nus-yam/ex-repair huggingface dataset:
Program: 13644
Project: 13644
Buggy source:
/** 
 * account falko@sensorberg.com https://manage.sensorberg.com/#/applications/edit/38eda3c5-649e-4178-9682-314d14abf1fe https://manage.sensorberg.com/#/campaign/edit/bd67e5ec-4426-4f51-b962-6beea2c82695 https://manage.sensorberg.com/#/beacon/view/14053e1f-567b-43e5-818f-811c700b7ae4
 */
public void test_enter_exit_action(){
  URLFactory.Conf env=URLFactory.switchToProductionEnvironment();
  androidPlattform.getTransport().setApiToken("String_Node_Str");
  ResolverListener mockListener=new ResolverListener(){
    @Override public void onResolutionFailed(    Resolution resolution,    Throwable cause){
      fail(cause.getMessage());
    }
    @Override public void onResolutionsFinished(    List<BeaconEvent> events){
      Assertions.assertThat(events).hasSize(1);
    }
  }
;
  tested.addResolverListener(mockListener);
  ResolutionConfiguration conf=new ResolutionConfiguration();
  conf.setScanEvent(new ScanEvent.Builder().withBeaconId(new BeaconId(UUID.fromString("String_Node_Str"),40122,43878)).withEventMask(ScanEventType.ENTRY.getMask()).build());
  Resolution resolution=tested.createResolution(conf);
  resolution.start();
  URLFactory.restorePreviousConf(env);
}

Fixed version (ground truth):
/** 
 * account falko@sensorberg.com https://manage.sensorberg.com/#/applications/edit/38eda3c5-649e-4178-9682-314d14abf1fe https://manage.sensorberg.com/#/campaign/edit/bd67e5ec-4426-4f51-b962-6beea2c82695 https://manage.sensorberg.com/#/beacon/view/14053e1f-567b-43e5-818f-811c700b7ae4
 */
public void test_enter_exit_action(){
  URLFactory.Conf env=URLFactory.switchToProductionEnvironment();
  androidPlattform.getTransport().setApiToken("String_Node_Str");
  ResolverListener mockListener=new ResolverListener(){
    @Override public void onResolutionFailed(    Resolution resolution,    Throwable cause){
      fail(cause.getMessage());
    }
    @Override public void onResolutionsFinished(    List<BeaconEvent> events){
      Assertions.assertThat(events).hasSize(0);
    }
  }
;
  tested.addResolverListener(mockListener);
  ResolutionConfiguration conf=new ResolutionConfiguration();
  conf.setScanEvent(new ScanEvent.Builder().withBeaconId(new BeaconId(UUID.fromString("String_Node_Str"),40122,43878)).withEventMask(ScanEventType.ENTRY.getMask()).build());
  Resolution resolution=tested.createResolution(conf);
  resolution.start();
  URLFactory.restorePreviousConf(env);
}
Program: 13645
Project: 13645
Buggy source:
private static String getAppVersionString(Context context){
  try {
    PackageInfo myInfo=context.getPackageManager().getPackageInfo(context.getPackageName(),0);
    return URLEncoder.encode(myInfo.versionName) + "String_Node_Str" + myInfo.versionCode;
  }
 catch (  PackageManager.NameNotFoundException e) {
    return "String_Node_Str";
  }
}

Fixed version (ground truth):
private static String getAppVersionString(Context context){
  try {
    PackageInfo myInfo=context.getPackageManager().getPackageInfo(context.getPackageName(),0);
    return URLEncoder.encode(myInfo.versionName) + "String_Node_Str" + myInfo.versionCode;
  }
 catch (  PackageManager.NameNotFoundException e) {
    return "String_Node_Str";
  }
catch (  NullPointerException e) {
    return "String_Node_Str";
  }
}
Program: 13646
Project: 13646
Buggy source:
/** 
 * Reads the contents of an InputStream into a byte[].
 */
private static byte[] streamToBytes(InputStream in,int length) throws IOException {
  byte[] bytes=new byte[length];
  int count;
  int pos=0;
  while (pos < length && ((count=in.read(bytes,pos,length - pos)) != -1)) {
    pos+=count;
  }
  if (pos != length) {
    throw new IOException("String_Node_Str" + length + "String_Node_Str"+ pos+ "String_Node_Str");
  }
  return bytes;
}

Fixed version (ground truth):
/** 
 * Reads the contents of an InputStream into a byte[].
 */
private static byte[] streamToBytes(InputStream in,int length) throws IOException {
  if (length < 0) {
    throw new IOException("String_Node_Str");
  }
  byte[] bytes=new byte[length];
  int count;
  int pos=0;
  while (pos < length && ((count=in.read(bytes,pos,length - pos)) != -1)) {
    pos+=count;
  }
  if (pos != length) {
    throw new IOException("String_Node_Str" + length + "String_Node_Str"+ pos+ "String_Node_Str");
  }
  return bytes;
}
Program: 13647
Project: 13647
Buggy source:
public BeaconEvent map(ResolveAction resolveAction){
  try {
    Action action=ActionFactory.getAction(resolveAction.type,resolveAction.content,UUID.fromString(UUIDUtils.addUuidDashes(resolveAction.eid)),resolveAction.delay * Constants.Time.ONE_SECOND);
    if (action == null) {
      return null;
    }
    return new BeaconEvent.Builder().withAction(action).withSuppressionTime(resolveAction.suppressionTime).withSendOnlyOnce(resolveAction.sendOnlyOnce).withDeliverAtDate(resolveAction.deliverAt).withTrigger(resolveAction.trigger).build();
  }
 catch (  JSONException e) {
    return null;
  }
}

Fixed version (ground truth):
public BeaconEvent map(ResolveAction resolveAction){
  try {
    Action action=ActionFactory.getAction(resolveAction.type,resolveAction.content,UUID.fromString(UUIDUtils.addUuidDashes(resolveAction.eid)),resolveAction.delay * Constants.Time.ONE_SECOND);
    if (action == null) {
      return null;
    }
    return new BeaconEvent.Builder().withAction(action).withSuppressionTime(resolveAction.suppressionTime * Constants.Time.ONE_SECOND).withSendOnlyOnce(resolveAction.sendOnlyOnce).withDeliverAtDate(resolveAction.deliverAt).withTrigger(resolveAction.trigger).build();
  }
 catch (  JSONException e) {
    return null;
  }
}
Program: 13650
Project: 13650
Buggy source:
private void createBootstrapperFromDiskConfiguration(){
  try {
    ServiceConfiguration diskConf=(ServiceConfiguration)FileHelper.getContentsOfFileOrNull(platform.getFile(SERVICE_CONFIGURATION));
    URLFactory.setLayoutURL(diskConf.resolverConfiguration.getResolverLayoutURL().toString());
    if (diskConf.isComplete()) {
      platform.getTransport().setApiToken(diskConf.resolverConfiguration.apiToken);
      bootstrapper=new InternalApplicationBootstrapper(platform);
    }
 else {
      Logger.log.logError("String_Node_Str");
    }
  }
 catch (  Exception e) {
    Logger.log.logError("String_Node_Str" + e);
    e.printStackTrace();
  }
}

