Program: 12481
Project: 12481
Buggy source:
private static String locationStr(Location location,int offset,boolean complement,Location location2) throws SBOLConversionException {
  int start;
  int end;
  String locationStr="String_Node_Str";
  boolean isCut=false;
  if (location instanceof Range) {
    Range range=(Range)location;
    start=offset + range.getStart();
    end=offset + range.getEnd();
  }
 else   if (location instanceof Cut) {
    Cut cut=(Cut)location;
    start=offset + cut.getAt();
    end=offset + cut.getAt() + 1;
    isCut=true;
  }
 else {
    throw new SBOLConversionException("String_Node_Str" + location.getIdentity() + "String_Node_Str");
  }
  if (location2 != null) {
    if (location2 instanceof Range) {
      Range range=(Range)location2;
      end=offset + range.getEnd();
    }
 else     if (location2 instanceof Cut) {
      Cut cut=(Cut)location2;
      end=offset + cut.getAt() + 1;
    }
  }
  if (complement) {
    locationStr+="String_Node_Str";
  }
  if (location.getAnnotation(new QName(GBNAMESPACE,STARTLESSTHAN,GBPREFIX)) != null) {
    locationStr+="String_Node_Str";
  }
  locationStr+=start;
  if (isCut) {
    locationStr+="String_Node_Str";
  }
 else   if (location.getAnnotation(new QName(GBNAMESPACE,SINGLEBASERANGE,GBPREFIX)) != null) {
    locationStr+="String_Node_Str";
  }
 else {
    locationStr+="String_Node_Str";
  }
  if (location.getAnnotation(new QName(GBNAMESPACE,ENDGREATERTHAN,GBPREFIX)) != null) {
    locationStr+="String_Node_Str";
  }
  locationStr+=end;
  if (complement) {
    locationStr+="String_Node_Str";
  }
  return locationStr;
}

Fixed version (ground truth):
private static String locationStr(Location location,int offset,boolean complement,Location location2) throws SBOLConversionException {
  int start;
  int end;
  String locationStr="String_Node_Str";
  boolean isCut=false;
  if (location instanceof Range) {
    Range range=(Range)location;
    start=offset + range.getStart();
    end=offset + range.getEnd();
  }
 else   if (location instanceof Cut) {
    Cut cut=(Cut)location;
    start=offset + cut.getAt();
    end=offset + cut.getAt() + 1;
    isCut=true;
  }
 else {
    throw new SBOLConversionException("String_Node_Str" + location.getIdentity() + "String_Node_Str");
  }
  if (location2 != null) {
    if (location2 instanceof Range) {
      Range range=(Range)location2;
      end=offset + range.getEnd();
    }
 else     if (location2 instanceof Cut) {
      Cut cut=(Cut)location2;
      end=offset + cut.getAt() + 1;
    }
  }
  if (complement) {
    locationStr+="String_Node_Str";
  }
  if (location.getAnnotation(new QName(GBCONVNAMESPACE,STARTLESSTHAN,GBCONVPREFIX)) != null) {
    locationStr+="String_Node_Str";
  }
  locationStr+=start;
  if (isCut) {
    locationStr+="String_Node_Str";
  }
 else   if (location.getAnnotation(new QName(GBCONVNAMESPACE,SINGLEBASERANGE,GBCONVPREFIX)) != null) {
    locationStr+="String_Node_Str";
  }
 else {
    locationStr+="String_Node_Str";
  }
  if (location.getAnnotation(new QName(GBCONVNAMESPACE,ENDGREATERTHAN,GBCONVPREFIX)) != null) {
    locationStr+="String_Node_Str";
  }
  locationStr+=end;
  if (complement) {
    locationStr+="String_Node_Str";
  }
  return locationStr;
}