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Showing content from https://github.com/stuart-lab/signac/issues/513 below:

The switch for pruning the non standard chromosomes is not implemented. · Issue #513 · stuart-lab/signac · GitHub

https://github.com/timoast/signac/blob/e0512d348adeda4a3f23a2e8f56d1fe09840e03c/R/utilities.R#L398

Hi!
Thanks a lot for the awesome package!

I could not get the GetGRangesFromEnsDb working with my Gasterosteus aculeatus genome, because it was leaving only "MT" chromosome.
It looks like the switch to not prune the non-standard chromosomes was not implemented in the code. It would also be great to have an option to supply a vector of the chromosomes to keep.


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