Fixed version (ground truth):
private void createBootstrapperFromDiskConfiguration(){
  try {
    ServiceConfiguration diskConf=(ServiceConfiguration)FileHelper.getContentsOfFileOrNull(platform.getFile(SERVICE_CONFIGURATION));
    if (diskConf.resolverConfiguration.getResolverLayoutURL() != null) {
      URLFactory.setLayoutURL(diskConf.resolverConfiguration.getResolverLayoutURL().toString());
    }
    if (diskConf.isComplete()) {
      platform.getTransport().setApiToken(diskConf.resolverConfiguration.apiToken);
      bootstrapper=new InternalApplicationBootstrapper(platform);
    }
 else {
      Logger.log.logError("String_Node_Str");
    }
  }
 catch (  Exception e) {
    Logger.log.logError("String_Node_Str" + e);
    e.printStackTrace();
  }
}
Program: 13656
Project: 13656
Buggy source:
public AnalysisRunner(SequenceFile file,File genomeBaseLocation){
  this.file=file;
  this.annotationSet=annotationSet;
  this.genomeBaseLocation=genomeBaseLocation;
  annotationFromNetwork=true;
}

Fixed version (ground truth):
public AnalysisRunner(SequenceFile file,File genomeBaseLocation){
  this.file=file;
  this.genomeBaseLocation=genomeBaseLocation;
  annotationFromNetwork=true;
}
Program: 13660
Project: 13660
Buggy source:
public Chromosome chr(){
  return chr;
}

Fixed version (ground truth):
/** 
 * Chromosome.
 * @return the chromosome
 */
public Chromosome chr(){
  return chr;
}
Program: 13661
Project: 13661
Buggy source:
private int getY(double y){
  return (getHeight() - 40) - (int)(((getHeight() - 80) / (maxY - minY)) * y);
}

Fixed version (ground truth):
private int getY(double y){
  return (getHeight() - 40) - (int)(((getHeight() - 80) / (maxY - minY)) * (y - minY));
}
Program: 13663
Project: 13663
Buggy source:
@Override public void makeReport(HTMLReportArchive report) throws XMLStreamException, IOException {
}

Fixed version (ground truth):
@Override public void makeReport(HTMLReportArchive report) throws XMLStreamException, IOException {
  super.writeTable(report,new ResultsTable());
}
Program: 13666
Project: 13666
Buggy source:
public QingCloudWSClient(String accessKeyId,String secretKey,String endPoint){
  this.accessKeyId=accessKeyId;
  this.secretKey=secretKey;
  if (endPoint != null && endPoint.trim().length() > 0) {
    this.endpoint=endPoint.trim();
  }
}

Fixed version (ground truth):
public QingCloudWSClient(String accessKeyId,String secretKey,String endPoint){
  this.accessKeyId=accessKeyId;
  this.secretKey=secretKey;
  if (endPoint != null && endPoint.trim().length() > 0) {
    this.endpoint=endPoint.trim();
    if (!this.endpoint.endsWith("String_Node_Str")) {
      this.endpoint+="String_Node_Str";
    }
  }
}
Program: 13667
Project: 13667
Buggy source:
public void setPublic_key(Integer public_key){
  this.public_key=public_key;
}

Fixed version (ground truth):
public void setPublic_key(String public_key){
  this.public_key=public_key;
}
Program: 13668
Project: 13668
Buggy source:
public Integer getPublic_key(){
  return public_key;
}

Fixed version (ground truth):
public String getPublic_key(){
  return public_key;
}
Program: 13669
Project: 13669
Buggy source:
public String post(String urlStr,Map<String,String> para) throws Exception {
  urlStr=preProcessUrl(urlStr);
  HttpURLConnection getCon=(HttpURLConnection)new URL(urlStr).openConnection();
  getCon.connect();
  String cookie=getCon.getHeaderField("String_Node_Str");
  cookie=cookie.substring(0,cookie.indexOf("String_Node_Str"));
  HttpURLConnection postCon=(HttpURLConnection)new URL(urlStr).openConnection();
  postCon.setRequestMethod("String_Node_Str");
  postCon.setDoOutput(true);
  postCon.setDoInput(true);
  postCon.setRequestProperty("String_Node_Str",cookie);
  OutputStream os=postCon.getOutputStream();
  OutputStreamWriter out=new OutputStreamWriter(os);
  Iterator<String> keys=para.keySet().iterator();
  while (keys.hasNext()) {
    String key=keys.next();
    String value=para.get(key);
    key=URLEncoder.encode(key,"String_Node_Str");
    value=URLEncoder.encode(value,"String_Node_Str");
    out.write(key + "String_Node_Str" + value);
  }
  out.close();
  InputStream is=postCon.getInputStream();
  StringBuffer sb=readStream(is);
  String resultFlag="String_Node_Str";
  int start=sb.indexOf(resultFlag);
  String result=sb.substring(start + resultFlag.length());
  return ResultConverter.convert2Xml(result);
}

