VSEARCH 2.23.0: Numerous fixes and documentation updates

README.md

@@ -37,7 +37,7 @@ 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/v2.22.1/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/v2.23.0/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
 
@@ -50,9 +50,9 @@ 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/v2.22.1.tar.gz
-tar xzf v2.22.1.tar.gz
-cd vsearch-2.22.1
+wget https://github.com/torognes/vsearch/archive/v2.23.0.tar.gz
+tar xzf v2.23.0.tar.gz
+cd vsearch-2.23.0
 ./autogen.sh
 ./configure CFLAGS="-O3" CXXFLAGS="-O3"
 make
@@ -81,48 +81,48 @@ Binary distributions are provided for x86-64 systems running GNU/Linux, macOS (v
 Download the appropriate executable for your system using the following commands if you are using a Linux x86_64 system:
 
 ```sh
-wget https://github.com/torognes/vsearch/releases/download/v2.22.1/vsearch-2.22.1-linux-x86_64.tar.gz
-tar xzf vsearch-2.22.1-linux-x86_64.tar.gz
+wget https://github.com/torognes/vsearch/releases/download/v2.23.0/vsearch-2.23.0-linux-x86_64.tar.gz
+tar xzf vsearch-2.23.0-linux-x86_64.tar.gz
 ```
 
 Or these commands if you are using a Linux ppc64le system:
 
 ```sh
-wget https://github.com/torognes/vsearch/releases/download/v2.22.1/vsearch-2.22.1-linux-ppc64le.tar.gz
-tar xzf vsearch-2.22.1-linux-ppc64le.tar.gz
+wget https://github.com/torognes/vsearch/releases/download/v2.23.0/vsearch-2.23.0-linux-ppc64le.tar.gz
+tar xzf vsearch-2.23.0-linux-ppc64le.tar.gz
 ```
 
 Or these commands if you are using a Linux aarch64 (arm64) system:
 
 ```sh
-wget https://github.com/torognes/vsearch/releases/download/v2.22.1/vsearch-2.22.1-linux-aarch64.tar.gz
-tar xzf vsearch-2.22.1-linux-aarch64.tar.gz
+wget https://github.com/torognes/vsearch/releases/download/v2.23.0/vsearch-2.23.0-linux-aarch64.tar.gz
+tar xzf vsearch-2.23.0-linux-aarch64.tar.gz
 ```
 
 Or these commands if you are using a Mac with an Apple Silicon CPU:
 
 ```sh
-wget https://github.com/torognes/vsearch/releases/download/v2.22.1/vsearch-2.22.1-macos-aarch64.tar.gz
-tar xzf vsearch-2.22.1-macos-aarch64.tar.gz
+wget https://github.com/torognes/vsearch/releases/download/v2.23.0/vsearch-2.23.0-macos-aarch64.tar.gz
+tar xzf vsearch-2.23.0-macos-aarch64.tar.gz
 ```
 
 Or these commands if you are using a Mac with an Intel CPU:
 
 ```sh
-wget https://github.com/torognes/vsearch/releases/download/v2.22.1/vsearch-2.22.1-macos-x86_64.tar.gz
-tar xzf vsearch-2.22.1-macos-x86_64.tar.gz
+wget https://github.com/torognes/vsearch/releases/download/v2.23.0/vsearch-2.23.0-macos-x86_64.tar.gz
+tar xzf vsearch-2.23.0-macos-x86_64.tar.gz
 ```
 
 Or if you are using Windows, download and extract (unzip) the contents of this file:
 
 ```
-https://github.com/torognes/vsearch/releases/download/v2.22.1/vsearch-2.22.1-win-x86_64.zip
+https://github.com/torognes/vsearch/releases/download/v2.23.0/vsearch-2.23.0-win-x86_64.zip
 ```
 
