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Add OptimizedDiploidExactAF to PerformanceTesting framework

This commit is contained in:
Mark DePristo 2012-10-04 22:10:28 -07:00
parent f800f3fb88
commit b924e9ebb4
1 changed files with 3 additions and 3 deletions
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6
protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationPerformanceTest.java
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@ -175,14 +175,14 @@ public class ExactAFCalculationPerformanceTest {
final boolean USE_GENERAL = false; final boolean USE_GENERAL = false;
final List<ExactAFCalculationTestBuilder.ModelType> modelTypes = USE_GENERAL final List<ExactAFCalculationTestBuilder.ModelType> modelTypes = USE_GENERAL
? Arrays.asList(ExactAFCalculationTestBuilder.ModelType.values()) ? Arrays.asList(ExactAFCalculationTestBuilder.ModelType.values())
: Arrays.asList(ExactAFCalculationTestBuilder.ModelType.DiploidExact); : Arrays.asList(ExactAFCalculationTestBuilder.ModelType.DiploidExact, ExactAFCalculationTestBuilder.ModelType.OptimizedDiploidExact);
final boolean ONLY_HUMAN_PRIORS = false; final boolean ONLY_HUMAN_PRIORS = false;
final List<ExactAFCalculationTestBuilder.PriorType> priorTypes = ONLY_HUMAN_PRIORS final List<ExactAFCalculationTestBuilder.PriorType> priorTypes = ONLY_HUMAN_PRIORS
? Arrays.asList(ExactAFCalculationTestBuilder.PriorType.values()) ? Arrays.asList(ExactAFCalculationTestBuilder.PriorType.values())
: Arrays.asList(ExactAFCalculationTestBuilder.PriorType.human); : Arrays.asList(ExactAFCalculationTestBuilder.PriorType.human);
final int MAX_N_SAMPLES_FOR_MULTI_ALLELIC = 100; final int MAX_N_SAMPLES_FOR_MULTI_ALLELIC = 200;
final List<Analysis> analyzes = new ArrayList<Analysis>(); final List<Analysis> analyzes = new ArrayList<Analysis>();
analyzes.add(new AnalyzeByACAndPL(coreColumns)); analyzes.add(new AnalyzeByACAndPL(coreColumns));
@ -191,7 +191,7 @@ public class ExactAFCalculationPerformanceTest {
for ( int iteration = 0; iteration < 1; iteration++ ) { for ( int iteration = 0; iteration < 1; iteration++ ) {
for ( final int nAltAlleles : Arrays.asList(1, 2) ) { for ( final int nAltAlleles : Arrays.asList(1, 2) ) {
for ( final int nSamples : Arrays.asList(1, 10, 100, 1000, 10000) ) { for ( final int nSamples : Arrays.asList(1, 10, 100, 200) ) {
if ( nSamples > MAX_N_SAMPLES_FOR_MULTI_ALLELIC && nAltAlleles > 1 ) if ( nSamples > MAX_N_SAMPLES_FOR_MULTI_ALLELIC && nAltAlleles > 1 )
continue; // skip things that will take forever! continue; // skip things that will take forever!