Publish Note 4 summary tables, confusion matrices, and expected benchmark metrics

README.md

@@ -27,6 +27,7 @@ xenofilx/gate-c/{rna-hg38,bs-pdx-graft-hg38,bs-pdx-srr36187610-host}/
 xenofilx/gate-d/bs-pdx-srr36187610/
 xenofilx/mixture/rna-pdx/<cell>/{graft.bam,host.bam,truth.tsv}
 xenofilx/mixture/bs-pdx/<cell>/{graft.hg19.bam,host.mm10.bam,truth.tsv}
+xenofilx/benchmark/tables/{note4-summary-table.csv,note4-confusion-matrix-table.csv,table-s5-gradient.tsv,table-s6-gradient.tsv,table-s7-parameter-grid.tsv}
 ```
 
 Each line in `provenance/files.jsonl` conforms to `provenance/schema.json`. The required `owner` object identifies the repository, workflow, validation gate, and assay. The required `derivation` object records the SRA accession, Paracloud source path, method, seed when applicable, and input/output counts.
@@ -41,6 +42,18 @@ Sources are human RRBS `SRR31480456` and mouse RRBS `SRR10025242`, aligned with
 
 Sources are human RNA-seq `SRR1039508` and mouse RNA-seq `SRR037954`, aligned with STAR; each cell carries 1,000,000 complete fragments (n=3 replicates per non-zero fraction). Every file's SHA-256 matches the value recorded by the evaluation manifests.
 
+## Benchmark tables and confusion matrices (Supplementary Note 4)
+
+`xenofilx/benchmark/tables/` publishes the machine-readable summary tables, confusion matrices, and audit manifests corresponding to Supplementary Tables S5, S6, and S7:
+
+- `note4-summary-table.csv` — Unified 117-row x 24-column cross-assay benchmark summary covering the RNA-seq 0–99% gradient (n=3), BS-seq 0–99% gradient (n=3, three arms), BS-seq 60% parameter grid (n=3, three arms), and authentic PDX accessions (`SRR30880970`, `SRR36187610`).
+- `note4-confusion-matrix-table.csv` — Comprehensive 446-row x 32-column table recording the full 2x2 confusion matrix (TP, FN, FP, TN exact integer counts and derived rates) for every single replicate (329 rows) and stratum mean (117 rows).
+- `table-s5-gradient.tsv` — RNA-seq 0–99% gradient benchmark table (14 non-zero points n=3).
+- `table-s6-gradient.tsv` — BS-seq 0–99% gradient benchmark table with modern, patched legacy, and conventional unpatched paths (all n=3).
+- `table-s7-parameter-grid.tsv` — 4x3 mismatch threshold and unmapped penalty factorial grid across all three paths (n=3).
+- `per-cell-expected-s5.json`, `per-cell-expected-s6.json`, `per-cell-expected-s7.json` — Machine-auditable per-cell reference metric targets used by CI parity gates.
+- `rna-mixture-cells.json` — Immutable fixture contract for all 43 RNA-PDX mixture cells.
+
 ## Validation policy
 
 - All supplied files are checksum-verified before use.

provenance/checksums.sha256

@@ -4,6 +4,15 @@
 4a52edbb89e8dbe40f1224fb13985b3ff891aa3e15f2f5997c0508b59f34975a  fastqcx/rna-pdx-srr30880970/R2.fastq.gz
 964d4d8548c6b92c96c545b988e7b0ec44a68d888c63464089ec4a04cbe4ed81  pairbam/gate-b/rna-pdx-srr30880970/hg38/input.bam
 68493088e6bf2810a66f4570c4209540db3456be504840c1339618eb887ab533  pairbam/gate-b/rna-pdx-srr30880970/hg38/input.bam.bai
+fa1c11af02016d8b7d5a05789b2f13bf952752655976527c001b41196569ee38  xenofilx/benchmark/tables/note4-confusion-matrix-table.csv
+9295986017ed427ddcd9783dc85d105ac2a8637cc5d9d30a808cbf9d3601f040  xenofilx/benchmark/tables/note4-summary-table.csv
+9012b874f500bb4358ae8cc970277a03f06237bd8a7cb229ad41913289c3fa5d  xenofilx/benchmark/tables/per-cell-expected-s5.json
+9a95a2710b3253bd272692bcd67bbc352053c7aeb32426a316beb768706fc68b  xenofilx/benchmark/tables/per-cell-expected-s6.json
+dca1a14f6cb73f8911956d47c29a2fcb092b6cda8a8aa655e9fe1559afd043fb  xenofilx/benchmark/tables/per-cell-expected-s7.json
+086e15ea342de34d53138912eccb7bd4ddb19c30f390f92045a77787cefcfdba  xenofilx/benchmark/tables/rna-mixture-cells.json
+4768efd2321a5f0b0f73b5e5007bd8018010805fefb261a3bbbad071c79b9136  xenofilx/benchmark/tables/table-s5-gradient.tsv
+eb7846d43e1fcef9736e4a87e53b8977284697b342d9a5f8248b6a438b3f96ae  xenofilx/benchmark/tables/table-s6-gradient.tsv
+e74b41a305a17292125c792cc68c8f1b789cddc17c9722dc04d377c5804c9f49  xenofilx/benchmark/tables/table-s7-parameter-grid.tsv
 ecaf4a19359074fafafd20f0baa5f994092d3af36437e538a726febfa4be61e6  xenofilx/gate-c/bs-pdx-graft-hg38/input.bam
 54acd4f37ca193e4295e2ba66eaf9814ede6201598fa0fa198dae0d6da5402d3  xenofilx/gate-c/bs-pdx-graft-hg38/input.bam.bai
 5a4287df6c8be3bb443c1864b70be9a52ded4a55e3158394b9642a9f2dce5c81  xenofilx/gate-c/bs-pdx-srr36187610-host/mm10/input.bam

provenance/files.jsonl

@@ -272,3 +272,12 @@
 {"schema_version": "otter.provenance.file/v1", "dataset_revision": "r7", "dataset_path": "xenofilx/mixture/rna-pdx/human0p99-replicate3/graft.bam", "file_role": "fixture", "file_format": "BAM", "owner": {"repository": "xenofilx", "workflow": "xenofilx-note4-gradient", "gate": "mixture", "assay": "RNA-PDX"}, "derivation": {"sra_accession": "SRR1039508", "paracloud_source_path": "/public3/home/scg9946/otter-gate6/evidence/gate6-human-mouse-rna-mixtures-20260903/staged/human0p99-replicate3/graft.bam", "method": "star_alignment_of_human_mouse_rnaseq_synthetic_mixture_to_hg38", "random_seed": "gate6-human-mouse-rna-v1"}, "counts": {"unit": "records", "input": null, "output": null}, "source_commit": "79581c16f0a4b06e713bdac510e9feda17545e05", "size_bytes": 127176344, "sha256": "0ece14487ee1943eb04ea4da5872959422ac55d7f2d6af33c9c99f2759c95bba", "created_at_utc": "2026-09-21T11:00:00Z", "notes": "Human-graft STAR alignment to hg38 for the RNA-PDX composition gradient cell human0p99-replicate3 (Supplementary Table S5)."}
 {"schema_version": "otter.provenance.file/v1", "dataset_revision": "r7", "dataset_path": "xenofilx/mixture/rna-pdx/human0p99-replicate3/host.bam", "file_role": "fixture", "file_format": "BAM", "owner": {"repository": "xenofilx", "workflow": "xenofilx-note4-gradient", "gate": "mixture", "assay": "RNA-PDX"}, "derivation": {"sra_accession": "SRR037954", "paracloud_source_path": "/public3/home/scg9946/otter-gate6/evidence/gate6-human-mouse-rna-mixtures-20260903/staged/human0p99-replicate3/host.bam", "method": "star_alignment_of_human_mouse_rnaseq_synthetic_mixture_to_mm10", "random_seed": "gate6-human-mouse-rna-v1"}, "counts": {"unit": "records", "input": null, "output": null}, "source_commit": "79581c16f0a4b06e713bdac510e9feda17545e05", "size_bytes": 30052021, "sha256": "7877f10f8e481f65e4593b798582dff3c53fc249c7611cfeff02843a9ffecc14", "created_at_utc": "2026-09-21T11:00:00Z", "notes": "Mouse-host STAR alignment to mm10 for the RNA-PDX composition gradient cell human0p99-replicate3 (Supplementary Table S5)."}
 {"schema_version": "otter.provenance.file/v1", "dataset_revision": "r7", "dataset_path": "xenofilx/mixture/rna-pdx/human0p99-replicate3/truth.tsv", "file_role": "expected_output", "file_format": "TSV", "owner": {"repository": "xenofilx", "workflow": "xenofilx-note4-gradient", "gate": "mixture", "assay": "RNA-PDX"}, "derivation": {"sra_accession": "SRR1039508", "paracloud_source_path": "/public3/home/scg9946/otter-gate6/evidence/gate6-human-mouse-rna-mixtures-20260903/staged/human0p99-replicate3/truth.tsv", "method": "construction_truth_manifest", "random_seed": "gate6-human-mouse-rna-v1"}, "counts": {"unit": "templates", "input": null, "output": 1000000}, "source_commit": "79581c16f0a4b06e713bdac510e9feda17545e05", "size_bytes": 59011146, "sha256": "6eeab3e9843c1bafc53a07de980ae0d532c0ff7e8254034d14abdd0624094029", "created_at_utc": "2026-09-21T11:00:00Z", "notes": "Per-fragment construction truth manifest (fragment_id, known_source) for human0p99-replicate3 (1,000,000 fragments)."}
+{"schema_version": "otter.provenance.file/v1", "dataset_revision": "r8", "dataset_path": "xenofilx/benchmark/tables/note4-summary-table.csv", "file_role": "metric", "file_format": "CSV", "owner": {"repository": "xenofilx", "workflow": "xenofilx-note4-gradient", "gate": "benchmark", "assay": "multi-omics"}, "derivation": {"sra_accession": "SRR1039508+SRR037954+SRR31480456+SRR10025242+SRR30880970+SRR36187610", "paracloud_source_path": "/public3/home/scg9946/otter-gate6/scratch-merge-test/note4-summary-table.csv", "method": "note4_cross_validation_aggregation", "random_seed": null}, "counts": {"unit": "records", "input": null, "output": null}, "source_commit": "79581c16f0a4b06e713bdac510e9feda17545e05", "size_bytes": 37985, "sha256": "9295986017ed427ddcd9783dc85d105ac2a8637cc5d9d30a808cbf9d3601f040", "created_at_utc": "2026-09-21T15:30:00Z", "notes": "Comprehensive multi-omics xenograft deconvolution summary table across RNA and BS gradients (n=3), parameter grid, and authentic PDX accessions."}
+{"schema_version": "otter.provenance.file/v1", "dataset_revision": "r8", "dataset_path": "xenofilx/benchmark/tables/note4-confusion-matrix-table.csv", "file_role": "metric", "file_format": "CSV", "owner": {"repository": "xenofilx", "workflow": "xenofilx-note4-gradient", "gate": "benchmark", "assay": "multi-omics"}, "derivation": {"sra_accession": "SRR1039508+SRR037954+SRR31480456+SRR10025242+SRR30880970+SRR36187610", "paracloud_source_path": "/public3/home/scg9946/otter-gate6/scratch-merge-test/note4-confusion-matrix-table.csv", "method": "note4_cross_validation_aggregation", "random_seed": null}, "counts": {"unit": "records", "input": null, "output": null}, "source_commit": "79581c16f0a4b06e713bdac510e9feda17545e05", "size_bytes": 153978, "sha256": "fa1c11af02016d8b7d5a05789b2f13bf952752655976527c001b41196569ee38", "created_at_utc": "2026-09-21T15:30:00Z", "notes": "Full 2x2 confusion matrix (TP, FN, FP, TN counts and derived rates) for every single replicate and stratum mean across all evaluated pipelines."}
