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VCFTester.h
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VCFTester.h
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///----------------------------------------------
// Copyright 2011 Wellcome Trust Sanger Institute
// Written by Jared Simpson (js18@sanger.ac.uk)
// Released under the GPL
//-----------------------------------------------
//
// VCFTester - Run dindel on each variant in a vcf file
//
#ifndef VCFTESTER_H
#define VCFTESTER_H
#include <list>
#include <stack>
#include <queue>
#include "GraphCompare.h"
#include "DindelRealignWindow.h"
#include "DindelUtil.h"
//
//
//
class VCFTester
{
public:
//
// Functions
//
VCFTester(const GraphCompareParameters& params);
~VCFTester();
// Process a read and all its kmers
void process(const VCFFile::VCFEntry& record);
private:
// Functions
std::string applyVariant(const std::string& in, int pos,
const std::string& ref, const std::string& alt);
//
// Data
//
GraphCompareParameters m_parameters;
GraphCompare m_graphComparer;
int m_returnCodes[DRC_NUM_CODES];
// Output file
VCFFile m_baseVCFFile;
VCFFile m_variantVCFFile;
VCFFile m_callsVCFFile;
};
#endif