VSEARCH 2.8.2: Reduced memory for dereplication and more

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/v2.8.1/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/v2.8.2/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/v2.8.1.tar.gz
-tar xzf v2.8.1.tar.gz
-cd vsearch-2.8.1
+wget https://github.com/torognes/vsearch/archive/v2.8.2.tar.gz
+tar xzf v2.8.2.tar.gz
+cd vsearch-2.8.2
 ./autogen.sh
 ./configure
 make
@@ -70,36 +70,36 @@ 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/v2.8.1/vsearch-2.8.1-linux-x86_64.tar.gz
-tar xzf vsearch-2.8.1-linux-x86_64.tar.gz
+wget https://github.com/torognes/vsearch/releases/download/v2.8.2/vsearch-2.8.2-linux-x86_64.tar.gz
+tar xzf vsearch-2.8.2-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/v2.8.1/vsearch-2.8.1-linux-ppc64le.tar.gz
-tar xzf vsearch-2.8.1-linux-ppc64le.tar.gz
+wget https://github.com/torognes/vsearch/releases/download/v2.8.2/vsearch-2.8.2-linux-ppc64le.tar.gz
+tar xzf vsearch-2.8.2-linux-ppc64le.tar.gz
 ```
 
 Or these commands if you are using a Mac:
 
 ```sh
-wget https://github.com/torognes/vsearch/releases/download/v2.8.1/vsearch-2.8.1-macos-x86_64.tar.gz
-tar xzf vsearch-2.8.1-macos-x86_64.tar.gz
+wget https://github.com/torognes/vsearch/releases/download/v2.8.2/vsearch-2.8.2-macos-x86_64.tar.gz
+tar xzf vsearch-2.8.2-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/v2.8.1/vsearch-2.8.1-win-x86_64.zip
+https://github.com/torognes/vsearch/releases/download/v2.8.2/vsearch-2.8.2-win-x86_64.zip
 ```
 
-Linux and Mac: You will now have the binary distribution in a folder called `vsearch-2.8.1-linux-x86_64` or `vsearch-2.8.1-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`.
+Linux and Mac: You will now have the binary distribution in a folder called `vsearch-2.8.2-linux-x86_64` or `vsearch-2.8.2-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-2.8.1-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-2.8.2-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/v2.8.1/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 `$MANPATH`. The manual in both formats is also available with the binary distribution. The manual in PDF form ([vsearch_manual.pdf](https://github.com/torognes/vsearch/releases/download/v2.8.1/vsearch_manual.pdf)) is also attached to the latest [release](https://github.com/torognes/vsearch/releases).
+**Documentation** The VSEARCH user's manual is available in the `man` folder in the form of a [man page](https://github.com/torognes/vsearch/blob/master/man/vsearch.1). A pdf version ([vsearch_manual.pdf](https://github.com/torognes/vsearch/releases/download/v2.8.2/vsearch_manual.pdf)) will be generated by `make`. To install the manpage manually, copy the `vsearch.1` file or a create a symbolic link to `vsearch.1` in a folder included in your `$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/v2.8.2/vsearch_manual.pdf)) is also attached to the latest [release](https://github.com/torognes/vsearch/releases).
 
 
 ## Plugins, packages, 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], [2.8.1], [[email protected]])
+AC_INIT([vsearch], [2.8.2], [[email protected]])
 AC_CANONICAL_TARGET
 AM_INIT_AUTOMAKE([subdir-objects])
 AC_LANG([C++])

man/vsearch.1

@@ -1,5 +1,5 @@
 .\" ============================================================================
-.TH vsearch 1 "June 22, 2018" "version 2.8.1" "USER COMMANDS"
+.TH vsearch 1 "August 21, 2018" "version 2.8.2" "USER COMMANDS"
 .\" ============================================================================
 .SH NAME
 vsearch \(em chimera detection, clustering, dereplication and
@@ -3398,6 +3398,14 @@ Added the fastq_maxdiffpct option to the fastq_mergepairs command.
 .TP
 .BR v2.8.1\~ "released June 22nd, 2018"
 Fixes for compilation warnings with GCC 8.
+.TP
+.BR v2.8.2\~ "released August 21st, 2018"
+Fix for wrong placement of semicolons in header lines in some cases
+when using the sizeout or xsize options. Reduced memory requirements
+for full-length dereplication in cases with many duplicate sequences.
+Improved wording of fastq_mergepairs report. Updated manual regarding
+use of sizein and sizeout with dereplication. Changed a compiler
+option.
 .RE
 .LP
 .\" ============================================================================

src/abundance.cc

@@ -149,12 +149,12 @@ void abundance_fprint_header_strip_size(FILE * fp,
     {
       if (start <= 1)
         {
-          if (end < header_length)
+          if (end < header_length - 1)
             fprintf(fp, "%s", header + end + 1);
         }
       else
         {
-          if (end == header_length)
+          if (end >= header_length - 1)
             fprintf(fp, "%.*s", start - 1, header);
           else
             fprintf(fp, "%.*s;%.*s",