Merge pull request #13 from ilia-kats/updates

update WFA2-lib, expose more options to Python

_custom_build.py

@@ -75,7 +75,7 @@ def get_extra_args(flags):
 # this has happened on multiple OS with/without `libomp-dev`
 # compiler = ccompiler.new_compiler()
 omp = 0 #1 if has_flag(compiler, "-fopenmp") else 0
-ret = run(f"cd pywfa/WFA2_lib; make clean all BUILD_WFA_PARALLEL={omp} BUILD_MINIMAL=1",
+ret = run(f"cd pywfa/WFA2_lib; make clean all BUILD_WFA_PARALLEL={omp} BUILD_TOOLS=0 BUILD_EXAMPLES=0",
           shell=True)
 if ret.returncode != 0:
     print("Unable to build WFA2_lib")

pywfa/WFA2_lib/.gitignore

@@ -0,0 +1,43 @@
+lib/
+bin/
+build/
+
+# Prerequisites
+*.d
+
+# Compiled Object files
+*.slo
+*.lo
+*.o
+*.obj
+
+# Precompiled Headers
+*.gch
+*.pch
+
+# Compiled Dynamic libraries
+*.so
+*.dylib
+*.dll
+
+# Fortran module files
+*.mod
+*.smod
+
+# Compiled Static libraries
+*.lai
+*.la
+*.a
+*.lib
+
+# Executables
+*.exe
+*.out
+*.app
+
+# Test output files
+tests/wfa.utest.log.correct
+tests/wfa.utest.log.mem
+tests/wfa.utest.log.time
+
+