Fixed version (ground truth):
public String post(String urlStr,Map<String,String> para) throws Exception {
  urlStr=preProcessUrl(urlStr);
  HttpURLConnection getCon=(HttpURLConnection)new URL(urlStr).openConnection();
  getCon.connect();
  String cookie=getCon.getHeaderField("String_Node_Str");
  cookie=cookie.substring(0,cookie.indexOf("String_Node_Str"));
  String nonceStr=findVMwareSessionNonce(getCon.getInputStream());
  HttpURLConnection postCon=(HttpURLConnection)new URL(urlStr).openConnection();
  postCon.setRequestMethod("String_Node_Str");
  postCon.setDoOutput(true);
  postCon.setDoInput(true);
  postCon.setRequestProperty("String_Node_Str",cookie);
  OutputStream os=postCon.getOutputStream();
  OutputStreamWriter out=new OutputStreamWriter(os);
  if (nonceStr != null) {
    out.write(NONCE + "String_Node_Str" + nonceStr);
  }
  Iterator<String> keys=para.keySet().iterator();
  while (keys.hasNext()) {
    String key=keys.next();
    String value=para.get(key);
    key=URLEncoder.encode(key,"String_Node_Str");
    value=URLEncoder.encode(value,"String_Node_Str");
    out.write(key + "String_Node_Str" + value);
  }
  out.close();
  InputStream is=postCon.getInputStream();
  StringBuffer sb=readStream(is);
  String resultFlag="String_Node_Str";
  int start=sb.indexOf(resultFlag);
  String result=sb.substring(start + resultFlag.length());
  return ResultConverter.convert2Xml(result);
}
Program: 13670
Project: 13670
Buggy source:
public InputStream post(String soapMsg) throws IOException {
  HttpURLConnection postCon=(HttpURLConnection)baseUrl.openConnection();
  if (connectTimeout > 0)   postCon.setConnectTimeout(connectTimeout);
  if (readTimeout > 0)   postCon.setReadTimeout(readTimeout);
  try {
    postCon.setRequestMethod("String_Node_Str");
  }
 catch (  ProtocolException e) {
    e.printStackTrace();
  }
  postCon.setDoOutput(true);
  postCon.setDoInput(true);
  postCon.setRequestProperty(SOAP_ACTION_HEADER,soapAction);
  if (cookie != null) {
    postCon.setRequestProperty("String_Node_Str",cookie);
  }
  OutputStream os=postCon.getOutputStream();
  OutputStreamWriter out=new OutputStreamWriter(os);
  out.write(soapMsg);
  out.close();
  InputStream is;
  try {
    is=postCon.getInputStream();
  }
 catch (  IOException ioe) {
    is=postCon.getErrorStream();
  }
  if (cookie == null) {
    cookie=postCon.getHeaderField("String_Node_Str");
  }
  return is;
}

Fixed version (ground truth):
public InputStream post(String soapMsg) throws IOException {
  HttpURLConnection postCon=(HttpURLConnection)baseUrl.openConnection();
  if (connectTimeout > 0)   postCon.setConnectTimeout(connectTimeout);
  if (readTimeout > 0)   postCon.setReadTimeout(readTimeout);
  try {
    postCon.setRequestMethod("String_Node_Str");
  }
 catch (  ProtocolException e) {
    e.printStackTrace();
  }
  postCon.setDoOutput(true);
  postCon.setDoInput(true);
  postCon.setRequestProperty(SOAP_ACTION_HEADER,soapAction);
  postCon.setRequestProperty("String_Node_Str","String_Node_Str");
  if (cookie != null) {
    postCon.setRequestProperty("String_Node_Str",cookie);
  }
  OutputStream os=postCon.getOutputStream();
  OutputStreamWriter out=new OutputStreamWriter(os,"String_Node_Str");
  out.write(soapMsg);
  out.close();
  InputStream is;
  try {
    is=postCon.getInputStream();
  }
 catch (  IOException ioe) {
    is=postCon.getErrorStream();
  }
  if (cookie == null) {
    cookie=postCon.getHeaderField("String_Node_Str");
  }
  return is;
}
Program: 13671
Project: 13671
Buggy source:
/** 
 * Copyright 2009 NetApp, contribution by Eric Forgette Modified by Steve Jin (sjin@vmware.com) This constructor builds a new ServiceInstance based on a ServiceInstance. The new ServiceInstance is effectively a clone of the first.  This clone will NOT become invalid when the first is logged out.
 * @author Eric Forgette (forgette@netapp.com)
 * @throws RemoteException 
 * @throws RuntimeFault 
 * @throws InvalidLogin 
 * @throws MalformedURLException 
 */
public ServiceInstance cloneSession(boolean ignoreCert) throws InvalidLogin, RuntimeFault, RemoteException, MalformedURLException {
  ServiceInstance oldsi=getServerConnection().getServiceInstance();
  ServerConnection oldsc=oldsi.getServerConnection();
  String ticket=oldsi.getSessionManager().acquireCloneTicket();
  VimPortType vimService=new VimPortType(oldsc.getUrl().toString(),ignoreCert);
  vimService.getWsc().setVimNameSpace(oldsc.getVimService().getWsc().getVimNameSpace());
  ServerConnection newsc=new ServerConnection(oldsc.getUrl(),vimService,null);
  ServiceInstance newsi=new ServiceInstance(newsc);
  newsc.setServiceInstance(newsi);
  UserSession userSession=newsi.getSessionManager().cloneSession(ticket);
  newsc.setUserSession(userSession);
  return newsi;
}

Fixed version (ground truth):
/** 
 * Copyright 2009 NetApp, contribution by Eric Forgette Modified by Steve Jin (sjin@vmware.com) This constructor builds a new ServiceInstance based on a ServiceInstance. The new ServiceInstance is effectively a clone of the first.  This clone will NOT become invalid when the first is logged out.
 * @author Eric Forgette (forgette@netapp.com)
 * @throws RemoteException 
 * @throws RuntimeFault 
 * @throws InvalidLogin 
 * @throws MalformedURLException 
 */
public ServiceInstance cloneSession(boolean ignoreCert) throws InvalidLogin, RuntimeFault, RemoteException, MalformedURLException {
  ServiceInstance oldsi=getServerConnection().getServiceInstance();
  ServerConnection oldsc=oldsi.getServerConnection();
  String ticket=oldsi.getSessionManager().acquireCloneTicket();
  VimPortType vimService=new VimPortType(oldsc.getUrl().toString(),ignoreCert);
  vimService.getWsc().setVimNameSpace(oldsc.getVimService().getWsc().getVimNameSpace());
  vimService.getWsc().setSoapActionOnApiVersion(oldsi.getAboutInfo().getApiVersion());
  ServerConnection newsc=new ServerConnection(oldsc.getUrl(),vimService,null);
  ServiceInstance newsi=new ServiceInstance(newsc);
  newsc.setServiceInstance(newsi);
  UserSession userSession=newsi.getSessionManager().cloneSession(ticket);
  newsc.setUserSession(userSession);
  return newsi;
}
Program: 13674
Project: 13674
Buggy source:
public Profile[] findAssociatedProfile(ManagedEntity entity) throws RuntimeFault, RemoteException {
  ManagedObjectReference[] mors=getVimService().findAssociatedProfile(getMOR(),entity.getMOR());
  Profile[] pfs=new Profile[mors.length];
  for (int i=0; i < mors.length; i++) {
    pfs[i]=new Profile(getServerConnection(),mors[i]);
  }
  return pfs;
}

Fixed version (ground truth):
public Profile[] findAssociatedProfile(ManagedEntity entity) throws RuntimeFault, RemoteException {
  ManagedObjectReference[] mors=getVimService().findAssociatedProfile(getMOR(),entity.getMOR());
  return convert2Profiles(mors);
}
Program: 13675
Project: 13675
Buggy source:
public Profile[] getProfile(){
  return (Profile[])getCurrentProperty("String_Node_Str");
}

