Change seqan3 for FM-index from sdsl-lite

CMakeLists.txt

@@ -1,22 +1,24 @@
-cmake_minimum_required(VERSION 3.4)
-project(unitig_query)
+cmake_minimum_required(VERSION 3.9) # CMP0069 NEW
+set(TARGET_NAME unitig_query)
+project("${TARGET_NAME}")
+add_compile_definitions(PYTHON_EXT)
+
 set(CMAKE_CXX_STANDARD 17)
-set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fconcepts")
-
-# find pthreads
-set(THREADS_PREFER_PTHREAD_FLAG ON)
-find_package(Threads REQUIRED)
-
-# check for conda environment
-IF( DEFINED ENV{CONDA_PREFIX} )
-  # set conda directory
-  SET(CONDA_DIR "$ENV{CONDA_PREFIX}")
-  # find Seqan3 packages
-  find_path(SEQAN3_CLONE_DIR name bin PATHS ${CONDA_DIR} NO_DEFAULT_PATH)
-  find_path(SEQAN3_INCLUDE_DIR name seqan PATHS ${SEQAN3_CLONE_DIR}/include NO_DEFAULT_PATH)
-  find_path(SEQAN3_SUBMODULES_DIR name submodules PATHS ${SEQAN3_INCLUDE_DIR}/seqan3 NO_DEFAULT_PATH)
+if(ENV{UC_INSTALL} EQUAL "conda")
+else()
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DFS_EXP -fconcepts")
+endif()
+
+IF(CMAKE_COMPILER_IS_GNUCC OR "$ENV{SKETCHLIB_INSTALL}" STREQUAL "conda")
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fopenmp")
 ENDIF()
 
+# gcc debug flags
+set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -O0")
+set(CMAKE_C_FLAGS_DEBUG "${CMAKE_C_FLAGS_DEBUG} -O0")
+
+# Vendored libraries
+include_directories(${CMAKE_CURRENT_SOURCE_DIR}/vendor)
 
 #Find include dirs for z and bifrost
 FIND_PATH(z_INCLUDE_DIR NAMES zlib.h HINTS ${CONDA_DIR}/include)
@@ -27,19 +29,48 @@ FIND_LIBRARY(z_LIBRARY NAMES z HINTS ${CONDA_DIR}/lib REQUIRED)
 FIND_LIBRARY(bifrost_LIBRARY NAMES bifrost HINTS ${CONDA_DIR}/lib REQUIRED)
 
 # Set package found as true
-FIND_PACKAGE_HANDLE_STANDARD_ARGS(z DEFAULT_MSG z_INCLUDE_DIR z_LIBRARY)
-FIND_PACKAGE_HANDLE_STANDARD_ARGS(bifrost DEFAULT_MSG bifrost_INCLUDE_DIR bifrost_LIBRARY)
+include(FindPackageHandleStandardArgs)
+find_package_handle_standard_args(z DEFAULT_MSG z_INCLUDE_DIR z_LIBRARY)
+find_package_handle_standard_args(bifrost DEFAULT_MSG bifrost_INCLUDE_DIR bifrost_LIBRARY)
 
 # Set dirs if multiple include/libraries found
 SET( z_INCLUDE_DIRS ${z_INCLUDE_DIR} )
 SET( z_LIBRARIES ${z_LIBRARY} )
-SET( bifrost_INCLUDE_DIRS ${z_INCLUDE_DIR} )
+SET( bifrost_INCLUDE_DIRS ${bifrost_INCLUDE_DIR} )
 SET( bifrost_LIBRARIES ${bifrost_LIBRARY} )
 
-# find SeqAn3 packages
-find_package(SeqAn3 REQUIRED HINTS ${CONDA_DIR}/share/cmake/seqan3)
+include_directories(${bifrost_INCLUDE_DIR})
+include_directories(${z_INCLUDE_DIR})
+
+add_library("${TARGET_NAME}" MODULE)
+execute_process(COMMAND pybind11-config --cmakedir OUTPUT_STRIP_TRAILING_WHITESPACE OUTPUT_VARIABLE pybind11_DIR)
+find_package(pybind11 2.6 CONFIG REQUIRED)
+
+target_sources("${TARGET_NAME}" PRIVATE src/map_strings.cpp src/map_bindings.cpp src/bifrost.cpp)
+
+set_target_properties("${TARGET_NAME}" PROPERTIES
+    CXX_VISIBILITY_PRESET "hidden"
+    PREFIX "${PYTHON_MODULE_PREFIX}"
+    SUFFIX "${PYTHON_MODULE_EXTENSION}"
+)
 
-find_package(pybind11 REQUIRED)
-pybind11_add_module(unitig_query src/map_strings.cpp src/map_bindings.cpp src/bifrost.cpp)
+include(CheckIPOSupported)
+check_ipo_supported(RESULT result)
+if(result)
+    set_target_properties("${TARGET_NAME}" PROPERTIES
+                          INTERPROCEDURAL_OPTIMIZATION ON)
+endif()
 
-target_link_libraries(unitig_query PRIVATE seqan3::seqan3 ${bifrost_LIBRARIES} ${z_LIBRARIES} Threads::Threads)
+target_link_libraries("${TARGET_NAME}" PRIVATE pybind11::module ${bifrost_LIBRARIES} ${z_LIBRARIES})
+if(DEFINED ENV{CONDA_PREFIX} AND (NOT APPLE OR CMAKE_COMPILER_IS_GNUCC OR ENV{UC_INSTALL} EQUAL "conda"))
+    target_link_libraries("${TARGET_NAME}" PRIVATE gomp)
+else()
+    find_package(OpenMP)
+    if(OpenMP_CXX_FOUND)
+        target_link_libraries("${TARGET_NAME}" PRIVATE OpenMP::OpenMP_CXX)
+    endif()
+endif()
+if(ENV{UC_INSTALL} EQUAL "conda")
+else()
+    target_link_libraries("${TARGET_NAME}" PRIVATE stdc++fs)
+endif()

azure-pipelines.yml

@@ -38,6 +38,7 @@ steps:
 # pushd src && make && make install && popd
 - script: |
     source activate unitig_caller_env
+    export UC_INSTALL=conda
     python -m pip install --no-deps --ignore-installed .
     cd test && python run_test.py
   displayName: 'Install and run_test.py'

environment.yml

@@ -3,7 +3,6 @@ channels:
   - conda-forge
   - bioconda
   - defaults
-  - r
 dependencies:
   - python
   - pip
@@ -12,5 +11,4 @@ dependencies:
   - zlib
   - bzip2
   - bifrost >=1.0.6
-  - seqan3 >=3.1.0
-  - pthread-stubs
+  - libgomp