small GWASTools patch to allow to use already built gds objects in Genotype Readers
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Karl Forner • 70
@karl-forner-2831
Last seen 4.2 years ago
Switzerland
Hello, This is a patch for GWASTools that allows to use gds instances instead of filenames as arguments of GdsGenotypeReader and GdsReader. Recent versions of gdsfmt have introduced new arguments for the openfn.gds function that creates gds objects: allow_duplicate and allow_fork. It is not possible to use a GdsGenotypeReader for example with mlcapply if the gds has not been opened with allow_fork=TRUE. To fix this I created a patch to be able to do: GdsGenotypeReader(openfn.gds(filename, allow_fork = TRUE, allow_duplicate = TRUE)). I first thought of using ... arguments, but they are already used (though not documented) in GdsGenotypeReader to init some class fields. I added some tests and updated the docs too. This is just a proof of concept, I'd be happy to discuss it and help fixing this problem. Best regards, Karl Forner [[alternative HTML version deleted]]
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