Commit 8f9cb2d8 authored by Steffen Möller's avatar Steffen Möller
Browse files

New upstream version 2.13.6

parent 59e4ea33

README.md

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@@ -34,7 +34,7 @@ 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/v2.13.5/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/v2.13.6/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
@@ -47,9 +47,9 @@ 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/v2.13.5.tar.gz

tar xzf v2.13.5.tar.gz

cd vsearch-2.13.5

wget https://github.com/torognes/vsearch/archive/v2.13.6.tar.gz

tar xzf v2.13.6.tar.gz

cd vsearch-2.13.6

./autogen.sh

./configure

make
@@ -78,43 +78,43 @@ 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/v2.13.5/vsearch-2.13.5-linux-x86_64.tar.gz

tar xzf vsearch-2.13.5-linux-x86_64.tar.gz

wget https://github.com/torognes/vsearch/releases/download/v2.13.6/vsearch-2.13.6-linux-x86_64.tar.gz

tar xzf vsearch-2.13.6-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/v2.13.5/vsearch-2.13.5-linux-ppc64le.tar.gz

tar xzf vsearch-2.13.5-linux-ppc64le.tar.gz

wget https://github.com/torognes/vsearch/releases/download/v2.13.6/vsearch-2.13.6-linux-ppc64le.tar.gz

tar xzf vsearch-2.13.6-linux-ppc64le.tar.gz

```



Or these commands if you are using a Linux aarch64 system:



```sh

wget https://github.com/torognes/vsearch/releases/download/v2.13.5/vsearch-2.13.5-linux-aarch64.tar.gz

tar xzf vsearch-2.13.5-linux-aarch64.tar.gz

wget https://github.com/torognes/vsearch/releases/download/v2.13.6/vsearch-2.13.6-linux-aarch64.tar.gz

tar xzf vsearch-2.13.6-linux-aarch64.tar.gz

```



Or these commands if you are using a Mac:



```sh

wget https://github.com/torognes/vsearch/releases/download/v2.13.5/vsearch-2.13.5-macos-x86_64.tar.gz

tar xzf vsearch-2.13.5-macos-x86_64.tar.gz

wget https://github.com/torognes/vsearch/releases/download/v2.13.6/vsearch-2.13.6-macos-x86_64.tar.gz

tar xzf vsearch-2.13.6-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/v2.13.5/vsearch-2.13.5-win-x86_64.zip

https://github.com/torognes/vsearch/releases/download/v2.13.6/vsearch-2.13.6-win-x86_64.zip

```



Linux and Mac: You will now have the binary distribution in a folder called `vsearch-2.13.5-linux-x86_64` or `vsearch-2.13.5-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-2.13.6-linux-x86_64` or `vsearch-2.13.6-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-2.13.5-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-2.13.6-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/v2.13.5/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/v2.13.5/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/v2.13.6/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/v2.13.6/vsearch_manual.pdf)) is also attached to the latest [release](https://github.com/torognes/vsearch/releases).





## Packages, plugins, and wrappers

configure.ac

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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], [2.13.5], [torognes@ifi.uio.no])

AC_INIT([vsearch], [2.13.6], [torognes@ifi.uio.no])

AC_CANONICAL_TARGET

AM_INIT_AUTOMAKE([subdir-objects])

AC_LANG([C++])

man/vsearch.1

+4 −1
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.\" ============================================================================

.TH vsearch 1 "July 2, 2019" "version 2.13.4" "USER COMMANDS"

.TH vsearch 1 "July 2, 2019" "version 2.13.6" "USER COMMANDS"

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

.SH NAME

vsearch \(em chimera detection, clustering, dereplication and
@@ -3841,6 +3841,9 @@ compilation on FreeBSD and NetBSD systems. 
.BR v2.13.5\~ "released July 2nd, 2019"

Added cut command to fragment sequences at restriction sites. Silenced

output from the fastq_stats command if quiet option was given. Updated manual.

.TP

.BR v2.13.6\~ "released July 2nd, 2019"

Added info about cut command to output of help command.

.RE

.LP

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

src/vsearch.cc

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@@ -4279,7 +4279,7 @@ void cmd_help() 
              " Data\n"

              "  --reverse FILENAME          specify FASTQ file with reverse reads\n"

              " Parameters\n"

              "  --fastq_allowmergestagger   Allow merging of staggered reads\n"

              "  --fastq_allowmergestagger   allow merging of staggered reads\n"

              "  --fastq_ascii INT           FASTQ input quality score ASCII base char (33)\n"

              "  --fastq_maxdiffpct REAL     maximum percentage diff. bases in overlap (100.0)\n"

              "  --fastq_maxdiffs INT        maximum number of different bases in overlap (10)\n"
@@ -4313,8 +4313,18 @@ void cmd_help() 
              "  --alnout FILENAME           filename for human-readable alignment output\n"

              "  --acceptall                 output all pairwise alignments\n"

              "\n"

              "Restriction site cutting\n"

              "  --cut FILENAME              filename of FASTA formatted input sequences\n"

              " Parameters\n"

              "  --cut_pattern STRING        pattern to match with ^ and _ at cut sites\n"

              " Output\n"

              "  --fastaout FILENAME         FASTA filename for fragments on forward strand\n"

              "  --fastaout_rev FILENAME     FASTA filename for fragments on reverse strand\n"

              "  --fastaout_discarded FN     FASTA filename for non-matching sequences\n"

              "  --fastaout_discarded_rev FN FASTA filename for non-matching, reverse compl.\n"

              "\n"

              "Reverse complementation\n"

              "  --fastx_revcomp FILENAME    Reverse-complement seqs in FASTA or FASTQ file\n"

              "  --fastx_revcomp FILENAME    reverse-complement seqs in FASTA or FASTQ file\n"

              " Parameters\n"

              "  --fastq_ascii INT           FASTQ input quality score ASCII base char (33)\n"

              "  --fastq_qmax INT            maximum base quality value for FASTQ input (41)\n"
@@ -4322,7 +4332,7 @@ void cmd_help() 
              " Output\n"

              "  --fastaout FILENAME         FASTA output filename\n"

              "  --fastqout FILENAME         FASTQ output filename\n"

              "  --label_suffix STRING       Label to append to identifier in the output\n"

              "  --label_suffix STRING       label to append to identifier in the output\n"

              "\n"

              "Searching\n"

              "  --search_exact FILENAME     filename of queries for exact match search\n"
@@ -4670,6 +4680,7 @@ void cmd_none() 
            "\n"

            "vsearch --allpairs_global FILENAME --id 0.5 --alnout FILENAME\n"

            "vsearch --cluster_size FILENAME --id 0.97 --centroids FILENAME\n"

            "vsearch --cut FILENAME --cut_pattern G^AATT_C --fastaout FILENAME\n"

            "vsearch --derep_fulllength FILENAME --output FILENAME\n"

            "vsearch --fastq_chars FILENAME\n"

            "vsearch --fastq_convert FILENAME --fastqout FILENAME --fastq_ascii 64\n"