Merge pull request #223 from DaehwanKimLab/release/2.2.0-rc

Release/2.2.0

.gitignore

@@ -1,19 +1,22 @@
 *~
 *.dSYM
 .DS_Store
+tags
 *-debug
 *-s
 *-l
 hisat2.xcodeproj/project.xcworkspace
 hisat2.xcodeproj/xcuserdata
 hisat2.xcodeproj/xcshareddata
+*.patch
 
 build_automaton
 build_index
 clean_alignment
 determinize
 gcsa_alignment
 gcsa_test
+hisat2-repeat
 
 hisat2_test/*.bt2
 hisat2_test/*.ht2
@@ -28,6 +31,13 @@ hisat2_test/genome*
 hisat2_test/2*
 hisat2_test/snp142*
 hisat2_test/testset*
+
+.idea
+.vscode
+
+.ht2lib-obj*
+*.a
+*.so
 docs/_site
 docs/*.lock
 docs/.*-cache

CMakeLists.txt

@@ -0,0 +1,247 @@
+cmake_minimum_required(VERSION 3.10)
+project(hisat2)
+
+# escape preprocessor definition 
+cmake_policy(SET CMP0005 NEW)
+
+if(NOT CMAKE_BUILD_TYPE)
+	set(CMAKE_BUILD_TYPE Release)
+endif()
+
+option(BOWTIE_MM "enable memory mapping" ON)
+option(BOWTIE_SHARED_MEM "enable shared memory mapping" OFF)
+option(USE_SRA "enable NCBI SRA Toolkit" OFF)
+
+set(CMAKE_CXX_STANDARD 11)
+set(CMAKE_VERBOSE_MAKEFILE true)
+set(CMAKE_EXPORT_COMPILE_COMMANDS on)
+set(NCBI_NGS_DIR ${NCBI_NGS_DIR})
+
+# Common Flag
+set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -m64 -g3 -Wall -msse2")
+
+# Debug/Release Flag
+set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -O0")
+set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -O3 -funroll-loops")
+
+set(INSTALL_DIR "${CMAKE_INSTALL_PREFIX}/bin" CACHE PATH "Installation directory for executables")
+
+if(MINGW OR CYGWIN)
+    option(BOWTIE_MM "Memory mapped files not supported on Windows" OFF)
+    option(BOWTIE_SHARED_MEM "Shared memory not supported on Windows" OFF)
+endif()
+
+if (USE_SRA AND APPLE)
+	set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -mmacosx-version-min=10.6")
+endif()
+
+set(HISAT2_BIN_LIST
+	hisat2-build-s
+	hisat2-build-l
+	hisat2-align-s
+	hisat2-align-l
+	hisat2-inspect-s
+	hisat2-inspect-l
+	hisat2-repeat
+    )
+
+set(HISAT2_LIB_LIST
+	hisat2lib
+	)
+
+
+# Source Codes
+set(SHARED_CPPS
+	alphabet.cpp
+	ccnt_lut.cpp
+	ds.cpp
+	edit.cpp
+	gfm.cpp
+	limit.cpp
+	multikey_qsort.cpp
+	random_source.cpp
+	reference.cpp
+	ref_read.cpp
+	shmem.cpp
+	tinythread.cpp
+	)
+
+set(SEARCH_CPPS
+	aligner_bt.cpp
+	aligner_cache.cpp
+	aligner_driver.cpp
+	aligner_result.cpp
+	aligner_seed.cpp
+	aligner_seed2.cpp
+	aligner_seed_policy.cpp
+	aligner_sw.cpp
+	aligner_sw_driver.cpp
+	aligner_swsse.cpp
+	aligner_swsse_ee_i16.cpp
+	aligner_swsse_ee_u8.cpp
+	aligner_swsse_loc_i16.cpp
+	aligner_swsse_loc_u8.cpp
+	aln_sink.cpp
+	dp_framer.cpp
+	outq.cpp
+	pat.cpp
+	pe.cpp
+	presets.cpp
+	qual.cpp
+	random_util.cpp
+	read_qseq.cpp
+	ref_coord.cpp mask.cpp
+	scoring.cpp
+	simple_func.cpp
+	splice_site.cpp
+	sse_util.cpp
+	unique.cpp
+	hisat2_main.cpp
+	hisat2.cpp
+	)
+
+set(BUILD_CPPS
+	diff_sample.cpp
+	hisat2_build_main.cpp
+	hisat2_build.cpp
+	)
+
+set(REPEAT_CPPS
+	aligner_bt.cpp
+	aligner_result.cpp
+	aligner_sw_driver.cpp
+	aligner_sw.cpp
+	aligner_swsse_ee_i16.cpp
+	aligner_swsse_ee_u8.cpp
+	aligner_swsse_loc_i16.cpp
+	aligner_swsse_loc_u8.cpp
+	aligner_swsse.cpp
+	bit_packed_array.cpp
+	bit_packed_array.h
+	dp_framer.cpp
+	mask.cpp
+	qual.cpp
+	repeat_builder.cpp
+	scoring.cpp
+	simple_func.cpp
+	diff_sample.cpp
+	hisat2_repeat_main.cpp
+	hisat2_repeat.cpp
+	)
+
+set(INSPECT_CPPS
+	hisat2_inspect.cpp
+	)
+
+
+set(HT2LIB_CPPS
+	hisat2lib/ht2_init.cpp
+	hisat2lib/ht2_repeat.cpp
