Merge pull request #2 from statgen/develop

Alpha2 Merge

.travis.yml

@@ -0,0 +1,27 @@
+language: cpp
+compiler: gcc
+dist: trusty
+sudo: required
+group: edge
+branches:
+  only:
+    - develop
+addons:
+  apt:
+    sources:
+      - george-edison55-precise-backports
+      - ubuntu-toolchain-r-test
+    packages:
+      - cmake-data
+      - cmake
+      - python-dev
+      - python-pip
+install:
+   - sudo pip install cget
+   - cget install -f ./requirements.txt
+script:
+  - cmake --version
+  - mkdir build && cd build
+  - cmake -DBUILD_TESTS=1 -DCMAKE_TOOLCHAIN_FILE=../cget/cget/cget.cmake ..
+  - make
+  - make CTEST_OUTPUT_ON_FAILURE=1 test

CMakeLists.txt

@@ -2,7 +2,7 @@ cmake_minimum_required(VERSION 3.2)
 project(savvy VERSION 1.0.0)
 include(CMakePackageConfigHelpers)
 
-set(CMAKE_CXX_STANDARD 14)
+set(CMAKE_CXX_STANDARD 11)
 
 #add_library(hts STATIC IMPORTED)
 #set_property(TARGET hts PROPERTY IMPORTED_LOCATION ${CMAKE_INSTALL_PREFIX}/lib/libhts.a)
@@ -16,49 +16,67 @@ endif()
 #find_package(shrinkwrap CONFIG REQUIRED)
 find_library(HTS_LIBRARY hts)
 find_library(ZLIB_LIBRARY z)
-#ZSTD can only likn statically since experimental functions are being used.
-find_library(ZSTD_LIBRARY NAMES ${CMAKE_STATIC_LIBRARY_PREFIX}zstd${CMAKE_STATIC_LIBRARY_SUFFIX})
+find_library(ZSTD_LIBRARY zstd)
 find_package(Threads)
 
 #get_target_property(SHRINKWRAP_LIBS shrinkwrap INTERFACE_LINK_LIBRARIES)
 
-add_definitions(-DSAVVY_VERSION="${PROJECT_VERSION}-alpha")
+add_definitions(-DSAVVY_VERSION="${PROJECT_VERSION}-alpha2")
 
 set(HEADER_FILES
     include/savvy/savvy.hpp include/savvy/reader.hpp include/savvy/m3vcf_reader.hpp include/savvy/sav_reader.hpp include/savvy/allele_status.hpp include/savvy/vcf_reader.hpp include/savvy/varint.hpp include/savvy/s1r.hpp include/savvy/site_info.hpp include/savvy/variant_iterator.hpp include/savvy/portable_endian.hpp include/savvy/region.hpp include/savvy/compressed_vector.hpp include/savvy/eigen3_vector.hpp include/savvy/ublas_vector.hpp include/savvy/armadillo_vector.hpp include/savvy/utility.hpp include/savvy/data_format.hpp)
 
 set(SOURCE_FILES
-    src/savvy.cpp src/reader.cpp src/m3vcf_reader.cpp include/savvy/sav_reader.hpp src/sav_reader.cpp include/savvy/test_class.hpp src/vcf_reader.cpp src/varint.cpp src/utility.cpp src/site_info.cpp src/region.cpp)
+    src/savvy/savvy.cpp src/savvy/reader.cpp src/savvy/m3vcf_reader.cpp include/savvy/sav_reader.hpp src/savvy/sav_reader.cpp include/test/test_class.hpp src/savvy/vcf_reader.cpp src/savvy/varint.cpp src/savvy/utility.cpp src/savvy/site_info.cpp src/savvy/region.cpp)
 
 add_library(savvy ${SOURCE_FILES} ${HEADER_FILES})
 target_link_libraries(savvy ${HTS_LIBRARY} ${ZLIB_LIBRARY} ${ZSTD_LIBRARY} ${CMAKE_THREAD_LIBS_INIT})
 target_include_directories(savvy PUBLIC $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include> $<INSTALL_INTERFACE:include>)
 
