Add macOS support (Apple Silicon and Intel)

README.md

@@ -45,6 +45,35 @@ At the moment, GLIMPSE2 performs imputation only from a reference panel of sampl
 
 To build the source code, please refer to the [step-by-step guide on the website](https://odelaneau.github.io/GLIMPSE/docs/installation).
 
+#### Building on macOS
+
+GLIMPSE2 supports macOS builds, including Apple Silicon (ARM64) devices. The build system automatically detects dependencies installed via Homebrew.
+
+**Prerequisites:**
+```bash
+# Install dependencies via Homebrew
+brew install boost htslib openssl@3 libdeflate
+```
+
+**Building:**
+```bash
+# Build all tools
+make
+
+# Or build individual tools
+make phase
+make chunk
+make ligate
+make split_reference
+make concordance
+```
+
+**Platform-specific notes:**
+
+- **⚠️ Performance Note (WIP):** On Apple Silicon and other ARM platforms, GLIMPSE2 currently uses scalar fallback implementations instead of AVX2 SIMD instructions. This means **significantly slower performance** compared to x86_64 with AVX2. Native ARM NEON optimizations are planned for future releases.
+- On x86_64 platforms, native AVX2/FMA instructions are used for optimal performance
+- The build system automatically detects the architecture and applies appropriate compiler flags
+
 #### Docker images
 
 ##### Dockerhub

chunk/makefile

@@ -15,6 +15,7 @@ LDFLAG=-O3
 
 #DYNAMIC LIBRARIES
 DYN_LIBS=-lz -lpthread -lbz2 -llzma -lcurl -lcrypto -ldeflate
+BASE_DYN_LIBS := $(DYN_LIBS)
 
 HFILE=$(shell find src -name *.h)
 CFILE=$(shell find src -name *.cpp)
@@ -25,6 +26,34 @@ NAME=$(shell basename $(CURDIR))
 BFILE=bin/GLIMPSE2_$(NAME)
 EXEFILE=bin/GLIMPSE2_$(NAME)_static
 
+BREW_AVAILABLE := $(shell command -v brew 2>/dev/null)
+BOOST_PREFIX_AUTO := $(if $(BREW_AVAILABLE),$(shell brew --prefix boost 2>/dev/null),)
+HTSLIB_PREFIX_AUTO := $(if $(BREW_AVAILABLE),$(shell brew --prefix htslib 2>/dev/null),)
+
+BOOST_INC_AUTO := $(if $(BOOST_PREFIX_AUTO),$(BOOST_PREFIX_AUTO)/include,)
+BOOST_LIB_DIR_AUTO := $(if $(BOOST_PREFIX_AUTO),$(BOOST_PREFIX_AUTO)/lib,)
+BOOST_LIB_IO_AUTO := $(firstword $(wildcard $(BOOST_LIB_DIR_AUTO)/libboost_iostreams.a $(BOOST_LIB_DIR_AUTO)/libboost_iostreams.dylib $(BOOST_LIB_DIR_AUTO)/libboost_iostreams.so))
+BOOST_LIB_PO_AUTO := $(firstword $(wildcard $(BOOST_LIB_DIR_AUTO)/libboost_program_options.a $(BOOST_LIB_DIR_AUTO)/libboost_program_options.dylib $(BOOST_LIB_DIR_AUTO)/libboost_program_options.so))
+BOOST_LIB_SE_AUTO := $(firstword $(wildcard $(BOOST_LIB_DIR_AUTO)/libboost_serialization.a $(BOOST_LIB_DIR_AUTO)/libboost_serialization.dylib $(BOOST_LIB_DIR_AUTO)/libboost_serialization.so))
+
+HTSLIB_INC_AUTO := $(if $(HTSLIB_PREFIX_AUTO),$(HTSLIB_PREFIX_AUTO)/include,)
+HTSLIB_LIB_AUTO := $(firstword $(wildcard $(HTSLIB_PREFIX_AUTO)/lib/libhts.a $(HTSLIB_PREFIX_AUTO)/lib/libhts.dylib $(HTSLIB_PREFIX_AUTO)/lib/libhts.so))
+
+OPENSSL_PREFIX_AUTO := $(if $(BREW_AVAILABLE),$(shell brew --prefix openssl@3 2>/dev/null),)
+LIBDEFLATE_PREFIX_AUTO := $(if $(BREW_AVAILABLE),$(shell brew --prefix libdeflate 2>/dev/null),)
+
+EXTRA_LDFLAGS_AUTO := $(strip $(if $(BOOST_LIB_DIR_AUTO),-L$(BOOST_LIB_DIR_AUTO)) $(if $(HTSLIB_PREFIX_AUTO),-L$(HTSLIB_PREFIX_AUTO)/lib) $(if $(OPENSSL_PREFIX_AUTO),-L$(OPENSSL_PREFIX_AUTO)/lib) $(if $(LIBDEFLATE_PREFIX_AUTO),-L$(LIBDEFLATE_PREFIX_AUTO)/lib))
+
+DEFAULT_BOOST_INC := $(or $(BOOST_INC_AUTO),/usr/include)
+DEFAULT_BOOST_LIB_IO := $(or $(BOOST_LIB_IO_AUTO),-lboost_iostreams)
+DEFAULT_BOOST_LIB_PO := $(or $(BOOST_LIB_PO_AUTO),-lboost_program_options)
+DEFAULT_BOOST_LIB_SE := $(or $(BOOST_LIB_SE_AUTO),-lboost_serialization)
+
+DEFAULT_HTSLIB_INC := $(or $(HTSLIB_INC_AUTO),/home/srubinac/git/htslib-1.17)
+DEFAULT_HTSLIB_LIB := $(or $(HTSLIB_LIB_AUTO),/home/srubinac/git/htslib-1.17/libhts.a)
+
+.DEFAULT_GOAL := auto
+
 #COMMIT_VERS=$(shell git rev-parse --short HEAD)
 #COMMIT_DATE=$(shell git log -1 --format=%cd --date=short)
 #CXXFLAG+= -D__COMMIT_ID__=\"$(COMMIT_VERS)\"
@@ -147,10 +176,19 @@ static_exe: BOOST_LIB_SE=/usr/local/lib/libboost_serialization.a
 static_exe: $(EXEFILE)
 
