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minimap2/Makefile

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Makefile
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use -msse4 by default, not -march
2017-07-19 01:56:51 +08:00
CFLAGS= -g -Wall -O2 -Wc++-compat
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=
r607: estimate sequence divergence Currently using the simplest method. There may be a more accurate estimate.
2017-12-07 05:14:39 +08:00
OBJS= kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o index.o chain.o align.o hit.o map.o format.o pe.o esterr.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
added support for arm neon
2017-12-15 14:42:19 +08:00
ifeq ($(arm_neon),)
r338: portable CPU dispatch, which is the default working with gcc, icc, clang and msvc.
2017-09-04 08:29:24 +08:00
ifeq ($(sse2only),)
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
else
OBJS+=ksw2_extz2_sse.o ksw2_extd2_sse.o ksw2_exts2_sse.o
endif
added support for arm neon
2017-12-15 14:42:19 +08:00
else
OBJS+=ksw2_extz2_neon.o ksw2_extd2_neon.o ksw2_exts2_neon.o
CFLAGS+=-D_FILE_OFFSET_BITS=64 -mfpu=neon -fsigned-char
INCLUDES+=-I sse2neon
endif
use -msse4 by default, not -march
2017-07-19 01:56:51 +08:00
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)
r315: added getopt from musl
2017-09-01 20:20:34 +08:00
minimap2:main.o getopt.o libminimap2.a
$(CC) $(CFLAGS) main.o getopt.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)
for better windows compatibility
2017-09-03 05:52:33 +08:00
sdust:sdust.c getopt.o kalloc.o kalloc.h kdq.h kvec.h kseq.h sdust.h
$(CC) -D_SDUST_MAIN $(CFLAGS) $< getopt.o kalloc.o -o $@ -lz
index can be compiled; not tested yet
2017-04-08 03:30:30 +08:00
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
r338: portable CPU dispatch, which is the default working with gcc, icc, clang and msvc.
2017-09-04 08:29:24 +08:00
$(CC) -c -msse4 $(CFLAGS) $(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
r338: portable CPU dispatch, which is the default working with gcc, icc, clang and msvc.
2017-09-04 08:29:24 +08:00
$(CC) -c $(CFLAGS) $(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
r338: portable CPU dispatch, which is the default working with gcc, icc, clang and msvc.
2017-09-04 08:29:24 +08:00
$(CC) -c -msse4 $(CFLAGS) $(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
r338: portable CPU dispatch, which is the default working with gcc, icc, clang and msvc.
2017-09-04 08:29:24 +08:00
$(CC) -c $(CFLAGS) $(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
r338: portable CPU dispatch, which is the default working with gcc, icc, clang and msvc.
2017-09-04 08:29:24 +08:00
$(CC) -c -msse4 $(CFLAGS) $(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
r338: portable CPU dispatch, which is the default working with gcc, icc, clang and msvc.
2017-09-04 08:29:24 +08:00
$(CC) -c $(CFLAGS) $(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
$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@
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 $@
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:
this is embarrassing: rename again to mappy
2017-09-17 12:05:30 +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
for better windows compatibility
2017-09-03 05:52:33 +08:00
getopt.o: getopt.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
for better windows compatibility
2017-09-03 05:52:33 +08:00
main.o: bseq.h minimap.h mmpriv.h getopt.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
index can be compiled; not tested yet
2017-04-08 03:30:30 +08:00
misc.o: minimap.h ksort.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
index can be compiled; not tested yet
2017-04-08 03:30:30 +08:00
sdust.o: kalloc.h kdq.h kvec.h sdust.h
sketch.o: kvec.h kalloc.h minimap.h