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VSEARCH 2.7.1: Fixes several Windows bugs
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torognes committed Feb 16, 2018
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28 changes: 14 additions & 14 deletions README.md
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Expand Up @@ -22,7 +22,7 @@ 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/v2.7.0/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/v2.7.1/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

Expand All @@ -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/v2.7.0.tar.gz
tar xzf v2.7.0.tar.gz
cd vsearch-2.7.0
wget https://github.com/torognes/vsearch/archive/v2.7.1.tar.gz
tar xzf v2.7.1.tar.gz
cd vsearch-2.7.1
./autogen.sh
./configure
make
Expand Down Expand Up @@ -68,36 +68,36 @@ 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/v2.7.0/vsearch-2.7.0-linux-x86_64.tar.gz
tar xzf vsearch-2.7.0-linux-x86_64.tar.gz
wget https://github.com/torognes/vsearch/releases/download/v2.7.1/vsearch-2.7.1-linux-x86_64.tar.gz
tar xzf vsearch-2.7.1-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/v2.7.0/vsearch-2.7.0-linux-ppc64le.tar.gz
tar xzf vsearch-2.7.0-linux-ppc64le.tar.gz
wget https://github.com/torognes/vsearch/releases/download/v2.7.1/vsearch-2.7.1-linux-ppc64le.tar.gz
tar xzf vsearch-2.7.1-linux-ppc64le.tar.gz
```

Or these commands if you are using a Mac:

```sh
wget https://github.com/torognes/vsearch/releases/download/v2.7.0/vsearch-2.7.0-macos-x86_64.tar.gz
tar xzf vsearch-2.7.0-macos-x86_64.tar.gz
wget https://github.com/torognes/vsearch/releases/download/v2.7.1/vsearch-2.7.1-macos-x86_64.tar.gz
tar xzf vsearch-2.7.1-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/v2.7.0/vsearch-2.7.0-win-x86_64.zip
https://github.com/torognes/vsearch/releases/download/v2.7.1/vsearch-2.7.1-win-x86_64.zip
```

Linux and Mac: You will now have the binary distribution in a folder called `vsearch-2.7.0-linux-x86_64` or `vsearch-2.7.0-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-2.7.1-linux-x86_64` or `vsearch-2.7.1-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-2.7.0-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-2.7.1-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/v2.7.0/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 `$MANPATH`. The manual in both formats is also available with the binary distribution. The manual in PDF form ([vsearch_manual.pdf](https://github.com/torognes/vsearch/releases/download/v2.7.0/vsearch_manual.pdf)) is also attached to the latest [release](https://github.com/torognes/vsearch/releases).
**Documentation** The VSEARCH user's manual is available in the `man` folder in the form of a [man page](https://github.com/torognes/vsearch/blob/master/man/vsearch.1). A pdf version ([vsearch_manual.pdf](https://github.com/torognes/vsearch/releases/download/v2.7.1/vsearch_manual.pdf)) will be generated by `make`. To install the manpage manually, copy the `vsearch.1` file or a create a symbolic link to `vsearch.1` in a folder included in your `$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/v2.7.1/vsearch_manual.pdf)) is also attached to the latest [release](https://github.com/torognes/vsearch/releases).


## Plugins, packages, and wrappers
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2 changes: 1 addition & 1 deletion configure.ac
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Expand Up @@ -2,7 +2,7 @@
# Process this file with autoconf to produce a configure script.

AC_PREREQ([2.63])
AC_INIT([vsearch], [2.7.0], [[email protected]])
AC_INIT([vsearch], [2.7.1], [[email protected]])
AC_CANONICAL_TARGET
AM_INIT_AUTOMAKE([subdir-objects])
AC_LANG([C++])
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7 changes: 6 additions & 1 deletion man/vsearch.1
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.\" ============================================================================
.TH vsearch 1 "February 13, 2018" "version 2.7.0" "USER COMMANDS"
.TH vsearch 1 "February 16, 2018" "version 2.7.1" "USER COMMANDS"
.\" ============================================================================
.SH NAME
vsearch \(em chimera detection, clustering, dereplication and
Expand Down Expand Up @@ -3315,6 +3315,11 @@ Added commands cluster_unoise, uchime2_denovo and uchime3_denovo
contributed by Davide Albanese based on Robert Edgar's
papers. Refactored fasta and fastq print functions as well as code for
extraction of abundance and other attributes from the headers.
.TP
.BR v2.7.1\~ "released February 16th, 2018"
Fix several bugs on Windows related to large files, use of "-" as a
file name to mean stdin or stdout, alignment errors, missed kmers and
corrupted UDB files. Added documentation of UDB-related commands.
.RE
.LP
.\" ============================================================================
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