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package org.broadinstitute.gatk.tools.walkers.phasing;
import htsjdk.samtools.reference.ReferenceSequenceFile;
import org.apache.log4j.Logger;
import org.broadinstitute.gatk.utils.GenomeLocParser;
import org.broadinstitute.gatk.utils.MathUtils;
import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils;
import htsjdk.variant.vcf.VCFHeader;
import htsjdk.variant.variantcontext.writer.VariantContextWriter;
import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
import org.broadinstitute.gatk.utils.exceptions.UserException;
import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile;
import htsjdk.variant.variantcontext.*;
import java.io.File;
import java.io.FileNotFoundException;
import java.util.*;
// Streams in VariantContext objects and streams out VariantContexts produced by merging phased segregating polymorphisms into MNP VariantContexts
class MergeSegregatingAlternateAllelesVCFWriter implements VariantContextWriter {
private VariantContextWriter innerWriter;
private GenomeLocParser genomeLocParser;
private ReferenceSequenceFile referenceFileForMNPmerging;
private VariantContextMergeRule vcMergeRule;
private PhasingUtils.AlleleMergeRule alleleMergeRule;
private String useSingleSample = null;
private boolean emitOnlyMergedRecords;
private VCFRecord vcfrWaitingToMerge;
private List<VCFRecord> filteredVcfrList;
private int numRecordsAttemptToMerge;
private int numRecordsSatisfyingMergeRule;
private int numMergedRecords;
private AltAlleleStatsForSamples altAlleleStats = null;
private Logger logger;
// Should we call innerWriter.close() in close()
private boolean takeOwnershipOfInner;
public MergeSegregatingAlternateAllelesVCFWriter(VariantContextWriter innerWriter, GenomeLocParser genomeLocParser, File referenceFile, VariantContextMergeRule vcMergeRule, PhasingUtils.AlleleMergeRule alleleMergeRule, String singleSample, boolean emitOnlyMergedRecords, Logger logger, boolean takeOwnershipOfInner, boolean trackAltAlleleStats) {
this.innerWriter = innerWriter;
this.genomeLocParser = genomeLocParser;
try {
this.referenceFileForMNPmerging = new CachingIndexedFastaSequenceFile(referenceFile);
}
catch(FileNotFoundException ex) {
throw new UserException.CouldNotReadInputFile(referenceFile,ex);
}
this.vcMergeRule = vcMergeRule;
this.alleleMergeRule = alleleMergeRule;
this.useSingleSample = singleSample;
this.emitOnlyMergedRecords = emitOnlyMergedRecords;
this.vcfrWaitingToMerge = null;
this.filteredVcfrList = new LinkedList<VCFRecord>();
this.numRecordsSatisfyingMergeRule = 0;
this.numMergedRecords = 0;
if (trackAltAlleleStats)
this.altAlleleStats = new AltAlleleStatsForSamples();
this.logger = logger;
this.takeOwnershipOfInner = takeOwnershipOfInner;
}
public MergeSegregatingAlternateAllelesVCFWriter(VariantContextWriter innerWriter, GenomeLocParser genomeLocParser, File referenceFile, int maxGenomicDistanceForMNP, Logger logger, boolean takeOwnershipOfInner) {
this(innerWriter, genomeLocParser, referenceFile, new DistanceMergeRule(maxGenomicDistanceForMNP, genomeLocParser), new SegregatingMNPmergeAllelesRule(), null, false, logger, takeOwnershipOfInner, true); // by default: consider all samples, emit all records, keep track of alt allele statistics
}
public void writeHeader(VCFHeader header) {
if (useSingleSample != null) { // only want to output context for one sample
Set<String> singSampSet = new TreeSet<String>();
singSampSet.add(useSingleSample);
header = new VCFHeader(header.getMetaDataInSortedOrder(), singSampSet);
}
innerWriter.writeHeader(header);
}
public void close() {
stopWaitingToMerge();
if (takeOwnershipOfInner)
innerWriter.close();
}
public void add(VariantContext vc) {
if (useSingleSample != null) { // only want to output context for one sample
Genotype sampGt = vc.getGenotype(useSingleSample);
if (sampGt != null) // TODO: subContextFromGenotypes() does not handle any INFO fields [AB, HaplotypeScore, MQ, etc.]. Note that even SelectVariants.subsetRecord() only handles AC,AN,AF, and DP!
