VSEARCH 2.29.0

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/v2.28.1/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/v2.29.0/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
 
@@ -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/v2.28.1.tar.gz
-tar xzf v2.28.1.tar.gz
-cd vsearch-2.28.1
+wget https://github.com/torognes/vsearch/archive/v2.29.0.tar.gz
+tar xzf v2.29.0.tar.gz
+cd vsearch-2.29.0
 ./autogen.sh
 ./configure CFLAGS="-O3" CXXFLAGS="-O3"
 make ARFLAGS="cr"
@@ -83,48 +83,48 @@ 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/v2.28.1/vsearch-2.28.1-linux-x86_64.tar.gz
-tar xzf vsearch-2.28.1-linux-x86_64.tar.gz
+wget https://github.com/torognes/vsearch/releases/download/v2.29.0/vsearch-2.29.0-linux-x86_64.tar.gz
+tar xzf vsearch-2.29.0-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/v2.28.1/vsearch-2.28.1-linux-ppc64le.tar.gz
-tar xzf vsearch-2.28.1-linux-ppc64le.tar.gz
+wget https://github.com/torognes/vsearch/releases/download/v2.29.0/vsearch-2.29.0-linux-ppc64le.tar.gz
+tar xzf vsearch-2.29.0-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/v2.28.1/vsearch-2.28.1-linux-aarch64.tar.gz
-tar xzf vsearch-2.28.1-linux-aarch64.tar.gz
+wget https://github.com/torognes/vsearch/releases/download/v2.29.0/vsearch-2.29.0-linux-aarch64.tar.gz
+tar xzf vsearch-2.29.0-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/v2.28.1/vsearch-2.28.1-macos-aarch64.tar.gz
-tar xzf vsearch-2.28.1-macos-aarch64.tar.gz
+wget https://github.com/torognes/vsearch/releases/download/v2.29.0/vsearch-2.29.0-macos-aarch64.tar.gz
+tar xzf vsearch-2.29.0-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/v2.28.1/vsearch-2.28.1-macos-x86_64.tar.gz
-tar xzf vsearch-2.28.1-macos-x86_64.tar.gz
+wget https://github.com/torognes/vsearch/releases/download/v2.29.0/vsearch-2.29.0-macos-x86_64.tar.gz
+tar xzf vsearch-2.29.0-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/v2.28.1/vsearch-2.28.1-win-x86_64.zip
+https://github.com/torognes/vsearch/releases/download/v2.29.0/vsearch-2.29.0-win-x86_64.zip
 ```
 
-Linux and Mac: You will now have the binary distribution in a folder called `vsearch-2.28.1-linux-x86_64` or `vsearch-2.28.1-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-2.29.0-linux-x86_64` or `vsearch-2.29.0-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-2.28.1-win-x86_64`. The vsearch executable is called
+called `vsearch-2.29.0-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
@@ -137,7 +137,7 @@ 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/v2.28.1/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 `$MANPATH`. The manual in both formats is also available with the binary distribution. The manual in PDF form ([vsearch_manual.pdf](https://github.com/torognes/vsearch/releases/download/v2.28.1/vsearch_manual.pdf)) is also attached to the latest [release](https://github.com/torognes/vsearch/releases).
+**Documentation** The VSEARCH user's manual is available in the `man` folder in the form of a [man page](https://github.com/torognes/vsearch/blob/master/man/vsearch.1). A pdf version ([vsearch_manual.pdf](https://github.com/torognes/vsearch/releases/download/v2.29.0/vsearch_manual.pdf)) will be generated by `make`. To install the manpage manually, copy the `vsearch.1` file or a create a symbolic link to `vsearch.1` in a folder included in your `$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/v2.29.0/vsearch_manual.pdf)) is also attached to the latest [release](https://github.com/torognes/vsearch/releases).
 
 
 ## Packages, plugins, and wrappers
@@ -181,7 +181,7 @@ 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 2.28.1 and later.
+On Windows these libraries are called `zlib1.dll` and `libbz2.dll`. These DLL's are included with the released distribution of vsearch 2.29.0 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], [2.28.1], [torognes@ifi.uio.no], [vsearch], [https://github.com/torognes/vsearch])
+AC_INIT([vsearch], [2.29.0], [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 "April 26, 2024" "version 2.28.1" "USER COMMANDS"
+.TH vsearch 1 "September 26, 2024" "version 2.29.0" "USER COMMANDS"
 .\" ============================================================================
 .SH NAME
 vsearch \(em a versatile open-source tool for microbiome analysis,
@@ -210,14 +210,15 @@ Needleman-Wunsch algorithm, making use of the Streaming SIMD
 Extensions (SSE2) of post-2003 x86-64 CPUs.  If SSE2 instructions are
 not available, \fBvsearch\fR exits with an error message. On Power8
 CPUs it will use AltiVec/VSX/VMX instructions, and on ARMv8 CPUs it
-will use Neon instructions. Memory usage increases rapidly with
-sequence length: for example comparing two sequences of length 1 kb
-requires 8 MB of memory per thread, and comparing two 10 kb sequences
-requires 800 MB of memory per thread. For comparisons involving
-sequences with a length product greater than 25 million (for example
-two sequences of length 5 kb), \fBvsearch\fR uses a slower alignment
-method described by Hirschberg (1975) and Myers and Miller (1988),
-with much smaller memory requirements.
