Makefile.common

## This Makefile store variable declarations shared for all libs/executables
##ROOT?=.
##################################################
## Third-party libs.
TABIX_INC = $(ROOT)/third/tabix
TABIX_LIB = $(ROOT)/third/tabix/libtabix.a

EIGEN_INC = $(ROOT)/third/eigen
EIGEN_LIB =  # Eigen are header files only

PCRE_INC = $(ROOT)/third/pcre/include
PCRE_LIB = $(ROOT)/third/pcre/lib/libpcreposix.a $(ROOT)/third/pcre/lib/libpcre.a

GSL_INC = $(ROOT)/third/gsl/include
GSL_LIB = $(ROOT)/third/gsl/lib/libgsl.a

ZLIB_INC = $(ROOT)/third/zlib
ZLIB_LIB = $(ROOT)/third/zlib/libz.a

BZIP2_INC = $(ROOT)/third/bzip2
BZIP2_LIB = $(ROOT)/third/bzip2/libbz2.a

NLOPT_INC = $(ROOT)/third/nlopt/include
NLOPT_LIB = $(ROOT)/third/nlopt/lib/libnlopt.a

BCF_INC = $(ROOT)/third/samtools/bcftools
BCF_LIB = $(ROOT)/third/samtools/bcftools/libbcf.a

SAMTOOLS_INC = $(ROOT)/third/samtools
SAMTOOLS_LIB = $(ROOT)/third/samtools/libbam.a

RAPIDJSON_INC = $(ROOT)/third/rapidjson/include
RAPIDJSON_LIB = # We only use its headers

SQLITE_INC = $(ROOT)/third/sqlite/include
SQLITE_LIB = $(ROOT)/third/sqlite/lib/libsqlite3.a

ZSTD_INC = $(ROOT)/third/zstd/lib
ZSTD_LIB = $(ROOT)/third/zstd/lib/libzstd.a

CNPY_INC = $(ROOT)/third/cnpy
CNPY_LIB = $(ROOT)/third/cnpy/libcnpy.a

THIRD_INC = $(BCF_INC) $(SAMTOOLS_INC) $(TABIX_INC) $(EIGEN_INC) $(PCRE_INC) $(GSL_INC) $(ZLIB_INC) $(BZIP2_INC) $(NLOPT_INC) $(RAPIDJSON_INC) $(SQLITE_INC) $(ZSTD_INC) $(CNPY_INC)
THIRD_LIB = $(BCF_LIB) $(SAMTOOLS_LIB) $(TABIX_LIB) $(PCRE_LIB) $(GSL_LIB) $(ZLIB_LIB) $(BZIP2_LIB) $(NLOPT_LIB) $(SQLITE_LIB) $(ZSTD_LIB) $(CNPY_LIB)
##################################################
## Our libs.
BASE_INC = $(ROOT)/base
BASE_LIB = $(ROOT)/base/lib-base.a
BASE_LIB_DBG = $(ROOT)/base/lib-dbg-base.a

VCF_INC = $(ROOT)/libVcf
VCF_LIB = $(ROOT)/libVcf/lib-vcf.a
VCF_LIB_DBG = $(ROOT)/libVcf/lib-dbg-vcf.a

BGEN_INC = $(ROOT)/libBgen
BGEN_LIB = $(ROOT)/libBgen/lib-bgen.a
BGEN_LIB_DBG = $(ROOT)/libBgen/lib-dbg-bgen.a

REGRESSION_INC = $(ROOT)/regression
REGRESSION_LIB = $(ROOT)/regression/lib-regression.a
REGRESSION_LIB_DBG = $(ROOT)/regression/lib-dbg-regression.a

GONCALO_INC = $(ROOT)/libsrc
GONCALO_LIB = $(ROOT)/libsrc/lib-goncalo.a
GONCALO_LIB_DBG = $(ROOT)/libsrc/lib-dbg-goncalo.a

##################################################
## Common compiler options
CXX ?= g++
DEFAULT_CXXFLAGS = -D__STDC_LIMIT_MACROS -std=c++0x -Wall -Wno-unused-function $(OPENMP_FLAG) -DGIT_VERSION="\"$(GIT_VERSION)\""

