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# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
EAPI=5
MODULE_AUTHOR=LDS
MODULE_VERSION=1.41
inherit perl-module toolchain-funcs
DESCRIPTION="Read SAM/BAM database files"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE=""
RDEPEND="
>=sci-biology/bioperl-1.6.9
>=sci-biology/samtools-1
"
DEPEND="${RDEPEND}
virtual/perl-ExtUtils-CBuilder
>=dev-perl/Module-Build-0.420.0
"
SRC_TEST=skip
# cannot load its own library, fundamentally b0rken
PATCHES=(
"${FILESDIR}"/${PN}-1.390.0-samtools-1.patch
)
src_prepare() {
find . -type f -exec chmod +w '{}' + || die
sed \
-e 's|my $HeaderFile = "bam.h";|my $HeaderFile = "bam/bam.h";|' \
-e 's|my $LibFile = "libbam.a";|my $LibFile = "libbam.so";|' \
-i Build.PL || die
sed \
-e 's|#include "bam.h"|#include "bam/bam.h"|' \
-e 's|#include "sam.h"|#include "bam/sam.h"|' \
-e 's|#include "khash.h"|#include "htslib/khash.h"|' \
-e 's|#include "faidx.h"|#include "htslib/faidx.h"|' \
-i lib/Bio/DB/Sam.xs c_bin/bam2bedgraph.c || die
perl-module_src_prepare
tc-export CC
}
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