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Finalizing IndependentAllelesDiploidExactAFCalc 

-- Updating integration tests, confirming that results for the original EXACT model are as expected given our new more rigorous application of likelihoods, priors, and posteriors
-- Fix basic logic bug in AFCalcResult.isPolymorphic and UnifiedGenotypeEngine, where isNonRef really meant isRef.  Not ideal.  Finally caught by some tests, but good god it almost made it into the code
-- Now takes the Math.abs of the phred-scaled confidence so that we don't see -0.0
-- Massive new suite of unit tests to ensure that bi-allelic and tri-allele events are called properly with all models, and that the IndependentAllelesDiploidExactAFCalc calls events with up to 4 alt alleles correctly.  ID'd some of the bugs below
-- Fix sort order bug in IndependentAllelesDiploidExactAFCalc caught by new unit tests
-- Fix bug in GeneralPloidyExactAFCalc where the AFCalcResult has meaningless values in the likelihoods when no there we no informative GLs.
This commit is contained in:
Mark DePristo 2012-10-15 07:40:09 -04:00
parent 1ac09ca81e
commit dcf8af42a8
13 changed files with 249 additions and 99 deletions
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30
protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactAFCalculationPerformanceTest.java → protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcPerformanceTest.java
View File

@ -23,8 +23,8 @@ import java.util.*;
* Time: 10:25 AM
* To change this template use File | Settings | File Templates.
*/
public class ExactAFCalculationPerformanceTest {
final static Logger logger = Logger.getLogger(ExactAFCalculationPerformanceTest.class);
public class AFCalcPerformanceTest {
final static Logger logger = Logger.getLogger(AFCalcPerformanceTest.class);
private static abstract class Analysis {
final GATKReport report;
@ -33,7 +33,7 @@ public class ExactAFCalculationPerformanceTest {
report = GATKReport.newSimpleReport(name, columns);
}
public abstract void run(final ExactAFCalculationTestBuilder testBuilder,
public abstract void run(final AFCalcTestBuilder testBuilder,
final List<Object> coreColumns);
public String getName() {
@ -50,7 +50,7 @@ public class ExactAFCalculationPerformanceTest {
super("AnalyzeByACAndPL", Utils.append(columns, "non.type.pls", "ac", "n.alt.seg", "other.ac"));
}
public void run(final ExactAFCalculationTestBuilder testBuilder, final List<Object> coreValues) {
public void run(final AFCalcTestBuilder testBuilder, final List<Object> coreValues) {
final SimpleTimer timer = new SimpleTimer();
for ( final int nonTypePL : Arrays.asList(100) ) {
@ -109,7 +109,7 @@ public class ExactAFCalculationPerformanceTest {
super("AnalyzeBySingletonPosition", Utils.append(columns, "non.type.pls", "position.of.singleton"));
}
public void run(final ExactAFCalculationTestBuilder testBuilder, final List<Object> coreValues) {
public void run(final AFCalcTestBuilder testBuilder, final List<Object> coreValues) {
final SimpleTimer timer = new SimpleTimer();
for ( final int nonTypePL : Arrays.asList(100) ) {
@ -143,7 +143,7 @@ public class ExactAFCalculationPerformanceTest {
super("AnalyzeByNonInformative", Utils.append(columns, "non.type.pls", "n.non.informative"));
}
public void run(final ExactAFCalculationTestBuilder testBuilder, final List<Object> coreValues) {
public void run(final AFCalcTestBuilder testBuilder, final List<Object> coreValues) {
final SimpleTimer timer = new SimpleTimer();
for ( final int nonTypePL : Arrays.asList(100) ) {
@ -212,9 +212,9 @@ public class ExactAFCalculationPerformanceTest {
final int nSamples = Integer.valueOf(args[1]);
final int ac = Integer.valueOf(args[2]);
final ExactAFCalculationTestBuilder testBuilder = new ExactAFCalculationTestBuilder(nSamples, 1,
final AFCalcTestBuilder testBuilder = new AFCalcTestBuilder(nSamples, 1,
AFCalcFactory.Calculation.EXACT_INDEPENDENT,
ExactAFCalculationTestBuilder.PriorType.human);
AFCalcTestBuilder.PriorType.human);
final VariantContext vc = testBuilder.makeACTest(new int[]{ac}, 0, 100);
@ -233,14 +233,14 @@ public class ExactAFCalculationPerformanceTest {
final List<ModelParams> modelParams = Arrays.asList(
new ModelParams(AFCalcFactory.Calculation.EXACT_REFERENCE, 10000, 10),
// new ModelParams(ExactAFCalculationTestBuilder.ModelType.GeneralExact, 100, 10),
// new ModelParams(AFCalcTestBuilder.ModelType.GeneralExact, 100, 10),
new ModelParams(AFCalcFactory.Calculation.EXACT_CONSTRAINED, 10000, 100),
new ModelParams(AFCalcFactory.Calculation.EXACT_INDEPENDENT, 10000, 1000));
final boolean ONLY_HUMAN_PRIORS = false;
final List<ExactAFCalculationTestBuilder.PriorType> priorTypes = ONLY_HUMAN_PRIORS
? Arrays.asList(ExactAFCalculationTestBuilder.PriorType.values())
: Arrays.asList(ExactAFCalculationTestBuilder.PriorType.human);
final List<AFCalcTestBuilder.PriorType> priorTypes = ONLY_HUMAN_PRIORS
? Arrays.asList(AFCalcTestBuilder.PriorType.values())
: Arrays.asList(AFCalcTestBuilder.PriorType.human);
final List<Analysis> analyzes = new ArrayList<Analysis>();
analyzes.add(new AnalyzeByACAndPL(coreColumns));
@ -252,9 +252,9 @@ public class ExactAFCalculationPerformanceTest {
for ( final int nSamples : Arrays.asList(1, 10, 100, 1000, 10000) ) {
for ( final ModelParams modelToRun : modelParams) {
if ( modelToRun.meetsConstraints(nAltAlleles, nSamples) ) {
for ( final ExactAFCalculationTestBuilder.PriorType priorType : priorTypes ) {
final ExactAFCalculationTestBuilder testBuilder
= new ExactAFCalculationTestBuilder(nSamples, nAltAlleles, modelToRun.modelType, priorType);
for ( final AFCalcTestBuilder.PriorType priorType : priorTypes ) {
final AFCalcTestBuilder testBuilder
= new AFCalcTestBuilder(nSamples, nAltAlleles, modelToRun.modelType, priorType);
for ( final Analysis analysis : analyzes ) {
logger.info(Utils.join("\t", Arrays.asList(iteration, nAltAlleles, nSamples, modelToRun.modelType, priorType, analysis.getName())));

