#include "variance/SampleStats.hh"
/**
 * Project     : CASAVA
 * Module      : $RCSfile: SampleStats.cpp,v $
 * @author     : Tony Cox
 * Copyright   : Copyright (c) Illumina 2008, 2009. All rights reserved.
 *
 ** 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).
 *
 */


namespace ca {
namespace variance_detection {



void SampleStats::print(void) const {
	printf("# Quality stats:\n# ");
	qualStats_[0].print();
	printf("# ");
	qualStats_[1].print();
	printf("# Score stats:\n# ");
	scoreStats_[0].print();
	printf("# ");
	scoreStats_[1].print();
	printf("# Offset stats:\n# ");
	offsetStats_.print();
	printf("# Spanning reads stats:\n# ");
	spanReadStats_[0].print();
	printf("# ");
	spanReadStats_[1].print();
} // ~print

void SampleStats::setThresholds(int numStandardDevs) {
	for (int i(0); i<2; i++) {
		qualThreshold_[i] =(int)(qualStats_[i].getMean()-(1.5
				*qualStats_[i].getStandardDeviation()));
		scoreThreshold_[i] =(int)(scoreStats_[i].getMean()-(1.5
				*scoreStats_[i].getStandardDeviation()));
		//		printf("# Read %d: min qual=%d, min score=%d\n", i+1,
		//	qualThreshold_[i], scoreThreshold_[i]);
	} // ~for

	minOffset_ = ((int)(offsetStats_.getMean() -(numStandardDevs
			*offsetStats_.getStandardDeviation())));
	maxOffset_ = ((int)(offsetStats_.getMean() +(numStandardDevs
			*offsetStats_.getStandardDeviation())));
	//	printf("# Offset min=%d max=%d\n", minOffset_, maxOffset_);
} // ~setThresholds

void SampleStats::printOffsetStats(void) const
{
  printf ("# offset min=%d max=%d mean=%f sd=%f se=%f\n",
	  minOffset_,
	  maxOffset_,
	  offsetStats_.getMean(),
	  offsetStats_.getStandardDeviation(),
	  offsetStats_.getStandardError());
}

}
} // end namespace casava{ namespace { applications