Program: 25509
Project: 25509
Buggy source:
private void alignTier() throws IOException {
  LOG.info("String_Node_Str");
  final List<HierarchicalStack> stacksWithMatches=tierStacks.stream().filter(HierarchicalStack::hasMatchPairs).collect(Collectors.toList());
  final List<HierarchicalStack> stacksToAlign;
  if (parameters.keepExisting(PipelineStep.ALIGN)) {
    stacksToAlign=stacksWithMatches.stream().filter(HierarchicalStack::requiresAlignment).collect(Collectors.toList());
    LOG.info("String_Node_Str",(stacksWithMatches.size() - stacksToAlign.size()),stacksWithMatches.size());
  }
 else {
    stacksToAlign=stacksWithMatches;
  }
  if (stacksToAlign.size() > 0) {
    final EMAlignerTool solver=new EMAlignerTool(new File(parameters.solverScript),new File(parameters.solverParametersTemplate));
    final Broadcast<EMAlignerTool> broadcastEMAlignerTool=sparkContext.broadcast(solver);
    final HierarchicalTierSolveFunction solveStacksFunction=new HierarchicalTierSolveFunction(parameters.boxBaseDataUrl,broadcastEMAlignerTool);
    for (    final HierarchicalStack tierStack : stacksToAlign) {
      driverTierRender.deleteStack(tierStack.getAlignedStackId().getStack(),null);
    }
    final JavaRDD<HierarchicalStack> rddTierStacksToAlign=sparkContext.parallelize(stacksToAlign);
    final JavaRDD<HierarchicalStack> rddTierStacksAfterAlignment=rddTierStacksToAlign.map(solveStacksFunction);
    final List<HierarchicalStack> tierStacksAfterAlignment=rddTierStacksAfterAlignment.collect();
    LOG.info("String_Node_Str");
    final Map<String,HierarchicalStack> nameToUpdatedStackMap=new HashMap<>(tierStacksAfterAlignment.size() * 2);
    for (    final HierarchicalStack tierStack : tierStacksAfterAlignment) {
      final String tierStackName=tierStack.getSplitStackId().getStack();
      LOG.info("String_Node_Str",tierStackName,tierStack.getAlignmentQuality());
      driverTierRender.setHierarchicalData(tierStackName,tierStack);
      nameToUpdatedStackMap.put(tierStackName,tierStack);
    }
    HierarchicalStack tierStack;
    HierarchicalStack updatedStack;
    for (int i=0; i < tierStacks.size(); i++) {
      tierStack=tierStacks.get(i);
      updatedStack=nameToUpdatedStackMap.get(tierStack.getSplitStackId().getStack());
      if (updatedStack != null) {
        tierStacks.set(i,updatedStack);
      }
    }
  }
 else {
    LOG.info("String_Node_Str");
  }
  LOG.info("String_Node_Str");
}

Fixed version (ground truth):
private void alignTier() throws IOException {
  LOG.info("String_Node_Str");
  final List<HierarchicalStack> stacksWithMatches=tierStacks.stream().filter(HierarchicalStack::hasMatchPairs).collect(Collectors.toList());
  final List<HierarchicalStack> stacksToAlign;
  if (parameters.keepExisting(PipelineStep.ALIGN)) {
    stacksToAlign=stacksWithMatches.stream().filter(HierarchicalStack::requiresAlignment).collect(Collectors.toList());
    LOG.info("String_Node_Str",(stacksWithMatches.size() - stacksToAlign.size()),stacksWithMatches.size());
  }
 else {
    stacksToAlign=stacksWithMatches;
  }
  if (stacksToAlign.size() > 0) {
    final EMAlignerTool solver=new EMAlignerTool(new File(parameters.solverScript),new File(parameters.solverParametersTemplate));
    final Broadcast<EMAlignerTool> broadcastEMAlignerTool=sparkContext.broadcast(solver);
    final HierarchicalTierSolveFunction solveStacksFunction=new HierarchicalTierSolveFunction(parameters.boxBaseDataUrl,broadcastEMAlignerTool);
    for (    final HierarchicalStack tierStack : stacksToAlign) {
      driverTierRender.deleteStack(tierStack.getAlignedStackId().getStack(),null);
    }
    final JavaRDD<HierarchicalStack> rddTierStacksToAlign=sparkContext.parallelize(stacksToAlign);
    final JavaRDD<HierarchicalStack> rddTierStacksAfterAlignment=rddTierStacksToAlign.map(solveStacksFunction);
    final List<HierarchicalStack> tierStacksAfterAlignment=rddTierStacksAfterAlignment.collect();
    LOG.info("String_Node_Str");
    final Map<String,HierarchicalStack> nameToUpdatedStackMap=new HashMap<>(tierStacksAfterAlignment.size() * 2);
    for (    final HierarchicalStack tierStack : tierStacksAfterAlignment) {
      final String tierStackName=tierStack.getSplitStackId().getStack();
      LOG.info("String_Node_Str",tierStackName,tierStack.getAlignmentQuality());
      persistHierarchicalData(tierStack);
      nameToUpdatedStackMap.put(tierStackName,tierStack);
    }
    HierarchicalStack tierStack;
    HierarchicalStack updatedStack;
    for (int i=0; i < tierStacks.size(); i++) {
      tierStack=tierStacks.get(i);
      updatedStack=nameToUpdatedStackMap.get(tierStack.getSplitStackId().getStack());
      if (updatedStack != null) {
        tierStacks.set(i,updatedStack);
      }
    }
  }
 else {
    LOG.info("String_Node_Str");
  }
  LOG.info("String_Node_Str");
}