Commit for Kiran; but this is now working, barring little exceptions that I've yet to run across...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3511 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl
parent
6febd0291d
commit
8f9e3e8ad7
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@ -5,6 +5,8 @@ import org.broad.tribble.vcf.VCFHeaderLine;
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import org.broadinstitute.sting.commandline.Argument;
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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.contexts.StratifiedAlignmentContext;
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import org.broadinstitute.sting.gatk.contexts.variantcontext.Allele;
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import org.broadinstitute.sting.gatk.contexts.variantcontext.Genotype;
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import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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@ -12,13 +14,16 @@ import org.broadinstitute.sting.gatk.refdata.VariantContextAdaptors;
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import org.broadinstitute.sting.gatk.walkers.LocusWalker;
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import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedArgumentCollection;
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import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine;
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import org.broadinstitute.sting.gatk.walkers.genotyper.VariantCallContext;
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import org.broadinstitute.sting.gatk.walkers.varianteval.MendelianViolationEvaluator;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.SampleUtils;
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import org.broadinstitute.sting.utils.StingException;
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import org.broadinstitute.sting.utils.genotype.vcf.VCFUtils;
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import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
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import org.broadinstitute.sting.utils.pileup.PileupElement;
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import java.io.PrintStream;
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import java.util.*;
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@ -33,14 +38,17 @@ import java.util.*;
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public class MendelianViolationClassifier extends LocusWalker<MendelianViolationClassifier.MendelianViolation, VCFWriter> {
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@Argument(shortName="f",fullName="familyPattern",required=true,doc="Pattern for the family structure (usage: mom+dad=child)")
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String familyStr = null;
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@Argument(shortName="ob",fullName="outputBed",required=true,doc="Output file to write the homozygous region information to")
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PrintStream bedOutput = null;
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/*
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****** PRIVATE CLASSES
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*********** PRIVATE CLASSES
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*/
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public class ExtendedTrioStructure extends MendelianViolationEvaluator.TrioStructure {
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public HashMap<String,HomozygosityRegion> homozygousRegions;
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public HashMap<String,Integer> homozygousRegionCounts;
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public HashMap<String,MendelianInfoKey> regionKeys;
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public ExtendedTrioStructure(String family) {
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MendelianViolationEvaluator.TrioStructure struct = MendelianViolationEvaluator.parseTrioDescription(family);
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@ -54,30 +62,144 @@ public class MendelianViolationClassifier extends LocusWalker<MendelianViolation
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homozygousRegions.put(dad,null);
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homozygousRegionCounts.put(child,0);
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homozygousRegionCounts.put(mom,0);
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homozygousRegionCounts.put(dad,0);
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regionKeys = new HashMap<String,MendelianInfoKey>(3);
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regionKeys.put(child,MendelianInfoKey.ChildHomozygosityRegion);
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regionKeys.put(mom,MendelianInfoKey.MotherHomozygosityRegion);
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regionKeys.put(dad,MendelianInfoKey.FatherHomozygosityRegion);
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}
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public void updateHomozygosityRegions(Map<String,Genotype> genotypes, GenomeLoc loc) {
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for ( Map.Entry<String,Genotype> memberGenotype : genotypes.entrySet() ) {
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if ( homozygousRegions.get(memberGenotype.getKey()) == null ) {
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// currently in a heterozygous region, update if possible
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if ( memberGenotype.getValue().isHom() ) {
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homozygousRegionCounts.put(memberGenotype.getKey(),homozygousRegionCounts.get(memberGenotype.getKey())+1);
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homozygousRegions.put(memberGenotype.getKey(),new HomozygosityRegion(loc));
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}
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} else {
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// potentially breaking a homozygous region
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if ( memberGenotype.getValue().isHom() ) {
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// no break, continuing
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homozygousRegions.get(memberGenotype.getKey()).callsWithinRegion++;
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} else {
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// break of homozygosity, reset region to null, print to file, do not update the count yet
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homozygousRegions.put(memberGenotype.getKey(),null);
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}
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}
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}
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}
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public void updateHomozygosityRegions(MendelianViolation v, PrintStream output) {
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if ( ! v.siteIsFiltered() ) {
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ArrayList<HomozygosityRegion> brokenRegions = new ArrayList<HomozygosityRegion>(3);
