+Author: Simon Ruderich <simon@ruderich.org>
+Date: Sat, 28 Apr 2012 19:09:02 UTC
+Description: Fix build system to enable hardening flags
+
--- tabix.orig/Makefile
+++ tabix/Makefile
-@@ -12,7 +12,7 @@
+@@ -1,5 +1,8 @@
+ CC= gcc
+-CFLAGS= -g -Wall -O2 -fPIC #-m64 #-arch ppc
++# Use flags when CFLAGS is not already defined in the environment.
++CFLAGS?= -g -Wall -O2
++# But always append special flags we need.
++CFLAGS+= -fPIC #-m64 #-arch ppc
+ DFLAGS= -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE
+ LOBJS= bgzf.o kstring.o knetfile.o index.o bedidx.o
+ AOBJS= main.o
+@@ -12,7 +15,7 @@
.SUFFIXES:.c .o
.c.o:
- $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
-+ $(CC) -c $(CPPFLAGS) $(CFLAGS) $(CXXFLAGS) $(DFLAGS) $(LDFLAGS) $(INCLUDES) $< -o $@
++ $(CC) -c $(CPPFLAGS) $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
all-recur lib-recur clean-recur cleanlocal-recur install-recur:
@target=`echo $@ | sed s/-recur//`; \
+@@ -29,19 +32,19 @@
+ lib:libtabix.a
+
+ libtabix.so.1:$(LOBJS)
+- $(CC) -shared -Wl,-soname,libtabix.so -o $@ $(LOBJS) -lc -lz
++ $(CC) $(CFLAGS) $(LDFLAGS) -shared -Wl,-soname,libtabix.so -o $@ $(LOBJS) -lc -lz
+
+ libtabix.1.dylib:$(LOBJS)
+- libtool -dynamic $(LOBJS) -o $@ -lc -lz
++ libtool $(CFLAGS) $(LDFLAGS) -dynamic $(LOBJS) -o $@ -lc -lz
+
+ libtabix.a:$(LOBJS)
+ $(AR) -cru $@ $(LOBJS)
+
+ tabix:lib $(AOBJS)
+- $(CC) $(CFLAGS) -o $@ $(AOBJS) -lm $(LIBPATH) -lz -L. -ltabix
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(AOBJS) -lm $(LIBPATH) -lz -L. -ltabix
+
+ bgzip:bgzip.o bgzf.o knetfile.o
+- $(CC) $(CFLAGS) -o $@ bgzip.o bgzf.o knetfile.o -lz
++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ bgzip.o bgzf.o knetfile.o -lz
+
+ TabixReader.class:TabixReader.java
+ javac -cp .:sam.jar TabixReader.java