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Require both overlap and breakend proximity for depth-only SV clustering #8962

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merged 2 commits into from
Sep 11, 2024
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Require both overlap and breakend proximity for depth-only SV clustering #8962

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736a02d
Require both overlap and breakend proximity for depth-only SV clustering
mwalker174 Aug 23, 2024
3036e50
Add comment about requiresOverlapAndProximity
mwalker174 Sep 11, 2024
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2 changes: 1 addition & 1 deletion src/main/java/org/broadinstitute/hellbender/tools/sv/cluster/CanonicalSVLinkage.java
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Expand Up @@ -45,7 +45,7 @@ public class CanonicalSVLinkage<T extends SVCallRecord> extends SVClusterLinkage

public static final double DEFAULT_RECIPROCAL_OVERLAP_DEPTH_ONLY = 0.8;
public static final double DEFAULT_SIZE_SIMILARITY_DEPTH_ONLY = 0;
public static final int DEFAULT_WINDOW_DEPTH_ONLY = 0;
public static final int DEFAULT_WINDOW_DEPTH_ONLY = 10000000;
public static final double DEFAULT_SAMPLE_OVERLAP_DEPTH_ONLY = 0;

public static final double DEFAULT_RECIPROCAL_OVERLAP_MIXED = 0.8;
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3 changes: 2 additions & 1 deletion src/main/java/org/broadinstitute/hellbender/tools/sv/cluster/ClusteringParameters.java
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Expand Up @@ -17,6 +17,7 @@ public class ClusteringParameters {

// if true, both reciprocal overlap and window criteria must be met
// if false, reciprocal overlap and/or window criteria must be met
// NOTE this is currently set to true in all tools but is being kept for possible future use
private final boolean requiresOverlapAndProximity;

// returns true if two given records are the correct type of pair for this parameter set
Expand Down Expand Up @@ -57,7 +58,7 @@ public boolean isValidPair(final SVCallRecord a, final SVCallRecord b) {
}

public static ClusteringParameters createDepthParameters(final double reciprocalOverlap, final double sizeSimilarity, final int window, final double sampleOverlap) {
return new ClusteringParameters(reciprocalOverlap, sizeSimilarity, window, sampleOverlap, false, (a,b) -> a.isDepthOnly() && b.isDepthOnly());
return new ClusteringParameters(reciprocalOverlap, sizeSimilarity, window, sampleOverlap, true, (a,b) -> a.isDepthOnly() && b.isDepthOnly());
}

public static ClusteringParameters createMixedParameters(final double reciprocalOverlap, final double sizeSimilarity, final int window, final double sampleOverlap) {
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2 changes: 1 addition & 1 deletion src/test/java/org/broadinstitute/hellbender/tools/sv/SVTestUtils.java
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Expand Up @@ -56,7 +56,7 @@ public static SVClusterEngine getNewDefaultMaxCliqueEngine() {
return new SVClusterEngine(SVClusterEngine.CLUSTERING_TYPE.MAX_CLIQUE, defaultCollapser::collapse, getNewDefaultLinkage(), hg38Dict);
}

public static final ClusteringParameters defaultDepthOnlyParameters = ClusteringParameters.createDepthParameters(0.8, 0, 0, 0);
public static final ClusteringParameters defaultDepthOnlyParameters = ClusteringParameters.createDepthParameters(0.8, 0, 10000000, 0);
public static final ClusteringParameters defaultMixedParameters = ClusteringParameters.createMixedParameters(0.8, 0, 1000, 0);
public static final ClusteringParameters defaultEvidenceParameters = ClusteringParameters.createPesrParameters(0.5, 0, 500, 0);