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// can only enter or break regions at unfiltered calls
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for( Map.Entry<String,Genotype> memberGenotype : v.getUnderlyingGenotypes().entrySet() ) {
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// for each family member
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if ( homozygousRegions.get(memberGenotype.getKey()) == null ) {
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// currently in a heterozygous region, update if possible
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if ( memberGenotype.getValue().isHom() ) {
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homozygousRegionCounts.put(memberGenotype.getKey(),homozygousRegionCounts.get(memberGenotype.getKey())+1);
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homozygousRegions.put(memberGenotype.getKey(),new HomozygosityRegion(v.getLocus()));
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if ( v.type != MendelianViolationType.NONE ) {
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v.addAttribute(regionKeys.get(memberGenotype.getKey()).getKey(),homozygousRegionCounts.get(memberGenotype.getKey()));
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}
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}
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} else {
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// potentially breaking a homozygous region
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if ( memberGenotype.getValue().isHom() ) {
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// no break, update the region
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HomozygosityRegion r = homozygousRegions.get(memberGenotype.getKey());
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r.lastSeen = v.getLocus();
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r.callsWithinRegion++;
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if ( v.type != MendelianViolationType.NONE ) {
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v.addAttribute(regionKeys.get(memberGenotype.getKey()).getKey(),homozygousRegionCounts.get(memberGenotype.getKey()));
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if ( v.type == MendelianViolationType.DE_NOVO_SNP ) {
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r.deNovoSNPsInRegion++;
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} else if ( v.type == MendelianViolationType.OPPOSITE_HOMOZYGOTE ) {
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r.oppositeHomsInRegion++;
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}
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}
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} else if ( memberGenotype.getValue().isHet() ) {
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// explicitly check for hets -- no calls are not counted -- this breaks a region so we print it
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homozygousRegions.get(memberGenotype.getKey()).finalize(v.getLocus(),memberGenotype.getKey(),homozygousRegionCounts.get(memberGenotype.getKey()));
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brokenRegions.add(homozygousRegions.get(memberGenotype.getKey()));
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homozygousRegions.put(memberGenotype.getKey(),null);
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}
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}
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}
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if ( brokenRegions.size() > 0 ) {
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Collections.sort(brokenRegions);
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}
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for ( HomozygosityRegion r : brokenRegions ) {
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output.printf("%s%n",r);
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}
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}
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}
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}
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public class HomozygosityRegion {
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public class HomozygosityRegion implements Comparable{
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public GenomeLoc regionStart;
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public GenomeLoc lastSeen;
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public GenomeLoc endedBy;
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public int callsWithinRegion;
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public int oppositeHomsInRegion;
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public int deNovoSNPsInRegion;
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private String parent;
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private int id;
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public HomozygosityRegion(GenomeLoc start) {
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regionStart = start;
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lastSeen = start;
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endedBy = null;
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callsWithinRegion = 0;
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oppositeHomsInRegion = 0;
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deNovoSNPsInRegion = 0;
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}
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public void finalize(GenomeLoc regionEnd,String parent, int id) {
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endedBy = regionEnd;
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this.parent = parent;
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this.id = id;
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}
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private int getSizeLowerBound() {
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return lastSeen.distance(regionStart);
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}
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private int getSizeOfFirstHomToFirstHet() {
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return endedBy.distance(regionStart);
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}
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public String toString() {
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return String.format("%s\t%d\t%d\t%s\t%d\t%d\t%d\t%d\t%d\t%d",regionStart.getContig(),regionStart.getStart(),lastSeen.getStart(),
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parent,id,getSizeLowerBound(),getSizeOfFirstHomToFirstHet(),callsWithinRegion,oppositeHomsInRegion,deNovoSNPsInRegion);
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}
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public int compareTo(Object o) {
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if ( ! ( o instanceof HomozygosityRegion) ) {
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return Integer.MIN_VALUE;
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}
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return this.regionStart.compareTo(((HomozygosityRegion) o).regionStart);
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}
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}
