[Demonstration 1]

[Buggy Method]
public String get_TrioAnalysis(String track, String id, String chr, long start, long end) {
    Document doc = XmlWriter.init(Consts.DATA_ROOT);
    int chrid = check_chromosome(chr);
    if (chrid >= 0) {
        Annotations vt = null;
        if (Externals.containsKey(track))
            vt = Externals.get(track);
        else if (Annos.containsKey(track))
            vt = Annos.get(track);
        else if (Pvar != null && track.startsWith("_") && track.substring(1).equals(Pvar.get_ID()))
            vt = Pvar;
        if (vt != null && vt.get_Type().equals(Consts.FORMAT_VCF) && vt.has_Parameter(VCF_HEADER_SAMPLE)) {
            VcfReader vr = new VcfReader(vt, chr);
            Element[] ele_temp = vr.write_trio(doc, id, chr, start, end, false);
        }
    }
    return XmlWriter.xml2string(doc);
}

[Buggy Hunk]
Element[] ele_temp = vr.write_trio(doc, id, chr, start, end, false);

[Patch]
Element[] ele_temp = vr.write_trio(doc, id, chr, start, end, false, false);

[Demonstration 2]

[Buggy Method]
public synchronized void clear() {
    timeElapsed = 0;
    //      neededTimeStep = 0.5;
    //      timeStep = 0.5;
    getPointMasses().clear();
}

[Buggy Hunk]
getPointMasses().clear();

[Patch]
pointMasses.clear();

[Demonstration 3]

[Buggy Method]
private static Element makePostRequest(String request, Map<String, String> formData) {
    System.out.println(request);
    try {
        return Jsoup.connect(request).userAgent(APIUtils.generateRandomUserAgent()).ignoreContentType(true).timeout(60 * 1000).data(formData).post().body();
    } catch (HttpStatusException e) {
        // TODO Auto-generated catch block
        if (e.getStatusCode() == 401) {
            System.out.println("A 401 exception has occured, slow down your requests and" + " double check your query parameters");
        } else if (e.getStatusCode() == 500) {
            System.out.println("A 500 exception has occured, there may have been a problem with the User Agent" + " post this issue on GitHub");
        } else {
            e.printStackTrace();
        }
    } catch (IOException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }
    return null;
}

[Buggy Hunk]
.userAgent(APIUtils.generateRandomUserAgent())

[Patch]
.userAgent(YikYakProfile.USER_AGENT + "" + YikYakAPI.getYikYakVersion())