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Fixing merge conflict

This commit is contained in:
Eric Banks 2012-08-27 12:16:51 -04:00
parent 63a9ae817a 3d476487c6
commit bedcdbdc5f
2 changed files with 1 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++;

1
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java
View File

@ -97,7 +97,6 @@ public class DepthPerAlleleBySample extends GenotypeAnnotation implements Standa
if (!vc.getAlleles().contains(a)) if (!vc.getAlleles().contains(a))
continue; // sanity check - shouldn't be needed continue; // sanity check - shouldn't be needed
alleleCounts.put(a,alleleCounts.get(a)+1); alleleCounts.put(a,alleleCounts.get(a)+1);
} }
final int[] counts = new int[alleleCounts.size()]; final int[] counts = new int[alleleCounts.size()];
counts[0] = alleleCounts.get(vc.getReference()); counts[0] = alleleCounts.get(vc.getReference());