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Mikaël Salson authored
When computing whether the alignment has too many differences we should not allow having a negative number of mismatches. So we have to make sure that length >= BOTTOM_TRIANGLE_SHIFT. But this is not enough: having only 1 match in 20 nucleotides doesn't make sense. Therefore we may allow a given fraction of the sequences to be matches just by chance. We could have used probabilities but this should be a rare case. I'm not sure that's worth it.
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