* samtools-0.1.9-2 (r797)

[samtools.git] / bam_sort.c

diff --git a/bam_sort.c b/bam_sort.c
index c992a68fd5ec4360a6d258885110e50193d3b4c8..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);
@@ -149,14 +153,13 @@ 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);