KAT Release V2.1.0

Introduced new python plotting engine.  Gnuplot plotting is still supported but python plotting is preferred.  The plotting engine can be controlled during configuration prior to compilation.

New documentation

Testing framework change from BOOST to gtest

Travis CI support added

SECT now outputs GC counts as well as CVG counts

KAT supports SOAP scaffolder output

Various bug fixes and improvements.

.gitignore

@@ -13,23 +13,19 @@
 /test-driver
 /*.pro.user*
 /doxygen-doc/
-/kat-0.2.1/
 /.metadata/
 /*.tar.gz
-/kat-0.3.3/
 /config.h
 config.h.in
 configure
 **/Makefile.in
 Makefile.in
 /*.log
 /*.scan
-/kat-1.0.3/
 /build-aux/
-/kat-1.0.4/
 /*.layout
 /nbproject/
-/kat-1.0.6/
+/kat-*/
 /libtool
 /kat
 /gcp/
@@ -41,7 +37,5 @@ Makefile.in
 /.libs/
 *.hpp
 *.Makefile.am.swp
-!/src/filter_sequence.hpp
-!/src/filter_kmer.hpp
-!/src/filter.hpp
-!/src/inc/distance_metrics.hpp
+*.pc
+*.la

.travis.yml

@@ -0,0 +1,41 @@
+language: cpp
+
+matrix:
+    include:
+            - os: linux
+              sudo: required
+              compiler: gcc
+              env: PLOT=none
+            - os: linux
+              sudo: required
+              compiler: gcc
+              env: PLOT=python
+            - os: linux
+              sudo: required
+              compiler: gcc
+              env: PLOT=gnuplot
+            - os: linux
+              sudo: required
+              compiler: gcc
+              env: COMPILER=GCC5 PLOT=python
+            - os: osx
+              compiler: clang
+
+# Setup compiler
+before_install:
+- ./.travis/before_install.sh
+
+# Install dependencies: (Boost and python, and setup KAT)
+install:
+- ./.travis/install.sh
+
+# Build KAT
+- ./autogen.sh
+
+# Make sure python's available at runtime (if necessary) and then build KAT and run tests
+script:
+- if [[ "$PLOT" == "python" ]] || [[ "$TRAVIS_OS_NAME" == "osx" ]]; then export PATH="$HOME/miniconda/bin:$PATH" && source activate test-environment && export LD_LIBRARY_PATH="$HOME/miniconda/envs/test-environment/lib:$LD_LIBRARY_PATH"; fi
+- ./configure --disable-silent-rules && make && make check && make distcheck
+
+
+

.travis/before_install.sh

@@ -0,0 +1,22 @@
+#!/bin/bash
+
+if [[ $TRAVIS_OS_NAME == 'osx' ]]; then
+    brew update
+else
+    sudo add-apt-repository -y ppa:ubuntu-toolchain-r/test
+    sudo apt-get update -qq
+    if [ "$COMPILER" == "GCC5" ]; then 
+        sudo apt-get install -qq g++-5
+        sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-5 100
+        sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-5 100
+        export CXX="g++-5"
+        export CC="gcc-5"        
+    else 
+        sudo apt-get install -qq g++-4.9
+        sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-4.9 100
+        sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-4.9 100
+        export CXX="g++-4.9"
+        export CC="gcc-4.9"
+    fi
+    gcc --version
+fi

.travis/install.sh

@@ -0,0 +1,51 @@
+#!/bin/bash
+
+if [[ $TRAVIS_OS_NAME == 'osx' ]]; then
+
+	# Install boost -- looks like boost 1.55.0_2 is already installed with brew
+	#brew install boost
+
+
+	# install anaconda
+	wget https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O miniconda.sh;
+	bash miniconda.sh -b -p $HOME/miniconda;
+	export PATH="$HOME/miniconda/bin:$PATH";
+	hash -r; 
+	conda config --set always_yes yes --set changeps1 no; 
+	conda update -q conda;  
+	conda info -a
+	conda create -q -n test-environment python=3.5 anaconda; 
+
+else
+
+	# Boost installation
+	wget -q http://sourceforge.net/projects/boost/files/boost/1.59.0/boost_1_59_0.tar.gz/download
+	mv download boost.tar.gz
+	tar -xf boost.tar.gz
+	cd boost_1_59_0
+	sudo ./bootstrap.sh --with-libraries=chrono,timer,program_options,filesystem,system
+	if [[ "$COMPILER" == "GCC5" ]]; then 
+		sudo ./b2 -d0 --toolset=gcc-5 install; 
+	else 
+		sudo ./b2 -d0 --toolset=gcc-4.9 install; 
+	fi
+	cd ..
+
+
+	# Plotting installation
+	if [[ "$PLOT" == "python" ]]; then 
+		wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
+		bash miniconda.sh -b -p $HOME/miniconda;
+		export PATH="$HOME/miniconda/bin:$PATH"; 
+		hash -r; 
+		conda config --set always_yes yes --set changeps1 no; 
+		conda update -q conda;	
+		conda info -a
+		conda create -q -n test-environment python=3.5 anaconda;	
+	elif [ "$PLOT" == "gnuplot" ]; then 
+		sudo apt-get install gnuplot
+		gnuplot --version; 
+	fi
+
+fi
+

AUTHORS

@@ -1,6 +1,6 @@
-Bernardo Clavijo <[email protected]>
-Daniel Mapleson <[email protected]>
-Darren Heavens <[email protected]>
-Sarah Ayling <[email protected]>
-Mario Caccamo <[email protected]>
-George Kettleborough <[email protected]>
+Daniel Mapleson (The software architect and developer)
+Gonzalo Garcia (KAT superuser and primary tester)
+George Kettleborough (For the recent python plotting functionality)
+Jon Wright (KAT superuser and documentation writer)
+Bernardo Clavijo (KAT's godfather, evangelist and all-round k-mer guru)
+