## /* The MIT License
## 
## Copyright (c) 2018-     Dana-Farber Cancer Institute
##               2017-2018 Broad Institute, Inc.
## 
## Permission is hereby granted, free of charge, to any person obtaining
## a copy of this software and associated documentation files (the
## "Software"), to deal in the Software without restriction, including
## without limitation the rights to use, copy, modify, merge, publish,
## distribute, sublicense, and/or sell copies of the Software, and to
## permit persons to whom the Software is furnished to do so, subject to
## the following conditions:
## 
## The above copyright notice and this permission notice shall be
## included in all copies or substantial portions of the Software.
## 
## THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
## EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
## MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
## NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
## BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
## ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
## CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
## SOFTWARE.
## Modified Copyright (C) 2021 Intel Corporation
##    Contacts: Saurabh Kalikar <saurabh.kalikar@intel.com>; 
## 	Vasimuddin Md <vasimuddin.md@intel.com>; Sanchit Misra <sanchit.misra@intel.com>; 
## 	Chirag Jain <chirag@iisc.ac.in>; Heng Li <hli@jimmy.harvard.edu>
## */
## 
CFLAGS=		-Wall -O2 -Wc++-compat #-Wextra
CPPFLAGS=	-DHAVE_KALLOC -march=native

OPT_FLAGS= -DVECTORIZED_CHAINING -DALIGN_AVX  
 
ifeq ($(lhash), 1)	
	OPT_FLAGS+=	-DLISA_HASH -DUINT64 -DVECTORIZE 
endif

ifeq ($(manual_profile), 1)
	CPPFLAGS+= -DMANUAL_PROFILING 
endif

ifeq ($(use_avx2), 1)
	OPT_FLAGS+= -DAPPLY_AVX2
endif

ifeq ($(disable_output), 1)
	CPPFLAGS+= -DDISABLE_OUTPUT
endif

ifeq ($(no_opt),)
	CPPFLAGS+= $(OPT_FLAGS)
endif

INCLUDES=	-I./ext/TAL/src/LISA-hash -I./ext/TAL/src/dynamic-programming 

OBJS=		kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o index.o chain.o align.o hit.o map.o format.o pe.o esterr.o splitidx.o ksw2_ll_sse.o
PROG=		minimap2
PROG_EXTRA=	sdust minimap2-lite
LIBS=		-lm -lz -lpthread 

CC=$(CXX)
ifeq ($(CC), g++)
	CC=g++ -std=c++11
endif

ifeq ($(arm_neon),) # if arm_neon is not defined
ifeq ($(sse2only),) # if sse2only is not defined
	OBJS+=ksw2_extz2_sse41.o ksw2_extd2_sse41.o ksw2_exts2_sse41.o ksw2_extz2_sse2.o ksw2_extd2_sse2.o ksw2_exts2_sse2.o ksw2_dispatch.o ksw2_extd2_avx.o
else                # if sse2only is defined
	OBJS+=ksw2_extz2_sse.o ksw2_extd2_sse.o ksw2_exts2_sse.o
endif
else				# if arm_neon is defined
	OBJS+=ksw2_extz2_neon.o ksw2_extd2_neon.o ksw2_exts2_neon.o
    INCLUDES+=-Isse2neon
ifeq ($(aarch64),)	#if aarch64 is not defined
	CFLAGS+=-D_FILE_OFFSET_BITS=64 -mfpu=neon -fsigned-char
else				#if aarch64 is defined
	CFLAGS+=-D_FILE_OFFSET_BITS=64 -fsigned-char
endif
endif

ifneq ($(asan),)
	CFLAGS+=-fsanitize=address
	LIBS+=-fsanitize=address
endif

ifneq ($(tsan),)
	CFLAGS+=-fsanitize=thread
	LIBS+=-fsanitize=thread
endif

.PHONY:all extra clean depend
.SUFFIXES:.c .o

.c.o:
		$(CC) -c $(CFLAGS) $(CPPFLAGS) $(INCLUDES) $< -o $@

all:$(PROG)

extra:all $(PROG_EXTRA)

minimap2:main.o libminimap2.a
		$(CC) $(CFLAGS) main.o -o $@ -L. -lminimap2 $(LIBS)

minimap2-lite:example.o libminimap2.a
		$(CC) $(CFLAGS) $< -o $@ -L. -lminimap2 $(LIBS)

libminimap2.a:$(OBJS)
		$(AR) -csru $@ $(OBJS)

sdust:sdust.c kalloc.o kalloc.h kdq.h kvec.h kseq.h ketopt.h sdust.h
		$(CC) -D_SDUST_MAIN $(CFLAGS) $< kalloc.o -o $@ -lz

multi:
		$(MAKE) clean
		$(MAKE)
		mv minimap2 mm2-fast
		$(MAKE) clean
		$(MAKE) lhash=1
		mv minimap2 mm2-fast-lhash
		$(MAKE) clean
		$(MAKE) no_opt=1
		mv minimap2 mm2-fast-no-opt

