#include <ctype.h>
#include "bam.h"
#include "khash.h"
+typedef char *str_p;
KHASH_MAP_INIT_STR(s, int)
+KHASH_MAP_INIT_STR(r2l, str_p)
-uint8_t *bam_aux_get(bam1_t *b, const char tag[2])
+void bam_aux_append(bam1_t *b, const char tag[2], char type, int len, uint8_t *data)
+{
+ int ori_len = b->data_len;
+ b->data_len += 3 + len;
+ b->l_aux += 3 + len;
+ if (b->m_data < b->data_len) {
+ b->m_data = b->data_len;
+ kroundup32(b->m_data);
+ b->data = (uint8_t*)realloc(b->data, b->m_data);
+ }
+ b->data[ori_len] = tag[0]; b->data[ori_len + 1] = tag[1];
+ b->data[ori_len + 2] = type;
+ memcpy(b->data + ori_len + 3, data, len);
+}
+
+uint8_t *bam_aux_get_core(bam1_t *b, const char tag[2])
+{
+ return bam_aux_get(b, tag);
+}
+
+#define __skip_tag(s) do { \
+ int type = toupper(*(s)); \
+ ++(s); \
+ if (type == 'C' || type == 'A') ++(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); } \
+ } 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) putchar(*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);
}
-void 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 *begin, int *end)
{
char *s, *p;
int i, l, k;
bam_init_header_hash(header);
h = (khash_t(s)*)header->hash;
-
+
l = strlen(str);
p = s = (char*)malloc(l+1);
/* squeeze out "," */
iter = kh_get(s, h, s); /* get the ref_id */
if (iter == kh_end(h)) { // name not found
*ref_id = -1; free(s);
- return;
+ return -1;
}
*ref_id = kh_value(h, iter);
if (i == k) { /* dump the whole sequence */
*begin = 0; *end = 1<<29; free(s);
- return;
+ return -1;
}
for (p = s + i + 1; i != k; ++i) if (s[i] == '-') break;
*begin = atoi(p);
*end = atoi(p);
} else *end = 1<<29;
if (*begin > 0) --*begin;
- assert(*begin <= *end);
free(s);
+ if (*begin > *end) {
+ fprintf(stderr, "[bam_parse_region] invalid region.\n");
+ return -1;
+ }
+ return 0;
}
int32_t bam_aux2i(const uint8_t *s)
if (type == 'Z' || type == 'H') return (char*)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)
+{
+ 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);
+}