16
protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactAFCalculationTestBuilder.java → protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcTestBuilder.java
View File

@ -11,11 +11,14 @@ import java.util.Arrays;
import java.util.Collections;
import java.util.List;
public class ExactAFCalculationTestBuilder {
public class AFCalcTestBuilder {
final static Allele A = Allele.create("A", true);
final static Allele C = Allele.create("C");
final static Allele G = Allele.create("G");
final static Allele T = Allele.create("T");
final static Allele AA = Allele.create("AA");
final static Allele AT = Allele.create("AT");
final static Allele AG = Allele.create("AG");
static int sampleNameCounter = 0;
@ -24,14 +27,19 @@ public class ExactAFCalculationTestBuilder {
final AFCalcFactory.Calculation modelType;
final PriorType priorType;
public ExactAFCalculationTestBuilder(final int nSamples, final int numAltAlleles,
final AFCalcFactory.Calculation modelType, final PriorType priorType) {
public AFCalcTestBuilder(final int nSamples, final int numAltAlleles,
final AFCalcFactory.Calculation modelType, final PriorType priorType) {
this.nSamples = nSamples;
this.numAltAlleles = numAltAlleles;
this.modelType = modelType;
this.priorType = priorType;
}
@Override
public String toString() {
return String.format("AFCalcTestBuilder nSamples=%d nAlts=%d model=%s prior=%s", nSamples, numAltAlleles, modelType, priorType);
}
public enum PriorType {
flat,
human
@ -113,7 +121,7 @@ public class ExactAFCalculationTestBuilder {
}
public List<Allele> getAlleles() {
return Arrays.asList(A, C, G, T).subList(0, numAltAlleles+1);
return Arrays.asList(A, C, G, T, AA, AT, AG).subList(0, numAltAlleles+1);
}
public List<Allele> getAlleles(final GenotypeType type, final int altI) {

18
protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/GeneralPloidyExactAFCalc.java
View File

@ -192,13 +192,19 @@ public class GeneralPloidyExactAFCalc extends ExactAFCalc {
set.getLog10Likelihoods()[0] = 0.0;
combinedPoolLikelihoods.add(set);
for (int p=1; p<genotypeLikelihoods.size(); p++) {
resultTracker.reset(); // TODO -- why is this here? It makes it hard to track the n evaluation
combinedPoolLikelihoods = fastCombineMultiallelicPool(combinedPoolLikelihoods, genotypeLikelihoods.get(p), combinedPloidy, ploidyPerPool,
numAlleles, log10AlleleFrequencyPriors, resultTracker);
combinedPloidy = ploidyPerPool + combinedPloidy; // total number of chromosomes in combinedLikelihoods
}
if ( genotypeLikelihoods.size() <= 1 ) {
// no meaningful GLs at all, just set the tracker to non poly values
resultTracker.reset(); // just mimic-ing call below
resultTracker.setLog10LikelihoodOfAFzero(0.0);
} else {
for (int p=1; p<genotypeLikelihoods.size(); p++) {
resultTracker.reset(); // TODO -- why is this here? It makes it hard to track the n evaluation
combinedPoolLikelihoods = fastCombineMultiallelicPool(combinedPoolLikelihoods, genotypeLikelihoods.get(p), combinedPloidy, ploidyPerPool,
numAlleles, log10AlleleFrequencyPriors, resultTracker);
combinedPloidy = ploidyPerPool + combinedPloidy; // total number of chromosomes in combinedLikelihoods
}
}
}
public static CombinedPoolLikelihoods fastCombineMultiallelicPool(final CombinedPoolLikelihoods originalPool, double[] newGL, int originalPloidy, int newGLPloidy, int numAlleles,

14
protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidyIntegrationTest.java
View File

