[med-svn] [SCM] bowtie2 branch, master, updated. upstream/2.0.6-59-g3df4b1c

[Alexandre Mestiashvili]

The following commit has been merged in the master branch:
commit 3df4b1c236e64261cb5b592b3555ebb70cb3e657
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Wed Feb 27 16:19:57 2013 +0100

    refreshed patches

diff --git a/debian/changelog b/debian/changelog
index 4de8c3c..65ad59c 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -4,6 +4,7 @@ bowtie2 (2.1.0-1) UNRELEASED; urgency=low
     Closes: #701686
     - d/rules: use help2man-wrapper instead of help2man to generate man pages
   * Imported Upstream version 2.1.0
+  * refreshed patches
 
  -- Alexandre Mestiashvili <alex at biotec.tu-dresden.de>  Wed, 27 Feb 2013 15:58:40 +0100
 
diff --git a/debian/patches/fix_makefile_machine_detection.patch b/debian/patches/fix_makefile_machine_detection.patch
index a527eae..3e5ace0 100644
--- a/debian/patches/fix_makefile_machine_detection.patch
+++ b/debian/patches/fix_makefile_machine_detection.patch
@@ -1,24 +1,24 @@
-Subject: Attemp to adapt build flags to built package on all supported 
- architectures.
-Origin: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Date: 2012-05-09
 --- bowtie2.orig/Makefile
 +++ bowtie2/Makefile
-@@ -108,20 +108,29 @@
+@@ -117,27 +117,29 @@
+ SEARCH_FRAGMENTS = $(wildcard search_*_phase*.c)
  VERSION = $(shell cat VERSION)
- EXTRA_FLAGS =
  
 -# Convert BITS=?? to a -m flag
 -BITS=32
 -ifeq (x86_64,$(shell uname -m))
 -BITS=64
 -endif
+-# msys will always be 32 bit so look at the cpu arch instead.
+-ifneq (,$(findstring AMD64,$(PROCESSOR_ARCHITEW6432)))
+-	ifeq (1,$(MINGW))
+-		BITS=64
+-	endif
+-endif
 -BITS_FLAG =
+-
 -ifeq (32,$(BITS))
--BITS_FLAG = -m32
--endif
--ifeq (64,$(BITS))
--BITS_FLAG = -m64
+-	BITS_FLAG = -m32
 -endif
 +ifeq (1,$(ENABLE_SSE))
 + ARCH := $(shell getconf LONG_BIT)
@@ -27,23 +27,25 @@ Date: 2012-05-09
 + BITS=32
 + BITS_FLAG = -m32
 + ifeq (64,$(ARCH))
-+	BITS=64
-+	BITS_FLAG = -m64
++       BITS=64
++       BITS_FLAG = -m64
 + endif
 + ifeq ($(UNAME),'Power Macintosh')
-+	ifeq (32,$(BITS))
-+		BITS_FLAG = -m32
-+		SSE_FLAG = 
-+	endif
-+	ifeq (64,$(BITS))
-+		BITS_FLAG = -m64
-+		SSE_FLAG =
-+	endif
++       ifeq (32,$(BITS))
++               BITS_FLAG = -m32
++               SSE_FLAG =
++       endif
++       ifeq (64,$(BITS))
++               BITS_FLAG = -m64
++               SSE_FLAG =
++       endif
 + endif
  
+-ifeq (64,$(BITS))
+-	BITS_FLAG = -m64
++ SSE_FLAG=-msse2
+ endif
 -SSE_FLAG=-msse2
-+ SSE_FLAG = -msse2
-+endif
  
  DEBUG_FLAGS    = -O0 -g3 $(BITS_FLAG) $(SSE_FLAG)
  DEBUG_DEFS     = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS)\""
diff --git a/debian/patches/hardening.patch b/debian/patches/hardening.patch
index 8e1a8b9..51f4b03 100644
--- a/debian/patches/hardening.patch
+++ b/debian/patches/hardening.patch
@@ -2,8 +2,8 @@ Subject: Patch injects hardening CPPFLAGS
 Origin: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 --- bowtie2.orig/Makefile
 +++ bowtie2/Makefile
-@@ -189,7 +189,8 @@
-      $(PTHREAD_DEF) \
+@@ -204,7 +204,8 @@
+      $(FILE_FLAGS) \
       $(PREF_DEF) \
       $(MM_DEF) \
 -     $(SHMEM_DEF)

-- 
ultrafast memory-efficient short read aligner