seq_util_test.cpp

//
// Strelka - Small Variant Caller
// Copyright (c) 2009-2018 Illumina, Inc.
//
// This program is free software: you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Software Foundation, either version 3 of the License, or
// at your option) any later version.
//
// This program is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
// GNU General Public License for more details.
//
// You should have received a copy of the GNU General Public License
// along with this program.  If not, see <http://www.gnu.org/licenses/>.
//
//


#include "boost/test/unit_test.hpp"

#include "blt_util/seq_util.hh"


BOOST_AUTO_TEST_SUITE( test_seq_util )


BOOST_AUTO_TEST_CASE( test_seq_repeat )
{
    std::string ru;
    unsigned count;

    static const std::string test0="";
    get_seq_repeat_unit(test0,ru,count);
    BOOST_REQUIRE_EQUAL(ru, "");
    BOOST_REQUIRE_EQUAL(count, 1u);

    static const std::string test1="AAAA";
    get_seq_repeat_unit(test1,ru,count);
    BOOST_REQUIRE_EQUAL(ru, "A");
    BOOST_REQUIRE_EQUAL(count, 4u);

    static const std::string test2="ACAC";
    get_seq_repeat_unit(test2,ru,count);
    BOOST_REQUIRE_EQUAL(ru, "AC");
    BOOST_REQUIRE_EQUAL(count, 2u);

    static const std::string test3="TACAC";
    get_seq_repeat_unit(test3,ru,count);
    BOOST_REQUIRE_EQUAL(ru, "TACAC");
    BOOST_REQUIRE_EQUAL(count, 1u);

    get_vcf_seq_repeat_unit(test3,ru,count);
    BOOST_REQUIRE_EQUAL(ru, "AC");
    BOOST_REQUIRE_EQUAL(count, 2u);
}


BOOST_AUTO_TEST_SUITE_END()