(Partial) Hamming distance

[traversc]

I'm looking for a function for partial hamming distance. It looks like it existed in an earlier version but was taken out.

Is it possible to put it back in?

[matthieugomez]

Sure. Could you give a code example of what you’d like to to?

…

On Thu, Oct 22, 2020 at 11:10 AM Travers ***@***.***> wrote: I'm looking for a function for partial hamming distance. It looks like it existed in an earlier version <https://libraries.io/github/matthieugomez/StringDistances.jl> but was taken out. Is it possible to put it back in? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#35>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABPPPXM3CWIDQPNLVN4FLGLSMBYSXANCNFSM4S3RP3GQ> .

[traversc]

Something simple like:

compare("GACT", "CGATTGCAATGCTA", Partial(Hamming()))

or

 findall(s, itr, Partial(Hamming()), min_score = 0.9)

An example use case would be as a first pass in PCR primer design, where a hamming might be more appropriate than levenshtein or other metric.

[matthieugomez]

The issue is that Hamming is already defined in Distances and so defining it on Strings is type piracy.

[traversc]

I'm a bit new to Julia, but can you simply name the function something else? The name isn't important, only what it does. Something like hammingstr or hamming2 etc.

[matthieugomez]

Ok, I now export a Hamming distance that is distinct from the one exported by Distances. Not super satisfied (this requires to do StringDistances.Hamming() when loading both Distances and StringDistances), but that's better than type piracy.