INCLUDE = $(THIRD_INC) $(REGRESSION_INC) $(VCF_INC) $(BGEN_INC) $(BASE_INC) $(GONCALO_INC)
LIB = $(REGRESSION_LIB) $(VCF_LIB) $(BGEN_LIB) $(BASE_LIB) $(GONCALO_LIB) $(THIRD_LIB) 
LIB_DBG = $(REGRESSION_LIB_DBG) $(VCF_LIB_DBG) $(BGEN_LIB_DBG) $(BASE_LIB_DBG) $(GONCALO_LIB_DBG) $(THIRD_LIB)
CXX_INCLUDE = $(addprefix -I, $(INCLUDE)) -I. -I$(ROOT)
CXX_LIB = $(LIB) -lm -lpthread
CXX_LIB_DBG = $(LIB_DBG) -lm -lpthread

##################################################
## Win32
ifneq ($(WIN32),)
CXX_LIB += -lws2_32
CXX_LIB_DBG += -lws2_32
endif

##################################################
## MKL library
USE_MKL ?=
MKL_ROOT = /home/zhanxw/intel/compilers_and_libraries
MKL_INCDIR = $(MKL_ROOT)/linux/mkl/include
MKL_LIBDIR = $(MKL_ROOT)/linux/mkl/lib/intel64/
MKL_RT_LIBDIR = $(MKL_ROOT)/linux/lib/intel64/
MKL_INC_FLAGS = -I $(MKL_INCDIR)

ifeq  ($(USE_MKL), dynamic)
  MKL_LINK_FLAGS = -L $(MKL_LIBDIR) \
                   -L $(MKL_RT_LIBDIR) \
                   -Wl,--start-group -lmkl_gnu_thread -lmkl_core -lmkl_intel_lp64 -Wl,--end-group \
                   -fopenmp -lm -ldl
else ifeq ($(USE_MKL), static)
  MKL_LINK_FLAGS = -Wl,--start-group \
                 ${MKL_ROOT}/linux/mkl/lib/intel64/libmkl_intel_lp64.a \
                 ${MKL_ROOT}/linux/mkl/lib/intel64/libmkl_core.a \
                 ${MKL_ROOT}/linux/mkl/lib/intel64/libmkl_intel_thread.a \
                 /home/zhanxw/intel/compilers_and_libraries_2016.3.210/linux/compiler/lib/intel64/libiomp5.a \
                 -Wl,--end-group -fopenmp -lpthread -lm -ldl
else ifeq ($(USE_MKL),)
else
  $(error "Unsupported paramter for USE_MKL")
endif

ifneq ($(USE_MKL),) 
  DEFAULT_CXXFLAGS += -DEIGEN_USE_MKL_ALL
  DEFAULT_CXXFLAGS += $(MKL_INC_FLAGS)
  CXX_INCLUDE += -DEIGEN_USE_MKL_ALL
  CXX_INCLUDE += $(MKL_INC_FLAGS)
  CXX_LIB += $(MKL_LINK_FLAGS)
endif

##################################################
## BLAS library
USE_BLAS = 
ifneq ($(USE_BLAS),)
  DEFAULT_CXXFLAGS += -DEIGEN_USE_BLAS #-DEIGEN_USE_LAPACKE
  DEFAULT_CXXFLAGS += 
  CXX_INCLUDE += -DEIGEN_USE_BLAS #-DEIGEN_USE_LAPACKE
  CXX_INCLUDE += 
  CXX_LIB += /home/zhanxw/software/OpenBLAS-0.2.18/libopenblas.a
endif

##################################################
## Platform dependent variables
ARCH := $(firstword $(shell uname -m))
SYS := $(firstword $(shell uname -s))
ifeq ($(SYS), Linux)
  STATIC_FLAG ?= -static
  OPENMP_FLAG = -fopenmp
endif

ifeq ($(SYS), Darwin)
  DEFAULT_CXXFLAGS += -m64
endif
##################################################
## format
##################################################
.PHONY: format
format: *.cpp *.h
	clang-format -i -style google $^


##################################################
## lint
##################################################
.PHONY: lint
lint: *.cpp *.h
	cpplint.py --filter=-legal/copyright $^


##################################################
## Git version
##################################################
GIT_VERSION := $(shell git rev-parse HEAD || echo Unknown)