From bf675098f2287735a37153fde27108db0b441816 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@live.co.uk>
Date: Thu, 24 Sep 2009 10:29:19 +0000
Subject: [PATCH]  * samtools-0.1.6-6 (r466)  * do not crash calmd when some
 sequences are absent from the reference.

---
 ChangeLog | 69 +++++++++++++++++++++++++++++++++++++++++++++++++++++++
 bam_md.c  |  5 +++-
 bamtk.c   |  2 +-
 3 files changed, 74 insertions(+), 2 deletions(-)

diff --git a/ChangeLog b/ChangeLog
index c0afc45..18b7d8a 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,72 @@
+------------------------------------------------------------------------
+r462 | lh3lh3 | 2009-09-16 09:51:07 +0100 (Wed, 16 Sep 2009) | 3 lines
+Changed paths:
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/faidx.c
+   M /trunk/samtools/knetfile.c
+   M /trunk/samtools/knetfile.h
+   M /trunk/samtools/razf.c
+   M /trunk/samtools/razf.h
+
+ * samtools-0.1.6-5 (r462)
+ * Added knetfile support in razf and faidx (on behalf of Petr Danecek)
+
+------------------------------------------------------------------------
+r460 | lh3lh3 | 2009-09-09 12:06:22 +0100 (Wed, 09 Sep 2009) | 2 lines
+Changed paths:
+   M /trunk/samtools/samtools.1
+
+fixed a formatting issue
+
+------------------------------------------------------------------------
+r459 | lh3lh3 | 2009-09-08 23:14:08 +0100 (Tue, 08 Sep 2009) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam_sort.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.6-4 (r459)
+ * make sort output the result to stdout when -o is in use
+
+------------------------------------------------------------------------
+r458 | lh3lh3 | 2009-09-07 10:10:28 +0100 (Mon, 07 Sep 2009) | 4 lines
+Changed paths:
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/faidx.c
+   M /trunk/samtools/faidx.h
+   M /trunk/samtools/samtools.1
+
+ * samtools-0.1.6-2 (r458)
+ * added more interface to faidx (by Nils)
+ * updated documentation
+
+------------------------------------------------------------------------
+r457 | lh3lh3 | 2009-09-05 21:12:04 +0100 (Sat, 05 Sep 2009) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam_sort.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.6-2 (r457)
+ * get rid of three assert() in bam_sort.c
+
+------------------------------------------------------------------------
+r456 | jmarshall | 2009-09-04 17:46:25 +0100 (Fri, 04 Sep 2009) | 3 lines
+Changed paths:
+   M /trunk/samtools/razf.c
+
+Return NULL from _razf_open() (and hence razf_open()/razf_open2())
+when opening the file fails.
+
+------------------------------------------------------------------------
+r453 | lh3lh3 | 2009-09-02 13:56:33 +0100 (Wed, 02 Sep 2009) | 2 lines
+Changed paths:
+   M /trunk/samtools/ChangeLog
+   M /trunk/samtools/NEWS
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/samtools.1
+   D /trunk/samtools/source.dot
+
+Release samtools-0.1.6
+
 ------------------------------------------------------------------------
 r451 | lh3lh3 | 2009-09-02 10:44:48 +0100 (Wed, 02 Sep 2009) | 4 lines
 Changed paths:
diff --git a/bam_md.c b/bam_md.c
index 8d07487..3ca7309 100644
--- a/bam_md.c
+++ b/bam_md.c
@@ -132,8 +132,11 @@ int bam_fillmd(int argc, char *argv[])
 				free(ref);
 				ref = fai_fetch(fai, fp->header->target_name[b->core.tid], &len);
 				tid = b->core.tid;
+				if (ref == 0)
+					fprintf(stderr, "[bam_fillmd] fail to find sequence '%s' in the reference.\n",
+							fp->header->target_name[tid]);
 			}
-			bam_fillmd1(b, ref, is_equal);
+			if (ref) bam_fillmd1(b, ref, is_equal);
 		}
 		samwrite(fpout, b);
 	}
diff --git a/bamtk.c b/bamtk.c
index a383c45..a9efb2b 100644
--- a/bamtk.c
+++ b/bamtk.c
@@ -9,7 +9,7 @@
 #endif
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.6-5 (r462)"
+#define PACKAGE_VERSION "0.1.6-6 (r466)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);
-- 
2.39.5