Enable Atropos-style matching based on sequence similarity - #891
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When migrating from the deprecated
atropostocutadapt, there was discordance in the results due to a difference in how the two algorithms scored alignments. It is simplest for us to migrate without changing downstream results, so we have added an optional mode that scores by sequence similarity. It resolves ties by choosing the first adapter, since errors are meant to be ignored in the scoring. This brings the two tools into full concordance to the extent of our testing.