vc = vc.subContextFromSample(sampGt.getSampleName());
else // asked for a sample that this vc does not contain, so ignore this vc:
return;
}
logger.debug("Next VC input = " + GATKVariantContextUtils.getLocation(genomeLocParser, vc));
boolean curVcIsNotFiltered = vc.isNotFiltered();
if (vcfrWaitingToMerge == null) {
logger.debug("NOT Waiting to merge...");
if (!filteredVcfrList.isEmpty())
throw new ReviewedGATKException("filteredVcfrList should be empty if not waiting to merge a vc!");
if (curVcIsNotFiltered) { // still need to wait before can release vc
logger.debug("Waiting for new variant " + GATKVariantContextUtils.getLocation(genomeLocParser, vc));
vcfrWaitingToMerge = new VCFRecord(vc, false);
}
else if (!emitOnlyMergedRecords) { // filtered records are never merged
logger.debug("DIRECTLY output " + GATKVariantContextUtils.getLocation(genomeLocParser, vc));
innerWriter.add(vc);
}
}
else { // waiting to merge vcfrWaitingToMerge
logger.debug("Waiting to merge " + GATKVariantContextUtils.getLocation(genomeLocParser, vcfrWaitingToMerge.vc));
if (!curVcIsNotFiltered) {
if (!emitOnlyMergedRecords) { // filtered records are never merged
logger.debug("Caching unprocessed output " + GATKVariantContextUtils.getLocation(genomeLocParser, vc));
filteredVcfrList.add(new VCFRecord(vc, false));
}
}
else { // waiting to merge vcfrWaitingToMerge, and curVcIsNotFiltered. So, attempt to merge them:
numRecordsAttemptToMerge++;
boolean shouldAttemptToMerge = vcMergeRule.shouldAttemptToMerge(vcfrWaitingToMerge.vc, vc);
logger.debug("shouldAttemptToMerge? = " + shouldAttemptToMerge);
/*
TODO: -- CONSIDER THE FOLLOWING EXAMPLE: WHAT DO WE WANT HERE??? --
If the following 3 genotypes originally exist for a sample [at sites 1, 2, and 3]:
1/1
0|1
0|1
Then, after merging the first two, we have [at sites 1 and 3]:
1/2
0|1
Then, not having merged would consider sites 2 and 3 as a MNP (since it's a diploid het site with haplotypes: REF-REF and ALT-ALT)
But, since we merged sites 1 and 2, we get that sites 1-2 and 3 are counted as two haplotypes of: ALT-REF and ALT-ALT
*/
if (altAlleleStats != null)
altAlleleStats.updateSampleStats(vcfrWaitingToMerge.vc, vc, shouldAttemptToMerge);
boolean mergedRecords = false;
if (shouldAttemptToMerge) {
numRecordsSatisfyingMergeRule++;
VariantContext mergedVc = PhasingUtils.mergeIntoMNP(genomeLocParser, vcfrWaitingToMerge.vc, vc, referenceFileForMNPmerging, alleleMergeRule);
if (mergedVc != null) {
mergedRecords = true;
Map<String, Object> addedAttribs = vcMergeRule.addToMergedAttributes(vcfrWaitingToMerge.vc, vc);
addedAttribs.putAll(mergedVc.getAttributes());
mergedVc = new VariantContextBuilder(mergedVc).attributes(addedAttribs).make();
vcfrWaitingToMerge = new VCFRecord(mergedVc, true);
numMergedRecords++;
}
}
if (!mergedRecords) {
stopWaitingToMerge();
vcfrWaitingToMerge = new VCFRecord(vc, false);
}
logger.debug("Merged? = " + mergedRecords);
}
}
}
private void stopWaitingToMerge() {
if (vcfrWaitingToMerge == null) {
if (!filteredVcfrList.isEmpty())
throw new ReviewedGATKException("filteredVcfrList should be empty if not waiting to merge a vc!");
return;
}
if (!emitOnlyMergedRecords || vcfrWaitingToMerge.resultedFromMerge)
innerWriter.add(vcfrWaitingToMerge.vc);
vcfrWaitingToMerge = null;
for (VCFRecord vcfr : filteredVcfrList)
innerWriter.add(vcfr.vc);
filteredVcfrList.clear();
}
/**
* Gets a string representation of this object.
