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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 vcf;
/**
* <p>Class {@code BasicGTRec} stores genotypes for a list of samples
* at a single marker. The phased or unphased status of each genotype is
* stored.</p>
*
* <p>Instances of class {@code BasicGTRec} are immutable.</p>
*
* @author Brian L. Browning {@code <browning@uw.edu>}
*/
public final class BasicGTRec implements GTRec {
private final Marker marker;
private final Samples samples;
private final int[] alleles;
private final boolean[] isPhased;
private final boolean allPhased;
/**
* Constructs a new {@code BasicGTRec} instance representing
* the specified VCF record's GT format field data.
*
* @param recParser the VCF record genotype data
* @throws IllegalArgumentException if a format error is detected
* in the VCF record
* @throws NullPointerException if {@code recParser == null}
*/
public BasicGTRec(VcfRecGTParser recParser) {
int nSamples = recParser.samples().size();
int nHaps = nSamples<<1;
int[] alleles0 = new int[nHaps];
boolean[] isPhased0 = new boolean[nSamples];
this.allPhased = recParser.storeAlleles(alleles0, isPhased0);
this.marker = recParser.marker();
this.samples = recParser.samples();
this.alleles = alleles0;
this.isPhased = isPhased0;
}
@Override
public Samples samples() {
return samples;
}
@Override
public int size() {
return 2*samples.size();
}
@Override
public Marker marker() {
return marker;
}
@Override
public boolean isPhased() {
return allPhased;
}
@Override
public boolean isPhased(int sample) {
return isPhased[sample];
}
@Override
public int allele1(int sample) {
return alleles[sample<<1];
}
@Override
public int allele2(int sample) {
return alleles[(sample<<1) | 0b1];
}
@Override
public int get(int hap) {
return alleles[hap];
}
@Override
public int[] alleles() {
return alleles.clone();
}
/**
* Returns the data represented by {@code this} as a VCF
* record with a GT format field. The returned VCF record
* will have missing QUAL and INFO fields, will have "PASS"
* in the filter field, and will have a GT format field.
* @return the data represented by {@code this} as a VCF
* record with a GT format field
*/
@Override
public String toString() {
return GTRec.toVcfRec(this);
}
}
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