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minimap2/Makefile

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Makefile
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r792: fixed -Wextra warnings and resolved #184
2018-06-20 03:26:58 +08:00
CFLAGS= -g -Wall -O2 -Wc++-compat #-Wextra
enabled kalloc (was a mistake) Not using kalloc leads to significant malloc overhead.
2017-06-27 03:41:55 +08:00
CPPFLAGS= -DHAVE_KALLOC
r337: support CPU dispatch for gcc-4.8+ using __builtin_cpu_supports()
2017-09-04 02:29:49 +08:00
INCLUDES=
write hits to tmp files (unfinished)
2018-07-15 00:15:10 +08:00
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
index can be compiled; not tested yet
2017-04-08 03:30:30 +08:00
PROG= minimap2
update dependency; delete minimap2-lite on clean
2017-07-19 02:48:46 +08:00
PROG_EXTRA= sdust minimap2-lite
index can be compiled; not tested yet
2017-04-08 03:30:30 +08:00
LIBS= -lm -lz -lpthread
use SSE compiler flags more precisely (#127)
2018-02-26 22:51:01 +08:00
ifeq ($(arm_neon),) # if arm_neon is not defined
ifeq ($(sse2only),) # if sse2only is not defined
r337: support CPU dispatch for gcc-4.8+ using __builtin_cpu_supports()
2017-09-04 02:29:49 +08:00
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
use SSE compiler flags more precisely (#127)
2018-02-26 22:51:01 +08:00
else # if sse2only is defined
r337: support CPU dispatch for gcc-4.8+ using __builtin_cpu_supports()
2017-09-04 02:29:49 +08:00
OBJS+=ksw2_extz2_sse.o ksw2_extd2_sse.o ksw2_exts2_sse.o
endif
added support for 64 bit ARM architectures
2018-06-11 12:23:03 +08:00
else # if arm_neon is defined
OBJS+=ksw2_extz2_neon.o ksw2_extd2_neon.o ksw2_exts2_neon.o
use SSE compiler flags more precisely (#127)
2018-02-26 22:51:01 +08:00
INCLUDES+=-Isse2neon
added support for 64 bit ARM architectures
2018-06-11 12:23:03 +08:00
ifeq ($(aarch64),) #if aarch64 is not defined
CFLAGS+=-D_FILE_OFFSET_BITS=64 -mfpu=neon -fsigned-char
else #if aarch64 is defined
CFLAGS+=-D_FILE_OFFSET_BITS=64 -fsigned-char
r794: fixed a bug in seed filtering
2018-06-20 22:26:29 +08:00
endif
added support for arm neon
2017-12-15 14:42:19 +08:00
endif
use -msse4 by default, not -march
2017-07-19 01:56:51 +08:00
added the asan and tsan targets to Makefile
2019-12-24 06:33:10 +08:00
ifneq ($(asan),)
CFLAGS+=-fsanitize=address
LIBS+=-fsanitize=address
endif
ifneq ($(tsan),)
CFLAGS+=-fsanitize=thread
LIBS+=-fsanitize=thread
endif
added PHONY and comments to makefile
2017-12-31 09:54:11 +08:00
.PHONY:all extra clean depend
index can be compiled; not tested yet
2017-04-08 03:30:30 +08:00
.SUFFIXES:.c .o
.c.o:
$(CC) -c $(CFLAGS) $(CPPFLAGS) $(INCLUDES) $< -o $@
all:$(PROG)
extra:all $(PROG_EXTRA)
r829: replaced musl's getopt with ketopt
2018-09-02 09:15:43 +08:00
minimap2:main.o libminimap2.a
$(CC) $(CFLAGS) main.o -o $@ -L. -lminimap2 $(LIBS)
index can be compiled; not tested yet
2017-04-08 03:30:30 +08:00
migrated minimap/example.c here.
