removes metamist file/analysis registration completely out of this codebase (we handle that at a pipeline level, this code is specific to CPG and no longer used)
removes metamist connection from the panel matching stage
creates a new script to connect to metamist and parse all required details into an extended PED file format. This is intended to be the only metamist-specific entrypoint, which other users could swap out for their own implementation
drops reliance on Peddy, instead using peds, parsing into a private model where required
MOI testing is done as independent trios, not as a whole family (i.e. for each affected participant, variant(s) will be accepted if the inheritance model works within the proband-parents trio. An affected/unaffected sibling/grandparent is not considered for the MOI to hold)
Proposed Changes
Frankly, a ridiculous number of changes
Chunky Changes
Various other
peds, parsing into a private model where requiredNext steps
Checklist