 #COMPILATION RULES
-all: desktop
+all: auto
+
+auto: BOOST_INC=$(DEFAULT_BOOST_INC)
+auto: BOOST_LIB_IO=$(DEFAULT_BOOST_LIB_IO)
+auto: BOOST_LIB_PO=$(DEFAULT_BOOST_LIB_PO)
+auto: BOOST_LIB_SE=$(DEFAULT_BOOST_LIB_SE)
+auto: HTSLIB_INC=$(DEFAULT_HTSLIB_INC)
+auto: HTSLIB_LIB=$(DEFAULT_HTSLIB_LIB)
+auto: AUTO_LDFLAG=$(strip $(LDFLAG) $(EXTRA_LDFLAGS_AUTO))
+auto: $(BFILE)
 
 $(BFILE): $(OFILE)
-	$(CXX) $(LDFLAG) $^ $(HTSLIB_LIB) $(BOOST_LIB_IO) $(BOOST_LIB_PO) $(BOOST_LIB_SE) $(BGEN_LIB) -o $@ $(DYN_LIBS)
+	$(CXX) $(AUTO_LDFLAG) $^ $(HTSLIB_LIB) $(BOOST_LIB_IO) $(BOOST_LIB_PO) $(BOOST_LIB_SE) $(BGEN_LIB) -o $@ $(DYN_LIBS)
 
 $(EXEFILE): $(OFILE)
 	$(CXX) $(LDFLAG) -static -static-libgcc -static-libstdc++ -pthread -o $(EXEFILE) $^ $(HTSLIB_LIB) $(BOOST_LIB_IO) $(BOOST_LIB_PO) $(BOOST_LIB_SE) -Wl,-Bstatic $(DYN_LIBS)

concordance/makefile

@@ -15,6 +15,7 @@ LDFLAG=-O3
 
 #DYNAMIC LIBRARIES
 DYN_LIBS=-lz -lpthread -lbz2 -llzma -lcurl -lcrypto -ldeflate
+BASE_DYN_LIBS := $(DYN_LIBS)
 
 HFILE=$(shell find src -name *.h)
 CFILE=$(shell find src -name *.cpp)
@@ -25,6 +26,34 @@ NAME=$(shell basename $(CURDIR))
 BFILE=bin/GLIMPSE2_$(NAME)
 EXEFILE=bin/GLIMPSE2_$(NAME)_static
 
