5 KHASH_MAP_INIT_STR(sm, int)
7 bam_sample_t *bam_smpl_init(void)
10 s = calloc(1, sizeof(bam_sample_t));
11 s->rg2smid = kh_init(sm);
15 void bam_smpl_destroy(bam_sample_t *sm)
19 khash_t(sm) *rg2smid = (khash_t(sm)*)sm->rg2smid;
21 for (i = 0; i < sm->n; ++i) free(sm->smpl[i]);
23 for (k = kh_begin(rg2smid); k != kh_end(rg2smid); ++k)
24 if (kh_exist(rg2smid, k)) free((char*)kh_key(rg2smid, k));
25 kh_destroy(sm, sm->rg2smid);
29 static void add_pair(bam_sample_t *sm, khash_t(sm) *sm2id, const char *key, const char *val)
33 khash_t(sm) *rg2smid = (khash_t(sm)*)sm->rg2smid;
34 k_rg = kh_get(sm, rg2smid, key);
35 if (k_rg != kh_end(rg2smid)) return; // duplicated @RG-ID
36 k_rg = kh_put(sm, rg2smid, strdup(key), &ret);
37 k_sm = kh_get(sm, sm2id, val);
38 if (k_sm == kh_end(sm2id)) { // absent
40 sm->m = sm->m? sm->m<<1 : 1;
41 sm->smpl = realloc(sm->smpl, sizeof(void*) * sm->m);
43 sm->smpl[sm->n] = strdup(val);
44 k_sm = kh_put(sm, sm2id, sm->smpl[sm->n], &ret);
45 kh_val(sm2id, k_sm) = sm->n++;
47 kh_val(rg2smid, k_rg) = kh_val(sm2id, k_sm);
50 int bam_smpl_add(bam_sample_t *sm, const char *fn, const char *txt)
52 const char *p = txt, *q, *r;
57 memset(&buf, 0, sizeof(kstring_t));
58 while ((q = strstr(p, "@RG")) != 0) {
61 if ((q = strstr(p, "\tID:")) != 0) q += 4;
62 if ((r = strstr(p, "\tSM:")) != 0) r += 4;
66 for (u = (char*)q; *u && *u != '\t' && *u != '\n'; ++u);
67 for (v = (char*)r; *v && *v != '\t' && *v != '\n'; ++v);
68 oq = *u; or = *v; *u = *v = '\0';
69 buf.l = 0; kputs(fn, &buf); kputc('/', &buf); kputs(q, &buf);
70 add_pair(sm, sm2id, buf.s, r);
76 if (n == 0) add_pair(sm, sm2id, fn, fn);
78 kh_destroy(sm, sm2id);
82 int bam_smpl_rg2smid(const bam_sample_t *sm, const char *fn, const char *rg, kstring_t *str)
85 khash_t(sm) *rg2smid = (khash_t(sm)*)sm->rg2smid;
88 kputs(fn, str); kputc('/', str); kputs(rg, str);
89 k = kh_get(sm, rg2smid, str->s);
90 } else k = kh_get(sm, rg2smid, fn);
91 return k == kh_end(rg2smid)? -1 : kh_val(rg2smid, k);