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integer_cst
2017 Apr 28
1
pairwiseAlignment Improvements
...on why the show method for the summary only shows mismatches, even if there are indels contained in it? This seems 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)
> alignm...