First commit for GA4GH common classes and Picard runner



 Hi Cassie,
 
 Yup, I was looking at old version of `Genomics.java` - wow some things changed quite a bit, but I like the new approach :)
 
 So based on the following example that I tested in `api-client-java` on [GenomicsSample.java](https://github.com/googlegenomics/api-client-java/blob/master/src/main/java/com/google/cloud/genomics/api/client/GenomicsSample.java):
 
  ```
   Genomics genomicsFactory = GenomicsFactory.builder("genomics_java_client").build().fromClientSecretsFile(new File(command.clientSecretsFilename));
 ```

 I can see that in [GenomicsFactory.java](https://github.com/googlegenomics/utils-java/blob/master/src/main/java/com/google/cloud/genomics/utils/GenomicsFactory.java), the `fromClientSecretsFile(...)` calls `fromCredential(Credential credential)`, which calls `create(credential, null)`.  Then in `private Genomics create(...)`, a new instance of `Genomics.Builder` object - called `builder` - instantiates the following from `Genomics.java`, and returns a `Genomics` object via `builder.build()`:
 
 ```
   public Builder(com.google.api.client.http.HttpTransport transport, com.google.api.client.json.JsonFactory jsonFactory,
        com.google.api.client.http.HttpRequestInitializer httpRequestInitializer) {
      super(
          transport,
          jsonFactory,
          DEFAULT_ROOT_URL,
          DEFAULT_SERVICE_PATH,
          httpRequestInitializer,
          false);
    }
 ```
 
 And of course when I look at `DEFAULT_ROOT_URL` and `DEFAULT_SERVICE_PATH`, they are like what you said:
 
 ```
  public static final String DEFAULT_ROOT_URL = "https://www.googleapis.com/";

  public static final String DEFAULT_SERVICE_PATH = "genomics/v1beta/";
 ```
 
 I just tested it with `api-client-java`, and it works!  Below are the changes I made to [GenomicsSample.java](https://github.com/googlegenomics/api-client-java/blob/master/src/main/java/com/google/cloud/genomics/api/client/GenomicsSample.java):
 
 * I added `import com.google.api.services.genomics.Genomics;` to the `import` section.
  
 * I replaced `GenomicsFactory genomicsFactory = ...` with:
 ```
   Genomics genomicsFactory = GenomicsFactory.builder("genomics_java_client").build().fromClientSecretsFile(new File(command.clientSecretsFilename));
```

* I then replaced `File dataStoreFile =...`, `command.setDataStoreFactory(...` and `command.handleRequest(...` with:

```
  command.handleRequest(genomicsFactory);
```

Thanks Cassie - that was fun! :)
~p