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Fixed issue causing VariantRecalibrator to sometimes fail if user provides duplicate -an options #8227

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merged 1 commit into from
Feb 28, 2023
Merged

Fixed issue causing VariantRecalibrator to sometimes fail if user provides duplicate -an options #8227

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2 changes: 1 addition & 1 deletion src/main/java/org/broadinstitute/hellbender/tools/walkers/vqsr/VariantDataManager.java
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Original file line number Diff line number Diff line change
Expand Up @@ -38,7 +38,7 @@ public VariantDataManager( final List<String> annotationKeys, final VariantRecal
this.data = Collections.emptyList();
final List<String> uniqueAnnotations = annotationKeys.stream().distinct().collect(Collectors.toList());
if (annotationKeys.size() != uniqueAnnotations.size()) {
logger.warn("Ignoring duplicate annotations for recalibration %s.", Utils.getDuplicatedItems(annotationKeys));
logger.warn("Ignoring duplicate annotations for recalibration {}", Utils.getDuplicatedItems(annotationKeys));
}
this.annotationKeys = new ArrayList<>( uniqueAnnotations );
this.VRAC = VRAC;
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6 changes: 3 additions & 3 deletions src/main/java/org/broadinstitute/hellbender/tools/walkers/vqsr/VariantRecalibrator.java
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Expand Up @@ -659,7 +659,7 @@ public Object onTraversalSuccess() {
engine.evaluateData(dataManager.getData(), goodModel, false);
if (goodModel.failedToConverge) {
if (outputModel != null) {
final GATKReport report = writeModelReport(goodModel, null, USE_ANNOTATIONS);
final GATKReport report = writeModelReport(goodModel, null, dataManager.getAnnotationKeys());
saveModelReport(report, outputModel);
}
throw new UserException.VQSRPositiveModelFailure("Positive training model failed to converge. One or more annotations " +
Expand All @@ -682,7 +682,7 @@ public Object onTraversalSuccess() {
engine.evaluateData(dataManager.getData(), badModel, true);

if (outputModel != null) {
final GATKReport report = writeModelReport(goodModel, badModel, USE_ANNOTATIONS);
final GATKReport report = writeModelReport(goodModel, badModel, dataManager.getAnnotationKeys());
saveModelReport(report, outputModel);
}

Expand Down Expand Up @@ -715,7 +715,7 @@ public Object onTraversalSuccess() {
goodModel,
badModel,
0.0,
dataManager.getAnnotationKeys().toArray(new String[USE_ANNOTATIONS.size()]));
dataManager.getAnnotationKeys().toArray(new String[dataManager.getAnnotationKeys().size()]));
}

if (VRAC.MODE == VariantRecalibratorArgumentCollection.Mode.INDEL) {
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18 changes: 17 additions & 1 deletion .../org/broadinstitute/hellbender/tools/walkers/vqsr/VariantRecalibratorIntegrationTest.java
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Expand Up @@ -174,6 +174,22 @@ public class VariantRecalibratorIntegrationTest extends CommandLineProgramTest {
" --" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE +" false"
};

final private String[] variantRecalibratorSamplingParamsWithDupes = {
" --variant " + getLargeVQSRTestDataDir() + "phase1.projectConsensus.chr20.1M-10M.raw.snps.vcf" +
" -L 20:1,000,000-10,000,000" +
" --resource:known,known=true,prior=10.0 " + getLargeVQSRTestDataDir() + "dbsnp_132_b37.leftAligned.20.1M-10M.vcf" +
" --resource:truth_training1,truth=true,training=true,prior=15.0 " + getLargeVQSRTestDataDir() + "sites_r27_nr.b37_fwd.20.1M-10M.vcf" +
" --resource:truth_training2,training=true,truth=true,prior=12.0 " + getLargeVQSRTestDataDir() + "Omni25_sites_1525_samples.b37.20.1M-10M.vcf" +
" -an QD -an HaplotypeScore -an HRun -an QD" +
" --trust-all-polymorphic" + // for speed
" --output %s" +
" -tranches-file %s" +
" --output-model " + modelReportFilename +
" -mode SNP --max-gaussians 3" + //reduce max gaussians so we have negative training data with the sampled input
" -sample-every 2" +
" --" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE +" false"
};

@Override
public String getToolTestDataDir(){
return toolsTestDir + "walkers/VQSR/";
Expand Down Expand Up @@ -404,7 +420,7 @@ public void testVariantRecalibratorSampling() throws IOException {
public void testVariantRecalibratorRScriptOutput() throws IOException {
final String inputFile = getLargeVQSRTestDataDir() + "phase1.projectConsensus.chr20.1M-10M.raw.snps.vcf";
final File unrunRscript = createTempFile("rscriptOutput", ".R");
final String args = StringUtils.join(variantRecalibratorSamplingParams, " ");
final String args = StringUtils.join(variantRecalibratorSamplingParamsWithDupes, " ");

final IntegrationTestSpec spec = new IntegrationTestSpec(
args +
Expand Down