Merge commit 'upstream/0.1.7a.dfsg'

[samtools.git] / bam_import.c

diff --git a/bam_import.c b/bam_import.c
index 1dc906eb49f36428460be547b1582ab52432f651..9d463d102bbb254ddf5a5b9bf32b5f216aac2187 100644 (file)
--- a/bam_import.c
+++ b/bam_import.c
@@ -10,6 +10,7 @@
 #endif
 #include "kstring.h"
 #include "bam.h"
+#include "sam_header.h"
 #include "kseq.h"
 #include "khash.h"
 
@@ -170,107 +171,26 @@ 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)
-{
-       kstring_t *rgid, *rglib;
-       char *p, *q, *s, *r;
-       int n = 0;
-
-       // free
-       if (h == 0) return 0;
-       bam_strmap_destroy(h->rg2lib); h->rg2lib = 0;
-       if (h->l_text < 3) return 0;
-       // parse @RG lines
-       h->rg2lib = bam_strmap_init();
-       rgid = calloc(1, sizeof(kstring_t));
-       rglib = calloc(1, sizeof(kstring_t));
-       s = h->text;
-       while ((s = strstr(s, "@RG")) != 0) {
-               if (rgid->l && rglib->l) {
-                       bam_strmap_put(h->rg2lib, rgid->s, rglib->s);
-                       ++n;
-               }
-               rgid->l = rglib->l = 0;
-               s += 3;
-               r = s;
-               if ((p = strstr(s, "ID:")) != 0) {
-                       q = p + 3;
-                       for (p = q; *p && *p != '\t' && *p != '\r' && *p != '\n'; ++p);
-                       kputsn(q, p - q, rgid);
-               } else {
-                       fprintf(stderr, "[bam_header_parse] missing ID tag in @RG lines.\n");
-                       break;
-               }
-               if (r < p) r = p;
-               if ((p = strstr(s, "LB:")) != 0) {
-                       q = p + 3;
-                       for (p = q; *p && *p != '\t' && *p != '\r' && *p != '\n'; ++p);
-                       kputsn(q, p - q, rglib);
-               } else {
-                       fprintf(stderr, "[bam_header_parse] missing LB tag in @RG lines.\n");
-                       break;
-               }
-               if (r < p) r = p;
-               s = r + 3;
-       }
-       if (rgid->l && rglib->l) {
-               bam_strmap_put(h->rg2lib, rgid->s, rglib->s);
-               ++n;
-       }
-       free(rgid->s); free(rgid);
-       free(rglib->s); free(rglib);
-       if (n == 0) {
-               bam_strmap_destroy(h->rg2lib);
-               h->rg2lib = 0;
-       }
-       return n;
-}
-
 int sam_header_parse(bam_header_t *h)
 {
+       char **tmp;
        int i;
-       char *s, *p, *q, *r;
-
-       // free
        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;
-       // count number of @SQ
-       s = h->text;
-       while ((s = strstr(s, "@SQ")) != 0) {
-               ++h->n_targets;
-               s += 3;
-       }
+       if (h->dict == 0) h->dict = sam_header_parse2(h->text);
+       tmp = sam_header2list(h->dict, "SQ", "SN", &h->n_targets);
        if (h->n_targets == 0) return 0;
-       h->target_len = (uint32_t*)calloc(h->n_targets, 4);
-       h->target_name = (char**)calloc(h->n_targets, sizeof(void*));
-       // parse @SQ lines
-       i = 0;
-       s = h->text;
-       while ((s = strstr(s, "@SQ")) != 0) {
-               s += 3;
-               r = s;
-               if ((p = strstr(s, "SN:")) != 0) {
-                       q = p + 3;
-                       for (p = q; *p && *p != '\t' && *p != '\r' && *p != '\n'; ++p);
-                       h->target_name[i] = (char*)calloc(p - q + 1, 1);
-                       strncpy(h->target_name[i], q, p - q);
-               } else goto header_err_ret;
-               if (r < p) r = p;
-               if ((p = strstr(s, "LN:")) != 0) h->target_len[i] = strtol(p + 3, 0, 10);
-               else goto header_err_ret;
-               if (r < p) r = p;
-               s = r + 3;
-               ++i;
-       }
-       sam_header_parse_rg(h);
+       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);
        return h->n_targets;
-
-header_err_ret:
-       fprintf(stderr, "[bam_header_parse] missing SN or LN tag in @SQ lines.\n");
-       free(h->target_len); free(h->target_name);
-       h->n_targets = 0; h->target_len = 0; h->target_name = 0;
-       return 0;
 }
 
 bam_header_t *sam_header_read(tamFile fp)