2017-07-19 02:43:43 +08:00
minimap2-lite:example.o libminimap2.a
$(CC) $(CFLAGS) $< -o $@ -L. -lminimap2 $(LIBS)
index can be compiled; not tested yet
2017-04-08 03:30:30 +08:00
libminimap2.a:$(OBJS)
$(AR) -csru $@ $(OBJS)
r829: replaced musl's getopt with ketopt
2018-09-02 09:15:43 +08:00
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 $@ -lz
index can be compiled; not tested yet
2017-04-08 03:30:30 +08:00
added PHONY and comments to makefile
2017-12-31 09:54:11 +08:00
# SSE-specific targets on x86/x86_64
use SSE compiler flags more precisely (#127)
2018-02-26 22:51:01 +08:00
ifeq ($(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
r337: support CPU dispatch for gcc-4.8+ using __builtin_cpu_supports()
2017-09-04 02:29:49 +08:00
ksw2_extz2_sse41.o:ksw2_extz2_sse.c ksw2.h kalloc.h
use SSE compiler flags more precisely (#127)
2018-02-26 22:51:01 +08:00
$(CC) -c $(CFLAGS) -msse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@
r337: support CPU dispatch for gcc-4.8+ using __builtin_cpu_supports()
2017-09-04 02:29:49 +08:00
ksw2_extz2_sse2.o:ksw2_extz2_sse.c ksw2.h kalloc.h
use SSE compiler flags more precisely (#127)
2018-02-26 22:51:01 +08:00
$(CC) -c $(CFLAGS) -msse2 -mno-sse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY $(INCLUDES) $< -o $@
r337: support CPU dispatch for gcc-4.8+ using __builtin_cpu_supports()
2017-09-04 02:29:49 +08:00
ksw2_extd2_sse41.o:ksw2_extd2_sse.c ksw2.h kalloc.h
use SSE compiler flags more precisely (#127)
2018-02-26 22:51:01 +08:00
$(CC) -c $(CFLAGS) -msse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@
r337: support CPU dispatch for gcc-4.8+ using __builtin_cpu_supports()
2017-09-04 02:29:49 +08:00
ksw2_extd2_sse2.o:ksw2_extd2_sse.c ksw2.h kalloc.h
use SSE compiler flags more precisely (#127)
2018-02-26 22:51:01 +08:00
$(CC) -c $(CFLAGS) -msse2 -mno-sse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY $(INCLUDES) $< -o $@
r337: support CPU dispatch for gcc-4.8+ using __builtin_cpu_supports()
2017-09-04 02:29:49 +08:00
ksw2_exts2_sse41.o:ksw2_exts2_sse.c ksw2.h kalloc.h
use SSE compiler flags more precisely (#127)
2018-02-26 22:51:01 +08:00
$(CC) -c $(CFLAGS) -msse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@
r337: support CPU dispatch for gcc-4.8+ using __builtin_cpu_supports()
2017-09-04 02:29:49 +08:00
ksw2_exts2_sse2.o:ksw2_exts2_sse.c ksw2.h kalloc.h
use SSE compiler flags more precisely (#127)
2018-02-26 22:51:01 +08:00
$(CC) -c $(CFLAGS) -msse2 -mno-sse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY $(INCLUDES) $< -o $@
r337: support CPU dispatch for gcc-4.8+ using __builtin_cpu_supports()
2017-09-04 02:29:49 +08:00
ksw2_dispatch.o:ksw2_dispatch.c ksw2.h
use SSE compiler flags more precisely (#127)
2018-02-26 22:51:01 +08:00
$(CC) -c $(CFLAGS) -msse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@
added PHONY and comments to makefile
2017-12-31 09:54:11 +08:00
# NEON-specific targets on ARM
added support for arm neon
2017-12-15 14:42:19 +08:00
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 $@
