/*
* The MIT License
*
* Copyright (c) 2014 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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* THE SOFTWARE.
*/
package picard.vcf.filter;
import htsjdk.samtools.util.CollectionUtil;
import htsjdk.variant.variantcontext.Allele;
import htsjdk.variant.variantcontext.Genotype;
import htsjdk.variant.variantcontext.GenotypesContext;
import htsjdk.variant.variantcontext.VariantContext;
import htsjdk.variant.variantcontext.VariantContextUtils;
import htsjdk.variant.vcf.VCFFilterHeaderLine;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
/**
* Filters out a record if the allele balance for heterozygotes is out of a defined range across all samples.
* The threshold is set as the minimum fraction of the data drawn from the less-represented allele - e.g. 0.3 would
* set that whichever allele has lower representation across all heterozygous individuals must account for at least 30% of the
* total observations.
*/
public class AlleleBalanceFilter implements VariantFilter {
/** The filter string used for sites that fail the allele balance filter. */
public static final String AB_FILTER = "AlleleBalance";
private final double hetAlleleBalance;
public AlleleBalanceFilter(final double hetAlleleBalance) {
this.hetAlleleBalance = hetAlleleBalance;
}
private static class Counts { int samples; int allele1; int allele2; }
@Override
public List<VCFFilterHeaderLine> headerLines() {
return CollectionUtil.makeList(new VCFFilterHeaderLine(AB_FILTER, "Heterozygote allele balance below required threshold."));
}
@Override
public String filter(final VariantContext ctx) {
if (ctx.getHetCount() == 0) return null;
final Map<List<Allele>, Counts> countsMap = new HashMap<List<Allele>, Counts>();
for (final Genotype gt : ctx.getGenotypesOrderedByName()) {
if (gt.isNoCall() || !gt.isHet()) continue;
final List<Allele> alleles = gt.getAlleles();
Counts counts = countsMap.get(alleles);
if (counts == null) {
counts = new Counts();
countsMap.put(alleles, counts);
}
counts.allele1 += gt.getAD()[ctx.getAlleleIndex(alleles.get(0))];
counts.allele2 += gt.getAD()[ctx.getAlleleIndex(alleles.get(1))];
}
for (final Counts counts : countsMap.values()) {
final int total = counts.allele1 + counts.allele2;
if (total > 0 && Math.min(counts.allele1, counts.allele2) / (double) total < this.hetAlleleBalance) return AB_FILTER;
}
return null;
}
}