Release minimap2-2.31 (r1302)

NEWS.md

@@ -1,3 +1,36 @@
+Release 2.31-r1302 (19 May 2026)
+--------------------------------
+
+Notable changes to minimap2:
+
+ * Bugfix: supplementary and secondary alignments were occasionally flagged
+   incorrectly.
+
+ * Bugfix: Smith-Waterman alignment for inversion alignment led to an
+   out-of-bound access in rare cases.
+
+Changes to paftools.js:
+
+ * New feature: new `sim2bed` subcommand to get a BED file from simulated
+   reads.
+
+ * New feature: new `badread2fa` subcommand to format reads simulated by
+   the Badread simulator.
+
+Change to the python binding:
+
+ * New feature: mappy optionally writes the `ds` tag.
+
+ * Bugfix: a use-after-free error (#1345)
+
+The two bugs in minimap2 had existed for years. They were caught by Jeremy Wang
+at UNC when he ported minimap2 to Rust. Due to the two bug fixes, this version
+occasionally produces alignment different from the last version.
+
+(2.31: 19 May 2026, r1302)
+
+
+
 Release 2.30-r1287 (15 June 2025)
 ---------------------------------
 

README.md

@@ -78,8 +78,8 @@ 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/v2.30/minimap2-2.30_x64-linux.tar.bz2 | tar -jxvf -
+curl -L https://github.com/lh3/minimap2/releases/download/v2.31/minimap2-2.31_x64-linux.tar.bz2 | tar -jxvf -
-./minimap2-2.30_x64-linux/minimap2
+./minimap2-2.31_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

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/v2.30/minimap2-2.30_x64-linux.tar.bz2 | tar jxf -
+curl -L https://github.com/lh3/minimap2/releases/download/v2.31/minimap2-2.31_x64-linux.tar.bz2 | tar jxf -
-cp minimap2-2.30_x64-linux/{minimap2,k8,paftools.js} .  # copy executables
+cp minimap2-2.31_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 -

minimap.h

@@ -5,7 +5,7 @@
 #include <stdio.h>
 #include <sys/types.h>
 
-#define MM_VERSION "2.30-r1299-dirty"
+#define MM_VERSION "2.31-r1302"
 
 #define MM_F_NO_DIAG       (0x001LL) // no exact diagonal hit
 #define MM_F_NO_DUAL       (0x002LL) // skip pairs where query name is lexicographically larger than target name

minimap2.1

@@ -1,4 +1,4 @@
-.TH minimap2 1 "15 June 2025" "minimap2-2.30 (r1287)" "Bioinformatics tools"
+.TH minimap2 1 "19 May 2026" "minimap2-2.31 (r1302)" "Bioinformatics tools"
 .SH NAME
 .PP
 minimap2 - mapping and alignment between collections of DNA sequences

misc/paftools.js

@@ -1,6 +1,6 @@
 #!/usr/bin/env k8
 
-var paftools_version = '2.30-r1287';
+var paftools_version = '2.31-r1302';
 
 /*****************************
  ***** Library functions *****

python/mappy.pyx

@@ -3,7 +3,7 @@ from libc.stdlib cimport free
 cimport cmappy
 import sys
 
-__version__ = '2.30'
+__version__ = '2.31'
 
 cmappy.mm_reset_timer()
 

setup.py

@@ -23,7 +23,7 @@ def readme():
 
 setup(
 	name = 'mappy',
-	version = '2.30',
+	version = '2.31',
 	url = 'https://github.com/lh3/minimap2',
 	description = 'Minimap2 python binding',
 	long_description = readme(),