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Add more granular variant specification and other minor changes #165
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First, thanks for working on this & helping to tackle these issues! Few high-level comments:
I would like to test this out if that's OK with you & will then give more concrete feedback. |
Just noting here our offline discussion:
Otherwise LGTM -- |
@jburos responded to all the above, and added an associated test as well as an error if a cache with the old format is present. I don't want to bother you over the weekend, so I'll probably go ahead and merge today or tomorrow. |
LGTM - thanks Tavi! Really like the out-of-date cache check. |
Added a few things to support some of my melanoma and lung work.
In this PR:
snv_vcf_paths
andindel_vcf_paths
and replacing with a dictionary fromsnv
to a list of VCF paths or MAF paths orVariantCollection
s.filter
ing of aCohort
..genome
property.Since removing
snv_vcf_paths
will break things, I'd be bumping the release up to0.5.0
. Also need to do more manual/automated testing to confirm no issues.