VSEARCH 2.30.1

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 [online documentation](https://torognes.github.io/vsearch/), or in the [manpage](https://github.com/torognes/vsearch/releases/download/v2.30.0/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.
+If you can't find an answer in [online documentation](https://torognes.github.io/vsearch/), or in the [manpage](https://github.com/torognes/vsearch/releases/download/v2.30.1/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.
 
 ## 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/v2.30.0.tar.gz
-tar xzf v2.30.0.tar.gz
-cd vsearch-2.30.0
+wget https://github.com/torognes/vsearch/archive/v2.30.1.tar.gz
+tar xzf v2.30.1.tar.gz
+cd vsearch-2.30.1
 ./autogen.sh
 ./configure CFLAGS="-O2" CXXFLAGS="-O2"
 make ARFLAGS="cr"
@@ -91,7 +91,7 @@ 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. `2.30.0`), `{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. `2.30.1`), `{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`.
 
 Or, if you are using Windows, download and extract (unzip) the contents of this file:
 
@@ -115,7 +115,7 @@ 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/v2.30.0/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 `$MANPATH`. The manual in both formats is also available with the binary distribution. The manual in PDF form ([vsearch_manual.pdf](https://github.com/torognes/vsearch/releases/download/v2.30.0/vsearch_manual.pdf)) is also attached to the latest [release](https://github.com/torognes/vsearch/releases).
+**Documentation:** The VSEARCH user's manual is available in the `man` folder in the form of a [man page](https://github.com/torognes/vsearch/blob/master/man/vsearch.1). A pdf version ([vsearch_manual.pdf](https://github.com/torognes/vsearch/releases/download/v2.30.1/vsearch_manual.pdf)) will be generated by `make`. To install the manpage manually, copy the `vsearch.1` file or a create a symbolic link to `vsearch.1` in a folder included in your `$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/v2.30.1/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], [2.30.0], [[email protected]], [vsearch], [https://github.com/torognes/vsearch])
+AC_INIT([vsearch], [2.30.1], [[email protected]], [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 "February 27, 2025" "version 2.30.0" "USER COMMANDS"
+.TH vsearch 1 "October 3, 2025" "version 2.30.1" "USER COMMANDS"
 .\" ============================================================================
 .SH NAME
 vsearch \(em a versatile open-source tool for microbiome analysis,
@@ -5059,7 +5059,6 @@ commands (\-\-sortbylength, \-\-sortbysize, \-\-shuffle,
 .IP -
 improve: code-coverage of our test-suite for the above-mentioned commands (1,210 new tests, 4,753 in total)
 .RE
-.LP
 .TP
 .BR v2.29.1\~ "released October 24th, 2024"
 Fix a segmentation fault that could occur during alignment in version
@@ -5099,6 +5098,61 @@ a quality scores below the given value. The new
 `\-\-fastq_truncee_rate` option for the same commands will truncate
 sequences at the first position where the number of expected errors
 per base is above the given value.
+.TP
+.BR v2.30.1\~ "released October 3rd, 2025"
+This version incorporates many code improvements, more extensive testing, better documentation and some minor bug fixes. List of changes:
+.RS
+.IP - 2
+fix: use-after-free introduced in commit de6c1d8 (Jun 13, 2024),
+.IP -
+fix: (harmless) out-of-bounds memory issue in  \-\-derep_prefix (commit 8a0a508b),
+.IP -
+fix: (harmless) memory leak in \-\-fastx_getseqs \-\-label_field (commit a9c42713),
+.IP -
+fix: (harmless) memory leak when using option \-\-userfields (\-\-allpairs_global commit 03b95bcf; \-\-cluster_* commit 2fde5472; \-\-search_exact commit 45cd56d6; \-\-usearch_global commit d83bfee9),
+.IP -
+fix: (harmless) valgrind error, use of uninitialized values (commit 8bab2444), also eliminates a pesky compilation warning,
+.IP -
+change: passing a negative value to \-\-fastq_truncee_rate is now an error (commit a120f371),
+.IP -
+change: passing a negative value to \-\-fastq_minqual is now an error (commit ff5b0c99),
+.IP -
+change: passing a non-ASCII symbol to \-\-join_padgap or \-\-join_padgapq is now an error (commit a708f5b3),
+.IP -
+change: when using \-\-gapopen "*" to forbid gap opening, the penalty is now set to INT_MAX (rather than 1,000). This might change alignment results for users who relied on the old behavior (thanks to Denis Filloux, issue #602, commit 96e9cf9e),
+.IP -
+change: when using command \-\-chimeras_denovo, \-\-tabbedout or \-\-alnout can be the only output files specified (commit d51f0a456300a0ea69c035ba3de23c5ecf3da348)
+.IP -
+change: when using command \-\-chimeras_denovo, option \-\-lengthout is now accepted (commit 3f55cc6b)
+.IP -
+change: when using command \-\-chimeras_denovo, option \-\-xlength is now accepted (commit 0fd346cd)
+.IP -
+add: compilation option GLIBCXX_DEBUG when compiling for debugging (commit 5cf4a6c1, option activates more runtime checks),
+.IP -
+add: official support for clang 20,
+.IP -
+add: initial support for clang 21, initial support for GCC 15,
+.IP -
+add: experimental support for clang 22,
+.IP -
+improve: more accurate line number when reporting illegal characters in fastq headers (commit 539084e9),
+.IP -
+improve: more accurate line number when reporting non-ASCII characters in fastq headers (commit 98a851ed),
+.IP -
+improve: remove checks for unneeded libraries during compilation (commit 249bb5d5276b1be6c9add60a538a16e1b9d0ebfb),
+.IP -
+improve: code quality (eliminates clang-tidy warnings),
+.IP -
+improve: documentation and help messages (issues #604),
+.IP -
+improve: complete refactoring and modernization of the command \-\-fastq_stats,
+.IP -
+improve: command \-\-fastq_stats is now up to twice faster (tested on x86-64),
+.IP -
+improve: extensive test-suites for \-\-fastq_stats and \-\-sff_convert,
+.IP -
+improve: code coverage of our test-suite
+.RE
 .\" ============================================================================
 .\" TODO:
 .\"