//
// 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 .
//
#ifndef __PAIRED_ALIGNMENT_FORMATTER_HPP__
#define __PAIRED_ALIGNMENT_FORMATTER_HPP__
//#include "RapMapUtils.hpp"
#include "Util.hpp"
template
struct PairedAlignmentFormatter {
PairedAlignmentFormatter(IndexPtrT indexIn) : index(indexIn),
read1Temp(1000, 'A'),
qual1Temp(1000, '~'),
read2Temp(1000, 'A'),
qual2Temp(1000, '~'),
cigarStr1(buff1, 1000),
cigarStr2(buff2, 1000),
use_qualities(false) {
}
bool enable_qualities() {
bool prev = use_qualities;
use_qualities = true;
return prev;
}
bool disable_qualities() {
bool prev = use_qualities;
use_qualities = false;
return prev;
}
// Data members
IndexPtrT index;
std::string read1Temp;
std::string qual1Temp;
std::string read2Temp;
std::string qual2Temp;
char buff1[1000];
char buff2[1000];
pufferfish::util::FixedWriter cigarStr1;
pufferfish::util::FixedWriter cigarStr2;
bool use_qualities;
std::string empty_qual{"*"};
};
#endif //__PAIR_ALIGNMENT_FORMATTER_HPP__