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//
// RapMap - Rapid and accurate mapping of short reads to transcriptomes using
// quasi-mapping.
// Copyright (C) 2015, 2016 Rob Patro, Avi Srivastava, Hirak Sarkar
//
// This file is part of RapMap.
//
// RapMap 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.
//
// RapMap 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 RapMap. If not, see <http://www.gnu.org/licenses/>.
//
#ifndef __PAIR_ALIGNMENT_FORMATTER_HPP__
#define __PAIR_ALIGNMENT_FORMATTER_HPP__
#include "RapMapUtils.hpp"
template <typename IndexPtrT>
struct PairAlignmentFormatter {
PairAlignmentFormatter(IndexPtrT indexIn) : index(indexIn),
read1Temp(1000, 'A'),
qual1Temp(1000, '~'),
read2Temp(1000, 'A'),
qual2Temp(1000, '~'),
cigarStr1(buff1, 1000),
cigarStr2(buff2, 1000) {
}
// Data members
IndexPtrT index;
std::string read1Temp;
std::string qual1Temp;
std::string read2Temp;
std::string qual2Temp;
char buff1[1000];
char buff2[1000];
rapmap::utils::FixedWriter cigarStr1;
rapmap::utils::FixedWriter cigarStr2;
};
#endif //__PAIR_ALIGNMENT_FORMATTER_HPP__
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