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README.md
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......@@ -34,7 +34,7 @@ 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/v2.13.5/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/v2.13.6/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
......@@ -47,9 +47,9 @@ 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/v2.13.5.tar.gz
tar xzf v2.13.5.tar.gz
cd vsearch-2.13.5
wget https://github.com/torognes/vsearch/archive/v2.13.6.tar.gz
tar xzf v2.13.6.tar.gz
cd vsearch-2.13.6
./autogen.sh
./configure
make
......@@ -78,43 +78,43 @@ 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/v2.13.5/vsearch-2.13.5-linux-x86_64.tar.gz
tar xzf vsearch-2.13.5-linux-x86_64.tar.gz
wget https://github.com/torognes/vsearch/releases/download/v2.13.6/vsearch-2.13.6-linux-x86_64.tar.gz
tar xzf vsearch-2.13.6-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/v2.13.5/vsearch-2.13.5-linux-ppc64le.tar.gz
tar xzf vsearch-2.13.5-linux-ppc64le.tar.gz
wget https://github.com/torognes/vsearch/releases/download/v2.13.6/vsearch-2.13.6-linux-ppc64le.tar.gz
tar xzf vsearch-2.13.6-linux-ppc64le.tar.gz
```
Or these commands if you are using a Linux aarch64 system:
```sh
wget https://github.com/torognes/vsearch/releases/download/v2.13.5/vsearch-2.13.5-linux-aarch64.tar.gz
tar xzf vsearch-2.13.5-linux-aarch64.tar.gz
wget https://github.com/torognes/vsearch/releases/download/v2.13.6/vsearch-2.13.6-linux-aarch64.tar.gz
tar xzf vsearch-2.13.6-linux-aarch64.tar.gz
```
Or these commands if you are using a Mac:
```sh
wget https://github.com/torognes/vsearch/releases/download/v2.13.5/vsearch-2.13.5-macos-x86_64.tar.gz
tar xzf vsearch-2.13.5-macos-x86_64.tar.gz
wget https://github.com/torognes/vsearch/releases/download/v2.13.6/vsearch-2.13.6-macos-x86_64.tar.gz
tar xzf vsearch-2.13.6-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/v2.13.5/vsearch-2.13.5-win-x86_64.zip
https://github.com/torognes/vsearch/releases/download/v2.13.6/vsearch-2.13.6-win-x86_64.zip
```
Linux and Mac: You will now have the binary distribution in a folder called `vsearch-2.13.5-linux-x86_64` or `vsearch-2.13.5-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`.
Linux and Mac: You will now have the binary distribution in a folder called `vsearch-2.13.6-linux-x86_64` or `vsearch-2.13.6-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`.
Windows: You will now have the binary distribution in a folder called `vsearch-2.13.5-win-x86_64`. The vsearch executable is called `vsearch.exe`. The manual in PDF format is called `vsearch_manual.pdf`.
Windows: You will now have the binary distribution in a folder called `vsearch-2.13.6-win-x86_64`. The vsearch executable is called `vsearch.exe`. The manual in PDF format is called `vsearch_manual.pdf`.
**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/v2.13.5/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 `$MANPATH`. The manual in both formats is also available with the binary distribution. The manual in PDF form ([vsearch_manual.pdf](https://github.com/torognes/vsearch/releases/download/v2.13.5/vsearch_manual.pdf)) is also attached to the latest [release](https://github.com/torognes/vsearch/releases).
**Documentation** The VSEARCH user's manual is available in the `man` folder in the form of a [man page](https://github.com/torognes/vsearch/blob/master/man/vsearch.1). A pdf version ([vsearch_manual.pdf](https://github.com/torognes/vsearch/releases/download/v2.13.6/vsearch_manual.pdf)) will be generated by `make`. To install the manpage manually, copy the `vsearch.1` file or a create a symbolic link to `vsearch.1` in a folder included in your `$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/v2.13.6/vsearch_manual.pdf)) is also attached to the latest [release](https://github.com/torognes/vsearch/releases).
## Packages, plugins, and wrappers
......
configure.ac
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......@@ -2,7 +2,7 @@
# Process this file with autoconf to produce a configure script.
AC_PREREQ([2.63])
AC_INIT([vsearch], [2.13.5], [torognes@ifi.uio.no])
AC_INIT([vsearch], [2.13.6], [torognes@ifi.uio.no])
AC_CANONICAL_TARGET
AM_INIT_AUTOMAKE([subdir-objects])
AC_LANG([C++])
......
debian/changelog
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vsearch (2.13.6-1) unstable; urgency=medium
* Team upload.
