feat: flag MHC credible sets based on lead

[d0choa]

This PR closes opentargets/issues#3469.

It implements:

• QC flag for MHC region in StudyLocus
• Add flag in study_locus_validation step
• New GenomicRegion class refactoring some pre-existing code

It's pending:

• Add new flag IN_MHC to orchestration config

[d0choa]

@DSuveges and @Daniel-Considine, this touches on code that you worked on in the past, so please feel free to raise any objections. I'm assigning the review to Szymon and Yakov. (I didn't want to assign everyone 😅)

[Daniel-Considine]

Looks all good to me

[DSuveges]

There's a comment in the src/gentropy/study_locus_validation.py file indicating a filtering for MHC, however I cannot find the logic to do so. Is it intentional? I suspect the comment should go, and a exclusion flag needs to be added to the orchestration.

[d0choa]

• Comment updated
• As said at the top, we need to add Add new flag IN_MHC to orchestration config, and that would be enough to handle the filtering using the generic valid_rows function.

[DSuveges]

Now the flagging comment is duplicated, but this is no way block the PR.

[d0choa]

that's why I shouldn't do commits from the web. Fixed now