VSEARCH 2.5.1: Fix bad minseqlength with makeudb_usearch command

README.md

@@ -35,9 +35,9 @@ 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/v2.5.0.tar.gz
-tar xzf v2.5.0.tar.gz
-cd vsearch-2.5.0
+wget https://github.com/torognes/vsearch/archive/v2.5.1.tar.gz
+tar xzf v2.5.1.tar.gz
+cd vsearch-2.5.1
 ./autogen.sh
 ./configure
 make
@@ -68,33 +68,33 @@ 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/v2.5.0/vsearch-2.5.0-linux-x86_64.tar.gz
-tar xzf vsearch-2.5.0-linux-x86_64.tar.gz
+wget https://github.com/torognes/vsearch/releases/download/v2.5.1/vsearch-2.5.1-linux-x86_64.tar.gz
+tar xzf vsearch-2.5.1-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/v2.5.0/vsearch-2.5.0-linux-ppc64le.tar.gz
-tar xzf vsearch-2.5.0-linux-ppc64le.tar.gz
+wget https://github.com/torognes/vsearch/releases/download/v2.5.1/vsearch-2.5.1-linux-ppc64le.tar.gz
+tar xzf vsearch-2.5.1-linux-ppc64le.tar.gz
 ```
 
 Or these commands if you are using a Mac:
 
 ```sh
-wget https://github.com/torognes/vsearch/releases/download/v2.5.0/vsearch-2.5.0-macos-x86_64.tar.gz
-tar xzf vsearch-2.5.0-macos-x86_64.tar.gz
+wget https://github.com/torognes/vsearch/releases/download/v2.5.1/vsearch-2.5.1-macos-x86_64.tar.gz
+tar xzf vsearch-2.5.1-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/v2.5.0/vsearch-2.5.0-win-x86_64.zip
+https://github.com/torognes/vsearch/releases/download/v2.5.1/vsearch-2.5.1-win-x86_64.zip
 ```
 
-Linux and Mac: You will now have the binary distribution in a folder called `vsearch-2.5.0-linux-x86_64` or `vsearch-2.5.0-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-2.5.1-linux-x86_64` or `vsearch-2.5.1-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-2.5.0-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-2.5.1-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) 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) is also attached to the latest [release](https://github.com/torognes/vsearch/releases). 
 

configure.ac

@@ -2,7 +2,7 @@
 # Process this file with autoconf to produce a configure script.
 
 AC_PREREQ([2.63])
-AC_INIT([vsearch], [2.5.0], [[email protected]])
+AC_INIT([vsearch], [2.5.1], [[email protected]])
 AC_CANONICAL_TARGET
 AM_INIT_AUTOMAKE([subdir-objects])
 AC_LANG([C++])

man/vsearch.1

@@ -1,5 +1,5 @@
 .\" ============================================================================
-.TH vsearch 1 "October 5, 2017" "version 2.5.0" "USER COMMANDS"
+.TH vsearch 1 "October 25, 2017" "version 2.5.1" "USER COMMANDS"
 .\" ============================================================================
 .SH NAME
 vsearch \(em chimera detection, clustering, dereplication and
@@ -3182,6 +3182,10 @@ fastq_eestats2, makeudb_usearch, udb2fasta, udbinfo, and udbstats. New
 general option: no_progress. New options minsize and maxsize to
 fastx_filter. Minor bug fixes, error message improvements and
 documentation updates.
+.TP
+.BR v2.5.1\~ "released October 25th, 2017"
+Fixed bug with bad default value of 1 instead of 32 for minseqlength
+when using the makeudb_usearch command.
 .RE
 .LP
 .\" ============================================================================

src/vsearch.cc

@@ -2021,7 +2021,8 @@ void args_init(int argc, char **argv)
   if (opt_minseqlength < 0)
     {
       if (opt_cluster_smallmem || opt_cluster_fast || opt_cluster_size ||
-          opt_usearch_global || opt_derep_fulllength || opt_derep_prefix )
+          opt_usearch_global || opt_derep_fulllength || opt_derep_prefix ||
+          opt_makeudb_usearch)
         opt_minseqlength = 32;
       else
         opt_minseqlength = 1;