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Second intermediate commit for indel pool caller - now works (more or less) in reference sample-free mode. Still needs a lot of cleanups/add more tests and not done w/refactoring quite yet

This commit is contained in:
Guillermo del Angel 2012-06-13 20:59:17 -04:00
parent 67c0569f9c
commit 92669a0468
1 changed files with 24 additions and 19 deletions
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43
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
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@ -30,12 +30,14 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.Requires;
import org.broadinstitute.sting.gatk.walkers.indels.PairHMMIndelErrorModel;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.Haplotype;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.variantcontext.*;
@ -48,7 +50,8 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
private boolean DEBUG = false;
private boolean ignoreSNPAllelesWhenGenotypingIndels = false;
private PairHMMIndelErrorModel pairModel;
private boolean allelesArePadded;
private static ThreadLocal<HashMap<PileupElement, LinkedHashMap<Allele, Double>>> indelLikelihoodMap =
new ThreadLocal<HashMap<PileupElement, LinkedHashMap<Allele, Double>>>() {
protected synchronized HashMap<PileupElement, LinkedHashMap<Allele, Double>> initialValue() {
@ -87,6 +90,7 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
private final static EnumSet<VariantContext.Type> allowableTypes = EnumSet.of(VariantContext.Type.INDEL, VariantContext.Type.MIXED);
public VariantContext getLikelihoods(final RefMetaDataTracker tracker,
final ReferenceContext ref,
final Map<String, AlignmentContext> contexts,
@ -95,28 +99,30 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
final boolean useBAQedPileup,
final GenomeLocParser locParser) {
if (tracker == null)
return null;
GenomeLoc loc = ref.getLocus();
if (!ref.getLocus().equals(lastSiteVisited)) {
// if (!ref.getLocus().equals(lastSiteVisited)) {
if (contextType == AlignmentContextUtils.ReadOrientation.COMPLETE) {
// starting a new site: clear allele list
lastSiteVisited = ref.getLocus();
indelLikelihoodMap.set(new HashMap<PileupElement, LinkedHashMap<Allele, Double>>());
haplotypeMap.clear();
alleleList = getInitialAlleleList(tracker, ref, contexts, contextType, locParser, UAC, ignoreSNPAllelesWhenGenotypingIndels);
Pair<List<Allele>,Boolean> pair = getInitialAlleleList(tracker, ref, contexts, contextType, locParser, UAC, ignoreSNPAllelesWhenGenotypingIndels);
alleleList = pair.first;
allelesArePadded = pair.second;
if (alleleList.isEmpty())
return null;
}
getHaplotypeMapFromAlleles(alleleList, ref, loc, haplotypeMap);
getHaplotypeMapFromAlleles(alleleList, ref, loc, haplotypeMap); // will update haplotypeMap adding elements
if (haplotypeMap == null || haplotypeMap.isEmpty())
return null;
// start making the VariantContext
// For all non-snp VC types, VC end location is just startLocation + length of ref allele including padding base.
final int endLoc = computeEndLocation(alleleList, loc);
final int endLoc = computeEndLocation(alleleList, loc,allelesArePadded);
final int eventLength = getEventLength(alleleList);
final VariantContextBuilder builder = new VariantContextBuilder("UG_call", loc.getContig(), loc.getStart(), endLoc, alleleList).referenceBaseForIndel(ref.getBase());
@ -160,14 +166,9 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
return indelLikelihoodMap.get();
}
public static int computeEndLocation(final List<Allele> alleles, final GenomeLoc loc) {
public static int computeEndLocation(final List<Allele> alleles, final GenomeLoc loc, final boolean allelesArePadded) {
Allele refAllele = alleles.get(0);
boolean allelesArePadded = true;
int endLoc = loc.getStart() + refAllele.length()-1;
/* if (refAllele.getBases().length == vc.getEnd()-vc.getStart()+1)
allelesArePadded = false;
*/
// todo FIXME!
if (allelesArePadded)
endLoc++;
@ -215,7 +216,7 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
}
public static List<Allele> getInitialAlleleList(final RefMetaDataTracker tracker,
public static Pair<List<Allele>,Boolean> getInitialAlleleList(final RefMetaDataTracker tracker,
final ReferenceContext ref,
final Map<String, AlignmentContext> contexts,
final AlignmentContextUtils.ReadOrientation contextType,
@ -224,6 +225,7 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
final boolean ignoreSNPAllelesWhenGenotypingIndels) {
List<Allele> alleles = new ArrayList<Allele>();
boolean allelesArePadded = true;
if (UAC.GenotypingMode == GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES) {
VariantContext vc = null;
for (final VariantContext vc_input : tracker.getValues(UAC.alleles, ref.getLocus())) {
@ -234,10 +236,9 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
break;
}
}
// ignore places where we don't have a variant
// ignore places where we don't have a variant
if (vc == null)
return alleles;
return new Pair<List<Allele>,Boolean>(alleles,false);
if (ignoreSNPAllelesWhenGenotypingIndels) {
// if there's an allele that has same length as the reference (i.e. a SNP or MNP), ignore it and don't genotype it
@ -250,11 +251,15 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
} else {
alleles.addAll(vc.getAlleles());
}
if ( vc.getReference().getBases().length == vc.getEnd()-vc.getStart()+1)
allelesArePadded = false;
} else {
alleles = IndelGenotypeLikelihoodsCalculationModel.computeConsensusAlleles(ref, contexts, contextType, locParser, UAC);
}
return alleles;
return new Pair<List<Allele>,Boolean> (alleles,allelesArePadded);
}
// Overload function in GenotypeLikelihoodsCalculationModel so that, for an indel case, we consider a deletion as part of the pileup,