diff --git a/README.md b/README.md index c5ccb5f6..c68b416f 100644 --- a/README.md +++ b/README.md @@ -24,7 +24,7 @@ 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/v2.11.0/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 the [VSEARCH documentation](https://github.com/torognes/vsearch/releases/download/v2.11.1/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 @@ -37,9 +37,9 @@ 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/v2.11.0.tar.gz -tar xzf v2.11.0.tar.gz -cd vsearch-2.11.0 +wget https://github.com/torognes/vsearch/archive/v2.11.1.tar.gz +tar xzf v2.11.1.tar.gz +cd vsearch-2.11.1 ./autogen.sh ./configure make @@ -68,43 +68,43 @@ 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/v2.11.0/vsearch-2.11.0-linux-x86_64.tar.gz -tar xzf vsearch-2.11.0-linux-x86_64.tar.gz +wget https://github.com/torognes/vsearch/releases/download/v2.11.1/vsearch-2.11.1-linux-x86_64.tar.gz +tar xzf vsearch-2.11.1-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/v2.11.0/vsearch-2.11.0-linux-ppc64le.tar.gz -tar xzf vsearch-2.11.0-linux-ppc64le.tar.gz +wget https://github.com/torognes/vsearch/releases/download/v2.11.1/vsearch-2.11.1-linux-ppc64le.tar.gz +tar xzf vsearch-2.11.1-linux-ppc64le.tar.gz ``` Or these commands if you are using a Linux aarch64 system: ```sh -wget https://github.com/torognes/vsearch/releases/download/v2.11.0/vsearch-2.11.0-linux-aarch64.tar.gz -tar xzf vsearch-2.11.0-linux-aarch64.tar.gz +wget https://github.com/torognes/vsearch/releases/download/v2.11.1/vsearch-2.11.1-linux-aarch64.tar.gz +tar xzf vsearch-2.11.1-linux-aarch64.tar.gz ``` Or these commands if you are using a Mac: ```sh -wget https://github.com/torognes/vsearch/releases/download/v2.11.0/vsearch-2.11.0-macos-x86_64.tar.gz -tar xzf vsearch-2.11.0-macos-x86_64.tar.gz +wget https://github.com/torognes/vsearch/releases/download/v2.11.1/vsearch-2.11.1-macos-x86_64.tar.gz +tar xzf vsearch-2.11.1-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/v2.11.0/vsearch-2.11.0-win-x86_64.zip +https://github.com/torognes/vsearch/releases/download/v2.11.1/vsearch-2.11.1-win-x86_64.zip ``` -Linux and Mac: You will now have the binary distribution in a folder called `vsearch-2.11.0-linux-x86_64` or `vsearch-2.11.0-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`. +Linux and Mac: You will now have the binary distribution in a folder called `vsearch-2.11.1-linux-x86_64` or `vsearch-2.11.1-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`. -Windows: You will now have the binary distribution in a folder called `vsearch-2.11.0-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-2.11.1-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/v2.11.0/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 `$MANPATH`. The manual in both formats is also available with the binary distribution. The manual in PDF form ([vsearch_manual.pdf](https://github.com/torognes/vsearch/releases/download/v2.11.0/vsearch_manual.pdf)) is also attached to the latest [release](https://github.com/torognes/vsearch/releases). +**Documentation** The VSEARCH user's manual is available in the `man` folder in the form of a [man page](https://github.com/torognes/vsearch/blob/master/man/vsearch.1). A pdf version ([vsearch_manual.pdf](https://github.com/torognes/vsearch/releases/download/v2.11.1/vsearch_manual.pdf)) will be generated by `make`. To install the manpage manually, copy the `vsearch.1` file or a create a symbolic link to `vsearch.1` in a folder included in your `$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/v2.11.1/vsearch_manual.pdf)) is also attached to the latest [release](https://github.com/torognes/vsearch/releases). ## Plugins, packages, and wrappers @@ -197,6 +197,7 @@ File | Description **fastqjoin.cc** | FASTQ paired-end reads joining **fastqops.cc** | FASTQ file statistics etc **fastx.cc** | Detection of FASTA and FASTQ files, wrapper for FASTA and FASTQ parsers +**filter.cc** | Trimming and filtering of sequences in FASTA and FASTQ files **kmerhash.cc** | Hash for kmers used by paired-end read merger **linmemalign.cc** | Linear memory global sequence aligner **maps.cc** | Various character mapping arrays diff --git a/configure.ac b/configure.ac index 9a3a1bb7..21075499 100644 --- a/configure.ac +++ b/configure.ac @@ -2,7 +2,7 @@ # Process this file with autoconf to produce a configure script. AC_PREREQ([2.63]) -AC_INIT([vsearch], [2.11.0], [torognes@ifi.uio.no]) +AC_INIT([vsearch], [2.11.1], [torognes@ifi.uio.no]) AC_CANONICAL_TARGET AM_INIT_AUTOMAKE([subdir-objects]) AC_LANG([C++]) diff --git a/man/vsearch.1 b/man/vsearch.1 index 3ae865dd..d0ae3ea5 100644 --- a/man/vsearch.1 +++ b/man/vsearch.1 @@ -1,5 +1,5 @@ .\" ============================================================================ -.TH vsearch 1 "February 13, 2019" "version 2.11.0" "USER COMMANDS" +.TH vsearch 1 "February 28, 2019" "version 2.11.1" "USER COMMANDS" .\" ============================================================================ .SH NAME vsearch \(em chimera detection, clustering, dereplication and @@ -3555,6 +3555,10 @@ Added ability to trim and filter paired-end reads using the reverse option with the fastx_filter and fastq_filter commands. Added \-\-xee option to remove ee attributes from FASTA headers. Minor invisible improvement to the progress indicator. +.TP +.BR v2.11.1\~ "released February 28th, 2019" +Minor change to the handling of the weak_id and id options when using +cluster_unoise. .RE .LP .\" ============================================================================ diff --git a/src/vsearch.cc b/src/vsearch.cc index 8152462a..c589c1cf 100644 --- a/src/vsearch.cc +++ b/src/vsearch.cc @@ -2874,7 +2874,7 @@ void cmd_cluster() if (!opt_cluster_unoise) if ((opt_id < 0.0) || (opt_id > 1.0)) fatal("Identity between 0.0 and 1.0 must be specified with --id"); - + if (opt_cluster_fast) cluster_fast(cmdline, progheader); else if (opt_cluster_smallmem)