return bam_aux_get(b, tag);
}
+#define __skip_tag(s) do { \
+ int type = toupper(*(s)); \
+ ++(s); \
+ if (type == 'Z' || type == 'H') { while (*(s)) ++(s); ++(s); } \
+ else if (type == 'B') (s) += 5 + bam_aux_type2size(*(s)) * (*(int32_t*)((s)+1)); \
+ else (s) += bam_aux_type2size(type); \
+ } while(0)
+
uint8_t *bam_aux_get(const bam1_t *b, const char tag[2])
{
uint8_t *s;
int y = tag[0]<<8 | tag[1];
s = bam1_aux(b);
while (s < b->data + b->data_len) {
- int type, x = (int)s[0]<<8 | s[1];
+ int x = (int)s[0]<<8 | s[1];
s += 2;
if (x == y) return s;
- type = toupper(*s); ++s;
- if (type == 'C') ++s;
- else if (type == 'S') s += 2;
- else if (type == 'I' || type == 'F') s += 4;
- else if (type == 'D') s += 8;
- else if (type == 'Z' || type == 'H') { while (*s) ++s; ++s; }
+ __skip_tag(s);
}
return 0;
}
+// s MUST BE returned by bam_aux_get()
+int bam_aux_del(bam1_t *b, uint8_t *s)
+{
+ uint8_t *p, *aux;
+ aux = bam1_aux(b);
+ p = s - 2;
+ __skip_tag(s);
+ memmove(p, s, b->l_aux - (s - aux));
+ b->data_len -= s - p;
+ b->l_aux -= s - p;
+ return 0;
+}
void bam_init_header_hash(bam_header_t *header)
{
return k == kh_end(h)? -1 : kh_value(h, k);
}
-int bam_parse_region(bam_header_t *header, const char *str, int *ref_id, int *begin, int *end)
+int bam_parse_region(bam_header_t *header, const char *str, int *ref_id, int *beg, int *end)
{
- char *s, *p;
- int i, l, k;
+ char *s;
+ int i, l, k, name_end;
khiter_t iter;
khash_t(s) *h;
bam_init_header_hash(header);
h = (khash_t(s)*)header->hash;
- l = strlen(str);
- p = s = (char*)malloc(l+1);
- /* squeeze out "," */
- for (i = k = 0; i != l; ++i)
- if (str[i] != ',' && !isspace(str[i])) s[k++] = str[i];
- s[k] = 0;
- for (i = 0; i != k; ++i) if (s[i] == ':') break;
- s[i] = 0;
- iter = kh_get(s, h, s); /* get the ref_id */
- if (iter == kh_end(h)) { // name not found
- *ref_id = -1; free(s);
- return -1;
- }
- *ref_id = kh_value(h, iter);
- if (i == k) { /* dump the whole sequence */
- *begin = 0; *end = 1<<29; free(s);
- return -1;
- }
- for (p = s + i + 1; i != k; ++i) if (s[i] == '-') break;
- *begin = atoi(p);
- if (i < k) {
- p = s + i + 1;
- *end = atoi(p);
- } else *end = 1<<29;
- if (*begin > 0) --*begin;
+ *ref_id = *beg = *end = -1;
+ name_end = l = strlen(str);
+ s = (char*)malloc(l+1);
+ // remove space
+ for (i = k = 0; i < l; ++i)
+ if (!isspace(str[i])) s[k++] = str[i];
+ s[k] = 0; l = k;
+ // determine the sequence name
+ for (i = l - 1; i >= 0; --i) if (s[i] == ':') break; // look for colon from the end
+ if (i >= 0) name_end = i;
+ if (name_end < l) { // check if this is really the end
+ int n_hyphen = 0;
+ for (i = name_end + 1; i < l; ++i) {
+ if (s[i] == '-') ++n_hyphen;
+ else if (!isdigit(s[i]) && s[i] != ',') break;
+ }
+ if (i < l || n_hyphen > 1) name_end = l; // malformated region string; then take str as the name
+ s[name_end] = 0;
+ iter = kh_get(s, h, s);
+ if (iter == kh_end(h)) { // cannot find the sequence name
+ iter = kh_get(s, h, str); // try str as the name
+ if (iter == kh_end(h)) {
+ if (bam_verbose >= 2) fprintf(stderr, "[%s] fail to determine the sequence name.\n", __func__);
+ free(s); return -1;
+ } else s[name_end] = ':', name_end = l;
+ }
+ } else iter = kh_get(s, h, str);
+ *ref_id = kh_val(h, iter);
+ // parse the interval
+ if (name_end < l) {
+ for (i = k = name_end + 1; i < l; ++i)
+ if (s[i] != ',') s[k++] = s[i];
+ s[k] = 0;
+ *beg = atoi(s + name_end + 1);
+ for (i = name_end + 1; i != k; ++i) if (s[i] == '-') break;
+ *end = i < k? atoi(s + i + 1) : 1<<29;
+ if (*beg > 0) --*beg;
+ } else *beg = 0, *end = 1<<29;
free(s);
- if (*begin > *end) {
- fprintf(stderr, "[bam_parse_region] invalid region.\n");
- return -1;
- }
- return 0;
+ return *beg <= *end? 0 : -1;
}
int32_t bam_aux2i(const uint8_t *s)
else return 0;
}
-/******************
- * rg2lib related *
- ******************/
-
-int bam_strmap_put(void *rg2lib, const char *rg, const char *lib)
-{
- int ret;
- khint_t k;
- khash_t(r2l) *h = (khash_t(r2l)*)rg2lib;
- char *key;
- if (h == 0) return 1;
- key = strdup(rg);
- k = kh_put(r2l, h, key, &ret);
- if (ret) kh_val(h, k) = strdup(lib);
- else {
- fprintf(stderr, "[bam_rg2lib_put] duplicated @RG ID: %s\n", rg);
- free(key);
- }
- return 0;
-}
-
-const char *bam_strmap_get(const void *rg2lib, const char *rg)
+#ifdef _WIN32
+double drand48()
{
- const khash_t(r2l) *h = (const khash_t(r2l)*)rg2lib;
- khint_t k;
- if (h == 0) return 0;
- k = kh_get(r2l, h, rg);
- if (k != kh_end(h)) return (const char*)kh_val(h, k);
- else return 0;
-}
-
-void *bam_strmap_dup(const void *rg2lib)
-{
- const khash_t(r2l) *h = (const khash_t(r2l)*)rg2lib;
- khash_t(r2l) *g;
- khint_t k, l;
- int ret;
- if (h == 0) return 0;
- g = kh_init(r2l);
- for (k = kh_begin(h); k < kh_end(h); ++k) {
- if (kh_exist(h, k)) {
- char *key = strdup(kh_key(h, k));
- l = kh_put(r2l, g, key, &ret);
- kh_val(g, l) = strdup(kh_val(h, k));
- }
- }
- return g;
-}
-
-void *bam_strmap_init()
-{
- return (void*)kh_init(r2l);
-}
-
-void bam_strmap_destroy(void *rg2lib)
-{
- khash_t(r2l) *h = (khash_t(r2l)*)rg2lib;
- khint_t k;
- if (h == 0) return;
- for (k = kh_begin(h); k < kh_end(h); ++k) {
- if (kh_exist(h, k)) {
- free((char*)kh_key(h, k)); free(kh_val(h, k));
- }
- }
- kh_destroy(r2l, h);
+ return (double)rand() / RAND_MAX;
}
+#endif
projects / samtools.git / blobdiff