added PHONY and comments to makefile
2017-12-31 09:54:11 +08:00
# other non-file targets
r337: support CPU dispatch for gcc-4.8+ using __builtin_cpu_supports()
2017-09-04 02:29:49 +08:00
index can be compiled; not tested yet
2017-04-08 03:30:30 +08:00
clean:
Release minimap2-2.8 (r672)
2018-02-02 01:27:15 +08:00
rm -fr gmon.out *.o a.out $(PROG) $(PROG_EXTRA) *~ *.a *.dSYM build dist mappy*.so mappy.c python/mappy.c mappy.egg*
index can be compiled; not tested yet
2017-04-08 03:30:30 +08:00
depend:
r159: use two-piece gap penalty
2017-07-08 22:26:00 +08:00
(LC_ALL=C; export LC_ALL; makedepend -Y -- $(CFLAGS) $(CPPFLAGS) -- *.c)
index can be compiled; not tested yet
2017-04-08 03:30:30 +08:00
# DO NOT DELETE
r159: use two-piece gap penalty
2017-07-08 22:26:00 +08:00
align.o: minimap.h mmpriv.h bseq.h ksw2.h kalloc.h
r440: better chain filtering for PE reads
2017-09-26 23:03:36 +08:00
bseq.o: bseq.h kvec.h kalloc.h kseq.h
separated formating printing for SAM in future; and for performance
2017-06-26 04:13:54 +08:00
chain.o: minimap.h mmpriv.h bseq.h kalloc.h
added esterr.o dependencies
2017-12-13 22:01:48 +08:00
esterr.o: mmpriv.h minimap.h bseq.h
update dependency; delete minimap2-lite on clean
2017-07-19 02:48:46 +08:00
example.o: minimap.h kseq.h
r281: don't open long gaps on query
2017-08-11 03:04:59 +08:00
format.o: kalloc.h mmpriv.h minimap.h bseq.h
r479: a bit code cleanup
2017-10-06 04:15:14 +08:00
hit.o: mmpriv.h minimap.h bseq.h kalloc.h khash.h
backup
2017-06-06 22:16:33 +08:00
index.o: kthread.h bseq.h minimap.h mmpriv.h kvec.h kalloc.h khash.h
index can be compiled; not tested yet
2017-04-08 03:30:30 +08:00
kalloc.o: kalloc.h
r159: use two-piece gap penalty
2017-07-08 22:26:00 +08:00
ksw2_extd2_sse.o: ksw2.h kalloc.h
separate out spliced alignment; not right yet
2017-08-13 06:54:32 +08:00
ksw2_exts2_sse.o: ksw2.h kalloc.h
r159: use two-piece gap penalty
2017-07-08 22:26:00 +08:00
ksw2_extz2_sse.o: ksw2.h kalloc.h
r229: a new way to prevent out-of-band backtrack
2017-07-30 11:52:30 +08:00
ksw2_ll_sse.o: ksw2.h kalloc.h
put option operations in another file
2018-01-26 21:38:37 +08:00
kthread.o: kthread.h
r829: replaced musl's getopt with ketopt
2018-09-02 09:15:43 +08:00
main.o: bseq.h minimap.h mmpriv.h ketopt.h
r479: a bit code cleanup
2017-10-06 04:15:14 +08:00
map.o: kthread.h kvec.h kalloc.h sdust.h mmpriv.h minimap.h bseq.h khash.h
put option operations in another file
2018-01-26 21:38:37 +08:00
map.o: ksort.h
misc.o: mmpriv.h minimap.h bseq.h ksort.h
options.o: mmpriv.h minimap.h bseq.h
r479: a bit code cleanup
2017-10-06 04:15:14 +08:00
pe.o: mmpriv.h minimap.h bseq.h kvec.h kalloc.h ksort.h
r829: replaced musl's getopt with ketopt
2018-09-02 09:15:43 +08:00
sdust.o: kalloc.h kdq.h kvec.h ketopt.h sdust.h
put option operations in another file
2018-01-26 21:38:37 +08:00
sketch.o: kvec.h kalloc.h mmpriv.h minimap.h bseq.h
r829: replaced musl's getopt with ketopt
2018-09-02 09:15:43 +08:00
splitidx.o: mmpriv.h minimap.h bseq.h