Commit 1920c746 authored by Steffen Möller's avatar Steffen Möller
Browse files

New upstream version 2.9.0

parent c89cbc05

README.md

+14 −14
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@@ -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/v2.8.5/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/v2.9.0/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.



## 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/v2.8.5.tar.gz

tar xzf v2.8.5.tar.gz

cd vsearch-2.8.5

wget https://github.com/torognes/vsearch/archive/v2.9.0.tar.gz

tar xzf v2.9.0.tar.gz

cd vsearch-2.9.0

./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/v2.8.5/vsearch-2.8.5-linux-x86_64.tar.gz

tar xzf vsearch-2.8.5-linux-x86_64.tar.gz

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

```



Or these commands if you are using a Linux ppc64le system:



```sh

wget https://github.com/torognes/vsearch/releases/download/v2.8.5/vsearch-2.8.5-linux-ppc64le.tar.gz

tar xzf vsearch-2.8.5-linux-ppc64le.tar.gz

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

```



Or these commands if you are using a Mac:



```sh

wget https://github.com/torognes/vsearch/releases/download/v2.8.5/vsearch-2.8.5-macos-x86_64.tar.gz

tar xzf vsearch-2.8.5-macos-x86_64.tar.gz

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

```



Or if you are using Windows, download and extract (unzip) the contents of this file:



```

https://github.com/torognes/vsearch/releases/download/v2.8.5/vsearch-2.8.5-win-x86_64.zip

https://github.com/torognes/vsearch/releases/download/v2.9.0/vsearch-2.9.0-win-x86_64.zip

```



Linux and Mac: You will now have the binary distribution in a folder called `vsearch-2.8.5-linux-x86_64` or `vsearch-2.8.5-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-2.9.0-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`.



Windows: You will now have the binary distribution in a folder called `vsearch-2.8.5-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-2.9.0-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/v2.8.5/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/v2.8.5/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/v2.9.0/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).





## Plugins, packages, and wrappers

configure.ac

+1 −1
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@@ -2,7 +2,7 @@ 
# Process this file with autoconf to produce a configure script.



AC_PREREQ([2.63])

AC_INIT([vsearch], [2.8.5], [torognes@ifi.uio.no])

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

AC_CANONICAL_TARGET

AM_INIT_AUTOMAKE([subdir-objects])

AC_LANG([C++])

man/vsearch.1

+41 −3
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.\" ============================================================================

.TH vsearch 1 "September 26, 2018" "version 2.8.5" "USER COMMANDS"

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

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

.SH NAME

vsearch \(em chimera detection, clustering, dereplication and
@@ -55,6 +55,10 @@ FASTA/FASTQ file processing: 
\-\-fastaout_discarded | \-\-fastqout | \-\-fastqout_discarded)

\fIoutputfile\fR [\fIoptions\fR]

.PP

\fBvsearch\fR \-\-fastq_join \fIfastqfile\fR \-\-reverse

\fIfastqfile\fR (\-\-fastaout | \-\-fastqout) \fIoutputfile\fR

[\fIoptions\fR]

.PP

\fBvsearch\fR \-\-fastq_mergepairs \fIfastqfile\fR \-\-reverse

\fIfastqfile\fR (\-\-fastaout | \-\-fastqout |

\-\-fastaout_notmerged_fwd | \-\-fastaout_notmerged_rev |
@@ -1091,6 +1095,22 @@ Shorten and/or filter sequences in the given FASTQ file. Similar to 
the \-\-fastx_filter command, but works only on FASTQ files. See

\-\-fastx_filter for details.

.TP

.BI \-\-fastq_join\0 filename

Join paired-end sequence reads into one sequence and add a gap between

them using a padding sequence. The sequences are not merged as with

the fastq_mergepairs command, but simply joined with a gap. The

forward reads are specified as the argument to this option and the

reverse reads are specified with the \-\-reverse option. The resulting

sequences consist of the forward read, the padding sequence and the

reverse complement of the reverse read. The padding sequence is

specified with the \-\-join_padgap option and the padding quality is

specified with the \-\-join_padgapq option. The default padding

sequence string is NNNNNNNN and the default padding quality string is

IIIIIIII, corresponding to a base quality score of 40 (a very high

quality score with error probability 0.0001). The joined sequences are

output to the file(s) specified with the \-\-fastaout or \-\-fastqout

options.

.TP

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

When using \-\-fastq_mergepairs, specify the maximum number of

non-matching nucleotides allowed in the overlap region. That option
@@ -1354,6 +1374,16 @@ file specified with the \-\-fastaout and/or \-\-fastqout options. If 
the input file is in FASTA format, the output can not be written back

to a FASTQ file due to missing base quality scores.

.TP

.BI \-\-join_padgap\~ string

When running \-\-fastq_join, use the \fIstring\fR as a sequence

padding string. The default is NNNNNNNN (8 N's).

.TP

.BI \-\-join_padgapq\~ string

When running \-\-fastq_join, use the \fIstring\fR as a quality padding

string. The default is a string of I's equal in length to the sequence

padding string. The letter I corresponds to a base quality score of 40

indicating a very high quality base with error probability of 0.0001.

.TP

.BI \-\-label_suffix\~ string

When using \-\-fastx_revcomp or \-\-fastq_mergepairs, add the suffix

\fIstring\fR to sequence headers.
@@ -1389,8 +1419,8 @@ Please see the description of the same option under Chimera detection 
for details.

.TP

.BI \-\-reverse \0filename

When using \-\-fastq_mergepairs, specify the FASTQ file containing

containing the reverse reads.

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

file containing containing the reverse reads.

.TP

.B \-\-xsize

Strip abundance information from the headers when writing the output
@@ -3418,6 +3448,14 @@ are in effect. 
.BR v2.8.5\~ "released September 26th, 2018"

Fixed a bug in fastq_eestats2 that caused the values for large lengths

to be much too high when the input sequences had varying lengths.

.TP

.BR v2.8.6\~ "released October 9th, 2018"

Fixed a bug introduced in version 2.8.2 that caused derep_fulllength

to include the full FASTA header in its output instead of stopping at

the first space (unless the notrunclabels option is in effect).

.TP

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

Added the fastq_join command.

.RE

.LP

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

src/Makefile.am

+2 −0
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@@ -30,6 +30,7 @@ dynlibs.h \ 
eestats.h \

fasta.h \

fastq.h \

fastqjoin.h \

fastqops.h \

fastx.h \

kmerhash.h \
@@ -108,6 +109,7 @@ dynlibs.cc \ 
eestats.cc \

fasta.cc \

fastq.cc \

fastqjoin.cc \

fastqops.cc \

fastx.cc \

kmerhash.cc \

src/derep.cc

+1 −1
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@@ -298,7 +298,7 @@ void derep_fulllength() 
  double median = 0.0;

  double average = 0.0;



  while(fastx_next(h, 0, chrmap_no_change))

  while(fastx_next(h, ! opt_notrunclabels, chrmap_no_change))

    {

      int64_t seqlen = fastx_get_sequence_length(h);