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GenomicMedLab / cool-seq-tool

https://coolseqtool.readthedocs.io
MIT License
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Add parameter for using GRCh37 sequences #371

Open jarbesfeld opened 1 month ago

jarbesfeld commented 1 month ago

Feature description

It is possible a user may want to represent GRCh37 data and not lift over to GRCh38. We should include a parameter that indicates if the user wants to lift over or not

Use case

There a fusion callers (such as GENIE) that may output GRCh37 genomic coordinates, and we want to represent those coordinates and not liftover to GRCh38.

Proposed solution

Add parameters in genomic_to_tx_segment that indicates what reference build the user would like to use and if liftover is needed.

Alternatives considered

No response

Implementation details

No response

Potential Impact

No response

Additional context

I can contribute to this

Contribution

None

jsstevenson commented 4 weeks ago

I wonder if there's a way that we could be defining these transformation functions more compositionally, so that you can construct these yourself instead of needing everything to be parameterized in the function