Fix Comp-Het test

[MattWellie]

Fixes

• Failed to call an expected Comp-Het in a production run
• Both variants in the comp-het were assigned Support and Cat6 (and maybe a couple of other categories)

Proposed Changes

• I'm confused - this seems like quite a core bug that should have cropped up before, but the code here hasn't been touched in a year. It definitely appears to be a bug, and suggests we've been under-reporting Comp-Hets in various cohorts

In AIP variant representation there are 3 types of category which can be assigned to a variant:

• support
• boolean (applies to all samples)
• sample (applies to subset of samples, e.g. de novo)

When testing that 2 variants can form a Comp-Het, we screen out cases where both variants are only supporting. The logic in this test was:

if var1 is support ONLY and var2 is support ONLY: fail

The method testing whether a variant is Support ONLY checked:

if variant.has_support and not variant.has_sample_category

missing out the boolean category case. The behaviour this has lead to is unintentional:

The only way to form a Comp-Het in AIP is when a variant with the Support category combines with a variant without the Support category, or where neither variant has the support category assigned.

This is an unintended consequence of the logic being too convoluted. This is a patch for the comp-het test, and I'll schedule a more detailed look into this.

Checklist

• [x] Linting checks pass

[MattWellie]

Also uses the built-in get_logger functionality, to make sure intended logs are really being printed