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
We call them Events Overlapping Primers and filter them together with reads that are potentially PRIMER DIMERS. This filter will also remove all events coming from reads with low alignment score - potential Off-targets.
amplicanFilter(aln, cfgT, PRIMER_DIMER)
(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.
(numeric) Value specifying buffer for PRIMER DIMER
detection. For a given read it will be recognized as PRIMER DIMER when
alignment will introduce gap of size bigger than:
(aln) Reduced by events classified as PRIMER DIMER or overlapping primers.
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