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/*
* Copyright (C) 2009-2012 Simon A. Berger
*
* This file is part of papara.
*
* papara 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.
*
* papara 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 papara. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef __align_utils_h__
#define __align_utils_h__
#include <vector>
#include <stdint.h>
namespace align_utils {
void trace_to_position_map( const std::vector< uint8_t >& gaps, std::vector< int > *map);
uint8_t decode_dna( int s );
void realize_trace( const std::vector<uint8_t> &seq, const std::vector<uint8_t> &tb, std::vector<uint8_t> *out );
}
#endif
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