/*
* 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
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package picard.vcf.filter;
import htsjdk.samtools.util.CloseableIterator;
import htsjdk.samtools.util.CloserUtil;
import htsjdk.samtools.util.ListMap;
import htsjdk.variant.variantcontext.Genotype;
import htsjdk.variant.variantcontext.GenotypeBuilder;
import htsjdk.variant.variantcontext.VariantContext;
import htsjdk.variant.variantcontext.VariantContextBuilder;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Set;
/**
* Iterator that dynamically applies filter strings to VariantContext records supplied by an underlying
* iterator. Returns all records from the underlying stream and does not remove any.
*
* @author tfennell
*/
public class FilterApplyingVariantIterator implements CloseableIterator<VariantContext> {
/** Filter string that is used to filter a Variant when all variant genotypes are filtered out. */
public static final String ALL_GTS_FILTERED = "AllGtsFiltered";
/** The "PASS"ing filter String. */
public static final String PASS_FILTER = "PASS";
private final Iterator<VariantContext> iterator;
private final VariantFilter[] filters;
private final GenotypeFilter[] gtFilters;
/**
* Constructs an iterator from an underlying iterator and the provided (possibly empty)
* collections of variant and genotype filters.
*/
public FilterApplyingVariantIterator(final Iterator<VariantContext> iterator,
final Collection<VariantFilter> filters,
final Collection<GenotypeFilter> gtFilters) {
this.iterator = iterator;
this.filters = filters.toArray(new VariantFilter[filters.size()]);
this.gtFilters = gtFilters.toArray(new GenotypeFilter[gtFilters.size()]);
}
/**
* Provides the next record from the underlying iterator after applying filter strings generated
* by the set of filters in use by the iterator.
*/
@Override
public VariantContext next() {
final VariantContext ctx = this.iterator.next();
final Set<String> filterStrings = new HashSet<String>();
// Collect variant level filters
for (final VariantFilter filter : this.filters) {
final String val = filter.filter(ctx);
if (val != null) filterStrings.add(val);
}
// Collect genotype level filters in a Map of Sample -> List<filter string>
final ListMap<String,String> gtFilterStrings = new ListMap<String,String>();
final Set<String> variantSamples = new HashSet<String>();
for (final Genotype gt : ctx.getGenotypes()) {
if (gt.isCalled() && !gt.isHomRef()) variantSamples.add(gt.getSampleName());
for (final GenotypeFilter filter : gtFilters) {
final String filterString = filter.filter(ctx,gt);
if (filterString != null) gtFilterStrings.add(gt.getSampleName(), filterString);
}
}
// If all genotypes are filtered apply a site level filter
if (gtFilterStrings.keySet().containsAll(variantSamples)) {
filterStrings.add(ALL_GTS_FILTERED);
}
// Make a builder and set the site level filter appropriately
final VariantContextBuilder builder = new VariantContextBuilder(ctx);
if (filterStrings.isEmpty()) {
builder.passFilters();
}
else {
builder.filters(filterStrings);
}
// Apply filters to the necessary genotypes
builder.noGenotypes();
final List<Genotype> newGenotypes = new ArrayList<Genotype>(ctx.getNSamples());
for (final Genotype gt : ctx.getGenotypes()) {
final GenotypeBuilder gtBuilder = new GenotypeBuilder(gt);
final List<String> filters = gtFilterStrings.get(gt.getSampleName());
if (filters == null || filters.isEmpty()) {
gtBuilder.filter(PASS_FILTER);
}
else {
gtBuilder.filters(filters);
}
newGenotypes.add(gtBuilder.make());
}
builder.genotypes(newGenotypes);
return builder.make();
}
@Override public boolean hasNext() { return this.iterator.hasNext(); }
@Override public void close() { CloserUtil.close(this.iterator); }
@Override public void remove() { throw new UnsupportedOperationException("remove() not supported by FilterApplyingVariantIterator."); }
}