* samtools-0.1.8-22 (r781)

[samtools.git] / bam_sort.c

diff --git a/bam_sort.c b/bam_sort.c
index 90ecddc26c171d112a698cdcba99bb03aebf6d69..76ab793196ca76fc5a63d619e230cf0fb5f59f1e 100644 (file)
--- a/bam_sort.c
+++ b/bam_sort.c
@@ -137,11 +137,15 @@ int bam_merge_core(int by_qname, const char *out, const char *headers, int n, ch
                                // check that they are consistent with the existing binary list
                                // of reference information.
                                if (hheaders->n_targets > 0) {
-                                       if (hout->n_targets != hheaders->n_targets)
+                                       if (hout->n_targets != hheaders->n_targets) {
                                                fprintf(stderr, "[bam_merge_core] number of @SQ headers in `%s' differs from number of target sequences", headers);
+                                               if (!reg) return -1;
+                                       }
                                        for (j = 0; j < hout->n_targets; ++j)
-                                               if (strcmp(hout->target_name[j], hheaders->target_name[j]) != 0)
+                                               if (strcmp(hout->target_name[j], hheaders->target_name[j]) != 0) {
                                                        fprintf(stderr, "[bam_merge_core] @SQ header '%s' in '%s' differs from target sequence", hheaders->target_name[j], headers);
+                                                       if (!reg) return -1;
+                                               }
                                }
                                swap_header_text(hout, hheaders);
                                bam_header_destroy(hheaders);