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/*++
Module Name:
AlignerStats.cpp
Abstract:
Common statistics for running single & paired alignment.
Authors:
Ravi Pandya, May, 2012
Environment:
User mode service.
Revision History:
Integrated from SingleAligner.cpp & PairedAligner.cpp
--*/
#include "stdafx.h"
#include "options.h"
#include "AlignerStats.h"
AbstractStats::~AbstractStats()
{}
AlignerStats::AlignerStats(AbstractStats* i_extra)
:
totalReads(0),
uselessReads(0),
singleHits(0),
multiHits(0),
notFound(0),
alignedAsPairs(0),
extra(i_extra),
lvCalls(0),
millisReading(0),
millisAligning(0),
millisWriting(0),
filtered(0),
extraAlignments(0),
sameComplement(0),
agForcedSingleEndAlignment(0),
agUsedSingleEndAlignment(0)
{
for (int i = 0; i <= AlignerStats::maxMapq; i++) {
mapqHistogram[i] = 0;
}
for (int i = 0; i < maxMaxHits; i++) {
countOfBestHitsByWeightDepth[i] = 0;
countOfAllHitsByWeightDepth[i] = 0;
probabilityMassByWeightDepth[i] = 0;
}
#if TIME_HISTOGRAM
countOfUnaligned = 0;
timeOfUnaligned = 0;
backwardsTimeStamps = 0;
totalBackwardsTimeStamps = 0;
for (unsigned i = 0; i < 31; i++) {
countByTimeBucket[i] = nanosByTimeBucket[i] = countByNM[i] = timeByNM[i] = 0;
}
for (unsigned i = 0; i <= 70; i++) {
countByMAPQ[i] = timeByMAPQ[i] = 0;
}
#endif // TIME_HISTOGRAM
}
AlignerStats::~AlignerStats()
{
if (extra != NULL) {
delete extra;
}
}
void
AlignerStats::printHistograms(
FILE* out)
{
// nothing
if (extra != NULL) {
extra->printHistograms(out);
}
}
void
AlignerStats::add(
const AbstractStats* i_other)
{
AlignerStats* other = (AlignerStats*) i_other;
totalReads += other->totalReads;
uselessReads += other->uselessReads;
singleHits += other->singleHits;
multiHits += other->multiHits;
notFound += other->notFound;
alignedAsPairs += other->alignedAsPairs;
lvCalls += other->lvCalls;
millisReading += other->millisReading;
millisAligning += other->millisAligning;
millisWriting += other->millisWriting;
filtered += other->filtered;
extraAlignments += other->extraAlignments;
sameComplement += other->sameComplement;
agForcedSingleEndAlignment += other->agForcedSingleEndAlignment;
agUsedSingleEndAlignment += other->agUsedSingleEndAlignment;
if (extra != NULL && other->extra != NULL) {
extra->add(other->extra);
}
for (int i = 0; i <= AlignerStats::maxMapq; i++) {
mapqHistogram[i] += other->mapqHistogram[i];
}
for (int i = 0; i < maxMaxHits; i++) {
countOfBestHitsByWeightDepth[i] += other->countOfBestHitsByWeightDepth[i];
countOfAllHitsByWeightDepth[i] += other->countOfAllHitsByWeightDepth[i];
probabilityMassByWeightDepth[i] = other->probabilityMassByWeightDepth[i];
}
#if TIME_HISTOGRAM
countOfUnaligned += other->countOfUnaligned;
timeOfUnaligned += other->timeOfUnaligned;
backwardsTimeStamps += other->backwardsTimeStamps;
totalBackwardsTimeStamps += other->totalBackwardsTimeStamps;
for (unsigned i = 0; i < 31; i++) {
countByTimeBucket[i] += other->countByTimeBucket[i];
nanosByTimeBucket[i] += other->nanosByTimeBucket[i];
countByNM[i] += other->countByNM[i];
timeByNM[i] += other->timeByNM[i];
}
for (unsigned i = 0; i < 71; i++) {
countByMAPQ[i] += other->countByMAPQ[i];
timeByMAPQ[i] += other->timeByMAPQ[i];
}
#endif // TIME_HISTOGRAM
}
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