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[samtools.git] / bam_sort.c

diff --git a/bam_sort.c b/bam_sort.c
index c992a68fd5ec4360a6d258885110e50193d3b4c8..90ecddc26c171d112a698cdcba99bb03aebf6d69 100644 (file)
--- a/bam_sort.c
+++ b/bam_sort.c
@@ -149,14 +149,13 @@ int bam_merge_core(int by_qname, const char *out, const char *headers, int n, ch
                        }
                } else { // validate multiple baf
                        if (hout->n_targets != hin->n_targets) {
-                               fprintf(stderr, "[bam_merge_core] file '%s' has different number of target sequences. Abort!\n", fn[i]);
-                               exit(1);
-                       }
-                       for (j = 0; j < hout->n_targets; ++j) {
-                               if (strcmp(hout->target_name[j], hin->target_name[j])) {
-                                       fprintf(stderr, "[bam_merge_core] different target sequence name: '%s' != '%s' in file '%s'. Abort!\n",
-                                                       hout->target_name[j], hin->target_name[j], fn[i]);
-                                       exit(1);
+                               fprintf(stderr, "[bam_merge_core] file '%s' has different number of target sequences. Continue anyway!\n", fn[i]);
+                       } else {
+                               for (j = 0; j < hout->n_targets; ++j) {
+                                       if (strcmp(hout->target_name[j], hin->target_name[j])) {
+                                               fprintf(stderr, "[bam_merge_core] different target sequence name: '%s' != '%s' in file '%s'. Continue anyway!\n",
+                                                               hout->target_name[j], hin->target_name[j], fn[i]);
+                                       }
                                }
                        }
                        bam_header_destroy(hin);