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/*
* Copyright (C) 2010 Regents of the University of Michigan
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
#include "SamStatistics.h"
#include <iomanip>
#include "SamFlag.h"
SamStatistics::SamStatistics()
{
reset();
}
SamStatistics::~SamStatistics()
{
reset();
}
void SamStatistics::reset()
{
myReadCount = 0;
myMappedReadCount = 0;
myPairedReadCount = 0;
myProperPairedReadCount = 0;
myBaseCount = 0;
myMappedReadBases = 0;
myDupReadCount = 0;
myQCFailureReadCount = 0;
}
bool SamStatistics::updateStatistics(SamRecord& samRecord)
{
// Each record has one read, so update the read count.
++myReadCount;
int32_t readLen = samRecord.getReadLength();
// Get the flag to determine the type or
// read (mapped, paired, proper paired).
uint16_t flag = samRecord.getFlag();
// If the read is mapped, update the mapped c
if(SamFlag::isMapped(flag))
{
++myMappedReadCount;
myMappedReadBases += readLen;
}
if(SamFlag::isPaired(flag))
{
++myPairedReadCount;
if(SamFlag::isProperPair(flag))
{
++myProperPairedReadCount;
}
}
if(SamFlag::isDuplicate(flag))
{
++myDupReadCount;
}
if(SamFlag::isQCFailure(flag))
{
++myQCFailureReadCount;
}
// Increment the total number of bases.
myBaseCount += readLen;
return(true);
}
void SamStatistics::print()
{
double DIVIDE_UNITS = 1000000;
std::string units = "(e6)";
std::cerr << std::fixed << std::setprecision(2);
// If total reads is less than DIVIDE_UNITS, just show the straight number.
if(myReadCount < DIVIDE_UNITS)
{
DIVIDE_UNITS = 1;
units.clear();
}
// Read Counts
std::cerr << "TotalReads" << units << "\t"
<< myReadCount/DIVIDE_UNITS << std::endl;
std::cerr << "MappedReads" << units << "\t"
<< myMappedReadCount/DIVIDE_UNITS << std::endl;
std::cerr << "PairedReads" << units << "\t"
<< myPairedReadCount/DIVIDE_UNITS << std::endl;
std::cerr << "ProperPair" << units << "\t"
<< myProperPairedReadCount/DIVIDE_UNITS << std::endl;
std::cerr << "DuplicateReads" << units << "\t"
<< myDupReadCount/DIVIDE_UNITS << std::endl;
std::cerr << "QCFailureReads" << units << "\t"
<< myQCFailureReadCount/DIVIDE_UNITS << std::endl;
std::cerr << std::endl;
// Read Percentages
std::cerr << "MappingRate(%)\t"
<< 100 * myMappedReadCount/(double)myReadCount << std::endl;
std::cerr << "PairedReads(%)\t"
<< 100 * myPairedReadCount/(double)myReadCount << std::endl;
std::cerr << "ProperPair(%)\t"
<< 100 * myProperPairedReadCount/(double)myReadCount << std::endl;
std::cerr << "DupRate(%)\t"
<< 100 * myDupReadCount/(double)myReadCount << std::endl;
std::cerr << "QCFailRate(%)\t"
<< 100 * myQCFailureReadCount/(double)myReadCount << std::endl;
std::cerr << std::endl;
// Base Counts
std::cerr << "TotalBases" << units << "\t"
<< myBaseCount/DIVIDE_UNITS << std::endl;
std::cerr << "BasesInMappedReads" << units << "\t"
<< myMappedReadBases/DIVIDE_UNITS << std::endl;
}
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