From 893a59e4dbf275012b3f0803ff6681639e5e740e Mon Sep 17 00:00:00 2001 From: Adam Novak Date: Tue, 30 Jun 2026 18:36:05 -0400 Subject: [PATCH 1/2] Sync up with upstream vcflib We still need a patch over upstream vcflib to fix static library compilation on Mac. --- Makefile | 8 +++++++- deps/vcflib | 2 +- 2 files changed, 8 insertions(+), 2 deletions(-) diff --git a/Makefile b/Makefile index 86348d4b74..b7dd6cffd1 100644 --- a/Makefile +++ b/Makefile @@ -776,9 +776,15 @@ $(LIB_DIR)/libtabixpp.a: $(LIB_DIR)/libhts.a $(TABIXPP_DIR)/*.cpp $(TABIXPP_DIR) # because there's no way to turn off vcflib's pybind11 build and pybind11 will # try and use the latest installed Python over the default one that probably # has headers. +# We now need to tell it to build in static mode so we get a static library. +# And we also now need to tell it to actually build its bundled WFA. +# +# Note that on MacOS we rely on the Makefile putting GNU coreutils on the PATH +# in order to avoid the dreaded "Could NOT find Threads". $(LIB_DIR)/libvcflib%a $(LIB_DIR)/libwfa2%a: $(LIB_DIR)/libhts.a $(LIB_DIR)/libtabixpp.a $(VCFLIB_DIR)/src/*.cpp $(VCFLIB_DIR)/src/*.hpp $(VCFLIB_DIR)/contrib/*/*.cpp $(VCFLIB_DIR)/contrib/*/*.h $(LIB_DIR)/cleaned_old_catch +rm -f $(VCFLIB_DIR)/contrib/WFA2-lib/VERSION - +cd $(VCFLIB_DIR) && rm -Rf build && mkdir build && cd build && PKG_CONFIG_PATH="$(CWD)/$(LIB_DIR)/pkgconfig:$(PKG_CONFIG_PATH)" cmake -DCMAKE_C_COMPILER="$(CC)" -DCMAKE_CXX_COMPILER="$(CXX)" -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DZIG=OFF -DCMAKE_C_FLAGS="$(CFLAGS)" -DCMAKE_CXX_FLAGS="$(CXXFLAGS) ${CPPFLAGS}" -DCMAKE_BUILD_TYPE=RelWithDebInfo -DCMAKE_INSTALL_PREFIX=$(CWD) -DCMAKE_PREFIX_PATH="/usr;$(OMP_PREFIXES)" -DPYTHON_EXECUTABLE="$(shell which python3)" .. && cmake --build . --target vcflib wfa2_static + +env + +cd $(VCFLIB_DIR) && rm -Rf build && mkdir build && cd build && PKG_CONFIG_PATH="$(CWD)/$(LIB_DIR)/pkgconfig:$(PKG_CONFIG_PATH)" cmake -DCMAKE_C_COMPILER="$(CC)" -DCMAKE_CXX_COMPILER="$(CXX)" -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DZIG=OFF -DCMAKE_C_FLAGS="$(CFLAGS)" -DCMAKE_CXX_FLAGS="$(CXXFLAGS) ${CPPFLAGS}" -DCMAKE_BUILD_TYPE=RelWithDebInfo -DCMAKE_INSTALL_PREFIX=$(CWD) -DCMAKE_PREFIX_PATH="/usr;$(OMP_PREFIXES)" -DPYTHON_EXECUTABLE="$(shell which python3)" -DBUILD_STATIC=ON -DWFA_GITMODULE=ON .. && cmake --build . --target vcflib wfa2_static +cp $(VCFLIB_DIR)/contrib/filevercmp/*.h* $(INC_DIR) +cp $(VCFLIB_DIR)/contrib/fastahack/*.h* $(INC_DIR) +cp $(VCFLIB_DIR)/contrib/smithwaterman/*.h* $(INC_DIR) diff --git a/deps/vcflib b/deps/vcflib index c65f20626d..41e285cb5a 160000 --- a/deps/vcflib +++ b/deps/vcflib @@ -1 +1 @@ -Subproject commit c65f20626d9fe96633181c4ab90f07b5560ddf5a +Subproject commit 41e285cb5a81917a85d352d493d13f96f6c37644 From 7ea75f06aaaccf66c3845641d46023406e4c1d57 Mon Sep 17 00:00:00 2001 From: Adam Novak Date: Wed, 1 Jul 2026 15:06:25 -0400 Subject: [PATCH 2/2] Use vcflib that points at vgteam url for fastahack --- deps/vcflib | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/deps/vcflib b/deps/vcflib index 41e285cb5a..174bcf52d0 160000 --- a/deps/vcflib +++ b/deps/vcflib @@ -1 +1 @@ -Subproject commit 41e285cb5a81917a85d352d493d13f96f6c37644 +Subproject commit 174bcf52d08dd40ebe4f6d2f85bb361e2624bd7f