Fixed version (ground truth):
public Profile[] getProfile(){
  ManagedObjectReference[] mors=(ManagedObjectReference[])getCurrentProperty("String_Node_Str");
  return convert2Profiles(mors);
}
Program: 13676
Project: 13676
Buggy source:
public static Object fromXML(String type,Element root) throws Exception {
  List<Element> subNodes=root.elements();
  if (subNodes.size() == 0) {
    return null;
  }
  if (type.startsWith("String_Node_Str")) {
    if (!type.endsWith("String_Node_Str")) {
      Element e=subNodes.get(0);
      return createMOR(e.attributeValue("String_Node_Str"),e.getText());
    }
 else {
      ManagedObjectReference[] mos=new ManagedObjectReference[subNodes.size()];
      for (int i=0; i < subNodes.size(); i++) {
        Element elem=(Element)subNodes.get(i);
        mos[i]=XmlGen.createMOR(elem.attributeValue("String_Node_Str"),elem.getText());
      }
      return mos;
    }
  }
 else   if (isBasicType(type)) {
    String[] vals=new String[subNodes.size()];
    for (int i=0; i < vals.length; i++) {
      vals[i]=subNodes.get(i).getText();
    }
    return parseValue(type,vals);
  }
 else   if (type.endsWith("String_Node_Str")) {
    String singleTypeName=type.substring(0,type.length() - 2);
    Element e=subNodes.get(0);
    String xsiType=e.attributeValue(XSI_TYPE);
    if (xsiType != null) {
      singleTypeName=xsiType;
    }
    Class clazz=getVimClass(singleTypeName);
    Object ao=Array.newInstance(clazz,subNodes.size());
    for (int i=0; i < subNodes.size(); i++) {
      Object o=fromXml(getVimClass(singleTypeName),subNodes.get(i));
      Array.set(ao,i,o);
    }
    return ao;
  }
 else {
    return fromXml(getVimClass(type),subNodes.get(0));
  }
}

Fixed version (ground truth):
public static Object fromXML(String type,Element root) throws Exception {
  List<Element> subNodes=root.elements();
  if (subNodes.size() == 0) {
    return null;
  }
  if (type.startsWith("String_Node_Str")) {
    if (!type.endsWith("String_Node_Str")) {
      Element e=subNodes.get(0);
      return createMOR(e.attributeValue("String_Node_Str"),e.getText());
    }
 else {
      ManagedObjectReference[] mos=new ManagedObjectReference[subNodes.size()];
      for (int i=0; i < subNodes.size(); i++) {
        Element elem=(Element)subNodes.get(i);
        mos[i]=XmlGen.createMOR(elem.attributeValue("String_Node_Str"),elem.getText());
      }
      return mos;
    }
  }
 else   if (isBasicType(type)) {
    String[] vals=new String[subNodes.size()];
    for (int i=0; i < vals.length; i++) {
      vals[i]=subNodes.get(i).getText();
    }
    return parseValue(type,vals);
  }
 else   if (type.endsWith("String_Node_Str")) {
    String arrayItemTypeName=type.substring(0,type.length() - 2);
    Class clazz=getVimClass(arrayItemTypeName);
    Object ao=Array.newInstance(clazz,subNodes.size());
    for (int i=0; i < subNodes.size(); i++) {
      Element e=subNodes.get(i);
      String xsiType=e.attributeValue(XSI_TYPE);
      Object o=fromXml(getVimClass(xsiType == null ? arrayItemTypeName : xsiType),subNodes.get(i));
      Array.set(ao,i,o);
    }
    return ao;
  }
 else {
    return fromXml(getVimClass(type),subNodes.get(0));
  }
}
Program: 13677
Project: 13677
Buggy source:
public OptionManager getOvfManager(){
  return (OptionManager)createMO(getServiceContent().getOvfManager());
}

Fixed version (ground truth):
public OvfManager getOvfManager(){
  return (OvfManager)createMO(getServiceContent().getOvfManager());
}
Program: 13678
Project: 13678
Buggy source:
public void watch(PropertyFilterSpec pfs){
  mom.watch(pfs);
}

Fixed version (ground truth):
/** 
 * Add PropertyFilterSpec for advanced settings
 * @param pfs the property filter spec which specifiesthe managed objects and properties to watch.
 */
public void watch(PropertyFilterSpec pfs){
  mom.watch(pfs);
}
Program: 13679
Project: 13679
Buggy source:
public Object getCopy(ManagedObjectReference mor,String propName){
  return getCopy(mor,propName);
}

Fixed version (ground truth):
/** 
 * Get a copy of the cached property. You can change the returned object as you like
 * @param mor Managed object reference
 * @param propName property name
 * @return the data object identified by the propName.NullObject.NULL if the data object is really null
 */
public Object getCopy(ManagedObjectReference mor,String propName){
  return getCopy(mor,propName);
}
Program: 13680
Project: 13680
Buggy source:
public Object get(ManagedObjectReference mor,String propName){
  Map<ManagedObjectReference,Map<String,Object>> items=cache.getCachedItems();
  Map<String,Object> moMap=items.get(mor);
  if (moMap != null) {
    return moMap.get(propName);
  }
  return null;
}

Fixed version (ground truth):
/** 
 * Get the value of cached property whose name is propName. You should NEVER change the returned data object.
 * @param mor Managed object reference pointing to the managed object
 * @param propName Property name
 * @return the data object identified by the propName.NullObject.NULL if the data object is really null
 */
public Object get(ManagedObjectReference mor,String propName){
  Map<ManagedObjectReference,Map<String,Object>> items=cache.getCachedItems();
  Map<String,Object> moMap=items.get(mor);
  if (moMap != null) {
    return moMap.get(propName);
  }
  return null;
}
Program: 13681
Project: 13681
Buggy source:
public ServiceInstance getServiceInstance(){
  return si;
}

Fixed version (ground truth):
/** 
 * Get the corresponding ServiceInstance
 * @return ServiceInstance object
 */
public ServiceInstance getServiceInstance(){
  return si;
}
Program: 13682
Project: 13682
Buggy source:
public boolean isReady(){
  return cache.isReady();
}

Fixed version (ground truth):
/** 
 * Check if the CacheInstance is ready for retrieval
 * @return true if ready; false otherwise
 */
public boolean isReady(){
  return cache.isReady();
}
Program: 13683
Project: 13683
Buggy source:
public void start(){
  mThread=new Thread(mom);
  mThread.setName("String_Node_Str" + si.getServerConnection().getUrl());
  mThread.start();
}

