[med-svn] [tophat] 02/03: debian/patches/hardening4samtols.patch: add hardening flags for embedded copy of samtools

[Alex Mestiashvili]

This is an automated email from the git hooks/post-receive script.

malex-guest pushed a commit to branch master
in repository tophat.

commit 093cb2f3e062927db421053ddf1cf50350cfce94
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Sun Oct 26 15:27:07 2014 +0100

    debian/patches/hardening4samtols.patch: add hardening flags for
     embedded copy of samtools
---
 debian/patches/hardening4samtols.patch | 22 ++++++++++++++++++++++
 debian/patches/series                  |  1 +
 2 files changed, 23 insertions(+)

diff --git a/debian/patches/hardening4samtols.patch b/debian/patches/hardening4samtols.patch
new file mode 100644
index 0000000..0c9cedd
--- /dev/null
+++ b/debian/patches/hardening4samtols.patch
@@ -0,0 +1,22 @@
+Subject: add hardening flags to embedded copy of samtools
+Author: Alex Mestiashvili <alex at biotec.tu-dresden.de>
+--- tophat.orig/src/samtools-0.1.18/Makefile
++++ tophat/src/samtools-0.1.18/Makefile
+@@ -1,5 +1,7 @@
+ CC=			gcc
+-CFLAGS=		-g -Wall -O2 #-m64 #-arch ppc
++CFLAGS=         $(shell dpkg-buildflags --get CFLAGS)
++LDFLAGS=        $(shell dpkg-buildflags --get LDFLAGS)
++
+ DFLAGS=		-D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0
+ KNETFILE_O=	knetfile.o
+ LOBJS=		bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o	\
+@@ -41,7 +43,7 @@
+ 		$(AR) -csru $@ $(LOBJS)
+ 
+ samtools_0.1.18:lib-recur $(AOBJS)
+-		$(CC) $(CFLAGS) -o $@ $(AOBJS) -Lbcftools $(LIBPATH) libbam.a -lbcf -lm -lz #$(LIBCURSES)
++		$(CC) $(CFLAGS) -o $@ $(AOBJS) -Lbcftools $(LIBPATH) libbam.a -lbcf -lm -lz $(LDFLAGS) #$(LIBCURSES) 
+ 
+ razip:razip.o razf.o $(KNETFILE_O)
+ 		$(CC) $(CFLAGS) -o $@ razf.o razip.o $(KNETFILE_O) -lz
diff --git a/debian/patches/series b/debian/patches/series
index d51df39..394aed0 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,4 @@
 fix_build_w_seqan1.4.patch
 fix_includes_path.patch
 bashism_in_shell_script.patch
+hardening4samtols.patch

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/tophat.git