#include <ctype.h>
#include "bam.h"
#include "khash.h"
-KHASH_MAP_INIT_INT(aux, uint8_t*)
+typedef char *str_p;
KHASH_MAP_INIT_STR(s, int)
+KHASH_MAP_INIT_STR(r2l, str_p)
+
+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 x = (int)s[0]<<8 | s[1];
+ s += 2;
+ if (x == y) return 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);
-}
-
-void bam_aux_init(bam1_t *b)
-{
- khash_t(aux) *h;
- uint8_t *s;
- if (b->hash == 0) {
- h = kh_init(aux);
- b->hash = h;
- } else {
- h = (khash_t(aux)*)b->hash;
- kh_clear(aux, h);
- }
- s = bam1_aux(b);
- while (s < b->data + b->data_len) {
- uint32_t x = (uint32_t)s[0]<<8 | s[1];
- int ret, type;
- khint_t k;
- s += 2; type = toupper(*s); ++s;
- k = kh_put(aux, h, x, &ret);
- kh_value(h, k) = s;
- if (type == 'C') ++s;
- else if (type == 'S') s += 2;
- else if (type == 'I') s += 4;
- else if (type == 'F') s += 4;
- else if (type == 'Z') { while (*s) putchar(*s++); ++s; }
+ if (*begin > *end) {
+ fprintf(stderr, "[bam_parse_region] invalid region.\n");
+ return -1;
}
+ return 0;
}
-void bam_aux_destroy(bam1_t *b)
-{
- khash_t(aux) *h = (khash_t(aux)*)b->hash;
- kh_destroy(aux, h);
- b->hash = 0;
-}
-static uint8_t *bam_aux_get_core(bam1_t *b, const char tag[2])
-{
- uint32_t x = (uint32_t)tag[0]<<8 | tag[1];
- khint_t k;
- khash_t(aux) *h;
- if (b->hash == 0) bam_aux_init(b);
- h = (khash_t(aux)*)b->hash;
- k = kh_get(aux, h, x);
- if (k == kh_end(h)) return 0;
- return kh_value(h, k);
-}
-int32_t bam_aux_geti(bam1_t *b, const char tag[2], int *err)
+
+int32_t bam_aux2i(const uint8_t *s)
{
int type;
- uint8_t *s = bam_aux_get_core(b, tag);
- *err = 0;
- if (s == 0) { *err = -1; return 0; }
+ if (s == 0) return 0;
type = *s++;
if (type == 'c') return (int32_t)*(int8_t*)s;
else if (type == 'C') return (int32_t)*(uint8_t*)s;
else if (type == 's') return (int32_t)*(int16_t*)s;
else if (type == 'S') return (int32_t)*(uint16_t*)s;
else if (type == 'i' || type == 'I') return *(int32_t*)s;
- else { *err = -2; return 0; }
+ else return 0;
}
-float bam_aux_getf(bam1_t *b, const char tag[2], int *err)
+
+float bam_aux2f(const uint8_t *s)
{
int type;
- uint8_t *s = bam_aux_get_core(b, tag);
- *err = 0;
type = *s++;
- if (s == 0) { *err = -1; return 0; }
+ if (s == 0) return 0.0;
if (type == 'f') return *(float*)s;
- else { *err = -2; return 0; }
+ else return 0.0;
}
-char bam_aux_getc(bam1_t *b, const char tag[2], int *err)
+
+double bam_aux2d(const uint8_t *s)
{
int type;
- uint8_t *s = bam_aux_get_core(b, tag);
- *err = 0;
type = *s++;
- if (s == 0) { *err = -1; return 0; }
- if (type == 'c') return *(char*)s;
- else { *err = -2; return 0; }
+ if (s == 0) return 0.0;
+ if (type == 'd') return *(double*)s;
+ else return 0.0;
}
-char *bam_aux_getZH(bam1_t *b, const char tag[2], int *err)
+
+char bam_aux2A(const uint8_t *s)
+{
+ int type;
+ type = *s++;
+ if (s == 0) return 0;
+ if (type == 'A') return *(char*)s;
+ else return 0;
+}
+
+char *bam_aux2Z(const uint8_t *s)
{
int type;
- uint8_t *s = bam_aux_get_core(b, tag);
- *err = 0;
type = *s++;
- if (s == 0) { *err = -1; return 0; }
+ if (s == 0) return 0;
if (type == 'Z' || type == 'H') return (char*)s;
- else { *err = -2; return 0; }
+ else return 0;
}
projects / samtools.git / blobdiff