New upstream version 2.10.2

## Getting Help

If you can't find an answer in the [VSEARCH documentation](https://github.com/torognes/vsearch/releases/download/v2.9.0/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/v2.10.2/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

**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/v2.9.0.tar.gz

tar xzf v2.9.0.tar.gz

cd vsearch-2.9.0

wget https://github.com/torognes/vsearch/archive/v2.10.2.tar.gz

tar xzf v2.10.2.tar.gz

cd vsearch-2.10.2

./autogen.sh

./configure

make

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/v2.9.0/vsearch-2.9.0-linux-x86_64.tar.gz

tar xzf vsearch-2.9.0-linux-x86_64.tar.gz

wget https://github.com/torognes/vsearch/releases/download/v2.10.2/vsearch-2.10.2-linux-x86_64.tar.gz

tar xzf vsearch-2.10.2-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/v2.9.0/vsearch-2.9.0-linux-ppc64le.tar.gz

tar xzf vsearch-2.9.0-linux-ppc64le.tar.gz

wget https://github.com/torognes/vsearch/releases/download/v2.10.2/vsearch-2.10.2-linux-ppc64le.tar.gz

tar xzf vsearch-2.10.2-linux-ppc64le.tar.gz

```

Or these commands if you are using a Mac:

```sh

wget https://github.com/torognes/vsearch/releases/download/v2.9.0/vsearch-2.9.0-macos-x86_64.tar.gz

tar xzf vsearch-2.9.0-macos-x86_64.tar.gz

wget https://github.com/torognes/vsearch/releases/download/v2.10.2/vsearch-2.10.2-macos-x86_64.tar.gz

tar xzf vsearch-2.10.2-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/v2.9.0/vsearch-2.9.0-win-x86_64.zip

