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CXX=g++
CXXFLAGS += -O3 -Wno-write-strings
#CFLAGS= -g -Wno-write-strings
LDLIBS += -lpthread
#CFLAGS+=-DPOPCNT
#CFLAGS+=-DPERFCOUNT
#CFLAGS+=-DDEBUG_STAT
#CFLAGS+=-DDEBUG_HASH_PRINT
#CFLAGS+=-DPAIRALIGN_NO_FILTER
#CFLAGS+=-DPAIRALIGN_BASIC
#CFLAGS+=-DPAIRALIGN_NW
#CFLAGS+=-DPAIRALIGN_BITVECTOR
all: wham wham-build
wham: makefile hash.o embedhash.o main.o sequence.o aligner.o interval.o edit_distance.o error.o short.o hitset.o perfcounters.o model.o writer.o
$(CXX) -o wham sequence.o hash.o embedhash.o main.o aligner.o interval.o edit_distance.o error.o short.o hitset.o model.o perfcounters.o writer.o $(LDLIBS)
wham-build: makefile hash.o embedhash.o builder.o sequence.o aligner.o interval.o edit_distance.o error.o short.o hitset.o model.o writer.o
$(CXX) -o wham-build sequence.o hash.o embedhash.o builder.o aligner.o interval.o edit_distance.o error.o short.o hitset.o model.o perfcounters.o writer.o $(LDLIBS)
wham-test: makefile unittest.o hash.o embedhash.o sequence.o aligner.o interval.o edit_distance.o error.o short.o hitset.o model.o
$(CXX) -o wham-test unittest.o sequence.o hash.o embedhash.o aligner.o interval.o edit_distance.o error.o short.o hitset.o model.o perfcounters.o $(LDLIBS)
unittest.o: makefile unittest.cpp bitread.h
$(CXX) -c $(CXXFLAGS) unittest.cpp
interval.o: makefile interval.cpp interval.h lib.h error.h
$(CXX) -c $(CXXFLAGS) interval.cpp
edit_distance.o: makefile edit_distance.cpp edit_distance.h error.h
$(CXX) -c $(CXXFLAGS) edit_distance.cpp
embedhash.o: makefile embedhash.cpp embedhash.h hash.h edit_distance.h sequence.h lib.h error.h hitset.h pair.h
$(CXX) -c $(CXXFLAGS) embedhash.cpp
hash.o: makefile hash.cpp hash.h edit_distance.h sequence.h lib.h error.h hitset.h pair.h
$(CXX) -c $(CXXFLAGS) hash.cpp
aligner.o: makefile aligner.cpp aligner.h hash.h sequence.h lib.h error.h short.h hitset.h
$(CXX) -c $(CXXFLAGS) aligner.cpp
main.o: makefile main.cpp hash.h aligner.h sequence.h lib.h error.h perfcounters.h rdtsc.h pair.h
$(CXX) -c $(CXXFLAGS) main.cpp
sequence.o: makefile sequence.cpp sequence.h lib.h error.h
$(CXX) -c $(CXXFLAGS) sequence.cpp
error.o: makefile error.h
$(CXX) -c $(CXXFLAGS) error.cpp
short.o: makefile short.cpp short.h sequence.h lib.h error.h
$(CXX) -c $(CXXFLAGS) short.cpp
hitset.o: makefile hitset.cpp hitset.h lib.h short.h
$(CXX) -c $(CXXFLAGS) hitset.cpp
model.o: makefile model.cpp model.h
$(CXX) -c $(CXXFLAGS) model.cpp
writer.o: makefile writer.cpp writer.h sequence.h short.h
$(CXX) -c $(CXXFLAGS) writer.cpp
builder.o: makefile builder.cpp hash.h aligner.h sequence.h lib.h error.h short.h
$(CXX) -c $(CXXFLAGS) builder.cpp
filter.o: makefile filter.cpp hash.h aligner.h sequence.h lib.h error.h short.h
$(CXX) -c $(CXXFLAGS) filter.cpp
sorter.o: makefile sorter.cpp aligner.h
$(CXX) -c $(CXXFLAGS) sorter.cpp
perfcounters.o: makefile perfcounters.cpp perfcounters.h
$(CXX) -c $(CXXFLAGS) perfcounters.cpp
clean:
rm -f wham wham-build *.o
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