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GraphAlignmentOperations.hh
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GraphAlignmentOperations.hh
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//
// Expansion Hunter
// Copyright (c) 2018 Illumina, Inc.
//
// Author: Egor Dolzhenko <edolzhenko@illumina.com>
//
// 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/>.
//
#pragma once
#include "graphalign/GraphAlignment.hh"
#include "graphalign/LinearAlignmentParameters.hh"
namespace ehunter
{
/**
* Adds softclips to the ends of the alignment
*
* @param alignment: any alignment
* @param leftSoftclipLen: length of the left softclip to add
* @param rightSoftclipLen: length of the right softclip to add
* @return extended alignment
*
* Example:
* GraphAlignment alignment = decodeGraphAlignment(1, "0[3M]1[3M]", &graph);
* GraphAlignment extendedAlignment = extendWithSoftclip(alignment, 5, 4);
* // extendedAlignment == decodeGraphAlignment(1, "0[5S3M]1[3M4S]", &graph);
*/
graphtools::GraphAlignment
extendWithSoftclip(const graphtools::GraphAlignment& alignment, int leftSoftclipLen, int rightSoftclipLen);
int getNumNonrepeatMatchesUpstream(graphtools::NodeId nodeId, graphtools::GraphAlignment alignment);
int getNumNonrepeatMatchesDownstream(graphtools::NodeId nodeId, graphtools::GraphAlignment alignment);
int scoreAlignmentToNonloopNodes(
graphtools::GraphAlignment alignment, LinearAlignmentParameters parameters = LinearAlignmentParameters());
int countFullOverlaps(graphtools::NodeId nodeId, graphtools::GraphAlignment alignment);
graphtools::GraphAlignment computeCanonicalAlignment(const std::list<graphtools::GraphAlignment>& alignments);
}