Functions to align flanks of breakpoing regions.

[charles-plessy]

                   TSD
query       …──────────━━━━━─────────━━━━━─────────────…
alignment    ...............              .............
target      …──────────━━━━━              ─────────────…

Service functions

Align breakpoints

pat          ++++
range  --------==========----------
sub                    ++++             (or ---- if rev = F)

alignBreakPoints <- function(gr, n = 20, reverseComplement = FALSE) {
  if (isFALSE(reverseComplement)) reverseComplement <- identity
  pairwiseAlignment(getSeq(gr |> flank(n, both = T, start = T)),
                    getSeq(gr |> flank(n, both = T, start = F)) |> reverseComplement(),
                    type="global")
}

Align ends

pat            ++++
range  --------==========----------
sub                  ++++             (or ---- if rev = F)

alignEnds <- function(gr, n = 20, reverseComplement = FALSE) {
  resize_ <- function(...) resize(...) |> trim() |> suppressWarnings()
  if (isFALSE(reverseComplement)) reverseComplement <- identity
  pairwiseAlignment(getSeq(gr |> resize_(n, fix = "start")),
                    getSeq(gr |> resize_(n, fix = "end")) |> reverseComplement(),
                    type="global")
}

Search for TSDs

pat            +
range  --------==========----------
sub                      +         

searchForTSDs <- function(gr, n = 8) {
  pairwiseAlignment(getSeq(gr |> resize(n, fix = "start")),
                    getSeq(gr |>  flank(n, start = F)),
                    type="global")
}

Align indels

                          ++++          ++++
query       …──────────────────────────────────────────…
target      …───────────────              ─────────────…
                          ++..............++

alignInDel <- function(gb) {
  list(
    q_l = getSeq(gb$query[1] |> flank(20, both = T, start = T))[[1]],
    trg = getSeq(gb[1]       |> flank(20, both = T, start = F))[[1]],
    q_r = getSeq(gb$query[2] |> flank(20, both = T, start = F))[[1]]
  ) |> as("DNAStringSet") |> msa::msaClustalW(order = "input")
}

Align to self

alignToSelf <- function(gr) {
  pairwiseAlignment(getSeq(gr),
                    getSeq(gr) |> reverseComplement(),
                    type="global")
}