64BIT_VERSION ?= yes
USEREADLINE ?= no
USEBOOST ?= no
RELEASE_DATE = "\"3/20/2017\""
VERSION = "\"1.39.5\""

# Optimize to level 3:
    CXXFLAGS += -O3 -std=c++0x
    LDFLAGS += -std=c++0x

ifeq  ($(strip $(64BIT_VERSION)),yes)
    #if you are a mac user use the following line
    #TARGET_ARCH += -arch x86_64

    #if you using cygwin to build Windows the following line
    CXX = x86_64-w64-mingw32-g++
    CC = x86_64-w64-mingw32-g++
    TARGET_ARCH += -m64 -static

    #if you are a linux user use the following line - specific processor builds in future??
    #CXXFLAGS += -mtune=generic

    CXXFLAGS += -DBIT_VERSION
endif


CXXFLAGS += -DRELEASE_DATE=${RELEASE_DATE} -DVERSION=${VERSION}

# if you do not want to use the readline library, set this to no.
# make sure you have the library installed
ifeq  ($(strip $(USEREADLINE)),yes)
    CXXFLAGS += -DUSE_READLINE
    LIBS += -lreadline
endif


#The boost libraries allow you to read gz files.
ifeq  ($(strip $(USEBOOST)),yes)
    #statically link so the boost install is not required on users machine
    BOOST_INCLUDE_DIR="/usr/local/include"
    BOOST_LIBRARY_DIR="/usr/local/lib"

    CXXFLAGS += -DUSE_BOOST -I ${BOOST_INCLUDE_DIR}

    LIBS += ${BOOST_LIBRARY_DIR}/libboost_iostreams.a

    #if mac
    LIBS += -lz

    #if linux or windows
    #LIBS += ${BOOST_LIBRARY_DIR}/libz.a
endif

#
# INCLUDE directories for mothur
#
#
    VPATH=source/calculators:source/chimera:source/classifier:source/clearcut:source/commands:source/communitytype:source/datastructures:source/metastats:source/randomforest:source/read:source/svm
    skipUchime := source/uchime_src/
    subdirs :=  $(sort $(dir $(filter-out  $(skipUchime), $(wildcard source/*/))))
    subDirIncludes = $(patsubst %, -I %, $(subdirs))
    subDirLinking =  $(patsubst %, -L%, $(subdirs))
    CXXFLAGS += -I. $(subDirIncludes)
    LDFLAGS += $(subDirLinking)


#
# Get the list of all .cpp files, rename to .o files
#
    OBJECTS=$(patsubst %.cpp,%.o,$(wildcard $(addsuffix *.cpp,$(subdirs))))
    OBJECTS+=$(patsubst %.c,%.o,$(wildcard $(addsuffix *.c,$(subdirs))))
    OBJECTS+=$(patsubst %.cpp,%.o,$(wildcard *.cpp))
    OBJECTS+=$(patsubst %.c,%.o,$(wildcard *.c))

mothur : $(OBJECTS) uchime
    $(CXX) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS) $(LIBS)
    strip mothur


uchime:
    cd source/uchime_src && ./mk && mv uchime ../../ && cd ..


install : mothur


%.o : %.c %.h
    $(COMPILE.c) $(OUTPUT_OPTION) $<
%.o : %.cpp %.h
    $(COMPILE.cpp) $(OUTPUT_OPTION) $<
%.o : %.cpp %.hpp
    $(COMPILE.cpp) $(OUTPUT_OPTION) $<



clean :
    @rm -f $(OBJECTS)
    @rm -f uchime