-Linux and Mac: You will now have the binary distribution in a folder called `vsearch-2.22.1-linux-x86_64` or `vsearch-2.22.1-macos-x86_64` in which you will find three subfolders `bin`, `man` and `doc`. We recommend making a copy or a symbolic link to the vsearch binary `bin/vsearch` in a folder included in your `$PATH`, and a copy or a symbolic link to the vsearch man page `man/vsearch.1` in a folder included in your `$MANPATH`. The PDF version of the manual is available in `doc/vsearch_manual.pdf`. Versions with statically compiled libraries are available for Linux systems. These have "-static" in their name, and could be used on systems that do not have all the necessary libraries installed.
+Linux and Mac: You will now have the binary distribution in a folder called `vsearch-2.23.0-linux-x86_64` or `vsearch-2.23.0-macos-x86_64` in which you will find three subfolders `bin`, `man` and `doc`. We recommend making a copy or a symbolic link to the vsearch binary `bin/vsearch` in a folder included in your `$PATH`, and a copy or a symbolic link to the vsearch man page `man/vsearch.1` in a folder included in your `$MANPATH`. The PDF version of the manual is available in `doc/vsearch_manual.pdf`. Versions with statically compiled libraries are available for Linux systems. These have "-static" in their name, and could be used on systems that do not have all the necessary libraries installed.
 
 **Windows**: You will now have the binary distribution in a folder
-called `vsearch-2.22.1-win-x86_64`. The vsearch executable is called
+called `vsearch-2.23.0-win-x86_64`. The vsearch executable is called
 `vsearch.exe`. The manual in PDF format is called
 `vsearch_manual.pdf`. If you want to be able to call `vsearch.exe`
 from any command prompt window, you can put the vsearch executable in
@@ -133,7 +133,7 @@ searching for it in the Start menu, `Edit` user variables, add
 your changes.
 
 
-**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/v2.22.1/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 `$MANPATH`. The manual in both formats is also available with the binary distribution. The manual in PDF form ([vsearch_manual.pdf](https://github.com/torognes/vsearch/releases/download/v2.22.1/vsearch_manual.pdf)) is also attached to the latest [release](https://github.com/torognes/vsearch/releases).
+**Documentation** The VSEARCH user's manual is available in the `man` folder in the form of a [man page](https://github.com/torognes/vsearch/blob/master/man/vsearch.1). A pdf version ([vsearch_manual.pdf](https://github.com/torognes/vsearch/releases/download/v2.23.0/vsearch_manual.pdf)) will be generated by `make`. To install the manpage manually, copy the `vsearch.1` file or a create a symbolic link to `vsearch.1` in a folder included in your `$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/v2.23.0/vsearch_manual.pdf)) is also attached to the latest [release](https://github.com/torognes/vsearch/releases).
 
 
 ## Packages, plugins, and wrappers

configure.ac

@@ -2,7 +2,7 @@
 # Process this file with autoconf to produce a configure script.
 
 AC_PREREQ([2.63])
-AC_INIT([vsearch], [2.22.1], [[email protected]], [vsearch], [https://github.com/torognes/vsearch])
+AC_INIT([vsearch], [2.23.0], [[email protected]], [vsearch], [https://github.com/torognes/vsearch])
 AC_CANONICAL_TARGET
 AM_INIT_AUTOMAKE([subdir-objects])
 AC_LANG([C++])

man/vsearch.1

@@ -1,5 +1,5 @@
 .\" ============================================================================
-.TH vsearch 1 "September 19, 2022" "version 2.22.1" "USER COMMANDS"
+.TH vsearch 1 "July 7, 2023" "version 2.23.0" "USER COMMANDS"
 .\" ============================================================================
 .SH NAME
 vsearch \(em a versatile open-source tool for microbiome analysis,
@@ -4810,6 +4810,18 @@ Add the derep_smallmem command for dereplication using little memory.
 .TP
 .BR v2.22.1\~ "released September 19th, 2022"
 Fix compiler warning.
+.TP
+.BR v2.23.0\~ "released July 7th, 2023"
+Update documentation. Add citation file. Modernize and improve
+code. Fix several minor bugs. Fix compilation with GCC 13. Print stats
+after fastq_mergepairs to log file instead of stderr. Handle sizein
+option correctly with dbmatched option for usearch_global. Allow
+maxseqlength option for makeudb_usearch. Fix memory allocation problem
+with chimera detection. Add lengthout and xlength options. Increase
+precision for eeout option. Add warning about sintax algorithm, random
+seed and multiple threads. Refactor chimera detection code. Add
+undocumented experimental long_chimeras_denovo command. Fix segfault
+with clustering. Add more references.
 .LP
 .\" ============================================================================
 .\" TODO: