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Scalability test for EXACT models

This commit is contained in:
Mark DePristo 2012-10-17 14:14:41 -04:00
parent c9e7a947c2
commit fa93681f51
2 changed files with 92 additions and 1 deletions
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6
protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcTestBuilder.java
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@ -45,12 +45,16 @@ public class AFCalcTestBuilder {
human
}
public int getNumAltAlleles() {
return numAltAlleles;
}
public int getnSamples() {
return nSamples;
}
public AFCalc makeModel() {
return AFCalcFactory.createAFCalc(modelType, nSamples, 4, 4, 2);
return AFCalcFactory.createAFCalc(modelType, nSamples, getNumAltAlleles(), getNumAltAlleles(), 2);
}
public double[] makePriors() {

87
protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcPerformanceUnitTest.java 100644
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@ -0,0 +1,87 @@
package org.broadinstitute.sting.gatk.walkers.genotyper.afcalc;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.testng.Assert;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
public class AFCalcPerformanceUnitTest extends BaseTest {
@DataProvider(name = "ScalingTests")
public Object[][] makepolyTestProviderLotsOfAlleles() {
List<Object[]> tests = new ArrayList<Object[]>();
// list of all high-quality models in the system
final List<AFCalcFactory.Calculation> biAllelicModels = Arrays.asList(
AFCalcFactory.Calculation.EXACT_INDEPENDENT,
AFCalcFactory.Calculation.EXACT_REFERENCE);
final List<AFCalcFactory.Calculation> multiAllelicModels = Arrays.asList(
AFCalcFactory.Calculation.EXACT_INDEPENDENT);
// for ( final int nonTypePLs : Arrays.asList(100) ) {
// for ( final int nSamples : Arrays.asList(10000) ) {
// final List<Integer> alleleCounts = Arrays.asList(50);
// for ( final int nAltAlleles : Arrays.asList(1) ) {
for ( final int nonTypePLs : Arrays.asList(100) ) {
for ( final int nSamples : Arrays.asList(100, 1000) ) {
final List<Integer> alleleCounts = Arrays.asList(0, 1, 2, 3, 4, 5, 10, 50, 500);
for ( final int nAltAlleles : Arrays.asList(1, 2, 3) ) {
final List<AFCalcFactory.Calculation> models = nAltAlleles > 1 ? multiAllelicModels : biAllelicModels;
for ( final AFCalcFactory.Calculation model : models ) {
for ( final List<Integer> ACs : Utils.makePermutations(alleleCounts, nAltAlleles, true) ) {
if ( MathUtils.sum(ACs) < nSamples * 2 ) {
final AFCalcTestBuilder testBuilder
= new AFCalcTestBuilder(nSamples, nAltAlleles, model, AFCalcTestBuilder.PriorType.human);
tests.add(new Object[]{testBuilder, ACs, nonTypePLs});
}
}
}
}
}
}
return tests.toArray(new Object[][]{});
}
private Pair<Integer, Integer> estNumberOfEvaluations(final AFCalcTestBuilder testBuilder, final VariantContext vc, final int nonTypePL) {
final int evalOverhead = 2; // 2
final int maxEvalsPerSamplePerAC = 3;
int minEvals = 0, maxEvals = 0;
for ( final Allele alt : vc.getAlternateAlleles() ) {
final int AC = vc.getCalledChrCount(alt);
minEvals += AC + evalOverhead; // everyone is hom-var
maxEvals += AC * maxEvalsPerSamplePerAC + 10;
}
return new Pair<Integer, Integer>(minEvals, maxEvals);
}
@Test(dataProvider = "ScalingTests")
private void testScaling(final AFCalcTestBuilder testBuilder, final List<Integer> ACs, final int nonTypePL) {
final AFCalc calc = testBuilder.makeModel();
final double[] priors = testBuilder.makePriors();
final VariantContext vc = testBuilder.makeACTest(ACs, 0, nonTypePL);
final AFCalcResult result = calc.getLog10PNonRef(vc, priors);
final Pair<Integer, Integer> expectedNEvaluation = estNumberOfEvaluations(testBuilder, vc, nonTypePL);
final int minEvals = expectedNEvaluation.getFirst();
final int maxEvals = expectedNEvaluation.getSecond();
logger.warn(" min " + minEvals + " obs " + result.getnEvaluations() + " max " + maxEvals + " for test " + testBuilder + " sum(ACs)=" + (int)MathUtils.sum(ACs));
Assert.assertTrue(result.getnEvaluations() >= minEvals,
"Actual number of evaluations " + result.getnEvaluations() + " < min number of evals " + minEvals);
Assert.assertTrue(result.getnEvaluations() <= maxEvals,
"Actual number of evaluations " + result.getnEvaluations() + " > max number of evals " + minEvals);
}
}