/*
* The MIT License
*
* Copyright (c) 2010 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.fingerprint;
import java.io.File;
import java.util.*;
/**
* Small class to represent a genetic fingerprint as a set of HaplotypeProbabilities
* objects that give the relative probabilities of each of the possible haplotypes
* at a locus.
*
* @author Tim Fennell
*/
public class Fingerprint extends TreeMap<HaplotypeBlock, HaplotypeProbabilities> {
private final String sample;
private final File source;
private final String info;
public Fingerprint(final String sample, final File source, final String info) {
this.sample = sample;
this.source = source;
this.info = info;
}
public String getSample() { return sample; }
public File getSource() { return source; }
public String getInfo() { return info; }
public String getPrintableId() {
return getSample() + "@" + (source == null ? "" : source.getName()) + (info == null ? "" : (":" + info));
}
public void add(final HaplotypeProbabilities h) {
put(h.getHaplotype(), h);
}
/**
* Merges the likelihoods from the supplied Fingerprint into the likelihoods for this fingerprint.
*/
public void merge(final Fingerprint other) {
final Set<HaplotypeBlock> haps = new HashSet<>();
haps.addAll(keySet());
haps.addAll(other.keySet());
for (final HaplotypeBlock haplotype : haps) {
HaplotypeProbabilities probabilities = get(haplotype);
final HaplotypeProbabilities otherProbabilities = other.get(haplotype);
if (probabilities == null) {
probabilities = otherProbabilities;
put(haplotype, probabilities);
} else if (otherProbabilities != null) {
probabilities.merge(otherProbabilities);
}
}
}
/**
* Attempts to filter out haplotypes that may have suspect genotyping by removing haplotypes that reach
* a minimum confidence score yet have a significant fraction of observations from a third or fourth allele.
*/
public void filterSuspectSites() {
final Iterator<Map.Entry<HaplotypeBlock, HaplotypeProbabilities>> iterator = entrySet().iterator();
while (iterator.hasNext()) {
final Map.Entry<HaplotypeBlock, HaplotypeProbabilities> entry = iterator.next();
final HaplotypeProbabilities p = entry.getValue();
if (p instanceof HaplotypeProbabilitiesFromSequence) {
final HaplotypeProbabilitiesFromSequence probs = (HaplotypeProbabilitiesFromSequence) p;
if (probs.getLodMostProbableGenotype() >= 3 && probs.getFractionUnexpectedAlleleObs() > 0.1) {
iterator.remove();
}
}
}
}
}