Release samtools-0.1.12

diff --git a/NEWS b/NEWS
index 478e718c79963a052e682bbc33cfa0de695076e0..9118140a48dd853050cb932179cb3dc04f103df7 100644 (file)
--- a/NEWS
+++ b/NEWS
@@ -1,3 +1,27 @@
+Beta release 0.1.12 (2 December, 2010)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+This is another bug fix release:
+
+ * Fixed a memory violation in mpileup, which causes segfault. Release
+   0.1.9 and above are affected.
+
+ * Fixed a memory violation in the indel caller, which does not causes
+   segfault, but may potentially affect deletion calls in an unexpected
+   way. Release 0.1.10 and above are affected.
+
+ * Fixed a bug in computing r-square in bcftools. Few are using this
+   functionality and it only has minor effect.
+
+ * Fixed a memory leak in bam_fetch().
+
+ * Fixed a bug in writing meta information to the BAM index for the last
+   sequence. This bug is invisible to most users, but it is a bug anyway.
+
+(0.1.12: 2 December 2010, r859)
+
+
+
 Beta release 0.1.11 (21 November, 2010)
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 

diff --git a/bam_index.c b/bam_index.c
index 0638a2e826a1ceb10f86a144ca42c78355bcae35..328f011c16ccf4a9a558702317ecdecfbcc5212a 100644 (file)
--- a/bam_index.c
+++ b/bam_index.c
@@ -212,7 +212,7 @@ bam_index_t *bam_index_core(bamFile fp)
        }
        if (save_tid >= 0) {
                insert_offset(idx->index[save_tid], save_bin, save_off, bam_tell(fp));
-               insert_offset(idx->index[save_tid], BAM_MAX_BIN, off_beg, off_end);
+               insert_offset(idx->index[save_tid], BAM_MAX_BIN, off_beg, bam_tell(fp));
                insert_offset(idx->index[save_tid], BAM_MAX_BIN, n_mapped, n_unmapped);
        }
        merge_chunks(idx);

diff --git a/bamtk.c b/bamtk.c
index 116c45f6ae69fef919ba162044ba00bce8d243db..32c8417cc4584277ac3f13af0daea52e2268648b 100644 (file)
--- a/bamtk.c
+++ b/bamtk.c
@@ -9,7 +9,7 @@
 #endif
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.11-1 (r858)"
+#define PACKAGE_VERSION "0.1.12 (r859)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);

diff --git a/samtools.1 b/samtools.1
index e0595607196e577f15227c5cef8af0c9f51de2d6..57f1aff50065ef54c470436108a5c69da8c73d84 100644 (file)
--- a/samtools.1
+++ b/samtools.1
@@ -1,4 +1,4 @@
-.TH samtools 1 "21 November 2010" "samtools-0.1.11" "Bioinformatics tools"
+.TH samtools 1 "2 December 2010" "samtools-0.1.12" "Bioinformatics tools"
 .SH NAME
 .PP
 samtools - Utilities for the Sequence Alignment/Map (SAM) format