Basic walker to count the number of (phased) hets in each exome target
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/*
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* Copyright (c) 2010, The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
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* OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting.oneoffprojects.phasing;
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import org.broad.tribble.util.variantcontext.Genotype;
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import org.broad.tribble.util.variantcontext.VariantContext;
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import org.broadinstitute.sting.commandline.Output;
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.filters.ZeroMappingQualityReadFilter;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
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import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
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import org.broadinstitute.sting.gatk.walkers.*;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.exceptions.UserException;
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import java.io.PrintStream;
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import java.util.*;
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/**
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* Walks along all variant ROD loci and verifies the phasing from the reads for user-defined pairs of sites.
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*/
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@Allows(value = {DataSource.REFERENCE})
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@Requires(value = {DataSource.REFERENCE}, referenceMetaData = @RMD(name = "variant", type = ReferenceOrderedDatum.class))
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@ReadFilters({ZeroMappingQualityReadFilter.class})
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// Filter out all reads with zero mapping quality
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public class CountHetPhasingInIntervalWalker extends RodWalker<Integer, Integer> {
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private LinkedList<String> rodNames = null;
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private GenomeLoc prevInterval = null;
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private MultiSampleIntervalStats intervalStats = null;
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@Output
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protected PrintStream out;
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public void initialize() {
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rodNames = new LinkedList<String>();
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rodNames.add("variant");
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intervalStats = new MultiSampleIntervalStats();
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}
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public boolean generateExtendedEvents() {
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return false;
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}
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public Integer reduceInit() {
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return 0;
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}
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/**
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* @param tracker the meta-data tracker
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* @param ref the reference base
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* @param context the context for the given locus
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* @return statistics of and list of all phased VariantContexts and their base pileup that have gone out of cacheWindow range.
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*/
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public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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if (tracker == null)
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return null;
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int processed = 1;
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List<GATKFeature> interval = tracker.getGATKFeatureMetaData("intervals", true);
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if (interval.size() != 1) {
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String error = "At " + ref.getLocus() + " : Must provide a track named 'intervals' with exactly ONE interval per locus in -L argument!";
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if (interval.size() < 1)
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throw new UserException(error);
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else // interval.size() > 1
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logger.warn(error);
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}
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// Take the FIRST interval covering this locus, and WARN about multiple intervals (above):
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GenomeLoc curInterval = interval.get(0).getLocation();
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logger.debug("refLocus: " + ref.getLocus() + "\tcurInterval = " + curInterval);
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boolean isNewInterval = (prevInterval == null || !curInterval.equals(prevInterval));
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if (isNewInterval)
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intervalStats.startNewInterval();
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boolean requireStartHere = true; // only see each VariantContext once
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boolean takeFirstOnly = false; // take as many entries as the VCF file has
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for (VariantContext vc : tracker.getVariantContexts(ref, rodNames, null, context.getLocation(), requireStartHere, takeFirstOnly)) {
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Map<String, Genotype> sampToGenotypes = vc.getGenotypes();
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for (Map.Entry<String, Genotype> sampEntry : sampToGenotypes.entrySet()) {
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Genotype gt = sampEntry.getValue();
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intervalStats.processHetSiteInInterval(sampEntry.getKey(), gt.isHet(), gt.isPhased());
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}
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}
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prevInterval = curInterval;
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return processed;
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}
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public Integer reduce(Integer addIn, Integer runningCount) {
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if (addIn == null)
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addIn = 0;
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return runningCount + addIn;
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}
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/**
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* @param result the number of reads and VariantContexts seen.
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*/
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public void onTraversalDone(Integer result) {
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intervalStats.finalizeStats();
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System.out.println("Processed " + result + " sites.");
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for (Map.Entry<String, MultiSampleIntervalStats.SingleSampleIntervalStats> sampleEntry : intervalStats.entrySet()) {
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out.println("Sample:\t" + sampleEntry.getKey());
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out.println(sampleEntry.getValue() + "\n");
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}
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}
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class MultiSampleIntervalStats {
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private Map<String, SingleSampleIntervalStats> sampleToStat;
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protected int numIntervals;
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public MultiSampleIntervalStats() {
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this.sampleToStat = new HashMap<String, SingleSampleIntervalStats>();
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this.numIntervals = 0;
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}
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public void processHetSiteInInterval(String sample, boolean isHet, boolean isPhased) {
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SingleSampleIntervalStats sampleStats = sampleToStat.get(sample);
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if (sampleStats == null) {
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sampleStats = new SingleSampleIntervalStats();
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sampleToStat.put(sample, sampleStats);
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}
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sampleStats.updateHetStats(isHet, isPhased);
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}
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public void finalizeStats() {
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for (SingleSampleIntervalStats stats : sampleToStat.values())
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stats.finalizeStats();
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}
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public Set<Map.Entry<String, SingleSampleIntervalStats>> entrySet() {
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return sampleToStat.entrySet();
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}
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public void startNewInterval() {
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finalizeStats();
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numIntervals++;
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}
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private class SingleSampleIntervalStats {
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public Map<PhasedHetsStat, Integer> hetStatInIntervalToCount;
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public int firstHetIsPhased;
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private int numHetsInCurrentInterval;
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private int numPhasedInCurrentInterval;
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public SingleSampleIntervalStats() {
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this.hetStatInIntervalToCount = new TreeMap<PhasedHetsStat, Integer>(); // implemented PhasedHetsStat.compareTo()
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this.firstHetIsPhased = 0;
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this.numHetsInCurrentInterval = 0;
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this.numPhasedInCurrentInterval = 0;
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}
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public void updateHetStats(boolean isHet, boolean isPhased) {
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if (isHet) {
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numHetsInCurrentInterval++;
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if (isPhased) {
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numPhasedInCurrentInterval++;
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if (numHetsInCurrentInterval == 1)
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firstHetIsPhased++;
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}
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}
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}
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public void finalizeStats() {
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if (numIntervals == 0) // have not yet seen any intervals
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return;
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PhasedHetsStat hetsAndPhased = new PhasedHetsStat(numHetsInCurrentInterval, numPhasedInCurrentInterval);
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Integer cnt = hetStatInIntervalToCount.get(hetsAndPhased);
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if (cnt == null)
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cnt = 0;
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hetStatInIntervalToCount.put(hetsAndPhased, cnt + 1);
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numHetsInCurrentInterval = 0;
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numPhasedInCurrentInterval = 0;
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}
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public String toString() {
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StringBuilder sb = new StringBuilder();
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sb.append("# of intervals: " + numIntervals + "\n");
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sb.append("First het is phased: " + firstHetIsPhased + "\n");
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sb.append("Distribution of number of phased / hets per interval:" + "\n");
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for (Map.Entry<PhasedHetsStat, Integer> hetStatEntry : hetStatInIntervalToCount.entrySet())
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sb.append(hetStatEntry.getKey() + "\t" + hetStatEntry.getValue() + "\n");
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return sb.toString();
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}
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}
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}
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class PhasedHetsStat implements Comparable<PhasedHetsStat> {
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public int numHets;
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public int numPhased;
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public PhasedHetsStat(int numHets, int numPhased) {
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this.numHets = numHets;
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this.numPhased = numPhased;
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}
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public int compareTo(PhasedHetsStat that) {
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if (this.numHets != that.numHets)
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return this.numHets - that.numHets;
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return this.numPhased - that.numPhased;
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}
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public String toString() {
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StringBuilder sb = new StringBuilder();
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sb.append(numPhased + " / " + numHets);
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return sb.toString();
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}
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}
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}
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