openvax / isovar / 36024955208

96%

master: 96%

Pull #369

github

Record why SV paths end and every collection setting; schema v3

Fixes #363.

- _extend reports why each path end stopped: observations_end,
  repeated_genomic_position or path_limit. Truncation was only in the
  global limitations, so a cut path looked like a natural end. Paths carry
  end_reasons; ORF export copies them and warns path_end_truncated.
- parameters.read_collection records every ReadCollector setting that can
  change the evidence: duplicate/secondary/QUAL policy, mate merging,
  end inference, trimming and each read-end profile's SHA-256. The ATP5MG
  example shows the adapter profile changes which paths are output.
- Records without a read name are reported as unnamed_records_skipped
  instead of disappearing.
- The output schema becomes isovar.sv_rna_candidates.v3. Field semantics
  and additions since v2 were introduced (null molecule counts, start and
  junction evidence, inclusion gates, the new frame status, moved
  parameters) are listed in CHANGELOG.md; the ORF exporter accepts v2 and v3.

Claude-Session: https://claude.ai/code/session_01P88BbC8f9t1eS48iqQdcEi

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