# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)

from spack import *


class Biobambam2(AutotoolsPackage):
    """Tools for early stage alignment file processing"""

    homepage = "https://gitlab.com/german.tischler/biobambam2"
    url      = "https://gitlab.com/german.tischler/biobambam2/-/archive/2.0.177-release-20201112105453/biobambam2-2.0.177-release-20201112105453.tar.gz"

    version('2.0.177', sha256='ad0a418fb49a31996a105a1a275c0d1dfc8b84aa91d48fa1efb6ff4fe1e74181',
            url='https://gitlab.com/german.tischler/biobambam2/-/archive/2.0.177-release-20201112105453/biobambam2-2.0.177-release-20201112105453.tar.gz')

    depends_on('autoconf', type='build')
    depends_on('automake', type='build')
    depends_on('libtool',  type='build')
    depends_on('m4',       type='build')
    depends_on('libmaus2')

    test_src_dir = 'test'

    def configure_args(self):
        args = ['--with-libmaus2={0}'.format(self.spec['libmaus2'].prefix)]
        return args

    def _fix_shortsort(self):
        """Fix the testshortsort.sh file copied during installation."""
        test_dir = join_path(self.install_test_root, self.test_src_dir)
        filter_file('../src/', '', join_path(test_dir, 'testshortsort.sh'))

    @run_after('install')
    def cache_test_sources(self):
        """Copy the test source files after the package is installed to an
        install test subdirectory for use during `spack test run`."""
        self.cache_extra_test_sources(self.test_src_dir)
        self._fix_shortsort()

    def test(self):
        test_dir = join_path(self.install_test_root, self.test_src_dir)
        self.run_test('sh', ['testshortsort.sh'],
                      expected='Alignments sorted by coordinate.',
                      work_dir=test_dir)