* samtools-0.1.7-1 (r515)

[samtools.git] / bam_import.c

diff --git a/bam_import.c b/bam_import.c
index 9d463d102bbb254ddf5a5b9bf32b5f216aac2187..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;