Release minimap2-2.24 (r1122)

lh3 · Dec 26, 2021 · fe35e67 · fe35e67
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diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,17 @@
+Release 2.24-r1122 (26 December 2021)
+-------------------------------------
+
+This release improves alignment around long poorly aligned regions. Older
+minimap2 may chain through such regions in rare cases which may result in
+missing alignments later. The issue has become worse since the the change of
+the chaining algorithm in v2.19. v2.23 implements an incomplete remedy. This
+release provides a better solution with a X-drop-like heuristic and by enabling
+two-bandwidth chaining in the assembly mode.
+
+(2.24: 26 December 2021, r1122)
+
+
+
 Release 2.23-r1111 (18 November 2021)
 -------------------------------------
 

diff --git 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/v2.23/minimap2-2.23_x64-linux.tar.bz2 | tar -jxvf -
-./minimap2-2.23_x64-linux/minimap2
+curl -L https://github.com/lh3/minimap2/releases/download/v2.24/minimap2-2.24_x64-linux.tar.bz2 | tar -jxvf -
+./minimap2-2.24_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
@@ -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/v2.23/minimap2-2.23_x64-linux.tar.bz2 | tar jxf -
-cp minimap2-2.23_x64-linux/{minimap2,k8,paftools.js} .  # copy executables
+curl -L https://github.com/lh3/minimap2/releases/download/v2.24/minimap2-2.24_x64-linux.tar.bz2 | tar jxf -
+cp minimap2-2.24_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
@@ -7,7 +7,7 @@
 #include "mmpriv.h"
 #include "ketopt.h"
 
-#define MM_VERSION "2.23-r1119-dirty"
+#define MM_VERSION "2.24-r1122"
 
 #ifdef __linux__
 #include <sys/resource.h>

diff --git a/minimap2.1 b/minimap2.1
@@ -1,4 +1,4 @@
-.TH minimap2 1 "18 December 2021" "minimap2-2.24 (r1121)" "Bioinformatics tools"
+.TH minimap2 1 "18 December 2021" "minimap2-2.24 (r1122)" "Bioinformatics tools"
 .SH NAME
 .PP
 minimap2 - mapping and alignment between collections of DNA sequences

diff --git a/misc/paftools.js b/misc/paftools.js
@@ -1,6 +1,6 @@
 #!/usr/bin/env k8
 
-var paftools_version = '2.23-r1111';
+var paftools_version = '2.24-r1122';
 
 /*****************************
  ***** Library functions *****

diff --git a/python/mappy.pyx b/python/mappy.pyx
@@ -3,7 +3,7 @@ from libc.stdlib cimport free
 cimport cmappy
 import sys
 
-__version__ = '2.23'
+__version__ = '2.24'
 
 cmappy.mm_reset_timer()
 

diff --git a/setup.py b/setup.py
@@ -23,7 +23,7 @@ def readme():
 
 setup(
 	name = 'mappy',
-	version = '2.23',
+	version = '2.24',
 	url = 'https://github.com/lh3/minimap2',
 	description = 'Minimap2 python binding',
 	long_description = readme(),