+{"schema_version": "otter.provenance.file/v1", "dataset_revision": "r8", "dataset_path": "xenofilx/benchmark/tables/table-s5-gradient.tsv", "file_role": "metric", "file_format": "TSV", "owner": {"repository": "xenofilx", "workflow": "xenofilx-note4-gradient", "gate": "benchmark", "assay": "multi-omics"}, "derivation": {"sra_accession": "SRR1039508+SRR037954+SRR31480456+SRR10025242+SRR30880970+SRR36187610", "paracloud_source_path": "/public3/home/scg9946/otter-gate6/scratch-merge-test/table-s5-gradient.tsv", "method": "note4_cross_validation_aggregation", "random_seed": null}, "counts": {"unit": "records", "input": null, "output": null}, "source_commit": "79581c16f0a4b06e713bdac510e9feda17545e05", "size_bytes": 760, "sha256": "4768efd2321a5f0b0f73b5e5007bd8018010805fefb261a3bbbad071c79b9136", "created_at_utc": "2026-09-21T15:30:00Z", "notes": "Supplementary Table S5: 0-99% RNA-seq composition gradient benchmark table (all non-zero fractions n=3)."}
+{"schema_version": "otter.provenance.file/v1", "dataset_revision": "r8", "dataset_path": "xenofilx/benchmark/tables/table-s6-gradient.tsv", "file_role": "metric", "file_format": "TSV", "owner": {"repository": "xenofilx", "workflow": "xenofilx-note4-gradient", "gate": "benchmark", "assay": "multi-omics"}, "derivation": {"sra_accession": "SRR1039508+SRR037954+SRR31480456+SRR10025242+SRR30880970+SRR36187610", "paracloud_source_path": "/public3/home/scg9946/otter-gate6/scratch-merge-test/table-s6-gradient.tsv", "method": "note4_cross_validation_aggregation", "random_seed": null}, "counts": {"unit": "records", "input": null, "output": null}, "source_commit": "79581c16f0a4b06e713bdac510e9feda17545e05", "size_bytes": 1272, "sha256": "eb7846d43e1fcef9736e4a87e53b8977284697b342d9a5f8248b6a438b3f96ae", "created_at_utc": "2026-09-21T15:30:00Z", "notes": "Supplementary Table S6: 0-99% BS-seq composition gradient benchmark table with all three tool paths (n=3)."}
+{"schema_version": "otter.provenance.file/v1", "dataset_revision": "r8", "dataset_path": "xenofilx/benchmark/tables/table-s7-parameter-grid.tsv", "file_role": "metric", "file_format": "TSV", "owner": {"repository": "xenofilx", "workflow": "xenofilx-note4-gradient", "gate": "benchmark", "assay": "multi-omics"}, "derivation": {"sra_accession": "SRR1039508+SRR037954+SRR31480456+SRR10025242+SRR30880970+SRR36187610", "paracloud_source_path": "/public3/home/scg9946/otter-gate6/scratch-merge-test/table-s7-parameter-grid.tsv", "method": "note4_cross_validation_aggregation", "random_seed": null}, "counts": {"unit": "records", "input": null, "output": null}, "source_commit": "79581c16f0a4b06e713bdac510e9feda17545e05", "size_bytes": 1337, "sha256": "e74b41a305a17292125c792cc68c8f1b789cddc17c9722dc04d377c5804c9f49", "created_at_utc": "2026-09-21T15:30:00Z", "notes": "Supplementary Table S7: 4x3 mismatch threshold and unmapped penalty factorial sensitivity grid with all three tool paths (n=3)."}
+{"schema_version": "otter.provenance.file/v1", "dataset_revision": "r8", "dataset_path": "xenofilx/benchmark/tables/rna-mixture-cells.json", "file_role": "reference_contract", "file_format": "JSON", "owner": {"repository": "xenofilx", "workflow": "xenofilx-note4-gradient", "gate": "benchmark", "assay": "multi-omics"}, "derivation": {"sra_accession": "SRR1039508+SRR037954+SRR31480456+SRR10025242+SRR30880970+SRR36187610", "paracloud_source_path": "/public3/home/scg9946/otter-gate6/scratch-merge-test/rna-mixture-cells.json", "method": "note4_cross_validation_aggregation", "random_seed": null}, "counts": {"unit": "records", "input": null, "output": null}, "source_commit": "79581c16f0a4b06e713bdac510e9feda17545e05", "size_bytes": 23911, "sha256": "086e15ea342de34d53138912eccb7bd4ddb19c30f390f92045a77787cefcfdba", "created_at_utc": "2026-09-21T15:30:00Z", "notes": "Supplementary Table S5 fixture contract pinning SHA-256 and byte sizes for all 43 RNA-PDX gradient cells."}
+{"schema_version": "otter.provenance.file/v1", "dataset_revision": "r8", "dataset_path": "xenofilx/benchmark/tables/per-cell-expected-s5.json", "file_role": "expected_output", "file_format": "JSON", "owner": {"repository": "xenofilx", "workflow": "xenofilx-note4-gradient", "gate": "benchmark", "assay": "multi-omics"}, "derivation": {"sra_accession": "SRR1039508+SRR037954+SRR31480456+SRR10025242+SRR30880970+SRR36187610", "paracloud_source_path": "/public3/home/scg9946/otter-gate6/scratch-merge-test/per-cell-expected-s5.json", "method": "note4_cross_validation_aggregation", "random_seed": null}, "counts": {"unit": "records", "input": null, "output": null}, "source_commit": "79581c16f0a4b06e713bdac510e9feda17545e05", "size_bytes": 9180, "sha256": "9012b874f500bb4358ae8cc970277a03f06237bd8a7cb229ad41913289c3fa5d", "created_at_utc": "2026-09-21T15:30:00Z", "notes": "Per-cell expected metric values for all 43 RNA gradient cells (n=3)."}
+{"schema_version": "otter.provenance.file/v1", "dataset_revision": "r8", "dataset_path": "xenofilx/benchmark/tables/per-cell-expected-s6.json", "file_role": "expected_output", "file_format": "JSON", "owner": {"repository": "xenofilx", "workflow": "xenofilx-note4-gradient", "gate": "benchmark", "assay": "multi-omics"}, "derivation": {"sra_accession": "SRR1039508+SRR037954+SRR31480456+SRR10025242+SRR30880970+SRR36187610", "paracloud_source_path": "/public3/home/scg9946/otter-gate6/scratch-merge-test/per-cell-expected-s6.json", "method": "note4_cross_validation_aggregation", "random_seed": null}, "counts": {"unit": "records", "input": null, "output": null}, "source_commit": "79581c16f0a4b06e713bdac510e9feda17545e05", "size_bytes": 13795, "sha256": "9a95a2710b3253bd272692bcd67bbc352053c7aeb32426a316beb768706fc68b", "created_at_utc": "2026-09-21T15:30:00Z", "notes": "Per-cell expected metric values for all 43 BS-seq gradient cells across three arms (n=3)."}
+{"schema_version": "otter.provenance.file/v1", "dataset_revision": "r8", "dataset_path": "xenofilx/benchmark/tables/per-cell-expected-s7.json", "file_role": "expected_output", "file_format": "JSON", "owner": {"repository": "xenofilx", "workflow": "xenofilx-note4-gradient", "gate": "benchmark", "assay": "multi-omics"}, "derivation": {"sra_accession": "SRR1039508+SRR037954+SRR31480456+SRR10025242+SRR30880970+SRR36187610", "paracloud_source_path": "/public3/home/scg9946/otter-gate6/scratch-merge-test/per-cell-expected-s7.json", "method": "note4_cross_validation_aggregation", "random_seed": null}, "counts": {"unit": "records", "input": null, "output": null}, "source_commit": "79581c16f0a4b06e713bdac510e9feda17545e05", "size_bytes": 11787, "sha256": "dca1a14f6cb73f8911956d47c29a2fcb092b6cda8a8aa655e9fe1559afd043fb", "created_at_utc": "2026-09-21T15:30:00Z", "notes": "Per-cell expected metric values for all 36 BS-seq 60% parameter grid cells across three arms (n=3)."}

xenofilx/benchmark/tables/note4-summary-table.csv

@@ -0,0 +1,118 @@
+assay,dataset,dataset_kind,metric_family,stratum_type,stratum_value,n_replicates,arm,arm_status,arm_pipeline,parameter_contract,recall_pct,specificity_pct,ppv_pct,f1_pct,filtered_fragments,input_fragments,modern_graft_fragments,legacy_graft_fragments,agreements,disagreements,modern_only_graft,legacy_only_graft,note
+RNA-seq,RNA gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,0%,1,modern_xenofilx,reported,"xenofilx, native strand-aware NM recalculation (bamdriver)",mm_threshold=4 unmapped_penalty=8 conventional_nm,,99.3968,,,,,,,,,,,pure-mouse control; no positive-class denominator
+RNA-seq,RNA gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,0%,1,legacy_xenofilter,reported,Picard SetNmMdAndUqTags (no bisulfite flag; not applicable to RNA) + R XenofilteR,mm_threshold=4 unmapped_penalty=8 conventional_nm,,99.3968,,,,,,,,,,,pure-mouse control; no positive-class denominator
+RNA-seq,RNA gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,0.1%,3,modern_xenofilx,reported,"xenofilx, native strand-aware NM recalculation (bamdriver)",mm_threshold=4 unmapped_penalty=8 conventional_nm,96.1667,99.3981,13.7896,,,,,,,,,,
+RNA-seq,RNA gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,0.1%,3,legacy_xenofilter,reported,Picard SetNmMdAndUqTags (no bisulfite flag; not applicable to RNA) + R XenofilteR,mm_threshold=4 unmapped_penalty=8 conventional_nm,96.1667,99.3981,13.7896,,,,,,,,,,"RNA has no bisulfite flag, so this is the conventional Picard path (decision-identical to modern)"
+RNA-seq,RNA gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,0.5%,3,modern_xenofilx,reported,"xenofilx, native strand-aware NM recalculation (bamdriver)",mm_threshold=4 unmapped_penalty=8 conventional_nm,96.5800,99.3980,44.6342,,,,,,,,,,
