VSEARCH 2.11.1: Fix handling of id and weak_id options for cluster_un…

…oise

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

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], [[email protected]])
+AC_INIT([vsearch], [2.11.1], [[email protected]])
 AC_CANONICAL_TARGET
 AM_INIT_AUTOMAKE([subdir-objects])
 AC_LANG([C++])

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
 .\" ============================================================================

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)