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dewyman avatar dewyman commented on July 1, 2024

Here is another special case that I found: c10882/f1p1/3230. This situation suggests that maybe we need to impose a similarity requirement on the exon matches. If the 3' or the 5' difference exceeds 10 basepairs, then it is not a match.
c10882-f1p1-3230_tnfrsf18

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dewyman avatar dewyman commented on July 1, 2024

Solution: Loose exon assignments and transcript pool approach

For each exon in query transcript:
- Fetch annotated exons that overlap with query exon
- match_pool := transcripts that contain these exons
- transcript pool := intersection(match_pool, previous transcript_pool)

By the end, the only transcripts left in the transcript pool are transcripts that contain overlap for every exon in the query transcript. A final cross-check of the total exons in the query and the annotation ensures that we don't report a transcript that has more exons than the query.

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