Merge commit 'upstream/0.5'

[pysam.git] / samtools / bam_aux.c

diff --git a/samtools/bam_aux.c b/samtools/bam_aux.c
deleted file mode 100644 (file)
index fbcd982..0000000
--- a/samtools/bam_aux.c
+++ /dev/null
@@ -1,182 +0,0 @@
-#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 == '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)
-{
-       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 *begin, int *end)
-{
-       char *s, *p;
-       int i, l, k;
-       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 0;
-       }
-       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;
-       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)
-{
-       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;
-}