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polyscan.h
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polyscan.h
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/*
* polyscan.h for MSIsensor
* Copyright (c) 2013 Beifang Niu && Kai Ye WUGSC All Rights Reserved.
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
#ifndef _POLYSCAN_H_
#define _POLYSCAN_H_
#include <map>
#include <vector>
#include <string>
#include <iostream>
#include <fstream>
#include <algorithm>
#include "param.h"
#include "structs.h"
#include "homo.h"
#include "window.h"
#include "sample.h"
class PolyScan
{
public:
PolyScan();
~PolyScan();
// user defined region
UserDefinedRegion region_one;
bool ifUserDefinedRegion;
void eliminate(const char ch, std::string & str);
bool ParseOneRegion(const std::string ®ion);
// read bed regions
bool ifUserDefinedBed;
std::map<std::string, bit16_t> chrMaptoIndex;
std::vector< BedChr > beds;
void LoadBeds(std::ifstream &fin);
void BedFilterorNot();
// load bam list file
std::vector< BamPairs > totalBamPairs;
std::vector< BamTumors > totalBamTumors;
//void LoadBams(std::ifstream &fin);
void LoadBams(const std::string &nBam, const std::string &tBam);
void LoadBam(const std::string &tBam);
unsigned int totalBamPairsNum;
unsigned int totalBamTumorsNum;
// load homos and microsatellites
unsigned long totalHomosites;
//std::vector< HomoSite * > totalSites;
std::vector< HomoSite > totalSites;
bool LoadHomosAndMicrosates(std::ifstream &fin);
void TestHomos();
std::vector< HomoSite > homosBuffer;
// windows
std::vector< Window > totalWindows;
void SplitWindows();
void TestWindows();
unsigned long totalWindowsNum;
// distribution
void InithializeDistributions();
void outputDistributions();
void releaseDistributions();
void GetHomoDistribution( Sample &oneSample, const std::string &prefix );
void GetHomoTumorDistribution( Sample &oneSample, const std::string &prefix );
protected:
// xxxxxx
// xxxx
};
#endif //_POLYSCAN_H_