5 KHASH_MAP_INIT_STR(s, int)
6 KHASH_MAP_INIT_STR(r2l, str_p)
8 void bam_aux_append(bam1_t *b, const char tag[2], char type, int len, uint8_t *data)
10 int ori_len = b->data_len;
11 b->data_len += 3 + len;
13 if (b->m_data < b->data_len) {
14 b->m_data = b->data_len;
15 kroundup32(b->m_data);
16 b->data = (uint8_t*)realloc(b->data, b->m_data);
18 b->data[ori_len] = tag[0]; b->data[ori_len + 1] = tag[1];
19 b->data[ori_len + 2] = type;
20 memcpy(b->data + ori_len + 3, data, len);
23 uint8_t *bam_aux_get_core(bam1_t *b, const char tag[2])
25 return bam_aux_get(b, tag);
28 uint8_t *bam_aux_get(const bam1_t *b, const char tag[2])
31 int y = tag[0]<<8 | tag[1];
33 while (s < b->data + b->data_len) {
34 int type, x = (int)s[0]<<8 | s[1];
37 type = toupper(*s); ++s;
39 else if (type == 'S') s += 2;
40 else if (type == 'I' || type == 'F') s += 4;
41 else if (type == 'D') s += 8;
42 else if (type == 'Z' || type == 'H') { while (*s) putchar(*s++); ++s; }
47 void bam_init_header_hash(bam_header_t *header)
49 if (header->hash == 0) {
53 header->hash = h = kh_init(s);
54 for (i = 0; i < header->n_targets; ++i) {
55 iter = kh_put(s, h, header->target_name[i], &ret);
56 kh_value(h, iter) = i;
61 void bam_destroy_header_hash(bam_header_t *header)
64 kh_destroy(s, (khash_t(s)*)header->hash);
67 int32_t bam_get_tid(const bam_header_t *header, const char *seq_name)
70 khash_t(s) *h = (khash_t(s)*)header->hash;
71 k = kh_get(s, h, seq_name);
72 return k == kh_end(h)? -1 : kh_value(h, k);
75 void bam_parse_region(bam_header_t *header, const char *str, int *ref_id, int *begin, int *end)
82 bam_init_header_hash(header);
83 h = (khash_t(s)*)header->hash;
86 p = s = (char*)malloc(l+1);
88 for (i = k = 0; i != l; ++i)
89 if (str[i] != ',' && !isspace(str[i])) s[k++] = str[i];
91 for (i = 0; i != k; ++i) if (s[i] == ':') break;
93 iter = kh_get(s, h, s); /* get the ref_id */
94 if (iter == kh_end(h)) { // name not found
95 *ref_id = -1; free(s);
98 *ref_id = kh_value(h, iter);
99 if (i == k) { /* dump the whole sequence */
100 *begin = 0; *end = 1<<29; free(s);
103 for (p = s + i + 1; i != k; ++i) if (s[i] == '-') break;
109 if (*begin > 0) --*begin;
110 assert(*begin <= *end);
114 int32_t bam_aux2i(const uint8_t *s)
117 if (s == 0) return 0;
119 if (type == 'c') return (int32_t)*(int8_t*)s;
120 else if (type == 'C') return (int32_t)*(uint8_t*)s;
121 else if (type == 's') return (int32_t)*(int16_t*)s;
122 else if (type == 'S') return (int32_t)*(uint16_t*)s;
123 else if (type == 'i' || type == 'I') return *(int32_t*)s;
127 float bam_aux2f(const uint8_t *s)
131 if (s == 0) return 0.0;
132 if (type == 'f') return *(float*)s;
136 double bam_aux2d(const uint8_t *s)
140 if (s == 0) return 0.0;
141 if (type == 'd') return *(double*)s;
145 char bam_aux2A(const uint8_t *s)
149 if (s == 0) return 0;
150 if (type == 'A') return *(char*)s;
154 char *bam_aux2Z(const uint8_t *s)
158 if (s == 0) return 0;
159 if (type == 'Z' || type == 'H') return (char*)s;
167 int bam_strmap_put(void *rg2lib, const char *rg, const char *lib)
171 khash_t(r2l) *h = (khash_t(r2l)*)rg2lib;
172 char *key = strdup(rg);
173 k = kh_put(r2l, h, key, &ret);
174 if (ret) kh_val(h, k) = strdup(lib);
176 fprintf(stderr, "[bam_rg2lib_put] duplicated @RG ID: %s\n", rg);
182 const char *bam_strmap_get(const void *rg2lib, const char *rg)
184 const khash_t(r2l) *h = (const khash_t(r2l)*)rg2lib;
186 k = kh_get(r2l, h, rg);
187 if (k != kh_end(h)) return (const char*)kh_val(h, k);
191 void *bam_strmap_dup(const void *rg2lib)
193 const khash_t(r2l) *h = (const khash_t(r2l)*)rg2lib;
194 khash_t(r2l) *g = kh_init(r2l);
197 for (k = kh_begin(h); k < kh_end(h); ++k) {
198 if (kh_exist(h, k)) {
199 char *key = strdup(kh_key(h, k));
200 l = kh_put(r2l, g, key, &ret);
201 kh_val(g, l) = strdup(kh_val(h, k));
207 void *bam_strmap_init()
209 return (void*)kh_init(r2l);
212 void bam_strmap_destroy(void *rg2lib)
214 khash_t(r2l) *h = (khash_t(r2l)*)rg2lib;
217 for (k = kh_begin(h); k < kh_end(h); ++k) {
218 if (kh_exist(h, k)) {
219 free((char*)kh_key(h, k)); free(kh_val(h, k));
225 /*** The following routines were implemented by Nils Homer for color-space support in tview ***/
227 char bam_aux_getCSi(bam1_t *b, int i)
229 uint8_t *c = bam_aux_get(b, "CS");
232 // return the base if the tag was not found
236 // adjust for strandedness and leading adaptor
237 if(bam1_strand(b)) i = strlen(cs) - 1 - i;
242 char bam_aux_getCQi(bam1_t *b, int i)
244 uint8_t *c = bam_aux_get(b, "CQ");
247 // return the base if the tag was not found
251 // adjust for strandedness
252 if(bam1_strand(b)) i = strlen(cq) - 1 - i;
256 char bam_aux_nt2int(char a)
277 char bam_aux_ntnt2cs(char a, char b)
279 a = bam_aux_nt2int(a);
280 b = bam_aux_nt2int(b);
281 if(4 == a || 4 == b) return '4';
282 return "0123"[(int)(a ^ b)];
285 char bam_aux_getCEi(bam1_t *b, int i)
288 uint8_t *c = bam_aux_get(b, "CS");
291 char cur_color, cor_color;
293 // return the base if the tag was not found
298 // adjust for strandedness and leading adaptor
299 if(bam1_strand(b)) { //reverse strand
300 cs_i = strlen(cs) - 1 - i;
302 cur_color = cs[cs_i];
304 prev_b = (0 == cs_i) ? cs[0] : bam_nt16_rev_table[bam1_seqi(bam1_seq(b), i+1)];
306 cur_b = bam_nt16_rev_table[bam1_seqi(bam1_seq(b), i)];
311 cur_color = cs[cs_i];
313 prev_b = (0 == i) ? cs[0] : bam_nt16_rev_table[bam1_seqi(bam1_seq(b), i-1)];
315 cur_b = bam_nt16_rev_table[bam1_seqi(bam1_seq(b), i)];
319 cor_color = bam_aux_ntnt2cs(prev_b, cur_b);
321 if(cur_color == cor_color) {