+BREW_AVAILABLE := $(shell command -v brew 2>/dev/null)
+BOOST_PREFIX_AUTO := $(if $(BREW_AVAILABLE),$(shell brew --prefix boost 2>/dev/null),)
+HTSLIB_PREFIX_AUTO := $(if $(BREW_AVAILABLE),$(shell brew --prefix htslib 2>/dev/null),)
+
+BOOST_INC_AUTO := $(if $(BOOST_PREFIX_AUTO),$(BOOST_PREFIX_AUTO)/include,)
+BOOST_LIB_DIR_AUTO := $(if $(BOOST_PREFIX_AUTO),$(BOOST_PREFIX_AUTO)/lib,)
+BOOST_LIB_IO_AUTO := $(firstword $(wildcard $(BOOST_LIB_DIR_AUTO)/libboost_iostreams.a $(BOOST_LIB_DIR_AUTO)/libboost_iostreams.dylib $(BOOST_LIB_DIR_AUTO)/libboost_iostreams.so))
+BOOST_LIB_PO_AUTO := $(firstword $(wildcard $(BOOST_LIB_DIR_AUTO)/libboost_program_options.a $(BOOST_LIB_DIR_AUTO)/libboost_program_options.dylib $(BOOST_LIB_DIR_AUTO)/libboost_program_options.so))
+BOOST_LIB_SE_AUTO := $(firstword $(wildcard $(BOOST_LIB_DIR_AUTO)/libboost_serialization.a $(BOOST_LIB_DIR_AUTO)/libboost_serialization.dylib $(BOOST_LIB_DIR_AUTO)/libboost_serialization.so))
+
+HTSLIB_INC_AUTO := $(if $(HTSLIB_PREFIX_AUTO),$(HTSLIB_PREFIX_AUTO)/include,)
+HTSLIB_LIB_AUTO := $(firstword $(wildcard $(HTSLIB_PREFIX_AUTO)/lib/libhts.a $(HTSLIB_PREFIX_AUTO)/lib/libhts.dylib $(HTSLIB_PREFIX_AUTO)/lib/libhts.so))
+
+OPENSSL_PREFIX_AUTO := $(if $(BREW_AVAILABLE),$(shell brew --prefix openssl@3 2>/dev/null),)
+LIBDEFLATE_PREFIX_AUTO := $(if $(BREW_AVAILABLE),$(shell brew --prefix libdeflate 2>/dev/null),)
+
+EXTRA_LDFLAGS_AUTO := $(strip $(if $(BOOST_LIB_DIR_AUTO),-L$(BOOST_LIB_DIR_AUTO)) $(if $(HTSLIB_PREFIX_AUTO),-L$(HTSLIB_PREFIX_AUTO)/lib) $(if $(OPENSSL_PREFIX_AUTO),-L$(OPENSSL_PREFIX_AUTO)/lib) $(if $(LIBDEFLATE_PREFIX_AUTO),-L$(LIBDEFLATE_PREFIX_AUTO)/lib))
+
+DEFAULT_BOOST_INC := $(or $(BOOST_INC_AUTO),/usr/include)
+DEFAULT_BOOST_LIB_IO := $(or $(BOOST_LIB_IO_AUTO),-lboost_iostreams)
+DEFAULT_BOOST_LIB_PO := $(or $(BOOST_LIB_PO_AUTO),-lboost_program_options)
+DEFAULT_BOOST_LIB_SE := $(or $(BOOST_LIB_SE_AUTO),-lboost_serialization)
+
+DEFAULT_HTSLIB_INC := $(or $(HTSLIB_INC_AUTO),/home/srubinac/git/htslib-1.17)
+DEFAULT_HTSLIB_LIB := $(or $(HTSLIB_LIB_AUTO),/home/srubinac/git/htslib-1.17/libhts.a)
+
+.DEFAULT_GOAL := auto
+
 #COMMIT_VERS=$(shell git rev-parse --short HEAD)
 #COMMIT_DATE=$(shell git log -1 --format=%cd --date=short)
 #CXXFLAG+= -D__COMMIT_ID__=\"$(COMMIT_VERS)\"
@@ -147,10 +176,19 @@ static_exe: BOOST_LIB_SE=/usr/local/lib/libboost_serialization.a
 static_exe: $(EXEFILE)
 
