Program: 56236
Project: 56236
Buggy source:
public void repairStages(){
  final Map<ExecutionGroupVertex,Integer> stageNumbers=new HashMap<ExecutionGroupVertex,Integer>();
  ExecutionGroupVertexIterator it=new ExecutionGroupVertexIterator(this,true,-1);
  while (it.hasNext()) {
    final ExecutionGroupVertex groupVertex=it.next();
    int precedingNumber=0;
    if (stageNumbers.containsKey(groupVertex)) {
      precedingNumber=stageNumbers.get(groupVertex).intValue();
    }
 else {
      stageNumbers.put(groupVertex,new Integer(precedingNumber));
    }
    for (int i=0; i < groupVertex.getNumberOfForwardLinks(); i++) {
      final ExecutionGroupEdge edge=groupVertex.getForwardEdge(i);
      if (!stageNumbers.containsKey(edge.getTargetVertex())) {
        if (edge.getChannelType() != ChannelType.FILE) {
          stageNumbers.put(edge.getTargetVertex(),new Integer(precedingNumber));
        }
 else {
          stageNumbers.put(edge.getTargetVertex(),new Integer(precedingNumber + 1));
        }
      }
 else {
        final int stageNumber=stageNumbers.get(edge.getTargetVertex()).intValue();
        if (edge.getChannelType() != ChannelType.FILE) {
          if (stageNumber != precedingNumber) {
            stageNumbers.put(edge.getTargetVertex(),(int)Math.max(precedingNumber,stageNumber));
          }
        }
 else {
          if (stageNumber != (precedingNumber + 1)) {
            stageNumbers.put(edge.getTargetVertex(),(int)Math.max(precedingNumber + 1,stageNumber));
          }
        }
      }
    }
  }
  it=new ExecutionGroupVertexIterator(this,false,-1);
  while (it.hasNext()) {
    final ExecutionGroupVertex groupVertex=it.next();
    final int succeedingNumber=stageNumbers.get(groupVertex);
    for (int i=0; i < groupVertex.getNumberOfBackwardLinks(); i++) {
      final ExecutionGroupEdge edge=groupVertex.getBackwardEdge(i);
      final int stageNumber=stageNumbers.get(edge.getSourceVertex());
      if (edge.getChannelType() == ChannelType.FILE) {
        if (stageNumber < (succeedingNumber - 1)) {
          stageNumbers.put(edge.getSourceVertex(),new Integer(succeedingNumber - 1));
        }
      }
 else {
        if (stageNumber != succeedingNumber) {
          LOG.error(edge.getSourceVertex() + "String_Node_Str" + edge.getTargetVertex()+ "String_Node_Str");
        }
      }
    }
  }
  this.stages.clear();
  final Iterator<ExecutionGroupVertex> it2=stageNumbers.keySet().iterator();
  while (it2.hasNext()) {
    final ExecutionGroupVertex groupVertex=it2.next();
    final int stageNumber=stageNumbers.get(groupVertex).intValue();
    while (this.stages.size() <= stageNumber) {
      this.stages.add(null);
    }
    ExecutionStage executionStage=this.stages.get(stageNumber);
    if (executionStage == null) {
      executionStage=new ExecutionStage(stageNumber);
      this.stages.set(stageNumber,executionStage);
    }
    executionStage.addStageMember(groupVertex);
    groupVertex.setExecutionStage(executionStage);
  }
}

Fixed version (ground truth):
public void repairStages(){
  final Map<ExecutionGroupVertex,Integer> stageNumbers=new HashMap<ExecutionGroupVertex,Integer>();
  ExecutionGroupVertexIterator it=new ExecutionGroupVertexIterator(this,true,-1);
  while (it.hasNext()) {
    final ExecutionGroupVertex groupVertex=it.next();
    int precedingNumber=0;
    if (stageNumbers.containsKey(groupVertex)) {
      precedingNumber=stageNumbers.get(groupVertex).intValue();
    }
 else {
      stageNumbers.put(groupVertex,Integer.valueOf(precedingNumber));
    }
    for (int i=0; i < groupVertex.getNumberOfForwardLinks(); i++) {
      final ExecutionGroupEdge edge=groupVertex.getForwardEdge(i);
      if (!stageNumbers.containsKey(edge.getTargetVertex())) {
        if (edge.getChannelType() != ChannelType.FILE) {
          stageNumbers.put(edge.getTargetVertex(),Integer.valueOf(precedingNumber));
        }
 else {
          stageNumbers.put(edge.getTargetVertex(),Integer.valueOf(precedingNumber + 1));
        }
      }
 else {
        final int stageNumber=stageNumbers.get(edge.getTargetVertex()).intValue();
        if (edge.getChannelType() != ChannelType.FILE) {
          if (stageNumber != precedingNumber) {
            stageNumbers.put(edge.getTargetVertex(),(int)Math.max(precedingNumber,stageNumber));
          }
        }
 else {
          if (stageNumber != (precedingNumber + 1)) {
            stageNumbers.put(edge.getTargetVertex(),(int)Math.max(precedingNumber + 1,stageNumber));
          }
        }
      }
    }
  }
  it=new ExecutionGroupVertexIterator(this,false,-1);
  while (it.hasNext()) {
    final ExecutionGroupVertex groupVertex=it.next();
    final int succeedingNumber=stageNumbers.get(groupVertex);
    for (int i=0; i < groupVertex.getNumberOfBackwardLinks(); i++) {
      final ExecutionGroupEdge edge=groupVertex.getBackwardEdge(i);
      final int stageNumber=stageNumbers.get(edge.getSourceVertex());
      if (edge.getChannelType() == ChannelType.FILE) {
        if (stageNumber < (succeedingNumber - 1)) {
          stageNumbers.put(edge.getSourceVertex(),Integer.valueOf(succeedingNumber - 1));
        }
      }
 else {
        if (stageNumber != succeedingNumber) {
          LOG.error(edge.getSourceVertex() + "String_Node_Str" + edge.getTargetVertex()+ "String_Node_Str");
        }
      }
    }
  }
  this.stages.clear();
  final Iterator<Map.Entry<ExecutionGroupVertex,Integer>> it2=stageNumbers.entrySet().iterator();
  while (it2.hasNext()) {
    final Map.Entry<ExecutionGroupVertex,Integer> entry=it2.next();
    final ExecutionGroupVertex groupVertex=entry.getKey();
    final int stageNumber=entry.getValue().intValue();
    while (this.stages.size() <= stageNumber) {
      this.stages.add(null);
    }
    ExecutionStage executionStage=this.stages.get(stageNumber);
    if (executionStage == null) {
      executionStage=new ExecutionStage(stageNumber);
      this.stages.set(stageNumber,executionStage);
    }
    executionStage.addStageMember(groupVertex);
    groupVertex.setExecutionStage(executionStage);
  }
}