From 581f2d7123f651d04c9e103b1c7ea8f7051e909a Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Tue, 6 Jul 2021 13:18:55 -0400
Subject: [PATCH] Release minimap2-2.21 (r1071)

---
 NEWS.md          | 11 +++++++++++
 README.md        |  4 ++--
 cookbook.md      |  4 ++--
 main.c           |  2 +-
 minimap2.1       |  6 +++---
 misc/paftools.js |  2 +-
 python/mappy.pyx |  2 +-
 setup.py         |  2 +-
 8 files changed, 22 insertions(+), 11 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index b770498f..425545ac 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,14 @@
+Release 2.21-r1071 (6 July 2021)
+--------------------------------
+
+This release fixed a regression in short-read mapping introduced in v2.19
+(#776). It also fixed invalid comparisons of uninitialized variables, though
+these are harmless (#752). Long-read alignment should be identical to v2.20.
+
+(2.21: 6 July 2021)
+
+
+
 Release 2.20-r1061 (27 May 2021)
 --------------------------------
 
diff --git a/README.md b/README.md
index d016a464..0bff2e48 100644
--- a/README.md
+++ b/README.md
@@ -74,8 +74,8 @@ Detailed evaluations are available from the [minimap2 paper][doi] or the
 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/v2.20/minimap2-2.20_x64-linux.tar.bz2 | tar -jxvf -
-./minimap2-2.20_x64-linux/minimap2
+curl -L https://github.com/lh3/minimap2/releases/download/v2.21/minimap2-2.21_x64-linux.tar.bz2 | tar -jxvf -
+./minimap2-2.21_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/cookbook.md b/cookbook.md
index d72e646c..8ff2bd0f 100644
--- a/cookbook.md
+++ b/cookbook.md
@@ -31,8 +31,8 @@ To acquire the data used in this cookbook and to install minimap2 and paftools,
 please follow the command lines below:
 ```sh
 # install minimap2 executables
-curl -L https://github.com/lh3/minimap2/releases/download/v2.20/minimap2-2.20_x64-linux.tar.bz2 | tar jxf -
-cp minimap2-2.20_x64-linux/{minimap2,k8,paftools.js} .  # copy executables
+curl -L https://github.com/lh3/minimap2/releases/download/v2.21/minimap2-2.21_x64-linux.tar.bz2 | tar jxf -
+cp minimap2-2.21_x64-linux/{minimap2,k8,paftools.js} .  # copy executables
 export PATH="$PATH:"`pwd`                               # put the current directory on PATH
 # download example datasets
 curl -L https://github.com/lh3/minimap2/releases/download/v2.10/cookbook-data.tgz | tar zxf -
diff --git a/main.c b/main.c
index cc586cb1..f4167d8b 100644
--- a/main.c
+++ b/main.c
@@ -7,7 +7,7 @@
 #include "mmpriv.h"
 #include "ketopt.h"
 
-#define MM_VERSION "2.20-r1080-dirty"
+#define MM_VERSION "2.21-r1071"
 
 #ifdef __linux__
 #include <sys/resource.h>
diff --git a/minimap2.1 b/minimap2.1
index 11bc4f58..a1c0fb81 100644
--- a/minimap2.1
+++ b/minimap2.1
@@ -1,4 +1,4 @@
-.TH minimap2 1 "27 May 2021" "minimap2-2.20 (r1061)" "Bioinformatics tools"
+.TH minimap2 1 "6 July 2021" "minimap2-2.21 (r1071)" "Bioinformatics tools"
 .SH NAME
 .PP
 minimap2 - mapping and alignment between collections of DNA sequences
@@ -592,8 +592,8 @@ Long-read splice alignment for PacBio CCS reads
 .B sr
 Short single-end reads without splicing
 .RB ( -k21
-.B -w11 --sr --frag=yes -A2 -B8 -O12,32 -E2,1 -r50 -p.5 -N20 -f1000,5000 -n2 -m20
-.B -s40 -g200 -2K50m --heap-sort=yes
+.B -w11 --sr --frag=yes -A2 -B8 -O12,32 -E2,1 -r100 -p.5 -N20 -f1000,5000 -n2 -m20
+.B -s40 -g100 -2K50m --heap-sort=yes
 .BR --secondary=no ).
 .TP
 .B ava-pb
diff --git a/misc/paftools.js b/misc/paftools.js
index 999aa78c..0c5c186d 100755
--- a/misc/paftools.js
+++ b/misc/paftools.js
@@ -1,6 +1,6 @@
 #!/usr/bin/env k8
 
-var paftools_version = '2.20-r1061';
+var paftools_version = '2.21-r1071';
 
 /*****************************
  ***** Library functions *****
diff --git a/python/mappy.pyx b/python/mappy.pyx
index 920bc0d2..838b5ad0 100644
--- a/python/mappy.pyx
+++ b/python/mappy.pyx
@@ -3,7 +3,7 @@ from libc.stdlib cimport free
 cimport cmappy
 import sys
 
-__version__ = '2.20'
+__version__ = '2.21'
 
 cmappy.mm_reset_timer()
 
diff --git a/setup.py b/setup.py
index c0b576a2..1a4d2277 100644
--- a/setup.py
+++ b/setup.py
@@ -23,7 +23,7 @@ def readme():
 
 setup(
 	name = 'mappy',
-	version = '2.20',
+	version = '2.21',
 	url = 'https://github.com/lh3/minimap2',
 	description = 'Minimap2 python binding',
 	long_description = readme(),