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/*
* Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
* Bowtie 2 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.
*
* Bowtie 2 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 Bowtie 2. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef ALIGNER_METRICS_H_
#define ALIGNER_METRICS_H_
#include <math.h>
#include <iostream>
#include "alphabet.h"
#include "timer.h"
#include "sstring.h"
using namespace std;
/**
* Borrowed from http://www.johndcook.com/standard_deviation.html,
* which in turn is borrowed from Knuth.
*/
class RunningStat {
public:
RunningStat() : m_n(0), m_tot(0.0) { }
void clear() {
m_n = 0;
m_tot = 0.0;
}
void push(float x) {
m_n++;
m_tot += x;
// See Knuth TAOCP vol 2, 3rd edition, page 232
if (m_n == 1) {
m_oldM = m_newM = x;
m_oldS = 0.0;
} else {
m_newM = m_oldM + (x - m_oldM)/m_n;
m_newS = m_oldS + (x - m_oldM)*(x - m_newM);
// set up for next iteration
m_oldM = m_newM;
m_oldS = m_newS;
}
}
int num() const {
return m_n;
}
double tot() const {
return m_tot;
}
double mean() const {
return (m_n > 0) ? m_newM : 0.0;
}
double variance() const {
return ( (m_n > 1) ? m_newS/(m_n - 1) : 0.0 );
}
double stddev() const {
return sqrt(variance());
}
private:
int m_n;
double m_tot;
double m_oldM, m_newM, m_oldS, m_newS;
};
/**
* Encapsulates a set of metrics that we would like an aligner to keep
* track of, so that we can possibly use it to diagnose performance
* issues.
*/
class AlignerMetrics {
public:
AlignerMetrics() :
curBacktracks_(0),
curBwtOps_(0),
first_(true),
curIsLowEntropy_(false),
curIsHomoPoly_(false),
curHadRanges_(false),
curNumNs_(0),
reads_(0),
homoReads_(0),
lowEntReads_(0),
hiEntReads_(0),
alignedReads_(0),
unalignedReads_(0),
threeOrMoreNReads_(0),
lessThanThreeNRreads_(0),
bwtOpsPerRead_(),
backtracksPerRead_(),
bwtOpsPerHomoRead_(),
backtracksPerHomoRead_(),
bwtOpsPerLoEntRead_(),
backtracksPerLoEntRead_(),
bwtOpsPerHiEntRead_(),
backtracksPerHiEntRead_(),
bwtOpsPerAlignedRead_(),
backtracksPerAlignedRead_(),
bwtOpsPerUnalignedRead_(),
backtracksPerUnalignedRead_(),
bwtOpsPer0nRead_(),
backtracksPer0nRead_(),
bwtOpsPer1nRead_(),
backtracksPer1nRead_(),
bwtOpsPer2nRead_(),
backtracksPer2nRead_(),
bwtOpsPer3orMoreNRead_(),
backtracksPer3orMoreNRead_(),
timer_(cout, "", false)
{ }
void printSummary() {
if(!first_) {
finishRead();
}
cout << "AlignerMetrics:" << endl;
cout << " # Reads: " << reads_ << endl;
float hopct = (reads_ > 0) ? (((float)homoReads_)/((float)reads_)) : (0.0f);
hopct *= 100.0f;
cout << " % homo-polymeric: " << (hopct) << endl;
float lopct = (reads_ > 0) ? ((float)lowEntReads_/(float)(reads_)) : (0.0f);
lopct *= 100.0f;
cout << " % low-entropy: " << (lopct) << endl;
float unpct = (reads_ > 0) ? ((float)unalignedReads_/(float)(reads_)) : (0.0f);
unpct *= 100.0f;
cout << " % unaligned: " << (unpct) << endl;
float npct = (reads_ > 0) ? ((float)threeOrMoreNReads_/(float)(reads_)) : (0.0f);
npct *= 100.0f;
cout << " % with 3 or more Ns: " << (npct) << endl;
cout << endl;
cout << " Total BWT ops: avg: " << bwtOpsPerRead_.mean() << ", stddev: " << bwtOpsPerRead_.stddev() << endl;
cout << " Total Backtracks: avg: " << backtracksPerRead_.mean() << ", stddev: " << backtracksPerRead_.stddev() << endl;
time_t elapsed = timer_.elapsed();
cout << " BWT ops per second: " << (bwtOpsPerRead_.tot()/elapsed) << endl;
