From be36d981cd3e7121992bb29d7a83d3d037e17bd2 Mon Sep 17 00:00:00 2001
From: John Marshall <jmarshall@users.sourceforge.net>
Date: Sun, 15 Dec 2019 18:14:49 +0000
Subject: [PATCH] Use $CPPFLAGS and $LDFLAGS if they are set

The bwa makefile doesn't set these two itself, but the environment
or make command line might set any of CC/CPPFLAGS/CFLAGS/LDFLAGS/LIBS.
Use $(CPPFLAGS) when compiling and $(LDFLAGS) when linking so they can
be used to customise the build. Remove $(DFLAGS) from link commands as
these preprocessor options are irrelevant for linking.
---
 Makefile | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/Makefile b/Makefile
index 7151435..37751bb 100644
--- a/Makefile
+++ b/Makefile
@@ -22,15 +22,15 @@ endif
 .SUFFIXES:.c .o .cc
 
 .c.o:
-		$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
+		$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $(CPPFLAGS) $< -o $@
 
 all:$(PROG)
 
 bwa:libbwa.a $(AOBJS) main.o
-		$(CC) $(CFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS)
+		$(CC) $(CFLAGS) $(LDFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS)
 
 bwamem-lite:libbwa.a example.o
-		$(CC) $(CFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS)
+		$(CC) $(CFLAGS) $(LDFLAGS) example.o -o $@ -L. -lbwa $(LIBS)
 
 libbwa.a:$(LOBJS)
 		$(AR) -csru $@ $(LOBJS)
@@ -39,7 +39,7 @@ clean:
 		rm -f gmon.out *.o a.out $(PROG) *~ *.a
 
 depend:
-	( LC_ALL=C ; export LC_ALL; makedepend -Y -- $(CFLAGS) $(DFLAGS) -- *.c )
+	( LC_ALL=C ; export LC_ALL; makedepend -Y -- $(CFLAGS) $(DFLAGS) $(CPPFLAGS) -- *.c )
 
 # DO NOT DELETE THIS LINE -- make depend depends on it.