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Development on GATK 4

There is a newer version: 4.6.0.0

package org.broadinstitute.hellbender.tools;

import org.broadinstitute.barclay.argparser.CommandLineProgramProperties;
import org.broadinstitute.barclay.help.DocumentedFeature;
import org.broadinstitute.hellbender.cmdline.programgroups.CoverageAnalysisProgramGroup;
import org.broadinstitute.hellbender.engine.FeatureContext;
import org.broadinstitute.hellbender.engine.ReadWalker;
import org.broadinstitute.hellbender.engine.ReferenceContext;
import org.broadinstitute.hellbender.utils.read.GATKRead;

/**
 * Calculate and print to the standard output the overall number of reads in a SAM/BAM/CRAM file
 *
 * Input
 * 
 *     A single BAM file
 * 
 *
 * Example
 *
 *  *   gatk CountReads \
 *     -I input_reads.bam
 * 
 */
@DocumentedFeature
@CommandLineProgramProperties(
	summary = "Count reads in a SAM/BAM/CRAM file.",
	oneLineSummary = "Count reads in a SAM/BAM/CRAM file",
    programGroup = CoverageAnalysisProgramGroup.class
)
public final class CountReads extends ReadWalker {

    private long count = 0;
    @Override
    public void apply( final GATKRead read, final ReferenceContext referenceContext, final FeatureContext featureContext ) {
        ++count;
    }

    @Override
    public Object onTraversalSuccess() {
        logger.info("CountReads counted " + count + " total reads");
        return count;
    }
}