Tavi Nathanson comments

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                                            Tavi Nathanson

Invalid biotype error when loading effects from TCGA-BLCA cohort

@jburos yup, should be fixed with the latest `varcode`.

Invalid biotype error when loading effects from TCGA-BLCA cohort

@jburos that `.pyc` code looks old; can you delete all the `.pyc`s and see if that helps? Are you using `0.4.0` there?

Allow the plot_boolean column to be a function

More generally, all columns in cohorts should be specifiable as functions. We can probably centralize that concept and get rid of some code.

Simplify Cohort default

Indeed, @jburos ran into this very issue: https://github.com/hammerlab/cohorts/issues/120#issue-171240320

Support stratified cohorts, as a way to combine more than one sample of patients

I like the idea of a `StratifiedCohort` class.

Find public or create simulated data for worked example

This seems related to https://github.com/hammerlab/cohorts/pull/112/commits/067efef7e9816cdc384a10853186ee425f7954ba

Modify isovar usage from >=3 to >=2 spanning reads

Or, at least, consider this modification

Throw failed-io error

@arahuja I think my logic was: I was running into issues where I had a few missing VCFs and wanted to load the others, but the `IOError` blew up the...

Throw failed-io error

We discussed offline that it's okay for incorrect paths to blow up the whole thing, and any logic to the contrary can live outside of `cohorts` since it's counter-intuitive.

Resolve overlap between epidisco and cohorts

Also related: tracking provenance. `cohorts` tracks `Python` package versions in `PROVENANCE` files inside the `cache` directory. I'm not sure how to pull out the software versions that `epidisco` used?