Swarm 2.2.0: Updated version number and manual

README.md

@@ -95,7 +95,7 @@ cap swarm's memory consumption.
 
 ## Install ##
 
-Get the latest binaries for GNU/Linux or MacOSX from
+Get the latest binaries for GNU/Linux or macOS from
 [the release page](https://github.com/torognes/swarm/releases "swarm
 tagged releases"). Get the source code from
 [GitHub](https://github.com/torognes/swarm "swarm public repository")
@@ -356,7 +356,7 @@ You are welcome to:
 If you want to try alternative free and open-source clustering
 methods, here are some links:
 
-* [Vsearch](https://github.com/torognes/vsearch)
+* [VSEARCH](https://github.com/torognes/vsearch)
 * [Oligotyping](http://merenlab.org/projects/oligotyping/)
 * [DNAclust](http://dnaclust.sourceforge.net/)
 * [Sumaclust](http://metabarcoding.org/sumatra)
@@ -365,6 +365,20 @@ methods, here are some links:
 
 ## Version history##
 
+### version 2.2.0 ###
+
+**swarm** 2.2.0 fixes several problems and improves usability.
+Corrected output to structure and uclust files when using fastidious
+mode. Corrected abundance output in some cases. Added check for
+duplicated sequences and fixed check for duplicated sequence
+IDs. Checks for empty sequences. Sorts sequences by additional fields
+to improve stability. Improves compatibility with compilers and
+operating systems.  Outputs sequences in upper case. Allows 64-bit
+abundances. Shows message when waiting for input from stdin. Improves
+error messages and warnings. Improves checking of command line
+options. Fixes remaining errors reported by test suite. Updates
+documentation.
+
 ### version 2.1.13 ###
 
 **swarm** 2.1.13 removes a bug in the progress bar when writing seeds.

man/swarm.1

@@ -1,5 +1,5 @@
 .\" ============================================================================
-.TH swarm 1 "July 6, 2017" "version 2.1.13" "USER COMMANDS"
+.TH swarm 1 "October 17, 2017" "version 2.2.0" "USER COMMANDS"
 .\" ============================================================================
 .SH NAME
 swarm \(em find clusters of nearly-identical nucleotide amplicons
@@ -389,6 +389,19 @@ New features and important modifications of \fBswarm\fR (short lived
 or minor bug releases are not mentioned):
 .RS
 .TP
+.BR v2.2.0\~ "released October 17, 2017"
+Version 2.2.0 fixes several problems and improves usability. Corrected
+output to structure and uclust files when using fastidious
+mode. Corrected abundance output in some cases. Added check for
+duplicated sequences and fixed check for duplicated sequence
+IDs. Checks for empty sequences. Sorts sequences by additional fields
+to improve stability. Improves compatibility with compilers and
+operating systems.  Outputs sequences in upper case. Allows 64-bit
+abundances. Shows message when waiting for input from stdin. Improves
+error messages and warnings. Improves checking of command line
+options. Fixes remaining errors reported by test suite. Updates
+documentation.
+.TP
 .BR v2.1.13\~ "released March 8, 2017"
 Version 2.1.13 removes a bug with the progress bar when writing seeds.
 .TP

src/swarm.h

@@ -54,7 +54,7 @@
 #define LINE_MAX 2048
 #endif
 
-#define SWARM_VERSION "2.1.13"
+#define SWARM_VERSION "2.2.0"
 #define WIDTH 32
 #define WIDTH_SHIFT 5
 #define BLOCKWIDTH 32