Program: 30560
Project: 30560
Buggy source:
public static Set<VCFHeaderLine> smartMergeHeaders(Collection<VCFHeader> headers,boolean emitWarnings) throws IllegalStateException {
  HashMap<String,VCFHeaderLine> map=new HashMap<String,VCFHeaderLine>();
  HeaderConflictWarner conflictWarner=new HeaderConflictWarner(emitWarnings);
  for (  VCFHeader source : headers) {
    for (    VCFHeaderLine line : source.getMetaDataInSortedOrder()) {
      String key=line.getKey();
      if (line instanceof VCFIDHeaderLine)       key=key + "String_Node_Str" + ((VCFIDHeaderLine)line).getID();
      if (map.containsKey(key)) {
        VCFHeaderLine other=map.get(key);
        if (line.equals(other)) {
        }
 else         if (!line.getClass().equals(other.getClass())) {
          throw new IllegalStateException("String_Node_Str" + line + "String_Node_Str"+ other);
        }
 else         if (line instanceof VCFFilterHeaderLine) {
          String lineName=((VCFFilterHeaderLine)line).getID();
          String otherName=((VCFFilterHeaderLine)other).getID();
          if (!lineName.equals(otherName))           throw new IllegalStateException("String_Node_Str" + line + "String_Node_Str"+ other);
        }
 else         if (line instanceof VCFCompoundHeaderLine) {
          VCFCompoundHeaderLine compLine=(VCFCompoundHeaderLine)line;
          VCFCompoundHeaderLine compOther=(VCFCompoundHeaderLine)other;
          if (!(compLine).equalsExcludingDescription(compOther)) {
            if (compLine.getType().equals(compOther.getType())) {
              conflictWarner.warn(line,"String_Node_Str" + line + "String_Node_Str"+ other);
              compOther.setNumberToUnbounded();
            }
 else             if (compLine.getType() == VCFHeaderLineType.Integer && compOther.getType() == VCFHeaderLineType.Float) {
              conflictWarner.warn(line,"String_Node_Str" + compOther);
              map.put(key,compOther);
            }
 else             if (compLine.getType() == VCFHeaderLineType.Float && compOther.getType() == VCFHeaderLineType.Integer) {
              conflictWarner.warn(line,"String_Node_Str" + compOther);
            }
 else {
              throw new IllegalStateException("String_Node_Str" + line + "String_Node_Str"+ other);
            }
          }
          if (!compLine.getDescription().equals(compOther.getDescription()))           conflictWarner.warn(line,"String_Node_Str" + compOther + "String_Node_Str"+ compLine);
        }
 else {
          conflictWarner.warn(line,"String_Node_Str" + line + "String_Node_Str"+ other);
        }
      }
 else {
        map.put(key,line);
      }
    }
  }
  return new HashSet<VCFHeaderLine>(map.values());
}

Fixed version (ground truth):
public static Set<VCFHeaderLine> smartMergeHeaders(final Collection<VCFHeader> headers,final boolean emitWarnings) throws IllegalStateException {
  final TreeMap<String,VCFHeaderLine> map=new TreeMap<String,VCFHeaderLine>();
  final HeaderConflictWarner conflictWarner=new HeaderConflictWarner(emitWarnings);
  for (  final VCFHeader source : headers) {
    for (    final VCFHeaderLine line : source.getMetaDataInSortedOrder()) {
      String key=line.getKey();
      if (line instanceof VCFIDHeaderLine)       key=key + "String_Node_Str" + ((VCFIDHeaderLine)line).getID();
      if (map.containsKey(key)) {
        final VCFHeaderLine other=map.get(key);
        if (line.equals(other)) {
        }
 else         if (!line.getClass().equals(other.getClass())) {
          throw new IllegalStateException("String_Node_Str" + line + "String_Node_Str"+ other);
        }
 else         if (line instanceof VCFFilterHeaderLine) {
          final String lineName=((VCFFilterHeaderLine)line).getID();
          final String otherName=((VCFFilterHeaderLine)other).getID();
          if (!lineName.equals(otherName))           throw new IllegalStateException("String_Node_Str" + line + "String_Node_Str"+ other);
        }
 else         if (line instanceof VCFCompoundHeaderLine) {
          final VCFCompoundHeaderLine compLine=(VCFCompoundHeaderLine)line;
          final VCFCompoundHeaderLine compOther=(VCFCompoundHeaderLine)other;
          if (!(compLine).equalsExcludingDescription(compOther)) {
            if (compLine.getType().equals(compOther.getType())) {
              conflictWarner.warn(line,"String_Node_Str" + line + "String_Node_Str"+ other);
              compOther.setNumberToUnbounded();
            }
 else             if (compLine.getType() == VCFHeaderLineType.Integer && compOther.getType() == VCFHeaderLineType.Float) {
              conflictWarner.warn(line,"String_Node_Str" + compOther);
              map.put(key,compOther);
            }
 else             if (compLine.getType() == VCFHeaderLineType.Float && compOther.getType() == VCFHeaderLineType.Integer) {
              conflictWarner.warn(line,"String_Node_Str" + compOther);
            }
 else {
              throw new IllegalStateException("String_Node_Str" + line + "String_Node_Str"+ other);
            }
          }
          if (!compLine.getDescription().equals(compOther.getDescription()))           conflictWarner.warn(line,"String_Node_Str" + compOther + "String_Node_Str"+ compLine);
        }
 else {
          conflictWarner.warn(line,"String_Node_Str" + line + "String_Node_Str"+ other);
        }
      }
 else {
        map.put(key,line);
      }
    }
  }
  return new LinkedHashSet<VCFHeaderLine>(map.values());
}