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BatchData.h
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BatchData.h
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/*
This file is part of MMR, the Read Multi-Mapper Resolution tool.
MMR 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 software 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.
A copy of the GNU General Public License is distributed with
MMR (file LICENSE). If not, see <http://www.gnu.org/licenses/>.
Written 2010-2015 by
Andre Kahles <akahles@cbio.mskcc.org>
Jonas Behr <jonas_behr@web.de>
Gunnar R\"atsch <raetsch@cbio.mskcc.org>
This work was funded by the Max Planck Society,
the German Research Foundation (DFG RA1894/2-1)
and Memorial Sloan Kettering Cancer Center.
*/
#ifndef __BATCHDATA_H__
#define __BATCHDATA_H__
#include <vector>
#include <map>
#include <unordered_map>
#include <list>
#include "Utils.h"
#include "GeneralData.h"
#include "Alignment.h"
using namespace std;
class BatchData {
public:
// reads
unordered_map <string, vector<Alignment>, hash<string> > read_map_left;
unordered_map <string, vector<Alignment>, hash<string> > read_map_right;
// active sets
unordered_map <string, vector<vector<Alignment>::iterator>, hash<string> > active_left_pair;
unordered_map <string, vector<vector<Alignment>::iterator>, hash<string> > active_right_pair;
list<unordered_map <string, vector<Alignment> >::iterator > active_left_single;
list<unordered_map <string, vector<Alignment> >::iterator > active_right_single;
// constructor
BatchData() {};
// destructor
~BatchData() {};
void parse_file();
void pre_filter_alignment_maps();
double get_total_min_loss();
void get_active_read_set();
unsigned int smooth_coverage_map_single(unsigned int &num_ambiguous);
unsigned int smooth_coverage_map_paired(unsigned int &num_ambiguous);
private:
unsigned int smooth_coverage_map_single_wrapper(list<unordered_map <string, vector<Alignment> >::iterator > &active_reads, unsigned int &num_ambiguous);
};
#endif