VSEARCH 1.0.16: Include code patches from Debian

README.md

@@ -32,22 +32,22 @@ If you can't find an answer in the VSEARCH documentation, please visit the [VSEA
 
 In the example below, VSEARCH will identify sequences in the file database.fsa that are at least 90% identical on the plus strand to the query sequences in the file queries.fsa and write the results to the file alnout.txt.
 
-`./vsearch-1.0.15-linux-x86_64 --usearch_global queries.fsa --db database.fsa --id 0.9 --alnout alnout.txt`
+`./vsearch-1.0.16-linux-x86_64 --usearch_global queries.fsa --db database.fsa --id 0.9 --alnout alnout.txt`
 
 ## Download and install
 
 The latest releases of VSEARCH are available [here](https://github.com/torognes/vsearch/releases).
 
-Binary executables of VSEARCH are available in the `bin` folder for [GNU/Linux on x86-64 systems](https://github.com/torognes/vsearch/blob/master/bin/vsearch-1.0.15-linux-x86_64) and [Apple Mac OS X on x86-64 systems](https://github.com/torognes/vsearch/blob/master/bin/vsearch-1.0.15-osx-x86_64). These executables include support for  input files compressed by zlib and bzip2 (with files usually ending in .gz or .bz2).
+Binary executables of VSEARCH are available in the `bin` folder for [GNU/Linux on x86-64 systems](https://github.com/torognes/vsearch/blob/master/bin/vsearch-1.0.16-linux-x86_64) and [Apple Mac OS X on x86-64 systems](https://github.com/torognes/vsearch/blob/master/bin/vsearch-1.0.16-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 in a folder included in your `$PATH` from `vsearch` to the appropriate binary. You may use the following commands (assuming `~/bin` is in your `$PATH`):
 
 ```sh
 cd ~
 mkdir -p bin
 cd bin
-wget https://github.com/torognes/vsearch/releases/download/v1.0.15/vsearch-1.0.15-linux-x86_64
-ln -s vsearch-1.0.15-linux-x86_64 vsearch
+wget https://github.com/torognes/vsearch/releases/download/v1.0.16/vsearch-1.0.16-linux-x86_64
+ln -s vsearch-1.0.16-linux-x86_64 vsearch
 ```
 
 Substitute `linux` with `osx` in those lines if you're on a Mac.
@@ -339,14 +339,22 @@ Some issues to work on:
 
 ## The VSEARCH team
 
-The following people have contributed to VSEARCH:
+The main contributors to VSEARCH:
 
-* Torbjørn Rognes (Coding, testing, documentation, evaluation)
-* Tomáš Flouri (Coding, testing)
-* Frédéric Mahé (Documentation, testing, feature suggestions)
-* Christopher Quince (Initiator, feature suggestions, evaluation)
-* Umer Zeeshan Ijaz (Feature suggestions)
-* Ben Nichols (evaluation)
+* Tom&aacute;&scaron; Flouri <[email protected]> (Coding, testing)
+* Umer Zeeshan Ijaz <[email protected]> (Feature suggestions)
+* Fr&eacute;d&eacute;ric Mah&eacute; <[email protected]> (Documentation, testing, feature suggestions)
+* Ben Nichols <[email protected]> (evaluation)
+* Christopher Quince <[email protected]> (Initiator, feature suggestions, evaluation)
+* Torbj&oslash;rn Rognes <[email protected]> (Coding, testing, documentation, evaluation)
+
+
+## Acknowledgements
+
+Thanks to the following for patches and other suggestions for improvements:
+
+* Jeff Epler <[email protected]>
+* Andreas Tille <[email protected]>
 
