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/*
Ray
Copyright (C) 2010, 2011, 2012 Sébastien Boisvert
http://DeNovoAssembler.SourceForge.Net/
This program 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, version 3 of the License.
This program 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 have received a copy of the GNU General Public License
along with this program (gpl-3.0.txt).
see <http://www.gnu.org/licenses/>
*/
#ifndef _CoverageDistribution
#define _CoverageDistribution
#include <code/Mock/constants.h>
#include <RayPlatform/core/types.h>
#include <map>
#include <string>
#include <vector>
#include <stdint.h>
using namespace std;
/*
*
* Given a distribution of coverage, CoverageDistribution computes
* the minimum coverage, and the peak coverage.
* \author Sébastien Boisvert
*/
class CoverageDistribution{
int m_minimumCoverage;
int m_peakCoverage;
int m_repeatCoverage;
void findPeak(vector<int>*x,vector<LargeCount>*y,vector<LargeCount>*rawValues);
vector<uint64_t> smoothData(vector<uint64_t>*a);
public:
CoverageDistribution(map<CoverageDepth,LargeCount>*distributionOfCoverage,string*file);
int getMinimumCoverage();
int getPeakCoverage();
int getRepeatCoverage();
};
#endif
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