VSEARCH 2.29.2

Author: torognes

README.md

@@ -39,7 +39,7 @@ Most of the nucleotide based commands and options in USEARCH version 7 are suppo
 
 ## Getting Help
 
-If you can't find an answer in the [VSEARCH documentation](https://github.com/torognes/vsearch/releases/download/v2.29.1/vsearch_manual.pdf), please visit the [VSEARCH Web Forum](https://groups.google.com/forum/#!forum/vsearch-forum) to post a question or start a discussion.
+If you can't find an answer in the [VSEARCH documentation](https://github.com/torognes/vsearch/releases/download/v2.29.2/vsearch_manual.pdf), please visit the [VSEARCH Web Forum](https://groups.google.com/forum/#!forum/vsearch-forum) to post a question or start a discussion.
 
 ## Example
 
@@ -52,9 +52,9 @@ In the example below, VSEARCH will identify sequences in the file database.fsa t
 **Source distribution** To download the source distribution from a [release](https://github.com/torognes/vsearch/releases) and build the executable and the documentation, use the following commands:
 
 ```
-wget https://github.com/torognes/vsearch/archive/v2.29.1.tar.gz
-tar xzf v2.29.1.tar.gz
-cd vsearch-2.29.1
+wget https://github.com/torognes/vsearch/archive/v2.29.2.tar.gz
+tar xzf v2.29.2.tar.gz
+cd vsearch-2.29.2
 ./autogen.sh
 ./configure CFLAGS="-O3" CXXFLAGS="-O3"
 make ARFLAGS="cr"
@@ -89,7 +89,7 @@ wget https://github.com/torognes/vsearch/releases/download/v{VERSION}/vsearch-{V
 tar xzf vsearch-{VERSION}-{OS}-{ARCH}.tar.gz
 ```
 
-Replace `{VERSION}` with the VSEARCH version number (e.g. `2.29.1`), `{OS}` with the target operating system (`linux` or `macos`), and `{ARCH}` with the architecture (`x86_64`, `aarch64`, `ppc64le`, `riscv64`, or `mips64el`). You could add `-static` after `{ARCH}` to get a statically compiled version for Linux (except x86_64). The name of the binary for the RHEL 7 and CentOS 7 Linux distributions ends in `-ubi7`.
+Replace `{VERSION}` with the VSEARCH version number (e.g. `2.29.2`), `{OS}` with the target operating system (`linux` or `macos`), and `{ARCH}` with the architecture (`x86_64`, `aarch64`, `ppc64le`, `riscv64`, or `mips64el`). You could add `-static` after `{ARCH}` to get a statically compiled version for Linux (except x86_64). The name of the binary for the RHEL 7 and CentOS 7 Linux distributions ends in `-ubi7`.
 
 Or, if you are using Windows, download and extract (unzip) the contents of this file:
 
@@ -113,7 +113,7 @@ and `zlib1.dll` files required for reading compressed input
 files. These DLL's have been obtained for mingw-w64 from the MSYS2
 platform.
 
-**Documentation:** The VSEARCH user's manual is available in the `man` folder in the form of a [man page](https://github.com/torognes/vsearch/blob/master/man/vsearch.1). A pdf version ([vsearch_manual.pdf](https://github.com/torognes/vsearch/releases/download/v2.29.1/vsearch_manual.pdf)) will be generated by `make`. To install the manpage manually, copy the `vsearch.1` file or a create a symbolic link to `vsearch.1` in a folder included in your `$MANPATH`. The manual in both formats is also available with the binary distribution. The manual in PDF form ([vsearch_manual.pdf](https://github.com/torognes/vsearch/releases/download/v2.29.1/vsearch_manual.pdf)) is also attached to the latest [release](https://github.com/torognes/vsearch/releases).
+**Documentation:** The VSEARCH user's manual is available in the `man` folder in the form of a [man page](https://github.com/torognes/vsearch/blob/master/man/vsearch.1). A pdf version ([vsearch_manual.pdf](https://github.com/torognes/vsearch/releases/download/v2.29.2/vsearch_manual.pdf)) will be generated by `make`. To install the manpage manually, copy the `vsearch.1` file or a create a symbolic link to `vsearch.1` in a folder included in your `$MANPATH`. The manual in both formats is also available with the binary distribution. The manual in PDF form ([vsearch_manual.pdf](https://github.com/torognes/vsearch/releases/download/v2.29.2/vsearch_manual.pdf)) is also attached to the latest [release](https://github.com/torognes/vsearch/releases).
 
 
 ## Packages, plugins, and wrappers
@@ -157,7 +157,7 @@ Compiling VSEARCH requires either GCC (`g++`) or `clang`, `make` and the autotoo
 
 VSEARCH will automatically check whether these libraries are available and load them dynamically.
 
-On Windows these libraries are called `zlib1.dll` and `libbz2.dll`. These DLL's are included with the released distribution of vsearch 2.29.1 and later.
+On Windows these libraries are called `zlib1.dll` and `libbz2.dll`. These DLL's are included with the released distribution of vsearch 2.29.2 and later.
 
 To create the PDF file with the manual the ps2pdf tool is required. It is part of the `ghostscript` package.
 

configure.ac

@@ -2,7 +2,7 @@
 # Process this file with autoconf to produce a configure script.
 
 AC_PREREQ([2.63])
-AC_INIT([vsearch], [2.29.1], [torognes@ifi.uio.no], [vsearch], [https://github.com/torognes/vsearch])
+AC_INIT([vsearch], [2.29.2], [torognes@ifi.uio.no], [vsearch], [https://github.com/torognes/vsearch])
 AC_CANONICAL_TARGET
 AM_INIT_AUTOMAKE([subdir-objects])
 AC_LANG([C++])

man/vsearch.1

@@ -1,7 +1,7 @@
 .\" import www macros (URL, TAG, MTO)
 .mso www.tmac
 .\" ============================================================================
-.TH vsearch 1 "October 24, 2024" "version 2.29.1" "USER COMMANDS"
+.TH vsearch 1 "December 20, 2024" "version 2.29.2" "USER COMMANDS"
 .\" ============================================================================
 .SH NAME
 vsearch \(em a versatile open-source tool for microbiome analysis,
@@ -4994,6 +4994,10 @@ improve: code-coverage of our test-suite for the above-mentioned commands (1,210
 Fix a segmentation fault that could occur during alignment in version
 2.29.0, for example with \-\-uchime_ref. Some improvements to code and
 documentation.
+.TP
+.BR v2.29.2\~ "released December 20th, 2024"
+Fix a segmentation fault during clustering when the set of clusters is empty.
+Initial documentation in markdown format available on GitHub Pages.
 .\" ============================================================================
 .\" TODO:
 .\"