unused argument : min.cov in toil-vg vcfeval

[zqfang]

toil-vg/src/toil_vg/vg_vcfeval.py

Line 551 in 99101f2

sveval_cmd += ', min.cov={}'.format(sv_overlap)

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]

@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]

We do pin a version here:

• https://github.com/vgteam/toil-vg/blob/master/src/toil_vg/vg_config.py#L211-L212
• https://github.com/vgteam/toil-vg/blob/master/src/toil_vg/vg_config.py#L523-L524