feat: --extended_orf_analysis routes hybrid GTF into genome-BAM ORF callers

[pinin4fjords]

Summary

Adds --extended_orf_analysis (default false) to opt into novel-ORF discovery on the hybrid annotation from #164. When the flag is on and a novel-transcript source is configured (--skip_stringtie false or --novel_gtf <path>), the hybrid GTF is routed to:

• Ribo-TISH predict: hybrid GTF on -g. The optional -a secondary annotation (added by feat(ribotish/predict): wire optional -a reference annotation through pipeline #179) is left empty in the extended path to avoid a known Ribo-TISH bug (TypeError: unsupported operand type(s) for +=: 'NoneType' and 'int' zhpn1024/ribotish#33, Incorporate check for 3nt periodicity #24) hit when both -g and -a share CDS rows. The hybrid GTF preserves canonical CDS records, so background calibration is intact.
• Ribotricer prepare-orfs: hybrid GTF directly. Ribotricer has no secondary-annotation concept; CDS-absent novel transcripts are auto-labelled novel in its ORF_type column.

RiboCode, riboWaltz, plastid, and Salmon-based quantification stay on the canonical backbone regardless of the flag. RiboCode in particular is gated by the transcriptome-BAM constraint and gets its own hybrid path in #171.

When --extended_orf_analysis true is set without a novel-transcript source, the pipeline warns and falls back to canonical (no-op rather than error, so users can compose flags incrementally).

Default behaviour is unchanged

With --extended_orf_analysis false, the workflow graph is identical to PR6 (feat/164-stringtie-novel).

Stacked PR notes

Seventh in the stack splitting #174. Targets #182 (feat/164-stringtie-novel).

Closes #165

🤖 Generated with Claude Code

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