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Add max_alt_alleles option to schema generation #18

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jeromekelleher opened this issue Feb 20, 2024 · 1 comment
Open

Add max_alt_alleles option to schema generation #18

jeromekelleher opened this issue Feb 20, 2024 · 1 comment

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@jeromekelleher
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Sometimes we do want to clip.

Probably the right thing to do here is to add a min_value and max_value values to the column schemas, and to np.clip() the values during sanitise.

@jeromekelleher
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Note that there are numerous thorny issue to deal with here, as we may not want to just keep the first k alleles but the k most frequent. Except for PL fields (for which we need local alleles anyway, #185) it doesn't see to cause too much problems, so I'm not sure this is much of a priority. Going to leave open for now, but we should probably close this issue after a while if nobody comes along with a compelling use-case.

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