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README.md
View file @ 2223cdf9
......@@ -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/v2.8.0/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/v2.8.5/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.
## 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/v2.8.0.tar.gz
tar xzf v2.8.0.tar.gz
cd vsearch-2.8.0
wget https://github.com/torognes/vsearch/archive/v2.8.5.tar.gz
tar xzf v2.8.5.tar.gz
cd vsearch-2.8.5
./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/v2.8.0/vsearch-2.8.0-linux-x86_64.tar.gz
tar xzf vsearch-2.8.0-linux-x86_64.tar.gz
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
```
Or these commands if you are using a Linux ppc64le system:
```sh
wget https://github.com/torognes/vsearch/releases/download/v2.8.0/vsearch-2.8.0-linux-ppc64le.tar.gz
tar xzf vsearch-2.8.0-linux-ppc64le.tar.gz
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
```
Or these commands if you are using a Mac:
```sh
wget https://github.com/torognes/vsearch/releases/download/v2.8.0/vsearch-2.8.0-macos-x86_64.tar.gz
tar xzf vsearch-2.8.0-macos-x86_64.tar.gz
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
```
Or if you are using Windows, download and extract (unzip) the contents of this file:
```
https://github.com/torognes/vsearch/releases/download/v2.8.0/vsearch-2.8.0-win-x86_64.zip
https://github.com/torognes/vsearch/releases/download/v2.8.5/vsearch-2.8.5-win-x86_64.zip
```
Linux and Mac: You will now have the binary distribution in a folder called `vsearch-2.8.0-linux-x86_64` or `vsearch-2.8.0-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-2.8.5-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`.
Windows: You will now have the binary distribution in a folder called `vsearch-2.8.0-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-2.8.5-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/v2.8.0/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 `$MANPATH`. The manual in both formats is also available with the binary distribution. The manual in PDF form ([vsearch_manual.pdf](https://github.com/torognes/vsearch/releases/download/v2.8.0/vsearch_manual.pdf)) is also attached to the latest [release](https://github.com/torognes/vsearch/releases).
**Documentation** The VSEARCH user's manual is available in the `man` folder in the form of a [man page](https://github.com/torognes/vsearch/blob/master/man/vsearch.1). A pdf version ([vsearch_manual.pdf](https://github.com/torognes/vsearch/releases/download/v2.8.5/vsearch_manual.pdf)) will be generated by `make`. To install the manpage manually, copy the `vsearch.1` file or a create a symbolic link to `vsearch.1` in a folder included in your `$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).
## Plugins, packages, 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], [2.8.0], [torognes@ifi.uio.no])
AC_INIT([vsearch], [2.8.5], [torognes@ifi.uio.no])
AC_CANONICAL_TARGET
AM_INIT_AUTOMAKE([subdir-objects])
AC_LANG([C++])
......@@ -14,8 +14,8 @@ MACOSX_DEPLOYMENT_TARGET="10.7"
# Set default gcc and g++ options
CFLAGS='-g'
CXXFLAGS='-g'
CFLAGS='-g -march=native'
CXXFLAGS='-g -march=native'
# Checks for programs.
AC_PROG_CXX
......
debian/changelog
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vsearch (2.8.5-1) unstable; urgency=medium
* New upstream version
* Standards-Version: 4.2.1
-- Andreas Tille <tille@debian.org> Wed, 26 Sep 2018 21:00:00 +0200
vsearch (2.8.0-1) unstable; urgency=medium
* New upstream version
......
debian/control
View file @ 2223cdf9
......@@ -10,7 +10,7 @@ Build-Depends: debhelper (>= 11~),
python-markdown,
ghostscript,
time
Standards-Version: 4.1.4
Standards-Version: 4.2.1
Vcs-Browser: https://salsa.debian.org/med-team/vsearch
Vcs-Git: https://salsa.debian.org/med-team/vsearch.git
Homepage: https://github.com/torognes/vsearch/
......
debian/patches/compilerflags.patch
View file @ 2223cdf9
......@@ -6,10 +6,10 @@ Author: Sascha Steinbiss <satta@debian.org>
# Set default gcc and g++ options
-CFLAGS='-g'
-CXXFLAGS='-g'
+#CFLAGS='-g'
+#CXXFLAGS='-g'
-CFLAGS='-g -march=native'
-CXXFLAGS='-g -march=native'
+#CFLAGS='-g -march=native'
+#CXXFLAGS='-g -march=native'
# Checks for programs.
AC_PROG_CXX
man/vsearch.1
View file @ 2223cdf9
.\" ============================================================================
.TH vsearch 1 "April 24, 2018" "version 2.8.0" "USER COMMANDS"
.TH vsearch 1 "September 26, 2018" "version 2.8.5" "USER COMMANDS"
.\" ============================================================================
.SH NAME
vsearch \(em chimera detection, clustering, dereplication and
......@@ -828,7 +828,8 @@ Dereplication and rereplication options:
Merge strictly identical sequences contained in
\fIfilename\fR. Identical sequences are defined as having the same
length and the same string of nucleotides (case insensitive, T and U
are considered the same).
are considered the same). See the options \-\-sizein and \-\-sizeout
to take into account and compute abundance values.
.TP
.BI \-\-derep_prefix \0filename
Merge sequences with identical prefixes contained in \fIfilename\fR.
......@@ -3394,6 +3395,29 @@ incorrect FASTA headers of consensus sequences after clustering.
.TP
.BR v2.8.0\~ "released April 24th, 2018"
Added the fastq_maxdiffpct option to the fastq_mergepairs command.
