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DEST_DIR = ~/bin
# CFLAGS = -O0 -g -Wall -Wextra -Wno-unused-result -fno-strict-aliasing -fsanitize=address -fsanitize=undefined
# Above is for debug out of bound addresses, must compile with -lASAN -lUBSAN if gcc instead of clang
CFLAGS += -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing
ALL = daligner HPC.daligner LAsort LAmerge LAsplit LAcat LAshow LA2ONE LAcheck ONE2LA
all: $(ALL)
daligner: daligner.c filter.c filter.h lsd.sort.c lsd.sort.h align.c align.h DB.c DB.h QV.c QV.h
$(CC) $(CFLAGS) -o daligner daligner.c filter.c lsd.sort.c align.c DB.c QV.c -lpthread -lm $(LDFLAGS)
HPC.daligner: HPC.daligner.c DB.c DB.h QV.c QV.h
$(CC) $(CFLAGS) -o HPC.daligner HPC.daligner.c DB.c QV.c -lm $(LDFLAGS)
LAsort: LAsort.c align.h DB.c DB.h QV.c QV.h
$(CC) $(CFLAGS) -o LAsort LAsort.c DB.c QV.c -lm $(LDFLAGS)
LAmerge: LAmerge.c align.h DB.c DB.h QV.c QV.h
$(CC) $(CFLAGS) -o LAmerge LAmerge.c DB.c QV.c -lm $(LDFLAGS)
LAshow: LAshow.c align.c align.h DB.c DB.h QV.c QV.h
$(CC) $(CFLAGS) -o LAshow LAshow.c align.c DB.c QV.c -lm $(LDFLAGS)
LA2ONE: LA2ONE.c align.c align.h DB.c DB.h QV.c QV.h ONElib.c ONElib.h
$(CC) $(CFLAGS) -o LA2ONE LA2ONE.c align.c DB.c QV.c ONElib.c -lm $(LDFLAGS)
LAcat: LAcat.c align.h DB.c DB.h QV.c QV.h
$(CC) $(CFLAGS) -o LAcat LAcat.c DB.c QV.c -lm $(LDFLAGS)
LAsplit: LAsplit.c align.h DB.c DB.h QV.c QV.h
$(CC) $(CFLAGS) -o LAsplit LAsplit.c DB.c QV.c -lm $(LDFLAGS)
LAcheck: LAcheck.c align.c align.h DB.c DB.h QV.c QV.h
$(CC) $(CFLAGS) -o LAcheck LAcheck.c align.c DB.c QV.c -lm $(LDFLAGS)
ONE2LA: ONE2LA.c align.c align.h DB.c DB.h QV.c QV.h ONElib.c ONElib.h
$(CC) $(CFLAGS) -o ONE2LA ONE2LA.c align.c DB.c QV.c ONElib.c -lm $(LDFLAGS)
clean:
rm -f $(ALL)
rm -fr *.dSYM
rm -f daligner.tar.gz
install:
install -d $(DESTDIR)/usr/bin
install $(ALL) $(DESTDIR)/usr/bin
package:
make clean
tar -zcf daligner.tar.gz README.md Makefile *.h *.c
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