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mcveanlab / treeseq-inference

Work for the tree sequence inference paper.

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Version of bgen library required to build the simplebgen module

XiaoleiZ opened this issue · comments

commented

Hi

I am trying to test the software in UKB data. One of the step required in the code is to build simplebgen module, which requires bgen library. I've used the newest version bgen 4.1.9 and it seems like it's not compatible with the file simplebgenmodule.c. Many functions used in the simplebgenmodule.c are not found in the current bgen library. Could you point to which version you have used or other alternatives to solve it?

Thank you!

commented

I'm afraid I don't have that information available @XiaoleiZ, sorry. It would be a version that was current at the time the preprint was release, so Nov 2018.

This code wasn't really intended to be reused on a long-term basis. We have some changes in the pipeline for tsinfer that will use sgkit to read data from files, that this will support bgen directly.