Finish Release-2.11

Updated documentation

Removed dependency on sphinx extensions in order to keep both readthedocs and homebrew happy.

Fixed representation of labels and plotting coordinates based on whether the matrix should be interpretted transposed or not.

Added shebang to python library files, in order for homebrew to be happy including them in the bin directory.

Author: maplesond

README.md

@@ -104,6 +104,13 @@ Both commands do the same thing.
 
 GNU GPL V3.  See COPYING file for more details.
 
+##Cite:
+
+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:
+
+Daniel Mapleson et al. 2016. KAT: A K-mer Analysis Toolkit to quality control NGS datasets and genome assemblies. bioRxiv doi: 10.1101/064733
+
 
 ##Authors:
 
@@ -118,7 +125,7 @@ See AUTHORS file for more details.
 
 ##Acknowledgements:
 
- * Affiliation: The Genome Analysis Centre (TGAC)
+ * Affiliation: Earlham Institute (EI)
  * Funding: The Biotechnology and Biological Sciences Research Council (BBSRC)
 
 We would also like to thank the authors of Jellyfish: https://github.com/gmarcais/Jellyfish; 

configure.ac

@@ -4,7 +4,7 @@
 
 # Autoconf initialistion.  Sets package name version and contact details
 AC_PREREQ([2.68])
-AC_INIT([kat],[2.1.0],[https://github.com/TGAC/KAT/issues],[kat],[https://github.com/TGAC/KAT])
+AC_INIT([kat],[2.1.1],[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

@@ -28,9 +28,7 @@
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = [
-    'sphinx.ext.pngmath',
-    'sphinx.ext.mathjax',
+extensions = [    
 ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -54,9 +52,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '2.1.0'
+version = '2.1.1'
 # The full version, including alpha/beta/rc tags.
-release = '2.1.0'
+release = '2.1.1'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

doc/source/conf.py.in

@@ -28,9 +28,7 @@ needs_sphinx = '1.3'
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = [
-    'sphinx.ext.pngmath',
-    'sphinx.ext.mathjax',
+extensions = [    
 ]
 
 # Add any paths that contain templates here, relative to this directory.

doc/source/images/contaminant_MP.png

@@ -43,8 +43,10 @@ selected and the size of your datasets.
 Citing
 ======
 
-We are currently planning to submit multiple publications around different aspects of KAT.
-In the meantime if you use KAT in your work, please reference our github page `https://github.com/TGAC/KAT <https://github.com/TGAC/KAT>`_
+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:
+
+Daniel Mapleson et al. 2016. KAT: A K-mer Analysis Toolkit to quality control NGS datasets and genome assemblies. bioRxiv doi: 10.1101/064733
 
 
 
@@ -54,7 +56,7 @@ Issues
 ======
 
 Should you discover any issues with spectre, 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@tgac.ac.uk
+Alternatively, contact Daniel Mapleson at: daniel.mapleson@earlham.ac.uk
 
 
 .. _availability:

doc/source/images/contaminant_PE.png

@@ -3,25 +3,26 @@
 K-mer spectra
 =============
 
-K-mer spectra is a representation of a dataset showing how many short
-fixed length words (y-axis) appear a certain number of times (x-axis). The k-mer 
-spectra is composed of distributions representing groups of motifs at different 
-frequencies in the sample, plus biases. Given not too many biases, this becomes 
-shape of the distributions provides a useful set of properties describing the 
-biological sample and the sequencing process and the amount of useful data in the
-dataset.
+A K-mer spectra is a graphical representation of a dataset showing how many short
+fixed length words (k-mers) appear a certain number of times.  The frequency of 
+occurance is plotted on the x-axis and the number of k-mers on the y-axis.  The 
+k-mer spectra is composed of distributions representing groups of motifs at different 
+frequencies in the sample, plus biases. Given not too many biases, the shape of the 
+distributions provides a useful set of properties describing the biological sample, 
+the sequencing process and the amount of useful data in the dataset.
 
-A typical nice 31-mer spectrum of S.cerevisae S288C WGS dataset is shown in the
+A typical 31-mer spectrum of S.cerevisae S288C WGS dataset is shown in the
 following figure:
 
 .. image:: images/kmer_spectra1.png
     :scale: 75%
 
 
-This is composed of an error component containing a huge amount of
-rare motifs, and a several other components as distributions with different modes
-according to how many times a motif appear on the genome. The decomposition
-showing this distributions can be seen here:
+This is composed of an error component containing a huge amount of rare motifs at 
+frequency < 7 arising from errors in the sequencing process, and a several other 
+components as distributions with different modes according to how many times a motif 
+appears on the genome (once, twice, three times etc.). The following plot shows the 
+decomposition of this distribution into it's component distributions:
 
 .. image:: images/kmer_spectra_breakdown.png
-    :scale: 50%
+    :scale: 50%