com.google.cloud.genomics.dataflow.functions.LikelihoodFnTest.java Source code

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

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/*
 * Copyright 2015 Google.
 *
 * 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;

import com.google.api.services.genomics.model.Position;
import com.google.cloud.genomics.dataflow.model.ReadCounts;
import com.google.cloud.genomics.dataflow.model.ReadQualityCount;
import com.google.cloud.genomics.dataflow.model.ReadQualityCount.Base;
import com.google.common.collect.ImmutableMap;

import junit.framework.TestCase;

import org.apache.commons.math3.util.Precision;
import org.junit.Test;
import org.junit.runner.RunWith;
import org.junit.runners.JUnit4;

import java.util.Map;

/**
 * Unit tests for {@link LikelihoodFn}.
 */
@RunWith(JUnit4.class)
public class LikelihoodFnTest extends TestCase {

    @Test
    public void testValue() {
        final double tolerance = 0.0000001; // slop factor for floating point comparisons
        final double alpha = 0.25;
        final int errPhred = 10; // P(err) = 0.1
        final double pRef = 0.6;

        Position position1 = new Position().setReferenceName("1").setPosition(123L);

        /*
         * Observe single REF read
         */
        ImmutableMap.Builder<Position, ReadCounts> countsBuilder = ImmutableMap.builder();
        ReadCounts rc = new ReadCounts();
        rc.setRefFreq(pRef);
        ReadQualityCount rqc = new ReadQualityCount();
        rqc.setBase(Base.REF);
        rqc.setQuality(errPhred);
        rqc.setCount(1);
        rc.addReadQualityCount(rqc);
        countsBuilder.put(position1, rc);
        Map<Position, ReadCounts> readCounts = countsBuilder.build();
        LikelihoodFn fn = new LikelihoodFn(readCounts);
        // Likelihood of a single REF with the parameters above
        final double likRef = 0.3354133333;
        assertEquals(Precision.compareTo(fn.value(alpha), Math.log(likRef), tolerance), 0);

        /*
         * Observe single NONREF read
         */
        countsBuilder = ImmutableMap.builder();
        rc = new ReadCounts();
        rc.setRefFreq(pRef);
        rqc = new ReadQualityCount();
        rqc.setBase(Base.NONREF);
        rqc.setQuality(errPhred);
        rqc.setCount(1);
        rc.addReadQualityCount(rqc);
        countsBuilder.put(position1, rc);
        readCounts = countsBuilder.build();
        fn = new LikelihoodFn(readCounts);
        // Likelihood of a single NONREF with the parameters above
        final double likNonref = 0.20368;
        assertEquals(Precision.compareTo(fn.value(alpha), Math.log(likNonref), tolerance), 0);

        /*
         * Observe single OTHER read
         */
        countsBuilder = ImmutableMap.builder();
        rc = new ReadCounts();
        rc.setRefFreq(pRef);
        rqc = new ReadQualityCount();
        rqc.setBase(Base.OTHER);
        rqc.setQuality(errPhred);
        rqc.setCount(1);
        rc.addReadQualityCount(rqc);
        countsBuilder.put(position1, rc);
        readCounts = countsBuilder.build();
        fn = new LikelihoodFn(readCounts);
        // Likelihood of a single OTHER with the parameters above
        final double likOther = 0.03850666667;
        assertEquals(Precision.compareTo(fn.value(alpha), Math.log(likOther), tolerance), 0);

        // Likelihood for reads at 2 different positions should be product of
        // likelihoods for individual reads
        Position position2 = new Position().setReferenceName("1").setPosition(124L);
        countsBuilder = ImmutableMap.builder();
        rc = new ReadCounts();
        rc.setRefFreq(pRef);
        rqc = new ReadQualityCount();
        rqc.setBase(Base.REF);
        rqc.setQuality(errPhred);
        rqc.setCount(1);
        rc.addReadQualityCount(rqc);
        countsBuilder.put(position1, rc);
        rc = new ReadCounts();
        rc.setRefFreq(pRef);
        rqc = new ReadQualityCount();
        rqc.setBase(Base.NONREF);
        rqc.setQuality(errPhred);
        rqc.setCount(1);
        rc.addReadQualityCount(rqc);
        countsBuilder.put(position2, rc);
        readCounts = countsBuilder.build();
        fn = new LikelihoodFn(readCounts);
        assertEquals(Precision.compareTo(fn.value(alpha), Math.log(likRef * likNonref), tolerance), 0);
    }
}