[codex] Extract transcript edits from assembled cDNA

[iskandr]

Summary

This PR extracts transcript-relative edits from the assembled local cDNA and threads them through the RNA phasing and varcode adapter surfaces.

It adds a transcript-anchored edit model so PhaseGroup can now distinguish:

• known somatic transcript edits
• known germline transcript edits
• unexplained transcript edits

It also updates the varcode adapter to emit the full observed transcript edit list for a matched transcript instead of only the focal variant edit.

Why

PhaseGroup previously carried only sequence-level metadata (cdna_sequences, mutant_protein_sequences, transcript ids/names). That was enough to say that assemblies existed, but not enough to answer which differences from the reference transcript were actually observed and whether those differences were explained by a known variant.

This change gets Isovar closer to a contig-backed phase/edit model without overclaiming a single full-length canonical haplotype transcript.

Validation

• ./lint.sh
• ./test.sh
• added focused regression tests for transcript-edit extraction, phase-group propagation, and varcode adapter behavior

Closes #180

[coveralls]

coverage: 93.517% (+0.3%) from 93.216% — codex/phase-group-transcript-edits into master