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new Makefile

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This commit is contained in:
Heng Li
2019-11-22 14:43:37 -05:00
parent b81b7f9213
commit 8ad76667f4
1 changed files with 48 additions and 12 deletions
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Makefile
+48 -12
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@@ -1,18 +1,54 @@
CC=g++
CXX= g++
CXXFLAGS= -g -O3 -msse4.2 -mpopcnt -fomit-frame-pointer -Winline -Wall
CPPFLAGS=
INCLUDES=
OBJS= Output.o CommandLines.o Process_Read.o Assembly.o kmer.o Hash_Table.o \
POA.o Correct.o Levenshtein_distance.o edlib.o Overlaps.o
EXE= ccs_assembly
LIBS= -lz -lpthread -lm
CFLAGS = -w -c -msse4.2 -mpopcnt -fomit-frame-pointer -Winline -O3 -lz
LDFLAGS = -lm -lz -lpthread -O3 -mpopcnt -msse4.2 -lz -w
ifneq ($(asan),)
CXXFLAGS+=-fsanitize=address
LIBS+=-fsanitize=address
endif
SOURCES = main.cpp Output.cpp CommandLines.cpp Process_Read.cpp Assembly.cpp kmer.cpp Hash_Table.cpp POA.cpp Correct.cpp Levenshtein_distance.cpp edlib.cpp Overlaps.cpp
OBJECTS = $(SOURCES:.c=.o)
EXECUTABLE = ccs_assembly
.SUFFIXES:.cpp .o
.PHONY:all clean depend
.cpp.o:
$(CXX) -c $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) $< -o $@
all: $(SOURCES) $(EXECUTABLE)
$(EXECUTABLE): $(OBJECTS)
$(CC) $(OBJECTS) -o $@ $(LDFLAGS)
all:$(EXE)
$(EXE):$(OBJS) main.o
$(CXX) $(CXXFLAGS) $^ -o $@ $(LIBS)
.c.o:
$(CC) $(CFLAGS) $< -o $@
clean:
rm -f *.o *~ \#* ccs_assembly
rm -fr gmon.out *.o a.out $(EXE) *~ *.a *.dSYM
depend:
(LC_ALL=C; export LC_ALL; makedepend -Y -- $(CPPFLAGS) $(DFLAGS) -- *.cpp)
# DO NOT DELETE
Assembly.o: Assembly.h Process_Read.h kseq.h Overlaps.h kvec.h kdq.h
Assembly.o: CommandLines.h kmer.h Hash_Table.h khash.h POA.h Correct.h
Assembly.o: Levenshtein_distance.h Output.h
CommandLines.o: CommandLines.h ketopt.h
Correct.o: Correct.h Hash_Table.h khash.h kmer.h Process_Read.h kseq.h
Correct.o: Overlaps.h kvec.h kdq.h CommandLines.h Levenshtein_distance.h
Correct.o: POA.h edlib.h Assembly.h
Hash_Table.o: Hash_Table.h khash.h kmer.h Process_Read.h kseq.h Overlaps.h
Hash_Table.o: kvec.h kdq.h CommandLines.h Correct.h Levenshtein_distance.h
Hash_Table.o: POA.h ksort.h
Levenshtein_distance.o: Levenshtein_distance.h
Output.o: Output.h CommandLines.h
Overlaps.o: Overlaps.h kvec.h kdq.h ksort.h Process_Read.h kseq.h
Overlaps.o: CommandLines.h
POA.o: POA.h Hash_Table.h khash.h kmer.h Process_Read.h kseq.h Overlaps.h
POA.o: kvec.h kdq.h CommandLines.h Correct.h Levenshtein_distance.h
Process_Read.o: Process_Read.h kseq.h Overlaps.h kvec.h kdq.h CommandLines.h
edlib.o: edlib.h
kmer.o: kmer.h Process_Read.h kseq.h Overlaps.h kvec.h kdq.h CommandLines.h
main.o: CommandLines.h Process_Read.h kseq.h Overlaps.h kvec.h kdq.h
main.o: Assembly.h Levenshtein_distance.h edlib.h