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

diff --git a/NEWS b/NEWS
index 6c2195e5929fab1dbe96b5fafc734a62443ec99c..91434f3ff72b34358644fe3dad36c5ef9b8cf8a5 100644 (file)
--- a/NEWS
+++ b/NEWS
@@ -1,3 +1,25 @@
+Beta release 0.1.11 (19 November, 2010)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+This is a bug fix release:
+
+ * Fixed a bug in random retrieval (since 0.1.8). It occurs when reads
+   are retrieved from a small region containing no reads.
+
+ * Fixed a bug in pileup (since 0.1.9). The bug causes an assertion
+   failure when the first CIGAR operation is a deletion.
+
+ * Improved fault tolerence in remote access.
+
+In addition, since 0.1.10, the `pileup' command has been deprecated by
+`mpileup' which is more powerful and more accurate. The `pileup' command
+will not be removed in the next few releases, but new features will not
+be added.
+
+(0.1.11: 19 November 2010, r842)
+
+
+
 Beta Release 0.1.10 (16 November, 2010)
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 

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;
                                }
                }