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public class MendelianViolation {
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private VariantContext trio;
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public MendelianViolationType type;
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private HashMap<String,Object> newAttributes;
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private HashMap<String,Integer> homozygosityRegions;
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public MendelianViolation(VariantContext context, MendelianViolationType violationType) {
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trio = context;
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type = violationType;
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newAttributes = new HashMap<String,Object>();
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newAttributes.put(MendelianInfoKey.ViolationType.getKey(),type);
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homozygosityRegions = new HashMap<String,Integer>(3);
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}
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public void addAttribute(String key, Object val) {
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@ -93,10 +215,49 @@ public class MendelianViolationClassifier extends LocusWalker<MendelianViolation
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return trio.isFiltered();
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}
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public void addRegions(HashMap<String,Integer> regionIDsByName ) {
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for ( Map.Entry<String,Integer> e : regionIDsByName.entrySet() ) {
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setRegion(e.getKey(),e.getValue());
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}
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}
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public void setRegion(String parent, int regionID) {
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homozygosityRegions.put(parent,regionID);
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}
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public boolean isInPreviousRegions(Map<String,Integer> otherRegions) {
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for ( String s : otherRegions.keySet() ) {
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if ( homozygosityRegions.get(s) >= otherRegions.get(s) ) {
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return false;
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}
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}
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return true;
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}
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public Map<String,Genotype> getUnderlyingGenotypes() {
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return trio.getGenotypes();
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}
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public GenomeLoc getLocus() {
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return trio.getLocation();
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}
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public byte getRefBase() {
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return trio.getReference().getBases()[0];
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}
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public Object getAttribute(String key) {
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if ( newAttributes.keySet().contains(key) ) {
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return newAttributes.get(key);
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} else {
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return trio.getAttribute(key);
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}
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}
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}
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/*
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********** PRIVATE ENUMS
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*************** PRIVATE ENUMS
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*/
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public enum MendelianViolationType {
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@ -118,16 +279,18 @@ public class MendelianViolationClassifier extends LocusWalker<MendelianViolation
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public enum MendelianInfoKey {
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ViolationType("MVT","String","\"The Mendelian violation type\""),
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ParentalDeletion("deletedParent","String","\"The parent from whom the child (putatively) inherited a deletion at opposite homozygous sites\""),
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ChildHomozygosityRegion("CHR","Integer","\"An identifier for the region of homozygosity in the child in which the opposite homozygote is located\""),
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ChildHomozygosityRegionSize("CHRS","Integer","\"The size of the region of homozygosity in the child in which the opposite homozygote is located\""),
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OppositeHomozygotesInRegion("CHROH","Integer","\"The number of opposite-homozygotes located in the region of homozygosity\""),
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TriAllelicQuality("TriAlQ","Integer","\"The variant quality of the third allele at putative tri-allelic sites\""),
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TriAllelicBase("TriAlB","String","\"The third allele at putative tri-allelic sites\""),
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NumCallsInRegion("REGION_NCALLS","Integer","\"The number of SNP calls found in the homozygosity region\""),
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ParentHomozygosityRegion("PHR","String","\"An identifier for the parent, and the region number, for the homozygosity region where the deNovo SNP is located\""),
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MotherHomozygosityRegion("MHR","String","\"An identifier for the mother's homozygosity region where the violation is located\""),
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FatherHomozygosityRegion("FHR","String","\"An identifier for the father's homozygosity region where the violation is located\""),
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ChildHomozygosityRegion("CHR","Integer","\"An identifier for the child's homozygosity region where the violation is located\""),
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ProportionOfParentAllele("PropParent","Double","\"The proportion of bases in the child that were the parent allele at deNovo SNP sites\""),
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/* ***************************************** UNUSED ************************************************ */
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NumCallsInRegion("REGION_NCALLS","Integer","\"The number of unfiltered SNP calls found in the homozygosity region\""),
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ChildHomozygosityRegionSize("CHRS","Integer","\"The size of the region of homozygosity in the child in which the opposite homozygote is located\""),
