--- genometools-1.4.1.orig/Makefile
+++ genometools-1.4.1/Makefile
@@ -25,6 +25,8 @@
             -I$(CURDIR)/src/external/bzip2-1.0.6 \
             -I$(CURDIR)/src/external/libtecla-1.6.1 \
             -I$(CURDIR)/src/external/samtools-0.1.18
+#Debian hardening
+CFLAGS+=`dpkg-buildflags --get CFLAGS` `dpkg-buildflags --get CPPFLAGS`
 # these variables are exported by the configuration script
 ifndef CC
   CC:=gcc
