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privefl / bigsnpr

R package for the analysis of massive SNP arrays.
https://privefl.github.io/bigsnpr/
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[snp_modifyBuild] add [local.chain] #492

Closed Hugolyu closed 5 months ago

Hugolyu commented 5 months ago

Add parameter to use local files local.chain and changed the url download from https://hgdownload.soe.ucsc.edu/

Hi Florian,

I've added a new parameter to use the local chain files in snp_modifyBuild, and documented it in man/snp_modifyBuild.Rd.

The URL changes were cse to soe and ftp to https. I've tested it on my own computer and it seems to be working fine, but you need to test it multiple times to check for any potential bugs.

This is my first try pull request, and I appreciate the opportunity!

I hope it works well and this addition is useful.

Best regards,

Hugo

privefl commented 5 months ago

I've made a few minor changes for my preference. And some versioning.

It is annoying I cannot really write unit tests for this function, because liftOver is not available in the tests.

privefl commented 5 months ago

Is it still working for you?

Hugolyu commented 5 months ago

Yes! Still works well for me! Many thanks.