* This revision is SERIOUSLY BUGGY. Please NOT use it.

[samtools.git] / bam_aux.c

diff --git a/bam_aux.c b/bam_aux.c
index f9be398f0e820d9b48b2002073039af1ebeb95d5..89e99f281adb652e144eea0a77074a1c6cec023a 100644 (file)
--- a/bam_aux.c
+++ b/bam_aux.c
@@ -1,26 +1,65 @@
 #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)
 {
@@ -50,7 +89,7 @@ int32_t bam_get_tid(const bam_header_t *header, const char *seq_name)
        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;
@@ -59,7 +98,7 @@ void bam_parse_region(bam_header_t *header, const char *str, int *ref_id, int *b
 
        bam_init_header_hash(header);
        h = (khash_t(s)*)header->hash;
-       
+
        l = strlen(str);
        p = s = (char*)malloc(l+1);
        /* squeeze out "," */
@@ -71,12 +110,12 @@ void bam_parse_region(bam_header_t *header, const char *str, int *ref_id, int *b
        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);
@@ -85,8 +124,12 @@ void bam_parse_region(bam_header_t *header, const char *str, int *ref_id, int *b
                *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)