Make CMAKE the default build script

* use add_compile_options instead of hardcode setting of the env variable
* remove lib from include directories
* add header files to the source list
* include htslib directories at the cmake build location (no longer using the git-submodule)
* remove git submodule and use htslib via cmake from now on.
* exclude tests from building by default
* build release by default, but tests in debug mode
* remove boost build files
* add cmake to travis
* add release / debug options to the build

.gitmodules

@@ -1,4 +0,0 @@
-[submodule "lib/htslib"]
-  path = lib/htslib
-  url = ../htslib.git
-  branch = broad

.travis.yml

@@ -15,14 +15,16 @@ before_install:
   - sudo apt-get -qq update;
 
 install:
-  - .travis_scripts/boost.sh 
+  - .travis_scripts/boost.sh
   - if [ "$CXX" == "clang++" ]; then .travis_scripts/clang.sh; fi
   - if [ "$CXX" == "g++"     ]; then .travis_scripts/gcc.sh; fi
 
 script:
-  - if [ "$TRAVIS_BRANCH" == "master" ]; then b2 -a toolset=${CC} test variant=production; fi
-  - b2 -a toolset=${CC} test variant=debug cxxflags=--coverage linkflags=--coverage
+  - mkdir build; pushd build;
+  - cmake .. && make debug && make -j 2 gamgee_test
+  - popd;
+  - build/test/gamgee_test
 
 after_success:
   - .travis_scripts/update_website_dox.sh 
-  - .travis_scripts/coveralls.sh 
+  - .travis_scripts/coveralls.sh

.travis_scripts/boost.sh

@@ -3,9 +3,3 @@
 # install boost libraries
 sudo apt-get install -qq boost1.55 
 
-# install boost build from sources in ${HOME}/boost-build
-git clone https://github.com/boostorg/build.git ${HOME}/boost-build
-cd ${HOME}/boost-build
-./bootstrap.sh --with-toolset=${CC}
-sudo ./b2 install 
-cd -

.travis_scripts/coveralls.sh

@@ -5,5 +5,6 @@
 if [ "$CXX" == "g++" ];
 then
   sudo pip install cpp-coveralls
-  coveralls -b . -r . -e lib -e test -e testdata -t ${COVERALLS_TOKEN}
+  cd build
+  coveralls -r ../ -e CMakeFiles -e contrib -e test -t ${COVERALLS_TOKEN}
 fi

.travis_scripts/gcc.sh

@@ -3,3 +3,17 @@
 wget ftp://gsapubftp-anonymous@ftp.broadinstitute.org/travis/gcc_4.9.1-1_amd64.deb
 sudo apt-get remove cpp libffi-dev
 sudo dpkg --install gcc_4.9.1-1_amd64.deb
+
+echo "BEGIN Eliminating old libstdc++"
+sudo rm /usr/lib/gcc/i586-mingw32msvc/4.2.1-sjlj/libstdc++.a
+sudo rm /usr/lib/gcc/i586-mingw32msvc/4.2.1-sjlj/libstdc++.la
+sudo rm /usr/lib/gcc/i586-mingw32msvc/4.2.1-sjlj/libstdc++_s.a
+sudo rm /usr/lib/gcc/i586-mingw32msvc/4.2.1-sjlj/libstdc++_sjlj_6.dll
+sudo rm /usr/lib/gcc/x86_64-linux-gnu/4.6/libstdc++.a
+sudo rm /usr/lib/gcc/x86_64-linux-gnu/4.6/libstdc++.so
+sudo rm /usr/lib/x86_64-linux-gnu/libstdc++.so.6
+sudo rm /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16
+echo "END Eliminating old libstdc++"
+
+export LD_LIBRARY_PATH=/usr/lib64
+sudo ln -s /usr/lib64/libstd* /usr/lib/x86_64-linux-gnu/

CMakeLists.txt

@@ -1,16 +1,32 @@
-cmake_minimum_required(VERSION 2.8.4)
+cmake_minimum_required(VERSION 2.8.7)
 project(gamgee)
 
 include(ExternalProject)
 
+## This is the right way to do this, but only supported in cmake 2.8.12
+#add_compile_options("-std=c++1y")
 set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++1y")
 
-find_package(Boost 1.56 COMPONENTS unit_test_framework REQUIRED)
+# Dependency: Boost Unit Test Framework (find in the system)
+find_package(Boost 1.55 COMPONENTS unit_test_framework REQUIRED)
+include_directories(${Boost_INCLUDE_DIRS})
+
+# Dependency: htslib (download and build)
+include("contrib/htslib.cmake")
 
 include_directories(gamgee)
-include_directories(gamgee/utils)
-include_directories(lib)
-include_directories(lib/htslib)
 
 add_subdirectory(gamgee)
 add_subdirectory(test)
+
+ADD_CUSTOM_TARGET(debug
+  COMMAND ${CMAKE_COMMAND} -DCMAKE_BUILD_TYPE=Debug ${CMAKE_SOURCE_DIR}
+  COMMAND ${CMAKE_COMMAND} --build ${CMAKE_BINARY_DIR} --target all
+  COMMENT "Switch CMAKE_BUILD_TYPE to Debug"
+  )
+
+ADD_CUSTOM_TARGET(release
+  COMMAND ${CMAKE_COMMAND} -DCMAKE_BUILD_TYPE=Release ${CMAKE_SOURCE_DIR}
+  COMMAND ${CMAKE_COMMAND} --build ${CMAKE_BINARY_DIR} --target all
+  COMMENT "Switch CMAKE_BUILD_TYPE to Release"
+  )

