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Drat, forgot the unit tests again

This commit is contained in:
Eric Banks 2012-06-12 19:00:47 -04:00
parent bacd25d1a4
commit bb77aa88c3
3 changed files with 18 additions and 19 deletions
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13
public/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/ReadCovariatesUnitTest.java
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@ -6,9 +6,6 @@ import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.testng.Assert;
import org.testng.annotations.Test;
import java.util.ArrayList;
import java.util.List;
/**
* @author carneiro
* @since 4/21/12
@ -38,11 +35,11 @@ public class ReadCovariatesUnitTest {
coCov.initialize(RAC);
cyCov.initialize(RAC);
List<Covariate> requestedCovariates = new ArrayList<Covariate>(4);
requestedCovariates.add(rgCov);
requestedCovariates.add(qsCov);
requestedCovariates.add(coCov);
requestedCovariates.add(cyCov);
Covariate[] requestedCovariates = new Covariate[4];
requestedCovariates[0] = rgCov;
requestedCovariates[1] = qsCov;
requestedCovariates[2] = coCov;
requestedCovariates[3] = cyCov;
ReadCovariates rc = RecalDataManager.computeCovariates(read, requestedCovariates);

11
public/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationReportUnitTest.java
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@ -37,7 +37,6 @@ public class RecalibrationReportUnitTest {
quantizationInfo.noQuantization();
final List<Covariate> requiredCovariates = new LinkedList<Covariate>();
final List<Covariate> optionalCovariates = new LinkedList<Covariate>();
final List<Covariate> requestedCovariates = new LinkedList<Covariate>();
final ReadGroupCovariate rgCovariate = new ReadGroupCovariate();
rgCovariate.initialize(RAC);
@ -60,10 +59,12 @@ public class RecalibrationReportUnitTest {
BQSRKeyManager cvKeyManager = new BQSRKeyManager(requiredCovariates, optionalCovariates);
keysAndTablesMap.put(cvKeyManager, new HashMap<Long, RecalDatum>());
for (Covariate cov : requiredCovariates)
requestedCovariates.add(cov);
for (Covariate cov : optionalCovariates)
requestedCovariates.add(cov);
final Covariate[] requestedCovariates = new Covariate[requiredCovariates.size() + optionalCovariates.size()];
int covariateIndex = 0;
for (final Covariate cov : requiredCovariates)
requestedCovariates[covariateIndex++] = cov;
for (final Covariate cov : optionalCovariates)
requestedCovariates[covariateIndex++] = cov;
final GATKSAMReadGroupRecord rg = new GATKSAMReadGroupRecord("id");
rg.setPlatform("illumina");

13
public/java/test/org/broadinstitute/sting/utils/recalibration/BaseRecalibrationUnitTest.java
View File

@ -48,7 +48,6 @@ public class BaseRecalibrationUnitTest {
RecalibrationArgumentCollection RAC = new RecalibrationArgumentCollection();
List<Covariate> requiredCovariates = new ArrayList<Covariate>();
List<Covariate> optionalCovariates = new ArrayList<Covariate>();
ArrayList<Covariate> requestedCovariates = new ArrayList<Covariate>();
dataManager = new org.broadinstitute.sting.gatk.walkers.recalibration.RecalDataManager(true, 4);
keysAndTablesMap = new LinkedHashMap<BQSRKeyManager, Map<Long, RecalDatum>>();
@ -74,10 +73,12 @@ public class BaseRecalibrationUnitTest {
BQSRKeyManager cvKeyManager = new BQSRKeyManager(requiredCovariates, optionalCovariates);
keysAndTablesMap.put(cvKeyManager, new HashMap<Long, RecalDatum>());
for (Covariate cov : requiredCovariates)
requestedCovariates.add(cov);
for (Covariate cov : optionalCovariates)
requestedCovariates.add(cov);
final Covariate[] requestedCovariates = new Covariate[requiredCovariates.size() + optionalCovariates.size()];
int covariateIndex = 0;
for (final Covariate cov : requiredCovariates)
requestedCovariates[covariateIndex++] = cov;
for (final Covariate cov : optionalCovariates)
requestedCovariates[covariateIndex++] = cov;
readCovariates = RecalDataManager.computeCovariates(read, requestedCovariates);
@ -112,7 +113,7 @@ public class BaseRecalibrationUnitTest {
}
QuantizationInfo quantizationInfo = new QuantizationInfo(quantizedQuals, qualCounts);
quantizationInfo.noQuantization();
baseRecalibration = new BaseRecalibration(quantizationInfo, keysAndTablesMap, requestedCovariates.toArray());
baseRecalibration = new BaseRecalibration(quantizationInfo, keysAndTablesMap, requestedCovariates);
}