Finish Release-2.4.1

Fixing bug with spectra-mx plotting script

Author: maplesond

configure.ac

@@ -4,7 +4,7 @@
 
 # Autoconf initialistion.  Sets package name version and contact details
 AC_PREREQ([2.68])
-AC_INIT([kat],[2.4.0],[https://github.com/TGAC/KAT/issues],[kat],[https://github.com/TGAC/KAT])
+AC_INIT([kat],[2.4.1],[https://github.com/TGAC/KAT/issues],[kat],[https://github.com/TGAC/KAT])
 AC_CONFIG_SRCDIR([src/kat.cc])
 AC_CONFIG_AUX_DIR([build-aux])
 AC_CONFIG_MACRO_DIR([m4])

doc/source/conf.py

@@ -52,9 +52,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '2.4.0'
+version = '2.4.1'
 # The full version, including alpha/beta/rc tags.
-release = '2.4.0'
+release = '2.4.1'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

doc/source/index.rst

@@ -44,12 +44,11 @@ selected and the size of your datasets.
 Citing
 ======
 
-The KAT paper is currently in submission.  In the meantime, if you use our software
-and wish to cite us please use our bioRxiv preprint:
+If you use KAT in your work and wish to cite us please use the following citation:
 
-Daniel Mapleson, Gonzalo Garcia Accinelli, George Kettleborough, Jonathan Wright, and Bernardo J. Clavijo. 
+Daniel Mapleson, Gonzalo Garcia Accinelli, George Kettleborough, Jonathan Wright, and Bernardo J. Clavijo.
 **KAT: A K-mer Analysis Toolkit to quality control NGS datasets and genome assemblies.**
-Bioinformatics, 2016. `doi: 10.1093/bioinformatics/btw663 <http://bioinformatics.oxfordjournals.org/content/early/2016/10/20/bioinformatics.btw663.abstract>`_
+Bioinformatics, 2016. [doi: 10.1093/bioinformatics/btw663](http://bioinformatics.oxfordjournals.org/content/early/2016/10/20/bioinformatics.btw663.abstract)
 
 
 
@@ -59,7 +58,7 @@ Issues
 ======
 
 Should you discover any issues with KAT, or wish to request a new feature please raise a `ticket here <https://github.com/TGAC/KAT/issues>`_.
-Alternatively, contact Daniel Mapleson at: daniel.mapleson@earlham.ac.uk; or Bernardo Clavijo at: [email protected].  
+Alternatively, contact Daniel Mapleson at: d.mapleson@gmail.com; or Bernardo Clavijo at: [email protected].  
 However, please consult the `Frequently Asked Questions <faq>`_ page first in case your 
 question is already answered there.
 

doc/source/walkthrough.rst

@@ -385,7 +385,8 @@ assembly completeness.  To this end we bundle a script with kat called kat_dista
 in either a spectra-cn matrix file, or kat histogram file as input, then proceeds to identify peaks
 and fit distributions to each one.  In the case of spectra-cn matrix files it also identifies peaks
 for each copy number for an assembly.  Alternatively, for matrix files generated by KAT GCP, it will also identify
-peaks associated with GC content.
+peaks associated with GC content.  Output from this tool consists of stdout logging as well as structured
+JSON output.  In addition, plots of the fitted distributions can be requested using the *--plot* option.
 
 The user can help to get correct predictions out of the tool by providing an approximate frequency for
 the homozygous part of the distribution.  By default, this is assumed to be the last peak.  For example,
@@ -401,7 +402,7 @@ might produce the following output for this tetraploid genome:
 .. image:: images/distanalysis_plot.png
     :scale: 100%
 
-
+As of KAT V2.4.0, this script is executed as a post-processing step to most KAT tools.
 
 Finding repetitive regions in assemblies
 ----------------------------------------

lib/Makefile.am

@@ -11,7 +11,6 @@ libkat_la_LDFLAGS = \
 	-L../deps/boost/build/lib
 
 libkat_la_SOURCES = \
-	src/gnuplot_i.cc \
 	src/matrix_metadata_extractor.cc \
 	src/input_handler.cc \
 	src/jellyfish_helper.cc \
@@ -21,7 +20,6 @@ library_includedir=$(includedir)/kat-@PACKAGE_VERSION@/kat
 
 KI = $(top_srcdir)/lib/include/kat
 library_include_HEADERS =   $(KI)/distance_metrics.hpp \
-			    $(KI)/gnuplot_i.hpp \
 			    $(KI)/input_handler.hpp \
 			    $(KI)/jellyfish_helper.hpp \
 			    $(KI)/kat_fs.hpp \