 #COMPILATION RULES
-all: desktop
+all: auto
+
+auto: BOOST_INC=$(DEFAULT_BOOST_INC)
+auto: BOOST_LIB_IO=$(DEFAULT_BOOST_LIB_IO)
+auto: BOOST_LIB_PO=$(DEFAULT_BOOST_LIB_PO)
+auto: BOOST_LIB_SE=$(DEFAULT_BOOST_LIB_SE)
+auto: HTSLIB_INC=$(DEFAULT_HTSLIB_INC)
+auto: HTSLIB_LIB=$(DEFAULT_HTSLIB_LIB)
+auto: AUTO_LDFLAG=$(strip $(LDFLAG) $(EXTRA_LDFLAGS_AUTO))
+auto: $(BFILE)
 
 $(BFILE): $(OFILE)
-	$(CXX) $(LDFLAG) $^ $(HTSLIB_LIB) $(BOOST_LIB_IO) $(BOOST_LIB_PO) $(BOOST_LIB_SE) $(BGEN_LIB) -o $@ $(DYN_LIBS)
+	$(CXX) $(AUTO_LDFLAG) $^ $(HTSLIB_LIB) $(BOOST_LIB_IO) $(BOOST_LIB_PO) $(BOOST_LIB_SE) $(BGEN_LIB) -o $@ $(DYN_LIBS)
 
 $(EXEFILE): $(OFILE)
 	$(CXX) $(LDFLAG) -static -static-libgcc -static-libstdc++ -pthread -o $(EXEFILE) $^ $(HTSLIB_LIB) $(BOOST_LIB_IO) $(BOOST_LIB_PO) $(BOOST_LIB_SE) -Wl,-Bstatic $(DYN_LIBS)

ligate/makefile

@@ -15,6 +15,7 @@ LDFLAG=-O3
 
 #DYNAMIC LIBRARIES
 DYN_LIBS=-lz -lpthread -lbz2 -llzma -lcurl -lcrypto -ldeflate
+BASE_DYN_LIBS := $(DYN_LIBS)
 
 HFILE=$(shell find src -name *.h)
 CFILE=$(shell find src -name *.cpp)
@@ -25,6 +26,34 @@ NAME=$(shell basename $(CURDIR))
 BFILE=bin/GLIMPSE2_$(NAME)
 EXEFILE=bin/GLIMPSE2_$(NAME)_static
 
