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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 blbutil.Utilities;
import vcf.XRefGT;
/**
* <p>Class {@code LowFreqPhaseIbs} identifies haplotypes that share a long
* IBS segment or a low frequency variant with a specified haplotype
* in a specified genomic interval.</p>
*
* <p>Instances of {@code LowFreqPhaseIbs} are immutable.</p>
*
* @author Brian L. Browning {@code <browning@uw.edu>}
*/
public final class LowFreqPhaseIbs {
private final PhaseData phaseData;
private final XRefGT allHaps;
private final LowFreqPbwtPhaseIbs fwdPhaseIbs;
private final LowFreqPbwtPhaseIbs bwdPhaseIbs;
/**
* Constructs a new {@code LowFreqPhaseIbs} object from the specified data.
*
* @param phaseData the current genotype phase estimates and parameter
* values
*
* @throws NullPointerException if {@code phaseData == null}
*/
public LowFreqPhaseIbs(PhaseData phaseData) {
CodedSteps codedSteps = phaseData.codedSteps();
this.phaseData = phaseData;
this.allHaps = codedSteps.allHaps();
this.fwdPhaseIbs = new LowFreqPbwtPhaseIbs(phaseData, codedSteps, false);
this.bwdPhaseIbs = new LowFreqPbwtPhaseIbs(phaseData, codedSteps, true);
}
/**
* Returns the input data for the next phase update.
* @return the input data for the next phase update
*/
public PhaseData phaseData() {
return phaseData;
}
/**
* Returns the estimated phased genotypes for the target and reference
* samples.
* @return the estimated phased genotypes for the target and reference
* samples
*/
public XRefGT allHaps() {
return allHaps;
}
/**
* Returns the IBS haplotype index for the specified haplotype in
* the specified genomic interval, when the PBWT is performed in
* order of increasing marker index.An index of {@code -1} is stored
* in an entry if no IBS haplotype is available.
* @param targHap a target haplotype index
* @param step an index of a genomic interval
* @return the IBS haplotype index from a forward analysis
* @throws IndexOutOfBoundsException if
* {@code targHap < 0 || targHap >= this.phaseData().targGT().nHaps()}
* @throws IndexOutOfBoundsException if
* {@code step < 0 || step >= this.phaseData().fpd().stage1Steps().size()}
*/
public int fwdIbsHap(int targHap, int step) {
return fwdPhaseIbs.ibsHap(targHap, step);
}
/**
* Returns the IBS haplotype index for the specified haplotype in
* the specified genomic interval, when the PBWT is performed in
* order of decreasing marker index. An index of {@code -1} is stored
* in an entry if no IBS haplotype is available.
* @param targHap a target haplotype index
* @param step an index of a genomic interval
* @return the IBS haplotype index from a backward analysis
* @throws IndexOutOfBoundsException if
* {@code targHap < 0 || targHap >= this.phaseData().targGT().nHaps()}
* @throws IndexOutOfBoundsException if
* {@code step < 0 || step >= this.phaseData().fpd().stage1Steps().size()}
*/
public int bwdIbsHap(int targHap, int step) {
return bwdPhaseIbs.ibsHap(targHap, step);
}
}
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