cout << " Backtracks per second: " << (backtracksPerRead_.tot()/elapsed) << endl;
cout << endl;
cout << " Homo-poly:" << endl;
cout << " BWT ops: avg: " << bwtOpsPerHomoRead_.mean() << ", stddev: " << bwtOpsPerHomoRead_.stddev() << endl;
cout << " Backtracks: avg: " << backtracksPerHomoRead_.mean() << ", stddev: " << backtracksPerHomoRead_.stddev() << endl;
cout << " Low-entropy:" << endl;
cout << " BWT ops: avg: " << bwtOpsPerLoEntRead_.mean() << ", stddev: " << bwtOpsPerLoEntRead_.stddev() << endl;
cout << " Backtracks: avg: " << backtracksPerLoEntRead_.mean() << ", stddev: " << backtracksPerLoEntRead_.stddev() << endl;
cout << " High-entropy:" << endl;
cout << " BWT ops: avg: " << bwtOpsPerHiEntRead_.mean() << ", stddev: " << bwtOpsPerHiEntRead_.stddev() << endl;
cout << " Backtracks: avg: " << backtracksPerHiEntRead_.mean() << ", stddev: " << backtracksPerHiEntRead_.stddev() << endl;
cout << endl;
cout << " Unaligned:" << endl;
cout << " BWT ops: avg: " << bwtOpsPerUnalignedRead_.mean() << ", stddev: " << bwtOpsPerUnalignedRead_.stddev() << endl;
cout << " Backtracks: avg: " << backtracksPerUnalignedRead_.mean() << ", stddev: " << backtracksPerUnalignedRead_.stddev() << endl;
cout << " Aligned:" << endl;
cout << " BWT ops: avg: " << bwtOpsPerAlignedRead_.mean() << ", stddev: " << bwtOpsPerAlignedRead_.stddev() << endl;
cout << " Backtracks: avg: " << backtracksPerAlignedRead_.mean() << ", stddev: " << backtracksPerAlignedRead_.stddev() << endl;
cout << endl;
cout << " 0 Ns:" << endl;
cout << " BWT ops: avg: " << bwtOpsPer0nRead_.mean() << ", stddev: " << bwtOpsPer0nRead_.stddev() << endl;
cout << " Backtracks: avg: " << backtracksPer0nRead_.mean() << ", stddev: " << backtracksPer0nRead_.stddev() << endl;
cout << " 1 N:" << endl;
cout << " BWT ops: avg: " << bwtOpsPer1nRead_.mean() << ", stddev: " << bwtOpsPer1nRead_.stddev() << endl;
cout << " Backtracks: avg: " << backtracksPer1nRead_.mean() << ", stddev: " << backtracksPer1nRead_.stddev() << endl;
cout << " 2 Ns:" << endl;
cout << " BWT ops: avg: " << bwtOpsPer2nRead_.mean() << ", stddev: " << bwtOpsPer2nRead_.stddev() << endl;
cout << " Backtracks: avg: " << backtracksPer2nRead_.mean() << ", stddev: " << backtracksPer2nRead_.stddev() << endl;
cout << " >2 Ns:" << endl;
cout << " BWT ops: avg: " << bwtOpsPer3orMoreNRead_.mean() << ", stddev: " << bwtOpsPer3orMoreNRead_.stddev() << endl;
cout << " Backtracks: avg: " << backtracksPer3orMoreNRead_.mean() << ", stddev: " << backtracksPer3orMoreNRead_.stddev() << endl;
cout << endl;
}
/**
*
*/
void nextRead(const BTDnaString& read) {
if(!first_) {
finishRead();
}
first_ = false;
//float ent = entropyDna5(read);
float ent = 0.0f;
curIsLowEntropy_ = (ent < 0.75f);
curIsHomoPoly_ = (ent < 0.001f);
curHadRanges_ = false;
curBwtOps_ = 0;
curBacktracks_ = 0;
// Count Ns
curNumNs_ = 0;
const size_t len = read.length();
for(size_t i = 0; i < len; i++) {
if((int)read[i] == 4) curNumNs_++;
}
}
/**
*
*/
void setReadHasRange() {
curHadRanges_ = true;
}
/**
* Commit the running statistics for this read to
*/
void finishRead() {
reads_++;
if(curIsHomoPoly_) homoReads_++;
else if(curIsLowEntropy_) lowEntReads_++;
else hiEntReads_++;
if(curHadRanges_) alignedReads_++;
else unalignedReads_++;
bwtOpsPerRead_.push((float)curBwtOps_);
backtracksPerRead_.push((float)curBacktracks_);
// Drill down by entropy
if(curIsHomoPoly_) {
bwtOpsPerHomoRead_.push((float)curBwtOps_);
