Merge commit 'upstream/0.5'

[pysam.git] / samtools / bam_aux.c.pysam.c

diff --git a/samtools/bam_aux.c.pysam.c b/samtools/bam_aux.c.pysam.c
new file mode 100644 (file)
index 0000000..a1c1890
--- /dev/null
+++ b/samtools/bam_aux.c.pysam.c
@@ -0,0 +1,189 @@
+#include "pysam.h"
+
+#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;
+}
+
+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(pysamerr, "[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;
+}
+
+#ifdef _WIN32
+double drand48()
+{
+       return (double)rand() / RAND_MAX;
+}
+#endif