%na%                    Replaces the NA values in a with corresponding
                        values in b
%null%                  Uses b if a is NULL
.constrict              constrict
.isSymbolic             Determining whether the variant is a symbolic
                        allele.
.pairwiseLCPrefix       vectorised pairwise longest common prefix
                        Returns the length of the longest common prefix
                        for each string pair
.svLen                  Returns the structural variant length of the
                        first allele
.testfile               Testthat helper utility to locate files used
                        for package tests
.testrecord             Loading a VCF containing the given records
.toVcfBreakendNotationAlt
                        Converts to breakend notation
.unXStringSet           converts an XStringSet to a character
StructuralVariantAnnotation
                        StructuralVariantAnnotation: a package for SV
                        annotation
align_breakpoints       Adjusting the nominal position of a pair of
                        partnered breakpoint.
breakendRanges          Extracting unpartnered breakend structural
                        variants as a GRanges
breakpointGRangesToVCF
                        Converts the given breakpoint GRanges object to
                        VCF format in breakend notation.
breakpointRanges        Extracting the structural variants as a
                        GRanges.
breakpointgr2bedpe      Converting breakpoint GRanges to BEDPE-like
                        dataframe
breakpointgr2pairs      Converts a breakpoint GRanges object to a Pairs
                        object
calculateReferenceHomology
                        Calculates the length of inexact homology
                        between the breakpoint sequence and the
                        reference
countBreakpointOverlaps
                        Counting overlapping breakpoints between two
                        breakpoint sets
elementExtract          Extracts the element of each element at the
                        given position
extractBreakpointSequence
                        Extracts the breakpoint sequence.
extractReferenceSequence
                        Returns the reference sequence around the
                        breakpoint position
findBreakpointOverlaps
                        Finding overlapping breakpoints between two
                        breakpoint sets
isStructural            Determining whether the variant is a structural
                        variant
isSymbolic              Determining whether the variant is a symbolic
                        allele.
partner                 GRanges representing the breakend coordinates
                        of structural variants #@export Partner
                        breakend for each breakend.
