IntGenotypeFieldAccessors.java

/*
* Copyright (c) 2012 The Broad Institute
* 
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
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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,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/

package htsjdk.variant.variantcontext.writer;

import htsjdk.variant.variantcontext.Genotype;
import htsjdk.variant.vcf.VCFConstants;

import java.util.HashMap;

/**
 * A convenient way to provide a single view on the many int and int[] field values we work with,
 * for writing out the values.  This class makes writing out the inline AD, GQ, PL, DP fields
 * easy and fast
 *
 * @author Mark DePristo
 * @since 6/12
 */
public class IntGenotypeFieldAccessors {
    // initialized once per writer to allow parallel writers to work
    private final HashMap<String, Accessor> intGenotypeFieldEncoders = new HashMap<String, Accessor>();

    public IntGenotypeFieldAccessors() {
        intGenotypeFieldEncoders.put(VCFConstants.DEPTH_KEY, new IntGenotypeFieldAccessors.DPAccessor());
        intGenotypeFieldEncoders.put(VCFConstants.GENOTYPE_ALLELE_DEPTHS, new IntGenotypeFieldAccessors.ADAccessor());
        intGenotypeFieldEncoders.put(VCFConstants.GENOTYPE_PL_KEY, new IntGenotypeFieldAccessors.PLAccessor());
        intGenotypeFieldEncoders.put(VCFConstants.GENOTYPE_QUALITY_KEY, new IntGenotypeFieldAccessors.GQAccessor());
    }

    /**
     * Return an accessor for field, or null if none exists
     * @param field
     * @return
     */
    public Accessor getAccessor(final String field) {
        return intGenotypeFieldEncoders.get(field);
    }

    public static abstract class Accessor {
        public abstract int[] getValues(final Genotype g);

        public final int getSize(final Genotype g) {
            final int[] v = getValues(g);
            return v == null ? 0 : v.length;
        }
    }

    private static abstract class AtomicAccessor extends Accessor {
        private final int[] singleton = new int[1];

        @Override
        public int[] getValues(final Genotype g) {
            singleton[0] = getValue(g);
            return singleton[0] == -1 ? null : singleton;
        }

        public abstract int getValue(final Genotype g);
    }

    public static class GQAccessor extends AtomicAccessor {
        @Override public int getValue(final Genotype g) { return Math.min(g.getGQ(), VCFConstants.MAX_GENOTYPE_QUAL); }
    }

    public static class DPAccessor extends AtomicAccessor {
        @Override public int getValue(final Genotype g) { return g.getDP(); }
    }

    public static class ADAccessor extends Accessor {
        @Override public int[] getValues(final Genotype g) { return g.getAD(); }
    }

    public static class PLAccessor extends Accessor {
        @Override public int[] getValues(final Genotype g) { return g.getPL(); }
    }
}