Added Bernardo's distribution analysis script, updated the README and…

… tweaked the interface for spectra-mx.

This is V1!

Makefile.am

@@ -8,7 +8,9 @@ EXTRA_DIST = README COPYING AUTHORS NEWS doxygen.cfg
 dist_noinst_SCRIPTS = autogen.sh
 
 # SCRIPTS TO ADD TO BIN DIR
-dist_bin_SCRIPTS = scripts/kat_comp_reads.sh
+dist_bin_SCRIPTS = \
+        scripts/kat_comp_reads.sh \
+        scripts/dist_analysis.py
 
 # SRC DIRS
 SUBDIRS = src tests

README

@@ -26,8 +26,7 @@ KAT is a suite of tools that analyse jellyfish kmer hashes.  The following tools
      - spectra-mx:   Creates a K-mer spectra plot for a set of K-mer histograms that are derived from
                      selected rows or columns in a matrix produced by the "comp".
 
-In addition, KAT contains a script for.... [ADD INFO ABOUT BERNARDOS SCRIPT HERE]
-
+In addition, KAT contains a python script for analysing the mathematical distributions present in the K-mer spectra in order to determine how much content is present in each peak.
 
 
 -------------------------------------------------------------------------------------------------------------
@@ -61,6 +60,8 @@ The Makefile for kat can take several goals.  Full details of common make goals
   - "make dist" - packages the installation into a tarballed distributable.
   - "make distcheck" - runs some sanity tests to ensure the tarballed distributable is likely to work.
 
+KAT also come with a python script called "dist_analysis.py", which allows the user to determine the amount of content under each peak in the K-mer spectra.  This script will automatically be moved into your selected install directory after running "make install".  However, before running this script you will need to install python and the python numpy and scipy libraries.  In future versions this script will be properly integrated into KAT as another subtool written in C++.
+
 
 -------------------------------------------------------------------------------------------------------------
 
@@ -70,6 +71,7 @@ After KAT has been installed, the following tools should be available:
 
   "kat" - a single executable binary file that contains a number of subtools.
   "kat_comp_reads.sh" - a bash script demonstrating a simple pipeline to compare the K-mers in two read files
+  "dist_analysis.py" - a python script for determining the amount of content in each peak in the K-mer spectra
 
 Running "kat --help" will bring up a list of available tools within kat.  To get help on any of these subtools simple type: "kat <tool> --help".  For example: "kat sect --help"; will show details on how to use the sequence coverage estimator tool.
 

configure

@@ -1,6 +1,6 @@
 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.69 for Kmer Analysis Toolkit (KAT) 0.3.5.
+# Generated by GNU Autoconf 2.69 for Kmer Analysis Toolkit (KAT) 1.0.1.
 #
 # Report bugs to <[email protected]>.
 #
@@ -580,8 +580,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='Kmer Analysis Toolkit (KAT)'
 PACKAGE_TARNAME='kat'
-PACKAGE_VERSION='0.3.5'
-PACKAGE_STRING='Kmer Analysis Toolkit (KAT) 0.3.5'
+PACKAGE_VERSION='1.0.1'
+PACKAGE_STRING='Kmer Analysis Toolkit (KAT) 1.0.1'
 PACKAGE_BUGREPORT='[email protected]'
 PACKAGE_URL='http://www.tgac.ac.uk'
 
@@ -1336,7 +1336,7 @@ if test "$ac_init_help" = "long"; then
   # Omit some internal or obsolete options to make the list less imposing.
   # This message is too long to be a string in the A/UX 3.1 sh.
   cat <<_ACEOF
-\`configure' configures Kmer Analysis Toolkit (KAT) 0.3.5 to adapt to many kinds of systems.
+\`configure' configures Kmer Analysis Toolkit (KAT) 1.0.1 to adapt to many kinds of systems.
 
 Usage: $0 [OPTION]... [VAR=VALUE]...
 
@@ -1402,7 +1402,7 @@ fi
 
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of Kmer Analysis Toolkit (KAT) 0.3.5:";;
+     short | recursive ) echo "Configuration of Kmer Analysis Toolkit (KAT) 1.0.1:";;
    esac
   cat <<\_ACEOF
 
@@ -1520,7 +1520,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-Kmer Analysis Toolkit (KAT) configure 0.3.5
+Kmer Analysis Toolkit (KAT) configure 1.0.1
 generated by GNU Autoconf 2.69
 
 Copyright (C) 2012 Free Software Foundation, Inc.
@@ -1776,7 +1776,7 @@ cat >config.log <<_ACEOF
 This file contains any messages produced by compilers while
 running configure, to aid debugging if configure makes a mistake.
 
-It was created by Kmer Analysis Toolkit (KAT) $as_me 0.3.5, which was
+It was created by Kmer Analysis Toolkit (KAT) $as_me 1.0.1, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
 
   $ $0 $@
@@ -2639,7 +2639,7 @@ fi
 
 # Define the identity of the package.
  PACKAGE='kat'
- VERSION='0.3.5'
+ VERSION='1.0.1'
 
 
 # Some tools Automake needs.
@@ -7065,7 +7065,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
 # report actual input values of CONFIG_FILES etc. instead of their
 # values after options handling.
 ac_log="
-This file was extended by Kmer Analysis Toolkit (KAT) $as_me 0.3.5, which was
+This file was extended by Kmer Analysis Toolkit (KAT) $as_me 1.0.1, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
 
   CONFIG_FILES    = $CONFIG_FILES
@@ -7132,7 +7132,7 @@ _ACEOF
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
 ac_cs_version="\\
-Kmer Analysis Toolkit (KAT) config.status 0.3.5
+Kmer Analysis Toolkit (KAT) config.status 1.0.1
 configured by $0, generated by GNU Autoconf 2.69,
   with options \\"\$ac_cs_config\\"
 

configure.ac

@@ -1,4 +1,4 @@
-AC_INIT([Kmer Analysis Toolkit (KAT)], [0.3.5], [[email protected]], [kat], [http://www.tgac.ac.uk])
+AC_INIT([Kmer Analysis Toolkit (KAT)], [1.0.1], [[email protected]], [kat], [http://www.tgac.ac.uk])
 AM_INIT_AUTOMAKE([1.11 -Wall no-define])
 
 AC_CONFIG_MACRO_DIR([m4])