+BREW_AVAILABLE := $(shell command -v brew 2>/dev/null)
+BOOST_PREFIX_AUTO := $(if $(BREW_AVAILABLE),$(shell brew --prefix boost 2>/dev/null),)
+HTSLIB_PREFIX_AUTO := $(if $(BREW_AVAILABLE),$(shell brew --prefix htslib 2>/dev/null),)
+
+BOOST_INC_AUTO := $(if $(BOOST_PREFIX_AUTO),$(BOOST_PREFIX_AUTO)/include,)
+BOOST_LIB_DIR_AUTO := $(if $(BOOST_PREFIX_AUTO),$(BOOST_PREFIX_AUTO)/lib,)
+BOOST_LIB_IO_AUTO := $(firstword $(wildcard $(BOOST_LIB_DIR_AUTO)/libboost_iostreams.a $(BOOST_LIB_DIR_AUTO)/libboost_iostreams.dylib $(BOOST_LIB_DIR_AUTO)/libboost_iostreams.so))
+BOOST_LIB_PO_AUTO := $(firstword $(wildcard $(BOOST_LIB_DIR_AUTO)/libboost_program_options.a $(BOOST_LIB_DIR_AUTO)/libboost_program_options.dylib $(BOOST_LIB_DIR_AUTO)/libboost_program_options.so))
+BOOST_LIB_SE_AUTO := $(firstword $(wildcard $(BOOST_LIB_DIR_AUTO)/libboost_serialization.a $(BOOST_LIB_DIR_AUTO)/libboost_serialization.dylib $(BOOST_LIB_DIR_AUTO)/libboost_serialization.so))
+
+HTSLIB_INC_AUTO := $(if $(HTSLIB_PREFIX_AUTO),$(HTSLIB_PREFIX_AUTO)/include,)
+HTSLIB_LIB_AUTO := $(firstword $(wildcard $(HTSLIB_PREFIX_AUTO)/lib/libhts.a $(HTSLIB_PREFIX_AUTO)/lib/libhts.dylib $(HTSLIB_PREFIX_AUTO)/lib/libhts.so))
+
+OPENSSL_PREFIX_AUTO := $(if $(BREW_AVAILABLE),$(shell brew --prefix openssl@3 2>/dev/null),)
+LIBDEFLATE_PREFIX_AUTO := $(if $(BREW_AVAILABLE),$(shell brew --prefix libdeflate 2>/dev/null),)
+
+EXTRA_LDFLAGS_AUTO := $(strip $(if $(BOOST_LIB_DIR_AUTO),-L$(BOOST_LIB_DIR_AUTO)) $(if $(HTSLIB_PREFIX_AUTO),-L$(HTSLIB_PREFIX_AUTO)/lib) $(if $(OPENSSL_PREFIX_AUTO),-L$(OPENSSL_PREFIX_AUTO)/lib) $(if $(LIBDEFLATE_PREFIX_AUTO),-L$(LIBDEFLATE_PREFIX_AUTO)/lib))
+
+DEFAULT_BOOST_INC := $(or $(BOOST_INC_AUTO),/usr/include)
+DEFAULT_BOOST_LIB_IO := $(or $(BOOST_LIB_IO_AUTO),-lboost_iostreams)
+DEFAULT_BOOST_LIB_PO := $(or $(BOOST_LIB_PO_AUTO),-lboost_program_options)
+DEFAULT_BOOST_LIB_SE := $(or $(BOOST_LIB_SE_AUTO),-lboost_serialization)
+
+DEFAULT_HTSLIB_INC := $(or $(HTSLIB_INC_AUTO),/home/srubinac/git/htslib-1.17)
+DEFAULT_HTSLIB_LIB := $(or $(HTSLIB_LIB_AUTO),/home/srubinac/git/htslib-1.17/libhts.a)
+
+.DEFAULT_GOAL := auto
+
 #COMMIT_VERS=$(shell git rev-parse --short HEAD)
 #COMMIT_DATE=$(shell git log -1 --format=%cd --date=short)
 #CXXFLAG+= -D__COMMIT_ID__=\"$(COMMIT_VERS)\"
@@ -147,10 +176,19 @@ static_exe: BOOST_LIB_SE=/usr/local/lib/libboost_serialization.a
 static_exe: $(EXEFILE)
 
 #COMPILATION RULES
-all: desktop
+all: auto
+
+auto: BOOST_INC=$(DEFAULT_BOOST_INC)
+auto: BOOST_LIB_IO=$(DEFAULT_BOOST_LIB_IO)
+auto: BOOST_LIB_PO=$(DEFAULT_BOOST_LIB_PO)
+auto: BOOST_LIB_SE=$(DEFAULT_BOOST_LIB_SE)
+auto: HTSLIB_INC=$(DEFAULT_HTSLIB_INC)
+auto: HTSLIB_LIB=$(DEFAULT_HTSLIB_LIB)
+auto: AUTO_LDFLAG=$(strip $(LDFLAG) $(EXTRA_LDFLAGS_AUTO))
+auto: $(BFILE)
 
 $(BFILE): $(OFILE)
-	$(CXX) $(LDFLAG) $^ $(HTSLIB_LIB) $(BOOST_LIB_IO) $(BOOST_LIB_PO) $(BOOST_LIB_SE) $(BGEN_LIB) -o $@ $(DYN_LIBS)
+	$(CXX) $(AUTO_LDFLAG) $^ $(HTSLIB_LIB) $(BOOST_LIB_IO) $(BOOST_LIB_PO) $(BOOST_LIB_SE) $(BGEN_LIB) -o $@ $(DYN_LIBS)
 
 $(EXEFILE): $(OFILE)
 	$(CXX) $(LDFLAG) -static -static-libgcc -static-libstdc++ -pthread -o $(EXEFILE) $^ $(HTSLIB_LIB) $(BOOST_LIB_IO) $(BOOST_LIB_PO) $(BOOST_LIB_SE) -Wl,-Bstatic $(DYN_LIBS)

makefile

@@ -1,14 +1,23 @@
 projects = chunk concordance ligate phase split_reference
 
-.PHONY: all $(projects)
+BOOST_INC := $(shell brew --prefix boost)/include
+BOOST_LIB := $(shell brew --prefix boost)/lib
+
+CXXFLAGS += -I$(BOOST_INC)
+LDFLAGS  += -L$(BOOST_LIB)
+LDLIBS   += -lboost_program_options
+
+.PHONY: all $(projects) clean
 
 all: $(projects)
 