@ -1,9 +1,9 @@
package org.broadinstitute.sting.gatk.walkers.genotyper;
import org.broadinstitute.sting.WalkerTest;
import org.testng.annotations.Test;
import java.util.Arrays;
import org.testng.annotations.Test;
/**
* Created by IntelliJ IDEA.
@ -60,31 +60,31 @@ public class UnifiedGenotyperGeneralPloidyIntegrationTest extends WalkerTest {
@Test(enabled = true)
public void testBOTH_GGA_Pools() {
PC_LSV_Test(String.format(" -maxAltAlleles 2 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s",LSV_ALLELES),"LSV_BOTH_GGA","BOTH","a636ae291a27843107294f3e7940b98a");
PC_LSV_Test(String.format(" -maxAltAlleles 2 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s",LSV_ALLELES),"LSV_BOTH_GGA","BOTH","6d60d9f3dfe8e1580214be0d170b0fff");
}
@Test(enabled = true)
public void testINDEL_GGA_Pools() {
PC_LSV_Test(String.format(" -maxAltAlleles 1 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s",LSV_ALLELES),"LSV_INDEL_GGA","INDEL","738fa68a3fc838b4bbad5c257f3e96fe");
PC_LSV_Test(String.format(" -maxAltAlleles 1 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s",LSV_ALLELES),"LSV_INDEL_GGA","INDEL","30abf3c1868a61145edbc08fe35c8150");
}
@Test(enabled = true)
public void testINDEL_maxAltAlleles2_ploidy3_Pools_noRef() {
PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","9bcf1f2c204a251ee2b0b6f17ed59a61");
PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","ef99bc0513d3267f43b84cb88a324376");
}
@Test(enabled = true)
public void testINDEL_maxAltAlleles2_ploidy1_Pools_noRef() {
PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 1","LSV_INDEL_DISC_NOREF_p1","INDEL","c73678eeaad574af9ed45045074828fa");
PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 1","LSV_INDEL_DISC_NOREF_p1","INDEL","8ca07270717641385fe5d2e07e530782");
}
@Test(enabled = true)
public void testMT_SNP_DISCOVERY_sp4() {
PC_MT_Test(CEUTRIO_BAM, " -maxAltAlleles 1 -ploidy 8", "MT_SNP_DISCOVERY_sp4","c32e10070e10d30d33e5b882c1f89413");
PC_MT_Test(CEUTRIO_BAM, " -maxAltAlleles 1 -ploidy 8", "MT_SNP_DISCOVERY_sp4","da84bf45f7080a46a7a78542b3a0629d");
}
@Test(enabled = true)
public void testMT_SNP_GGA_sp10() {
PC_MT_Test(CEUTRIO_BAM, String.format(" -maxAltAlleles 1 -ploidy 20 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s",NA12891_CALLS), "MT_SNP_GGA_sp10", "d1b48f6f3a175fcba9aec6d427005a45");
PC_MT_Test(CEUTRIO_BAM, String.format(" -maxAltAlleles 1 -ploidy 20 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s",NA12891_CALLS), "MT_SNP_GGA_sp10", "f8ea18ec6a717a77fdf8c5f2482d8d8d");
}
}

137
protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcUnitTest.java
View File

