1 files changed, 3 insertions, 1 deletions
diff --git a/Makefile b/Makefile
index 68f95d4..e23c3c1 100644
--- a/Makefile
+++ b/Makefile
@@ -306,7 +306,9 @@ DEFS := -fno-strict-aliasing \
   $(FILE_FLAGS) \
   $(PREF_DEF) \
   $(MM_DEF) \
-  $(SHMEM_DEF)
+  $(SHMEM_DEF) \
+  $(CPPFLAGS) \
+  $(CFLAGS)
 
 # set compiler flags for all sanitized builds
 ifdef BOWTIE2_BIN_LIST_SAN