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Obscure error when aligning sequences with gaps #46

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jakobnissen opened this issue Feb 15, 2021 · 0 comments
Open

Obscure error when aligning sequences with gaps #46

jakobnissen opened this issue Feb 15, 2021 · 0 comments

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@jakobnissen
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MWE:

model = AffineGapScoreModel(EDNAFULL, gap_open=-12, gap_extend=-2)
pairalign(LocalAlignment(), dna"A-A", dna"AAA", model)

Errors with:
ERROR: LoadError: BoundsError: attempt to access 15×15 Matrix{Int64} at index [0, 1]

It seems clear to me that the problem is that the alignment do not have an entry in the score table for matching to a deletion (a deletion being decoded to 0), and so it goes out of bounds.
The solution here should be to throw an error if the sequence contains any gaps

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