From 8d81da7d336811d1ace69c7a9632aa35a8f8f248 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Torbj=C3=B8rn=20Rognes?= Date: Wed, 26 Sep 2018 18:23:26 +0200 Subject: [PATCH] VSEARCH 2.8.5: Fix bug with fastq_eestats2 --- README.md | 28 ++++++++++++++-------------- configure.ac | 2 +- man/vsearch.1 | 6 +++++- src/eestats.cc | 9 --------- 4 files changed, 20 insertions(+), 25 deletions(-) diff --git a/README.md b/README.md index cd4bc088..b4c78e5a 100644 --- a/README.md +++ b/README.md @@ -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/v2.8.4/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/v2.8.4.tar.gz -tar xzf v2.8.4.tar.gz -cd vsearch-2.8.4 +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/v2.8.4/vsearch-2.8.4-linux-x86_64.tar.gz -tar xzf vsearch-2.8.4-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/v2.8.4/vsearch-2.8.4-linux-ppc64le.tar.gz -tar xzf vsearch-2.8.4-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/v2.8.4/vsearch-2.8.4-macos-x86_64.tar.gz -tar xzf vsearch-2.8.4-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/v2.8.4/vsearch-2.8.4-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-2.8.4-linux-x86_64` or `vsearch-2.8.4-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-2.8.4-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/v2.8.4/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 `$MANPATH`. The manual in both formats is also available with the binary distribution. The manual in PDF form ([vsearch_manual.pdf](https://github.com/torognes/vsearch/releases/download/v2.8.4/vsearch_manual.pdf)) is also attached to the latest [release](https://github.com/torognes/vsearch/releases). +**Documentation** The VSEARCH user's manual is available in the `man` folder in the form of a [man page](https://github.com/torognes/vsearch/blob/master/man/vsearch.1). A pdf version ([vsearch_manual.pdf](https://github.com/torognes/vsearch/releases/download/v2.8.5/vsearch_manual.pdf)) will be generated by `make`. To install the manpage manually, copy the `vsearch.1` file or a create a symbolic link to `vsearch.1` in a folder included in your `$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 diff --git a/configure.ac b/configure.ac index 2bbe80af..9a329ddb 100644 --- a/configure.ac +++ b/configure.ac @@ -2,7 +2,7 @@ # Process this file with autoconf to produce a configure script. AC_PREREQ([2.63]) -AC_INIT([vsearch], [2.8.4], [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++]) diff --git a/man/vsearch.1 b/man/vsearch.1 index 3c3574e8..a52acf48 100644 --- a/man/vsearch.1 +++ b/man/vsearch.1 @@ -1,5 +1,5 @@ .\" ============================================================================ -.TH vsearch 1 "September 3, 2018" "version 2.8.4" "USER COMMANDS" +.TH vsearch 1 "September 26, 2018" "version 2.8.5" "USER COMMANDS" .\" ============================================================================ .SH NAME vsearch \(em chimera detection, clustering, dereplication and @@ -3414,6 +3414,10 @@ Fix for segmentation fault for \-\-derep_fulllength with \-\-uc. 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 .\" ============================================================================ diff --git a/src/eestats.cc b/src/eestats.cc index da99abd8..59015b77 100644 --- a/src/eestats.cc +++ b/src/eestats.cc @@ -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();