Clarify bite calculation: documentation and code comments

[Copilot]

bite (classification column 25) and bite_junction (junction column 13) lacked meaningful descriptions, making it impossible to understand what the fields represent or where they originate without reading the source.

Changes

• docs/Understanding-the-output-of-SQANTI3-QC.md

  • bite (col 25): Expanded to explain it reflects whether any junction in the isoform has bite_junction == TRUE; mono-exonic transcripts default to NA; cross-references junction glossary.
  • bite_junction (col 13): Explained the exact TRUE condition (novel intron extends past reference splice sites on both ends), the relationship to diff_to_Ref_start_site/diff_to_Ref_end_site, and that known junctions are always FALSE.

• src/classification_steps.py: Added inline comments documenting the sign semantics of min_diff_s/min_diff_e and the logic behind the bite_junction formula:

  # min_diff_s = d - closest_donor: negative if query donor is upstream of (inside) the adjacent exon
  # min_diff_e = closest_acceptor - a: negative if query acceptor is downstream of (inside) the adjacent exon
  # bite_junction TRUE when min_diff_s <= 0 AND min_diff_e <= 0, at least one strictly negative
  "bite_junction": "TRUE" if ((min_diff_s<0 or min_diff_e<0) and not(min_diff_s>0 or min_diff_e>0)) else "FALSE",

• src/qc_computations.py: Added comment on the bite aggregation: once any junction sets it TRUE, subsequent FALSE junctions do not override it.

---

✨ Let Copilot coding agent set things up for you — coding agent works faster and does higher quality work when set up for your repo.