# SSE-specific targets on x86/x86_64

ifeq ($(arm_neon),)   # if arm_neon is defined, compile this target with the default setting (i.e. no -msse2)
ksw2_ll_sse.o:ksw2_ll_sse.c ksw2.h kalloc.h
		$(CC) -c $(CFLAGS) -msse2 $(CPPFLAGS) $(INCLUDES) $< -o $@
endif

ksw2_extz2_sse41.o:ksw2_extz2_sse.c ksw2.h kalloc.h
		$(CC) -c $(CFLAGS) -msse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@

ksw2_extz2_sse2.o:ksw2_extz2_sse.c ksw2.h kalloc.h
		$(CC) -c $(CFLAGS) -msse2 -mno-sse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY $(INCLUDES) $< -o $@

ksw2_extd2_sse41.o:ksw2_extd2_sse.c ksw2.h kalloc.h
		$(CC) -c $(CFLAGS) -msse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@

ksw2_extd2_sse2.o:ksw2_extd2_sse.c ksw2.h kalloc.h
		$(CC) -c $(CFLAGS) -msse2 -mno-sse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY $(INCLUDES) $< -o $@

ksw2_exts2_sse41.o:ksw2_exts2_sse.c ksw2.h kalloc.h
		$(CC) -c $(CFLAGS) -msse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@

ksw2_exts2_sse2.o:ksw2_exts2_sse.c ksw2.h kalloc.h
		$(CC) -c $(CFLAGS) -msse2 -mno-sse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY $(INCLUDES) $< -o $@

ksw2_dispatch.o:ksw2_dispatch.c ksw2.h
		$(CC) -c $(CFLAGS) -msse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@

# NEON-specific targets on ARM

ksw2_extz2_neon.o:ksw2_extz2_sse.c ksw2.h kalloc.h
		$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ $(INCLUDES) $< -o $@

ksw2_extd2_neon.o:ksw2_extd2_sse.c ksw2.h kalloc.h
		$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ $(INCLUDES) $< -o $@

ksw2_exts2_neon.o:ksw2_exts2_sse.c ksw2.h kalloc.h
		$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ $(INCLUDES) $< -o $@

# other non-file targets

clean:
		rm -fr gmon.out *.o a.out $(PROG) $(PROG_EXTRA) *~ *.a *.dSYM build dist mappy*.so mappy.c python/mappy.c mappy.egg*

depend:
		(LC_ALL=C; export LC_ALL; makedepend -Y -- $(CFLAGS) $(CPPFLAGS) -- *.c)

# DO NOT DELETE

align.o: minimap.h mmpriv.h bseq.h ksw2.h kalloc.h
bseq.o: bseq.h kvec.h kalloc.h kseq.h
chain.o: minimap.h mmpriv.h bseq.h kalloc.h
esterr.o: mmpriv.h minimap.h bseq.h
example.o: minimap.h kseq.h
format.o: kalloc.h mmpriv.h minimap.h bseq.h
hit.o: mmpriv.h minimap.h bseq.h kalloc.h khash.h
index.o: kthread.h bseq.h minimap.h mmpriv.h kvec.h kalloc.h khash.h
kalloc.o: kalloc.h
ksw2_extd2_sse.o: ksw2.h kalloc.h
ksw2_exts2_sse.o: ksw2.h kalloc.h
ksw2_extz2_sse.o: ksw2.h kalloc.h
ksw2_ll_sse.o: ksw2.h kalloc.h
kthread.o: kthread.h
main.o: bseq.h minimap.h mmpriv.h ketopt.h
map.o: kthread.h kvec.h kalloc.h sdust.h mmpriv.h minimap.h bseq.h khash.h
map.o: ksort.h
misc.o: mmpriv.h minimap.h bseq.h ksort.h
options.o: mmpriv.h minimap.h bseq.h
pe.o: mmpriv.h minimap.h bseq.h kvec.h kalloc.h ksort.h
sdust.o: kalloc.h kdq.h kvec.h ketopt.h sdust.h
sketch.o: kvec.h kalloc.h mmpriv.h minimap.h bseq.h
splitidx.o: mmpriv.h minimap.h bseq.h