From: Michael R. Crusoe <michael.crusoe@gmail.com>
Subject: Compile using CPPFLAGS

Set by Debian and other distributions or users
--- delly.orig/Makefile
+++ delly/Makefile
@@ -58,10 +58,10 @@
 	if [ -r src/htslib/Makefile ]; then cd src/htslib && make && make lib-static && cd ../../ && touch .htslib; fi
 
 src/delly: ${SUBMODULES} $(SOURCES)
-	$(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS)
+	$(CXX) $(CPPFLAGS) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS)
 
 src/dpe: ${SUBMODULES} $(SOURCES)
-	$(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS)
+	$(CXX) $(CPPFLAGS) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS)
 
 install: ${BUILT_PROGRAMS}
 	mkdir -p ${bindir}
