--- makefile.orig	1999-03-11 15:13:20.000000000 +0900
+++ makefile	2007-12-11 13:19:39.000000000 +0900
@@ -23,8 +23,8 @@
 #*****************************************************************************/
 
 # Makefile for swat, phrap, cross_match, phrapview; also swprobs (currently inactivated)
-CC= cc
-CFLAGS= -O2
+CC?= cc
+#CFLAGS= -O2
 LFLAGS= -lm
 
 SWATOBJS= swat.o weibull.o
@@ -55,11 +55,11 @@
 
 manyreads:  
 	touch swat.h;
-	make CFLAGS="-O2 -DMANYREADS" phrap cross_match;
+	make CFLAGS="$(CFLAGS) -DMANYREADS" phrap cross_match;
 	mv phrap phrap.manyreads;
 	mv cross_match cross_match.manyreads;
 	touch swat.h;
-	make CFLAGS="-O2 -DLONGREADS" phrap;
+	make CFLAGS="$(CFLAGS) -DLONGREADS" phrap;
 	mv phrap phrap.longreads;
 	touch swat.h;
 	make phrap cross_match;
