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# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=5
inherit toolchain-funcs
DESCRIPTION="Bisulfite-aware short read mapper, FM-index, no InDel support"
HOMEPAGE="http://compbio.cs.ucr.edu/brat/"
SRC_URI="http://compbio.cs.ucr.edu/brat/downloads/${P}.tar.gz"
LICENSE="GPL-3"
SLOT="0"
IUSE=""
KEYWORDS="~amd64 ~x86"
DEPEND=""
RDEPEND="!sci-biology/brat"
src_prepare() {
sed \
-e "s:-Wl,-O1 : :g" \
-e "s:g++:$(tc-getCXX):g" \
-e "s:-O3:${CFLAGS} ${LDFLAGS}:g" \
-e "s:-w:-Wall:g" \
-i Makefile || die
}
src_install() {
dobin brat_bw build_bw trim acgt-count remove-dupl convert_to_sam
# possible FILLE_COLLISION with sci-biology/brat (probably some binaries just do the same)
# dobin ${PN} ${PN}-large trim acgt-count ${PN}-large-build rev-compl check-strands remove-dupl convert-to-sam
dodoc README
newdoc {'User Manual BRAT_2_0_1.pdf','User_Manual_BRAT_2_0_1.pdf'}
}
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