Imported Upstream version 0.1.6~dfsg

[samtools.git] / bam_aux.c

diff --git a/bam_aux.c b/bam_aux.c
index 7482500ef08a53f3471858793112d9c72263e33a..d0d733fc467bfa9af7d2f032b83ffb47840ef18a 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);
 }
 
        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) {
 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;
                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;
 }
        }
        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)
 {
 
 void bam_init_header_hash(bam_header_t *header)
 {