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• ReadIndexWithCounts.java

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org.campagnelab.dl.somatic.mappers.ReadIndexWithCounts Maven / Gradle / Ivy

package org.campagnelab.dl.somatic.mappers;

import it.unimi.dsi.fastutil.ints.IntOpenHashSet;
import it.unimi.dsi.fastutil.ints.IntSet;

import java.util.List;

/**
 * Created by fac2003 on 6/3/16.
 */
public class ReadIndexWithCounts extends GenotypeCount {
    private IntSet readIndices = new IntOpenHashSet();

    public ReadIndexWithCounts() {
    }

    public void set(List readIndicesForwardStrandList, List readIndicesReverseStrandList) {
        readIndices.clear();
        readIndices.addAll(readIndicesForwardStrandList);
        readIndices.addAll(readIndicesReverseStrandList);
    }

    public float getDistinctReadIndices() {
        return readIndices.size();
    }
}