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GenomicMedLab / cool-seq-tool

https://coolseqtool.readthedocs.io
MIT License
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Add start/end residue mode parameter #330

Closed korikuzma closed 2 months ago

korikuzma commented 2 months ago

Feature description

Currently, residue_mode is used to describe the input positions residue mode. We should add an end residue mode parameter.

Use case

In this Variation Normalizer PR, I had to do a hacky +1 since g_to_grch38 returns inter-residue mode but we need residue mode at this step. It would be nice to specify the end residue mode needed.

Proposed solution

No response

Alternatives considered

No response

Implementation details

No response

Potential Impact

No response

Additional context

No response

Contribution

None

jsstevenson commented 2 months ago

We're a ways out from this, but I think it'd be nice to start thinking about API consistency throughout CST -- rather than adding an extra argument to optionally alter the output coordinate mode here, I wonder if there are more generic ways to handle this for all functions that return positions (maybe a decorator?)

korikuzma commented 2 months ago

After conversations, I think I should revisit this in Variation Normalizer and not add additional complexity / confusion in Cool-Seq-Tool. We also want people to use inter-residue coordinates, so this would help enforce this. I'm going to close. We can re-open if this is actually needed.