*
* @return
*/
@Override
public String toString() {
return getClass().getName();
}
private static class VCFRecord {
public VariantContext vc;
public boolean resultedFromMerge;
public VCFRecord(VariantContext vc, boolean resultedFromMerge) {
this.vc = vc;
this.resultedFromMerge = resultedFromMerge;
}
}
private class AltAlleleStats {
public int numSuccessiveGenotypes;
public int numSuccessiveGenotypesAttemptedToBeMerged;
public int oneSampleMissing;
public int atLeastOneSampleNotCalledOrFiltered;
public int segregationUnknown;
public int eitherNotVariant;
public int bothInPairHaveVariant;
public int ref_ref_pair;
public int ref_alt_pair;
public int alt_ref_pair;
public int alt_alt_pair;
public int MNPsites;
public int CHetSites;
public AltAlleleStats() {
this.numSuccessiveGenotypes = 0;
this.numSuccessiveGenotypesAttemptedToBeMerged = 0;
this.oneSampleMissing = 0;
this.atLeastOneSampleNotCalledOrFiltered = 0;
this.segregationUnknown = 0;
this.eitherNotVariant = 0;
this.bothInPairHaveVariant = 0;
this.ref_ref_pair = 0;
this.ref_alt_pair = 0;
this.alt_ref_pair = 0;
this.alt_alt_pair = 0;
this.MNPsites = 0;
this.CHetSites = 0;
}
public String toString() {
StringBuilder sb = new StringBuilder();
sb.append("Sample missing:\t" + oneSampleMissing + "\n");
sb.append("Not called or filtered:\t" + atLeastOneSampleNotCalledOrFiltered + "\n");
sb.append("* Number of successive pairs of genotypes:\t" + numSuccessiveGenotypes + "\n");
sb.append("Number of successive pairs of genotypes with " + vcMergeRule + ":\t" + numSuccessiveGenotypesAttemptedToBeMerged + "\n");
sb.append("Unknown segregation, " + vcMergeRule + ":\t" + segregationUnknown + "\n");
sb.append("Not variant at least one of pair, segregation known, " + vcMergeRule + ":\t" + eitherNotVariant + "\n");
sb.append("* Variant at both, segregation known, " + vcMergeRule + ":\t" + percentageString(bothInPairHaveVariant, numSuccessiveGenotypes) + "\n");
sb.append("[Total haplotypes at pairs:\t" + (ref_ref_pair + ref_alt_pair + alt_ref_pair + alt_alt_pair) + "\n");
sb.append("REF-REF:\t" + ref_ref_pair + "\n");
sb.append("REF-ALT:\t" + ref_alt_pair + "\n");
sb.append("ALT-REF:\t" + alt_ref_pair + "\n");
sb.append("ALT-ALT:\t" + alt_alt_pair + "]\n");
int hetAfterHetSites = MNPsites + CHetSites;
sb.append("* Het-Het sites (with REF allele present at each):\t" + percentageString(hetAfterHetSites, bothInPairHaveVariant) + "\n");
sb.append("* MNPs:\t" + percentageString(MNPsites, hetAfterHetSites) + "\n");
sb.append("Compound Hets:\t" + CHetSites + "\n");
return sb.toString();
}
private String percentageString(int count, int baseCount) {
int NUM_DECIMAL_PLACES = 1;
String percent = new Formatter().format("%." + NUM_DECIMAL_PLACES + "f", MathUtils.percentage(count, baseCount)).toString();
return count + " (" + percent + "%)";
}
}
private class AltAlleleStatsForSamples {
private Map<String, AltAlleleStats> sampleStats;
public AltAlleleStatsForSamples() {
this.sampleStats = new HashMap<String, AltAlleleStats>();
}
public void updateSampleStats(VariantContext vc1, VariantContext vc2, boolean shouldAttemptToMerge) {
if (vc1.isFiltered() || vc2.isFiltered())
return;
Set<String> allSamples = new TreeSet<String>(vc1.getSampleNames());
allSamples.addAll(vc2.getSampleNames());
for (String samp : allSamples) {
AltAlleleStats aas = sampleStats.get(samp);
if (aas == null) {
aas = new AltAlleleStats();
sampleStats.put(samp, aas);
}
Genotype gt1 = vc1.getGenotype(samp);
Genotype gt2 = vc2.getGenotype(samp);
if (gt1 == null || gt2 == null) {
aas.oneSampleMissing++;
}
else if (gt1.isNoCall() || gt1.isFiltered() || gt2.isNoCall() || gt2.isFiltered()) {
aas.atLeastOneSampleNotCalledOrFiltered++;
}
else {
aas.numSuccessiveGenotypes++;
if (shouldAttemptToMerge) {
aas.numSuccessiveGenotypesAttemptedToBeMerged++;
if (!PhasingUtils.alleleSegregationIsKnown(gt1, gt2)) {
aas.segregationUnknown++;
logger.debug("Unknown segregation of alleles [not phased] for " + samp + " at " + GATKVariantContextUtils.getLocation(genomeLocParser, vc1) + ", " + GATKVariantContextUtils.getLocation(genomeLocParser, vc2));
}
else if (gt1.isHomRef() || gt2.isHomRef()) {
