1 package org.broadinstitute.hellbender.engine;
2 
3 import org.broadinstitute.barclay.argparser.CommandLineProgramProperties;
4 import org.broadinstitute.hellbender.cmdline.TestProgramGroup;
5 
6 /**
7  * A Dummy / Placeholder class that can be used where a {@link GATKTool} is required.
8  * DO NOT USE THIS FOR ANYTHING OTHER THAN TESTING.
9  * THIS MUST BE IN THE ENGINE PACKAGE DUE TO SCOPE ON `features`!
10  * Created by jonn on 9/19/18.
11  */
12 @CommandLineProgramProperties(
13         summary = "A dummy GATKTool to help test Funcotator.",
14         oneLineSummary = "Dummy dumb dumb tool for testing.",
15         programGroup = TestProgramGroup.class
16 )
17 public final class DummyPlaceholderGatkTool extends GATKTool {
18 
DummyPlaceholderGatkTool()19     public DummyPlaceholderGatkTool() {
20         parseArgs(new String[]{});
21         onStartup();
22     }
23 
24     @Override
traverse()25     public void traverse() {
26 
27     }
28 
29     @Override
initializeFeatures()30     void initializeFeatures(){
31         features = new FeatureManager(this, FeatureDataSource.DEFAULT_QUERY_LOOKAHEAD_BASES, cloudPrefetchBuffer, cloudIndexPrefetchBuffer,
32                 getGenomicsDBOptions());
33     }
34 }
35