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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;

import java.util.Collections;
import java.util.List;

/**
 * An argument collection for use with tools that accept one or more input files containing reads
 * (eg., BAM/SAM/CRAM files), and require at least one such input.
 */
public final class RequiredReadInputArgumentCollection extends ReadInputArgumentCollection {
    private static final long serialVersionUID = 1L;

    @Argument(fullName = StandardArgumentDefinitions.INPUT_LONG_NAME, shortName = StandardArgumentDefinitions.INPUT_SHORT_NAME, doc = "BAM/SAM/CRAM file containing reads", optional = false, common = true)
    @WorkflowInput(optionalCompanions = StandardArgumentDefinitions.INPUT_INDEX_COMPANION)
    public List readFilesNames;

    /**
     * Get the list of BAM/SAM/CRAM inputs specified at the command line.
     * GATKPath is the preferred format, as this can handle both local disk and NIO direct access to cloud storage.
     */
    public List getReadPathSpecifiers() { return Collections.unmodifiableList(readFilesNames);}
}