@ -370,7 +370,7 @@ public class AFCalcUnitTest extends BaseTest {
final VariantContext vc2 = new VariantContextBuilder("x","1", 1, 1, Arrays.asList(A, C)).make();
final VariantContext vc3 = new VariantContextBuilder("x","1", 1, 1, Arrays.asList(A, C, G)).make();
final ExactAFCalculationTestBuilder.PriorType priorType = ExactAFCalculationTestBuilder.PriorType.flat;
final AFCalcTestBuilder.PriorType priorType = AFCalcTestBuilder.PriorType.flat;
final List<AFCalcFactory.Calculation> constrainedModel = Arrays.asList(AFCalcFactory.Calculation.EXACT_CONSTRAINED);
@ -413,13 +413,13 @@ public class AFCalcUnitTest extends BaseTest {
@Test(enabled = true && ! DEBUG_ONLY, dataProvider = "PNonRef")
private void testPNonRef(final VariantContext vcRoot,
AFCalcFactory.Calculation modelType,
ExactAFCalculationTestBuilder.PriorType priorType,
AFCalcTestBuilder.PriorType priorType,
final List<Genotype> genotypes,
final double expectedPNonRef,
final double tolerance,
final int nNonInformative) {
final ExactAFCalculationTestBuilder testBuilder
= new ExactAFCalculationTestBuilder(1, vcRoot.getNAlleles()-1, modelType, priorType);
final AFCalcTestBuilder testBuilder
= new AFCalcTestBuilder(1, vcRoot.getNAlleles()-1, modelType, priorType);
final VariantContextBuilder vcb = new VariantContextBuilder(vcRoot);
vcb.genotypes(genotypes);
@ -448,7 +448,7 @@ public class AFCalcUnitTest extends BaseTest {
return tests.toArray(new Object[][]{});
}
@Test(enabled = true && ! DEBUG_ONLY, dataProvider = "Models")
@Test(enabled = true & ! DEBUG_ONLY, dataProvider = "Models")
public void testBiallelicPriors(final AFCalc model) {
for ( int REF_PL = 10; REF_PL <= 20; REF_PL += 10 ) {
@ -464,8 +464,12 @@ public class AFCalcUnitTest extends BaseTest {
final double pRefWithPrior = AB.getLikelihoods().getAsVector()[0] + priors[0];
final double pHetWithPrior = AB.getLikelihoods().getAsVector()[1] + priors[1] - Math.log10(0.5);
final double nonRefPost = Math.pow(10, pHetWithPrior) / (Math.pow(10, pRefWithPrior) + Math.pow(10, pHetWithPrior));
final double log10NonRefPost = Math.log10(nonRefPost);
if ( nonRefPost < 0.1 )
if ( ! Double.isInfinite(log10NonRefPost) )
Assert.assertEquals(resultTracker.getLog10PosteriorOfAFGT0(), log10NonRefPost, 1e-2);
if ( nonRefPost >= 0.9 )
Assert.assertTrue(resultTracker.isPolymorphic(C, -1));
final int expectedMLEAC = 1; // the MLE is independent of the prior
@ -475,4 +479,125 @@ public class AFCalcUnitTest extends BaseTest {
}
}
}
@Test(enabled = true && ! DEBUG_ONLY, dataProvider = "Models")
// --------------------------------------------------------------------------------
//
// Test that polymorphic sites (bi and tri) are properly called
//
// --------------------------------------------------------------------------------
@DataProvider(name = "polyTestProvider")
public Object[][] makePolyTestProvider() {
List<Object[]> tests = new ArrayList<Object[]>();
// list of all high-quality models in the system
final List<AFCalcFactory.Calculation> models = Arrays.asList(
AFCalcFactory.Calculation.EXACT,
AFCalcFactory.Calculation.EXACT_REFERENCE,
AFCalcFactory.Calculation.EXACT_INDEPENDENT);
// note that we cannot use small PLs here or the thresholds are hard to set
for ( final int nonTypePLs : Arrays.asList(100, 1000) ) {
for ( final AFCalcFactory.Calculation model : models ) {
for ( final int allele1AC : Arrays.asList(0, 1, 2, 10, 100, 1000, 10000) ) {
for ( final int nSamples : Arrays.asList(1, 10, 100, 1000, 10000) ) {
// for ( final int nonTypePLs : Arrays.asList(10) ) {
// for ( final AFCalcFactory.Calculation model : models ) {
// for ( final int allele1AC : Arrays.asList(100) ) {
// for ( final int nSamples : Arrays.asList(1000) ) {
if ( nSamples < allele1AC ) continue;
final double pPerSample = Math.pow(10, nonTypePLs / -10.0);
final double errorFreq = pPerSample * nSamples;
final boolean poly1 = allele1AC > errorFreq && (nonTypePLs * allele1AC) > 30;
// bi-allelic tests
{
final AFCalcTestBuilder testBuilder
= new AFCalcTestBuilder(nSamples, 1, model, AFCalcTestBuilder.PriorType.human);
final List<Integer> ACs = Arrays.asList(allele1AC);
tests.add(new Object[]{testBuilder, ACs, nonTypePLs, Arrays.asList(poly1)});
}
// multi-allelic tests
for ( final int allele2AC : Arrays.asList(0, 1, 2, 10, 20, 50) ) {
if ( nSamples < allele2AC || allele1AC + allele2AC > nSamples || nSamples > 100 || nSamples == 1)
continue;
final AFCalcTestBuilder testBuilder
= new AFCalcTestBuilder(nSamples, 2, model, AFCalcTestBuilder.PriorType.human);
final List<Integer> ACs = Arrays.asList(allele1AC, allele2AC);
final boolean poly2 = allele2AC > errorFreq && (nonTypePLs * allele2AC) > 90;
tests.add(new Object[]{testBuilder, ACs, nonTypePLs, Arrays.asList(poly1, poly2)});
}
}
}
}
}
return tests.toArray(new Object[][]{});
}
@Test(enabled = true && ! DEBUG_ONLY, dataProvider = "polyTestProvider")
public void testCallingGeneral(final AFCalcTestBuilder testBuilder, final List<Integer> ACs, final int nonTypePL, final List<Boolean> expectedPoly ) {
testCalling(testBuilder, ACs, nonTypePL, expectedPoly);
}
@DataProvider(name = "polyTestProviderLotsOfAlleles")
public Object[][] makepolyTestProviderLotsOfAlleles() {
List<Object[]> tests = new ArrayList<Object[]>();
// list of all high-quality models in the system
final List<AFCalcFactory.Calculation> models = Arrays.asList(AFCalcFactory.Calculation.EXACT_INDEPENDENT);
final List<Integer> alleleCounts = Arrays.asList(0, 1, 2, 3, 4, 5, 10, 20);
final int nonTypePLs = 1000;
final int nAlleles = 4;
for ( final AFCalcFactory.Calculation model : models ) {
for ( final List<Integer> ACs : Utils.makePermutations(alleleCounts, nAlleles, true) ) {
final List<Boolean> isPoly = new ArrayList<Boolean>(ACs.size());
for ( final int ac : ACs ) isPoly.add(ac > 0);
final double acSum = MathUtils.sum(ACs);
for ( final int nSamples : Arrays.asList(1, 10, 100) ) {
if ( nSamples < acSum ) continue;
final AFCalcTestBuilder testBuilder
= new AFCalcTestBuilder(nSamples, nAlleles, model, AFCalcTestBuilder.PriorType.human);
tests.add(new Object[]{testBuilder, ACs, nonTypePLs, isPoly});
}
}
}
return tests.toArray(new Object[][]{});
}
@Test(enabled = true && ! DEBUG_ONLY, dataProvider = "polyTestProviderLotsOfAlleles")
public void testCallingLotsOfAlleles(final AFCalcTestBuilder testBuilder, final List<Integer> ACs, final int nonTypePL, final List<Boolean> expectedPoly ) {
testCalling(testBuilder, ACs, nonTypePL, expectedPoly);
}
private void testCalling(final AFCalcTestBuilder testBuilder, final List<Integer> ACs, final int nonTypePL, final List<Boolean> expectedPoly) {
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);
boolean anyPoly = false;
for ( final boolean onePoly : expectedPoly ) anyPoly = anyPoly || onePoly;
if ( anyPoly )
Assert.assertTrue(result.getLog10PosteriorOfAFGT0() > -1);
for ( int altI = 1; altI < result.getAllelesUsedInGenotyping().size(); altI++ ) {
final int i = altI - 1;
final Allele alt = result.getAllelesUsedInGenotyping().get(altI);
// must be getCalledChrCount because we cannot ensure that the VC made has our desired ACs
Assert.assertEquals(result.getAlleleCountAtMLE(alt), vc.getCalledChrCount(alt));
Assert.assertEquals(result.isPolymorphic(alt, -1), (boolean)expectedPoly.get(i), "isPolymorphic for allele " + alt + " " + result.getLog10PosteriorOfAFGt0ForAllele(alt));
}
}
}

12
protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ConstrainedAFCalculationModelUnitTest.java
View File