pywfa/WFA2_lib/CMakeLists.txt

@@ -0,0 +1,226 @@
+# For Debian currently with
+#
+#   cd build
+#   cmake -DCMAKE_BUILD_TYPE=RelWithDebInfo ..
+#   make
+#   make test
+#   make install
+# See below option statements and the README for build information
+
+cmake_minimum_required(VERSION 3.16)
+project(wfa2lib)
+
+set(CMAKE_CXX_STANDARD 17)
+
+include(FeatureSummary)
+include(GNUInstallDirs)
+
+find_package(PkgConfig REQUIRED)
+
+feature_summary(
+  FATAL_ON_MISSING_REQUIRED_PACKAGES
+  WHAT REQUIRED_PACKAGES_NOT_FOUND)
+
+# ---- Options
+
+option(OPENMP "Enable OpenMP" OFF) # enables WFA_PARALLEL
+option(PROFILING "Enable profiling" OFF)
+option(ASAN "Use address sanitiser" OFF)
+option(EXTRA_FLAGS "Add optimization flags for C/C++ compiler" OFF)
+
+# include(CheckIPOSupported) # adds lto
+# check_ipo_supported(RESULT ipo_supported OUTPUT output)
+
+# ---- Dependencies
+
+if(OPENMP)
+  include(FindOpenMP)
+  set(OPTIMIZE_FLAGS "-DWFA_PARALLEL")
+endif(OPENMP)
+
+if(EXTRA_FLAGS)
+  set(OPTIMIZE_FLAGS "${OPTIMIZE_FLAGS} ${EXTRA_FLAGS}")
+endif(EXTRA_FLAGS)
+
+find_package(Threads)
+set_package_properties(Threads PROPERTIES TYPE REQUIRED)
+
+# ---- Build switches
+set(CMAKE_POSITION_INDEPENDENT_CODE ON)
+# set(CMAKE_INTERPROCEDURAL_OPTIMIZATION ${ipo_supported})
+
+if(NOT CMAKE_BUILD_TYPE)
+  set(CMAKE_BUILD_TYPE Release CACHE STRING
+          "Choose the type of build, options are: Release|Debug|RelWithDebInfo (for distros)." FORCE)
+endif()
+
+if (${CMAKE_BUILD_TYPE} MATCHES Release)
+  set(OPTIMIZE_FLAGS "${OPTIMIZE_FLAGS} -march=native -D_FILE_OFFSET_BITS=64")
+endif()
+
+if ((${CMAKE_BUILD_TYPE} MATCHES Release) OR (${CMAKE_BUILD_TYPE} MATCHES RelWithDebInfo))
+  SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OPTIMIZE_FLAGS}")
+  SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OPTIMIZE_FLAGS}")
+endif ()
+
+if (${CMAKE_BUILD_TYPE} MATCHES "Debug")
+  set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OPTIMIZE_FLAGS}")
+  set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OPTIMIZE_FLAGS}")
+  add_definitions(-Wfatal-errors)
+endif ()
+
+if (ASAN)
+  set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fsanitize=address  -fno-omit-frame-pointer -fno-common")
+  set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=address  -fno-omit-frame-pointer -fno-common")
+endif(ASAN)
+
+if(PROFILING)
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -g")
+endif(PROFILING)
+
+if(GPROF)
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
+endif(GPROF)
+
+# ---- Include files
+
+file(GLOB INCLUDES
+  wavefront/*.h*
+  )
+file(GLOB UTILS_INCLUDES
+  utils/*.h*
+  )
+file(GLOB ALIGNMENT_INCLUDES
+  alignment/*.h*
+  )
+file(GLOB SYSTEM_INCLUDES
+  system/*.h*
+  )
+
+set(wfa2lib_SOURCE
+  wavefront/wavefront_align.c
+  wavefront/wavefront_aligner.c
+  wavefront/wavefront_attributes.c
+  wavefront/wavefront_backtrace_buffer.c
+  wavefront/wavefront_backtrace.c
+  wavefront/wavefront_backtrace_offload.c
+  wavefront/wavefront_bialign.c
+  wavefront/wavefront_bialigner.c
+  wavefront/wavefront.c
+  wavefront/wavefront_components.c
+  wavefront/wavefront_compute_affine2p.c
+  wavefront/wavefront_compute_affine.c
+  wavefront/wavefront_compute.c
+  wavefront/wavefront_compute_edit.c
+  wavefront/wavefront_compute_linear.c
+  wavefront/wavefront_debug.c
+  wavefront/wavefront_display.c
+  wavefront/wavefront_extend.c
+  wavefront/wavefront_heuristic.c
+  wavefront/wavefront_pcigar.c
+  wavefront/wavefront_penalties.c
+  wavefront/wavefront_plot.c
+  wavefront/wavefront_sequences.c
+  wavefront/wavefront_slab.c
+  wavefront/wavefront_unialign.c
+  wavefront/wavefront_termination.c
+  wavefront/wavefront_extend_kernels_avx.c
+  wavefront/wavefront_extend_kernels.c
+  system/mm_stack.c
+  system/mm_allocator.c
+  system/profiler_counter.c
+  system/profiler_timer.c
+  utils/bitmap.c
+  utils/dna_text.c
+  utils/sequence_buffer.c
+  utils/vector.c
+  utils/commons.c
+  utils/heatmap.c
+  alignment/affine2p_penalties.c
+  alignment/affine_penalties.c
+  alignment/cigar.c
+  alignment/score_matrix.c
+)
+
+add_library(wfa2_static
+    ${wfa2lib_SOURCE}
+    )
+add_library(wfa2 SHARED ${wfa2lib_SOURCE})
+set_target_properties(wfa2_static PROPERTIES OUTPUT_NAME wfa2)
+set_target_properties(wfa2 PROPERTIES SOVERSION 0)
+target_include_directories(wfa2 PUBLIC . wavefront utils)
+target_include_directories(wfa2_static PUBLIC . wavefront utils)
+add_library(wfa2::wfa2 ALIAS wfa2)
+add_library(wfa2::wfa2_static ALIAS wfa2_static)
+
+if(OPENMP)
+  target_link_libraries(wfa2_static PRIVATE OpenMP::OpenMP_C)
+  target_link_libraries(wfa2 PRIVATE OpenMP::OpenMP_C)
+endif(OPENMP)
+
+# ---- C++ binding library
+
+set(wfa2cpp_SOURCE
+  bindings/cpp/WFAligner.cpp
+)
+file(GLOB CPP_INCLUDES
+  bindings/cpp/*.h*
+  )
+add_library(wfa2cpp_static STATIC ${wfa2cpp_SOURCE})
+add_library(wfa2cpp SHARED ${wfa2cpp_SOURCE})
+set_target_properties(wfa2cpp PROPERTIES SOVERSION 0)
+set_target_properties(wfa2cpp_static PROPERTIES OUTPUT_NAME wfa2cpp)
+target_link_libraries(wfa2cpp PUBLIC wfa2)
+target_link_libraries(wfa2cpp_static PUBLIC wfa2_static)
+add_library(wfa2::wfa2cpp ALIAS wfa2cpp)
+add_library(wfa2::wfa2cpp_static ALIAS wfa2cpp_static)
+
+if(OPENMP)
+  target_link_libraries(wfa2cpp_static PRIVATE OpenMP::OpenMP_CXX)
+  target_link_libraries(wfa2cpp PRIVATE OpenMP::OpenMP_CXX)
+endif(OPENMP)
+
+# ---- Get version
+
+file (STRINGS "VERSION.txt" BUILD_NUMBER)
+add_definitions(-DWFA2LIB_VERSION="${BUILD_NUMBER}")
+add_definitions(-DVERSION="${BUILD_NUMBER}")
+
+set(wfa2lib_LIBS
+)
+
+# add_dependencies(wfa2lib ${wfa2lib_DEPS})
+
+# ---- Build all
+
+# ---- Test
+
+enable_testing()
+
+
+function(add_wfa_test)
+  add_test(
+    NAME wfa2lib
+    COMMAND ./tests/wfa.utest.sh
+    WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
+    )
+endfunction()
+
+add_wfa_test()
+
+# ---- Install
+
+# Do not install anything when used with FetchContent
+if(CMAKE_CURRENT_SOURCE_DIR STREQUAL CMAKE_SOURCE_DIR)
+  install(TARGETS wfa2_static ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR} )
+  install(TARGETS wfa2 ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR} )
+
+  install(FILES ${INCLUDES} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/wfa2lib/wavefront)
+  install(FILES ${UTILS_INCLUDES} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/wfa2lib/utils)
+  install(FILES ${ALIGNMENT_INCLUDES} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/wfa2lib/alignment)
+  install(FILES ${SYSTEM_INCLUDES} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/wfa2lib/system)
+
+  install(TARGETS wfa2cpp ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
+  install(TARGETS wfa2cpp_static ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
+  install(FILES ${CPP_INCLUDES} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/wfa2lib/bindings/cpp)
+endif()

