Command
=======
/usr/local/bin/python3 \
  /tmp/nxf.fooQvEe3k0/nextflow-bin/compare_fusions_with_adjudication.py \
  --fusion \
  --test \
  test_harmonized_calls.tsv \
  --truth \
  truth_harmonized_calls.tsv \
  --patient-id-list \
  patient_id_list.txt \
  --gene-list \
  selected_gene_list.txt \
  --output-dir \
  . \
  --alternative-confirmation \
  alt_truth_harmonized_calls.tsv \
  --test-filters \
  FILTER==PASS \
  --truth-filters \
  FILTER==PASS \
  --alt-confirmation-filters \
  FILTER==PASS \
  --starfusion-filters \
  F \
  --starfusion-filters \
  U \
  --starfusion-filters \
  S \
  --starfusion-filters \
  I \
  --starfusion-filters \
  O \
  --starfusion-filters \
  N \
  --starfusion-filters \
  _ \
  --starfusion-filters \
  R \
  --starfusion-filters \
  E \
  --starfusion-filters \
  A \
  --starfusion-filters \
  D \
  --starfusion-filters \
  S \
  --starfusion-filters \
  '>' \
  --starfusion-filters \
  = \
  --starfusion-filters \
  8 \
  --arriba-filters \
  A \
  --arriba-filters \
  R \
  --arriba-filters \
  _ \
  --arriba-filters \
  C \
  --arriba-filters \
  O \
  --arriba-filters \
  N \
  --arriba-filters \
  F \
  --arriba-filters \
  I \
  --arriba-filters \
  D \
  --arriba-filters \
  E \
  --arriba-filters \
  N \
  --arriba-filters \
  C \
  --arriba-filters \
  E \
  --npa-fusion-catalog-from-truth

Standard output
===============
=== Fusion mode ===
Loading test...
  244540 rows
Loading truth...
  214 rows
  Test after filters: 20800 rows
  Truth after filters: 214 rows
  Arriba after per-caller filters: 445 rows
  STAR-Fusion after per-caller filters: 56 rows
  Test after per-caller filters: 501 rows
  Patient IDs in list: 76
  In test: 40, in truth: 6, both: 6
  NPA catalog:
    definition: filtered primary truth FUSION_ID_norm union filtered test FUSION_ID_norm
    |M| unique fusion events: 5
    primary truth IDs=5, test IDs=83, overlap=4, truth-only=1, test-only=79
    patient-fusion matrix cells: 76 x 5 = 380
    alternative confirmation IDs=0 (not added to M; used only for adjudicated NPA reference)
  NPA counts: primary neg_agree=373, neg_denom=374, npa_fp=1; adjudicated neg_agree=373, neg_denom=374, npa_fp=1
  Wrote fusion_adjudication_status.tsv (6 main + 93 fp_audit rows; fp original=93, adjudicated FP=93, TP_rescued=0)
  Wrote fusion_adjudication_summary.tsv
  Wrote fusion_adjudication_summary_long.tsv
  Wrote fusion_adjudication_report.txt

Report (fusion_adjudication_report.txt)
=======================================
Fusion adjudication:
# events in primary truth: Fusion = 6
# patient IDs in comparison: 76

Primary-only performance:
Sensitivity/PPA:
     Variant     Filter      Goal       Cur. Perform. [95% CI]
     Fusion      FILTER==PASS 90.0%      83.3%        (0.359, 0.996)

Precision/PPV:
     Variant     Filter      Goal       Cur. Perform. [95% CI]
     Fusion      FILTER==PASS 95.0%      5.1%         (0.017, 0.115)

NPA:
     Variant     Filter      Goal       Cur. Perform. [95% CI]
     Fusion      FILTER==PASS 99.0%      99.7%        (0.985, 1.000)

Adjudicated performance:
Sensitivity/PPA:
     Variant     Filter      Goal       Cur. Perform. [95% CI]
     Fusion      FILTER==PASS 90.0%      83.3%        (0.359, 0.996)

Precision/PPV:
     Variant     Filter      Goal       Cur. Perform. [95% CI]
     Fusion      FILTER==PASS 95.0%      5.1%         (0.017, 0.115)

NPA:
     Variant     Filter      Goal       Cur. Perform. [95% CI]
     Fusion      FILTER==PASS 99.0%      99.7%        (0.985, 1.000)
  Wrote fusion_adjudication_20260606_215950.log