* New upstream version
* debhelper-compat 12
* Standards-Version: 4.4.0
-- Steffen Moeller <moeller@debian.org> Sat, 03 Aug 2019 14:55:58 +0200
vsearch (2.13.5-1) unstable; urgency=medium
* New upstream version
......
debian/control
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......@@ -4,13 +4,13 @@ Uploaders: Tim Booth <tbooth@ceh.ac.uk>,
Andreas Tille <tille@debian.org>
Section: science
Priority: optional
Build-Depends: debhelper (>= 12~),
Build-Depends: debhelper-compat (= 12),
zlib1g-dev,
libbz2-dev,
python-markdown,
ghostscript,
time
Standards-Version: 4.3.0
Standards-Version: 4.4.0
Vcs-Browser: https://salsa.debian.org/med-team/vsearch
Vcs-Git: https://salsa.debian.org/med-team/vsearch.git
Homepage: https://github.com/torognes/vsearch/
......
man/vsearch.1
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.\" ============================================================================
.TH vsearch 1 "July 2, 2019" "version 2.13.4" "USER COMMANDS"
.TH vsearch 1 "July 2, 2019" "version 2.13.6" "USER COMMANDS"
.\" ============================================================================
.SH NAME
vsearch \(em chimera detection, clustering, dereplication and
......@@ -3841,6 +3841,9 @@ compilation on FreeBSD and NetBSD systems.
.BR v2.13.5\~ "released July 2nd, 2019"
Added cut command to fragment sequences at restriction sites. Silenced
output from the fastq_stats command if quiet option was given. Updated manual.
.TP
.BR v2.13.6\~ "released July 2nd, 2019"
Added info about cut command to output of help command.
.RE
.LP
.\" ============================================================================
......
src/vsearch.cc
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......@@ -4279,7 +4279,7 @@ void cmd_help()
" Data\n"
" --reverse FILENAME specify FASTQ file with reverse reads\n"
" Parameters\n"
" --fastq_allowmergestagger Allow merging of staggered reads\n"
" --fastq_allowmergestagger allow merging of staggered reads\n"
" --fastq_ascii INT FASTQ input quality score ASCII base char (33)\n"
" --fastq_maxdiffpct REAL maximum percentage diff. bases in overlap (100.0)\n"
" --fastq_maxdiffs INT maximum number of different bases in overlap (10)\n"
......@@ -4313,8 +4313,18 @@ void cmd_help()
" --alnout FILENAME filename for human-readable alignment output\n"
" --acceptall output all pairwise alignments\n"
"\n"
"Restriction site cutting\n"
" --cut FILENAME filename of FASTA formatted input sequences\n"
" Parameters\n"
" --cut_pattern STRING pattern to match with ^ and _ at cut sites\n"
" Output\n"
" --fastaout FILENAME FASTA filename for fragments on forward strand\n"
" --fastaout_rev FILENAME FASTA filename for fragments on reverse strand\n"
" --fastaout_discarded FN FASTA filename for non-matching sequences\n"
" --fastaout_discarded_rev FN FASTA filename for non-matching, reverse compl.\n"
"\n"
"Reverse complementation\n"
" --fastx_revcomp FILENAME Reverse-complement seqs in FASTA or FASTQ file\n"
" --fastx_revcomp FILENAME reverse-complement seqs in FASTA or FASTQ file\n"
" Parameters\n"
" --fastq_ascii INT FASTQ input quality score ASCII base char (33)\n"
" --fastq_qmax INT maximum base quality value for FASTQ input (41)\n"
......@@ -4322,7 +4332,7 @@ void cmd_help()
" Output\n"
" --fastaout FILENAME FASTA output filename\n"
" --fastqout FILENAME FASTQ output filename\n"
" --label_suffix STRING Label to append to identifier in the output\n"
" --label_suffix STRING label to append to identifier in the output\n"
"\n"
"Searching\n"
" --search_exact FILENAME filename of queries for exact match search\n"
......@@ -4670,6 +4680,7 @@ void cmd_none()
"\n"
"vsearch --allpairs_global FILENAME --id 0.5 --alnout FILENAME\n"
"vsearch --cluster_size FILENAME --id 0.97 --centroids FILENAME\n"
"vsearch --cut FILENAME --cut_pattern G^AATT_C --fastaout FILENAME\n"
"vsearch --derep_fulllength FILENAME --output FILENAME\n"
"vsearch --fastq_chars FILENAME\n"
"vsearch --fastq_convert FILENAME --fastqout FILENAME --fastq_ascii 64\n"
......