 
 ## Citing VSEARCH

doc/vsearch.1

@@ -1,5 +1,5 @@
 .\" ============================================================================
-.TH vsearch 1 "February 18, 2015" "version 1.0.15" "USER COMMANDS"
+.TH vsearch 1 "February 19, 2015" "version 1.0.16" "USER COMMANDS"
 .\" ============================================================================
 .SH NAME
 vsearch \(em chimera detection, clustering, dereplication, masking, pairwise alignment, searching, shuffling and sorting of amplicons from metagenomic projects.
@@ -1415,7 +1415,7 @@ only sequences with an abundance equal to or greater than 2:
 .\" 
 .\" ============================================================================
 .SH AUTHORS
-Implementation by Torbjørn Rognes and Tomas Flouri, documentation by Frédéric Mahé.
+Implementation by Torbjørn Rognes and Tomás Flouri, documentation by Frédéric Mahé.
 .\" ============================================================================
 .SH REPORTING BUGS
 Submit suggestions and bug-reports at
@@ -1427,7 +1427,7 @@ curmudgeont e-mail to Torbjørn Rognes <[email protected]>.
 Source code and binaries are available at <https://github.com/torognes/vsearch>.
 .\" ============================================================================
 .SH COPYRIGHT
-Copyright (C) 2014, 2015 Torbjørn Rognes, Frédéric Mahé and Tomas Flouri.
+Copyright (C) 2014, 2015 Torbjørn Rognes, Frédéric Mahé and Tomás Flouri.
 .PP
 This program is free software: you can redistribute it and/or modify
 it under the terms of the GNU Affero General Public License as

src/arch.cc

@@ -1,5 +1,5 @@
 /*
-    Copyright (C) 2014 Torbjorn Rognes
+    Copyright (C) 2014-2015 Torbjorn Rognes, Jeff Epler
 
     This program is free software: you can redistribute it and/or modify
     it under the terms of the GNU Affero General Public License as
@@ -37,17 +37,39 @@ unsigned long arch_get_memused()
 
 unsigned long arch_get_memtotal()
 {
-#ifdef __APPLE__
+#if defined(_SC_PHYS_PAGES) && defined(_SC_PAGESIZE)
+
+  long phys_pages = sysconf(_SC_PHYS_PAGES);
+  long pagesize = sysconf(_SC_PAGESIZE);
+
+  if ((phys_pages == -1) || (pagesize == -1))
+    fatal("Cannot determine amount of RAM");
+
+  // sysconf(3) notes that pagesize * phys_pages can overflow, such as
+  // when long is 32-bits and there's more than 4GB RAM.  Since vsearch
+  // apparently targets LP64 systems like x86_64 linux, this will not
+  // arise in practice on the intended platform.
+
+  if (pagesize > LONG_MAX / phys_pages)
+    return LONG_MAX;
+  else
+    return pagesize * phys_pages;
+
+#elif defined(__APPLE__)
+
   int mib [] = { CTL_HW, HW_MEMSIZE };
   int64_t ram = 0;
   size_t length = sizeof(ram);
   if(-1 == sysctl(mib, 2, &ram, &length, NULL, 0))
     fatal("Cannot determine amount of RAM");
   return ram;
+
 #else
+
   struct sysinfo si;
   if (sysinfo(&si))
     fatal("Cannot determine amount of RAM");
   return si.totalram * si.mem_unit;
+
 #endif
 }

src/vsearch.h

@@ -20,7 +20,6 @@
 */
 
 #include <sys/types.h>
-#include <sys/sysctl.h>
 #include <sys/stat.h>
 #include <sys/time.h>
 #include <sys/resource.h>
@@ -40,12 +39,14 @@
 #include <unistd.h>
 #include <float.h>
 
-#include <city.h>
-
-#ifndef __APPLE__
+#ifdef __APPLE__
+#include <sys/sysctl.h>
+#else
 #include <sys/sysinfo.h>
 #endif
 
+#include <city.h>
+
 #ifdef HAVE_ZLIB
 #include <zlib.h>
 #endif
@@ -84,7 +85,7 @@
 #include "allpairs.h"
 
 #define PROG_NAME "vsearch"
-#define PROG_VERSION "v1.0.15"
+#define PROG_VERSION "v1.0.16"
 
 #ifdef __APPLE__
 #define PROG_ARCH "osx_x86_64"