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Makefile
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Makefile
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# =========================================
# MOSAIK Banded Smith-Waterman Makefile
# (c) 2009 Michael Stromberg & Wan-Ping Lee
# =========================================
# ----------------------------------
# define our source and object files
# ----------------------------------
SOURCES= smithwaterman.cpp BandedSmithWaterman.cpp SmithWatermanGotoh.cpp Repeats.cpp LeftAlign.cpp IndelAllele.cpp
OBJECTS= $(SOURCES:.cpp=.o) disorder.o
OBJECTS_NO_MAIN= disorder.o BandedSmithWaterman.o SmithWatermanGotoh.o Repeats.o LeftAlign.o IndelAllele.o
# ----------------
# compiler options
# ----------------
CFLAGS=-Wall -O3
LDFLAGS=-Wl,-s
#CFLAGS=-g
PROGRAM=smithwaterman
LIBS=
all: $(PROGRAM) sw.o
.PHONY: all
disorder.o: disorder.c disorder.h
g++ -c -o disorder.o disorder.c
sw.o: $(OBJECTS_NO_MAIN)
ld -r $(OBJECTS_NO_MAIN) -o sw.o
$(PROGRAM): $(OBJECTS)
@echo " * linking $(PROGRAM)"
@$(CXX) $(LDFLAGS) $(CFLAGS) -o $@ $^ $(LIBS)
.PHONY: clean
clean:
@echo "Cleaning up."
@rm -f *.o $(PROGRAM) *~