t*)g->data;
74 g->len = n * (n + 1) / 2;
75 for (l = k = 0; l < n_smpl; ++l) {
76 uint8_t *dl = d + l * x;
77 for (j = 0; j < g->len; ++j) d[k++] = dl[z[j]];
86 int bcf_gl2pl(bcf1_t *b)
89 int i, n_smpl = b->n_smpl;
93 if (strstr(b->fmt, "PL")) return -1;
94 if ((p = strstr(b->fmt, "GL")) == 0) return -1;
96 for (i = 0; i < b->n_gi; ++i)
97 if (b->gi[i].fmt == bcf_str2int("GL", 2))
100 g->fmt = bcf_str2int("PL", 2);
101 g->len /= 4; // 4 == sizeof(float)
102 d0 = (float*)g->data; d1 = (uint8_t*)g->data;
103 for (i = 0; i < n_smpl * g->len; ++i) {
104 int x = (int)(-10. * d0[i] + .499);
105 if (x > 255) x = 255;
111 /* FIXME: this function will fail given AB:GTX:GT. BCFtools never
112 * produces such FMT, but others may do. */
113 int bcf_fix_gt(bcf1_t *b)
119 // check the presence of the GT FMT
120 if ((s = strstr(b->fmt, ":GT")) == 0) return 0; // no GT or GT is already the first
121 if (s[3] != '\0' && s[3] != ':') return 0; // :GTX in fact
122 tmp = bcf_str2int("GT", 2);
123 for (i = 0; i < b->n_gi; ++i)
124 if (b->gi[i].fmt == tmp) break;
125 if (i == b->n_gi) return 0; // no GT in b->gi; probably a bug...
127 // move GT to the first
128 for (; i > 0; --i) b->gi[i] = b->gi[i-1];
130 memmove(b->fmt + 3, b->fmt, s + 1 - b->fmt);
131 b->fmt[0] = 'G'; b->fmt[1] = 'T'; b->fmt[2] = ':';