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OppositeHomozygotesInRegion("CHROH","Integer","\"The number of opposite-homozygotes located in the region of homozygosity\""),
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ParentHomozygosityRegionSize("PHRS","Integer","\"The size of the parental homozygosity region where the deNovo SNP is located\""),
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DeNovoSNPsInRegion("PHRDN","Integer","\"The number of deNovo SNP events located in the same region of parental homozygosity where the deNovo SNP is located\""),
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ProportionOfParentAllele("PropParent","Double","\"The proportion of bases in the child that were the parent allele at deNovo SNP sites\"");
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DeNovoSNPsInRegion("PHRDN","Integer","\"The number of deNovo SNP events located in the same region of parental homozygosity where the deNovo SNP is located\"");
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String keyName;
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@ -150,23 +313,22 @@ public class MendelianViolationClassifier extends LocusWalker<MendelianViolation
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}
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/*
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*********** PRIVATE DATA
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**************** PRIVATE DATA
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*/
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private ExtendedTrioStructure trioStructure;
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private UnifiedGenotyperEngine engine;
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private ArrayList<VariantContext> contextBuffer;
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/*
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*********** INITIALIZE
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***************** INITIALIZE
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*/
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public void initialize() {
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trioStructure = new ExtendedTrioStructure(familyStr);
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contextBuffer = new ArrayList<VariantContext>(5000);
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UnifiedArgumentCollection uac = new UnifiedArgumentCollection();
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uac.MIN_BASE_QUALTY_SCORE = 10;
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uac.MIN_MAPPING_QUALTY_SCORE = 10;
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uac.STANDARD_CONFIDENCE_FOR_CALLING = 30;
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engine = new UnifiedGenotyperEngine(getToolkit(),uac);
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logger.info("Mom: "+trioStructure.mom+" Dad: "+trioStructure.dad+" Child: "+trioStructure.child);
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}
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/*
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@ -187,7 +349,7 @@ public class MendelianViolationClassifier extends LocusWalker<MendelianViolation
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}
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/*
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*********** MAP
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*************** MAP
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*/
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public MendelianViolation map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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if ( tracker == null ) {
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@ -199,16 +361,20 @@ public class MendelianViolationClassifier extends LocusWalker<MendelianViolation
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private MendelianViolation assessViolation(VariantContext varContext, RefMetaDataTracker tracker, ReferenceContext reference, AlignmentContext context) {
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MendelianViolation violation;
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if ( MendelianViolationEvaluator.isViolation(varContext,trioStructure) ) {
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if ( isDeNovo(varContext) ) {
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violation = assessDeNovo(varContext,tracker,reference,context);
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} else if ( isOppositeHomozygote(varContext) ) {
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violation = assessOppositeHomozygote(varContext,tracker,reference,context);
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if ( varContext != null ) {
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if ( MendelianViolationEvaluator.isViolation(varContext,trioStructure) ) {
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if ( isDeNovo(varContext) ) {
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violation = assessDeNovo(varContext,tracker,reference,context);
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} else if ( isOppositeHomozygote(varContext) ) {
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violation = assessOppositeHomozygote(varContext,tracker,reference,context);
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} else {
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throw new StingException("Mendelian violation that is neither deNovo nor opposite homozygote. Should never see this.");
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}
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} else {
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throw new StingException("Mendelian violation that is neither deNovo nor opposite homozygote. Should never see this.");
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violation = new MendelianViolation(varContext,MendelianViolationType.NONE);
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}
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} else {
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violation = new MendelianViolation(varContext,MendelianViolationType.NONE);
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violation = null;
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}
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return violation;
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@ -232,26 +398,93 @@ public class MendelianViolationClassifier extends LocusWalker<MendelianViolation
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return true;
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}
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/*
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************ ASSESS DE NOVO AND OPPOSITE HOMOZYGOTES
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*/
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private MendelianViolation assessDeNovo(VariantContext trio, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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// todo -- implement me
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return new MendelianViolation(trio,MendelianViolationType.DE_NOVO_SNP);
