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/* Copyright (C) 2013 Ion Torrent Systems, Inc. All Rights Reserved */
//! @file SampleManager.h
//! @ingroup VariantCaller
//! @brief Manages sample and read group names
#ifndef SAMPLEMANAGER_H
#define SAMPLEMANAGER_H
#include <map>
#include <vector>
#include <string>
#include "api/SamHeader.h"
#include "api/BamAlignment.h"
using namespace std;
using namespace BamTools;
class SampleManager {
public:
SampleManager() : num_samples_(0), primary_sample_(0) {}
~SampleManager() {}
void Initialize (const SamHeader& bam_header, string& sample_name, const string& force_sample_name);
bool IdentifySample(const BamAlignment& alignment, int& sample_index, bool& primary_sample) const;
int num_samples_;
vector<string> sample_names_;
map<string,int> read_group_to_sample_idx_;
int primary_sample_;
};
#endif //SAMPLEMANAGER_H
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