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Removing some more usages of extended events. Not done yet, but almost there.

This commit is contained in:
Eric Banks 2012-03-30 01:51:37 -04:00
parent ad6ace2439
commit b21889812d
2 changed files with 16 additions and 31 deletions
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17
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
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@ -35,16 +35,10 @@ import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.Haplotype; import org.broadinstitute.sting.utils.Haplotype;
import org.broadinstitute.sting.utils.clipping.ReadClipper;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.exceptions.StingException; import org.broadinstitute.sting.utils.exceptions.StingException;
import org.broadinstitute.sting.utils.pileup.ExtendedEventPileupElement;
import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.broadinstitute.sting.utils.variantcontext.*; import org.broadinstitute.sting.utils.variantcontext.*;
import java.util.*; import java.util.*;
@ -183,7 +177,7 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
} }
final int eventLength = altAllele.getBaseString().length() - refAllele.getBaseString().length(); final int eventLength = altAllele.getBaseString().length() - refAllele.getBaseString().length();
final int hsize = (int) ref.getWindow().size() - Math.abs(eventLength) - 1; final int hsize = ref.getWindow().size() - Math.abs(eventLength) - 1;
final int numPrefBases = ref.getLocus().getStart() - ref.getWindow().getStart() + 1; final int numPrefBases = ref.getLocus().getStart() - ref.getWindow().getStart() + 1;
if (hsize <= 0) { if (hsize <= 0) {
@ -208,12 +202,8 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
for (Map.Entry<String, AlignmentContext> sample : contexts.entrySet()) { for (Map.Entry<String, AlignmentContext> sample : contexts.entrySet()) {
AlignmentContext context = AlignmentContextUtils.stratify(sample.getValue(), contextType); AlignmentContext context = AlignmentContextUtils.stratify(sample.getValue(), contextType);
ReadBackedPileup pileup = null; if (context.hasBasePileup()) {
if (context.hasExtendedEventPileup()) final ReadBackedPileup pileup = context.getBasePileup();
pileup = context.getExtendedEventPileup();
else if (context.hasBasePileup())
pileup = context.getBasePileup();
if (pileup != null) { if (pileup != null) {
final double[] genotypeLikelihoods = pairModel.computeReadHaplotypeLikelihoods(pileup, haplotypeMap, ref, eventLength, getIndelLikelihoodMap()); final double[] genotypeLikelihoods = pairModel.computeReadHaplotypeLikelihoods(pileup, haplotypeMap, ref, eventLength, getIndelLikelihoodMap());
GenotypeLikelihoods likelihoods = GenotypeLikelihoods.fromLog10Likelihoods(genotypeLikelihoods); GenotypeLikelihoods likelihoods = GenotypeLikelihoods.fromLog10Likelihoods(genotypeLikelihoods);
@ -231,6 +221,7 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
} }
} }
} }
}
return builder.genotypes(genotypes).make(); return builder.genotypes(genotypes).make();
} }

6
public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
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@ -275,9 +275,6 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
if (context.hasBasePileup()) { if (context.hasBasePileup()) {
numReads = context.getBasePileup().getNumberOfElements(); numReads = context.getBasePileup().getNumberOfElements();
} }
else if (context.hasExtendedEventPileup()) {
numReads = context.getExtendedEventPileup().getNumberOfElements();
}
PhasingStats addInPhaseStats = new PhasingStats(numReads, 1); PhasingStats addInPhaseStats = new PhasingStats(numReads, 1);
phaseStats.addIn(addInPhaseStats); phaseStats.addIn(addInPhaseStats);
} }
@ -1115,9 +1112,6 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
if (alignment.hasBasePileup()) { if (alignment.hasBasePileup()) {
pileup = alignment.getBasePileup(); pileup = alignment.getBasePileup();
} }
else if (alignment.hasExtendedEventPileup()) {
pileup = alignment.getExtendedEventPileup();
}
if (pileup != null) { if (pileup != null) {
// filter the read-base pileup based on min base and mapping qualities: // filter the read-base pileup based on min base and mapping qualities:
pileup = pileup.getBaseAndMappingFilteredPileup(MIN_BASE_QUALITY_SCORE, MIN_MAPPING_QUALITY_SCORE); pileup = pileup.getBaseAndMappingFilteredPileup(MIN_BASE_QUALITY_SCORE, MIN_MAPPING_QUALITY_SCORE);