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HaplotypeCaller now creates MNP and complex substitutions by using LD information to decide if events segregate together on haplotypes. Added unit test.

This commit is contained in:
Ryan Poplin 2012-07-02 16:37:39 -04:00
parent b6093ff02c
commit b807ff63ef
1 changed files with 9 additions and 0 deletions
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9
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ClippingRankSumTest.java
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@ -25,6 +25,9 @@ public class ClippingRankSumTest extends RankSumTest {
public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("ClippingRankSum", 1, VCFHeaderLineType.Float, "Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases")); } public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("ClippingRankSum", 1, VCFHeaderLineType.Float, "Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases")); }
protected void fillQualsFromPileup(byte ref, List<Byte> alts, ReadBackedPileup pileup, List<Double> refQuals, List<Double> altQuals) { protected void fillQualsFromPileup(byte ref, List<Byte> alts, ReadBackedPileup pileup, List<Double> refQuals, List<Double> altQuals) {
return;
// This working implementation below needs to be tested for the UG pipeline
/*
for ( final PileupElement p : pileup ) { for ( final PileupElement p : pileup ) {
if ( isUsableBase(p) ) { if ( isUsableBase(p) ) {
if ( p.getBase() == ref ) { if ( p.getBase() == ref ) {
@ -34,6 +37,7 @@ public class ClippingRankSumTest extends RankSumTest {
} }
} }
} }
*/
} }
protected void fillQualsFromPileup(final Allele ref, final List<Allele> alts, final int refLoc, final Map<Allele, List<GATKSAMRecord>> stratifiedContext, final List<Double> refQuals, final List<Double> altQuals) { protected void fillQualsFromPileup(final Allele ref, final List<Allele> alts, final int refLoc, final Map<Allele, List<GATKSAMRecord>> stratifiedContext, final List<Double> refQuals, final List<Double> altQuals) {
@ -53,6 +57,10 @@ public class ClippingRankSumTest extends RankSumTest {
} }
protected void fillIndelQualsFromPileup(ReadBackedPileup pileup, List<Double> refQuals, List<Double> altQuals) { protected void fillIndelQualsFromPileup(ReadBackedPileup pileup, List<Double> refQuals, List<Double> altQuals) {
return;
// This working implementation below needs to be tested for the UG pipeline
/*
// equivalent is whether indel likelihoods for reads corresponding to ref allele are more likely than reads corresponding to alt allele ? // equivalent is whether indel likelihoods for reads corresponding to ref allele are more likely than reads corresponding to alt allele ?
HashMap<PileupElement,LinkedHashMap<Allele,Double>> indelLikelihoodMap = IndelGenotypeLikelihoodsCalculationModel.getIndelLikelihoodMap(); HashMap<PileupElement,LinkedHashMap<Allele,Double>> indelLikelihoodMap = IndelGenotypeLikelihoodsCalculationModel.getIndelLikelihoodMap();
for (final PileupElement p: pileup) { for (final PileupElement p: pileup) {
@ -78,5 +86,6 @@ public class ClippingRankSumTest extends RankSumTest {
altQuals.add((double)AlignmentUtils.getNumHardClippedBases(p.getRead())); altQuals.add((double)AlignmentUtils.getNumHardClippedBases(p.getRead()));
} }
} }
*/
} }
} }