From f63484f911793ee8a389c3e7c00f127a1d2f790a Mon Sep 17 00:00:00 2001
From: Diane Trout <diane@caltech.edu>
Date: Fri, 21 Dec 2012 17:10:29 -0800
Subject: [PATCH] Update use-dpkg-buildflags to work with the libtool version
 of the makefile

---
 debian/patches/use-dpkg-buildflags.patch | 58 ++++++++++--------------
 1 file changed, 24 insertions(+), 34 deletions(-)

diff --git a/debian/patches/use-dpkg-buildflags.patch b/debian/patches/use-dpkg-buildflags.patch
index 0275175..7367fb7 100644
--- a/debian/patches/use-dpkg-buildflags.patch
+++ b/debian/patches/use-dpkg-buildflags.patch
@@ -2,48 +2,38 @@ Author: Simon Ruderich <simon@ruderich.org>
 Date: Sat, 28 Apr 2012 19:09:02 UTC
 Description: Fix build system to enable hardening flags
 
---- a/Makefile
-+++ b/Makefile
-@@ -1,5 +1,8 @@
- CC=			gcc
--CFLAGS=		-g -Wall -O2 -fPIC #-m64 #-arch ppc
+Index: tabix/Makefile
+===================================================================
+--- tabix.orig/Makefile	2012-12-21 16:51:42.000000000 -0800
++++ tabix/Makefile	2012-12-21 16:54:56.446027398 -0800
+@@ -1,5 +1,6 @@
+ CC=		gcc
+-CFLAGS=		-g -Wall -O2
 +# 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 -DBGZF_CACHE
- LOBJS=		bgzf.o kstring.o knetfile.o index.o bedidx.o
- AOBJS=		main.o
-@@ -12,7 +15,7 @@
- .SUFFIXES:.c .o
+ LOBJS=		bgzf.lo kstring.lo knetfile.lo index.lo bedidx.lo
+ AOBJS=		main.lo
+@@ -30,18 +31,18 @@
+ .SUFFIXES:.c .o .lo
  
- .c.o:
--		$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
-+		$(CC) -c $(CPPFLAGS) $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
+ .c.lo:
+-		$(LIBTOOL) $(LTFLAGS) --mode=compile $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $<
++		$(LIBTOOL) $(LTFLAGS) --mode=compile $(CC) -c $(CPPFLAGS) $(CFLAGS) $(DFLAGS) $(INCLUDES) $<
  
- all-recur lib-recur clean-recur cleanlocal-recur install-recur:
- 		@target=`echo $@ | sed s/-recur//`; \
-@@ -29,19 +32,19 @@
- lib:libtabix.a
+ all:$(PROG) $(LIBNAME)
  
- 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
+ $(LIBNAME):$(LOBJS)
+-	$(LIBTOOL) $(LTFLAGS) --mode=link $(CC) $(CFLAGS) -version-info $(LIBVERSION) -rpath /usr/lib $(LOBJS) -o $@ -lc -lz
++	$(LIBTOOL) $(LTFLAGS) --mode=link $(CC) $(CFLAGS) $(LDFLAGS) -version-info $(LIBVERSION) -rpath /usr/lib $(LOBJS) -o $@ -lc -lz
  
- libtabix.1.dylib:$(LOBJS)
--		libtool -dynamic $(LOBJS) -o $@ -lc -lz
-+		libtool $(CFLAGS) $(LDFLAGS) -dynamic $(LOBJS) -o $@ -lc -lz
+ tabix:$(AOBJS) $(LIBNAME)
+-	$(LIBTOOL) $(LTFLAGS) --mode=link $(CC) $(CFLAGS) -o $@ $(AOBJS) $(LIBNAME) -lm -lz
++	$(LIBTOOL) $(LTFLAGS) --mode=link $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(AOBJS) $(LIBNAME) -lm -lz
  
- libtabix.a:$(LOBJS)
- 		$(AR) -csru $@ $(LOBJS)
- 
- tabix:lib $(AOBJS)
--		$(CC) $(CFLAGS) -o $@ $(AOBJS) -L. -ltabix -lm $(LIBPATH) -lz
-+		$(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(AOBJS) -L. -ltabix -lm $(LIBPATH) -lz
- 
- bgzip:bgzip.o bgzf.o knetfile.o
--		$(CC) $(CFLAGS) -o $@ bgzip.o bgzf.o knetfile.o -lz
-+		$(CC) $(CFLAGS) $(LDFLAGS) -o $@ bgzip.o bgzf.o knetfile.o -lz
+ bgzip:$(BOBJS)
+-	$(LIBTOOL) $(LTFLAGS) --mode=link $(CC) $(CFLAGS) -o $@  $(BOBJS) $(LIBNAME) -lz
++	$(LIBTOOL) $(LTFLAGS) --mode=link $(CC) $(CFLAGS) $(LDFLAGS) -o $@  $(BOBJS) $(LIBNAME) -lz
  
  TabixReader.class:TabixReader.java
  		javac -cp .:sam.jar TabixReader.java
-- 
2.30.2