From 2d7ec75d504b49cdcc9bd208e97d74179d1c1f3b Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Tue, 27 Mar 2018 11:45:44 -0400
Subject: [PATCH] Release minimap2-2.10 (r761)

---
 NEWS.md    | 47 +++++++++++++++++++++++++++++++++++++++++++++++
 README.md  |  5 ++---
 main.c     |  2 +-
 minimap2.1 |  2 +-
 setup.py   |  2 +-
 5 files changed, 52 insertions(+), 6 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index 5c32cfa..d6bb920 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,50 @@
+Release 2.10-r761 (27 March 2018)
+---------------------------------
+
+Changes to minimap2:
+
+ * Optionally output the MD tag for compatibility with existing tools (#63,
+   #118 and #137).
+
+ * Use SSE compiler flags more precisely to prevent compiling errors on certain
+   machines (#127).
+
+ * Added option --min-occ-floor to set a minimum occurrence threshold. Presets
+   intended for assembly-to-reference alignment set this option to 100. This
+   option alleviates issues with regions having high copy numbers (#107).
+
+ * Exit with non-zero code on file writing errors (e.g. disk full; #103 and
+   #132).
+
+ * Added option -y to copy FASTA/FASTQ comments in query sequences to the
+   output (#136).
+
+ * Added the asm20 preset for alignments between genomes at 5-10% sequence
+   divergence.
+
+ * Changed the band-width in the ava-ont preset from 500 to 2000. Oxford
+   Nanopore reads may contain long deletion sequencing errors that break
+   chaining.
+
+Changes to mappy, the Python binding:
+
+ * Fixed a typo in Align.seq() (#126).
+
+Changes to paftools.js, the companion script:
+
+ * Command sam2paf now converts the MD tag to cs.
+
+ * Support VCF output for assembly-to-reference variant calling (#109).
+
+This version should produce identical alignment for read overlapping, RNA-seq
+read mapping, and genomic read mapping. We have also added a cook book to show
+the variety uses of minimap2 on real datasets. Please see cookbook.md in the
+minimap2 source code directory.
+
+(2.10: 27 March 2017, r761)
+
+
+
 Release 2.9-r720 (23 February 2018)
 -----------------------------------
 
diff --git a/README.md b/README.md
index 5950025..dae44fe 100644
--- a/README.md
+++ b/README.md
@@ -68,9 +68,8 @@ Detailed evaluations are available from the [minimap2 preprint][preprint].
 Minimap2 is optimized for x86-64 CPUs. You can acquire precompiled binaries from
 the [release page][release] with:
 ```sh
-curl -L https://github.com/lh3/minimap2/releases/download/v2.9/minimap2-2.9_x64-linux.tar.bz2 \
-  | tar -jxvf -
-./minimap2-2.9_x64-linux/minimap2
+curl -L https://github.com/lh3/minimap2/releases/download/v2.10/minimap2-2.10_x64-linux.tar.bz2 | tar -jxvf -
+./minimap2-2.10_x64-linux/minimap2
 ```
 If you want to compile from the source, you need to have a C compiler, GNU make
 and zlib development files installed. Then type `make` in the source code
diff --git a/main.c b/main.c
index 315b8c7..2192a89 100644
--- a/main.c
+++ b/main.c
@@ -10,7 +10,7 @@
 #include "getopt.h"
 #endif
 
-#define MM_VERSION "2.9-r753-dirty"
+#define MM_VERSION "2.10-r761"
 
 #ifdef __linux__
 #include <sys/resource.h>
diff --git a/minimap2.1 b/minimap2.1
index 6011634..4214708 100644
--- a/minimap2.1
+++ b/minimap2.1
@@ -1,4 +1,4 @@
-.TH minimap2 1 "15 March 2018" "minimap2-2.9-dirty (r746)" "Bioinformatics tools"
+.TH minimap2 1 "27 March 2018" "minimap2-2.10 (r761)" "Bioinformatics tools"
 .SH NAME
 .PP
 minimap2 - mapping and alignment between collections of DNA sequences
diff --git a/setup.py b/setup.py
index 0f70fe8..aaba928 100644
--- a/setup.py
+++ b/setup.py
@@ -23,7 +23,7 @@ def readme():
 
 setup(
 	name = 'mappy',
-	version = '2.9',
+	version = '2.10',
 	url = 'https://github.com/lh3/minimap2',
 	description = 'Minimap2 python binding',
 	long_description = readme(),