Fixed version (ground truth):
/** 
 * Start the caching service. Called after specifying the managed objects and their properties to watch.
 */
public void start(){
  mThread=new Thread(mom);
  mThread.setName("String_Node_Str" + si.getServerConnection().getUrl());
  mThread.start();
}
Program: 13684
Project: 13684
Buggy source:
public void destroy(){
  mom.cleanUp();
  mThread.stop();
  si=null;
  mom=null;
  cache=null;
  mThread=null;
}

Fixed version (ground truth):
/** 
 * Destrory the caching service when no longer needed.
 */
public void destroy(){
  mom.cleanUp();
  mThread.stop();
  si=null;
  mom=null;
  cache=null;
  mThread=null;
}
Program: 13685
Project: 13685
Buggy source:
public void update(Observable obj,Object arg){
  if (arg instanceof PropertyFilterUpdate[]) {
    PropertyFilterUpdate[] pfus=(PropertyFilterUpdate[])arg;
    for (int i=0; pfus != null && i < pfus.length; i++) {
      ObjectUpdate[] ous=pfus[i].getObjectSet();
      for (int j=0; j < ous.length; j++) {
        ManagedObjectReference mor=ous[j].getObj();
        if (!items.containsKey(mor)) {
          items.put(mor,new ConcurrentHashMap<String,Object>());
        }
        Map<String,Object> moMap=items.get(mor);
        PropertyChange[] pcs=ous[j].getChangeSet();
        for (int k=0; k < pcs.length; k++) {
          moMap.put(pcs[k].getName(),pcs[k].getVal());
        }
      }
    }
  }
  isReady=true;
}

Fixed version (ground truth):
public void update(Observable obj,Object arg){
  if (arg instanceof PropertyFilterUpdate[]) {
    PropertyFilterUpdate[] pfus=(PropertyFilterUpdate[])arg;
    for (int i=0; pfus != null && i < pfus.length; i++) {
      ObjectUpdate[] ous=pfus[i].getObjectSet();
      for (int j=0; j < ous.length; j++) {
        ManagedObjectReference mor=ous[j].getObj();
        if (!items.containsKey(mor)) {
          items.put(mor,new ConcurrentHashMap<String,Object>());
        }
        Map<String,Object> moMap=items.get(mor);
        PropertyChange[] pcs=ous[j].getChangeSet();
        for (int k=0; k < pcs.length; k++) {
          Object value=pcs[k].getVal();
          value=value == null ? NULL : value;
          moMap.put(pcs[k].getName(),value);
        }
      }
    }
  }
  isReady=true;
}
Program: 13686
Project: 13686
Buggy source:
private static void fieldToXML(StringBuffer sb,String fName,String typeName,Object obj){
  if (typeName.endsWith("String_Node_Str")) {
    ManagedObjectReference mor=(ManagedObjectReference)obj;
    sb.append("String_Node_Str" + fName + "String_Node_Str"+ mor.type+ "String_Node_Str");
    sb.append(mor.val);
    sb.append("String_Node_Str" + fName + "String_Node_Str");
    return;
  }
  boolean isComplexType=typeName.startsWith(PACKAGE_NAME);
  if (!isComplexType) {
    sb.append("String_Node_Str" + fName + "String_Node_Str");
    sb.append(obj);
    sb.append("String_Node_Str" + fName + "String_Node_Str");
  }
 else {
    String realFieldType=obj.getClass().getCanonicalName();
    if (realFieldType.equals(typeName)) {
      sb.append(toXML(fName,obj,null));
    }
 else {
      int lastDot=realFieldType.lastIndexOf("String_Node_Str");
      String nameSpaceType=realFieldType.substring(lastDot + 1);
      sb.append(toXML(fName,obj,nameSpaceType));
    }
  }
}

Fixed version (ground truth):
private static void fieldToXML(StringBuffer sb,String fName,String typeName,Object obj){
  if (typeName.endsWith("String_Node_Str")) {
    ManagedObjectReference mor=(ManagedObjectReference)obj;
    sb.append("String_Node_Str" + fName + "String_Node_Str"+ mor.type+ "String_Node_Str");
    sb.append(mor.val);
    sb.append("String_Node_Str" + fName + "String_Node_Str");
    return;
  }
  boolean isComplexType=typeName.startsWith(PACKAGE_NAME);
  if (!isComplexType) {
    sb.append("String_Node_Str" + fName + "String_Node_Str");
    if (typeName.endsWith("String_Node_Str")) {
      sb.append(DatatypeConverter.printDateTime((Calendar)obj));
    }
 else {
      sb.append(obj);
    }
    sb.append("String_Node_Str" + fName + "String_Node_Str");
  }
 else {
    String realFieldType=obj.getClass().getCanonicalName();
    if (realFieldType.equals(typeName)) {
      sb.append(toXML(fName,obj,null));
    }
 else {
      int lastDot=realFieldType.lastIndexOf("String_Node_Str");
      String nameSpaceType=realFieldType.substring(lastDot + 1);
      sb.append(toXML(fName,obj,nameSpaceType));
    }
  }
}
Program: 13693
Project: 13693
Buggy source:
public static Object convertProperty(Object dynaPropVal){
  Object propertyValue=null;
  Class propClass=dynaPropVal.getClass();
  String propName=propClass.getName();
  if (propName.indexOf("String_Node_Str") != -1) {
    String methodName=propName.substring(propName.indexOf("String_Node_Str") + "String_Node_Str".length());
    try {
      Method getMethod=propClass.getMethod("String_Node_Str" + methodName,(Class[])null);
      if (getMethod == null) {
        getMethod=propClass.getMethod("String_Node_Str" + methodName.toLowerCase(),(Class[])null);
      }
      propertyValue=getMethod.invoke(dynaPropVal,(Object[])null);
    }
 catch (    Exception e) {
      e.printStackTrace();
    }
  }
 else   if (dynaPropVal.getClass().isArray()) {
    propertyValue=dynaPropVal;
  }
 else {
    propertyValue=dynaPropVal;
  }
  return propertyValue;
}

