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