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/*
* Copyright (C) 2014-2021 Brian L. Browning
*
* This file is part of Beagle
*
* Beagle 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.
*
* Beagle 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/>.
*/
package phase;
import main.Par;
/**
* <p>Class {@code PbwtIbsData} contains parameters and data for finding
* haplotypes that share an IBS segment with a target haplotype.</p>
*
* @author Brian L. Browning {@code <browning@uw.edu>}
*/
public class PbwtIbsData {
private static final int BURNIN_CANDIDATES = 100;
private static final int MAX_PHASE_CANDIDATES = 90;
private static final int MIN_PHASE_CANDIDATES = 5;
private static final float MAX_BACKOFF_CM = 0.3f;
private final CodedSteps codedSteps;
private final int nHaps;
private final int nTargHaps;
private final int nCandidates;
private final int nOverlapSteps;
private final int maxBackoffSteps;
private final int stepsPerBatch;
private final int nBatches;
/**
* Constructs a new {@code PbwtIbsData} instance from the specified data.
* @param phaseData the current genotype phase estimates and parameter
* values
* @param codedSteps the coded steps
* @throws IllegalArgumentException if
* {@code phaseData.fpd().stage1Steps() != codedSteps.steps()}
* @throws IllegalArgumentException if
* {@code phaseData.fpd().stage1XRefGT()!=codedSteps.refHaps()}
* @throws IllegalArgumentException if
* {@code phaseData.fpd().targGT().samples()!=codedSteps.targSamples()}
* @throws NullPointerException if
* {@code phaseData == null || codedSteps == null}
*/
public PbwtIbsData(PhaseData phaseData, CodedSteps codedSteps) {
checkConsistency(phaseData, codedSteps);
FixedPhaseData fpd = phaseData.fpd();
Par par = fpd.par();
int nSteps = codedSteps.steps().size();
int nThreads = par.nthreads();
int nIts = par.burnin() + par.iterations();
this.codedSteps = codedSteps;
this.nHaps = fpd.nHaps();
this.nTargHaps = phaseData.fpd().targGT().nHaps();
this.nCandidates = phaseData.it()<nIts ? nCandidates1(phaseData)
: nCandidates2(phaseData);
this.nOverlapSteps = (int) Math.rint(par.buffer() / fpd.ibsStep());
this.maxBackoffSteps = (int) Math.rint(MAX_BACKOFF_CM / fpd.ibsStep());
this.stepsPerBatch = (nSteps + nThreads - 1) / nThreads;
this.nBatches = (nSteps + stepsPerBatch - 1) / stepsPerBatch;
}
private static void checkConsistency(PhaseData phaseData,
CodedSteps codedSteps) {
FixedPhaseData fpd = phaseData.fpd();
if (fpd.stage1Steps()!=codedSteps.steps()
|| fpd.stage1XRefGT()!=codedSteps.refHaps()
|| fpd.targGT().samples()!=codedSteps.targSamples()) {
throw new IllegalArgumentException("inconsistent data");
}
}
private static int nCandidates1(PhaseData phaseData) {
int nCandidates = BURNIN_CANDIDATES;
int it = phaseData.it();
Par par = phaseData.fpd().par();
if (it>=par.burnin()) {
double nItsRemaining = par.burnin() + par.iterations() - it;
double p = (double) nItsRemaining / par.iterations();
nCandidates = (int) Math.round(p*MAX_PHASE_CANDIDATES);
nCandidates = Math.max(nCandidates, MIN_PHASE_CANDIDATES);
}
return Math.min(nCandidates, phaseData.fpd().nHaps());
}
private static int nCandidates2(PhaseData phaseData) {
FixedPhaseData fpd = phaseData.fpd();
int nHaps = fpd.nHaps();
float rare = fpd.par().rare();
float scaleFactor = 0.5f;
int nCandidates = (int) Math.floor(scaleFactor * rare * nHaps);
nCandidates = Math.max(nCandidates, MIN_PHASE_CANDIDATES);
return Math.min(nCandidates, nHaps);
}
/**
* Returns the coded steps.
* @return the codedSteps
*/
public CodedSteps codedSteps() {
return codedSteps;
}
/**
* Returns the total number of target and reference haplotypes.
* @return the total number of target and reference haplotypes
*/
public int nHaps() {
return nHaps;
}
/**
* Returns the number of target haplotypes.
* @return the number of target haplotypes
*/
public int nTargHaps() {
return nTargHaps;
}
/**
* Returns the number of candidate haplotypes
* @return the number of candidate haploytpes
*/
public int nCandidates() {
return nCandidates;
}
/**
* Returns the number of overlap steps
* @return the number of overlap steps
*/
public int nOverlapSteps() {
return nOverlapSteps;
}
/**
* Returns the number of backoff steps
* @return the number of backoff steps
*/
public int maxBackoffSteps() {
return maxBackoffSteps;
}
/**
* Returns the number of steps per batch
* @return the number of steps per batch
*/
public int stepsPerBatch() {
return stepsPerBatch;
}
/**
* Returns the number of batches.
* @return the number of batches
*/
public int nBatches() {
return nBatches;
}
}
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