/**
 ** Copyright (c) 2007-2010 Illumina, Inc.
 **
 ** This software is covered by the "Illumina Genome Analyzer Software
 ** License Agreement" and the "Illumina Source Code License Agreement",
 ** and certain third party copyright/licenses, and any user of this
 ** source file is bound by the terms therein (see accompanying files
 ** Illumina_Genome_Analyzer_Software_License_Agreement.pdf and
 ** Illumina_Source_Code_License_Agreement.pdf and third party
 ** copyright/license notices).
 **
 ** This file is part of the Consensus Assessment of Sequence And VAriation
 ** (CASAVA) software package.
 **
 **/

#ifndef INDELREADSSTATS_H
#define INDELREADSSTATS_H

#include <iostream>
#include <sstream>
#include <fstream>
#include <cstdio>
#include <cassert>
#include <cstdlib>
#include <vector>
#include <cmath>
#include <string>
#include <map>

#include "variance/export.h"

using namespace std;

// Stats file format
const unsigned int STAT_MACHINE_NAME_IDX   = 0;
const unsigned int STAT_RUN_NUM_IDX        = 1;
const unsigned int STAT_LANE_NUM_IDX       = 2;
const unsigned int STAT_INS_SIZE_MEAN_IDX  = 3;
const unsigned int STAT_INS_SIZE_SD_IDX    = 4;

class IndelReadsStats
{
 public:
  IndelReadsStats() {}
  ~IndelReadsStats() {}

  /*
  const string getMachineName() const {
    return(this->machineName);
  }
  */

  //
  // Access functions
  //

  double getMeanInsSize(string m, int r, int l);
  double getSdInsSize(string m, int r, int l);
  string toString();

  //
  // Manipuation fucntions
  //
  void load(string file);

  // Auxillary functions (static)

 private:
  map<string, string> machineNames;
  map<string, int>    runNums;
  map<string, int>    laneNums;

  map<string, double> meanInsSize;
  map<string, double> sdInsSize;

  vector<string> keys;

  //vector<string> machineNames;
  //vector<int>    runNums;
  //vector<int>    laneNums;
  //vector<double> meanInsSize;
  //vector<double> sdInsSize;
};

#endif

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