Very often alignments return deletions that are not real deletions, but
rather artifact of incomplete reads eg.:
ACTGAAAAA------- <- this "deletion" should be filtered ACTG----ACTGACTG
(data.frame) Should contain events from alignments in GRanges style with columns eg. seqnames, width, start, end.
(data.frame) Needs columns Forward_Primer, ReversePrimer and Amplicon.
(logical vector) where TRUE indicates events that are overlapping primers
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