 $(projects):
-	$(MAKE) -C $@ $(COMPILATION_ENV)
+	$(MAKE) -C $@ $(COMPILATION_ENV) \
+		CXXFLAGS="$(CXXFLAGS)" \
+		LDFLAGS="$(LDFLAGS)" \
+		LDLIBS="$(LDLIBS)"
 
 clean:
 	for dir in $(projects); do \
-	$(MAKE) $@ -C $$dir; \
+		$(MAKE) -C $$dir clean; \
 	done
-

phase/makefile

@@ -9,12 +9,14 @@ dummy_build_folder_obj := $(shell mkdir -p obj)
 #COMPILER & LINKER FLAGS
 CXXFLAG=-O3 -Wno-ignored-attributes
 LDFLAG=-O3
+HOST_ARCH := $(shell uname -m)
 
 #CXXFLAG=-O0 -g -Wno-ignored-attributes
 #LDFLAG=-O0
 
 #DYNAMIC LIBRARIES
 DYN_LIBS=-lz -lpthread -lbz2 -llzma -lcurl -lcrypto -ldeflate
+BASE_DYN_LIBS := $(DYN_LIBS)
 
 HFILE=$(shell find src -name *.h)
 CFILE=$(shell find src -name *.cpp)
@@ -25,13 +27,45 @@ NAME=$(shell basename $(CURDIR))
 BFILE=bin/GLIMPSE2_$(NAME)
 EXEFILE=bin/GLIMPSE2_$(NAME)_static
 
+BREW_AVAILABLE := $(shell command -v brew 2>/dev/null)
+BOOST_PREFIX_AUTO := $(if $(BREW_AVAILABLE),$(shell brew --prefix boost 2>/dev/null),)
+HTSLIB_PREFIX_AUTO := $(if $(BREW_AVAILABLE),$(shell brew --prefix htslib 2>/dev/null),)
+
+BOOST_INC_AUTO := $(if $(BOOST_PREFIX_AUTO),$(BOOST_PREFIX_AUTO)/include,)
+BOOST_LIB_DIR_AUTO := $(if $(BOOST_PREFIX_AUTO),$(BOOST_PREFIX_AUTO)/lib,)
+BOOST_LIB_IO_AUTO := $(firstword $(wildcard $(BOOST_LIB_DIR_AUTO)/libboost_iostreams.a $(BOOST_LIB_DIR_AUTO)/libboost_iostreams.dylib $(BOOST_LIB_DIR_AUTO)/libboost_iostreams.so))
+BOOST_LIB_PO_AUTO := $(firstword $(wildcard $(BOOST_LIB_DIR_AUTO)/libboost_program_options.a $(BOOST_LIB_DIR_AUTO)/libboost_program_options.dylib $(BOOST_LIB_DIR_AUTO)/libboost_program_options.so))
+BOOST_LIB_SE_AUTO := $(firstword $(wildcard $(BOOST_LIB_DIR_AUTO)/libboost_serialization.a $(BOOST_LIB_DIR_AUTO)/libboost_serialization.dylib $(BOOST_LIB_DIR_AUTO)/libboost_serialization.so))
+
+HTSLIB_INC_AUTO := $(if $(HTSLIB_PREFIX_AUTO),$(HTSLIB_PREFIX_AUTO)/include,)
+HTSLIB_LIB_AUTO := $(firstword $(wildcard $(HTSLIB_PREFIX_AUTO)/lib/libhts.a $(HTSLIB_PREFIX_AUTO)/lib/libhts.dylib $(HTSLIB_PREFIX_AUTO)/lib/libhts.so))
+
+OPENSSL_PREFIX_AUTO := $(if $(BREW_AVAILABLE),$(shell brew --prefix openssl@3 2>/dev/null),)
+LIBDEFLATE_PREFIX_AUTO := $(if $(BREW_AVAILABLE),$(shell brew --prefix libdeflate 2>/dev/null),)
+
+EXTRA_LDFLAGS_AUTO := $(strip $(if $(BOOST_LIB_DIR_AUTO),-L$(BOOST_LIB_DIR_AUTO)) $(if $(HTSLIB_PREFIX_AUTO),-L$(HTSLIB_PREFIX_AUTO)/lib) $(if $(OPENSSL_PREFIX_AUTO),-L$(OPENSSL_PREFIX_AUTO)/lib) $(if $(LIBDEFLATE_PREFIX_AUTO),-L$(LIBDEFLATE_PREFIX_AUTO)/lib))
+
+DEFAULT_BOOST_INC := $(or $(BOOST_INC_AUTO),/usr/include)
+DEFAULT_BOOST_LIB_IO := $(or $(BOOST_LIB_IO_AUTO),-lboost_iostreams)
+DEFAULT_BOOST_LIB_PO := $(or $(BOOST_LIB_PO_AUTO),-lboost_program_options)
+DEFAULT_BOOST_LIB_SE := $(or $(BOOST_LIB_SE_AUTO),-lboost_serialization)
+
+DEFAULT_HTSLIB_INC := $(or $(HTSLIB_INC_AUTO),/home/srubinac/git/htslib-1.17)
+DEFAULT_HTSLIB_LIB := $(or $(HTSLIB_LIB_AUTO),/home/srubinac/git/htslib-1.17/libhts.a)
+
+.DEFAULT_GOAL := auto
+
 #COMMIT_VERS=$(shell git rev-parse --short HEAD)
 #COMMIT_DATE=$(shell git log -1 --format=%cd --date=short)
 #CXXFLAG+= -D__COMMIT_ID__=\"$(COMMIT_VERS)\"
 #CXXFLAG+= -D__COMMIT_DATE__=\"$(COMMIT_DATE)\"
 
