diff -ur ../exonerate-2.2.0.orig/src/program/Makefile.am ./src/program/Makefile.am
--- ../exonerate-2.2.0.orig/src/program/Makefile.am	2008-02-08 17:35:36.000000000 +0000
+++ ./src/program/Makefile.am	2012-02-23 16:31:14.000000000 +0000
@@ -67,9 +67,9 @@
 BUILT_SOURCES = c4_model_archive.a
 BOOTSTRAPPER = $(top_srcdir)/src/model/bootstrapper
 c4_model_archive.h: $(BOOTSTRAPPER)
-	$(BOOTSTRAPPER) --compiled no
+	CFLAGS="$(CFLAGS)" $(BOOTSTRAPPER) --compiled no
 c4_model_archive.a: $(BOOTSTRAPPER)
-	$(BOOTSTRAPPER) --compiled no
+	CFLAGS="$(CFLAGS)" $(BOOTSTRAPPER) --compiled no
 
 # Special viterbi.o and scheduler.o for compiled model linking
 viterbi.o: $(top_srcdir)/src/c4/viterbi.c