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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.FloatArray;
import ints.IntArray;
import ints.WrappedIntArray;
import phase.SamplePhase.ClustType;
/**
* <p>Class {@code MarkerCluster} represents a partition of markers into
* contiguous marker clusters.</p>
*
* <p>Instances of class {@code MarkerCluster} are immutable.</p>
*
* @author Brian L. Browning {@code <browning@uw.edu>}
*/
public class MarkerCluster {
private final SamplePhase samplePhase;
private final int[] clusterToEnd;
private final IntArray unphHetClusters;
private final FloatArray pRecomb;
/**
* Constructs a new {@code MarkerCluster} instance from the specified data.
*
* @param phaseData the input data for the next genotype phasing iteration
* @param sample a sample index
* @throws IndexOutOfBoundsException if
* {@code sample < 0 || sample >= phaseData.targGT().nSamples()}
* @throws NullPointerException if {@code phaseData == null}
*/
public MarkerCluster(PhaseData phaseData, int sample) {
this.samplePhase = phaseData.estPhase().get(sample);
this.clusterToEnd = samplePhase.clustEnds();
this.unphHetClusters = unphHetClusters(samplePhase);
this.pRecomb = pClustRecomb(phaseData.pRecomb(), clusterToEnd);
}
private static IntArray unphHetClusters(SamplePhase samplePhase) {
int nUnph = samplePhase.nUnphased();
int nClusters = samplePhase.nClusters();
int[] unphHetClusters = new int[nUnph];
int index = 0;
for (int c=0; c<nClusters; ++c) {
if (samplePhase.clustType(c)==ClustType.UNPHASED_HET) {
unphHetClusters[index++] = c;
}
}
return new WrappedIntArray(unphHetClusters);
}
private static FloatArray pClustRecomb(FloatArray pRecomb,
int[] cluster2End) {
int nClusters = cluster2End.length;
float[] pClustRecomb = new float[nClusters];
int start = cluster2End[0];
for (int j=1; j<nClusters; ++j) {
int end = cluster2End[j];
float pNoRecomb = 1.0f;
for (int k=start; k<end; ++k) {
pNoRecomb *= (1.0f - pRecomb.get(k));
}
pClustRecomb[j] = 1.0f - pNoRecomb;
start = end;
}
return new FloatArray(pClustRecomb);
}
/**
* Return the estimated haplotypes.
* @return the estimated haplotypes
*/
public SamplePhase samplePhase() {
return samplePhase;
}
/**
* Returns the number of clusters
* @return the number of clusters
*/
public int nClusters() {
return clusterToEnd.length;
}
/**
* Returns the inclusive start marker for the cluster.
* @param index a cluster index
* @return the inclusive start marker for the cluster
* @throws IndexOutOfBoundsException if
* {@code index < 0 || index >= this.nClusteres()}
*/
public int clusterStart(int index) {
return index==0 ? 0 : clusterToEnd[index-1];
}
/**
* Returns the exclusive end marker for the cluster.
* @param index a cluster index
* @return the exclusive marker for the cluster
* @throws IndexOutOfBoundsException if
* {@code index < 0 || index >= this.nClusteres()}
*/
public int clusterEnd(int index) {
return clusterToEnd[index];
}
/**
* Return a {@code FloatArray} of size {@code this.nClusters()}
* whose {@code k}-th element is the probability of transitioning to a
* random HMM state between the {@code k}-th cluster and the
* previous cluster.
* @return a {@code FloatArray} of size {@code this.nClusters()}
* whose {@code k}-th element is the probability of transitioning to a
* random HMM state between the {@code k}-th cluster and the
* previous cluster
*/
public FloatArray pRecomb() {
return pRecomb;
}
/**
* Returns a sorted list of cluster indices in increasing order for which
* the cluster contains an unphased heterozygote.
* @return a sorted list of cluster indices in increasing order for which
* the cluster contains an unphased heterozygote
*/
public IntArray unphasedHetClusters() {
return unphHetClusters;
}
/**
* Returns {@code true} if the cluster has an unphased heterozygous genotype,
* and returns {@code false} otherwise.
* @param cluster a cluster index
* @return {@code true} if the cluster has an unphased heterozygous genotype,
* and returns {@code false} otherwise
* @throws IndexOutOfBoundsException if
* {@code cluster < 0 || cluster >= this.nClusters()}
*/
public boolean isUnphasedHet(int cluster) {
return samplePhase.clustType(cluster)==ClustType.UNPHASED_HET;
}
/**
* Returns {@code true} if the cluster has a phased heterozygous genotype,
* and returns {@code false} otherwise.
* @param cluster a cluster index
* @return {@code true} if the cluster has a phased heterozygous genotype,
* and returns {@code false} otherwise
* @throws IndexOutOfBoundsException if
* {@code cluster < 0 || cluster >= this.nClusters()}
*/
public boolean isPhasedHet(int cluster) {
return samplePhase.clustType(cluster)==ClustType.PHASED_HET;
}
/**
* Returns {@code true} if the cluster is a heterozygous genotype,
* and returns {@code false} otherwise.
* @param cluster a cluster index
* @return {@code true} if the cluster is a heterozygous genotype,
* and {@code false} otherwise
* @throws IndexOutOfBoundsException if
* {@code cluster < 0 || cluster >= this.nClusters()}
*/
public boolean isHet(int cluster) {
ClustType clustType = samplePhase.clustType(cluster);
return clustType==ClustType.UNPHASED_HET
|| clustType==ClustType.PHASED_HET;
}
/**
* Returns {@code true} if the cluster has a missing genotype, and
* returns {@code false} otherwise.
* @param cluster a cluster index
* @return {@code true} if the cluster has a missing genotype
* @throws IndexOutOfBoundsException if
* {@code cluster < 0 || cluster >= this.nClusters()}
*/
public boolean isMissingGT(int cluster) {
return samplePhase.clustType(cluster) == ClustType.MISSING_GT;
}
/**
* Returns {@code true} if the cluster is a masked heterozygote genotype,
* and returns {@code false} otherwise.
* @param cluster a cluster index
* @return {@code true} if the cluster is a masked heterozygote genotype
* @throws IndexOutOfBoundsException ift
* {@code cluster < 0 || cluster >= this.nClusters()}
*/
public boolean isMaskedHet(int cluster) {
return samplePhase.clustType(cluster) == ClustType.MASKED_HET;
}
/**
* Returns {@code true} if the cluster has a missing genotype or a
* masked heterozygote genotype, and returns {@code false} otherwise.
* @param cluster a cluster index
* @return {@code true} if the cluster has a missing genotype or a
* masked heterozygote genotype, and returns {@code false} otherwise
* @throws IndexOutOfBoundsException if
* {@code cluster < 0 || cluster >= this.nClusters()}
*/
public boolean isMissingGtOrMaskedHet(int cluster) {
ClustType clustType = samplePhase.clustType(cluster);
return clustType == ClustType.MISSING_GT
|| clustType==ClustType.MASKED_HET;
}
}
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