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
extractBreakpointSequence
                        Extracts the breakpoint sequence.
extractReferenceSequence
                        Returns the reference sequence around the
                        breakpoint position
findBreakpointOverlaps
                        Finding overlapping breakpoints between two
                        breakpoint sets
findInsDupOverlaps      Finds duplication events that are reported as
                        inserts. As sequence alignment algorithms do no
                        allow backtracking, long read-based variant
                        callers will frequently report small
                        duplication as insertion events. Whilst both
                        the duplication and insertion representations
                        result in the same sequence, this
                        representational difference is problematic when
                        comparing variant call sets.
findTransitiveCalls     Identifies potential transitive imprecise calls
                        that can be explained by traversing multiple
                        breakpoints.
hasPartner              Determines whether this breakend has a valid
                        partner in this GRanges
isStructural            Determining whether the variant is a structural
                        variant
isSymbolic              Determining whether the variant is a symbolic
                        allele.
numtDetect              Detecting nuclear mitochondria fusion events.
partner                 GRanges representing the breakend coordinates
                        of structural variants #@export Partner
                        breakend for each breakend.
rtDetect                Detecting retrotranscript insertion in nuclear
                        genomes.
simpleEventLength       Length of event if interpreted as an isolated
                        breakpoint.
simpleEventType         Type of simplest explanation of event. Possible
                        types are: | Type | Description | | BND |
                        Single breakend | | CTX | Interchromosomal
                        translocation | | INV | Inversion. | | DUP |
                        Tandem duplication | | INS | Insertion | | DEL
                        | Deletion |
