QC.h

//
// QC.h
//
// Header file for QC.cpp
//
//
// Author: Iain Bancarz <ib5@sanger.ac.uk>
//
// Redistribution and use in source and binary forms, with or without 
// modification, are permitted provided that the following conditions are met:
// 1. Redistributions of source code must retain the above copyright notice, 
// this list of conditions and the following disclaimer.
// 2. Redistributions in binary form must reproduce the above copyright 
// notice, this list of conditions and the following disclaimer in the 
// documentation and/or other materials provided with the distribution.
// 3. Neither the name of Genome Research Ltd nor the names of the 
// contributors may be used to endorse or promote products derived from 
// software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR 
// IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES 
// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. 
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// BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF 
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//

#ifndef _QC_H
#define _QC_H

#include <ctime>
#include <iostream>
#include <stdlib.h>  

#include "Sim.h"

using namespace std;

class QC {
 public:  
  static const int VERBOSE_FREQ = 1000; // frequency of verbose output
  static const int TIME_BUFFER = 100; // max size in bytes of timestamp string
  static const bool CLEANUP = true; // reset all Nan/infinity inputs to zero

  QC(string simPath, bool verbose);
  void close(void);
  void writeMagnitude(string outPath, bool verbose);
  void writeXydiff(string outPath, bool verbose);

 private:
  Sim *qcsim;
  uint16_t *intensity_int_array;
  float *intensity_float_array;

  void getNextMagnitudes(float magnitudes[], char* sampleName, Sim *sim);
  void magnitudeByProbe(float magByProbe[], bool verbose);
  void magnitudeBySample(float magBySample[], float magByProbe[], 
			 char sampleNames[][Sim::SAMPLE_NAME_SIZE+1],
			 bool verbose);
  void xydiffBySample(float xydBySample[], 
		      char sampleNames[][Sim::SAMPLE_NAME_SIZE+1]);
  void timeText(char *buffer);

};

#endif	// _QC_H