diff options
Diffstat (limited to 'Makefile')
| -rw-r--r-- | Makefile | 26 |
1 files changed, 19 insertions, 7 deletions
@@ -64,7 +64,12 @@ endif BITS := 32 ifneq (,$(findstring $(shell uname -m), x86_64 amd64)) BITS := 64 - SSE_FLAG := -msse2 + ifeq (1, $(SSE_AVX2)) + SSE_FLAG := -mavx2 -faligned-new -DSSE_AVX2 + else + SSE_FLAG := -msse2 + endif + POPCNT_CAPABILITY ?= 1 else ifneq (,$(findstring $(shell uname -m), aarch64 arm64 s390x ppc64 ppc64le)) BITS := 64 @@ -74,6 +79,13 @@ else ifneq (,$(findstring $(shell uname -m), aarch64 arm64 s390x ppc64 ppc64le)) POPCNT_CAPABILITY ?= 0 endif +ifdef USE_SAIS + CPPFLAGS += -Ithird_party/libsais/include + CXXFLAGS += -fopenmp -DUSE_SAIS + LDFLAGS += -Lthird_party/libsais/lib + LDLIBS += -lsais +endif + # msys will always be 32 bit so look at the cpu arch instead. ifneq (,$(findstring AMD64,$(PROCESSOR_ARCHITEW6432))) ifeq (1,$(MINGW)) @@ -176,6 +188,7 @@ SEARCH_CPPS := qual.cpp pat.cpp sam.cpp \ ifeq (1, $(WITH_ZSTD)) LDLIBS += -lzstd + CXXFLAGS += -DWITH_ZSTD SHARED_CPPS += zstd_decompress.cpp endif @@ -305,7 +318,6 @@ endif # # bowtie2-build targets # - bowtie2-build-s-sanitized bowtie2-build-s: bt2_build.cpp $(SHARED_CPPS) $(HEADERS) $(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(CXXFLAGS) \ $(DEFS) -DBOWTIE2 $(NOASSERT_FLAGS) -Wall \ @@ -544,16 +556,16 @@ static-libs: cd $(CURDIR)/.tmp ; \ DL=$$( ( which wget >/dev/null 2>&1 && echo "wget --no-check-certificate" ) || echo "curl -LOk") ; \ if [ ! -f "$(CURDIR)/.tmp/include/zlib.h" ] ; then \ - $$DL https://zlib.net/zlib-1.2.11.tar.gz && tar xzf zlib-1.2.11.tar.gz && cd zlib-1.2.11 ; \ + $$DL https://zlib.net/zlib-1.2.13.tar.gz && tar xzf zlib-1.2.13.tar.gz && cd zlib-1.2.13 ; \ $(if $(MINGW), mingw32-make -f win32/Makefile.gcc, ./configure --static && make) ; \ cp zlib.h zconf.h $(CURDIR)/.tmp/include && cp libz.a $(CURDIR)/.tmp/lib ; \ - rm -f zlib-1.2.11 ; \ + rm -f zlib-1.2.13 ; \ fi ; \ if [ ! -f "$(CURDIR)/.tmp/include/zstd.h" ]; then \ cd $(CURDIR)/.tmp ; \ - $$DL https://github.com/facebook/zstd/releases/download/v1.4.9/zstd-1.4.9.tar.gz && tar xzf zstd-1.4.9.tar.gz ; \ - cd zstd-1.4.9 && $(MAKE) ; \ - cd $(CURDIR)/.tmp/zstd-1.4.9/lib && cp zstd.h $(CURDIR)/.tmp/include && cp libzstd.a $(CURDIR)/.tmp/lib ; \ + $$DL https://github.com/facebook/zstd/releases/download/v1.5.1/zstd-1.5.1.tar.gz && tar xzf zstd-1.5.1.tar.gz ; \ + cd zstd-1.5.1 && $(MAKE) lib ; \ + cd $(CURDIR)/.tmp/zstd-1.5.1/lib && cp zstd.h $(CURDIR)/.tmp/include && cp libzstd.a $(CURDIR)/.tmp/lib ; \ fi .PHONY: sra-deps |