From 8e709f1738b62c62b07a1d4e6decd19275756595 Mon Sep 17 00:00:00 2001
From: Diane Trout <diane@caltech.edu>
Date: Wed, 19 Dec 2012 10:56:25 -0800
Subject: [PATCH] Clean up my patches

Add a end-of-file newline to series and remove the
duplicate patch to enable shared libraries.
---
 debian/patches/series    |  3 ++-
 debian/patches/use-shlib | 38 --------------------------------------
 2 files changed, 2 insertions(+), 39 deletions(-)
 delete mode 100644 debian/patches/use-shlib

diff --git a/debian/patches/series b/debian/patches/series
index 180fd32..8310354 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,4 @@
 no-pileup-tests.patch
 razip-oom-check
-build-so
\ No newline at end of file
+build-so
+
diff --git a/debian/patches/use-shlib b/debian/patches/use-shlib
deleted file mode 100644
index e747a11..0000000
--- a/debian/patches/use-shlib
+++ /dev/null
@@ -1,38 +0,0 @@
-Index: samtools-0.1.17/Makefile
-===================================================================
---- samtools-0.1.17.orig/Makefile	2011-07-25 21:00:44.145494440 -0700
-+++ samtools-0.1.17/Makefile	2011-07-25 21:09:46.265494761 -0700
-@@ -1,5 +1,5 @@
- CC=			gcc
--CFLAGS=		-g -Wall -O2 #-m64 #-arch ppc
-+CFLAGS=		-g -Wall -O2 -fPIC #-m64 #-arch ppc
- DFLAGS=		-D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1
- KNETFILE_O=	knetfile.o
- LOBJS=		bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o	\
-@@ -35,13 +35,13 @@
- .PHONY:all lib clean cleanlocal
- .PHONY:all-recur lib-recur clean-recur cleanlocal-recur install-recur
- 
--lib:libbam.a
-+lib:libbam.so.1
- 
- libbam.a:$(LOBJS)
- 		$(AR) -csru $@ $(LOBJS)
- 
- samtools:lib-recur $(AOBJS)
--		$(CC) $(CFLAGS) -o $@ $(AOBJS) -Lbcftools $(LIBPATH) libbam.a -lbcf $(LIBCURSES) -lm -lz
-+		$(CC) $(CFLAGS) -o $@ $(AOBJS) -Lbcftools $(LIBPATH) -L. -lbam -lbcf $(LIBCURSES) -lm -lz
- 
- razip:razip.o razf.o $(KNETFILE_O)
- 		$(CC) $(CFLAGS) -o $@ razf.o razip.o $(KNETFILE_O) -lz
-@@ -75,8 +75,9 @@
- libbam.1.dylib-local:$(LOBJS)
- 		libtool -dynamic $(LOBJS) -o libbam.1.dylib -lc -lz
- 
--libbam.so.1-local:$(LOBJS)
-+libbam.so.1:$(LOBJS)
- 		$(CC) -shared -Wl,-soname,libbam.so -o libbam.so.1 $(LOBJS) -lc -lz
-+		ln -s $@ libbam.so
- 
- dylib:
- 		@$(MAKE) cleanlocal; \
-- 
2.30.2