pywfa/WFA2_lib/Makefile

@@ -5,6 +5,7 @@ FOLDER_BIN=bin
 FOLDER_BUILD=build
 FOLDER_BUILD_CPP=build/cpp
 FOLDER_LIB=lib
+FOLDER_TESTS=tests
 
 UNAME=$(shell uname)
 
@@ -16,17 +17,14 @@ CC_FLAGS=-Wall -g -fPIC
 AR=ar
 AR_FLAGS=-rsc
 
-ifndef BUILD_EXAMPLES
-BUILD_EXAMPLES=0
+ifndef BUILD_EXAMPLES 
+BUILD_EXAMPLES=1
 endif
-ifndef BUILD_TOOLS
+ifndef BUILD_TOOLS 
 BUILD_TOOLS=1
 endif
 ifndef BUILD_WFA_PARALLEL
-BUILD_WFA_PARALLEL=1
-endif
-ifndef BUILD_MINIMAL
-BUILD_MINIMAL=0
+BUILD_WFA_PARALLEL=0
 endif
 
 ###############################################################################
@@ -38,18 +36,12 @@ SUBDIRS=alignment \
         system \
         utils \
         wavefront
-ifeq ($(BUILD_MINIMAL),0)
-    SUBDIRS+=bindings/cpp
+ifeq ($(BUILD_TOOLS),1)        
+    APPS+=tools/generate_dataset \
+          tools/align_benchmark
 endif
-
-ifeq ($(BUILD_MINIMAL),0)
-    ifeq ($(BUILD_TOOLS),1)
-        APPS+=tools/generate_dataset \
-              tools/align_benchmark
-    endif
-    ifeq ($(BUILD_EXAMPLES),1)
-        APPS+=examples
-    endif
+ifeq ($(BUILD_EXAMPLES),1)        
+    APPS+=examples
 endif
 
 all: CC_FLAGS+=-O3 -march=native #-flto -ffat-lto-objects
@@ -69,29 +61,26 @@ asan: build
 # Build rules
 ###############################################################################
 build: setup
-build: $(SUBDIRS)
-build: lib_wfa
+build: $(SUBDIRS) 
+build: lib_wfa 
 build: $(APPS)
 
 setup:
-	$( if ($(BUILD_MINIMAL),0) $(@mkdir -p $(FOLDER_BUILD_CPP)))
-	@mkdir -p $(FOLDER_BIN) $(FOLDER_BUILD) $(FOLDER_LIB)
-
+	@mkdir -p $(FOLDER_BIN) $(FOLDER_BUILD) $(FOLDER_BUILD_CPP) $(FOLDER_LIB)
+
 lib_wfa: $(SUBDIRS)
 	$(AR) $(AR_FLAGS) $(LIB_WFA) $(FOLDER_BUILD)/*.o 2> /dev/null
-	$( if ($(BUILD_MINIMAL),0) $(AR) $((AR_FLAGS) $(LIB_WFA_CPP) $(FOLDER_BUILD)/*.o $(FOLDER_BUILD_CPP)/*.o 2> /dev/null))
 
 clean:
-	rm -rf $(FOLDER_BIN) $(FOLDER_BUILD) $(FOLDER_LIB)
-	$(MAKE)
-
+	rm -rf $(FOLDER_BIN) $(FOLDER_BUILD) $(FOLDER_LIB) 2> /dev/null
+
 ###############################################################################
 # Subdir rule
 ###############################################################################
 export
 $(SUBDIRS):
 	$(MAKE) --directory=$@ all
-
+	
 $(APPS):
 	$(MAKE) --directory=$@ all