+RNA-seq,RNA gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,0.5%,3,legacy_xenofilter,reported,Picard SetNmMdAndUqTags (no bisulfite flag; not applicable to RNA) + R XenofilteR,mm_threshold=4 unmapped_penalty=8 conventional_nm,96.5800,99.3980,44.6342,,,,,,,,,,"RNA has no bisulfite flag, so this is the conventional Picard path (decision-identical to modern)"
+RNA-seq,RNA gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,1%,3,modern_xenofilx,reported,"xenofilx, native strand-aware NM recalculation (bamdriver)",mm_threshold=4 unmapped_penalty=8 conventional_nm,96.5867,99.3977,61.8321,,,,,,,,,,
+RNA-seq,RNA gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,1%,3,legacy_xenofilter,reported,Picard SetNmMdAndUqTags (no bisulfite flag; not applicable to RNA) + R XenofilteR,mm_threshold=4 unmapped_penalty=8 conventional_nm,96.5867,99.3977,61.8321,,,,,,,,,,"RNA has no bisulfite flag, so this is the conventional Picard path (decision-identical to modern)"
+RNA-seq,RNA gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,2%,3,modern_xenofilx,reported,"xenofilx, native strand-aware NM recalculation (bamdriver)",mm_threshold=4 unmapped_penalty=8 conventional_nm,96.6650,99.3967,76.5808,,,,,,,,,,
+RNA-seq,RNA gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,2%,3,legacy_xenofilter,reported,Picard SetNmMdAndUqTags (no bisulfite flag; not applicable to RNA) + R XenofilteR,mm_threshold=4 unmapped_penalty=8 conventional_nm,96.6650,99.3967,76.5808,,,,,,,,,,"RNA has no bisulfite flag, so this is the conventional Picard path (decision-identical to modern)"
+RNA-seq,RNA gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,5%,3,modern_xenofilx,reported,"xenofilx, native strand-aware NM recalculation (bamdriver)",mm_threshold=4 unmapped_penalty=8 conventional_nm,96.6300,99.3953,89.3742,,,,,,,,,,
+RNA-seq,RNA gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,5%,3,legacy_xenofilter,reported,Picard SetNmMdAndUqTags (no bisulfite flag; not applicable to RNA) + R XenofilteR,mm_threshold=4 unmapped_penalty=8 conventional_nm,96.6300,99.3953,89.3742,,,,,,,,,,"RNA has no bisulfite flag, so this is the conventional Picard path (decision-identical to modern)"
+RNA-seq,RNA gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,10%,3,modern_xenofilx,reported,"xenofilx, native strand-aware NM recalculation (bamdriver)",mm_threshold=4 unmapped_penalty=8 conventional_nm,96.5883,99.3956,94.6688,,,,,,,,,,
+RNA-seq,RNA gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,10%,3,legacy_xenofilter,reported,Picard SetNmMdAndUqTags (no bisulfite flag; not applicable to RNA) + R XenofilteR,mm_threshold=4 unmapped_penalty=8 conventional_nm,96.5883,99.3956,94.6688,,,,,,,,,,"RNA has no bisulfite flag, so this is the conventional Picard path (decision-identical to modern)"
+RNA-seq,RNA gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,25%,3,modern_xenofilx,reported,"xenofilx, native strand-aware NM recalculation (bamdriver)",mm_threshold=4 unmapped_penalty=8 conventional_nm,96.5844,99.3920,98.1466,,,,,,,,,,
+RNA-seq,RNA gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,25%,3,legacy_xenofilter,reported,Picard SetNmMdAndUqTags (no bisulfite flag; not applicable to RNA) + R XenofilteR,mm_threshold=4 unmapped_penalty=8 conventional_nm,96.5844,99.3920,98.1466,,,,,,,,,,"RNA has no bisulfite flag, so this is the conventional Picard path (decision-identical to modern)"
+RNA-seq,RNA gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,50%,3,modern_xenofilx,reported,"xenofilx, native strand-aware NM recalculation (bamdriver)",mm_threshold=4 unmapped_penalty=8 conventional_nm,96.5631,99.3885,99.3708,,,,,,,,,,
+RNA-seq,RNA gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,50%,3,legacy_xenofilter,reported,Picard SetNmMdAndUqTags (no bisulfite flag; not applicable to RNA) + R XenofilteR,mm_threshold=4 unmapped_penalty=8 conventional_nm,96.5631,99.3885,99.3708,,,,,,,,,,"RNA has no bisulfite flag, so this is the conventional Picard path (decision-identical to modern)"
+RNA-seq,RNA gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,60%,3,modern_xenofilx,reported,"xenofilx, native strand-aware NM recalculation (bamdriver)",mm_threshold=4 unmapped_penalty=8 conventional_nm,96.5645,99.3863,99.5781,,,,,,,,,,
+RNA-seq,RNA gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,60%,3,legacy_xenofilter,reported,Picard SetNmMdAndUqTags (no bisulfite flag; not applicable to RNA) + R XenofilteR,mm_threshold=4 unmapped_penalty=8 conventional_nm,96.5645,99.3863,99.5781,,,,,,,,,,"RNA has no bisulfite flag, so this is the conventional Picard path (decision-identical to modern)"
+RNA-seq,RNA gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,70%,3,modern_xenofilx,reported,"xenofilx, native strand-aware NM recalculation (bamdriver)",mm_threshold=4 unmapped_penalty=8 conventional_nm,96.5687,99.3886,99.7294,,,,,,,,,,
+RNA-seq,RNA gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,70%,3,legacy_xenofilter,reported,Picard SetNmMdAndUqTags (no bisulfite flag; not applicable to RNA) + R XenofilteR,mm_threshold=4 unmapped_penalty=8 conventional_nm,96.5687,99.3886,99.7294,,,,,,,,,,"RNA has no bisulfite flag, so this is the conventional Picard path (decision-identical to modern)"
+RNA-seq,RNA gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,80%,3,modern_xenofilx,reported,"xenofilx, native strand-aware NM recalculation (bamdriver)",mm_threshold=4 unmapped_penalty=8 conventional_nm,96.5712,99.3752,99.8385,,,,,,,,,,
+RNA-seq,RNA gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,80%,3,legacy_xenofilter,reported,Picard SetNmMdAndUqTags (no bisulfite flag; not applicable to RNA) + R XenofilteR,mm_threshold=4 unmapped_penalty=8 conventional_nm,96.5712,99.3752,99.8385,,,,,,,,,,"RNA has no bisulfite flag, so this is the conventional Picard path (decision-identical to modern)"
+RNA-seq,RNA gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,90%,3,modern_xenofilx,reported,"xenofilx, native strand-aware NM recalculation (bamdriver)",mm_threshold=4 unmapped_penalty=8 conventional_nm,96.5636,99.3680,99.9273,,,,,,,,,,
+RNA-seq,RNA gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,90%,3,legacy_xenofilter,reported,Picard SetNmMdAndUqTags (no bisulfite flag; not applicable to RNA) + R XenofilteR,mm_threshold=4 unmapped_penalty=8 conventional_nm,96.5636,99.3680,99.9273,,,,,,,,,,"RNA has no bisulfite flag, so this is the conventional Picard path (decision-identical to modern)"
+RNA-seq,RNA gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,95%,3,modern_xenofilx,reported,"xenofilx, native strand-aware NM recalculation (bamdriver)",mm_threshold=4 unmapped_penalty=8 conventional_nm,96.5609,99.3680,99.9656,,,,,,,,,,
+RNA-seq,RNA gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,95%,3,legacy_xenofilter,reported,Picard SetNmMdAndUqTags (no bisulfite flag; not applicable to RNA) + R XenofilteR,mm_threshold=4 unmapped_penalty=8 conventional_nm,96.5609,99.3680,99.9656,,,,,,,,,,"RNA has no bisulfite flag, so this is the conventional Picard path (decision-identical to modern)"
+RNA-seq,RNA gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,99%,3,modern_xenofilx,reported,"xenofilx, native strand-aware NM recalculation (bamdriver)",mm_threshold=4 unmapped_penalty=8 conventional_nm,96.5654,99.3600,99.9933,,,,,,,,,,
+RNA-seq,RNA gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,99%,3,legacy_xenofilter,reported,Picard SetNmMdAndUqTags (no bisulfite flag; not applicable to RNA) + R XenofilteR,mm_threshold=4 unmapped_penalty=8 conventional_nm,96.5654,99.3600,99.9933,,,,,,,,,,"RNA has no bisulfite flag, so this is the conventional Picard path (decision-identical to modern)"
+bisulfite-seq,BS gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,0%,1,modern_xenofilx,reported,"xenofilx, native strand-aware NM recalculation (bamdriver)",mm_threshold=6 unmapped_penalty=8 strand_aware_bisulfite_nm,,99.9182,,,,,,,,,,,pure-mouse control; no positive-class denominator
+bisulfite-seq,BS gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,0%,1,legacy_picard_xenofilter,reported,Picard SetNmMdAndUqTags IS_BISULFITE_SEQUENCE=true + R XenofilteR,mm_threshold=6 unmapped_penalty=8 strand_aware_bisulfite_nm,,99.9188,,,,,,,,,,,pure-mouse control; no positive-class denominator
+bisulfite-seq,BS gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,0%,1,conventional_picard_xenofilter,reported,Picard SetNmMdAndUqTags without IS_BISULFITE_SEQUENCE + R XenofilteR,mm_threshold=6 unmapped_penalty=8 strand_aware_bisulfite_nm,,99.9279,,,,,,,,,,,pure-mouse control; no positive-class denominator
+bisulfite-seq,BS gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,0.1%,3,modern_xenofilx,reported,"xenofilx, native strand-aware NM recalculation (bamdriver)",mm_threshold=6 unmapped_penalty=8 strand_aware_bisulfite_nm,54.0333,99.9215,40.8200,,,,,,,,,,
+bisulfite-seq,BS gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,0.1%,3,legacy_picard_xenofilter,reported,Picard SetNmMdAndUqTags IS_BISULFITE_SEQUENCE=true + R XenofilteR,mm_threshold=6 unmapped_penalty=8 strand_aware_bisulfite_nm,53.3333,99.9219,40.6281,,,,,,,,,,
