.breakpointRanges	breakpointRanges
align_breakpoints	align_breakpoints
breakendRanges	breakendRanges
breakendRanges,VCF-method	breakendRanges
breakpointgr2bedpe	breakpointgr2bedpe
breakpointgr2pairs	pairs2breakpointgr
breakpointGRangesToVCF	breakpointGRangesToVCF
breakpointRanges	breakpointRanges
breakpointRanges,VCF-method	breakpointRanges
calculateReferenceHomology	calculateReferenceHomology
countBreakpointOverlaps	countBreakpointOverlaps
elementExtract	elementExtract
extractBreakpointSequence	extractBreakpointSequence
extractReferenceSequence	extractReferenceSequence
findBreakpointOverlaps	findBreakpointOverlaps
findInsDupOverlaps	findInsDupOverlaps
findTransitiveCalls	findTransitiveCalls
hasPartner	hasPartner
isStructural	isStructural
isStructural,CollapsedVCF-method	isStructural
isStructural,ExpandedVCF-method	isStructural
isStructural,VCF-method	isStructural
isSymbolic	isSymbolic
isSymbolic,CollapsedVCF-method	isSymbolic
isSymbolic,ExpandedVCF-method	isSymbolic
numtDetect	numtDetect
pairs2breakpointgr	pairs2breakpointgr
partner	partner
rtDetect	rtDetect
simpleEventLength	simpleEventLength
simpleEventType	simpleEventType
StructuralVariantAnnotation	StructuralVariantAnnotation