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2 changes: 1 addition & 1 deletion src/test/java/org/broadinstitute/hellbender/tools/sv/cluster/SVClusterEngineTest.java
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Expand Up @@ -26,7 +26,7 @@ public class SVClusterEngineTest {

private final SVClusterEngine engine = SVTestUtils.defaultSingleLinkageEngine;

private static final ClusteringParameters depthOnlyParametersSizeSimilarity = ClusteringParameters.createDepthParameters(0.1, 0.5, 0, 0);
private static final ClusteringParameters depthOnlyParametersSizeSimilarity = ClusteringParameters.createDepthParameters(0.1, 0.5, 10000000, 0);
private static final ClusteringParameters mixedParametersSizeSimilarity = ClusteringParameters.createMixedParameters(0.1, 0.5, 5000, 0);
private static final ClusteringParameters evidenceParametersSizeSimilarity = ClusteringParameters.createPesrParameters(0.1, 0.5, 5000, 0);
private final CanonicalSVLinkage<SVCallRecord> linkageSizeSimilarity = new CanonicalSVLinkage<>(SVTestUtils.hg38Dict, false);
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2 changes: 1 addition & 1 deletion ...oadinstitute/hellbender/tools/walkers/sv/JointGermlineCNVSegmentationIntegrationTest.java
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Expand Up @@ -204,7 +204,7 @@ public void testOverlappingEvents(final List<File> inputVcfs) {
.add(JointGermlineCNVSegmentation.MODEL_CALL_INTERVALS_LONG_NAME, getToolTestDataDir() + "intervals.chr22.interval_list")
.addInterval("22:22,538,114-23,538,437")
.add(JointGermlineCNVSegmentation.CLUSTERING_INTERVAL_OVERLAP_LONG_NAME, 0.8)
.add(JointGermlineCNVSegmentation.CLUSTERING_BREAKEND_WINDOW_LONG_NAME, 0);
.add(JointGermlineCNVSegmentation.CLUSTERING_BREAKEND_WINDOW_LONG_NAME, 10000000);

inputVcfs.forEach(vcf -> args.addVCF(vcf));

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16 changes: 8 additions & 8 deletions src/test/java/org/broadinstitute/hellbender/tools/walkers/sv/SVClusterIntegrationTest.java
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Expand Up @@ -113,7 +113,7 @@ public void testMergeHelper(final boolean omitMembers) {
.add(SVCluster.ALGORITHM_LONG_NAME, SVCluster.CLUSTER_ALGORITHM.SINGLE_LINKAGE)
.add(SVClusterEngineArgumentsCollection.DEPTH_SAMPLE_OVERLAP_FRACTION_NAME, 0)
.add(SVClusterEngineArgumentsCollection.DEPTH_INTERVAL_OVERLAP_FRACTION_NAME, 1)
.add(SVClusterEngineArgumentsCollection.DEPTH_BREAKEND_WINDOW_NAME, 0)
.add(SVClusterEngineArgumentsCollection.DEPTH_BREAKEND_WINDOW_NAME, 10000000)
.add(SVClusterEngineArgumentsCollection.MIXED_SAMPLE_OVERLAP_FRACTION_NAME, 0)
.add(SVClusterEngineArgumentsCollection.MIXED_INTERVAL_OVERLAP_FRACTION_NAME, 1)
.add(SVClusterEngineArgumentsCollection.MIXED_BREAKEND_WINDOW_NAME, 0)
Expand Down Expand Up @@ -188,7 +188,7 @@ public void testClusterSingleLinkage() {
.add(StandardArgumentDefinitions.REFERENCE_LONG_NAME, REFERENCE_PATH)
.add(SVClusterEngineArgumentsCollection.DEPTH_SAMPLE_OVERLAP_FRACTION_NAME, 0)
.add(SVClusterEngineArgumentsCollection.DEPTH_INTERVAL_OVERLAP_FRACTION_NAME, 0.5)
.add(SVClusterEngineArgumentsCollection.DEPTH_BREAKEND_WINDOW_NAME, 2000)
.add(SVClusterEngineArgumentsCollection.DEPTH_BREAKEND_WINDOW_NAME, 10000000)
.add(SVClusterEngineArgumentsCollection.MIXED_SAMPLE_OVERLAP_FRACTION_NAME, 0)
.add(SVClusterEngineArgumentsCollection.MIXED_INTERVAL_OVERLAP_FRACTION_NAME, 0.1)
.add(SVClusterEngineArgumentsCollection.MIXED_BREAKEND_WINDOW_NAME, 2000)
Expand All @@ -204,7 +204,7 @@ public void testClusterSingleLinkage() {