+bisulfite-seq,BS gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,0.1%,3,conventional_picard_xenofilter,reported,Picard SetNmMdAndUqTags without IS_BISULFITE_SEQUENCE + R XenofilteR,mm_threshold=6 unmapped_penalty=8 strand_aware_bisulfite_nm,0.0000,99.9292,0.0000,,,,,,,,,,unpatched baseline; sensitivity collapse is the load-bearing contrast
+bisulfite-seq,BS gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,0.5%,3,modern_xenofilx,reported,"xenofilx, native strand-aware NM recalculation (bamdriver)",mm_threshold=6 unmapped_penalty=8 strand_aware_bisulfite_nm,52.9200,99.9216,77.2219,,,,,,,,,,
+bisulfite-seq,BS gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,0.5%,3,legacy_picard_xenofilter,reported,Picard SetNmMdAndUqTags IS_BISULFITE_SEQUENCE=true + R XenofilteR,mm_threshold=6 unmapped_penalty=8 strand_aware_bisulfite_nm,52.2933,99.9219,77.0967,,,,,,,,,,
+bisulfite-seq,BS gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,0.5%,3,conventional_picard_xenofilter,reported,Picard SetNmMdAndUqTags without IS_BISULFITE_SEQUENCE + R XenofilteR,mm_threshold=6 unmapped_penalty=8 strand_aware_bisulfite_nm,0.0133,99.9292,0.0883,,,,,,,,,,unpatched baseline; sensitivity collapse is the load-bearing contrast
+bisulfite-seq,BS gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,1%,3,modern_xenofilx,reported,"xenofilx, native strand-aware NM recalculation (bamdriver)",mm_threshold=6 unmapped_penalty=8 strand_aware_bisulfite_nm,51.6067,99.9201,86.7137,,,,,,,,,,
+bisulfite-seq,BS gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,1%,3,legacy_picard_xenofilter,reported,Picard SetNmMdAndUqTags IS_BISULFITE_SEQUENCE=true + R XenofilteR,mm_threshold=6 unmapped_penalty=8 strand_aware_bisulfite_nm,50.9067,99.9206,86.6245,,,,,,,,,,
+bisulfite-seq,BS gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,1%,3,conventional_picard_xenofilter,reported,Picard SetNmMdAndUqTags without IS_BISULFITE_SEQUENCE + R XenofilteR,mm_threshold=6 unmapped_penalty=8 strand_aware_bisulfite_nm,0.0100,99.9287,0.1443,,,,,,,,,,unpatched baseline; sensitivity collapse is the load-bearing contrast
+bisulfite-seq,BS gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,2%,3,modern_xenofilx,reported,"xenofilx, native strand-aware NM recalculation (bamdriver)",mm_threshold=6 unmapped_penalty=8 strand_aware_bisulfite_nm,52.2317,99.9218,93.1659,,,,,,,,,,
+bisulfite-seq,BS gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,2%,3,legacy_picard_xenofilter,reported,Picard SetNmMdAndUqTags IS_BISULFITE_SEQUENCE=true + R XenofilteR,mm_threshold=6 unmapped_penalty=8 strand_aware_bisulfite_nm,51.5383,99.9221,93.1087,,,,,,,,,,
+bisulfite-seq,BS gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,2%,3,conventional_picard_xenofilter,reported,Picard SetNmMdAndUqTags without IS_BISULFITE_SEQUENCE + R XenofilteR,mm_threshold=6 unmapped_penalty=8 strand_aware_bisulfite_nm,0.0050,99.9293,0.1395,,,,,,,,,,unpatched baseline; sensitivity collapse is the load-bearing contrast
+bisulfite-seq,BS gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,5%,3,modern_xenofilx,reported,"xenofilx, native strand-aware NM recalculation (bamdriver)",mm_threshold=6 unmapped_penalty=8 strand_aware_bisulfite_nm,52.0120,99.9200,97.1594,,,,,,,,,,
+bisulfite-seq,BS gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,5%,3,legacy_picard_xenofilter,reported,Picard SetNmMdAndUqTags IS_BISULFITE_SEQUENCE=true + R XenofilteR,mm_threshold=6 unmapped_penalty=8 strand_aware_bisulfite_nm,51.3520,99.9205,97.1411,,,,,,,,,,
+bisulfite-seq,BS gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,5%,3,conventional_picard_xenofilter,reported,Picard SetNmMdAndUqTags without IS_BISULFITE_SEQUENCE + R XenofilteR,mm_threshold=6 unmapped_penalty=8 strand_aware_bisulfite_nm,0.0053,99.9285,0.4015,,,,,,,,,,unpatched baseline; sensitivity collapse is the load-bearing contrast
+bisulfite-seq,BS gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,10%,3,modern_xenofilx,reported,"xenofilx, native strand-aware NM recalculation (bamdriver)",mm_threshold=6 unmapped_penalty=8 strand_aware_bisulfite_nm,51.9807,99.9202,98.6376,,,,,,,,,,
+bisulfite-seq,BS gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,10%,3,legacy_picard_xenofilter,reported,Picard SetNmMdAndUqTags IS_BISULFITE_SEQUENCE=true + R XenofilteR,mm_threshold=6 unmapped_penalty=8 strand_aware_bisulfite_nm,51.3210,99.9207,98.6291,,,,,,,,,,
+bisulfite-seq,BS gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,10%,3,conventional_picard_xenofilter,reported,Picard SetNmMdAndUqTags without IS_BISULFITE_SEQUENCE + R XenofilteR,mm_threshold=6 unmapped_penalty=8 strand_aware_bisulfite_nm,0.0070,99.9287,1.0858,,,,,,,,,,unpatched baseline; sensitivity collapse is the load-bearing contrast
+bisulfite-seq,BS gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,25%,3,modern_xenofilx,reported,"xenofilx, native strand-aware NM recalculation (bamdriver)",mm_threshold=6 unmapped_penalty=8 strand_aware_bisulfite_nm,52.0021,99.9199,99.5399,,,,,,,,,,
+bisulfite-seq,BS gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,25%,3,legacy_picard_xenofilter,reported,Picard SetNmMdAndUqTags IS_BISULFITE_SEQUENCE=true + R XenofilteR,mm_threshold=6 unmapped_penalty=8 strand_aware_bisulfite_nm,51.3475,99.9202,99.5361,,,,,,,,,,
+bisulfite-seq,BS gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,25%,3,conventional_picard_xenofilter,reported,Picard SetNmMdAndUqTags without IS_BISULFITE_SEQUENCE + R XenofilteR,mm_threshold=6 unmapped_penalty=8 strand_aware_bisulfite_nm,0.0080,99.9276,3.5592,,,,,,,,,,unpatched baseline; sensitivity collapse is the load-bearing contrast
+bisulfite-seq,BS gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,50%,3,modern_xenofilx,reported,"xenofilx, native strand-aware NM recalculation (bamdriver)",mm_threshold=6 unmapped_penalty=8 strand_aware_bisulfite_nm,52.0909,99.9197,99.8460,,,,,,,,,,
+bisulfite-seq,BS gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,50%,3,legacy_picard_xenofilter,reported,Picard SetNmMdAndUqTags IS_BISULFITE_SEQUENCE=true + R XenofilteR,mm_threshold=6 unmapped_penalty=8 strand_aware_bisulfite_nm,51.4305,99.9201,99.8450,,,,,,,,,,
+bisulfite-seq,BS gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,50%,3,conventional_picard_xenofilter,reported,Picard SetNmMdAndUqTags without IS_BISULFITE_SEQUENCE + R XenofilteR,mm_threshold=6 unmapped_penalty=8 strand_aware_bisulfite_nm,0.0066,99.9275,8.3327,,,,,,,,,,unpatched baseline; sensitivity collapse is the load-bearing contrast
+bisulfite-seq,BS gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,60%,3,modern_xenofilx,reported,"xenofilx, native strand-aware NM recalculation (bamdriver)",mm_threshold=6 unmapped_penalty=8 strand_aware_bisulfite_nm,52.0024,99.9179,99.8949,,,,,,,,,,
+bisulfite-seq,BS gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,60%,3,legacy_picard_xenofilter,reported,Picard SetNmMdAndUqTags IS_BISULFITE_SEQUENCE=true + R XenofilteR,mm_threshold=6 unmapped_penalty=8 strand_aware_bisulfite_nm,51.3501,99.9184,99.8942,,,,,,,,,,
+bisulfite-seq,BS gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,60%,3,conventional_picard_xenofilter,reported,Picard SetNmMdAndUqTags without IS_BISULFITE_SEQUENCE + R XenofilteR,mm_threshold=6 unmapped_penalty=8 strand_aware_bisulfite_nm,0.0068,99.9256,11.9381,,,,,,,,,,unpatched baseline; sensitivity collapse is the load-bearing contrast
+bisulfite-seq,BS gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,70%,3,modern_xenofilx,reported,"xenofilx, native strand-aware NM recalculation (bamdriver)",mm_threshold=6 unmapped_penalty=8 strand_aware_bisulfite_nm,52.0225,99.9188,99.9331,,,,,,,,,,
+bisulfite-seq,BS gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,70%,3,legacy_picard_xenofilter,reported,Picard SetNmMdAndUqTags IS_BISULFITE_SEQUENCE=true + R XenofilteR,mm_threshold=6 unmapped_penalty=8 strand_aware_bisulfite_nm,51.3680,99.9191,99.9326,,,,,,,,,,
+bisulfite-seq,BS gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,70%,3,conventional_picard_xenofilter,reported,Picard SetNmMdAndUqTags without IS_BISULFITE_SEQUENCE + R XenofilteR,mm_threshold=6 unmapped_penalty=8 strand_aware_bisulfite_nm,0.0069,99.9267,17.9501,,,,,,,,,,unpatched baseline; sensitivity collapse is the load-bearing contrast
+bisulfite-seq,BS gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,80%,3,modern_xenofilx,reported,"xenofilx, native strand-aware NM recalculation (bamdriver)",mm_threshold=6 unmapped_penalty=8 strand_aware_bisulfite_nm,52.0097,99.9153,99.9593,,,,,,,,,,
+bisulfite-seq,BS gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,80%,3,legacy_picard_xenofilter,reported,Picard SetNmMdAndUqTags IS_BISULFITE_SEQUENCE=true + R XenofilteR,mm_threshold=6 unmapped_penalty=8 strand_aware_bisulfite_nm,51.3543,99.9157,99.9590,,,,,,,,,,
+bisulfite-seq,BS gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,80%,3,conventional_picard_xenofilter,reported,Picard SetNmMdAndUqTags without IS_BISULFITE_SEQUENCE + R XenofilteR,mm_threshold=6 unmapped_penalty=8 strand_aware_bisulfite_nm,0.0070,99.9235,26.5814,,,,,,,,,,unpatched baseline; sensitivity collapse is the load-bearing contrast
