Bump to version 2.2.3.

Author: MikkelSchubert

AdapterRemoval.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "ADAPTERREMOVAL" "1" "Oct 01, 2017" "2.2.2" "AdapterRemoval"
+.TH "ADAPTERREMOVAL" "1" "Jan 22, 2019" "2.2.3" "AdapterRemoval"
 .SH NAME
 AdapterRemoval \- Fast short-read adapter trimming and processing
 .
@@ -153,8 +153,7 @@ Output file to which containing paired reads for which the mate has been discard
 .INDENT 0.0
 .TP
 .B \-\-outputcollapsed file
-If –collapsed is set, contains overlapping mate\-pairs which have been merged into a single read (PE mode) or reads for which the adapter was identified by a minimum overlap, indicating that the entire template molecule is present. This does not include which have subsequently been trimmed due to low\-quality or ambiguous nucleotides. Default filename is
-‘basename.collapsed’
+If –collapsed is set, contains overlapping mate\-pairs which have been merged into a single read (PE mode) or reads for which the adapter was identified by a minimum overlap, indicating that the entire template molecule is present. This does not include which have subsequently been trimmed due to low\-quality or ambiguous nucleotides. Default filename is ‘basename.collapsed’
 .UNINDENT
 .INDENT 0.0
 .TP

CHANGES.md

@@ -1,4 +1,4 @@
-### Unpublished
+### Version 2.2.3 - 2019-01-22
 
   * Added support for trimming reads by a fixed amount: --trim5p N --trim3p N.
     Different values may be given for each mate: --trim5p N1 N2. Trimming is
@@ -9,6 +9,12 @@
     the corresponding bases on the two mates differ, and if both have the same
     quality score. The default behavior is to select one of the two bases at
     random.
+  * Fixed reporting of line numbers in error messages.
+  * Added conda installation instructions, courtesy of Maxime Borry (maxibor).
+  * Fixed reading mate 2 adapters specified via --adapter-list. Adapters would
+    be used in the reverse orientation compared to --adapter2. Courtesy of
+    Karolis (KarolisM).
+  * Fixed various typos and improved help/error messages.
 
 
 ### Version 2.2.2 - 2017-07-17

docs/conf.py

@@ -54,9 +54,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = u'2.2.2'
+version = u'2.2.3'
 # The full version, including alpha/beta/rc tags.
-release = u'2.2.2'
+release = u'2.2.3'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

src/main.hpp

@@ -31,7 +31,7 @@ namespace ar
 {
 
 const std::string NAME = "AdapterRemoval";
-const std::string VERSION = "ver. 2.2.2";
+const std::string VERSION = "ver. 2.2.3";
 const std::string HELPTEXT = \
     "This program searches for and removes remnant adapter sequences from\n"
     "your read data.  The program can analyze both single end and paired end\n"