The alignment below induces terminal gaps in the subject. This is not indicated as an indel. So, from looking at the meta-data of the alignment only, one may think that it is a 'perfect' alignment.
Is that behaviour expected or desired?
aln <- pwalign::pairwiseAlignment("CCGGATCG", "ATCG", type = "global-local")
aln
Global-Local PairwiseAlignmentsSingleSubject (1 of 1)
pattern: CCGGATCG
subject: [1] ----ATCG
score: -18.07298
pwalign::indel(aln)
An object of class "InDel"
Slot "insertion":
IRangesList object of length 1:
[[1]]
IRanges object with 0 ranges and 0 metadata columns:
start end width
<integer> <integer> <integer>
Slot "deletion":
IRangesList object of length 1:
[[1]]
IRanges object with 0 ranges and 0 metadata columns:
start end width
<integer> <integer> <integer>
The alignment below induces terminal gaps in the subject. This is not indicated as an indel. So, from looking at the meta-data of the alignment only, one may think that it is a 'perfect' alignment.
Is that behaviour expected or desired?