prepareOl: Prepare SV overlaps before annotation
In jmonlong/sveval: SV evaluation

prepareOl

R Documentation

Prepare SV overlaps before annotation

Description

Prepare SV overlaps before annotation

Usage

prepareOl(
  query,
  subject,
  min.rol = 0.1,
  max.ins.dist = 1,
  range.seq.comp = FALSE,
  ins.seq.comp = FALSE,
  nb.cores = 1,
  by.gt = FALSE
)

Arguments

`query`	a query GRanges object
`subject`	a subject GRanges object
`min.rol`	minimum reciprocal overlap for deletions and other "ranges" SVs. Default is 0.1
`max.ins.dist`	maximum distance for insertions to be clustered.
`range.seq.comp`	compare sequence instead of overlapping deletions/inversion/etc. Default is FALSE.
`ins.seq.comp`	compare sequence instead of insertion sizes. Default is FALSE.
`nb.cores`	number of processors to use. Default is 1.
`by.gt`	should the variants be split by genotype? Default is FALSE, i.e. all variants with an alternate allele (ac>0) is considered 'called'.

Value

a GRanges with information about pairs of SVs in query and subject that overlap

`GRange`	intersected ranges (for "ranges" SVs)
`queryHits`	the id of the input query
`subjectHits`	the id of the input subject
`querSize`	the size of the input query
`subjectSize`	the size of the input subject
`interSize`	the size of the intersection (e.g. range, ins size, ins seq alignment)
`type`	the SV type of the pair