Assert.assertEquals(header.getSampleNamesInOrder(), Arrays.asList("HG00096", "HG00129", "HG00140", "NA18945", "NA18956"));

Assert.assertEquals(records.size(), 1338);
Assert.assertEquals(records.size(), 1344);

// Check for one record
int expectedRecordsFound = 0;
Expand Down Expand Up @@ -255,7 +255,7 @@ public void testAgainstSimpleImplementation() {
.add(StandardArgumentDefinitions.REFERENCE_LONG_NAME, REFERENCE_PATH)
.add(SVClusterEngineArgumentsCollection.DEPTH_SAMPLE_OVERLAP_FRACTION_NAME, 0)
.add(SVClusterEngineArgumentsCollection.DEPTH_INTERVAL_OVERLAP_FRACTION_NAME, 0.5)
.add(SVClusterEngineArgumentsCollection.DEPTH_BREAKEND_WINDOW_NAME, 2000)
.add(SVClusterEngineArgumentsCollection.DEPTH_BREAKEND_WINDOW_NAME, 10000000)
.add(SVClusterEngineArgumentsCollection.MIXED_SAMPLE_OVERLAP_FRACTION_NAME, 0)
.add(SVClusterEngineArgumentsCollection.MIXED_INTERVAL_OVERLAP_FRACTION_NAME, 0.1)
.add(SVClusterEngineArgumentsCollection.MIXED_BREAKEND_WINDOW_NAME, 2000)
Expand All @@ -279,7 +279,7 @@ public void testAgainstSimpleImplementation() {
final Pair<VCFHeader, List<VariantContext>> testVcf = VariantContextTestUtils.readEntireVCFIntoMemory(output.getAbsolutePath());

