[bwa] Add patch to fix build on i386 by disabling SSE2

[verdurin]

commit 99585d0f7326adbf6d7f61da0ac914ce7264c91d
Author: Adam Huffman <bloch at verdurin.com>
Date:   Sun May 13 21:15:01 2012 +0100

    Add patch to fix build on i386 by disabling SSE2

 bwa-nosse2-i386.patch |   11 +++++++++++
 bwa.spec              |    9 ++++++++-
 2 files changed, 19 insertions(+), 1 deletions(-)
---
diff --git a/bwa-nosse2-i386.patch b/bwa-nosse2-i386.patch
new file mode 100644
index 0000000..b9b9ea5
--- /dev/null
+++ b/bwa-nosse2-i386.patch
@@ -0,0 +1,11 @@
+--- bwa-0.6.1/Makefile	2011-11-28 14:55:02.000000000 +0000
++++ bwa-0.6.1.new/Makefile	2012-05-13 20:52:46.889400339 +0100
+@@ -2,7 +2,7 @@
+ CXX=		g++
+ CFLAGS=		-g -Wall -O2
+ CXXFLAGS=	$(CFLAGS)
+-DFLAGS=		-DHAVE_PTHREAD #-D_NO_SSE2 #-D_FILE_OFFSET_BITS=64
++DFLAGS=		-DHAVE_PTHREAD -D_NO_SSE2 #-D_FILE_OFFSET_BITS=64
+ OBJS=		QSufSort.o bwt_gen.o utils.o bwt.o bwtio.o bwtaln.o bwtgap.o \
+ 			is.o bntseq.o bwtmisc.o bwtindex.o ksw.o stdaln.o simple_dp.o \
+ 			bwaseqio.o bwase.o bwape.o kstring.o cs2nt.o \
diff --git a/bwa.spec b/bwa.spec
index 7d2baf7..d32710b 100644
--- a/bwa.spec
+++ b/bwa.spec
@@ -1,6 +1,6 @@
 Name:           bwa
 Version:        0.6.1
-Release:        1%{?dist}
+Release:        2%{?dist}
 Summary:        Burrows-Wheeler Alignment tool
 
 Group:          Applications/Engineering
@@ -18,6 +18,10 @@ reference genome (e.g. human genome). It has two major components, one
 for read shorter than 150bp and the other for longer reads.
 
 %prep
+#Avoid SSE2 on i386
+%ifarch i386
+patch -p1 -b .bwa-nosse-i386.patch bwa-nosse-i386.patch 
+%endif
 %setup -q
 
 
@@ -50,6 +54,9 @@ rm -rf %{buildroot}
 
 
 %changelog
+* Sun May 13 2012 Adam Huffman <verdurin at fedoraproject.org> - 0.6.1-2
+- add patch to avoid SSE2 on i386
+
 * Wed Jan 11 2012 Adam Huffman <verdurin at fedoraproject.org> - 0.6.1-1
 - update to 0.6.1