+bisulfite-seq,BS gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,90%,3,modern_xenofilx,reported,"xenofilx, native strand-aware NM recalculation (bamdriver)",mm_threshold=6 unmapped_penalty=8 strand_aware_bisulfite_nm,52.0161,99.9200,99.9829,,,,,,,,,,
+bisulfite-seq,BS gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,90%,3,legacy_picard_xenofilter,reported,Picard SetNmMdAndUqTags IS_BISULFITE_SEQUENCE=true + R XenofilteR,mm_threshold=6 unmapped_penalty=8 strand_aware_bisulfite_nm,51.3586,99.9203,99.9828,,,,,,,,,,
+bisulfite-seq,BS gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,90%,3,conventional_picard_xenofilter,reported,Picard SetNmMdAndUqTags without IS_BISULFITE_SEQUENCE + R XenofilteR,mm_threshold=6 unmapped_penalty=8 strand_aware_bisulfite_nm,0.0070,99.9287,46.7696,,,,,,,,,,unpatched baseline; sensitivity collapse is the load-bearing contrast
+bisulfite-seq,BS gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,95%,3,modern_xenofilx,reported,"xenofilx, native strand-aware NM recalculation (bamdriver)",mm_threshold=6 unmapped_penalty=8 strand_aware_bisulfite_nm,52.0212,99.9220,99.9921,,,,,,,,,,
+bisulfite-seq,BS gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,95%,3,legacy_picard_xenofilter,reported,Picard SetNmMdAndUqTags IS_BISULFITE_SEQUENCE=true + R XenofilteR,mm_threshold=6 unmapped_penalty=8 strand_aware_bisulfite_nm,51.3645,99.9227,99.9921,,,,,,,,,,
+bisulfite-seq,BS gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,95%,3,conventional_picard_xenofilter,reported,Picard SetNmMdAndUqTags without IS_BISULFITE_SEQUENCE + R XenofilteR,mm_threshold=6 unmapped_penalty=8 strand_aware_bisulfite_nm,0.0071,99.9293,65.7875,,,,,,,,,,unpatched baseline; sensitivity collapse is the load-bearing contrast
+bisulfite-seq,BS gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,99%,3,modern_xenofilx,reported,"xenofilx, native strand-aware NM recalculation (bamdriver)",mm_threshold=6 unmapped_penalty=8 strand_aware_bisulfite_nm,52.0165,99.8933,99.9979,,,,,,,,,,
+bisulfite-seq,BS gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,99%,3,legacy_picard_xenofilter,reported,Picard SetNmMdAndUqTags IS_BISULFITE_SEQUENCE=true + R XenofilteR,mm_threshold=6 unmapped_penalty=8 strand_aware_bisulfite_nm,51.3599,99.8967,99.9980,,,,,,,,,,
+bisulfite-seq,BS gradient 0-99%,synthetic_gradient,classification_metrics,human_fraction,99%,3,conventional_picard_xenofilter,reported,Picard SetNmMdAndUqTags without IS_BISULFITE_SEQUENCE + R XenofilteR,mm_threshold=6 unmapped_penalty=8 strand_aware_bisulfite_nm,0.0069,99.9067,87.9740,,,,,,,,,,unpatched baseline; sensitivity collapse is the load-bearing contrast
+bisulfite-seq,BS 60% parameter grid,synthetic_grid,classification_metrics,threshold_penalty,t5_p8,3,modern_xenofilx,reported,"xenofilx, native strand-aware NM recalculation (bamdriver)",mm_threshold=5 unmapped_penalty=8 strand_aware_bisulfite_nm,51.6177,99.9181,,68.0647,"310,034",,,,,,,,
+bisulfite-seq,BS 60% parameter grid,synthetic_grid,classification_metrics,threshold_penalty,t5_p8,3,legacy_picard_xenofilter,reported,Picard SetNmMdAndUqTags IS_BISULFITE_SEQUENCE=true + R XenofilteR,mm_threshold=5 unmapped_penalty=8 strand_aware_bisulfite_nm,50.5244,99.9185,,67.1069,"303,472",,,,,,,,
+bisulfite-seq,BS 60% parameter grid,synthetic_grid,classification_metrics,threshold_penalty,t5_p8,3,conventional_picard_xenofilter,reported,Picard SetNmMdAndUqTags without IS_BISULFITE_SEQUENCE + R XenofilteR,mm_threshold=5 unmapped_penalty=8 strand_aware_bisulfite_nm,0.0046,99.9258,,0.0092,325,,,,,,,,unpatched; recall stays near zero at every audited threshold
+bisulfite-seq,BS 60% parameter grid,synthetic_grid,classification_metrics,threshold_penalty,t5_p10,3,modern_xenofilx,reported,"xenofilx, native strand-aware NM recalculation (bamdriver)",mm_threshold=5 unmapped_penalty=10 strand_aware_bisulfite_nm,51.6177,99.9181,,68.0647,"310,034",,,,,,,,
+bisulfite-seq,BS 60% parameter grid,synthetic_grid,classification_metrics,threshold_penalty,t5_p10,3,legacy_picard_xenofilter,reported,Picard SetNmMdAndUqTags IS_BISULFITE_SEQUENCE=true + R XenofilteR,mm_threshold=5 unmapped_penalty=10 strand_aware_bisulfite_nm,50.5244,99.9185,,67.1069,"303,472",,,,,,,,
+bisulfite-seq,BS 60% parameter grid,synthetic_grid,classification_metrics,threshold_penalty,t5_p10,3,conventional_picard_xenofilter,reported,Picard SetNmMdAndUqTags without IS_BISULFITE_SEQUENCE + R XenofilteR,mm_threshold=5 unmapped_penalty=10 strand_aware_bisulfite_nm,0.0046,99.9258,,0.0092,325,,,,,,,,unpatched; recall stays near zero at every audited threshold
+bisulfite-seq,BS 60% parameter grid,synthetic_grid,classification_metrics,threshold_penalty,t5_p12,3,modern_xenofilx,reported,"xenofilx, native strand-aware NM recalculation (bamdriver)",mm_threshold=5 unmapped_penalty=12 strand_aware_bisulfite_nm,51.6177,99.9181,,68.0647,"310,034",,,,,,,,
+bisulfite-seq,BS 60% parameter grid,synthetic_grid,classification_metrics,threshold_penalty,t5_p12,3,legacy_picard_xenofilter,reported,Picard SetNmMdAndUqTags IS_BISULFITE_SEQUENCE=true + R XenofilteR,mm_threshold=5 unmapped_penalty=12 strand_aware_bisulfite_nm,50.5244,99.9185,,67.1069,"303,472",,,,,,,,
+bisulfite-seq,BS 60% parameter grid,synthetic_grid,classification_metrics,threshold_penalty,t5_p12,3,conventional_picard_xenofilter,reported,Picard SetNmMdAndUqTags without IS_BISULFITE_SEQUENCE + R XenofilteR,mm_threshold=5 unmapped_penalty=12 strand_aware_bisulfite_nm,0.0046,99.9258,,0.0092,325,,,,,,,,unpatched; recall stays near zero at every audited threshold
+bisulfite-seq,BS 60% parameter grid,synthetic_grid,classification_metrics,threshold_penalty,t6_p8,3,modern_xenofilx,reported,"xenofilx, native strand-aware NM recalculation (bamdriver)",mm_threshold=6 unmapped_penalty=8 strand_aware_bisulfite_nm,52.0024,99.9179,,68.3985,"312,343",,,,,,,,
+bisulfite-seq,BS 60% parameter grid,synthetic_grid,classification_metrics,threshold_penalty,t6_p8,3,legacy_picard_xenofilter,reported,Picard SetNmMdAndUqTags IS_BISULFITE_SEQUENCE=true + R XenofilteR,mm_threshold=6 unmapped_penalty=8 strand_aware_bisulfite_nm,51.3501,99.9184,,67.8316,"308,427",,,,,,,,prespecified production baseline
+bisulfite-seq,BS 60% parameter grid,synthetic_grid,classification_metrics,threshold_penalty,t6_p8,3,conventional_picard_xenofilter,reported,Picard SetNmMdAndUqTags without IS_BISULFITE_SEQUENCE + R XenofilteR,mm_threshold=6 unmapped_penalty=8 strand_aware_bisulfite_nm,0.0068,99.9256,,0.0135,338,,,,,,,,unpatched; recall stays near zero at every audited threshold
+bisulfite-seq,BS 60% parameter grid,synthetic_grid,classification_metrics,threshold_penalty,t6_p10,3,modern_xenofilx,reported,"xenofilx, native strand-aware NM recalculation (bamdriver)",mm_threshold=6 unmapped_penalty=10 strand_aware_bisulfite_nm,52.0024,99.9179,,68.3985,"312,343",,,,,,,,
+bisulfite-seq,BS 60% parameter grid,synthetic_grid,classification_metrics,threshold_penalty,t6_p10,3,legacy_picard_xenofilter,reported,Picard SetNmMdAndUqTags IS_BISULFITE_SEQUENCE=true + R XenofilteR,mm_threshold=6 unmapped_penalty=10 strand_aware_bisulfite_nm,51.3501,99.9184,,67.8316,"308,427",,,,,,,,
+bisulfite-seq,BS 60% parameter grid,synthetic_grid,classification_metrics,threshold_penalty,t6_p10,3,conventional_picard_xenofilter,reported,Picard SetNmMdAndUqTags without IS_BISULFITE_SEQUENCE + R XenofilteR,mm_threshold=6 unmapped_penalty=10 strand_aware_bisulfite_nm,0.0068,99.9256,,0.0135,338,,,,,,,,unpatched; recall stays near zero at every audited threshold
+bisulfite-seq,BS 60% parameter grid,synthetic_grid,classification_metrics,threshold_penalty,t6_p12,3,modern_xenofilx,reported,"xenofilx, native strand-aware NM recalculation (bamdriver)",mm_threshold=6 unmapped_penalty=12 strand_aware_bisulfite_nm,52.0024,99.9179,,68.3985,"312,343",,,,,,,,
+bisulfite-seq,BS 60% parameter grid,synthetic_grid,classification_metrics,threshold_penalty,t6_p12,3,legacy_picard_xenofilter,reported,Picard SetNmMdAndUqTags IS_BISULFITE_SEQUENCE=true + R XenofilteR,mm_threshold=6 unmapped_penalty=12 strand_aware_bisulfite_nm,51.3501,99.9184,,67.8316,"308,427",,,,,,,,
+bisulfite-seq,BS 60% parameter grid,synthetic_grid,classification_metrics,threshold_penalty,t6_p12,3,conventional_picard_xenofilter,reported,Picard SetNmMdAndUqTags without IS_BISULFITE_SEQUENCE + R XenofilteR,mm_threshold=6 unmapped_penalty=12 strand_aware_bisulfite_nm,0.0068,99.9256,,0.0135,338,,,,,,,,unpatched; recall stays near zero at every audited threshold
+bisulfite-seq,BS 60% parameter grid,synthetic_grid,classification_metrics,threshold_penalty,t7_p8,3,modern_xenofilx,reported,"xenofilx, native strand-aware NM recalculation (bamdriver)",mm_threshold=7 unmapped_penalty=8 strand_aware_bisulfite_nm,52.2246,99.9177,,68.5904,"313,677",,,,,,,,
+bisulfite-seq,BS 60% parameter grid,synthetic_grid,classification_metrics,threshold_penalty,t7_p8,3,legacy_picard_xenofilter,reported,Picard SetNmMdAndUqTags IS_BISULFITE_SEQUENCE=true + R XenofilteR,mm_threshold=7 unmapped_penalty=8 strand_aware_bisulfite_nm,51.6993,99.9181,,68.1357,"310,524",,,,,,,,