+will use Neon instructions. On other systems it can use the SIMD
+Everywhere (simde) library, if available. Memory usage increases
+rapidly with sequence length: for example comparing two sequences of
+length 1 kb requires 8 MB of memory per thread, and comparing two 10
+kb sequences requires 800 MB of memory per thread. For comparisons
+involving sequences with a length product greater than 25 million (for
+example two sequences of length 5 kb), \fBvsearch\fR uses a slower
+alignment method described by Hirschberg (1975) and Myers and Miller
+(1988), with much smaller memory requirements.
 .\" ----------------------------------------------------------------------------
 .SS Input
 \fBvsearch\fR accept as input fasta or fastq files containing one or
@@ -4098,8 +4099,7 @@ greater than 2:
 .\"
 .\" ============================================================================
 .SH AUTHORS
-Implementation by Torbjørn Rognes and Tomás Flouri, documentation by
-Frédéric Mahé.
+Implementation and documentation by Torbjørn Rognes, Frédéric Mahé and Tomás Flouri.
 .PP
 .\" ============================================================================
 .SH CITATION
@@ -4934,6 +4934,60 @@ ensure reproducibility of the random choices in the algorithm.
 .BR v2.28.1\~ "released April 26th, 2024"
 Fix a segmentation fault that could occur with the blast6out and
 output_no_hits options.
+.TP
+.BR v2.29.0\~ "released September 26th, 2024"
+This version fixes seven bugs (see changelog below), adds
+initial support for RISC-V architectures, and improves code quality
+and code testing (1,210 new tests):
+.RS
+.IP - 2
+add: experimental support for RISCV64 and other 64-bit little-endian
+architectures, thanks to Michael R. Crusoe and his fellow Debian
+developers (issue #566),
+.IP -
+add: official support for clang-19 and gcc 14,
+.IP -
+add: beta support for clang-20,
+.IP -
+remove: unused \-\-output option for command \-\-fastq_stats (issue #572),
+.IP -
+fix: bug in \-\-sintax when selecting the best lineage (only low
+confidence values below 0.5 were affected) (issue #573),
+.IP -
+fix: out-of-bounds error in \-\-fastq_stats when processing empty
+reads (issue #571),
+.IP -
+fix: bug in \-\-cut, patterns with multiple cutting sites were not
+detected (commit 4c4f9fa70f14b28d50185dbf322cf5727087e86a),
+.IP -
+fix: memory error (segmentation fault) when using \-\-derep_id and
+\-\-strand (issue #565),
+.IP -
+fix: \-\-fastq_join now obeys to \-\-quiet and \-\-log options
+(commit 87f968b09f17c17ebf8db00aebe86e89b13a3948),
+.IP -
+fix: \-\-fastq_join quality padding is now also set to Q40 when
+quality offset is 64 (commit be0bf9b48d782286c4ce38f0bf1a4c82bd230250),
+.IP -
+fix: (partial) \-\-fastq_join's handling of abundance annotations
+(commit f2bbcb421dc2f4dfa6603b9f31ec3e4598c1b591),
+.IP -
+improve: additional safeguards to validate input values and to make
+sure that they are within acceptable limits. Changes concern options
+\-\-abskew (commit a530dd8990f8a05cb25fc0b6a5da5a14d28fbedd) and
+\-\-fastq_maxdiffs (commit 4b254db7f120bfd49e86185ef3cd9070c236f940),
+.IP -
+improve: code quality (1.3k+ commits, 6k+ clang-tidy warnings eliminated),
+.IP -
+improve: documentation and help messages (issue #568),
+.IP -
+improve: complete refactoring and modernization of a subset of
+commands (\-\-sortbylength, \-\-sortbysize, \-\-shuffle,
+\-\-rereplicate, \-\-cut, \-\-fastq_join, \-\-fasta2fastq,
+\-\-fastq_chars),
+.IP -
+improve: code-coverage of our test-suite for the above-mentioned commands (1,210 new tests, 4,753 in total)
+.RE
 .LP
 .\" ============================================================================
 .\" TODO: