mm2-fast-v2.22 init

Makefile

@@ -1,6 +1,42 @@
 CFLAGS=		-g -Wall -O2 -Wc++-compat #-Wextra
-CPPFLAGS=	-DHAVE_KALLOC
-INCLUDES=
+CPPFLAGS=	-DHAVE_KALLOC #-march=native #-DALIGN_AVX -DPARALLEL_CHAINING #-DMANUAL_PROFILING
+COMP_FLAG = -march=native
+
+ifeq ($(avx2_compile), 1)
+	COMP_FLAG = -mavx2
+endif
+
+#CPPFLAGS=	-DHAVE_KALLOC -mavx2 -DALIGN_AVX -DAPPLY_AVX2 -DPARALLEL_CHAINING #-DLISA_HASH -DUINT64 -DVECTORIZE #-DMANUAL_PROFILING
+#CPPFLAGS=	-DHAVE_KALLOC -mavx2 -DPARALLEL_CHAINING  #-DMANUAL_PROFILING
+
+OPT_FLAGS= -DPARALLEL_CHAINING -DALIGN_AVX -DAPPLY_AVX2 
+OPT_FLAGS+=$(COMP_FLAG)
+ifeq ($(lhash_index), 1)	
+	CPPFLAGS+=	-DLISA_INDEX 
+endif
+ifeq ($(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=
+#INCLUDES=	-I./ext/TAL_offline/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 \
 			lchain.o align.o hit.o seed.o map.o format.o pe.o esterr.o splitidx.o \
 			ksw2_ll_sse.o
@@ -10,7 +46,7 @@ LIBS=		-lm -lz -lpthread
 
 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
+	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