.TP
.BR v2.8.1\~ "released June 22nd, 2018"
Fixes for compilation warnings with GCC 8.
.TP
.BR v2.8.2\~ "released August 21st, 2018"
Fix for wrong placement of semicolons in header lines in some cases
when using the sizeout or xsize options. Reduced memory requirements
for full-length dereplication in cases with many duplicate sequences.
Improved wording of fastq_mergepairs report. Updated manual regarding
use of sizein and sizeout with dereplication. Changed a compiler
option.
.TP
.BR v2.8.3\~ "released August 31st, 2018"
Fix for segmentation fault for \-\-derep_fulllength with \-\-uc.
.TP
.BR v2.8.4\~ "released September 3rd, 2018"
Further reduce memory requirements for dereplication when not using
the uc option. Fix output during subsampling when quiet or log options
are in effect.
.TP
.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.
.RE
.LP
.\" ============================================================================
......@@ -3403,7 +3427,3 @@ Added the fastq_maxdiffpct option to the fastq_mergepairs command.
.\" visualize and output to pdf
.\" man -l vsearch.1
.\" man -t ./doc/vsearch.1 | ps2pdf - > ./doc/vsearch_manual.pdf
.\"
.\" INSTALL (sysadmin)
.\" gzip -c vsearch.1 > vsearch.1.gz
.\" mv vsearch.1.gz /usr/share/man/man1/
src/abundance.cc
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......@@ -149,12 +149,12 @@ void abundance_fprint_header_strip_size(FILE * fp,
{
if (start <= 1)
{
if (end < header_length)
if (end < header_length - 1)
fprintf(fp, "%s", header + end + 1);
}
else
{
if (end == header_length)
if (end >= header_length - 1)
fprintf(fp, "%.*s", start - 1, header);
else
fprintf(fp, "%.*s;%.*s",
......
src/align.cc
View file @ 2223cdf9
......@@ -85,7 +85,7 @@ inline void pushop(char newop, char ** cigarendp, char * op, int * count)
char buf[25];
int len = sprintf(buf, "%d", *count);
*cigarendp -= len;
strncpy(*cigarendp, buf, (size_t)len);
memcpy(*cigarendp, buf, (size_t)len);
}
*op = newop;
*count = 1;
......@@ -102,7 +102,7 @@ inline void finishop(char ** cigarendp, char * op, int * count)
char buf[25];
int len = sprintf(buf, "%d", *count);
*cigarendp -= len;
strncpy(*cigarendp, buf, (size_t)len);
memcpy(*cigarendp, buf, (size_t)len);
}
*op = 0;
*count = 0;
......
src/derep.cc
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This diff is collapsed.
src/eestats.cc
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......@@ -465,15 +465,6 @@ void fastq_eestats2()
}
}
for (int x = 0; x < len_steps; x++)
{
uint64_t len_cutoff = opt_length_cutoffs_shortest + x * opt_length_cutoffs_increment;
if (len < len_cutoff)
for (int y = 0; y < opt_ee_cutoffs_count; y++)
if (ee <= opt_ee_cutoffs_values[y])
count_table[x * opt_ee_cutoffs_count + y]++;
}
progress_update(fastq_get_position(h));
}
progress_done();
......
src/mergepairs.cc
View file @ 2223cdf9
......@@ -1366,7 +1366,7 @@ void fastq_mergepairs()
if (failed_repeat)
fprintf(stderr,
"%10" PRIu64 " potential tandem repeat\n",
"%10" PRIu64 " multiple potential alignments\n",
failed_repeat);
if (failed_maxdiffs)
......
src/subsample.cc
View file @ 2223cdf9
......@@ -111,9 +111,14 @@ void subsample()
for(int i=0; i<dbsequencecount; i++)
mass_total += db_getabundance(i);
if (! opt_quiet)
fprintf(stderr, "Got %" PRIu64 " reads from %d amplicons\n",
mass_total, dbsequencecount);
if (opt_log)
fprintf(fp_log, "Got %" PRIu64 " reads from %d amplicons\n",
mass_total, dbsequencecount);
int * abundance = (int*) xmalloc(dbsequencecount * sizeof(int));
......@@ -229,7 +234,10 @@ void subsample()
xfree(abundance);
if (! opt_quiet)
fprintf(stderr, "Subsampled %" PRIu64 " reads from %d amplicons\n", n, samples);
if (opt_log)
fprintf(fp_log, "Subsampled %" PRIu64 " reads from %d amplicons\n", n, samples);
db_free();
......
src/util.cc
View file @ 2223cdf9
......@@ -60,6 +60,8 @@
#include "vsearch.h"
//#define SHOW_RUSAGE
static const char * progress_prompt;
static uint64_t progress_next;
static uint64_t progress_size;
......@@ -186,7 +188,7 @@ int64_t getusec(void)
void show_rusage()
{
#if 0
#ifdef SHOW_RUSAGE
double user_time = 0.0;
double system_time = 0.0;
......
src/vsearch.h
View file @ 2223cdf9
......@@ -58,7 +58,9 @@
*/
#define __STDC_CONSTANT_MACROS 1
#define __STDC_FORMAT_MACROS 1
#define __STDC_LIMIT_MACROS 1
#define __restrict
#ifdef HAVE_CONFIG_H
......@@ -87,6 +89,7 @@
#include <fcntl.h>
#include <unistd.h>
#include <float.h>
#include <stdint.h>
#include <inttypes.h>
#include <stdarg.h>
......