+bisulfite-seq,BS 60% parameter grid,synthetic_grid,classification_metrics,threshold_penalty,t7_p8,3,conventional_picard_xenofilter,reported,Picard SetNmMdAndUqTags without IS_BISULFITE_SEQUENCE + R XenofilteR,mm_threshold=7 unmapped_penalty=8 strand_aware_bisulfite_nm,0.0105,99.9253,,0.0210,362,,,,,,,,unpatched; recall stays near zero at every audited threshold
+bisulfite-seq,BS 60% parameter grid,synthetic_grid,classification_metrics,threshold_penalty,t7_p10,3,modern_xenofilx,reported,"xenofilx, native strand-aware NM recalculation (bamdriver)",mm_threshold=7 unmapped_penalty=10 strand_aware_bisulfite_nm,52.2246,99.9177,,68.5904,"313,677",,,,,,,,
+bisulfite-seq,BS 60% parameter grid,synthetic_grid,classification_metrics,threshold_penalty,t7_p10,3,legacy_picard_xenofilter,reported,Picard SetNmMdAndUqTags IS_BISULFITE_SEQUENCE=true + R XenofilteR,mm_threshold=7 unmapped_penalty=10 strand_aware_bisulfite_nm,51.6993,99.9181,,68.1357,"310,524",,,,,,,,
+bisulfite-seq,BS 60% parameter grid,synthetic_grid,classification_metrics,threshold_penalty,t7_p10,3,conventional_picard_xenofilter,reported,Picard SetNmMdAndUqTags without IS_BISULFITE_SEQUENCE + R XenofilteR,mm_threshold=7 unmapped_penalty=10 strand_aware_bisulfite_nm,0.0105,99.9253,,0.0210,362,,,,,,,,unpatched; recall stays near zero at every audited threshold
+bisulfite-seq,BS 60% parameter grid,synthetic_grid,classification_metrics,threshold_penalty,t7_p12,3,modern_xenofilx,reported,"xenofilx, native strand-aware NM recalculation (bamdriver)",mm_threshold=7 unmapped_penalty=12 strand_aware_bisulfite_nm,52.2246,99.9177,,68.5904,"313,677",,,,,,,,
+bisulfite-seq,BS 60% parameter grid,synthetic_grid,classification_metrics,threshold_penalty,t7_p12,3,legacy_picard_xenofilter,reported,Picard SetNmMdAndUqTags IS_BISULFITE_SEQUENCE=true + R XenofilteR,mm_threshold=7 unmapped_penalty=12 strand_aware_bisulfite_nm,51.6993,99.9181,,68.1357,"310,524",,,,,,,,
+bisulfite-seq,BS 60% parameter grid,synthetic_grid,classification_metrics,threshold_penalty,t7_p12,3,conventional_picard_xenofilter,reported,Picard SetNmMdAndUqTags without IS_BISULFITE_SEQUENCE + R XenofilteR,mm_threshold=7 unmapped_penalty=12 strand_aware_bisulfite_nm,0.0105,99.9253,,0.0210,362,,,,,,,,unpatched; recall stays near zero at every audited threshold
+bisulfite-seq,BS 60% parameter grid,synthetic_grid,classification_metrics,threshold_penalty,t8_p8,3,modern_xenofilx,reported,"xenofilx, native strand-aware NM recalculation (bamdriver)",mm_threshold=8 unmapped_penalty=8 strand_aware_bisulfite_nm,52.2941,99.9176,,68.6504,"314,094",,,,,,,,
+bisulfite-seq,BS 60% parameter grid,synthetic_grid,classification_metrics,threshold_penalty,t8_p8,3,legacy_picard_xenofilter,reported,Picard SetNmMdAndUqTags IS_BISULFITE_SEQUENCE=true + R XenofilteR,mm_threshold=8 unmapped_penalty=8 strand_aware_bisulfite_nm,51.8356,99.9177,,68.2539,"311,343",,,,,,,,
+bisulfite-seq,BS 60% parameter grid,synthetic_grid,classification_metrics,threshold_penalty,t8_p8,3,conventional_picard_xenofilter,reported,Picard SetNmMdAndUqTags without IS_BISULFITE_SEQUENCE + R XenofilteR,mm_threshold=8 unmapped_penalty=8 strand_aware_bisulfite_nm,0.0149,99.9249,,0.0298,390,,,,,,,,unpatched; recall stays near zero at every audited threshold
+bisulfite-seq,BS 60% parameter grid,synthetic_grid,classification_metrics,threshold_penalty,t8_p10,3,modern_xenofilx,reported,"xenofilx, native strand-aware NM recalculation (bamdriver)",mm_threshold=8 unmapped_penalty=10 strand_aware_bisulfite_nm,52.2941,99.9176,,68.6504,"314,094",,,,,,,,
+bisulfite-seq,BS 60% parameter grid,synthetic_grid,classification_metrics,threshold_penalty,t8_p10,3,legacy_picard_xenofilter,reported,Picard SetNmMdAndUqTags IS_BISULFITE_SEQUENCE=true + R XenofilteR,mm_threshold=8 unmapped_penalty=10 strand_aware_bisulfite_nm,51.8356,99.9177,,68.2539,"311,343",,,,,,,,
+bisulfite-seq,BS 60% parameter grid,synthetic_grid,classification_metrics,threshold_penalty,t8_p10,3,conventional_picard_xenofilter,reported,Picard SetNmMdAndUqTags without IS_BISULFITE_SEQUENCE + R XenofilteR,mm_threshold=8 unmapped_penalty=10 strand_aware_bisulfite_nm,0.0149,99.9249,,0.0298,390,,,,,,,,unpatched; recall stays near zero at every audited threshold
+bisulfite-seq,BS 60% parameter grid,synthetic_grid,classification_metrics,threshold_penalty,t8_p12,3,modern_xenofilx,reported,"xenofilx, native strand-aware NM recalculation (bamdriver)",mm_threshold=8 unmapped_penalty=12 strand_aware_bisulfite_nm,52.2941,99.9176,,68.6504,"314,094",,,,,,,,
+bisulfite-seq,BS 60% parameter grid,synthetic_grid,classification_metrics,threshold_penalty,t8_p12,3,legacy_picard_xenofilter,reported,Picard SetNmMdAndUqTags IS_BISULFITE_SEQUENCE=true + R XenofilteR,mm_threshold=8 unmapped_penalty=12 strand_aware_bisulfite_nm,51.8356,99.9177,,68.2539,"311,343",,,,,,,,
+bisulfite-seq,BS 60% parameter grid,synthetic_grid,classification_metrics,threshold_penalty,t8_p12,3,conventional_picard_xenofilter,reported,Picard SetNmMdAndUqTags without IS_BISULFITE_SEQUENCE + R XenofilteR,mm_threshold=8 unmapped_penalty=12 strand_aware_bisulfite_nm,0.0149,99.9249,,0.0298,390,,,,,,,,unpatched; recall stays near zero at every audited threshold
+RNA-seq,RNA-PDX authentic,authentic_pdx,membership_counts,accession,SRR30880970,1,modern_xenofilx,reported,"xenofilx, native strand-aware NM recalculation (bamdriver)",mm_threshold=4 unmapped_penalty=8 conventional_nm,,,,,,32097614,30773947,,32097614,0,,,"single authentic accession; no construction truth, so no recall is defined. Source: rna-pdx-comparison.json"
+RNA-seq,RNA-PDX authentic,authentic_pdx,membership_counts,accession,SRR30880970,1,legacy_xenofilter,reported,Picard SetNmMdAndUqTags (no bisulfite flag; not applicable to RNA) + R XenofilteR,mm_threshold=4 unmapped_penalty=8 conventional_nm,,,,,,32097614,,30773947,32097614,0,0,0,"digest matches xenofilx exactly, so the two arms are decision-identical"
+RNA-seq,RNA-PDX authentic,authentic_pdx,membership_counts,accession,SRR30880970,1,conventional_picard_xenofilter,not_applicable,Picard SetNmMdAndUqTags without IS_BISULFITE_SEQUENCE + R XenofilteR,mm_threshold=4 unmapped_penalty=8 conventional_nm,,,,,,32097614,,,32097614,0,,,"RNA has no bisulfite deamination, so IS_BISULFITE_SEQUENCE is undefined and this arm cannot exist; the legacy_xenofilter arm above already is the conventional Picard path"
+bisulfite-seq,BS-PDX authentic,authentic_pdx,membership_counts,accession,SRR36187610,1,modern_xenofilx,reported,"xenofilx, native strand-aware NM recalculation (bamdriver)",mm_threshold=6 unmapped_penalty=8 strand_aware_bisulfite_nm,,,,,,45160030,45120923,,44044790,1115240,,,"single authentic accession; no construction truth, so no recall is defined. Source: bs-pdx-comparison.json"
+bisulfite-seq,BS-PDX authentic,authentic_pdx,membership_counts,accession,SRR36187610,1,legacy_picard_xenofilter,reported,Picard SetNmMdAndUqTags against C-to-T / G-to-A converted references + R XenofilteR,mm_threshold=6 unmapped_penalty=8 strand_aware_bisulfite_nm,,,,,,45160030,,44005685,44044790,1115240,1115239,1,"legacy arm uses converted-reference strand-partitioned Picard, not the IS_BISULFITE_SEQUENCE flag"
+bisulfite-seq,BS-PDX authentic,authentic_pdx,membership_counts,accession,SRR36187610,1,conventional_picard_xenofilter,not_measured_at_this_accession,Picard SetNmMdAndUqTags without IS_BISULFITE_SEQUENCE + R XenofilteR,mm_threshold=6 unmapped_penalty=8 strand_aware_bisulfite_nm,,,,,,45160030,,,44044790,1115240,,,the unpatched arm was not run on this authentic accession; its bisulfite measurements are in the synthetic gradient and parameter-grid rows above

xenofilx/benchmark/tables/per-cell-expected-s5.json

@@ -0,0 +1,346 @@
+{
+  "human0-replicate1": {
+    "legacy_ppv": "0.0000",
+    "legacy_recall": "N/A",
+    "legacy_spec": "99.3968",
+    "modern_ppv": "0.0000",
+    "modern_recall": "N/A",
+    "modern_spec": "99.3968"
+  },
+  "human0p001-replicate1": {
+    "legacy_ppv": "13.7561",
+    "legacy_recall": "96.1000",
+    "legacy_spec": "99.3969",
+    "modern_ppv": "13.7561",
+    "modern_recall": "96.1000",
+    "modern_spec": "99.3969"
+  },
+  "human0p001-replicate2": {
+    "legacy_ppv": "13.6790",
+    "legacy_recall": "96.3000",
+    "legacy_spec": "99.3917",
+    "modern_ppv": "13.6790",
+    "modern_recall": "96.3000",
+    "modern_spec": "99.3917"
+  },
+  "human0p001-replicate3": {
+    "legacy_ppv": "13.9336",
+    "legacy_recall": "96.1000",
+    "legacy_spec": "99.4058",
+    "modern_ppv": "13.9336",
+    "modern_recall": "96.1000",
+    "modern_spec": "99.4058"
+  },
+  "human0p005-replicate1": {
+    "legacy_ppv": "44.5421",
+    "legacy_recall": "96.3000",
+    "legacy_spec": "99.3975",
+    "modern_ppv": "44.5421",
+    "modern_recall": "96.3000",
+    "modern_spec": "99.3975"
+  },
+  "human0p005-replicate2": {
+    "legacy_ppv": "44.3853",
+    "legacy_recall": "96.6800",
+    "legacy_spec": "99.3913",
+    "modern_ppv": "44.3853",
+    "modern_recall": "96.6800",
+    "modern_spec": "99.3913"
+  },
+  "human0p005-replicate3": {
+    "legacy_ppv": "44.9754",
+    "legacy_recall": "96.7600",
+    "legacy_spec": "99.4051",
+    "modern_ppv": "44.9754",
