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LIBS is totally busted for deletions. Putting a check in AD for bad pileup event bases so that we don't produce busted alleles. We must fix LIBS ASAP.

This commit is contained in:
Eric Banks 2012-08-27 12:13:12 -04:00
parent dcc972a557
commit 3d476487c6
2 changed files with 6 additions and 1 deletions
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1
public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java
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@ -318,6 +318,7 @@ public class LocusIteratorByState extends LocusIterator {
continue; continue;
if (op == CigarOperator.D) { if (op == CigarOperator.D) {
// TODO -- LIBS is totally busted for deletions so that reads with Ds right before Is in their CIGAR are broken; must fix
if (readInfo.includeReadsWithDeletionAtLoci()) { // only add deletions to the pileup if we are authorized to do so if (readInfo.includeReadsWithDeletionAtLoci()) { // only add deletions to the pileup if we are authorized to do so
pile.add(new PileupElement(read, readOffset, true, isBeforeDeletion, isAfterDeletion, isBeforeInsertion, isAfterInsertion, isNextToSoftClip, null, nextOp == CigarOperator.D ? nextElementLength : -1)); pile.add(new PileupElement(read, readOffset, true, isBeforeDeletion, isAfterDeletion, isBeforeInsertion, isAfterInsertion, isNextToSoftClip, null, nextOp == CigarOperator.D ? nextElementLength : -1));
size++; size++;

6
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java
View File

@ -88,7 +88,11 @@ public class DepthPerAlleleBySample extends GenotypeAnnotation implements Standa
for ( PileupElement p : pileup ) { for ( PileupElement p : pileup ) {
if ( p.isBeforeInsertion() ) { if ( p.isBeforeInsertion() ) {
final Allele insertion = Allele.create((char)refBase + p.getEventBases(), false); final String eventBases = p.getEventBases();
if ( eventBases == null )
continue;
final Allele insertion = Allele.create((char)refBase + eventBases, false);
if ( alleleCounts.containsKey(insertion) ) { if ( alleleCounts.containsKey(insertion) ) {
alleleCounts.put(insertion, alleleCounts.get(insertion)+1); alleleCounts.put(insertion, alleleCounts.get(insertion)+1);
} }