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SHELL ?= /bin/sh
PROG ?= soap
DEBUG ?= NO
STATIC ?= NO
PROFILE ?= NO
PTHREADS ?= YES
CC ?= gcc
DEBUG_FLAGS ?= -g3 -Wall -O2
PROFILE_FLAGS ?= -fprofile-arcs -ftest-coverage -pg
RELEASE_FLAGS ?= -O3 -funroll-loops -maccumulate-outgoing-args -fomit-frame-pointer
STATIC_FLAGS ?= -static
DFLAGS ?= -DMAKE_TIME=\""`date`"\"
LDFLAGS ?=
CPPFLAGS ?=
LIBS ?= -lm
#TARBALL_EXCLUDE = "*.(o,gz,zip)"
#ZIP_EXCLUDE = *.o *.gz *.zip
ifeq (YES, $(STATIC))
CFLAGS += $(STATIC_FLAGS)
endif
ifeq (YES, $(DEBUG))
CFLAGS += $(DEBUG_FLAGS) $(STATIC_FLAGS)
CFLAGS += -DDEBUG
# PTHREADS = NO
else
CFLAGS += $(RELEASE_FLAGS)
endif
ifeq (YES, $(PTHREADS))
LIBS += -lpthread
CFLAGS += -DPTHREADS
endif
CFLAGS += $(DFLAGS)
ifeq (YES, $(PROFILE))
CFLAGS += $(PROFILE_FLAGS)
endif
OBJ = SeqIO.o MiscUtilities.o MemManager.o TextConverter.o r250.o DNACount.o HSP.o Timing.o BWT.o extratools.o soapio.o BWTAln.o Match.o PairMatch.o stdaln.o kstring.o soap.o
.SUFFIX: .c .o
.c.o:
$(CC) $(CPPFLAGS) -c $(CFLAGS) $< -o $@
all: $(PROG)
$(PROG): $(OBJ)
$(CC) $(CPPFLAGS) $(CFLAGS) $(OBJ) -o $@ $(LDFLAGS) $(LIBS)
SeqIO.o:SeqIO.h
r250.o: r250.h
DNACount.o:DNACount.h
HSP.o:HSP.h
MiscUtilities.o:MiscUtilities.h
MemManager.o:MemManager.h
TextConverter.o:TextConverter.h
extratools.o:extratools.h BWT.h MiscUtilities.h MemManager.h TextConverter.h Timing.h HSP.h kstring.h
soapio.o:soapio.h SeqIO.h
BWT.o:BWT.h
BWTAln.o:BWTAln.h BWT.h
Match.o:Match.h BWTAln.h soapio.h
PairMatch.o:Match.h BWTAln.h stdaln.h
MiscUtilities.o:MiscUtilities.h
MemManager.o:MemManager.h
TextConverter.o:TextConverter.h
stdaln.o:stdaln.h
kstring.o:kstring.h
clean:
rm -f *.o $(PROG)
.PHONY: clean
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