Fixed version (ground truth):
public static Object convertProperty(Object dynaPropVal){
  Object propertyValue=null;
  Class propClass=dynaPropVal.getClass();
  String propName=propClass.getName();
  if (propName.indexOf("String_Node_Str") != -1) {
    String methodName=propName.substring(propName.indexOf("String_Node_Str") + "String_Node_Str".length());
    try {
      Method getMethod=null;
      try {
        getMethod=propClass.getMethod("String_Node_Str" + methodName,(Class[])null);
      }
 catch (      NoSuchMethodException nsme) {
        getMethod=propClass.getMethod("String_Node_Str" + methodName.toLowerCase(),(Class[])null);
      }
      propertyValue=getMethod.invoke(dynaPropVal,(Object[])null);
    }
 catch (    Exception e) {
      e.printStackTrace();
    }
  }
 else   if (dynaPropVal.getClass().isArray()) {
    propertyValue=dynaPropVal;
  }
 else {
    propertyValue=dynaPropVal;
  }
  return propertyValue;
}
Program: 13695
Project: 13695
Buggy source:
/** 
 * Find a VM by its location on a datastore
 * @param datacenter The datacenter within which it searches.
 * @param dPath The datastore path, for example, "[storage1] WinXP/WinXP.vmx".
 * @return A VirtualMachine that pointed by the dPath
 * @throws RemoteException 
 * @throws RuntimeFault 
 * @throws InvalidDatastore 
 */
public VirtualMachine findByDatastorePath(Datacenter datacenter,String dPath) throws InvalidDatastore, RuntimeFault, RemoteException {
  if (datacenter == null) {
    throw new IllegalArgumentException("String_Node_Str");
  }
  ManagedObjectReference mor=getVimService().findByDatastorePath(getMOR(),datacenter.getMOR(),dPath);
  return new VirtualMachine(getServerConnection(),mor);
}

Fixed version (ground truth):
/** 
 * Find a VM by its location on a datastore
 * @param datacenter The datacenter within which it searches.
 * @param dPath The datastore path, for example, "[storage1] WinXP/WinXP.vmx".
 * @return A VirtualMachine that pointed by the dPath
 * @throws RemoteException 
 * @throws RuntimeFault 
 * @throws InvalidDatastore 
 */
public VirtualMachine findByDatastorePath(Datacenter datacenter,String dPath) throws InvalidDatastore, RuntimeFault, RemoteException {
  if (datacenter == null) {
    throw new IllegalArgumentException("String_Node_Str");
  }
  ManagedObjectReference mor=getVimService().findByDatastorePath(getMOR(),datacenter.getMOR(),dPath);
  return (VirtualMachine)MorUtil.createExactManagedEntity(getServerConnection(),mor);
}
Program: 13696
Project: 13696
Buggy source:
protected void splitChromosomes(Configuration hConf) throws URISyntaxException, IOException {
  parseDictFile(hConf);
  reduces=(int)(1.75 * nodes * reducerContainersPerNode);
  int tmpReduces=reduces + 1;
  Logger.DEBUG("String_Node_Str" + reduces);
  double factor=0.95;
  int factoredReduces=reduces;
  ChromosomeSplitter splitter=null;
  while (tmpReduces > reduces) {
    if (bedFile != null)     splitter=new ChromosomeSplitter(dict,bedFile,factoredReduces);
 else     if (readCountsPerRegionFile != null)     splitter=new ChromosomeSplitter(dict,readCountsPerRegionFile,factoredReduces,reorderRegions);
 else     splitter=new ChromosomeSplitter(dict,factoredReduces);
    tmpReduces=splitter.getRegionCount();
    factoredReduces=(int)(factoredReduces * factor);
  }
  String bedRegions=out + "String_Node_Str";
  splitter.exportSplitter(bedRegions,hConf);
  reduces=splitter.getRegionCount();
  Logger.DEBUG("String_Node_Str" + reduces);
  HalvadeConf.setBedRegions(hConf,bedRegions);
}

Fixed version (ground truth):
protected void splitChromosomes(Configuration hConf,int nReduces) throws URISyntaxException, IOException {
  parseDictFile(hConf);
  if (nReduces == 0)   reduces=(int)(1.75 * nodes * reducerContainersPerNode);
 else   reduces=nReduces;
  int tmpReduces=reduces + 1;
  Logger.DEBUG("String_Node_Str" + reduces);
  double factor=0.95;
  int factoredReduces=reduces;
  ChromosomeSplitter splitter=null;
  while (tmpReduces > reduces) {
    if (bedFile != null)     splitter=new ChromosomeSplitter(dict,bedFile,factoredReduces);
 else     if (readCountsPerRegionFile != null)     splitter=new ChromosomeSplitter(dict,readCountsPerRegionFile,factoredReduces,reorderRegions);
 else     splitter=new ChromosomeSplitter(dict,factoredReduces);
    tmpReduces=splitter.getRegionCount();
    factoredReduces=(int)(factoredReduces * factor);
  }
  String bedRegions=out + "String_Node_Str";
  splitter.exportSplitter(bedRegions,hConf);
  reduces=splitter.getRegionCount();
  Logger.DEBUG("String_Node_Str" + reduces);
  HalvadeConf.setBedRegions(hConf,bedRegions);
}
Program: 13703
Project: 13703
Buggy source:
@Override protected void setup(Context context) throws IOException, InterruptedException {
  totalValCount=0;
  totalKeyCount=0;
  keyFactors=new ArrayList<>();
  tmpDir=HalvadeConf.getScratchTempDir(context.getConfiguration());
  refDir=HalvadeConf.getRefDirOnScratch(context.getConfiguration());
  requireUploadToHDFS=refDir.startsWith(tmpDir);
  out=HalvadeConf.getOutDir(context.getConfiguration());
  jobId=context.getJobID().toString();
  taskId=context.getTaskAttemptID().toString();
  taskId=taskId.substring(taskId.indexOf("String_Node_Str"));
  mergeJS=tmpDir + taskId + "String_Node_Str";
  File file=new File(mergeJS);
  threads=HalvadeConf.getReducerThreads(context.getConfiguration());
  try {
    mem=Long.parseLong(context.getConfiguration().get("String_Node_Str"));
  }
 catch (  NumberFormatException ex) {
    mem=0;
  }
  bin=checkBinaries(context);
  try {
    ref=HalvadeFileUtils.downloadGATKIndex(context,taskId);
  }
 catch (  URISyntaxException ex) {
    Logger.EXCEPTION(ex);
    throw new InterruptedException();
  }
  bw=new BufferedWriter(new FileWriter(file.getAbsoluteFile()));
  Logger.DEBUG("String_Node_Str" + mergeJS);
}

