Sync vcflib

Makefile

@@ -778,9 +778,15 @@ $(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)