# Description: Burrows-Wheeler Aligner
# URL: http://bio-bwa.sourceforge.net/
# Maintainer: Petar Petrov, slackalaxy at gmail dot com
# Depends on:

name=bwa
version=0.7.17
release=2
source=(https://sourceforge.net/projects/bio-bwa/files/$name-$version.tar.bz2)

build() {
	cd $name-$version
	
	# Use our CFLAGS/CXXFLAGS
	sed -i "/^C.*.*FLAGS/s/=/+=/" Makefile

	# Thanks to Willy for the -msse2 fix!
	CFLAGS="$CFLAGS -msse2 -fcommon" \
	CXXFLAGS="$CXXFLAGS" \
	make

	install -D -m755 $name $PKG/usr/bin/$name
	install -D -m644 $name.1 $PKG/usr/share/man/man1/$name.1

	mkdir -p $PKG/usr/share/$name
	cp -a qualfa2fq.pl xa2multi.pl $PKG/usr/share/$name
}