In merging, if -R is specified, do not abort if the sequence dictionary is different.

[samtools.git] / bam_sort.c

diff --git a/bam_sort.c b/bam_sort.c
index e4cc02f899c5ae724463bf7acb18f8fb4826f771..01f7016dd9a35ef27cf4cc232d7529b25d67880b 100644 (file)
--- a/bam_sort.c
+++ b/bam_sort.c
@@ -170,12 +170,12 @@ int bam_merge_core(int by_qname, const char *out, const char *headers, int n, ch
                if (hheaders->n_targets > 0) {
                        if (hout->n_targets != hheaders->n_targets) {
                                fprintf(stderr, "[bam_merge_core] number of @SQ headers in '%s' differs from number of target sequences\n", headers);
-                               return -1;
+                               if (!reg) return -1;
                        }
                        for (j = 0; j < hout->n_targets; ++j)
                                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\n", hheaders->target_name[j], headers);
-                                       return -1;
+                                       if (!reg) return -1;
                                }
                }