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vgteam / toil-vg

Distributed and cloud computing framework for vg
Apache License 2.0
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unused argument : `min.cov` in toil-vg vcfeval #835

Open zqfang opened 3 years ago

zqfang commented 3 years ago

https://github.com/vgteam/toil-vg/blob/99101f2b79a540c09c9774881807059b289b5d42/src/toil_vg/vg_vcfeval.py#L551

I've install the new sveval package from R. 

BiocManager::install('jmonlong/sveval')

Change min.cov to min.ol could let the toil vdfeval work without issues

I don't know how this will affect the older version of toil-vg

adamnovak commented 3 years ago

@glennhickey It looks like you wrote this part, but also it's @jmonlong's package

Can we just change this to min.ol? How long has the new sveval package been out?

I think we might end up installing sveval from the internet when we use it; I don't think we pin a version or package it in a container.

glennhickey commented 3 years ago

We do pin a version here: