Update exon selection offset to consider cases where breakpoint occurs before or after a transcript

[jarbesfeld]

Describe the bug

There are cases where a breakpoint can occur before or after a transcript (i.e. in the untranslated region, or UTR). We should check for these cases when selecting the adjacent exon.

Steps to reproduce

resp = test_egc_mapper._get_adjacent_exon(
        tx_exons_genomic_coords=nm_152263_exons_genomic_coords,
        start=154192102,
        strand=Strand.POSITIVE,
    )

Expected behavior

This should output 1, since this occurs two bases before the transcription start site of exon 1

Current behavior

This returns exon 10, as it iterates through the whole exon list since this breakpoint occurs outside of the transcript range

Possible reason(s)

No response

Suggested fix

No response

Branch, commit, and/or version

Main branch

Screenshots

No response

Environment details

Mac M1

Additional details

No response

Contribution

Yes, I can create a PR for this fix.

[korikuzma]

@jarbesfeld is this similar to #361?

[jarbesfeld]

@korikuzma Yes this includes a fix to the logic described in #361. I realized when looking at the GENIE data that there can be breakpoint before or after the transcript (e.g. Promoter of AOC4P(+):3Kb from tx start), so I thought it would be good to add this fix