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MendelianViolation violation = new MendelianViolation(trio,MendelianViolationType.DE_NOVO_SNP);
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// look for mis-genotyped sites by examining the proportion of the parent-allele bases in the child --
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// as a spoeedup we do this only at non-filtered sites
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if ( ! trio.isFiltered() ) {
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Allele parental = trio.getGenotype(trioStructure.mom).getAllele(0); // guaranteed homozygous
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int numParental = 0;
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int total = 0;
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for ( PileupElement e : StratifiedAlignmentContext.splitContextBySample(context.getBasePileup()).get(trioStructure.child).getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getBasePileup() ) {
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if ( e.getQual() >= 10 && e.getMappingQual() >= 10 ) {
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total++;
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if ( e.getBase() == parental.getBases()[0] ) {
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numParental++;
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}
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}
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}
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violation.addAttribute(MendelianInfoKey.ProportionOfParentAllele.getKey(), ((double) numParental)/total);
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}
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return violation;
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}
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private MendelianViolation assessOppositeHomozygote(VariantContext trio, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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// todo -- implement me
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return new MendelianViolation(trio,MendelianViolationType.OPPOSITE_HOMOZYGOTE);
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MendelianViolation violation = new MendelianViolation(trio,MendelianViolationType.OPPOSITE_HOMOZYGOTE);
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logger.debug(getParentalDeletion(trio));
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violation.addAttribute(MendelianInfoKey.ParentalDeletion.getKey(),getParentalDeletion(trio));
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// look for tri-allelic sites mis-called as hom -- as a speedup we do this only at non-filtered, non genotype error sites
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if ( ! trio.isFiltered() && ! violation.getAttribute(MendelianInfoKey.ParentalDeletion.getKey()).equals("genotypeError") ) {
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Map<String, StratifiedAlignmentContext> stratCon = StratifiedAlignmentContext.splitContextBySample(context.getBasePileup());
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int conf = 0;
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Allele alt = null;
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for ( Map.Entry<String,StratifiedAlignmentContext> stratifiedEntry : stratCon.entrySet() ) {
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VariantCallContext call = engine.runGenotyper(tracker,ref,stratifiedEntry.getValue().getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE));
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if ( call != null && call.confidentlyCalled ) {
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||||
if ( call.vc.isSNP() ) {
|
||||
if ( ! call.vc.getAlternateAllele(0).basesMatch(trio.getAlternateAllele(0)) ) {
|
||||
if ( alt == null ) {
|
||||
alt = call.vc.getAlternateAllele(0);
|
||||
conf = (int) Math.floor(10*call.vc.getNegLog10PError());
|
||||
} else {
|
||||
conf += (int) Math.floor(10*call.vc.getNegLog10PError());
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
if ( alt != null ) {
|
||||
violation.addAttribute(MendelianInfoKey.TriAllelicBase.getKey(),alt.toString());
|
||||
violation.addAttribute(MendelianInfoKey.TriAllelicQuality.getKey(),conf);
|
||||
}
|
||||
}
|
||||
|
||||
return violation;
|
||||
}
|
||||
|
||||
private String getParentalDeletion(VariantContext trio) {
|
||||
// case 1, mom and dad are both hom, so missing is the one whose alleles don't match the child
|
||||
if ( trio.getGenotype(trioStructure.mom).isHom() && trio.getGenotype(trioStructure.dad).isHom() ) {
|
||||
if ( trio.getGenotype(trioStructure.mom).isHomRef() == trio.getGenotype(trioStructure.child).isHomRef() ) {
|
||||
// mom and child both hom ref or hom var
|
||||
return trioStructure.dad;
|
||||
} else if ( trio.getGenotype(trioStructure.dad).isHomRef() == trio.getGenotype(trioStructure.child).isHomRef() ) {
|
||||
return trioStructure.mom;
|
||||
} else {
|
||||
// child matches neither parent
|
||||
return "genotypeError";
|
||||
}
|
||||
} else { // case 2, either mom or dad is het - the hom must be the missing allele
|
||||
return trio.getGenotype(trioStructure.mom).isHet() ? trioStructure.dad : trioStructure.mom;
|
||||
}
|
||||
}
|
||||
|
||||
/*
|
||||
*********** REDUCE
|
||||
*************** REDUCE
|
||||
*/
|
||||
public VCFWriter reduce(MendelianViolation variant, VCFWriter writer) {
|
||||
if ( variant != null ) {
|
||||
if ( ! variant.siteIsFiltered() ) {
|
||||
// todo -- fill me in
|
||||
} else { /* just add filtered variants to output if they're wanted */
|
||||
contextBuffer.add(variant.toVariantContext());
|
||||
}
|
||||
trioStructure.updateHomozygosityRegions(variant,bedOutput);
|
||||
writer.addRecord(VariantContextAdaptors.toVCF(variant.toVariantContext(),variant.getRefBase()));
|
||||
}
|
||||
|
||||
return writer;
|
||||
|
|
@ -261,9 +494,24 @@ public class MendelianViolationClassifier extends LocusWalker<MendelianViolation
|
|||
********** ON TRAVERSAL DONE
|
||||
*/
|
||||
public void onTraversalDone(VCFWriter writer) {
|
||||
while ( contextBuffer.size() > 0 ) {
|
||||
VariantContext vc = contextBuffer.remove(0);
|
||||
writer.addRecord(VariantContextAdaptors.toVCF(vc,vc.getReference().getBases()[0]));
|
||||
Map<String,HomozygosityRegion> regions = trioStructure.homozygousRegions;
|
||||
Map<String,Integer> counts = trioStructure.homozygousRegionCounts;
|
||||
for ( Map.Entry<String,HomozygosityRegion> entryRegion : regions.entrySet() ) {
|
||||
if ( entryRegion.getValue() != null ) {
|
||||
logger.info("---------------- REGION NOT FINALIZED -----------------");
|
||||
logger.info(String.format("%s,%s,%s,%d,%d",entryRegion.getKey(),entryRegion.getValue().regionStart,entryRegion.getValue().lastSeen,
|
||||
entryRegion.getValue().deNovoSNPsInRegion,entryRegion.getValue().oppositeHomsInRegion));
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/*
|
||||
***************** STATIC METHODS
|
||||
*/
|
||||
|
||||
public static String getBedFileHeader() {
|
||||
return String.format("%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s","Chrom","first_seen_hom","last_seen_hom","first_seen_het",
|
||||
"sample_name","region_id","homozygous_region_size", "size_to_first_het","calls_within_region",
|
||||
"opposite_homozygotes_in_region","deNovo_SNPs_in_region");
|
||||
}
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue