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 * copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the
 * Software is furnished to do so, subject to the following
 * conditions:
 *
 * The above copyright notice and this permission notice shall be
 * included in all copies or substantial portions of the Software.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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 * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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 * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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package org.broadinstitute.sting.gatk.walkers.recalibration;

import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.recalibration.BaseRecalibration;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;

import java.util.Arrays;

/**
 * Created by IntelliJ IDEA.
 * User: rpoplin
 * Date: 9/26/11
 */

public class ContextCovariate implements ExperimentalCovariate {

    private int CONTEXT_SIZE;
    private String allN = "";

    // Initialize any member variables using the command-line arguments passed to the walkers
    @Override
    public void initialize(final RecalibrationArgumentCollection RAC) {
        CONTEXT_SIZE = RAC.CONTEXT_SIZE;

        if (CONTEXT_SIZE <= 0)
            throw new UserException("Context Size must be positive, if you don't want to use the context covariate, just turn it off instead");

        // initialize allN given the size of the context
        for (int i = 0; i < CONTEXT_SIZE; i++)
            allN += "N";
    }

    @Override
    public void getValues(final GATKSAMRecord read, final Comparable[] comparable) {
        byte[] bases = read.getReadBases();
        for (int i = 0; i < read.getReadLength(); i++)
            comparable[i] = (i < CONTEXT_SIZE) ? allN : new String(Arrays.copyOfRange(bases, i - CONTEXT_SIZE, i));
    }

    // Used to get the covariate's value from input csv file in TableRecalibrationWalker
    @Override
    public final Comparable getValue(final String str) {
        return str;
    }
}