 ifeq ($(NAME),phase)
- CXXFLAG+=-mavx2 -mfma
+ ifeq ($(HOST_ARCH),x86_64)
+  CXXFLAG+=-mavx2 -mfma
+ else
+  $(info Skipping AVX2/FMA flags for architecture $(HOST_ARCH))
+ endif
 endif
 
 COMMIT_VERS=3bed6d9
@@ -147,10 +181,19 @@ static_exe: BOOST_LIB_SE=/usr/local/lib/libboost_serialization.a
 static_exe: $(EXEFILE)
 
 #COMPILATION RULES
-all: desktop
+all: auto
+
+auto: BOOST_INC=$(DEFAULT_BOOST_INC)
+auto: BOOST_LIB_IO=$(DEFAULT_BOOST_LIB_IO)
+auto: BOOST_LIB_PO=$(DEFAULT_BOOST_LIB_PO)
+auto: BOOST_LIB_SE=$(DEFAULT_BOOST_LIB_SE)
+auto: HTSLIB_INC=$(DEFAULT_HTSLIB_INC)
+auto: HTSLIB_LIB=$(DEFAULT_HTSLIB_LIB)
+auto: AUTO_LDFLAG=$(strip $(LDFLAG) $(EXTRA_LDFLAGS_AUTO))
+auto: $(BFILE)
 
 $(BFILE): $(OFILE)
-	$(CXX) $(LDFLAG) $^ $(HTSLIB_LIB) $(BOOST_LIB_IO) $(BOOST_LIB_PO) $(BOOST_LIB_SE) $(BGEN_LIB) -o $@ $(DYN_LIBS)
+	$(CXX) $(AUTO_LDFLAG) $^ $(HTSLIB_LIB) $(BOOST_LIB_IO) $(BOOST_LIB_PO) $(BOOST_LIB_SE) $(BGEN_LIB) -o $@ $(DYN_LIBS)
 
 $(EXEFILE): $(OFILE)
 	$(CXX) $(LDFLAG) -static -static-libgcc -static-libstdc++ -pthread -o $(EXEFILE) $^ $(HTSLIB_LIB) $(BOOST_LIB_IO) $(BOOST_LIB_PO) $(BOOST_LIB_SE) -Wl,-Bstatic $(DYN_LIBS)

phase/src/models/imputation_hmm.h

@@ -28,7 +28,7 @@
 
 #include <utils/otools.h>
 #include <containers/conditioning_set.h>
-#include <immintrin.h>
+#include "simd_compat.h"
 #include <boost/align/aligned_allocator.hpp>
 
 template <typename T>

phase/src/models/phasing_hmm.h

@@ -28,7 +28,7 @@
 
 #include <utils/otools.h>
 #include <containers/conditioning_set.h>
-#include <immintrin.h>
+#include "simd_compat.h"
 #include <boost/align/aligned_allocator.hpp>
 
 template <typename T>