CC=g++
CFLAGS=-O2 -g3 -Wall -c -fmessage-length=0 -ansi -Wno-unused-variable -Wno-unused-but-set-variable
LDFLAGS=-static
LIB=-lgsl -lgslcblas -lbpp-phyl -lbpp-seq -lbpp-core
BPP=/usr/
LIBPATH=-L$(BPP)/lib/
SRC=-I$(BPP)/include/
EXEC=reads2snp

all: $(EXEC)

reads2snp: Dmultinomiale.o Factorial.o Gamma.o Logvrais.o QuantileBeta.o LnL.o  Posdata.o Contigdata.o Reads2snp.o Paraclean.o main.o 
	$(CC) $(LIBPATH) -o $@ $^ $(LIB) $(LDFLAGS) 

Dmultinomiale.o: ./Stat/Dmultinomiale.cpp
	$(CC) $(SRC) -o $@ "Stat/Dmultinomiale.cpp" $(CFLAGS) 

Factorial.o: ./Stat/Factorial.cpp
	$(CC) $(SRC) -o $@ "Stat/Factorial.cpp" $(CFLAGS) 

Gamma.o: ./Stat/Gamma.cpp
	$(CC) $(SRC) -o $@ "Stat/Gamma.cpp" $(CFLAGS) 

Logvrais.o: ./Stat/Logvrais.cpp
	$(CC) $(SRC) -o $@ "Stat/Logvrais.cpp" $(CFLAGS) 

QuantileBeta.o: ./Stat/QuantileBeta.cpp
	$(CC) $(SRC) -o $@ "Stat/QuantileBeta.cpp" $(CFLAGS) 

LnL.o: ./Reads2snp/LnL.cpp
	$(CC) $(SRC) -o $@ "Reads2snp/LnL.cpp" $(CFLAGS) 

Posdata.o: ./Reads2snp/Posdata.cpp
	$(CC) $(SRC) -o $@ "Reads2snp/Posdata.cpp" $(CFLAGS) 

Contigdata.o: ./Reads2snp/Contigdata.cpp
	$(CC) $(SRC) -o $@ "Reads2snp/Contigdata.cpp" $(CFLAGS) 

Geno2pfas.o: ./Geno2pfas.hpp
	$(CC) $(SRC) -o $@ "Geno2pfas.hpp" $(CFLAGS)
	
Pfasclean.o: ./Pfasclean.hpp
	$(CC) $(SRC) -o $@ "Pfasclean.hpp" $(CFLAGS)

Reads2snp.o: ./Reads2snp/Reads2snp.cpp
	$(CC) $(SRC) -o $@ "Reads2snp/Reads2snp.cpp" $(CFLAGS) 

Paraclean.o: ./Paraclean/Paraclean.cpp
	$(CC) $(SRC) -o $@ "Paraclean/Paraclean.cpp" $(CFLAGS) 

main.o: main.cpp
	$(CC) $(SRC) -o $@ "main.cpp" $(CFLAGS)