@ -47,9 +47,9 @@ public class ConstrainedAFCalculationModelUnitTest extends BaseTest {
@Test(enabled = true, dataProvider = "MaxACsToVisit")
public void testMaxACsToVisit(final int nSamples, final List<Integer> requestedACs, final int nNonInformative, final AFCalcFactory.Calculation modelType) {
final int nAlts = requestedACs.size();
final ExactAFCalculationTestBuilder testBuilder
= new ExactAFCalculationTestBuilder(nSamples, nAlts, modelType,
ExactAFCalculationTestBuilder.PriorType.human);
final AFCalcTestBuilder testBuilder
= new AFCalcTestBuilder(nSamples, nAlts, modelType,
AFCalcTestBuilder.PriorType.human);
final VariantContext vc = testBuilder.makeACTest(requestedACs, nNonInformative, 100);
final int[] maxACsToVisit = ((ConstrainedDiploidExactAFCalc)testBuilder.makeModel()).computeMaxACs(vc);
@ -113,9 +113,9 @@ public class ConstrainedAFCalculationModelUnitTest extends BaseTest {
private void testMakeACByGenotype(final VariantContext vcRoot, final Genotype g) {
final VariantContext vc = new VariantContextBuilder(vcRoot).genotypes(g).make();
final ExactAFCalculationTestBuilder testBuilder
= new ExactAFCalculationTestBuilder(1, vc.getNAlleles()-1, AFCalcFactory.Calculation.EXACT_CONSTRAINED,
ExactAFCalculationTestBuilder.PriorType.human);
final AFCalcTestBuilder testBuilder
= new AFCalcTestBuilder(1, vc.getNAlleles()-1, AFCalcFactory.Calculation.EXACT_CONSTRAINED,
AFCalcTestBuilder.PriorType.human);
final int[] maxACsToVisit = ((ConstrainedDiploidExactAFCalc)testBuilder.makeModel()).computeMaxACs(vc);

18
protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
View File

@ -21,17 +21,17 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerMultiSample() {
HCTest(CEUTRIO_BAM, "", "5b751474ad0aef4cdb53f094e605f97c");
HCTest(CEUTRIO_BAM, "", "a305107a5ec889152aa2efbe90b249d7");
}
@Test
public void testHaplotypeCallerSingleSample() {
HCTest(NA12878_BAM, "", "60efcd2d2722087e900f6365985d18bf");
HCTest(NA12878_BAM, "", "0c2217ec81f19790a6d1f98ebf8cf70d");
}
@Test
public void testHaplotypeCallerMultiSampleGGA() {
HCTest(CEUTRIO_BAM, "--max_alternate_alleles_for_indels 3 -gt_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf", "71bec55320a2f07af0d54be9d7735322");
HCTest(CEUTRIO_BAM, "--max_alternate_alleles_for_indels 3 -gt_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf", "0396c7352ab8ab98b03dca36299a0ddf");
}
private void HCTestComplexVariants(String bam, String args, String md5) {
@ -42,7 +42,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerMultiSampleComplex() {
HCTestComplexVariants(CEUTRIO_BAM, "", "966da0de8466d21d79f1523488dff6bd");
HCTestComplexVariants(CEUTRIO_BAM, "", "2cfb7d830d5a7eb7bc754b5f688a27a5");
}
private void HCTestSymbolicVariants(String bam, String args, String md5) {
@ -53,7 +53,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerSingleSampleSymbolic() {
HCTestSymbolicVariants(NA12878_CHR20_BAM, "", "8043b0451a4384e678a93600b34afce7");
HCTestSymbolicVariants(NA12878_CHR20_BAM, "", "d511848a46083c0d0b2495f65f162c2e");
}
private void HCTestIndelQualityScores(String bam, String args, String md5) {
@ -64,20 +64,20 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerSingleSampleIndelQualityScores() {
HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "ea6539e05faf10ffaf76f2d16907c47a");
HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "98d82d74e8d6a778290bee6c0df6d092");
}
@Test
public void HCTestProblematicReadsModifiedInActiveRegions() {
final String base = String.format("-T HaplotypeCaller -R %s -I %s", REF, privateTestDir + "haplotype-problem-4.bam") + " --no_cmdline_in_header -o %s -minPruning 3";
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("8d092b25f40456e618eef91fdce8adf0"));
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("7e112ea4623617f1f7f8f562f54aa2aa"));
executeTest("HCTestProblematicReadsModifiedInActiveRegions: ", spec);
}
@Test
public void HCTestStructuralIndels() {
final String base = String.format("-T HaplotypeCaller -R %s -I %s", REF, privateTestDir + "AFR.structural.indels.bam") + " --no_cmdline_in_header -o %s -minPruning 6 -L 20:8187565-8187800 -L 20:18670537-18670730";
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("c29e61810c056b52a47baae0696931ea"));
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("c642dcd93771f6f084d55de31f180d1b"));
executeTest("HCTestStructuralIndels: ", spec);
}
@ -91,7 +91,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
public void HCTestReducedBam() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T HaplotypeCaller -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "bamExample.ReducedRead.ADAnnotation.bam -o %s -L 1:67,225,396-67,288,518", 1,
Arrays.asList("864abe729828248333aee14818c1d2e1"));
Arrays.asList("79af83432dc4a1768b3ebffffc4d2b8f"));
executeTest("HC calling on a ReducedRead BAM", spec);
}

11
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
View File

@ -385,7 +385,7 @@ public class UnifiedGenotyperEngine {
final boolean isNonRef = AFresult.isPolymorphic(alternateAllele, UAC.STANDARD_CONFIDENCE_FOR_EMITTING / -10.0);
// if the most likely AC is not 0, then this is a good alternate allele to use
if ( ! isNonRef ) {
if ( isNonRef ) {
myAlleles.add(alternateAllele);
alleleCountsofMLE.add(AFresult.getAlleleCountAtMLE(alternateAllele));
bestGuessIsRef = false;
@ -398,9 +398,12 @@ public class UnifiedGenotyperEngine {
}
final double PoFGT0 = Math.pow(10, AFresult.getLog10PosteriorOfAFGT0());
final double phredScaledConfidence = ! bestGuessIsRef || UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES
? -10 * AFresult.getLog10PosteriorOfAFEq0()
: -10 * AFresult.getLog10PosteriorOfAFGT0();
// note the math.abs is necessary because -10 * 0.0 => -0.0 which isn't nice
final double phredScaledConfidence =
Math.abs(! bestGuessIsRef || UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES
? -10 * AFresult.getLog10PosteriorOfAFEq0()
: -10 * AFresult.getLog10PosteriorOfAFGT0());
// return a null call if we don't pass the confidence cutoff or the most likely allele frequency is zero
if ( UAC.OutputMode != OUTPUT_MODE.EMIT_ALL_SITES && !passesEmitThreshold(phredScaledConfidence, bestGuessIsRef) ) {

