File f = new File(“D:/a.txt”);
File f1 = new File(“D:/b.txt”);
File file =new File(“D:/c.txt”);

    Reader rea = null;
    Reader rea1 = null;
    StringBuilder s = new StringBuilder();
    StringBuilder s1 = new StringBuilder();
    try {
        FileWriter fop=new FileWriter(file);
        rea = new InputStreamReader(new FileInputStream(f));
        rea1 = new InputStreamReader(new FileInputStream(f1));
        int tempbyte;
        while ((tempbyte = rea.read()) != -1) {
            if (((char) tempbyte) != '\r') {
                s.append(String.valueOf((char) tempbyte));
            }
        }
        int tempbyte1;
        while ((tempbyte1 = rea1.read()) != -1) {
            if (((char) tempbyte1) != '\r') {
                s1.append(String.valueOf((char) tempbyte1));
            }
        }
        String[] split = s.toString().split("\\s+");
        String[] split2 = s1.toString().split("\\s+");


        for (int j = 0; j < split2.length; j++) {
            fop.write(split2[j]+"2\n");
            System.out.println(split2[j]+"2\n");
            if(j<split.length){
                System.out.println(split[j]+"1\n");
                fop.write(split[j]+"1\n");
            }

        }
        fop.flush();
        rea.close();
        rea1.close();
        fop.close();

    } catch (FileNotFoundException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }