From c957fcdfce937652394b3b9489f0c6706d64c75d Mon Sep 17 00:00:00 2001 From: Heng Li Date: Sat, 20 Nov 2010 03:26:36 +0000 Subject: [PATCH] In merging, if -R is specified, do not abort if the sequence dictionary is different. --- NEWS | 22 ++++++++++++++++++++++ bam_sort.c | 4 ++-- 2 files changed, 24 insertions(+), 2 deletions(-) diff --git a/NEWS b/NEWS index 6c2195e..91434f3 100644 --- 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 e4cc02f..01f7016 100644 --- 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; } } -- 2.39.2