VSEARCH 2.8.5: Fix bug with fastq_eestats2

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

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], [[email protected]])
+AC_INIT([vsearch], [2.8.5], [[email protected]])
 AC_CANONICAL_TARGET
 AM_INIT_AUTOMAKE([subdir-objects])
 AC_LANG([C++])

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

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();