Fixed version (ground truth):
@Override protected void setup(Context context) throws IOException, InterruptedException {
  totalValCount=0;
  totalKeyCount=0;
  keyFactors=new ArrayList<>();
  tmpDir=HalvadeConf.getScratchTempDir(context.getConfiguration());
  refDir=HalvadeConf.getRefDirOnScratch(context.getConfiguration());
  requireUploadToHDFS=!HalvadeConf.getRefDirIsSet(context.getConfiguration());
  out=HalvadeConf.getOutDir(context.getConfiguration());
  jobId=context.getJobID().toString();
  taskId=context.getTaskAttemptID().toString();
  taskId=taskId.substring(taskId.indexOf("String_Node_Str"));
  mergeJS=tmpDir + taskId + "String_Node_Str";
  File file=new File(mergeJS);
  threads=HalvadeConf.getReducerThreads(context.getConfiguration());
  try {
    mem=Long.parseLong(context.getConfiguration().get("String_Node_Str"));
  }
 catch (  NumberFormatException ex) {
    mem=0;
  }
  bin=checkBinaries(context);
  try {
    ref=HalvadeFileUtils.downloadGATKIndex(context,taskId);
  }
 catch (  URISyntaxException ex) {
    Logger.EXCEPTION(ex);
    throw new InterruptedException();
  }
  bw=new BufferedWriter(new FileWriter(file.getAbsoluteFile()));
  Logger.DEBUG("String_Node_Str" + mergeJS);
}
Program: 13704
Project: 13704
Buggy source:
public static boolean getFixQualEnc(Configuration conf){
  String s=conf.get(fixQualEnc);
  if (s.equalsIgnoreCase("String_Node_Str"))   return true;
 else   return false;
}

Fixed version (ground truth):
public static boolean getFixQualEnc(Configuration conf){
  return conf.getBoolean(fixQualEnc,false);
}
Program: 13705
Project: 13705
Buggy source:
public static void setFixQualEnc(Configuration conf,boolean val){
  if (val)   conf.set(fixQualEnc,"String_Node_Str");
 else   conf.set(fixQualEnc,"String_Node_Str");
}

Fixed version (ground truth):
public static void setFixQualEnc(Configuration conf,boolean val){
  conf.setBoolean(fixQualEnc,val);
}
Program: 13706
Project: 13706
Buggy source:
@Override protected void map(LongWritable key,SAMRecordWritable value,Context context) throws IOException, InterruptedException {
  try {
    value.get().getSAMString();
  }
 catch (  StringIndexOutOfBoundsException e) {
    Logger.DEBUG("String_Node_Str");
  }
catch (  IllegalArgumentException ex) {
    Logger.DEBUG("String_Node_Str" + value.get().getReadName());
    Logger.EXCEPTION(ex);
  }
  instance.writePairedSAMRecordToContext(value.get(),false);
}

Fixed version (ground truth):
@Override protected void map(LongWritable key,SAMRecordWritable value,Context context) throws IOException, InterruptedException {
  try {
    value.get().getSAMString();
    instance.writePairedSAMRecordToContext(value.get(),false);
  }
 catch (  StringIndexOutOfBoundsException e) {
    Logger.DEBUG("String_Node_Str");
  }
catch (  IllegalArgumentException ex) {
    Logger.DEBUG("String_Node_Str" + value.get().getReadName());
    Logger.EXCEPTION(ex);
  }
}
Program: 13707
Project: 13707
Buggy source:
public HashSet<Integer> getRegions(SAMRecord sam,int read1Ref){
  int readLength=sam.getReadLength();
  int beginpos1=sam.getAlignmentStart();
  HashSet<Integer> keys=new HashSet();
  if (read1Ref >= 0)   Collections.addAll(keys,getKey(sam.getReferenceName(),beginpos1,beginpos1 + readLength));
  return keys;
}

Fixed version (ground truth):
public HashSet<Integer> getRegions(SAMRecord sam,int read1Ref){
  int beginpos1=sam.getAlignmentStart();
  int endpos1=sam.getAlignmentEnd();
  HashSet<Integer> keys=new HashSet();
  if (read1Ref >= 0)   Collections.addAll(keys,getKey(sam.getReferenceName(),beginpos1,endpos1));
  return keys;
}
Program: 13712
Project: 13712
Buggy source:
@Override public int run(String[] strings) throws Exception {
  int ret=0;
  try {
    Configuration halvadeConf=getConf();
    halvadeOpts=new HalvadeOptions();
    int optReturn=halvadeOpts.GetOptions(strings,halvadeConf);
    if (optReturn != 0)     return optReturn;
    String halvadeDir=halvadeOpts.out + "String_Node_Str";
    if (!halvadeOpts.justCombine) {
      if (halvadeOpts.rnaPipeline) {
        if (!halvadeOpts.useBamInput) {
          ret=runPass1RNAJob(halvadeConf,halvadeOpts.out + "String_Node_Str");
          if (ret != 0) {
            Logger.DEBUG("String_Node_Str");
            System.exit(-1);
          }
          HalvadeConf.setIsPass2(halvadeConf,true);
        }
        ret=runHalvadeJob(halvadeConf,halvadeDir,HalvadeResourceManager.RNA_SHMEM_PASS2);
      }
 else {
        ret=runHalvadeJob(halvadeConf,halvadeDir,HalvadeResourceManager.DNA);
      }
      if (ret != 0) {
        Logger.DEBUG("String_Node_Str");
        System.exit(-2);
      }
    }
    if (!halvadeOpts.dryRun) {
      if (halvadeOpts.combineVcf)       runCombineJob(halvadeDir,halvadeOpts.out + "String_Node_Str",false);
      if (halvadeOpts.gff != null)       runCombineJob(halvadeDir,halvadeOpts.out + "String_Node_Str",true);
    }
  }
 catch (  IOException|ClassNotFoundException|IllegalArgumentException|IllegalStateException|InterruptedException|URISyntaxException e) {
    Logger.EXCEPTION(e);
  }
  return ret;
}

Fixed version (ground truth):
@Override public int run(String[] strings) throws Exception {
  int ret=0;
  try {
    Configuration halvadeConf=getConf();
    halvadeOpts=new HalvadeOptions();
    int optReturn=halvadeOpts.GetOptions(strings,halvadeConf);
    if (optReturn != 0)     return optReturn;
    String halvadeDir=halvadeOpts.out + "String_Node_Str";
    if (!halvadeOpts.justCombine) {
      if (halvadeOpts.rnaPipeline) {
        if (!halvadeOpts.useBamInput) {
          ret=runPass1RNAJob(halvadeConf,halvadeOpts.out + "String_Node_Str");
          if (ret != 0) {
            Logger.DEBUG("String_Node_Str");
            System.exit(-1);
          }
          HalvadeConf.setIsPass2(halvadeConf,true);
        }
        ret=runHalvadeJob(halvadeConf,halvadeDir,HalvadeResourceManager.RNA_SHMEM_PASS2);
      }
 else {
        ret=runHalvadeJob(halvadeConf,halvadeDir,HalvadeResourceManager.DNA);
      }
      if (ret != 0) {
        Logger.DEBUG("String_Node_Str");
        System.exit(-2);
      }
    }
    if (!halvadeOpts.dryRun && !halvadeOpts.mergeBam) {
      if (halvadeOpts.combineVcf)       runCombineJob(halvadeDir,halvadeOpts.out + "String_Node_Str",false);
      if (halvadeOpts.gff != null)       runCombineJob(halvadeDir,halvadeOpts.out + "String_Node_Str",true);
    }
  }
 catch (  IOException|ClassNotFoundException|IllegalArgumentException|IllegalStateException|InterruptedException|URISyntaxException e) {
    Logger.EXCEPTION(e);
  }
  return ret;
}
Program: 13713
Project: 13713
Buggy source:
public void runCombineVariants(String[] inputs,String output,String ref) throws InterruptedException {
  ArrayList<String> command=new ArrayList<String>();
  String[] gatkcmd={java,mem,"String_Node_Str",gatk,"String_Node_Str","String_Node_Str",multiThreadingTypes[0],"String_Node_Str" + threads,"String_Node_Str",ref,"String_Node_Str",output,"String_Node_Str","String_Node_Str","String_Node_Str"};
  command.addAll(Arrays.asList(gatkcmd));
  if (inputs != null) {
    for (    String input : inputs) {
      command.add("String_Node_Str");
      command.add(input);
    }
  }
  String customArgs=HalvadeConf.getCustomArgs(context.getConfiguration(),"String_Node_Str","String_Node_Str");
  command=CommandGenerator.addToCommand(command,customArgs);
  Object[] objectList=command.toArray();
  long estimatedTime=runProcessAndWait("String_Node_Str",Arrays.copyOf(objectList,objectList.length,String[].class));
  if (context != null)   context.getCounter(HalvadeCounters.TIME_GATK_COMBINE_VCF).increment(estimatedTime);
}