13
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcResult.java
View File

@ -230,7 +230,7 @@ public class AFCalcResult {
* @return true if there's enough confidence (relative to log10minPNonRef) to reject AF == 0
*/
public boolean isPolymorphic(final Allele allele, final double log10minPNonRef) {
return getLog10PosteriorOfAFGt0ForAllele(allele) < log10minPNonRef;
return getLog10PosteriorOfAFGt0ForAllele(allele) >= log10minPNonRef;
}
/**
@ -267,7 +267,14 @@ public class AFCalcResult {
for ( int i = 0; i < log10LikelihoodsOfAC.length; i++ )
log10UnnormalizedPosteriors[i] = log10LikelihoodsOfAC[i] + log10PriorsOfAC[i];
return MathUtils.normalizeFromLog10(log10UnnormalizedPosteriors, true, true);
// necessary because the posteriors may be so skewed that the log-space normalized value isn't
// good, so we have to try both log-space normalization as well as the real-space normalization if the
// result isn't good
final double[] logNormalized = MathUtils.normalizeFromLog10(log10UnnormalizedPosteriors, true, true);
if ( goodLog10ProbVector(logNormalized, logNormalized.length, true) )
return logNormalized;
else
return MathUtils.normalizeFromLog10(log10UnnormalizedPosteriors, true, false);
}
/**
@ -287,7 +294,7 @@ public class AFCalcResult {
return false;
}
if ( shouldSumToOne && MathUtils.compareDoubles(MathUtils.sumLog10(vector), 1.0, 1e-2) != 0 )
if ( shouldSumToOne && MathUtils.compareDoubles(MathUtils.sumLog10(vector), 1.0, 1e-4) != 0 )
return false;
return true; // everything is good

5
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalc.java
View File

@ -38,7 +38,7 @@ public class IndependentAllelesDiploidExactAFCalc extends DiploidExactAFCalc {
private final static class CompareAFCalcResultsByPNonRef implements Comparator<AFCalcResult> {
@Override
public int compare(AFCalcResult o1, AFCalcResult o2) {
return -1 * Double.compare(o1.getLog10LikelihoodOfAFGT0(), o2.getLog10LikelihoodOfAFGT0());
return Double.compare(o1.getLog10LikelihoodOfAFGT0(), o2.getLog10LikelihoodOfAFGT0());
}
}
@ -82,7 +82,8 @@ public class IndependentAllelesDiploidExactAFCalc extends DiploidExactAFCalc {
// TODO -- can be easily optimized (currently looks at all GLs via getGLs)
for ( int i = 0; i < allGLs.size(); i++ ) {
final double[] GLs = allGLs.get(i);
log10LikelihoodOfHomRef += MathUtils.normalizeFromLog10(GLs, true)[0];
log10LikelihoodOfHomRef += GLs[0];
//log10LikelihoodOfHomRef += MathUtils.normalizeFromLog10(GLs, true)[0];
}
return log10LikelihoodOfHomRef;