logger.debug("gt1.isHomRef() || gt2.isHomRef() for " + samp + " at " + GATKVariantContextUtils.getLocation(genomeLocParser, vc1) + ", " + GATKVariantContextUtils.getLocation(genomeLocParser, vc2));
aas.eitherNotVariant++;
}
else { // BOTH gt1 and gt2 have at least one variant allele (so either hets, or homozygous variant):
aas.bothInPairHaveVariant++;
List<Allele> site1Alleles = gt1.getAlleles();
List<Allele> site2Alleles = gt2.getAlleles();
Iterator<Allele> all2It = site2Alleles.iterator();
for (Allele all1 : site1Alleles) {
Allele all2 = all2It.next(); // this is OK, since alleleSegregationIsKnown(gt1, gt2)
if (all1.isReference()) {
if (all2.isReference())
aas.ref_ref_pair++;
else
aas.ref_alt_pair++;
}
else { // all1.isNonReference()
if (all2.isReference())
aas.alt_ref_pair++;
else
aas.alt_alt_pair++;
}
}
// Check MNPs vs. CHets:
if (containsRefAllele(site1Alleles) && containsRefAllele(site2Alleles)) {
logger.debug("HET-HET for " + samp + " at " + GATKVariantContextUtils.getLocation(genomeLocParser, vc1) + ", " + GATKVariantContextUtils.getLocation(genomeLocParser, vc2));
if (logger.isDebugEnabled() && !(gt1.isHet() && gt2.isHet()))
throw new ReviewedGATKException("Since !gt1.isHomRef() && !gt2.isHomRef(), yet both have ref alleles, they BOTH must be hets!");
// There's the potential to only have REF-ALT, ALT-REF (CHet), or possibly ALT-ALT together (MNP)
boolean hasMNP = false;
all2It = site2Alleles.iterator();
for (Allele all1 : site1Alleles) {
Allele all2 = all2It.next(); // this is OK, since alleleSegregationIsKnown(gt1, gt2)
if (all1.isNonReference() && all2.isNonReference()) {
hasMNP = true; // has at least one haplotype of ALT-ALT that segregates!
break;
}
}
if (hasMNP)
aas.MNPsites++;
else
aas.CHetSites++;
}
}
}
}
}
}
private boolean containsRefAllele(List<Allele> siteAlleles) {
for (Allele all : siteAlleles) {
if (all.isReference())
return true;
}
return false;
}
public String toString() {
StringBuilder sb = new StringBuilder();
sb.append("-------------------------------------------------------------------------\n");
sb.append("Per-sample alternate allele statistics [" + vcMergeRule + "]\n");
sb.append("-------------------------------------------------------------------------");
for (Map.Entry<String, AltAlleleStats> sampAltAllStatsEntry : sampleStats.entrySet()) {
String samp = sampAltAllStatsEntry.getKey();
AltAlleleStats stats = sampAltAllStatsEntry.getValue();
sb.append("\n* Sample:\t" + samp + "\n" + stats);
}
return sb.toString();
}
}
}
/*
External classes:
*/
abstract class VariantContextMergeRule {
abstract public boolean shouldAttemptToMerge(VariantContext vc1, VariantContext vc2);
public Map<String, Object> addToMergedAttributes(VariantContext vc1, VariantContext vc2) {
return new HashMap<String, Object>();
}
}
class DistanceMergeRule extends VariantContextMergeRule {
private int maxGenomicDistanceForMNP;
private GenomeLocParser genomeLocParser;
public DistanceMergeRule(int maxGenomicDistanceForMNP, GenomeLocParser genomeLocParser) {
this.maxGenomicDistanceForMNP = maxGenomicDistanceForMNP;
this.genomeLocParser = genomeLocParser;
}
public boolean shouldAttemptToMerge(VariantContext vc1, VariantContext vc2) {
return minDistance(vc1, vc2) <= maxGenomicDistanceForMNP;
}
public String toString() {
return "Merge distance <= " + maxGenomicDistanceForMNP;
}
public int minDistance(VariantContext vc1, VariantContext vc2) {
return GATKVariantContextUtils.getLocation(genomeLocParser, vc1).minDistance(GATKVariantContextUtils.getLocation(genomeLocParser, vc2));
}
}
class ExistsDoubleAltAlleleMergeRule extends PhasingUtils.AlleleMergeRule {
public boolean allelesShouldBeMerged(VariantContext vc1, VariantContext vc2) {
return PhasingUtils.someSampleHasDoubleNonReferenceAllele(vc1, vc2);
}
public String toString() {
return super.toString() + ", some sample has a MNP of ALT alleles";
}
}
class SegregatingMNPmergeAllelesRule extends ExistsDoubleAltAlleleMergeRule {
public SegregatingMNPmergeAllelesRule() {
super();
}
public boolean allelesShouldBeMerged(VariantContext vc1, VariantContext vc2) {
// Must be interesting AND consistent:
return super.allelesShouldBeMerged(vc1, vc2) && PhasingUtils.doubleAllelesSegregatePerfectlyAmongSamples(vc1, vc2);
}
public String toString() {
return super.toString() + ", all alleles segregate consistently";
}
}