Add --report_json flag for machine-readable export of report tables

[TianYuan-Liu]

Summary

• Adds a new --report_json CLI flag that exports all SQANTI3 report tables as a structured JSON file ({prefix}_report_tables.json)
• Works alongside any --report format (html/pdf/both) and also with --report skip to produce only JSON without HTML/PDF output
• JSON includes: metadata, summary counts (isoform/gene classification), splice junction classification, polyA motifs, CAGE peaks, and quality metrics (RT-switching, non-canonical SJ, NMD, SJ coverage)

Changes

• src/qc_argparse.py — new --report_json CLI flag (boolean, default False)
• src/qc_output.py — forward flag to R script as 6th argument
• src/qc_pipeline.py — run R script when --report skip --report_json is used
• src/parallel.py — mirror wiring for parallel/chunked execution
• src/write_parameters.py — log ReportJSON parameter
• src/utilities/report_qc/SQANTI3_report.R — export_tables_to_json() function using jsonlite, accept "skip" format, fixed pdf/html branch logic
• test/integration/test_report_json.py — 4 integration tests covering: JSON+HTML, JSON+skip, no-flag backward compatibility, quality metrics structure

JSON structure

{
  "metadata": { "generated_at": "...", "classification_file": "...", "junction_file": "..." },
  "summary": {
    "unique_genes": 123,
    "unique_isoforms": 456,
    "isoform_classification": [{"category": "FSM", "n_isoforms": 100}, ...],
    "gene_classification": [{"category": "FSM", "n_genes": 50}, ...],
    "splice_junction_classification": [{"category": "canonical_known", "n_sjs": 200, "percent": 95.2}, ...]
  },
  "polya": { "by_category": [...], "motif_frequency": [...] },
  "cage": { "by_category": [...] },
  "quality_metrics": {
    "rt_switching": [{"structural_category": "...", "count": 5, "total": 100, "percent": 5.0}],
    "noncanonical_sj": [...],
    "nmd_prediction": [...],
    "sj_coverage": [...]
  }
}

Validation

All JSON values validated against classification/junction files on example data — counts match exactly.

Closes #218

Test plan

• Run sqanti3_qc.py --report_json with example data and verify JSON output
• Run sqanti3_qc.py --report skip --report_json and verify JSON-only output
• Run without --report_json and verify no JSON file is created
• Run integration tests: pytest test/integration/test_report_json.py -v

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