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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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41
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
View File

@ -35,16 +35,10 @@ 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.clipping.ReadClipper;
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.pileup.ExtendedEventPileupElement;
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.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.broadinstitute.sting.utils.variantcontext.*;
import java.util.*;
@ -183,7 +177,7 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
}
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;
if (hsize <= 0) {
@ -208,26 +202,23 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
for (Map.Entry<String, AlignmentContext> sample : contexts.entrySet()) {
AlignmentContext context = AlignmentContextUtils.stratify(sample.getValue(), contextType);
ReadBackedPileup pileup = null;
if (context.hasExtendedEventPileup())
pileup = context.getExtendedEventPileup();
else if (context.hasBasePileup())
pileup = context.getBasePileup();
if (context.hasBasePileup()) {
final ReadBackedPileup pileup = context.getBasePileup();
if (pileup != null) {
final double[] genotypeLikelihoods = pairModel.computeReadHaplotypeLikelihoods(pileup, haplotypeMap, ref, eventLength, getIndelLikelihoodMap());
GenotypeLikelihoods likelihoods = GenotypeLikelihoods.fromLog10Likelihoods(genotypeLikelihoods);
if (pileup != null) {
final double[] genotypeLikelihoods = pairModel.computeReadHaplotypeLikelihoods(pileup, haplotypeMap, ref, eventLength, getIndelLikelihoodMap());
GenotypeLikelihoods likelihoods = GenotypeLikelihoods.fromLog10Likelihoods(genotypeLikelihoods);
HashMap<String, Object> attributes = new HashMap<String, Object>();
attributes.put(VCFConstants.DEPTH_KEY, getFilteredDepth(pileup));
attributes.put(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY, likelihoods);
genotypes.add(new Genotype(sample.getKey(), noCall, Genotype.NO_LOG10_PERROR, null, attributes, false));
HashMap<String, Object> attributes = new HashMap<String, Object>();
attributes.put(VCFConstants.DEPTH_KEY, getFilteredDepth(pileup));
attributes.put(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY, likelihoods);
genotypes.add(new Genotype(sample.getKey(), noCall, Genotype.NO_LOG10_PERROR, null, attributes, false));
if (DEBUG) {
System.out.format("Sample:%s Alleles:%s GL:", sample.getKey(), alleleList.toString());
for (int k = 0; k < genotypeLikelihoods.length; k++)
System.out.format("%1.4f ", genotypeLikelihoods[k]);
System.out.println();
if (DEBUG) {
System.out.format("Sample:%s Alleles:%s GL:", sample.getKey(), alleleList.toString());
for (int k = 0; k < genotypeLikelihoods.length; k++)
System.out.format("%1.4f ", genotypeLikelihoods[k]);
System.out.println();
}
}
}
}

6
public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
View File

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