Merged branch release-0.1.1 into master

.travis.yml

@@ -1,69 +1,98 @@
 sudo: required
 dist: trusty
 
-language: cpp
+language: generic
 osx_image: xcode8
 
-before_install:
+install:
+  ############################################################################
+  # All the Linux dependencies are installed in ${TRAVIS_BUILD_DIR}/deps/
+  ############################################################################
+  - DEPS_DIR="${TRAVIS_BUILD_DIR}/deps"
+  - mkdir -p ${DEPS_DIR} && cd ${DEPS_DIR}
+
+  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then export DEBIAN_FRONTEND=noninteractive; fi
+  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sudo apt-get update -qy; fi
+
+  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew update; fi
+
+  ############################################################################
+  # Install CMake
+  ############################################################################
   - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then
-      sudo add-apt-repository ppa:george-edison55/cmake-3.x -y;
-      sudo apt-get update -q;
-      sudo apt-get upgrade cmake -y;
-      sudo apt-get install python3 -y;
-      sudo apt-get upgrade libboost-all-dev -y;
-      git clone https://github.com/samtools/htslib.git;
-      cd htslib && autoheader && autoconf && ./configure && make && sudo make install;
+      CMAKE_URL="https://cmake.org/files/v3.6/cmake-3.6.2-Linux-x86_64.tar.gz";
+      mkdir -p cmake && travis_retry wget --no-check-certificate --quiet -O - "${CMAKE_URL}" | tar --strip-components=1 -xz -C cmake;
+      export PATH=${DEPS_DIR}/cmake/bin:${PATH};
+    else
+      brew outdated cmake || brew upgrade cmake;
     fi
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then
-      brew update;
-      brew outdated cmake || upgrade cmake;
+
+  ############################################################################
+  # Install Boost
+  ############################################################################
+  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then
+      BOOST_VERSION=trunk;
+      BOOST_DIR=${DEPS_DIR}/boost-${BOOST_VERSION};
+      BOOST_URL="http://github.com/boostorg/boost.git";
+      travis_retry git clone --depth 1 --recursive --quiet ${BOOST_URL} ${BOOST_DIR} || exit 1;
+      cd ${BOOST_DIR} && ./bootstrap.sh && ./b2 headers;
+      cd ${BOOST_DIR}/tools/build && ./bootstrap.sh && ./b2 install --prefix=${DEPS_DIR}/b2;
+      export PATH=${DEPS_DIR}/b2/bin:${PATH};
+    fi
+
+  ############################################################################
+  # Install Python3
+  ############################################################################
+  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then
+      sudo apt-get install python3 -qy;
+    else
       brew install python3;
-      brew outdated boost || upgrade boost;
+    fi
+
+  ############################################################################
+  # Install htslib
+  ############################################################################
+  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then
+      git clone https://github.com/samtools/htslib.git;
+      cd htslib && autoheader && autoconf && ./configure && make && sudo make install;
+    else
       brew tap homebrew/science;
       brew install htslib;
     fi
 
 matrix:
   include:
-  - os: linux
-    compiler: gcc
-    addons:
-      apt:
-        sources:
-          - ubuntu-toolchain-r-test
-      packages:
-        - g++-6
-    env: COMPILER=g++-6
-  - os: linux
-    compiler: clang
-    addons:
-      apt:
-        sources:
-          - ubuntu-toolchain-r-test
-          - llvm-toolchain-precise-3.8
-      packages:
-        - clang-3.8
-    env: COMPILER=clang++-3.8
+#  - os: linux
+#    compiler: gcc
+#    addons:
+#      apt:
+#        sources:
+#          - ubuntu-toolchain-r-test
+#      packages:
+#        - g++-6
+#    env: COMPILER=g++
+#  - os: linux
+#    compiler: clang
+#    addons:
+#      apt:
+#        sources:
+#          - ubuntu-toolchain-r-test
+#          - llvm-toolchain-precise-3.8
+#      packages:
+#        - clang-3.8
+#    env: COMPILER=clang++
   - os: osx
     compiler: clang
-    addons:
-      apt:
-        sources:
-          - ubuntu-toolchain-r-test
-          - llvm-toolchain-precise-3.8
-        packages:
-          - clang-3.8
-    install: export PATH=/usr/local/clang/bin:$PATH
-    env: COMPILER=clang++-3.8
-  - os: osx
-    compiler: gcc
-    addons:
-      apt:
-        sources:
-          - ubuntu-toolchain-r-test
-        packages:
-          - g++-6
-    env: COMPILER=g++-6
+    before_install:
+      - brew install --with-clang llvm
+      - brew outdated boost || brew upgrade boost
+    env: COMPILER=clang++
+
+before_script:
+  - cd "${TRAVIS_BUILD_DIR}"
 
 script:
-  - ./install.py --compiler=$COMPILER
+  - ./install.py --compiler=$COMPILER
+
+notifications:
+  email: false

