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213 lines (196 loc) · 4.88 KB
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#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)
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 == '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 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;
}
int bam_aux_drop_other(bam1_t *b, uint8_t *s)
{
if (s) {
uint8_t *p, *aux;
aux = bam1_aux(b);
p = s - 2;
__skip_tag(s);
memmove(aux, p, s - p);
b->data_len -= b->l_aux - (s - p);
b->l_aux = s - p;
} else {
b->data_len -= b->l_aux;
b->l_aux = 0;
}
return 0;
}
void bam_init_header_hash(bam_header_t *header)
{
if (header->hash == 0) {
int ret, i;
khiter_t iter;
khash_t(s) *h;
header->hash = h = kh_init(s);
for (i = 0; i < header->n_targets; ++i) {
iter = kh_put(s, h, header->target_name[i], &ret);
kh_value(h, iter) = i;
}
}
}
void bam_destroy_header_hash(bam_header_t *header)
{
if (header->hash)
kh_destroy(s, (khash_t(s)*)header->hash);
}
int32_t bam_get_tid(const bam_header_t *header, const char *seq_name)
{
khint_t k;
khash_t(s) *h = (khash_t(s)*)header->hash;
k = kh_get(s, h, seq_name);
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 *beg, int *end)
{
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;
*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);
return *beg <= *end? 0 : -1;
}
int32_t bam_aux2i(const uint8_t *s)
{
int type;
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 return 0;
}
float bam_aux2f(const uint8_t *s)
{
int type;
type = *s++;
if (s == 0) return 0.0;
if (type == 'f') return *(float*)s;
else return 0.0;
}
double bam_aux2d(const uint8_t *s)
{
int type;
type = *s++;
if (s == 0) return 0.0;
if (type == 'd') return *(double*)s;
else return 0.0;
}
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;
type = *s++;
if (s == 0) return 0;
if (type == 'Z' || type == 'H') return (char*)s;
else return 0;
}
#ifdef _WIN32
double drand48()
{
return (double)rand() / RAND_MAX;
}
#endif