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Implemented HET case with binomial distribution. Separated events from normal events and for now skip all extended events. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6059 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
droazen 2011-06-22 22:55:24 +00:00
parent 26d837f59e
commit ea47ccf032
1 changed files with 21 additions and 18 deletions
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39
java/src/org/broadinstitute/sting/playground/gatk/walkers/replication_validation/ReplicationValidationWalker.java
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@ -5,6 +5,8 @@ import com.google.common.collect.ArrayListMultimap;
import com.sun.xml.internal.ws.client.BindingProviderProperties; import com.sun.xml.internal.ws.client.BindingProviderProperties;
import net.sf.samtools.SAMFileHeader; import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMReadGroupRecord; import net.sf.samtools.SAMReadGroupRecord;
import org.broad.tribble.util.variantcontext.Allele;
import org.broad.tribble.util.variantcontext.Genotype;
import org.broad.tribble.util.variantcontext.VariantContext; import org.broad.tribble.util.variantcontext.VariantContext;
import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.commandline.Output;
@ -90,20 +92,20 @@ public class ReplicationValidationWalker extends LocusWalker<Integer, Long> impl
/** /**
* Calculates he probability of the data (reference sample reads) given the phred scaled site quality score. * Calculates he probability of the data (reference sample reads) given the phred scaled site quality score.
* @param data - array of bases from the reference sample * @param data - array of bases from the reference sample
* @param refBase - base from the reference sequence for this site * @param refBases - base from the reference sequence for this site
* @param phredScaledPrior - phred scaled expected site quality (prior) * @param phredScaledPrior - phred scaled expected site quality (prior)
* @return an array of log10 probabilities of site qualities ranging from Q1-Q40. * @return an array of log10 probabilities of site qualities ranging from Q1-Q40.
*/ */
private double[] buildErrorModel (byte[] data, byte refBase, byte phredScaledPrior) { private double[] buildErrorModel (byte[] data, Collection<Byte> refBases, byte phredScaledPrior) {
double [] model = new double[maxQualityScore+1]; double [] model = new double[maxQualityScore+1];
int coverage = data.length; int coverage = data.length;
int mismatches = getNumberOfMismatches(data, refBase); int mismatches = getNumberOfMismatches(data, refBases);
int matches = coverage - mismatches; int matches = coverage - mismatches;
for (byte q=0; q<=maxQualityScore; q++) { for (byte q=0; q<=maxQualityScore; q++) {
double probMismatch = MathUtils.phredScaleToProbability(q); double probMismatch = MathUtils.phredScaleToProbability(q);
model[q] = MathUtils.phredScaleToLog10Probability(phredScaledPrior) + model[q] = MathUtils.phredScaleToLog10Probability(phredScaledPrior) +
Math.log10(Arithmetic.binomial(coverage, mismatches)) + MathUtils.log10BinomialCoefficient(coverage, mismatches) +
mismatches * Math.log10(probMismatch) + mismatches * Math.log10(probMismatch) +
matches * Math.log10(1-probMismatch); matches * Math.log10(1-probMismatch);
} }
@ -116,10 +118,10 @@ public class ReplicationValidationWalker extends LocusWalker<Integer, Long> impl
* @param refBase the reference sample base to compare to * @param refBase the reference sample base to compare to
* @return number of bases in data that are different from refBase * @return number of bases in data that are different from refBase
*/ */
private int getNumberOfMismatches(byte[] data, byte refBase) { private int getNumberOfMismatches(byte[] data, Collection<Byte> refBase) {
int mismatches = 0; int mismatches = 0;
for (byte seqBase : data) { for (byte seqBase : data) {
if (seqBase != refBase) if (!refBase.contains(seqBase))
mismatches++; mismatches++;
} }
return mismatches; return mismatches;
@ -158,11 +160,15 @@ public class ReplicationValidationWalker extends LocusWalker<Integer, Long> impl
// Get reference base from VCF or Reference // Get reference base from VCF or Reference
VariantContext referenceContext = tracker.getVariantContext(ref, REFERENCE_ROD_NAME, context.getLocation()); VariantContext referenceContext = tracker.getVariantContext(ref, REFERENCE_ROD_NAME, context.getLocation());
byte trueReferenceBase; ArrayList<Byte> trueReferenceBase = new ArrayList<Byte>();
if (referenceContext.isIndel()) {
return 0; // TODO: add special treatment for extended events. For Now just skip these altogether.
}
// Site is not a variant, take from the reference // Site is not a variant, take from the reference
if (referenceContext == null) { if (referenceContext == null) {
trueReferenceBase = ref.getBase(); trueReferenceBase.add(ref.getBase());
} }
// Site has a VCF entry -- is variant // Site has a VCF entry -- is variant
@ -172,14 +178,13 @@ public class ReplicationValidationWalker extends LocusWalker<Integer, Long> impl
return 0; return 0;
} }
// Site is HomVar -- easy, take the only alt allele. Genotype referenceGenotype = referenceContext.getGenotype(referenceSampleName);
else if (referenceContext.getGenotype(referenceSampleName).isHomVar()) { List<Allele> referenceAlleles = referenceGenotype.getAlleles();
trueReferenceBase = referenceContext.getAlternateAllele(0).getBases()[0]; for (Allele allele : referenceAlleles) {
} byte [] bases = allele.getBases();
for (byte b : bases) {
// TODO: treat HET cases specially? trueReferenceBase.add(b);
else { }
return 0;
} }
} }
@ -197,8 +202,6 @@ public class ReplicationValidationWalker extends LocusWalker<Integer, Long> impl
ReadBackedPileup poolPileup = lanePileup.getPileupForSampleNames(samples); ReadBackedPileup poolPileup = lanePileup.getPileupForSampleNames(samples);
//System.out.println(ref.getLocus().getContig() + ":" + ref.getLocus().getStart());
// create a reference pileup to build error model // create a reference pileup to build error model
ReadBackedPileup referenceSamplePileup = lanePileup.getPileupForSampleName(referenceSampleName); ReadBackedPileup referenceSamplePileup = lanePileup.getPileupForSampleName(referenceSampleName);