| Chunk |
|---|
| Conflicting content |
|---|
if (op == CigarOperator.D) {
if (readInfo.includeReadsWithDeletionAtLoci()) { // only add deletions to the pileup if we are authorized to do so
<<<<<<< HEAD
int leftAlignedStart = (eventStartOffset < 0) ? readOffset : eventStartOffset;
pile.add(new PileupElement(read, leftAlignedStart, true, nextOp == CigarOperator.I, nextOp == CigarOperator.S || (state.getGenomeOffset() == 0 && read.getSoftStart() != read.getAlignmentStart())));
=======
pile.add(new PileupElement(read, readOffset, true, nextOp == CigarOperator.I, false));
>>>>>>> 7f70612bebde5a535426d925562212097563a82e
size++;
nDeletions++;
if (read.getMappingQuality() == 0) |
| Solution content |
|---|
if (op == CigarOperator.D) {
if (readInfo.includeReadsWithDeletionAtLoci()) { // only add deletions to the pileup if we are authorized to do so
pile.add(new PileupElement(read, readOffset, true, nextOp == CigarOperator.I, nextOp == CigarOperator.S || (state.getGenomeOffset() == 0 && read.getSoftStart() != read.getAlignmentStart())));
size++;
nDeletions++;
if (read.getMappingQuality() == 0) |
| File |
|---|
| LocusIteratorByState.java |
| Developer's decision |
|---|
| Manual |
| Kind of conflict |
|---|
| Attribute |
| Method invocation |
| Variable |