VSEARCH 2.4.2: Improved paired-end merging

README.md

@@ -35,9 +35,9 @@ 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/v2.4.1.tar.gz
-tar xzf v2.4.1.tar.gz
-cd vsearch-2.4.1
+wget https://github.com/torognes/vsearch/archive/v2.4.2.tar.gz
+tar xzf v2.4.2.tar.gz
+cd vsearch-2.4.2
 ./autogen.sh
 ./configure
 make
@@ -68,33 +68,33 @@ 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/v2.4.1/vsearch-2.4.1-linux-x86_64.tar.gz
-tar xzf vsearch-2.4.1-linux-x86_64.tar.gz
+wget https://github.com/torognes/vsearch/releases/download/v2.4.2/vsearch-2.4.2-linux-x86_64.tar.gz
+tar xzf vsearch-2.4.2-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/v2.4.1/vsearch-2.4.1-linux-ppc64le.tar.gz
-tar xzf vsearch-2.4.1-linux-ppc64le.tar.gz
+wget https://github.com/torognes/vsearch/releases/download/v2.4.2/vsearch-2.4.2-linux-ppc64le.tar.gz
+tar xzf vsearch-2.4.2-linux-ppc64le.tar.gz
 ```
 
 Or these commands if you are using a Mac:
 
 ```sh
-wget https://github.com/torognes/vsearch/releases/download/v2.4.1/vsearch-2.4.1-macos-x86_64.tar.gz
-tar xzf vsearch-2.4.1-macos-x86_64.tar.gz
+wget https://github.com/torognes/vsearch/releases/download/v2.4.2/vsearch-2.4.2-macos-x86_64.tar.gz
+tar xzf vsearch-2.4.2-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/v2.4.1/vsearch-2.4.1-win-x86_64.zip
+https://github.com/torognes/vsearch/releases/download/v2.4.2/vsearch-2.4.2-win-x86_64.zip
 ```
 
-Linux and Mac: You will now have the binary distribution in a folder called `vsearch-2.4.1-linux-x86_64` or `vsearch-2.4.1-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-2.4.2-linux-x86_64` or `vsearch-2.4.2-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-2.4.1-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-2.4.2-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/doc/vsearch.1). A pdf version (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) is also attached to the latest [release](https://github.com/torognes/vsearch/releases). 
 

configure.ac

@@ -2,7 +2,7 @@
 # Process this file with autoconf to produce a configure script.
 
 AC_PREREQ([2.63])
-AC_INIT([vsearch], [2.4.1], [[email protected]])
+AC_INIT([vsearch], [2.4.2], [[email protected]])
 AC_CANONICAL_TARGET
 AM_INIT_AUTOMAKE([subdir-objects])
 AC_LANG([C++])

man/vsearch.1

@@ -1,5 +1,5 @@
 .\" ============================================================================
-.TH vsearch 1 "March 1, 2017" "version 2.4.1" "USER COMMANDS"
+.TH vsearch 1 "March 10, 2017" "version 2.4.2" "USER COMMANDS"
 .\" ============================================================================
 .SH NAME
 vsearch \(em chimera detection, clustering, dereplication and
@@ -1054,7 +1054,7 @@ with the \-\-fastq_maxns are also discarded (no limit by
 default). Staggered reads are not merged unless the
 \-\-fastq_allowmergestagger option is specified. The minimum length of
 the overlap region between the reads may be specified with the
-\-\-minovlen option (default 10), and the overlap region may not
+\-\-minovlen option (default 16), and the overlap region may not
 include more mismatches than specified with the \-\-maxdiffs option (5
 by default), otherwise the read pair is discarded. The mimimum and
 maximum length of the merged sequence may be specified with the
@@ -3058,6 +3058,11 @@ command in help text.
 Fixed an overflow bug in fastq_stats and fastq_eestats affecting
 analysis of very large FASTQ files. Fixed maximum memory usage
 reporting on Windows.
+.TP
+.BR v2.4.2\~ "released March 10th, 2017"
+Default value for fastq_minovlen increased to 16 in accordance with
+help text and for compatibility with usearch. Minor changes for
+improved accuracy of paired-end read merging.
 .RE
 .LP
 .\" ============================================================================

src/mergepairs.cc

@@ -61,12 +61,11 @@
 #include "vsearch.h"
 
 #define INPUTCHUNKSIZE 10000
-#define SCOREMETHOD 2
 
 /* scores */
 
 const double alpha = 4.0;
-const double beta = -5.0;
+const double beta = -22.0;
 
 /* static variables */
 
@@ -207,11 +206,7 @@ void precompute_qual()
 
           p = 1.0 - px - py + px * py * 4.0 / 3.0;
 
-#if SCOREMETHOD == 2
-          match_score[x][y] = alpha * p + beta * (1.0 - p);
-#else
           match_score[x][y] = alpha * p;
-#endif
 
           /* Mismatch */
 
@@ -221,11 +216,7 @@ void precompute_qual()
 
           p = 1.0 - (px + py) / 3.0 + px * py * 4.0 / 9.0;
 
-#if SCOREMETHOD == 2
-          mism_score[x][y] = alpha * (1.0 - p) + beta * p;
-#else
           mism_score[x][y] = beta * p;
-#endif
 
         }
     }
@@ -462,7 +453,6 @@ double overlap_score(merge_data_t * ip,
 
 int64_t optimize(merge_data_t * ip)
 {
-  //  int64_t i1 = opt_fastq_minovlen;
   int64_t i1 = 1;
 
   i1 = MAX(i1, ip->fwd_trunc + ip->rev_trunc - opt_fastq_maxmergelen);
@@ -582,7 +572,6 @@ void process(merge_data_t * ip)
   if (!skip)
     ip->offset = optimize(ip);
 
-  //  if (ip->offset)
   if (ip->offset >= opt_fastq_minovlen)
     merge(ip);
 }