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A wrapper around the GenotypeLikelihoods class for the UnifiedGenotyper. This wrapper incorporates both strand-based likelihoods and a combined likelihoods over both strands. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1777 348d0f76-0448-11de-a6fe-93d51630548a
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ebanks 2009-10-07 19:57:37 +00:00
parent 5bdcc2b4dc
commit 203c626fc2
1 changed files with 58 additions and 0 deletions
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java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotypeLikelihoods.java 100755
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package org.broadinstitute.sting.gatk.walkers.genotyper;
import org.broadinstitute.sting.utils.ReadBackedPileup;
import net.sf.samtools.SAMRecord;
/**
A wrapper around the GenotypeLikelihoods class for the UnifiedGenotyper.
This class incorporates both strand-based likelihoods and a combined likelihoods over both strands.
*/
public class UnifiedGenotypeLikelihoods {
private GenotypeLikelihoods forwardStrandGL;
private GenotypeLikelihoods reverseStrandGL;
private GenotypeLikelihoods combinedGL;
public UnifiedGenotypeLikelihoods(BaseMismatchModel baseModel, DiploidGenotypePriors priors, EmpiricalSubstitutionGenotypeLikelihoods.SequencerPlatform defaultPlatform, boolean VERBOSE) {
forwardStrandGL = GenotypeLikelihoodsFactory.makeGenotypeLikelihoods(baseModel, priors, defaultPlatform);
forwardStrandGL.setVerbose(VERBOSE);
reverseStrandGL = GenotypeLikelihoodsFactory.makeGenotypeLikelihoods(baseModel, priors, defaultPlatform);
reverseStrandGL.setVerbose(VERBOSE);
combinedGL = GenotypeLikelihoodsFactory.makeGenotypeLikelihoods(baseModel, priors, defaultPlatform);
combinedGL.setVerbose(VERBOSE);
}
public GenotypeLikelihoods getForwardStrandGenotypeLikelihoods() { return forwardStrandGL; }
public GenotypeLikelihoods getReverseStrandGenotypeLikelihoods() { return reverseStrandGL; }
public GenotypeLikelihoods getGenotypeLikelihoods() { return combinedGL; }
public void add(ReadBackedPileup pileup) {
for (int i = 0; i < pileup.getReads().size(); i++) {
int offset = pileup.getOffsets().get(i);
// ignore deletions
if ( offset == -1 )
continue;
SAMRecord read = pileup.getReads().get(i);
char base = read.getReadString().charAt(offset);
add(base, read, offset);
}
}
public void add(char base, SAMRecord read, int offset) {
if ( !read.getReadNegativeStrandFlag() )
forwardStrandGL.add(base, read.getBaseQualities()[offset], read, offset);
else
reverseStrandGL.add(base, read.getBaseQualities()[offset], read, offset);
combinedGL.add(base, read.getBaseQualities()[offset], read, offset);
}
public void setPriors(DiploidGenotypePriors priors) {
forwardStrandGL.setPriors(priors);
reverseStrandGL.setPriors(priors);
combinedGL.setPriors(priors);
}
}