+    "modern_recall": "96.7600",
+    "modern_spec": "99.4051"
+  },
+  "human0p01-replicate1": {
+    "legacy_ppv": "61.7854",
+    "legacy_recall": "96.4100",
+    "legacy_spec": "99.3977",
+    "modern_ppv": "61.7854",
+    "modern_recall": "96.4100",
+    "modern_spec": "99.3977"
+  },
+  "human0p01-replicate2": {
+    "legacy_ppv": "61.5870",
+    "legacy_recall": "96.7100",
+    "legacy_spec": "99.3907",
+    "modern_ppv": "61.5870",
+    "modern_recall": "96.7100",
+    "modern_spec": "99.3907"
+  },
+  "human0p01-replicate3": {
+    "legacy_ppv": "62.1239",
+    "legacy_recall": "96.6400",
+    "legacy_spec": "99.4048",
+    "modern_ppv": "62.1239",
+    "modern_recall": "96.6400",
+    "modern_spec": "99.4048"
+  },
+  "human0p02-replicate1": {
+    "legacy_ppv": "76.5692",
+    "legacy_recall": "96.6150",
+    "legacy_spec": "99.3966",
+    "modern_ppv": "76.5692",
+    "modern_recall": "96.6150",
+    "modern_spec": "99.3966"
+  },
+  "human0p02-replicate2": {
+    "legacy_ppv": "76.3990",
+    "legacy_recall": "96.7250",
+    "legacy_spec": "99.3902",
+    "modern_ppv": "76.3990",
+    "modern_recall": "96.7250",
+    "modern_spec": "99.3902"
+  },
+  "human0p02-replicate3": {
+    "legacy_ppv": "76.7743",
+    "legacy_recall": "96.6550",
+    "legacy_spec": "99.4033",
+    "modern_ppv": "76.7743",
+    "modern_recall": "96.6550",
+    "modern_spec": "99.4033"
+  },
+  "human0p05-replicate1": {
+    "legacy_ppv": "89.3540",
+    "legacy_recall": "96.6060",
+    "legacy_spec": "99.3942",
+    "modern_ppv": "89.3540",
+    "modern_recall": "96.6060",
+    "modern_spec": "99.3942"
+  },
+  "human0p05-replicate2": {
+    "legacy_ppv": "89.2861",
+    "legacy_recall": "96.7540",
+    "legacy_spec": "99.3889",
+    "modern_ppv": "89.2861",
+    "modern_recall": "96.7540",
+    "modern_spec": "99.3889"
+  },
+  "human0p05-replicate3": {
+    "legacy_ppv": "89.4824",
+    "legacy_recall": "96.5300",
+    "legacy_spec": "99.4028",
+    "modern_ppv": "89.4824",
+    "modern_recall": "96.5300",
+    "modern_spec": "99.4028"
+  },
+  "human0p1-replicate1": {
+    "legacy_ppv": "94.6217",
+    "legacy_recall": "96.5520",
+    "legacy_spec": "99.3902",
+    "modern_ppv": "94.6217",
+    "modern_recall": "96.5520",
+    "modern_spec": "99.3902"
+  },
+  "human0p1-replicate2": {
+    "legacy_ppv": "94.6539",
+    "legacy_recall": "96.6520",
+    "legacy_spec": "99.3934",
+    "modern_ppv": "94.6539",
+    "modern_recall": "96.6520",
+    "modern_spec": "99.3934"
+  },
+  "human0p1-replicate3": {
+    "legacy_ppv": "94.7308",
+    "legacy_recall": "96.5610",
+    "legacy_spec": "99.4032",
+    "modern_ppv": "94.7308",
+    "modern_recall": "96.5610",
+    "modern_spec": "99.4032"
+  },
+  "human0p25-replicate1": {
+    "legacy_ppv": "98.1383",
+    "legacy_recall": "96.6144",
+    "legacy_spec": "99.3891",
+    "modern_ppv": "98.1383",
+    "modern_recall": "96.6144",
+    "modern_spec": "99.3891"
+  },
+  "human0p25-replicate2": {
+    "legacy_ppv": "98.1249",
+    "legacy_recall": "96.6016",
+    "legacy_spec": "99.3847",
+    "modern_ppv": "98.1249",
+    "modern_recall": "96.6016",
+    "modern_spec": "99.3847"
+  },
+  "human0p25-replicate3": {
+    "legacy_ppv": "98.1768",
+    "legacy_recall": "96.5372",
+    "legacy_spec": "99.4024",
+    "modern_ppv": "98.1768",
+    "modern_recall": "96.5372",
+    "modern_spec": "99.4024"
+  },
+  "human0p5-replicate1": {
+    "legacy_ppv": "99.3797",
+    "legacy_recall": "96.5726",
+    "legacy_spec": "99.3972",
+    "modern_ppv": "99.3797",
+    "modern_recall": "96.5726",
+    "modern_spec": "99.3972"
+  },
+  "human0p5-replicate2": {
+    "legacy_ppv": "99.3655",
+    "legacy_recall": "96.5584",
+    "legacy_spec": "99.3834",
+    "modern_ppv": "99.3655",
+    "modern_recall": "96.5584",
+    "modern_spec": "99.3834"
+  },
+  "human0p5-replicate3": {
+    "legacy_ppv": "99.3671",
+    "legacy_recall": "96.5584",
+    "legacy_spec": "99.3850",
+    "modern_ppv": "99.3671",
+    "modern_recall": "96.5584",
+    "modern_spec": "99.3850"
+  },
+  "human0p6-replicate1": {
+    "legacy_ppv": "99.5848",
+    "legacy_recall": "96.5723",
+    "legacy_spec": "99.3960",
+    "modern_ppv": "99.5848",
+    "modern_recall": "96.5723",
+    "modern_spec": "99.3960"
+  },
+  "human0p6-replicate2": {
+    "legacy_ppv": "99.5707",
+    "legacy_recall": "96.5590",
+    "legacy_spec": "99.3755",
+    "modern_ppv": "99.5707",
+    "modern_recall": "96.5590",
+    "modern_spec": "99.3755"
+  },
+  "human0p6-replicate3": {
+    "legacy_ppv": "99.5787",
+    "legacy_recall": "96.5622",
+    "legacy_spec": "99.3873",
+    "modern_ppv": "99.5787",
+    "modern_recall": "96.5622",
+    "modern_spec": "99.3873"
+  },
+  "human0p7-replicate1": {
+    "legacy_ppv": "99.7417",
+    "legacy_recall": "96.5731",
+    "legacy_spec": "99.4163",
+    "modern_ppv": "99.7417",
+    "modern_recall": "96.5731",
+    "modern_spec": "99.4163"
+  },
+  "human0p7-replicate2": {
+    "legacy_ppv": "99.7212",
+    "legacy_recall": "96.5736",
+    "legacy_spec": "99.3700",
+    "modern_ppv": "99.7212",
+    "modern_recall": "96.5736",
+    "modern_spec": "99.3700"
+  },
+  "human0p7-replicate3": {
+    "legacy_ppv": "99.7253",
+    "legacy_recall": "96.5593",
+    "legacy_spec": "99.3793",
+    "modern_ppv": "99.7253",
+    "modern_recall": "96.5593",
+    "modern_spec": "99.3793"
+  },
+  "human0p8-replicate1": {
+    "legacy_ppv": "99.8451",
+    "legacy_recall": "96.5844",
+    "legacy_spec": "99.4005",
+    "modern_ppv": "99.8451",
+    "modern_recall": "96.5844",
+    "modern_spec": "99.4005"
+  },
+  "human0p8-replicate2": {
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+    "legacy_recall": "96.5736",
+    "legacy_spec": "99.3490",
+    "modern_ppv": "99.8318",
+    "modern_recall": "96.5736",
+    "modern_spec": "99.3490"
+  },
+  "human0p8-replicate3": {
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+    "legacy_recall": "96.5557",
+    "legacy_spec": "99.3760",
+    "modern_ppv": "99.8387",
+    "modern_recall": "96.5557",
+    "modern_spec": "99.3760"
+  },
+  "human0p9-replicate1": {
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+    "legacy_recall": "96.5800",
+    "legacy_spec": "99.3990",
+    "modern_ppv": "99.9309",
+    "modern_recall": "96.5800",
+    "modern_spec": "99.3990"
+  },
+  "human0p9-replicate2": {
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+    "legacy_recall": "96.5580",
+    "legacy_spec": "99.3490",
+    "modern_ppv": "99.9251",
+    "modern_recall": "96.5580",
+    "modern_spec": "99.3490"
+  },
+  "human0p9-replicate3": {
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+    "legacy_recall": "96.5529",
+    "legacy_spec": "99.3560",
+    "modern_ppv": "99.9259",
+    "modern_recall": "96.5529",
+    "modern_spec": "99.3560"
+  },
+  "human0p95-replicate1": {
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+    "legacy_recall": "96.5773",
+    "legacy_spec": "99.3740",
+    "modern_ppv": "99.9659",
+    "modern_recall": "96.5773",
+    "modern_spec": "99.3740"
+  },
+  "human0p95-replicate2": {
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+    "legacy_recall": "96.5539",
+    "legacy_spec": "99.3420",
+    "modern_ppv": "99.9641",
+    "modern_recall": "96.5539",
+    "modern_spec": "99.3420"
+  },
+  "human0p95-replicate3": {
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+    "legacy_recall": "96.5516",
+    "legacy_spec": "99.3880",
+    "modern_ppv": "99.9667",
+    "modern_recall": "96.5516",
+    "modern_spec": "99.3880"
+  },
+  "human0p99-replicate1": {
+    "legacy_ppv": "99.9927",
+    "legacy_recall": "96.5833",
+    "legacy_spec": "99.3000",
+    "modern_ppv": "99.9927",
+    "modern_recall": "96.5833",
+    "modern_spec": "99.3000"
+  },
+  "human0p99-replicate2": {
+    "legacy_ppv": "99.9945",
+    "legacy_recall": "96.5565",
+    "legacy_spec": "99.4700",
+    "modern_ppv": "99.9945",
+    "modern_recall": "96.5565",
+    "modern_spec": "99.4700"
+  },
+  "human0p99-replicate3": {
+    "legacy_ppv": "99.9928",
+    "legacy_recall": "96.5564",
+    "legacy_spec": "99.3100",
+    "modern_ppv": "99.9928",
+    "modern_recall": "96.5564",
+    "modern_spec": "99.3100"
+  }
+}

xenofilx/benchmark/tables/per-cell-expected-s6.json

@@ -0,0 +1,475 @@
+{
+  "human0-replicate1": {
+    "conventional_ppv": "0.0000",
+    "conventional_recall": "N/A",
+    "conventional_spec": "99.9279",
+    "legacy_ppv": "0.0000",
+    "legacy_recall": "N/A",
+    "legacy_spec": "99.9188",
+    "modern_ppv": "0.0000",
+    "modern_recall": "N/A",
+    "modern_spec": "99.9182"
+  },
+  "human0p001-replicate1": {
+    "conventional_ppv": "0.0000",
+    "conventional_recall": "0.0000",
+    "conventional_spec": "99.9244",
+    "legacy_ppv": "38.3073",
+    "legacy_recall": "51.6000",
+    "legacy_spec": "99.9168",
+    "modern_ppv": "38.3481",
+    "modern_recall": "52.0000",
+    "modern_spec": "99.9163"
+  },
+  "human0p001-replicate2": {
+    "conventional_ppv": "0.0000",
+    "conventional_recall": "0.0000",
+    "conventional_spec": "99.9310",
+    "legacy_ppv": "41.3580",
