package org.broadinstitute.hellbender.tools.examples; import htsjdk.tribble.Feature; import htsjdk.tribble.bed.BEDFeature; import htsjdk.variant.variantcontext.VariantContext; import org.broadinstitute.barclay.argparser.Argument; import org.broadinstitute.barclay.argparser.CommandLineProgramProperties; import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions; import org.broadinstitute.hellbender.cmdline.programgroups.ExampleProgramGroup; import org.broadinstitute.hellbender.engine.*; import org.broadinstitute.hellbender.utils.read.GATKRead; import java.io.File; import java.io.PrintStream; /** * Example/toy program that shows how to implement the FeatureWalker interface. Prints supplied features * along with overlapping reads/reference bases/variants (if present). */ @CommandLineProgramProperties( summary = "Example tool that prints features supplied to the specified output file (stdout if none provided), along with overlapping reads/reference bases/variants (if provided)", oneLineSummary = "Example tool that prints features with optional contextual data", programGroup = ExampleProgramGroup.class, omitFromCommandLine = true ) public final class ExampleFeatureWalker extends FeatureWalker<BEDFeature> { @Argument(fullName = StandardArgumentDefinitions.OUTPUT_LONG_NAME, shortName = StandardArgumentDefinitions.OUTPUT_SHORT_NAME, doc = "Output file (if not provided, defaults to STDOUT)", common = false, optional = true) private GATKPath outputFile = null; @Argument(fullName="auxiliaryVariants", shortName="av", doc="Auxiliary set of variants", optional=true) private FeatureInput<VariantContext> auxiliaryVariants; private PrintStream outputStream = null; @Argument(shortName = "F", fullName = "feature_file", doc = "Feature file (eg., VCF or BED file)") public File featuresFile; @Override public void onTraversalStart() { outputStream = outputFile != null ? new PrintStream(outputFile.getOutputStream()) : System.out; } @Override protected boolean isAcceptableFeatureType(Class<? extends Feature> featureType) { return featureType.isAssignableFrom(BEDFeature.class); } @Override public File getDrivingFeatureFile() { return featuresFile; } @Override public void apply(final BEDFeature feature, final ReadsContext readsContext, final ReferenceContext referenceContext, final FeatureContext featureContext) { outputStream.println("Current feature: " + toBedFeatureString(feature)); if ( referenceContext.hasBackingDataSource() ) { printReferenceBases(referenceContext); } if ( readsContext.hasBackingDataSource() ) { printReads(readsContext); } if ( featureContext.hasBackingDataSource() ) { printVariants(featureContext); } } private static String toBedFeatureString(Feature feature) { //Note: BEDFeatures have no toString methods and render as useless pointers return feature.getClass().getCanonicalName()+ ":" + feature.getContig() + ":" + feature.getStart() + "-" + feature.getEnd(); } private void printReferenceBases( final ReferenceContext refContext ) { outputStream.printf("\tOverlapping reference bases: %s\n\n", new String(refContext.getBases())); } private void printReads( final ReadsContext readsContext ) { for ( final GATKRead read : readsContext ) { outputStream.printf("\tOverlapping read at %s:%d-%d\n", read.getContig(), read.getStart(), read.getEnd()); } outputStream.println(); } private void printVariants( final FeatureContext featureContext ) { for ( final VariantContext variant : featureContext.getValues(auxiliaryVariants) ) { outputStream.printf("\tOverlapping variant at %s:%d-%d. Ref: %s Alt(s): %s\n", variant.getContig(), variant.getStart(), variant.getEnd(), variant.getReference(), variant.getAlternateAlleles()); } outputStream.println(); } @Override public void closeTool() { if ( outputStream != null ) { outputStream.close(); } } }