* samtools-0.1.6-18 (r493)

[samtools.git] / bam_import.c

diff --git a/bam_import.c b/bam_import.c
index 427140db9cbe9e3c80d173b0d69e31b1774c3037..9d463d102bbb254ddf5a5b9bf32b5f216aac2187 100644 (file)
--- a/bam_import.c
+++ b/bam_import.c
@@ -171,36 +171,25 @@ static inline void append_text(bam_header_t *header, kstring_t *str)
        header->text[header->l_text] = 0;
 }
 
-int sam_header_parse_rg(bam_header_t *h)
-{
-       if (h->dict == 0) h->dict = sam_header_parse2(h->text);
-       if (h->rg2lib) h->rg2lib = sam_header2tbl(h->dict, "RG", "ID", "LB");
-       return sam_tbl_size(h->rg2lib);
-}
-
 int sam_header_parse(bam_header_t *h)
 {
-       void *tbl;
        char **tmp;
        int i;
        free(h->target_len); free(h->target_name);
        h->n_targets = 0; h->target_len = 0; h->target_name = 0;
        if (h->l_text < 3) return 0;
        if (h->dict == 0) h->dict = sam_header_parse2(h->text);
-       tbl = sam_header2tbl(h->dict, "SQ", "SN", "LN");
-       h->n_targets = sam_tbl_size(tbl);
-       if (h->n_targets == 0) {
-               sam_tbl_destroy(tbl);
-               return 0;
-       }
-       h->target_len = (uint32_t*)calloc(h->n_targets, 4);
-       h->target_name = (char**)calloc(h->n_targets, sizeof(void*));
-       tmp = (char**)calloc(h->n_targets, sizeof(void*));
-       sam_tbl_pair(tbl, h->target_name, tmp);
+       tmp = sam_header2list(h->dict, "SQ", "SN", &h->n_targets);
+       if (h->n_targets == 0) return 0;
+       h->target_name = calloc(h->n_targets, sizeof(void*));
+       for (i = 0; i < h->n_targets; ++i)
+               h->target_name[i] = strdup(tmp[i]);
+       free(tmp);
+       tmp = sam_header2list(h->dict, "SQ", "LN", &h->n_targets);
+       h->target_len = calloc(h->n_targets, 4);
        for (i = 0; i < h->n_targets; ++i)
                h->target_len[i] = atoi(tmp[i]);
        free(tmp);
-       sam_tbl_destroy(tbl);
        return h->n_targets;
 }