*

[samtools.git] / bam_aux.c

diff --git a/bam_aux.c b/bam_aux.c
index 640004d9baf340465fdb1df1c2045464b6f82eda..6a82d9affb8e4d0341cf3ae26997e4e1bc72f594 100644 (file)
--- a/bam_aux.c
+++ b/bam_aux.c
@@ -19,30 +19,48 @@ void bam_aux_append(bam1_t *b, const char tag[2], char type, int len, uint8_t *d
        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];
+               printf("%c%c\n", s[0], 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)
 {