Added VCF header

[samtools.git] / bam_import.c

diff --git a/bam_import.c b/bam_import.c
index 2b4fb7e03f956e6ea35a2216c5c853c414fa0aa4..3a4a5cdf64611d1aa23e98b703976fc85beda117 100644 (file)
--- a/bam_import.c
+++ b/bam_import.c
@@ -116,7 +116,7 @@ static bam_header_t *hash2header(const kh_ref_t *hash)
 bam_header_t *sam_header_read2(const char *fn)
 {
        bam_header_t *header;
-       int c, dret, ret;
+       int c, dret, ret, error = 0;
        gzFile fp;
        kstream_t *ks;
        kstring_t *str;
@@ -135,6 +135,10 @@ bam_header_t *sam_header_read2(const char *fn)
                ks_getuntil(ks, 0, str, &dret);
                len = atoi(str->s);
                k = kh_put(ref, hash, s, &ret);
+               if (ret == 0) {
+                       fprintf(stderr, "[sam_header_read2] duplicated sequence name: %s\n", s);
+                       error = 1;
+               }
                kh_value(hash, k) = (uint64_t)len<<32 | i;
                if (dret != '\n')
                        while ((c = ks_getc(ks)) != '\n' && c != -1);
@@ -143,6 +147,7 @@ bam_header_t *sam_header_read2(const char *fn)
        gzclose(fp);
        free(str->s); free(str);
        fprintf(stderr, "[sam_header_read2] %d sequences loaded.\n", kh_size(hash));
+       if (error) return 0;
        header = hash2header(hash);
        kh_destroy(ref, hash);
        return header;
@@ -171,13 +176,6 @@ 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)
 {
        char **tmp;
@@ -186,10 +184,14 @@ int sam_header_parse(bam_header_t *h)
        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);
-       h->target_name = sam_header2list(h->dict, "SQ", "SN", &h->n_targets);
+       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 = (uint32_t*)calloc(h->n_targets, 4);
+       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);