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Check breakpoint distance for each CPX interval and overall in SVConcordance #9324

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Merged
epiercehoffman merged 1 commit into from
Feb 4, 2026
+28 −5
Merged

Check breakpoint distance for each CPX interval and overall in SVConcordance #9324

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33 changes: 28 additions & 5 deletions src/main/java/org/broadinstitute/hellbender/tools/sv/cluster/CanonicalSVLinkage.java
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Original file line number Diff line number Diff line change
Expand Up @@ -189,6 +189,11 @@ private static CanonicalLinkageResult clusterTogetherWithParams(final SVCallReco
private static CanonicalLinkageResult testComplexIntervals(final SVCallRecord a, final SVCallRecord b, final double overlapThreshold,
final double sizeSimilarityThreshold, final int window,
final double sampleOverlapThreshold) {
final Integer overallBreakpointDistance1 = getFirstBreakpointProximity(a, b);
final Integer overallBreakpointDistance2 = getSecondBreakpointProximity(a, b);
if (!(testBreakendProximity(overallBreakpointDistance1, overallBreakpointDistance2, window))) {
return new CanonicalLinkageResult(false);
}
final List<SVCallRecord.ComplexEventInterval> intervalsA = a.getComplexEventIntervals();
final List<SVCallRecord.ComplexEventInterval> intervalsB = b.getComplexEventIntervals();
if (intervalsA.size() != intervalsB.size()) {
Expand All @@ -198,14 +203,14 @@ private static CanonicalLinkageResult testComplexIntervals(final SVCallRecord a,
final Iterator<SVCallRecord.ComplexEventInterval> iterB = intervalsB.iterator();
for (int i = 0; i < intervalsA.size(); i++) {
final SVCallRecord.ComplexEventInterval cpxIntervalA = iterA.next();
final SVCallRecord.ComplexEventInterval cpxIintervalB = iterB.next();
if (cpxIntervalA.getIntervalSVType() != cpxIintervalB.getIntervalSVType()) {
final SVCallRecord.ComplexEventInterval cpxIntervalB = iterB.next();
if (cpxIntervalA.getIntervalSVType() != cpxIntervalB.getIntervalSVType()) {
return new CanonicalLinkageResult(false);
}
final Integer breakpointDistance1 = getFirstBreakpointProximity(a, b);
final Integer breakpointDistance2 = getSecondBreakpointProximity(a, b);
final Integer breakpointDistance1 = getFirstBreakpointProximity(cpxIntervalA, cpxIntervalB);
final Integer breakpointDistance2 = getSecondBreakpointProximity(cpxIntervalA, cpxIntervalB);
final SimpleInterval intervalA = cpxIntervalA.getInterval();
final SimpleInterval intervalB = cpxIintervalB.getInterval();
final SimpleInterval intervalB = cpxIntervalB.getInterval();
final Double reciprocalOverlap = computeReciprocalOverlap(intervalA, intervalB);
final Double sizeSimilarity = computeSizeSimilarity(intervalA.size(), intervalB.size());
if (!(testReciprocalOverlap(reciprocalOverlap, overlapThreshold)
Expand Down Expand Up @@ -272,6 +277,15 @@ private static Integer getFirstBreakpointProximity(final SVCallRecord a, final S
}
}

private static Integer getFirstBreakpointProximity(final SVCallRecord.ComplexEventInterval a,
final SVCallRecord.ComplexEventInterval b) {
if (a.getContig().equals(b.getContig())) {
return Math.abs(a.getStart() - b.getStart());
} else {
return null;
}
}

private static Integer getSecondBreakpointProximity(final SVCallRecord a, final SVCallRecord b) {
if (a.getContigB().equals(b.getContigB())) {
return Math.abs(a.getPositionB() - b.getPositionB());
Expand All @@ -280,6 +294,15 @@ private static Integer getSecondBreakpointProximity(final SVCallRecord a, final
}
}

private static Integer getSecondBreakpointProximity(final SVCallRecord.ComplexEventInterval a,
final SVCallRecord.ComplexEventInterval b) {
if (a.getContig().equals(b.getContig())) {
return Math.abs(a.getEnd() - b.getEnd());
} else {
return null;
}
}

/**
* Gets event length
*/
Expand Down
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