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Chain contigs in pairwise alignments

Source: R/chain_contigs.R
chain_contigs.Rd

Description TBW

Usage

chain_contigs(gb, tol = Inf, drop.within = FALSE)

Arguments

gb

GBreaks object of the pairwise alignment.

tol

Unaligned region of width lesser than or equal to tol in both the reference and query case will be bridged in coalescing.

drop.within

Discard the chains that are included in other chains.

Value

TBW

See also

Other Colinearity functions: GOC(), bridgeRegions(), coalesce_contigs(), dist2next(), filterColinearRegions(), flagColinearAlignments(), flagPairs()

Author

Charles Plessy

Examples

chain_contigs(exampleInversion)
#> GBreaks object with 2 ranges and 2 metadata columns:
#>       seqnames    ranges strand |        query     score
#>          <Rle> <IRanges>  <Rle> |    <GRanges> <integer>
#>   [1]     chrA   100-400      + | chrB:100-400       301
#>   [2]     chrA   210-291      - | chrB:210-291        82
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome