VSEARCH 1.4.5: Fix memory allocation bug when reading long FASTA sequ…

…ences

README.md

@@ -36,9 +36,9 @@ 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 using Autotools, use the following commands:
 ```
-wget https://github.com/torognes/vsearch/archive/v1.4.4.tar.gz
-tar xzf v1.4.4.tar.gz
-cd vsearch-1.4.4
+wget https://github.com/torognes/vsearch/archive/v1.4.5.tar.gz
+tar xzf v1.4.5.tar.gz
+cd vsearch-1.4.5
 ./autogen.sh
 ./configure
 make
@@ -61,18 +61,18 @@ make install  # as root or sudo make install
 **Binary distribution** Starting with version 1.4.0, binary distribution files (.tar.gz) for GNU/Linux on x86-64 and Apple Mac OS X on x86-64 containing pre-compiled binaries as well as the documentation (man and pdf files) will be made available as part of each [release](https://github.com/torognes/vsearch/releases). The included executables include support for input files compressed by zlib and bzip2 (with files usually ending in `.gz` or `.bz2`). Download the appropriate executable for your system using the following commands if you are using a Linux system:
 
 ```sh
-wget https://github.com/torognes/vsearch/releases/download/v1.4.4/vsearch-1.4.4-linux-x86_64.tar.gz
-tar xzf vsearch-1.4.4-linux-x86_64.tar.gz
+wget https://github.com/torognes/vsearch/releases/download/v1.4.5/vsearch-1.4.5-linux-x86_64.tar.gz
+tar xzf vsearch-1.4.5-linux-x86_64.tar.gz
 ```
 
 Or these commands if you are using a Mac:
 
 ```sh
-wget https://github.com/torognes/vsearch/releases/download/v1.4.4/vsearch-1.4.4-osx-x86_64.tar.gz
-tar xzf vsearch-1.4.4-osx-x86_64.tar.gz
+wget https://github.com/torognes/vsearch/releases/download/v1.4.5/vsearch-1.4.5-osx-x86_64.tar.gz
+tar xzf vsearch-1.4.5-osx-x86_64.tar.gz
 ```
 
-You will now have the binary distribution in a folder called something like `vsearch-1.4.4-linux-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`.
+You will now have the binary distribution in a folder called something like `vsearch-1.4.5-linux-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`.
 
 
 **Binaries** Older VSEARCH binaries (until version 1.1.3) are available [here](https://github.com/torognes/vsearch/releases) for [GNU/Linux on x86-64 systems](https://github.com/torognes/vsearch/blob/master/bin/vsearch-1.1.3-linux-x86_64) and [Apple Mac OS X on x86-64 systems](https://github.com/torognes/vsearch/blob/master/bin/vsearch-1.1.3-osx-x86_64). These executables include support for input files compressed by zlib and bzip2 (with files usually ending in `.gz` or `.bz2`). Download the appropriate executable and make a symbolic link to the vsearch binary in a folder included in your `$PATH`. You may use the following commands, assuming `~/bin` is in your `$PATH` (substitute `linux` with `osx` in those lines if you're on a Mac):

configure.ac

@@ -2,7 +2,7 @@
 # Process this file with autoconf to produce a configure script.
 
 AC_PREREQ([2.63])
-AC_INIT([vsearch], [1.4.4], [[email protected]])
+AC_INIT([vsearch], [1.4.5], [[email protected]])
 AM_INIT_AUTOMAKE([subdir-objects])
 AC_LANG([C++])
 AC_CONFIG_SRCDIR([src/vsearch.cc])

man/vsearch.1

@@ -1,5 +1,5 @@
 .\" ============================================================================
-.TH vsearch 1 "October 3, 2015" "version 1.4.3" "USER COMMANDS"
+.TH vsearch 1 "October 6, 2015" "version 1.4.5" "USER COMMANDS"
 .\" ============================================================================
 .SH NAME
 vsearch \(em chimera detection, clustering, dereplication, FASTA/FASTQ file processing, masking, pairwise alignment, searching, shuffling, sorting and subsampling of amplicons from metagenomic projects.
@@ -2013,6 +2013,9 @@ OS X.
 .TP
 .BR v1.4.4\~ "released October 3rd, 2015"
 Remove debug message.
+.TP
+.BR v1.4.5\~ "released October 6rd, 2015"
+Fix memory allocation bug when reading long FASTA sequences.
 .RE
 .LP
 .\" ============================================================================

src/fasta.cc

@@ -322,8 +322,8 @@ void buffer_extend(struct fasta_buffer_s * buffer, char * buf, unsigned long len
       /* alloc space for len more characters + terminating zero,
          but round up to nearest block size */
       buffer->alloc = 
-        (FASTA_BUFFER_ALLOC * 
-         ((buffer->length + len) / FASTA_BUFFER_ALLOC) + 1);
+        FASTA_BUFFER_ALLOC * 
+        (((buffer->length + len) / FASTA_BUFFER_ALLOC) + 1);
       buffer->data = (char*) xrealloc(buffer->data, buffer->alloc);
     }