From: Michael R. Crusoe <michael.crusoe@gmail.com>
Subject: Pass CPPFLAGS
--- libvcflib.orig/Makefile
+++ libvcflib/Makefile
@@ -146,7 +146,7 @@
 
 GIT_VERSION ?= $(shell git describe --abbrev=4 --dirty --always)
 
-CXXFLAGS = -O3 -D_FILE_OFFSET_BITS=64 -std=c++0x
+CXXFLAGS += -O3 -D_FILE_OFFSET_BITS=64 -std=c++0x
 #CXXFLAGS = -O2
 #CXXFLAGS = -pedantic -Wall -Wshadow -Wpointer-arith -Wcast-qual
 
@@ -161,9 +161,8 @@
 gprof:
 	$(MAKE) CXXFLAGS="$(CXXFLAGS) -pg" all
 
-$(OBJECTS): $(SOURCES) $(HEADERS) $(TABIX) multichoose pre $(SMITHWATERMAN) $(FILEVERCMP)
 $(OBJECTS): $(SOURCES) $(HEADERS) multichoose pre $(SMITHWATERMAN) $(FILEVERCMP)
-	$(CXX) -c $(CFLAGS) -fPIC -o $@ src/$(*F).cpp $(INCLUDES) $(LDFLAGS) $(CXXFLAGS) && cp src/*.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
+	$(CXX) $(CPPFLAGS) -c $(CFLAGS) -fPIC -o $@ src/$(*F).cpp $(INCLUDES) $(LDFLAGS) $(CXXFLAGS) && cp src/*.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
 
 multichoose: pre
 	echo "Source does not contain dir multichoose"
@@ -182,18 +181,18 @@
 	#cp /usr/share/gnulib/lib/filevercmp.* filevercmp
 	#echo 'Proper use of filevercmp would be: `gnulib-tool --import filevercmp` - but it needs ./configure.ac'
 	#We here go with quilt patches from upstream files
-	cd filevercmp && $(CXX) $(CXXFLAGS) -fPIC -c filevercmp.c
+	cd filevercmp && $(CXX) $(CPPFLAGS) $(CXXFLAGS) -fPIC -c filevercmp.c
 	ln -sf ../filevercmp/filevercmp.h $(VCF_LIB_LOCAL)/$(INC_DIR)/filevercmp.h
 
 $(SHORTBINS): pre
 	$(MAKE) $(BIN_DIR)/$@
 
 $(BINS): $(BIN_SOURCES) libvcflib.so $(OBJECTS) $(SMITHWATERMAN) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP) pre intervaltree
-	$(CXX) src/$(notdir $@).cpp -o $@ $(INCLUDES) $(LDFLAGS) $(CXXFLAGS) -DVERSION=\"$(GIT_VERSION)\"
+	$(CXX) $(CPPFLAGS) $(HTS_LDFLAGS) src/$(notdir $@).cpp -o $@ $(INCLUDES) $(LDFLAGS) $(CXXFLAGS) -DVERSION=\"$(GIT_VERSION)\"
 
 libvcflib.so: $(OBJECTS) $(SMITHWATERMAN) $(REPEATS) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP) pre
 	# ar rs libvcflib.a $(OBJECTS) $(SSW) $(FILEVERCMP)
-	gcc -shared  -Wl,-soname -Wl,libvcflib.so.1 -o libvcflib.so.1 $(OBJECTS) $(SSW) $(FILEVERCMP)
+	gcc $(HTS_LDFLAGS) -shared  -Wl,-soname -Wl,libvcflib.so.1 -o libvcflib.so.1 $(OBJECTS) $(SSW) $(FILEVERCMP)
 	ln -s libvcflib.so.1 libvcflib.so
 	cp -a libvcflib.so* $(LIB_DIR)
 