contrib/htslib.cmake

@@ -1,16 +1,20 @@
 # build htslib
-set(htslib_PREFIX ${CMAKE_BINARY_DIR}/contrib/htslib-prefix)
+set(htslib_PREFIX ${CMAKE_BINARY_DIR}/contrib/htslib)
 ExternalProject_Add(htslib
     PREFIX ${htslib_PREFIX}
     GIT_REPOSITORY "https://github.com/broadinstitute/htslib.git"
-    # NOTE: gamgee tracks the 'broad' branch
-    # we should always sync to a commit from that branch for consistency
     GIT_TAG broad
     BUILD_IN_SOURCE 1
     CONFIGURE_COMMAND ""
-    BUILD_COMMAND ${MAKE}
+    BUILD_COMMAND make lib-static -j 4
     INSTALL_COMMAND ""
-    )
+    LOG_DOWNLOAD 0
+    LOG_UPDATE 0
+    LOG_CONFIGURE 0
+    LOG_BUILD 0
+    LOG_TEST 0
+    LOG_INSTALL 0
+)
 
 include_directories(${htslib_PREFIX}/src/htslib)
 set(htslib_LIB ${htslib_PREFIX}/src/htslib/libhts.a)

gamgee/CMakeLists.txt

@@ -1,40 +1,97 @@
 set(SOURCE_FILES
-    utils/file_utils.cpp
-    utils/genotype_utils.cpp
-    utils/hts_memory.cpp
-    utils/utils.cpp
-    utils/variant_field_type.cpp
-    utils/variant_utils.cpp
     base_quals.cpp
+    base_quals.h
     cigar.cpp
+    cigar.h
+    exceptions.h
     fastq.cpp
+    fastq.h
     fastq_iterator.cpp
+    fastq_iterator.h
     fastq_reader.cpp
+    fastq_reader.h
+    gamgee.h
     genotype.cpp
+    genotype.h
     indexed_sam_iterator.cpp
+    indexed_sam_iterator.h
+    indexed_sam_reader.h
     indexed_variant_iterator.cpp
+    indexed_variant_iterator.h
+    indexed_variant_reader.h
+    individual_field.h
+    individual_field_iterator.h
+    individual_field_value.h
+    individual_field_value_iterator.h
     interval.cpp
+    interval.h
+    missing.h
     multiple_variant_iterator.cpp
+    multiple_variant_iterator.h
+    multiple_variant_reader.h
     read_bases.cpp
+    read_bases.h
     read_group.cpp
+    read_group.h
     reference_iterator.cpp
+    reference_iterator.h
     reference_map.cpp
-    sam.cpp
+    reference_map.h
     sam_builder.cpp
     sam_builder_data_field.cpp
+    sam_builder_data_field.h
+    sam_builder.h
+    sam.cpp
+    sam.h
     sam_header.cpp
+    sam_header.h
     sam_iterator.cpp
+    sam_iterator.h
     sam_pair_iterator.cpp
+    sam_pair_iterator.h
+    sam_reader.h
+    sam_tag.h
     sam_writer.cpp
+    sam_writer.h
+    shared_field.h
+    shared_field_iterator.h
     synced_variant_iterator.cpp
-    variant.cpp
+    synced_variant_iterator.h
+    synced_variant_reader.h
+    utils/file_utils.cpp
+    utils/file_utils.h
+    utils/genotype_utils.cpp
+    utils/genotype_utils.h
+    utils/hts_memory.cpp
+    utils/hts_memory.h
+    utils/short_value_optimized_storage.h
+    utils/utils.cpp
+    utils/utils.h
+    utils/variant_field_type.cpp
+    utils/variant_field_type.h
+    utils/variant_utils.cpp
+    utils/variant_utils.h
     variant_builder.cpp
+    variant_builder.h
+    variant_builder_individual_field.h
     variant_builder_individual_region.cpp
+    variant_builder_individual_region.h
     variant_builder_shared_region.cpp
-    variant_header.cpp
+    variant_builder_shared_region.h
+    variant.cpp
+    variant_filters.h
+    variant_filters_iterator.h
+    variant.h
     variant_header_builder.cpp
+    variant_header_builder.h
+    variant_header.cpp
+    variant_header.h
     variant_iterator.cpp
+    variant_iterator.h
+    variant_reader.h
     variant_writer.cpp
+    variant_writer.h
+    zip.h
     )
 
 add_library(gamgee STATIC ${SOURCE_FILES})

test/CMakeLists.txt

@@ -21,11 +21,10 @@ set(SOURCE_FILES
     variant_reader_test.cpp
     variant_test.cpp)
 
-include("../contrib/htslib.cmake")
+add_executable(gamgee_test EXCLUDE_FROM_ALL ${SOURCE_FILES})
 
-include_directories(${Boost_INCLUDE_DIRS})
-
-add_executable(gamgee_test ${SOURCE_FILES})
-target_compile_definitions(gamgee_test PUBLIC -DBOOST_TEST_DYN_LINK)
+## This is the right way to do this, but only supported in cmake 2.8.12
+# target_compile_definitions(gamgee_test PUBLIC -DBOOST_TEST_DYN_LINK)
+set_property(TARGET gamgee_test PROPERTY COMPILE_DEFINITIONS BOOST_TEST_DYN_LINK)
 target_link_libraries(gamgee_test gamgee ${htslib_LIB} ${Boost_LIBRARIES} pthread z)
 add_dependencies(gamgee_test htslib)