final ReferenceSequenceFile referenceSequenceFile = ReferenceUtils.createReferenceReader(new GATKPath(REFERENCE_PATH));
final ClusteringParameters depthParameters = ClusteringParameters.createDepthParameters(0.5, 0, 2000, 0);
final ClusteringParameters depthParameters = ClusteringParameters.createDepthParameters(0.5, 0, 10000000, 0);
final ClusteringParameters mixedParameters = ClusteringParameters.createMixedParameters(0.1, 0, 2000, 0);
final ClusteringParameters pesrParameters = ClusteringParameters.createPesrParameters(0.1, 0, 500, 0);
final SVClusterEngine engine = SVClusterEngineFactory.createCanonical(
Expand Down Expand Up @@ -347,7 +347,7 @@ public void testClusterMaxClique(final boolean fastMode) {
.add(SVCluster.ALGORITHM_LONG_NAME, SVCluster.CLUSTER_ALGORITHM.MAX_CLIQUE)
.add(SVClusterEngineArgumentsCollection.DEPTH_SAMPLE_OVERLAP_FRACTION_NAME, 0)
.add(SVClusterEngineArgumentsCollection.DEPTH_INTERVAL_OVERLAP_FRACTION_NAME, 0.5)
.add(SVClusterEngineArgumentsCollection.DEPTH_BREAKEND_WINDOW_NAME, 2000)
.add(SVClusterEngineArgumentsCollection.DEPTH_BREAKEND_WINDOW_NAME, 10000000)
.add(SVClusterEngineArgumentsCollection.MIXED_SAMPLE_OVERLAP_FRACTION_NAME, 0)
.add(SVClusterEngineArgumentsCollection.MIXED_INTERVAL_OVERLAP_FRACTION_NAME, 0.1)
.add(SVClusterEngineArgumentsCollection.MIXED_BREAKEND_WINDOW_NAME, 2000)
Expand Down Expand Up @@ -414,7 +414,7 @@ public void testClusterSampleOverlap() {
.add(SVCluster.ALGORITHM_LONG_NAME, SVCluster.CLUSTER_ALGORITHM.SINGLE_LINKAGE)
.add(SVClusterEngineArgumentsCollection.DEPTH_SAMPLE_OVERLAP_FRACTION_NAME, 0.5)
.add(SVClusterEngineArgumentsCollection.DEPTH_INTERVAL_OVERLAP_FRACTION_NAME, 0.5)
.add(SVClusterEngineArgumentsCollection.DEPTH_BREAKEND_WINDOW_NAME, 2000)
.add(SVClusterEngineArgumentsCollection.DEPTH_BREAKEND_WINDOW_NAME, 10000000)
.add(SVClusterEngineArgumentsCollection.MIXED_SAMPLE_OVERLAP_FRACTION_NAME, 0.5)
.add(SVClusterEngineArgumentsCollection.MIXED_INTERVAL_OVERLAP_FRACTION_NAME, 0.1)
.add(SVClusterEngineArgumentsCollection.MIXED_BREAKEND_WINDOW_NAME, 2000)
Expand Down Expand Up @@ -478,7 +478,7 @@ public void testAllosome() {
.add(StandardArgumentDefinitions.REFERENCE_LONG_NAME, REFERENCE_PATH)
.add(SVClusterEngineArgumentsCollection.DEPTH_SAMPLE_OVERLAP_FRACTION_NAME, 0)
.add(SVClusterEngineArgumentsCollection.DEPTH_INTERVAL_OVERLAP_FRACTION_NAME, 0.5)
.add(SVClusterEngineArgumentsCollection.DEPTH_BREAKEND_WINDOW_NAME, 2000)
.add(SVClusterEngineArgumentsCollection.DEPTH_BREAKEND_WINDOW_NAME, 10000000)
.add(SVClusterEngineArgumentsCollection.MIXED_SAMPLE_OVERLAP_FRACTION_NAME, 0)
.add(SVClusterEngineArgumentsCollection.MIXED_INTERVAL_OVERLAP_FRACTION_NAME, 0.1)
.add(SVClusterEngineArgumentsCollection.MIXED_BREAKEND_WINDOW_NAME, 2000)
Expand Down
12 changes: 6 additions & 6 deletions ...est/java/org/broadinstitute/hellbender/tools/walkers/sv/SVConcordanceIntegrationTest.java
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Expand Up @@ -53,7 +53,7 @@ public void testRefPanel() {
.add(StandardArgumentDefinitions.SEQUENCE_DICTIONARY_NAME, GATKBaseTest.FULL_HG38_DICT)
.add(SVClusterEngineArgumentsCollection.DEPTH_SAMPLE_OVERLAP_FRACTION_NAME, 0)
.add(SVClusterEngineArgumentsCollection.DEPTH_INTERVAL_OVERLAP_FRACTION_NAME, 0.5)
.add(SVClusterEngineArgumentsCollection.DEPTH_BREAKEND_WINDOW_NAME, 2000)
.add(SVClusterEngineArgumentsCollection.DEPTH_BREAKEND_WINDOW_NAME, 10000000)
.add(SVClusterEngineArgumentsCollection.MIXED_SAMPLE_OVERLAP_FRACTION_NAME, 0)
.add(SVClusterEngineArgumentsCollection.MIXED_INTERVAL_OVERLAP_FRACTION_NAME, 0.1)
.add(SVClusterEngineArgumentsCollection.MIXED_BREAKEND_WINDOW_NAME, 2000)
Expand All @@ -69,7 +69,7 @@ public void testRefPanel() {
final Pair<VCFHeader, List<VariantContext>> outputVcf = VariantContextTestUtils.readEntireVCFIntoMemory(output.getAbsolutePath());