Fixed version (ground truth):
public void runCombineVariants(String[] inputs,String output,String ref) throws InterruptedException {
  ArrayList<String> command=new ArrayList<String>();
  command.addAll(java);
  String[] gatkcmd={mem,"String_Node_Str",gatk,"String_Node_Str","String_Node_Str",multiThreadingTypes[0],"String_Node_Str" + threads,"String_Node_Str",ref,"String_Node_Str",output,"String_Node_Str","String_Node_Str","String_Node_Str"};
  command.addAll(Arrays.asList(gatkcmd));
  if (inputs != null) {
    for (    String input : inputs) {
      command.add("String_Node_Str");
      command.add(input);
    }
  }
  String customArgs=HalvadeConf.getCustomArgs(context.getConfiguration(),"String_Node_Str","String_Node_Str");
  command=CommandGenerator.addToCommand(command,customArgs);
  Object[] objectList=command.toArray();
  long estimatedTime=runProcessAndWait("String_Node_Str",Arrays.copyOf(objectList,objectList.length,String[].class));
  if (context != null)   context.getCounter(HalvadeCounters.TIME_GATK_COMBINE_VCF).increment(estimatedTime);
}
Program: 13714
Project: 13714
Buggy source:
public void runSplitNCigarReads(String input,String output,String ref,String region,int newMaxQualScore) throws InterruptedException {
  String[] command={java,mem,"String_Node_Str",gatk,"String_Node_Str","String_Node_Str","String_Node_Str",ref,"String_Node_Str",input,"String_Node_Str",output,"String_Node_Str","String_Node_Str","String_Node_Str","String_Node_Str","String_Node_Str","String_Node_Str" + newMaxQualScore,"String_Node_Str","String_Node_Str","String_Node_Str","String_Node_Str",region};
  String customArgs=HalvadeConf.getCustomArgs(context.getConfiguration(),"String_Node_Str","String_Node_Str");
  long estimatedTime=runProcessAndWait("String_Node_Str",AddCustomArguments(command,customArgs));
  if (context != null)   context.getCounter(HalvadeCounters.TIME_GATK_INDEL_REALN).increment(estimatedTime);
}

Fixed version (ground truth):
public void runSplitNCigarReads(String input,String output,String ref,String region,int newMaxQualScore) throws InterruptedException {
  String[] command={mem,"String_Node_Str",gatk,"String_Node_Str","String_Node_Str","String_Node_Str",ref,"String_Node_Str",input,"String_Node_Str",output,"String_Node_Str","String_Node_Str","String_Node_Str","String_Node_Str","String_Node_Str","String_Node_Str" + newMaxQualScore,"String_Node_Str","String_Node_Str","String_Node_Str","String_Node_Str",region};
  String customArgs=HalvadeConf.getCustomArgs(context.getConfiguration(),"String_Node_Str","String_Node_Str");
  long estimatedTime=runProcessAndWait("String_Node_Str",AddCustomArguments(command,customArgs));
  if (context != null)   context.getCounter(HalvadeCounters.TIME_GATK_INDEL_REALN).increment(estimatedTime);
}
Program: 13715
Project: 13715
Buggy source:
public void runVariantFiltration(String input,String output,String ref,String region,int window,int cluster,double minFS,double maxQD) throws InterruptedException {
  String[] command={java,mem,"String_Node_Str",gatk,"String_Node_Str","String_Node_Str","String_Node_Str",ref,"String_Node_Str",input,"String_Node_Str",output,"String_Node_Str",region,"String_Node_Str","String_Node_Str" + window,"String_Node_Str","String_Node_Str" + cluster,"String_Node_Str","String_Node_Str","String_Node_Str","String_Node_Str" + roundOneDecimal(minFS),"String_Node_Str","String_Node_Str","String_Node_Str","String_Node_Str" + roundOneDecimal(maxQD)};
  String customArgs=HalvadeConf.getCustomArgs(context.getConfiguration(),"String_Node_Str","String_Node_Str");
  long estimatedTime=runProcessAndWait("String_Node_Str",AddCustomArguments(command,customArgs));
  if (context != null)   context.getCounter(HalvadeCounters.TIME_GATK_INDEL_REALN).increment(estimatedTime);
}

Fixed version (ground truth):
public void runVariantFiltration(String input,String output,String ref,String region,int window,int cluster,double minFS,double maxQD) throws InterruptedException {
  String[] command={mem,"String_Node_Str",gatk,"String_Node_Str","String_Node_Str","String_Node_Str",ref,"String_Node_Str",input,"String_Node_Str",output,"String_Node_Str",region,"String_Node_Str","String_Node_Str" + window,"String_Node_Str","String_Node_Str" + cluster,"String_Node_Str","String_Node_Str","String_Node_Str","String_Node_Str" + roundOneDecimal(minFS),"String_Node_Str","String_Node_Str","String_Node_Str","String_Node_Str" + roundOneDecimal(maxQD)};
  String customArgs=HalvadeConf.getCustomArgs(context.getConfiguration(),"String_Node_Str","String_Node_Str");
  long estimatedTime=runProcessAndWait("String_Node_Str",AddCustomArguments(command,customArgs));
  if (context != null)   context.getCounter(HalvadeCounters.TIME_GATK_INDEL_REALN).increment(estimatedTime);
}