68
public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
View File

@ -28,7 +28,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMultiSamplePilot1() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
baseCommand + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10,022,000-10,025,000", 1,
Arrays.asList("cafd404f1b4f53586f7aa7a7084b91da"));
Arrays.asList("fe9c0e9e4b4ee4677145748cdd2285ff"));
executeTest("test MultiSample Pilot1", spec);
}
@ -36,7 +36,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testWithAllelesPassedIn1() {
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
baseCommand + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + privateTestDir + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1,
Arrays.asList("9a760dffbb299bda4934bcb4f7aad42a"));
Arrays.asList("bc15123620e1134f799005d71d1180fe"));
executeTest("test MultiSample Pilot2 with alleles passed in", spec1);
}
@ -44,7 +44,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testWithAllelesPassedIn2() {
WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
baseCommand + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + privateTestDir + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1,
Arrays.asList("8391146877aa7801ffdb3aa954bf2965"));
Arrays.asList("1ba7afccc8552f20d72d0b62237558e3"));
executeTest("test MultiSample Pilot2 with alleles passed in and emitting all sites", spec2);
}
@ -52,7 +52,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testSingleSamplePilot2() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,100,000", 1,
Arrays.asList("85b79ff7910f218dd59595d03ffe6ccc"));
Arrays.asList("57e409dbb12e0d85cd8af73db221b1fc"));
executeTest("test SingleSample Pilot2", spec);
}
@ -60,7 +60,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMultipleSNPAlleles() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -glm BOTH --dbsnp " + b37dbSNP129 + " -I " + privateTestDir + "multiallelic.snps.bam -o %s -L " + privateTestDir + "multiallelic.snps.intervals", 1,
Arrays.asList("cceb34ffbd2dbc45b8821f86ea255284"));
Arrays.asList("772e14d8c908044c04053d204bad69ef"));
executeTest("test Multiple SNP alleles", spec);
}
@ -76,7 +76,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testReverseTrim() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -glm INDEL -I " + validationDataLocation + "CEUTrio.HiSeq.b37.chr20.10_11mb.bam -o %s -L 20:10289124 -L 20:10090289", 1,
Arrays.asList("00f54a0097e710c0f7b001444c237e32"));
Arrays.asList("1fb69aa3857e921191997daa73f1b687"));
executeTest("test reverse trim", spec);
}
@ -84,7 +84,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMismatchedPLs() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -glm INDEL -I " + privateTestDir + "mismatchedPLs.bam -o %s -L 1:24020341", 1,
Arrays.asList("b3fae6bf4c620458f4259dbc93125e37"));
Arrays.asList("d210ee1baa75dd4a0c63aef6b1fa7a8a"));
executeTest("test mismatched PLs", spec);
}
@ -94,7 +94,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
//
// --------------------------------------------------------------------------------------------------------------
private final static String COMPRESSED_OUTPUT_MD5 = "712e87db5e278e92bd36e96d377303c6";
private final static String COMPRESSED_OUTPUT_MD5 = "367c0355b4e7b10c2988e5c41f44b3d2";
@Test
public void testCompressedOutput() {
@ -115,7 +115,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
// Note that we need to turn off any randomization for this to work, so no downsampling and no annotations
String md5 = "306943dd63111e2e64388cd2e2de6c01";
String md5 = "360d1274c1072a1ae9868e4e106c2650";
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
baseCommand + " -dt NONE -G none -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,075,000", 1,
@ -147,7 +147,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMinBaseQualityScore() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 --min_base_quality_score 26", 1,
Arrays.asList("f73dec2e77f14c170f7b6a8eee5793ff"));
Arrays.asList("6ae4a219c7b9c837fcbf12edeeac3c0c"));
executeTest("test min_base_quality_score 26", spec);
}
@ -155,7 +155,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testSLOD() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R " + b36KGReference + " --no_cmdline_in_header -glm BOTH --dbsnp " + b36dbSNP129 + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000", 1,
Arrays.asList("da7a5a3aa1c9f401896c34199c535954"));
Arrays.asList("c7429e670ba477bf9a6bbee2fb41c5a9"));
executeTest("test SLOD", spec);
}
@ -163,7 +163,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testNDA() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
baseCommand + " --annotateNDA -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000", 1,
Arrays.asList("07f5962f790673a1299f3a0f56579b65"));
Arrays.asList("abd8e33e649cc11b55e200d3940cc7e2"));
executeTest("test NDA", spec);
}
@ -171,23 +171,23 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testCompTrack() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R " + b36KGReference + " --no_cmdline_in_header -glm BOTH -comp:FOO " + b36dbSNP129 + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000", 1,
Arrays.asList("22037eac40a3b1df3086c2d7b27f0d5f"));
Arrays.asList("8a9b424e00cdbe6b5e73d517335b2186"));
executeTest("test using comp track", spec);
}
@Test
public void testOutputParameterSitesOnly() {
testOutputParameters("-sites_only", "92db524b334f1416e595c711abc2d798");
testOutputParameters("-sites_only", "97ba874eafc9884a4de027a84c036311");
}
@Test
public void testOutputParameterAllConfident() {
testOutputParameters("--output_mode EMIT_ALL_CONFIDENT_SITES", "7bb6375fddc461c72d44f261f6d4b3c7");
testOutputParameters("--output_mode EMIT_ALL_CONFIDENT_SITES", "f9ea04d96eeef29e71d37e60518c2579");
}
@Test
public void testOutputParameterAllSites() {
testOutputParameters("--output_mode EMIT_ALL_SITES", "2104dac76fa2a58a92c72b331c7f2095");
testOutputParameters("--output_mode EMIT_ALL_SITES", "67739a3ccf30975bcaef8a563e4b80cf");
}
private void testOutputParameters(final String args, final String md5) {
@ -201,7 +201,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testConfidence() {
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 -stand_call_conf 10 ", 1,
Arrays.asList("7326eb84d8418546a408b68839a0a47e"));
Arrays.asList("9addd225a985178339a0c49dc5fdc220"));
executeTest("test confidence 1", spec1);
}
@ -209,7 +209,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testConfidence2() {
WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 -stand_emit_conf 10 ", 1,
Arrays.asList("7326eb84d8418546a408b68839a0a47e"));
Arrays.asList("9addd225a985178339a0c49dc5fdc220"));
executeTest("test confidence 2", spec2);
}
@ -220,12 +220,12 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
// --------------------------------------------------------------------------------------------------------------
@Test
public void testHeterozyosity1() {
testHeterozosity( 0.01, "7aed8361e692eff559e6bca88752db0d" );
testHeterozosity( 0.01, "f1c4c8e701b2334bf3c4f12fc395fec8" );
}
@Test
public void testHeterozyosity2() {
testHeterozosity( 1.0 / 1850, "989e65bb7337117d31cd615163a8ac84" );
testHeterozosity( 1.0 / 1850, "7fbbf4a21d6bf0026bfdadbb3c086fbe" );
}
private void testHeterozosity(final double arg, final String md5) {
@ -249,7 +249,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -o %s" +
" -L 1:10,000,000-10,100,000",
1,
Arrays.asList("c155587aa0410f43d7ccc57e1ae09a68"));
Arrays.asList("5d19e3077e0cabbb364f68676a09ebe0"));
executeTest(String.format("test multiple technologies"), spec);
}
@ -268,7 +268,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -L 1:10,000,000-10,100,000" +
" -baq CALCULATE_AS_NECESSARY",
1,
Arrays.asList("0748a711c6154f8d85847afb79aead94"));
Arrays.asList("8a1931095f70523ad11cb99b30df7b84"));
executeTest(String.format("test calling with BAQ"), spec);
}
@ -287,7 +287,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -o %s" +
" -L 1:10,000,000-10,500,000",
1,
Arrays.asList("6aa034f669ec09ac4f5a28624cbe1830"));
Arrays.asList("64a491b5276fd5d1cd04260ea3e63cf7"));
executeTest(String.format("test indel caller in SLX"), spec);
}
@ -302,7 +302,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -minIndelCnt 1" +
" -L 1:10,000,000-10,100,000",
1,
Arrays.asList("ba7a011d0c665acc4455d58a6ab28716"));
Arrays.asList("f63a8b8061e6c5999408d34798061895"));
executeTest(String.format("test indel caller in SLX with low min allele count"), spec);
}
@ -315,7 +315,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -o %s" +
" -L 1:10,000,000-10,500,000",
1,
Arrays.asList("4f7d80f4f53ef0f0959414cb30097482"));
Arrays.asList("c9d684ff2f2a9083480db6e962d612a9"));
executeTest(String.format("test indel calling, multiple technologies"), spec);
}
@ -325,7 +325,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + privateTestDir + "indelAllelesForUG.vcf -I " + validationDataLocation +
"pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
Arrays.asList("95986d0c92436d3b9c1f1be9c768a368"));
Arrays.asList("833fd97c6f32d7af6c9c088a78e51f68"));
executeTest("test MultiSample Pilot2 indels with alleles passed in", spec);
}
@ -335,7 +335,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
baseCommandIndels + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles "
+ privateTestDir + "indelAllelesForUG.vcf -I " + validationDataLocation +
"pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
Arrays.asList("cecd3e35a817e299e97e8f7bbf083d2c"));
Arrays.asList("95b73c24c68dc475516571d9f49dfb1e"));
executeTest("test MultiSample Pilot2 indels with alleles passed in and emitting all sites", spec);
}
@ -343,13 +343,13 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMultiSampleIndels1() {
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
baseCommandIndels + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10450700-10551000", 1,
Arrays.asList("af04b81f0548ca22b8d1f6bf223b336e"));
Arrays.asList("3bdbf48de30bac58f3bcbc5bf3aa63aa"));
List<File> result = executeTest("test MultiSample Pilot1 CEU indels", spec1).getFirst();
WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + result.get(0).getAbsolutePath() + " -I " + validationDataLocation +
"low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10450700-10551000", 1,
Arrays.asList("c7792e27477ecf99893a76ecbac5c2f9"));
Arrays.asList("beee9457d7cea42006ac45400db5e873"));
executeTest("test MultiSample Pilot1 CEU indels using GENOTYPE_GIVEN_ALLELES", spec2);
}
@ -371,7 +371,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -o %s" +
" -L 20:10,000,000-10,100,000",
1,
Arrays.asList("59ff26d7e5ca2503ebe9f74902251551"));
Arrays.asList("945a2f994eaced8efdf8de24b58f2680"));
executeTest(String.format("test UG with base indel quality scores"), spec);
}
@ -405,7 +405,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMinIndelFraction0() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
assessMinIndelFraction + " -minIndelFrac 0.0", 1,
Arrays.asList("f99f9a917529bfef717fad97f725d5df"));
Arrays.asList("ba4fafec383fb988f20c8cf53dd3e9a0"));
executeTest("test minIndelFraction 0.0", spec);
}
@ -413,7 +413,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMinIndelFraction25() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
assessMinIndelFraction + " -minIndelFrac 0.25", 1,
Arrays.asList("eac2cd649bd5836068350eb4260aaea7"));
Arrays.asList("4c57a88de275105156aaafc6f9041365"));
executeTest("test minIndelFraction 0.25", spec);
}
@ -435,7 +435,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testNsInCigar() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -I " + validationDataLocation + "testWithNs.bam -o %s -L 8:141799600-141814700", 1,
Arrays.asList("22c9fd65ce3298bd7fbf400c9c209f29"));
Arrays.asList("e8ebfaac0804b782f22ab8ea35152735"));
executeTest("test calling on reads with Ns in CIGAR", spec);
}
@ -449,7 +449,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testReducedBam() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -I " + privateTestDir + "bamExample.ReducedRead.ADAnnotation.bam -o %s -L 1:67,225,396-67,288,518", 1,
Arrays.asList("84486c88a0fd1ae996a6402490db8492"));
Arrays.asList("bbf16e1873e525ee5975021cfb8988cf"));
executeTest("test calling on a ReducedRead BAM", spec);
}