backtracksPerHomoRead_.push((float)curBacktracks_);
} else if(curIsLowEntropy_) {
bwtOpsPerLoEntRead_.push((float)curBwtOps_);
backtracksPerLoEntRead_.push((float)curBacktracks_);
} else {
bwtOpsPerHiEntRead_.push((float)curBwtOps_);
backtracksPerHiEntRead_.push((float)curBacktracks_);
}
// Drill down by whether it aligned
if(curHadRanges_) {
bwtOpsPerAlignedRead_.push((float)curBwtOps_);
backtracksPerAlignedRead_.push((float)curBacktracks_);
} else {
bwtOpsPerUnalignedRead_.push((float)curBwtOps_);
backtracksPerUnalignedRead_.push((float)curBacktracks_);
}
if(curNumNs_ == 0) {
lessThanThreeNRreads_++;
bwtOpsPer0nRead_.push((float)curBwtOps_);
backtracksPer0nRead_.push((float)curBacktracks_);
} else if(curNumNs_ == 1) {
lessThanThreeNRreads_++;
bwtOpsPer1nRead_.push((float)curBwtOps_);
backtracksPer1nRead_.push((float)curBacktracks_);
} else if(curNumNs_ == 2) {
lessThanThreeNRreads_++;
bwtOpsPer2nRead_.push((float)curBwtOps_);
backtracksPer2nRead_.push((float)curBacktracks_);
} else {
threeOrMoreNReads_++;
bwtOpsPer3orMoreNRead_.push((float)curBwtOps_);
backtracksPer3orMoreNRead_.push((float)curBacktracks_);
}
}
// Running-total of the number of backtracks and BWT ops for the
// current read
uint32_t curBacktracks_;
uint32_t curBwtOps_;
protected:
bool first_;
// true iff the current read is low entropy
bool curIsLowEntropy_;
// true if current read is all 1 char (or very close)
bool curIsHomoPoly_;
// true iff the current read has had one or more ranges reported
bool curHadRanges_;
// number of Ns in current read
int curNumNs_;
// # reads
uint32_t reads_;
// # homo-poly reads
uint32_t homoReads_;
// # low-entropy reads
uint32_t lowEntReads_;
// # high-entropy reads
uint32_t hiEntReads_;
// # reads with alignments
uint32_t alignedReads_;
// # reads without alignments
uint32_t unalignedReads_;
// # reads with 3 or more Ns
uint32_t threeOrMoreNReads_;
// # reads with < 3 Ns
uint32_t lessThanThreeNRreads_;
// Distribution of BWT operations per read
RunningStat bwtOpsPerRead_;
RunningStat backtracksPerRead_;
// Distribution of BWT operations per homo-poly read
RunningStat bwtOpsPerHomoRead_;
RunningStat backtracksPerHomoRead_;
// Distribution of BWT operations per low-entropy read
RunningStat bwtOpsPerLoEntRead_;
RunningStat backtracksPerLoEntRead_;
// Distribution of BWT operations per high-entropy read
RunningStat bwtOpsPerHiEntRead_;
RunningStat backtracksPerHiEntRead_;
// Distribution of BWT operations per read that "aligned" (for
// which a range was arrived at - range may not have necessarily
// lead to an alignment)
RunningStat bwtOpsPerAlignedRead_;
RunningStat backtracksPerAlignedRead_;
// Distribution of BWT operations per read that didn't align
RunningStat bwtOpsPerUnalignedRead_;
RunningStat backtracksPerUnalignedRead_;
// Distribution of BWT operations/backtracks per read with no Ns
RunningStat bwtOpsPer0nRead_;
RunningStat backtracksPer0nRead_;
// Distribution of BWT operations/backtracks per read with one N
RunningStat bwtOpsPer1nRead_;
RunningStat backtracksPer1nRead_;
// Distribution of BWT operations/backtracks per read with two Ns
RunningStat bwtOpsPer2nRead_;
RunningStat backtracksPer2nRead_;
// Distribution of BWT operations/backtracks per read with three or
// more Ns
RunningStat bwtOpsPer3orMoreNRead_;
RunningStat backtracksPer3orMoreNRead_;
Timer timer_;
};
#endif /* ALIGNER_METRICS_H_ */
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