org.broadinstitute.hellbender.cmdline.argumentcollections.RequiredReferenceInputArgumentCollection Maven / Gradle / Ivy

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package org.broadinstitute.hellbender.cmdline.argumentcollections;

import org.broadinstitute.barclay.argparser.Argument;
import org.broadinstitute.barclay.argparser.WorkflowInput;
import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;
import org.broadinstitute.hellbender.engine.GATKPath;

/**
 * An argument collection for use with tools that require a reference file as input.
 */
public final class RequiredReferenceInputArgumentCollection extends ReferenceInputArgumentCollection {
    private static final long serialVersionUID = 1L;

    @Argument(fullName = StandardArgumentDefinitions.REFERENCE_LONG_NAME, shortName = StandardArgumentDefinitions.REFERENCE_SHORT_NAME, doc = "Reference sequence file", optional = false)
    @WorkflowInput(requiredCompanions = { StandardArgumentDefinitions.REFERENCE_INDEX_COMPANION, StandardArgumentDefinitions.REFERENCE_DICTIONARY_COMPANION})
    private GATKPath referenceInputPathSpecifier;

    @Override
    public GATKPath getReferenceSpecifier() {
        return referenceInputPathSpecifier;
    }
}