-add_executable(savvy-test src/test.cpp src/test_class.cpp include/savvy/test_class.hpp)
-target_link_libraries(savvy-test savvy)
+add_executable(sav
+               src/sav/main.cpp
+               src/sav/export.cpp include/sav/export.hpp
+               src/sav/import.cpp include/sav/import.hpp
+               src/sav/index.cpp include/sav/index.hpp
+               src/sav/merge.cpp include/sav/merge.hpp
+               src/sav/sort.cpp include/sav/sort.hpp
+               src/sav/utility.cpp include/sav/utility.hpp)
+target_link_libraries(sav savvy)
 
-add_executable(bcf2m3vcf src/bcf2m3vcf.cpp)
-target_link_libraries(bcf2m3vcf savvy)
+#add_executable(bcf2m3vcf src/sav/bcf2m3vcf.cpp)
+#target_link_libraries(bcf2m3vcf savvy)
 
-add_executable(vcf2sav src/vcf2sav.cpp)
-target_link_libraries(vcf2sav savvy)
+#add_executable(sav-sample-sort src/sav/sav_sample_sort.cpp)
+#target_link_libraries(sav-sample-sort savvy)
 
-add_executable(sav2vcf src/sav2vcf.cpp)
-target_link_libraries(sav2vcf savvy)
+#add_executable(savvy-speed-test src/test/savvy_speed_test.cpp)
+#target_link_libraries(savvy-speed-test savvy)
 
-add_executable(sav-sample-sort src/sav_sample_sort.cpp)
-target_link_libraries(sav-sample-sort savvy)
 
-add_executable(savvy-speed-test src/savvy_speed_test.cpp)
-target_link_libraries(savvy-speed-test savvy)
+if(BUILD_TESTS)
+    enable_testing()
+
+    add_definitions(-DSAVVYT_VCF_FILE=\"${CMAKE_CURRENT_SOURCE_DIR}/test_file.vcf\"
+                    -DSAVVYT_SAV_FILE_HARD=\"${CMAKE_CURRENT_SOURCE_DIR}/test_file_hard.sav\"
+                    -DSAVVYT_SAV_FILE_DOSE=\"${CMAKE_CURRENT_SOURCE_DIR}/test_file_dose.sav\"
+                    -DSAVVYT_MARKER_COUNT_HARD=28
+                    -DSAVVYT_MARKER_COUNT_DOSE=20)
+
+    add_executable(savvy-test src/test/main.cpp src/test/test_class.cpp include/test/test_class.hpp)
+    target_link_libraries(savvy-test savvy)
+
+    add_test(convert_file_test savvy-test convert-file)
+    add_test(subset_test savvy-test subset)
+    add_test(varint_test savvy-test varint)
+endif()
 
 if(BUILD_SLR_EXAMPLES)
-    add_executable(slr-examples src/slr_examples.cpp)
+    add_executable(slr-examples src/test/slr_examples.cpp)
     target_link_libraries(slr-examples savvy armadillo)
 
     find_library(OPENCL_LIB OpenCL)
 
-    add_executable(linreg-ttest src/linreg_ttest.cpp)
+    add_executable(linreg-ttest src/test/linreg_ttest.cpp)
     target_link_libraries(linreg-ttest savvy ${OPENCL_LIB})
 endif()
 
@@ -67,6 +85,8 @@ install(TARGETS savvy EXPORT ${PROJECT_NAME}-config
         LIBRARY DESTINATION lib
         ARCHIVE DESTINATION lib)
 
+install(TARGETS sav RUNTIME DESTINATION bin)
+
 install(EXPORT ${PROJECT_NAME}-config DESTINATION share/${PROJECT_NAME})
 write_basic_package_version_file(${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}-config-version.cmake COMPATIBILITY SameMajorVersion)
 install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}-config-version.cmake DESTINATION share/${PROJECT_NAME})