CC=g++ -g -static -static-libgcc -static-libstdc++
CFLAGS=-O2 -march=x86-64 #-W -Wall
OPT=#-fast #-mtune=native #-ftree-vectorize -ffast-math #-funroll-loops
MATH =-lm
DEBUG=-g
BIOPHYL=/usr/lib/Bpp1.9/libbpp-phyl.a
BIONUC=/usr/lib/Bpp1.9/libbpp-numcalc.a
BIOUT=/usr/lib/Bpp1.9/libbpp-utils.a
BIOSEQ=/usr/lib/Bpp1.9/libbpp-seq.a
RM=rm -f
ARCH=#-arch i386
GSL=/usr/lib/libgsl.a /usr/lib/libgslcblas.a #-I/sw/include -L/sw/lib

all:	BCFasta.o file_manip.o Blosum.o create.o caps

caps: caps.cpp file_manip.o create.o BCFasta.o Blosum.o
	$(CC) $(CFLAGS) $(OPT) $(GSL) $(ARCH) $(BIOPHYL) $(BIOUT) $(BIONUC) $(BIOSEQ) -o caps caps.cpp file_manip.o BCFasta.o create.o Blosum.o
Blosum.o: Blosum.cpp
	$(CC) $(CFLAGS) $(OPT) -c Blosum.cpp
create.o: create.cpp
	$(CC) $(OPT) $(CFLAGS) -c create.cpp
file_manip.o: file_manip.cpp
	$(CC) $(OPT) $(CFLAGS) -c file_manip.cpp
BCFasta.o: BCFasta.cpp
	$(CC) $(OPT) $(CFLAGS) -c BCFasta.cpp
clean:
	$(RM) *.o *~ caps
cleanout:
	$(RM) *.o *~ caps *.csv *.out