@Override protected Collection<ArgumentTypeDescriptor> getArgumentTypeDescriptors() { List<ArgumentTypeDescriptor> typeDescriptors = new ArrayList<ArgumentTypeDescriptor>(); typeDescriptors.add(new VCFWriterArgumentTypeDescriptor(GATKEngine,System.out,Collections.<Object>emptyList())); typeDescriptors.add(new SAMFileWriterArgumentTypeDescriptor(GATKEngine,System.out)); typeDescriptors.add(new OutputStreamArgumentTypeDescriptor(GATKEngine,System.out)); return typeDescriptors; }
ArgumentDefinition defaultArgumentDefinition = createDefaultArgumentDefinition(source); ArgumentMatchValue writerFileName = getArgumentValue(defaultArgumentDefinition,matches); File writerFile = writerFileName != null ? writerFileName.asFile() : null; : new VariantContextWriterStub(engine, defaultOutputStream, argumentSources); stub.setCompressed(isCompressed(writerFileName == null ? null: writerFileName.asString())); parsingEngine.addTags(stub,getArgumentTags(matches)); engine.addOutput(stub);
/** * Subclasses of CommandLinePrograms can provide their own types of command-line arguments. * @return A collection of type descriptors generating implementation-dependent placeholders. */ protected Collection<ArgumentTypeDescriptor> getArgumentTypeDescriptors() { return Arrays.asList( new VCFWriterArgumentTypeDescriptor(engine,System.out,argumentSources), new SAMFileWriterArgumentTypeDescriptor(engine,System.out), new OutputStreamArgumentTypeDescriptor(engine,System.out) ); }
@Override public Collection<ArgumentTypeDescriptor> getArgumentTypeDescriptors() { final GenomeAnalysisEngine engine = new GenomeAnalysisEngine(); return Arrays.asList( new SAMFileWriterArgumentTypeDescriptor(engine, System.out), new OutputStreamArgumentTypeDescriptor(engine, System.out), new VCFWriterArgumentTypeDescriptor(engine, System.out, null)); }