4
public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
View File

@ -190,7 +190,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants -R " + b36KGReference + " -regenotype -sn NA12892 --variant " + testFile + " -o %s --no_cmdline_in_header",
1,
Arrays.asList("52cb2f150559ca1457e9df7ec153dbb4")
Arrays.asList("549321a2543608f214ab4893ab478be6")
);
executeTest("testRegenotype--" + testFile, spec);
@ -216,7 +216,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants -R " + b36KGReference + " -regenotype -sn NA12892 --variant " + testFile + " -o %s --no_cmdline_in_header",
1,
Arrays.asList("52cb2f150559ca1457e9df7ec153dbb4")
Arrays.asList("549321a2543608f214ab4893ab478be6")
);
executeTest("testRemoveMLEAndRegenotype--" + testFile, spec);

2
public/java/test/org/broadinstitute/sting/utils/nanoScheduler/NanoSchedulerIntegrationTest.java
View File

@ -21,7 +21,7 @@ public class NanoSchedulerIntegrationTest extends WalkerTest {
for ( final int nct : Arrays.asList(1, 2) ) {
// tests.add(new Object[]{ "SNP", "a1c7546f32a8919a3f3a70a04b2e8322", nt, nct });
//// tests.add(new Object[]{ "INDEL", "0a6d2be79f4f8a4b0eb788cc4751b31b", nt, nct });
tests.add(new Object[]{ "BOTH", "081d077786ac0af24e9f97259a55209c", nt, nct });
tests.add(new Object[]{ "BOTH", "78ce72d8f9d029313f5f2ceb02bb9822", nt, nct });
}
return tests.toArray(new Object[][]{});