https://github.com/torognes/vsearch/releases/download/v2.10.2/vsearch-2.10.2-win-x86_64.zip

```

Linux and Mac: You will now have the binary distribution in a folder called `vsearch-2.9.0-linux-x86_64` or `vsearch-2.9.0-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-2.10.2-linux-x86_64` or `vsearch-2.10.2-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-2.9.0-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-2.10.2-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/v2.9.0/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/v2.9.0/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/v2.10.2/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/v2.10.2/vsearch_manual.pdf)) is also attached to the latest [release](https://github.com/torognes/vsearch/releases).

## Plugins, packages, and wrappers

# Process this file with autoconf to produce a configure script.

AC_PREREQ([2.63])

AC_INIT([vsearch], [2.9.0], [torognes@ifi.uio.no])

AC_INIT([vsearch], [2.10.2], [torognes@ifi.uio.no])

AC_CANONICAL_TARGET

AM_INIT_AUTOMAKE([subdir-objects])

AC_LANG([C++])

# Set default gcc and g++ options

CFLAGS='-g -march=native'

CXXFLAGS='-g -march=native'

CFLAGS='-g'

CXXFLAGS='-g'

# Checks for programs.

AC_PROG_CXX

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

.TH vsearch 1 "October 10, 2018" "version 2.9.0" "USER COMMANDS"

.TH vsearch 1 "December 10, 2018" "version 2.10.2" "USER COMMANDS"

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

.SH NAME

vsearch \(em chimera detection, clustering, dereplication and

\fBvsearch\fR \-\-fastx_revcomp \fIfastxfile\fR (\-\-fastaout |

\-\-fastqout) \fIoutputfile\fR [\fIoptions\fR]

.PP

\fBvsearch\fR \-\-sff_convert \fIsff-file\fR \-\-fastqout

\fIoutputfile\fR [\fIoptions\fR]

.PP

.RE

Masking:

.RS

.TP

.BI \-\-rereplicate \0filename

Duplicate each sequence the number of times indicated by the abundance

of each sequence in the specified file. The sequence labels are

identical for the same sequence, unless \-\-relabel, \-\-relabel_sha1

or \-\-relabel_md5 is used to create unique labels. Output is written

to the file specified with the \-\-output option, in FASTA format. The

output file does not contain abundance information unless \-\-sizeout

is specified, in which case an abundance of 1 is used.

of each sequence in the specified file (option \-\-sizein is always

implied). The sequence labels are identical for the same sequence,

unless \-\-relabel, \-\-relabel_sha1 or \-\-relabel_md5 is used to

create unique labels. Output is written to the file specified with the

\-\-output option, in FASTA format. The output file does not contain

abundance information unless \-\-sizeout is specified, in which case

an abundance of 1 is used.

.TP

.B \-\-sizein

Take into account the abundance annotations present in the input fasta

file (search for the pattern '[>;]size=\fIinteger\fR[;]' in sequence

headers).

headers). That option is active by default when rereplicating.

.TP

.B \-\-sizeout

Add abundance annotations to the output fasta file (add the pattern

\-\-fastq_stats, \-\-fastq_eestats, and \-\-fastq_eestats2

commands. Sequences may be shortened, filtered and converted by the

\-\-fastq_filter or \-\-fastx_filter commands. Paired-end reads can be

merged using the \-\-fastq_mergepairs command. Finally, the

\-\-fastx_revcomp command reverse-complements sequences.

merged using the \-\-fastq_mergepairs command. The \-\-fastx_revcomp

command reverse-complements sequences. Finally, the \-\-sff_convert

command can be used to convert SFF files to FASTQ.

.PP

.TP 9

.B \-\-eeout

Solexa, Illumina 1.3+ and Illumina 1.5+ formats (phred+64).

.TP

.BI \-\-fastq_asciiout\~ "positive integer"

When using \-\-fastq_convert, define the ASCII character number used

as the basis for the FASTQ quality score when writing FASTQ output

files. The default is 33.

When using \-\-fastq_convert or \-\-sff_convert, define the ASCII

character number used as the basis for the FASTQ quality score when

writing FASTQ output files. The default is 33.

.TP

.BI \-\-fastq_chars \0filename

Summarize the composition of sequence and quality strings contained in

quality encoding of the input file must be specified with the

\-\-fastq_ascii option (either 33 or 64, the default is 33), and the

output quality encoding must be specified with the \-\-fastq_asciiout

option (default 33). The mimimum and maximum output quality scores may

option (default 33). The minimum and maximum output quality scores may

be limited using the \-\-fastq_qminout and \-\-fastq_qmaxout

options. The output file is specified with the \-\-fastqout option.

.TP

1.8+ files.

.TP

.BI \-\-fastq_qmaxout\~ "positive integer"

When using \-\-fastq_convert, specify the maximum quality score used

when writing FASTQ files. The default is 41, which is usual for recent

Sanger/Illumina 1.8+ files. Older formats may use a maximum quality

score of 40.

When using \-\-fastq_convert or \-\-sff_convert, specify the maximum

quality score used when writing FASTQ files. The default is 41, which

is usual for recent Sanger/Illumina 1.8+ files. Older formats may use

a maximum quality score of 40.

.TP

.BI \-\-fastq_qmin\~ "positive integer"

Specify the minimum quality score accepted for FASTQ files. The

files. Older formats may use scores between -5 and 2.

.TP

.BI \-\-fastq_qminout\~ "positive integer"

When using \-\-fastq_convert, specify the minimum quality score used

when writing FASTQ files. The default is 0, which is usual for

Sanger/Illumina 1.8+ files. Older versions of the format may use

scores between -5 and 2.

When using \-\-fastq_convert or \-\-sff_convert, specify the minimum

quality score used when writing FASTQ files. The default is 0, which

is usual for Sanger/Illumina 1.8+ files. Older versions of the format

may use scores between -5 and 2.

.TP

.BI \-\-fastq_stats \0filename

Analyze a FASTQ file and report the number of reads it contains. The

When using \-\-fastq_mergepairs or \-\-fastq_join, specify the FASTQ

file containing containing the reverse reads.

.TP

.BI \-\-sff_convert \0filename

Convert the given SFF file to FASTQ. The FASTQ output file is

specified with the \-\-fastqout option. The sequence may be clipped as

specied in the SFF file if the option \-\-sff_clip is specified,

otherwise no clipping occurs. Bases that would have been clipped are

converted to lower case, while the rest is in upper case. The output

quality encoding may be specified with the \-\-fastq_asciiout option

(default 33). The minimum and maximum output quality scores may be

limited using the \-\-fastq_qminout and \-\-fastq_qmaxout options.

.TP

.BI \-\-sff_clip

Specifies that the sequences converted by the \-\-sff_convert command

should be clipped in both ends as indicated in the SFF file. By

default no clipping is performed.

.TP

.B \-\-xsize

Strip abundance information from the headers when writing the output

file.

.TP

.BR v2.9.0\~ "released October 10th, 2018"

Added the fastq_join command.

.TP

.BR v2.9.1\~ "released October 29th, 2018"

Changed compiler options that select the target cpu and tuning to

allow the software to run on any 64-bit x86 system, while tuning for

more modern variants. Avoid illegal instruction error on some

architectures. Update documentation of rereplicate command.

.TP

.BR v2.10.0\~ "released December 6th, 2018"

Added the sff_convert commmand to convert SFF files to FASTQ. Added

some additional option argument checks. Fixed segmentation fault bug

after some fatal errors when a log file was specified.

.TP

.BR v2.10.1\~ "released December 7th, 2018"

Improved sff_convert command. It will now read several variants of the

SFF format. It is also able to read from a pipe. Warnings are given if

there are minor problems. Errors messages have been improved. Minor

speed and memory usage improvements.

.TP

.BR v2.10.2\~ "released December 10th, 2018"

Fixed bug in sintax with reversed order of domain and kingdom.

.RE

.LP

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

if TARGET_PPC

AM_CXXFLAGS=-Wall -Wsign-compare -O3 -g -mcpu=power8

else

AM_CXXFLAGS=-Wall -Wsign-compare -O3 -g

AM_CXXFLAGS=-Wall -Wsign-compare -O3 -g -march=x86-64 -mtune=generic

endif

AM_CFLAGS=$(AM_CXXFLAGS)

search.h \

searchcore.h \

searchexact.h \

sffconvert.h \

showalign.h \

sha1.h \

shuffle.h \

if TARGET_WIN

libcityhash_a_CXXFLAGS = -Wall -Wno-sign-compare -O3 -g -D_MSC_VER

libcityhash_a_CXXFLAGS = $(AM_CXXFLAGS) -Wno-sign-compare -D_MSC_VER

__top_builddir__bin_vsearch_LDFLAGS = -static

__top_builddir__bin_vsearch_LDADD = libregex.a libcityhash.a libcpu_ssse3.a libcpu_sse2.a

else

libcityhash_a_CXXFLAGS = -Wall -Wno-sign-compare -O3 -g

libcityhash_a_CXXFLAGS = $(AM_CXXFLAGS) -Wno-sign-compare

if TARGET_PPC

__top_builddir__bin_vsearch_LDADD = libcityhash.a libcpu.a

search.cc \

searchcore.cc \

searchexact.cc \

sffconvert.cc \

sha1.c \

showalign.cc \

shuffle.cc \