#'@title getInsSeqs
#'@description Get insertion sequences
#'@author Helen Lindsay
#'@rdname getInsSeqs
#'@export
setGeneric("getInsSeqs", function(alignments, ...) {
standardGeneric("getInsSeqs")})
#'@rdname getInsSeqs
setMethod("getInsSeqs", signature("GAlignments"),
function(alignments, ...){
.checkForMcols(alignments, "seq", "gappedRef")
ins_on_qry <- cigarRangesAlongQuerySpace(cigar(alignments),
ops = "I")
extractAt(mcols(alignments)$seq, ins_on_qry)
})
# get clipped seqs
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