com.google.cloud.genomics.dataflow.functions.ibs.SharedMinorAllelesCalculator.java Source code

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Here is the source code for com.google.cloud.genomics.dataflow.functions.ibs.SharedMinorAllelesCalculator.java

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/*
 * Copyright (C) 2014 Google Inc.
 *
 * Licensed under the Apache License, Version 2.0 (the "License"); you may not
 * use this file except in compliance with the License. You may obtain a copy of
 * the License at
 *
 * http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS, WITHOUT
 * WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the
 * License for the specific language governing permissions and limitations under
 * the License.
 */
package com.google.cloud.genomics.dataflow.functions.ibs;

import com.google.common.base.Predicate;
import com.google.common.collect.Iterables;
import com.google.genomics.v1.VariantCall;

/**
 * Computes the similarity of two calls based on whether they share a minor allele or not.
 */
public class SharedMinorAllelesCalculator implements CallSimilarityCalculator {

    private final boolean isReferenceMajor;

    public SharedMinorAllelesCalculator(boolean isReferenceMajor) {
        this.isReferenceMajor = isReferenceMajor;
    }

    private boolean hasMinorAllele(VariantCall call) {
        return Iterables.any(call.getGenotypeList(), new Predicate<Integer>() {

            @Override
            public boolean apply(Integer genotype) {
                if (isReferenceMajor) {
                    return genotype > 0;
                } else {
                    return genotype == 0;
                }
            }

        });
    }

    @Override
    public double similarity(VariantCall call1, VariantCall call2) {
        if (call1.getCallSetName().equals(call2.getCallSetName())) {
            return 1.0;
        }
        if (hasMinorAllele(call1) && hasMinorAllele(call2)) {
            return 1.0;
        } else {
            return 0.0;
        }
    }

}