+	hisat2lib/ht2_index.cpp
+	)
+
+
+string(TIMESTAMP BUILD_DATE)
+file(STRINGS VERSION HISAT2_VERSION)
+execute_process(COMMAND ${CMAKE_CXX_COMPILER} -v OUTPUT_VARIABLE COMPILER_VERSION)
+
+add_definitions(
+	-DBOWTIE2
+    -DBUILD_HOST="${CMAKE_HOST_SYSTEM}"
+	-DBUILD_TIME="${BUILD_DATE}"
+    -DCOMPILER_VERSION="${CMAKE_CXX_COMPILER} ${CMAKE_CXX_COMPILER_VERSION}"
+    -DHISAT2_VERSION="${HISAT2_VERSION}"
+	-D_LARGEFILE_SOURCE
+	-D_FILE_OFFSET_BITS=64
+	-D_GNU_SOURCE
+	-DPOPCNT_CAPABILITY
+	)
+
+
+include_directories(third_party)
+
+link_libraries(
+	pthread
+	)
+
+
+if(BOWTIE_MM)
+	add_definitions(-DBOWTIE_MM)
+endif()
+
+if(BOWTIE_SHARED_MEM)
+	add_definitions(-DBOWTIE_SHARED_MEM)
+endif()
+
+include_directories(${PROJECT_SOURCE_DIR})
+add_definitions(-DCOMPILER_OPTIONS="${CMAKE_CXX_FLAGS}")
+
+add_library(hisat2lib_static STATIC ${HT2LIB_CPPS} ${SHARED_CPPS})
+add_library(hisat2lib_shared SHARED ${HT2LIB_CPPS} ${SHARED_CPPS})
+add_custom_target(ht2lib)
+add_dependencies(ht2lib hisat2lib_static hisat2lib_shared)
+
+set_target_properties(hisat2lib_static PROPERTIES OUTPUT_NAME hisat2lib)
+set_target_properties(hisat2lib_shared PROPERTIES OUTPUT_NAME hisat2lib)
+
+
+
+
+
+add_executable(hisat2-align-s ${SEARCH_CPPS} ${SHARED_CPPS})
+add_executable(hisat2-align-l ${SEARCH_CPPS} ${SHARED_CPPS})
+add_executable(hisat2-build-s ${BUILD_CPPS} ${SHARED_CPPS})
+add_executable(hisat2-build-l ${BUILD_CPPS} ${SHARED_CPPS})
+add_executable(hisat2-inspect-s ${INSPECT_CPPS} ${SHARED_CPPS})
+add_executable(hisat2-inspect-l ${INSPECT_CPPS} ${SHARED_CPPS})
+add_executable(hisat2-repeat ${REPEAT_CPPS} ${SHARED_CPPS})
+set_target_properties(${HISAT2_BIN_LIST} PROPERTIES DEBUG_POSTFIX "-debug")
+set_target_properties(hisat2-align-l hisat2-build-l hisat2-inspect-l hisat2-repeat 
+	PROPERTIES COMPILE_FLAGS "${COMPILE_FLAGS} -DBOWTIE_64BIT_INDEX")
+
+target_compile_options(hisat2-inspect-s PUBLIC "-DHISAT2_INSPECT_MAIN")
+target_compile_options(hisat2-inspect-l PUBLIC "-DHISAT2_INSPECT_MAIN")
+
+target_compile_options(hisat2-build-s PUBLIC "-DMASSIVE_DATA_RLCSA")
+
+target_compile_options(hisat2lib_static PUBLIC "-fPIC")
+target_include_directories(hisat2lib_static PUBLIC hisat2lib)
+target_include_directories(hisat2lib_shared PUBLIC hisat2lib)
+
+if(USE_SRA)
+	if(NOT NCBI_NGS_DIR)
+		message(FATAL_ERROR "You should set NCBI_NGS_DIR path. cmake3 .... -DNCBI_NGS_DIR=/path/to/ngs")
+	endif()
+	#set(NCBI_NGS_DIR /home/parkch/.local/ngs)
+
+	target_compile_options(hisat2-align-s PUBLIC "-DUSE_SRA")
+	target_compile_options(hisat2-align-l PUBLIC "-DUSE_SRA")
+	target_include_directories(hisat2-align-s PUBLIC "${NCBI_NGS_DIR}/include")
+	target_include_directories(hisat2-align-l PUBLIC "${NCBI_NGS_DIR}/include")
+
+	set(NCBI_LIBS 
+		${NCBI_NGS_DIR}/lib64/libncbi-ngs-c++-static.a
+		${NCBI_NGS_DIR}/lib64/libngs-c++-static.a
+		${NCBI_NGS_DIR}/lib64/libncbi-vdb-static.a
+		${CMAKE_DL_LIBS}
+		)
+
+	target_link_libraries(hisat2-align-s ${NCBI_LIBS})
+	target_link_libraries(hisat2-align-l ${NCBI_LIBS})
+endif()
+
+add_custom_target(hisat2-all)
+add_dependencies(hisat2-all
+		hisat2-align-s
+		hisat2-align-l
+		hisat2-build-s
+		hisat2-build-l
+		hisat2-inspect-s
+		hisat2-inspect-l
+		hisat2-repeat)
+
+#
+# Examples
+#
+#target_compile_options(hisat2-inspect-s PUBLIC $<$<CONFIG:DEBUG>:-DDEBUGONLY>)
+#target_compile_options(hisat2-inspect-s PUBLIC $<$<CONFIG:RELEASE>:-DRELEASEONLY>)