$NetBSD: patch-Makefile,v 1.3 2023/05/18 14:05:15 bacon Exp $

# Respect env, add librt for NetBSD

--- Makefile.orig	2017-10-23 17:10:17.000000000 +0000
+++ Makefile
@@ -1,6 +1,6 @@
-CC=			gcc
+CC?=			gcc
 #CC=			clang --analyze
-CFLAGS=		-g -Wall -Wno-unused-function -O2
+CFLAGS?=		-g -Wall -Wno-unused-function -O2
 WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS
 AR=			ar
 DFLAGS=		-DHAVE_PTHREAD $(WRAP_MALLOC)
@@ -12,11 +12,14 @@ AOBJS=		bwashm.o bwase.o bwaseqio.o bwtg
 			bwtsw2_chain.o fastmap.o bwtsw2_pair.o
 PROG=		bwa
 INCLUDES=	
-LIBS=		-lm -lz -lpthread
+LDFLAGS+=	-lm -lz -lpthread
 SUBDIRS=	.
 
 ifeq ($(shell uname -s),Linux)
-	LIBS += -lrt
+	LDFLAGS += -lrt
+endif
+ifeq ($(shell uname -s),NetBSD)
+	LDFLAGS += -lrt
 endif
 
 .SUFFIXES:.c .o .cc
@@ -27,10 +30,10 @@ endif
 all:$(PROG)
 
 bwa:libbwa.a $(AOBJS) main.o
-		$(CC) $(CFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS)
+		$(CC) $(CFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LDFLAGS)
 
 bwamem-lite:libbwa.a example.o
-		$(CC) $(CFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS)
+		$(CC) $(CFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LDFLAGS)
 
 libbwa.a:$(LOBJS)
 		$(AR) -csru $@ $(LOBJS)