search for: gaacgaggacc

...eems arbitrary and also misleading, because it always gives a false impression that there are no indels. Could the return data types consistently be made to be IRanges ? Sometimes it's IntegerList, sometimes it's IRanges. For example, > A 11-letter "DNAString" instance seq: GAACGAGGACC > B 8-letter "DNAString" instance seq: GGACGAGC > alignment <- pairwiseAlignment(A, B, gapOpening = 0, gapExtension = 1, substitutionMatrix = substitutions) > alignment at subject@mismatch IntegerList of length 1 [[1]] 2 > alignment at subject@indel IRangesList of length...