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a) Bug fixes for last commit related to PileupElements (unit tests are forthcoming). b) Changes needed to make pool caller work in GENOTYPE_GIVEN_ALLELES mode c) Bug fix (yet again) for UG when GENOTYPE_GIVEN_ALLELES and EMIT_ALL_SITES are on, when there's no coverage at site and when input vcf has genotypes: output vcf would still inherit genotypes from input vcf. Now, we just build vc from scratch instead of initializing from input vc. We just take location and alleles from vc

This commit is contained in:
Guillermo del Angel 2012-02-24 10:27:59 -05:00
parent 6866a41914
commit c9a4c74f7a
3 changed files with 9 additions and 1 deletions
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2
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
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@ -253,7 +253,7 @@ public class UnifiedGenotyperEngine {
VariantContext vcInput = UnifiedGenotyperEngine.getVCFromAllelesRod(tracker, ref, rawContext.getLocation(), false, logger, UAC.alleles);
if ( vcInput == null )
return null;
vc = new VariantContextBuilder(vcInput).source("UG_call").noID().referenceBaseForIndel(ref.getBase()).attributes(new HashMap<String, Object>()).filters(new HashSet<String>()).make();
vc = new VariantContextBuilder("UG_call", ref.getLocus().getContig(), ref.getLocus().getStart(), ref.getLocus().getStart(), vcInput.getAlleles()).make();
} else {
// deal with bad/non-standard reference bases
if ( !Allele.acceptableAlleleBases(new byte[]{ref.getBase()}) )

3
public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java
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@ -69,6 +69,9 @@ public class PileupElement implements Comparable<PileupElement> {
eventLength = -1;
}
public PileupElement(final GATKSAMRecord read, final int offset, final boolean isDeletion, final boolean isBeforeDeletion, final boolean isBeforeInsertion, final boolean isNextToSoftClip) {
this(read,offset, isDeletion, isBeforeDeletion, isBeforeInsertion, isNextToSoftClip, null, -1);
}
public boolean isDeletion() {
return isDeletion;
}

5
public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileupImpl.java
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@ -99,6 +99,11 @@ public class ReadBackedExtendedEventPileupImpl extends AbstractReadBackedPileup<
protected ExtendedEventPileupElement createNewPileupElement(GATKSAMRecord read, int offset, boolean isDeletion, boolean isBeforeDeletion, boolean isBeforeInsertion, boolean isNextToSoftClip) {
throw new UnsupportedOperationException("Not enough information provided to create a new pileup element");
}
@Override
protected ExtendedEventPileupElement createNewPileupElement(GATKSAMRecord read, int offset, boolean isDeletion, boolean isBeforeDeletion, boolean isBeforeInsertion,
boolean isNextToSoftClip,String nextEventBases, int nextEventLength) {
throw new UnsupportedOperationException("Not enough information provided to create a new pileup element");
}
/**