Program: 50435
Project: 50435
Buggy source:
/** 
 * Skip all entries that have position before (targetIndex,position). This method will use the alignment index to skip directly to the closest chunk start before the entry identified by targetIndex and position.
 * @param targetIndex The index of the target sequence to skip to.
 * @param position    The position on the target sequence.
 * @return The next entry, at position or past position (if not entry at position is found).
 * @throws IOException If an error occurs reading the alignment header. The header is accessed to check that the alignment is sorted.
 */
public final Alignments.AlignmentEntry skipTo(final int targetIndex,final int position) throws IOException {
{
    Bucket bucket;
    while (!entryHeap.isEmpty()) {
      bucket=entryHeap.first();
      if (bucket.entry.getTargetIndex() < targetIndex || bucket.entry.getPosition() < position) {
        Bucket removed=entryHeap.dequeue();
        nextLoadedForReader[removed.readerIndex]=false;
      }
 else {
        break;
      }
    }
  }
  for (  final int readerIndex : readersWithMoreEntries) {
    if (!nextLoadedForReader[readerIndex]) {
      activeIndex=readerIndex;
      final AlignmentReader reader=readers[activeIndex];
      final Alignments.AlignmentEntry alignmentEntry=reader.skipTo(targetIndex,position);
      if (alignmentEntry == null) {
        readersWithMoreEntries.remove(activeIndex);
      }
 else {
        nextLoadedForReader[readerIndex]=true;
        final Bucket bucket=buckets[readerIndex];
        bucket.entry=alignmentEntry;
        bucket.readerIndex=readerIndex;
        entryHeap.enqueue(bucket);
      }
    }
  }
  if (entryHeap.isEmpty())   return null;
  final Bucket bucket=entryHeap.dequeue();
  nextLoadedForReader[bucket.readerIndex]=false;
  hasNext=false;
  final Alignments.AlignmentEntry alignmentEntry=bucket.entry;
  final int newQueryIndex=mergedQueryIndex(alignmentEntry.getQueryIndex());
  if (adjustQueryIndices) {
    return alignmentEntry.newBuilderForType().mergeFrom(alignmentEntry).setQueryIndex(newQueryIndex).build();
  }
 else {
    return alignmentEntry;
  }
}

Fixed version (ground truth):
/** 
 * Skip all entries that have position before (targetIndex,position). This method will use the alignment index to skip directly to the closest chunk start before the entry identified by targetIndex and position.
 * @param targetIndex The index of the target sequence to skip to.
 * @param position    The position on the target sequence.
 * @return The next entry, at position or past position (if not entry at position is found).
 * @throws IOException If an error occurs reading the alignment header. The header is accessed to check that the alignment is sorted.
 */
public final Alignments.AlignmentEntry skipTo(final int targetIndex,final int position) throws IOException {
{
    Bucket bucket;
    while (!entryHeap.isEmpty()) {
      bucket=entryHeap.first();
      if (bucket.entry.getTargetIndex() < targetIndex || bucket.entry.getPosition() < position) {
        Bucket removed=entryHeap.dequeue();
        nextLoadedForReader[removed.readerIndex]=false;
      }
 else {
        break;
      }
    }
  }
  for (  final int readerIndex : readersWithMoreEntries) {
    if (!nextLoadedForReader[readerIndex]) {
      activeIndex=readerIndex;
      final AlignmentReader reader=readers[activeIndex];
      final Alignments.AlignmentEntry alignmentEntry=reader.skipTo(targetIndex,position);
      if (alignmentEntry == null) {
        readersWithMoreEntries.remove(activeIndex);
      }
 else {
        nextLoadedForReader[readerIndex]=true;
        final Bucket bucket=buckets[readerIndex];
        bucket.entry=alignmentEntry;
        bucket.readerIndex=readerIndex;
        entryHeap.enqueue(bucket);
      }
    }
  }
  if (entryHeap.isEmpty())   return null;
  final Bucket bucket=entryHeap.dequeue();
  nextLoadedForReader[bucket.readerIndex]=false;
  hasNext=false;
  final Alignments.AlignmentEntry alignmentEntry=bucket.entry;
  activeIndex=bucket.readerIndex;
  final int newQueryIndex=mergedQueryIndex(alignmentEntry.getQueryIndex());
  if (adjustQueryIndices) {
    return alignmentEntry.newBuilderForType().mergeFrom(alignmentEntry).setQueryIndex(newQueryIndex).build();
  }
 else {
    return alignmentEntry;
  }
}