README.md

@@ -1,6 +1,6 @@
 ![Octopus Logo](logo.png)
 
-[![Build Status](https://travis-ci.com/luntergroup/octopus.svg?token=U9L3a7MWio2P3XpPT3JV&branch=master)](https://travis-ci.com/luntergroup/octopus)
+[![Build Status](https://travis-ci.org/luntergroup/octopus.svg?branch=master)](https://travis-ci.org/luntergroup/octopus)
 [![MIT license](http://img.shields.io/badge/license-MIT-brightgreen.svg)](http://opensource.org/licenses/MIT)
 [![Gitter](https://badges.gitter.im/octopus-caller/Lobby.svg)](https://gitter.im/octopus-caller/Lobby?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge)
 

src/CMakeLists.txt

@@ -44,7 +44,8 @@ set(BASICS_SOURCES
     basics/aligned_read.hpp
     basics/aligned_read.cpp
     basics/mappable_reference_wrapper.hpp
-)
+    basics/ploidy_map.hpp
+    basics/ploidy_map.cpp)
 
 set(CONTAINERS_SOURCES
     containers/mappable_flat_multi_set.hpp

src/basics/ploidy_map.cpp

@@ -0,0 +1,46 @@
+// Copyright (c) 2016 Daniel Cooke
+// Use of this source code is governed by the MIT license that can be found in the LICENSE file.
+
+#include "ploidy_map.hpp"
+
+#include <iterator>
+
+namespace octopus {
+
+PloidyMap::PloidyMap(unsigned organism)
+: organism_ {organism}
+{}
+
+void PloidyMap::set(const ContigName& contig, unsigned ploidy)
+{
+    contigs_.emplace(contig, ploidy);
+}
+
+void PloidyMap::set(const SampleName& sample, const ContigName& contig, unsigned ploidy)
+{
+    sample_contigs_[sample].emplace(contig, ploidy);
+}
+
+unsigned PloidyMap::organism() const noexcept
+{
+    return organism_;
+}
+
+unsigned PloidyMap::operator()(const SampleName& sample, const ContigName& contig) const noexcept
+{
+    const auto sample_itr = sample_contigs_.find(sample);
+    if (sample_itr != std::cend(sample_contigs_)) {
+        const auto contig_itr = sample_itr->second.find(contig);
+        if (contig_itr != std::cend(sample_itr->second)) {
+            return contig_itr->second;
+        }
+    } else {
+        const auto contig_itr = contigs_.find(contig);
+        if (contig_itr != std::cend(contigs_)) {
+            return contig_itr->second;
+        }
+    }
+    return organism_;
+}
+
+} // namespace octopus

src/basics/ploidy_map.hpp

@@ -0,0 +1,41 @@
+// Copyright (c) 2016 Daniel Cooke
+// Use of this source code is governed by the MIT license that can be found in the LICENSE file.
+
+#ifndef ploidy_map_hpp
+#define ploidy_map_hpp
+
+#include <unordered_map>
+
+#include "config/common.hpp"
+
+namespace octopus {
+
+class PloidyMap
+{
+public:
+    PloidyMap(unsigned organism = 2);
+
+    PloidyMap(const PloidyMap&)            = default;
+    PloidyMap& operator=(const PloidyMap&) = default;
+    PloidyMap(PloidyMap&&)                 = default;
+    PloidyMap& operator=(PloidyMap&&)      = default;
+
+    ~PloidyMap() = default;
+
+    void set(const SampleName& sample, const ContigName& contig, unsigned ploidy);
+    void set(const ContigName& contig, unsigned ploidy);
+
+    unsigned organism() const noexcept;
+    unsigned operator()(const SampleName& sample, const ContigName& contig) const noexcept;
+
+private:
+    using ContigPloidyMap = std::unordered_map<ContigName, unsigned>;
+
+    unsigned organism_;
+    ContigPloidyMap contigs_;
+    std::unordered_map<SampleName, ContigPloidyMap> sample_contigs_;
+};
+
+} // namespace octopus
+
+#endif