// -*- mode: c++; indent-tabs-mode: nil; -*-
//
// Manta - Structural Variant and Indel Caller
// Copyright (c) 2013-2016 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/>.
//
//

///
/// \author Chris Saunders
///

#include "manta/JunctionIdGenerator.hh"



void
JunctionIdGenerator::
getId(
    const EdgeInfo& edge,
    const SVCandidate& sv,
    const bool isRNA,
    SVId& svId)
{
    using namespace EXTENDED_SV_TYPE;

    svId.svType=(getExtendedSVType(sv, isRNA));

    svId.localId = str(_SVIdFormatter % label(svId.svType) % edge.locusIndex % edge.nodeIndex1 % edge.nodeIndex2
                       % sv.candidateIndex %  sv.assemblyAlignIndex % sv.assemblySegmentIndex );

    if      (isSVTransloc(svId.svType))
    {
        svId.mateId = svId.localId + ":1";
        svId.localId = svId.localId + ":0";
    }
    else
    {
        svId.mateId.clear();
    }
}