final SAMSequenceDictionary dictionary = SVTestUtils.hg38Dict;
final ClusteringParameters depthParameters = ClusteringParameters.createDepthParameters(0.5, 0, 2000, 0);
final ClusteringParameters depthParameters = ClusteringParameters.createDepthParameters(0.5, 0, 10000000, 0);
final ClusteringParameters mixedParameters = ClusteringParameters.createMixedParameters(0.1, 0, 2000, 0);
final ClusteringParameters pesrParameters = ClusteringParameters.createPesrParameters(0.1, 0, 500, 0);
final SVConcordanceLinkage linkage = new SVConcordanceLinkage(dictionary);
Expand Down Expand Up @@ -180,7 +180,7 @@ public void testSelf() {
.add(SVClusterEngineArgumentsCollection.DEPTH_SAMPLE_OVERLAP_FRACTION_NAME, 0)
.add(SVClusterEngineArgumentsCollection.DEPTH_INTERVAL_OVERLAP_FRACTION_NAME, 0.5)
.add(SVClusterEngineArgumentsCollection.DEPTH_SIZE_SIMILARITY_NAME, 0)
.add(SVClusterEngineArgumentsCollection.DEPTH_BREAKEND_WINDOW_NAME, 2000)
.add(SVClusterEngineArgumentsCollection.DEPTH_BREAKEND_WINDOW_NAME, 10000000)
.add(SVClusterEngineArgumentsCollection.MIXED_SAMPLE_OVERLAP_FRACTION_NAME, 0)
.add(SVClusterEngineArgumentsCollection.MIXED_INTERVAL_OVERLAP_FRACTION_NAME, 0.1)
.add(SVClusterEngineArgumentsCollection.MIXED_SIZE_SIMILARITY_NAME, 0)
Expand All @@ -197,7 +197,7 @@ public void testSelf() {
final Pair<VCFHeader, List<VariantContext>> outputVcf = VariantContextTestUtils.readEntireVCFIntoMemory(output.getAbsolutePath());

final SAMSequenceDictionary dictionary = SVTestUtils.hg38Dict;
final ClusteringParameters depthParameters = ClusteringParameters.createDepthParameters(0.5, 0, 2000, 0);
final ClusteringParameters depthParameters = ClusteringParameters.createDepthParameters(0.5, 0, 10000000, 0);
final ClusteringParameters mixedParameters = ClusteringParameters.createMixedParameters(0.1, 0, 2000, 0);
final ClusteringParameters pesrParameters = ClusteringParameters.createPesrParameters(0.1, 0, 500, 0);
final SVConcordanceLinkage linkage = new SVConcordanceLinkage(dictionary);
Expand Down Expand Up @@ -279,7 +279,7 @@ private void assertPerfectConcordance(final File output, final String evalVcfPat
final Pair<VCFHeader, List<VariantContext>> outputVcf = VariantContextTestUtils.readEntireVCFIntoMemory(output.getAbsolutePath());

final SAMSequenceDictionary dictionary = SVTestUtils.hg38Dict;
final ClusteringParameters depthParameters = ClusteringParameters.createDepthParameters(0.5, 0, 2000, 0);
final ClusteringParameters depthParameters = ClusteringParameters.createDepthParameters(0.5, 0, 10000000, 0);
final ClusteringParameters mixedParameters = ClusteringParameters.createMixedParameters(0.1, 0, 2000, 0);
final ClusteringParameters pesrParameters = ClusteringParameters.createPesrParameters(0.1, 0, 500, 0);
final SVConcordanceLinkage linkage = new SVConcordanceLinkage(dictionary);
Expand Down Expand Up @@ -331,7 +331,7 @@ public void testSitesOnly() {
.add(StandardArgumentDefinitions.SEQUENCE_DICTIONARY_NAME, GATKBaseTest.FULL_HG38_DICT)
.add(SVClusterEngineArgumentsCollection.DEPTH_SAMPLE_OVERLAP_FRACTION_NAME, 0)
.add(SVClusterEngineArgumentsCollection.DEPTH_INTERVAL_OVERLAP_FRACTION_NAME, 0.5)
.add(SVClusterEngineArgumentsCollection.DEPTH_BREAKEND_WINDOW_NAME, 2000)
.add(SVClusterEngineArgumentsCollection.DEPTH_BREAKEND_WINDOW_NAME, 10000000)
.add(SVClusterEngineArgumentsCollection.MIXED_SAMPLE_OVERLAP_FRACTION_NAME, 0)
.add(SVClusterEngineArgumentsCollection.MIXED_INTERVAL_OVERLAP_FRACTION_NAME, 0.1)
.add(SVClusterEngineArgumentsCollection.MIXED_BREAKEND_WINDOW_NAME, 2000)
Expand Down
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