--- longread-one/Makefile.orig	2019-09-04 04:22:49 UTC
+++ longread-one/Makefile
@@ -1,12 +1,12 @@
-CC_EXEC = gcc
 OPT_LEVEL = 3
 
 include ../makefile.version
 include make.version
 
-CCFLAGS = -mtune=core2 ${MACOS} -O${OPT_LEVEL} -Wall  -DMAKE_FOR_EXON  -D MAKE_STANDALONE  -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\"${SUBREAD_VERSION}\" ${WARNING_LEVEL} ${MINGW32}
-LDFLAGS =  -lpthread -lz -lm -O${OPT_LEVEL} -DMAKE_FOR_EXON -D MAKE_STANDALONE # -DREPORT_ALL_THE_BEST
-CC = ${CC_EXEC}  ${CCFLAGS}  -fmessage-length=0  -ggdb
+CC ?= gcc
+CFLAGS += -DMAKE_FOR_EXON  -D MAKE_STANDALONE  -D_FILE_OFFSET_BITS=64 \
+	-DSUBREAD_VERSION=\"${SUBREAD_VERSION}\" ${WARNING_LEVEL} ${MINGW32}
+LDFLAGS +=  -lpthread -lz -lm -O${OPT_LEVEL} -DMAKE_FOR_EXON -D MAKE_STANDALONE # -DREPORT_ALL_THE_BEST
 
 ALL_LIBS=LRMsorted-hashtable LRMbase-index LRMchro-event LRMhelper LRMseek-zlib LRMfile-io LRMhashtable
 ALL_OBJECTS=$(addsuffix .o, ${ALL_LIBS})
@@ -20,8 +20,8 @@ clean:
 	rm -f *.o LRM
 
 LRM: longread-mapping.c  ${ALL_OBJECTS} 
-	${CC} -o LRM longread-mapping.c   ${ALL_OBJECTS}  ${LDFLAGS}
+	${CC} -o LRM ${CFLAGS} longread-mapping.c   ${ALL_OBJECTS}  ${LDFLAGS}
 
 $(ALL_OBJECTS): $(ALL_C) $(ALL_H)
-	$(CC) -o $@ -c $(subst .o,.c,$@)
+	$(CC) -o $@ -c ${CFLAGS} $(subst .o,.c,$@)