Merge commit 'upstream/0.1.10'

[samtools.git] / bam_aux.c

diff --git a/bam_aux.c b/bam_aux.c
index 7482500ef08a53f3471858793112d9c72263e33a..fbcd9822b233dab64f6c861fb332846acb951ce7 100644 (file)
--- a/bam_aux.c
+++ b/bam_aux.c
@@ -25,24 +25,41 @@ 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) ++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)
 {
@@ -98,7 +115,7 @@ int bam_parse_region(bam_header_t *header, const char *str, int *ref_id, int *be
        *ref_id = kh_value(h, iter);
        if (i == k) { /* dump the whole sequence */
                *begin = 0; *end = 1<<29; free(s);
-               return -1;
+               return 0;
        }
        for (p = s + i + 1; i != k; ++i) if (s[i] == '-') break;
        *begin = atoi(p);
@@ -163,70 +180,3 @@ char *bam_aux2Z(const uint8_t *s)
        if (type == 'Z' || type == 'H') return (char*)s;
        else return 0;
 }
-
-/******************
- * rg2lib related *
- ******************/
-
-int bam_strmap_put(void *rg2lib, const char *rg, const char *lib)
-{
-       int ret;
-       khint_t k;
-       khash_t(r2l) *h = (khash_t(r2l)*)rg2lib;
-       char *key;
-       if (h == 0) return 1;
-       key = strdup(rg);
-       k = kh_put(r2l, h, key, &ret);
-       if (ret) kh_val(h, k) = strdup(lib);
-       else {
-               fprintf(stderr, "[bam_rg2lib_put] duplicated @RG ID: %s\n", rg);
-               free(key);
-       }
-       return 0;
-}
-
-const char *bam_strmap_get(const void *rg2lib, const char *rg)
-{
-       const khash_t(r2l) *h = (const khash_t(r2l)*)rg2lib;
-       khint_t k;
-       if (h == 0) return 0;
-       k = kh_get(r2l, h, rg);
-       if (k != kh_end(h)) return (const char*)kh_val(h, k);
-       else return 0;
-}
-
-void *bam_strmap_dup(const void *rg2lib)
-{
-       const khash_t(r2l) *h = (const khash_t(r2l)*)rg2lib;
-       khash_t(r2l) *g;
-       khint_t k, l;
-       int ret;
-       if (h == 0) return 0;
-       g = kh_init(r2l);
-       for (k = kh_begin(h); k < kh_end(h); ++k) {
-               if (kh_exist(h, k)) {
-                       char *key = strdup(kh_key(h, k));
-                       l = kh_put(r2l, g, key, &ret);
-                       kh_val(g, l) = strdup(kh_val(h, k));
-               }
-       }
-       return g;
-}
-
-void *bam_strmap_init()
-{
-       return (void*)kh_init(r2l);
-}
-
-void bam_strmap_destroy(void *rg2lib)
-{
-       khash_t(r2l) *h = (khash_t(r2l)*)rg2lib;
-       khint_t k;
-       if (h == 0) return;
-       for (k = kh_begin(h); k < kh_end(h); ++k) {
-               if (kh_exist(h, k)) {
-                       free((char*)kh_key(h, k)); free(kh_val(h, k));
-               }
-       }
-       kh_destroy(r2l, h);
-}