org.broadinstitute.hellbender.tools.examples.ExampleReadWalkerWithReference Maven / Gradle / Ivy

Show more of this group Show more artifacts with this name
Show all versions of gatk Show documentation

Development on GATK 4

There is a newer version: 4.6.0.0

package org.broadinstitute.hellbender.tools.examples;

import org.broadinstitute.barclay.argparser.CommandLineProgramProperties;
import org.broadinstitute.barclay.argparser.Argument;
import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;
import org.broadinstitute.hellbender.cmdline.programgroups.ExampleProgramGroup;
import org.broadinstitute.hellbender.engine.FeatureContext;
import org.broadinstitute.hellbender.engine.GATKPath;
import org.broadinstitute.hellbender.engine.ReadWalker;
import org.broadinstitute.hellbender.engine.ReferenceContext;
import org.broadinstitute.hellbender.utils.read.GATKRead;

import java.io.PrintStream;

/**
 * Example/toy program that prints reads from the provided file or files with corresponding reference bases
 * (if a reference is provided). Intended to show how to implement the ReadWalker interface.
 */
@CommandLineProgramProperties(
        summary = "Prints reads from the provided file(s) with corresponding reference bases (if a reference is provided) to the specified output file (or STDOUT if none specified)",
        oneLineSummary = "Print reads with reference context",
        programGroup = ExampleProgramGroup.class,
        omitFromCommandLine = true
)
public final class ExampleReadWalkerWithReference extends ReadWalker {

    @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 OUTPUT_FILE = null;

    private PrintStream outputStream = null;

    @Override
    public void onTraversalStart() {
        outputStream = OUTPUT_FILE != null ? new PrintStream(OUTPUT_FILE.getOutputStream()) : System.out;
    }

    @Override
    public void apply( GATKRead read, ReferenceContext referenceContext, FeatureContext featureContext ) {
        outputStream.printf("Read at %s:%d-%d:\n%s\n", read.getContig(), read.getStart(), read.getEnd(), read.getBasesString());
        if ( referenceContext.hasBackingDataSource() )
            outputStream.println("Reference Context:\n" + new String(referenceContext.getBases()));
        outputStream.println();
    }

    @Override
    public void closeTool() {
        if ( outputStream != null ) {
            outputStream.close();
        }
    }
}