+    "legacy_recall": "53.6000",
+    "legacy_spec": "99.9239",
+    "modern_ppv": "41.7365",
+    "modern_recall": "54.8000",
+    "modern_spec": "99.9234"
+  },
+  "human0p001-replicate3": {
+    "conventional_ppv": "0.0000",
+    "conventional_recall": "0.0000",
+    "conventional_spec": "99.9321",
+    "legacy_ppv": "42.2188",
+    "legacy_recall": "54.8000",
+    "legacy_spec": "99.9249",
+    "modern_ppv": "42.3755",
+    "modern_recall": "55.3000",
+    "modern_spec": "99.9247"
+  },
+  "human0p005-replicate1": {
+    "conventional_ppv": "0.2649",
+    "conventional_recall": "0.0400",
+    "conventional_spec": "99.9243",
+    "legacy_ppv": "75.5247",
+    "legacy_recall": "51.1000",
+    "legacy_spec": "99.9168",
+    "modern_ppv": "75.5790",
+    "modern_recall": "51.5600",
+    "modern_spec": "99.9163"
+  },
+  "human0p005-replicate2": {
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+    "conventional_recall": "0.0000",
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+    "legacy_ppv": "77.7974",
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+    "legacy_spec": "99.9240",
+    "modern_ppv": "78.0093",
+    "modern_recall": "53.9200",
+    "modern_spec": "99.9236"
+  },
+  "human0p005-replicate3": {
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+    "conventional_recall": "0.0000",
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+    "modern_ppv": "78.0774",
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+  },
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+    "modern_recall": "50.8000",
+    "modern_spec": "99.9164"
+  },
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+    "modern_recall": "52.1000",
+    "modern_spec": "99.9189"
+  },
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+  },
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+    "modern_spec": "99.9161"
+  },
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+  },
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+    "modern_ppv": "93.4219",
+    "modern_recall": "52.0500",
+    "modern_spec": "99.9252"
+  },
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+  },
+  "human0p05-replicate2": {
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+    "modern_recall": "52.1000",
+    "modern_spec": "99.9189"
+  },
+  "human0p05-replicate3": {
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+    "conventional_recall": "0.0100",
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+    "legacy_ppv": "97.3382",
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+    "legacy_spec": "99.9260",
+    "modern_ppv": "97.3553",
+    "modern_recall": "52.0520",
+    "modern_spec": "99.9256"
+  },
+  "human0p1-replicate1": {
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+    "modern_recall": "51.9060",
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+  },
+  "human0p1-replicate2": {
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+    "conventional_recall": "0.0090",
+    "conventional_spec": "99.9288",
+    "legacy_ppv": "98.6300",
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+    "modern_ppv": "98.6366",
+    "modern_recall": "52.0890",
+    "modern_spec": "99.9200"
+  },
+  "human0p1-replicate3": {
+    "conventional_ppv": "1.2759",
+    "conventional_recall": "0.0080",
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+    "legacy_ppv": "98.6979",
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+    "modern_ppv": "98.7060",
+    "modern_recall": "51.9470",
+    "modern_spec": "99.9243"
+  },
+  "human0p25-replicate1": {
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+    "conventional_recall": "0.0080",
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+    "modern_recall": "52.0164",
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+  },
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+    "modern_spec": "99.9199"
+  },
+  "human0p25-replicate3": {
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+    "modern_ppv": "99.5651",
+    "modern_recall": "51.9220",
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+  },
+  "human0p5-replicate1": {
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+    "conventional_recall": "0.0068",
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+    "legacy_ppv": "99.8451",
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+    "modern_spec": "99.9198"
+  },
+  "human0p5-replicate2": {
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+    "modern_ppv": "99.8453",
+    "modern_recall": "52.1386",
+    "modern_spec": "99.9192"
+  },
+  "human0p5-replicate3": {
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+    "conventional_recall": "0.0052",
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+    "modern_ppv": "99.8464",
+    "modern_recall": "52.0132",
+    "modern_spec": "99.9200"
+  },
+  "human0p6-replicate1": {
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+    "conventional_recall": "0.0077",
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+    "modern_ppv": "99.8946",
+    "modern_recall": "51.9847",
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+  },
+  "human0p6-replicate2": {
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+    "conventional_recall": "0.0078",
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+    "legacy_ppv": "99.8918",
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+    "modern_ppv": "99.8925",
+    "modern_recall": "52.0303",
+    "modern_spec": "99.9160"
+  },
+  "human0p6-replicate3": {
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+    "modern_recall": "51.9922",
+    "modern_spec": "99.9200"
+  },
+  "human0p7-replicate1": {
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+    "modern_recall": "52.0049",
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+  },
+  "human0p7-replicate2": {
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+  },
+  "human0p7-replicate3": {
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+  },
+  "human0p8-replicate1": {
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+    "modern_recall": "51.9683",
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+  },
+  "human0p8-replicate2": {
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+    "modern_recall": "52.0467",
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+  },
+  "human0p8-replicate3": {
+    "conventional_ppv": "23.5897",
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+    "modern_recall": "52.0140",
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+  },
+  "human0p9-replicate1": {
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+    "modern_recall": "51.9982",
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+  },
+  "human0p9-replicate2": {
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+    "modern_recall": "52.0458",
+    "modern_spec": "99.9110"
+  },
+  "human0p9-replicate3": {
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+    "modern_recall": "52.0042",
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+  },
+  "human0p95-replicate1": {
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+}

xenofilx/benchmark/tables/per-cell-expected-s7.json

@@ -0,0 +1,398 @@
+{
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+}

xenofilx/benchmark/tables/rna-mixture-cells.json

@@ -0,0 +1,752 @@
+{
+  "schema_version": "otter.xenofilx-note4-rna-gradient/v1",
+  "description": "Input contract for reproducing Supplementary Table S5 from published otter-data RNA-PDX fixtures.",
+  "sources": {
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+    "mouse_rnaseq": "SRR037954"
+  },
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+    "modern_nm_semantics": "conventional_reference_nm",
+    "comparison_unit": "unique_fragment_membership"
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+}

xenofilx/benchmark/tables/table-s5-gradient.tsv

@@ -0,0 +1,16 @@
+fraction	modern_recall	legacy_recall	modern_spec	legacy_spec	modern_ppv	n
+0	N/A	N/A	99.3968	99.3968	N/A	1
+0.001	96.1667	96.1667	99.3981	99.3981	13.7896	3
+0.005	96.5800	96.5800	99.3980	99.3980	44.6342	3
+0.01	96.5867	96.5867	99.3977	99.3977	61.8321	3
+0.02	96.6650	96.6650	99.3967	99.3967	76.5808	3
+0.05	96.6300	96.6300	99.3953	99.3953	89.3742	3
+0.1	96.5883	96.5883	99.3956	99.3956	94.6688	3
+0.25	96.5844	96.5844	99.3920	99.3920	98.1466	3
+0.5	96.5631	96.5631	99.3885	99.3885	99.3708	3
+0.6	96.5645	96.5645	99.3863	99.3863	99.5781	3
+0.7	96.5687	96.5687	99.3886	99.3886	99.7294	3
+0.8	96.5712	96.5712	99.3752	99.3752	99.8385	3
+0.9	96.5636	96.5636	99.3680	99.3680	99.9273	3
+0.95	96.5609	96.5609	99.3680	99.3680	99.9656	3
+0.99	96.5654	96.5654	99.3600	99.3600	99.9933	3

xenofilx/benchmark/tables/table-s6-gradient.tsv

@@ -0,0 +1,16 @@
+fraction	modern_recall	legacy_recall	conventional_recall	modern_spec	legacy_spec	conventional_spec	modern_ppv	legacy_ppv	conventional_ppv	n
+0	N/A	N/A	N/A	99.9182	99.9188	99.9279	N/A	N/A	N/A	1
+0.001	54.0333	53.3333	0.0000	99.9215	99.9219	99.9292	40.8200	40.6281	0.0000	3
+0.005	52.9200	52.2933	0.0133	99.9216	99.9219	99.9292	77.2219	77.0967	0.0883	3
+0.01	51.6067	50.9067	0.0100	99.9201	99.9206	99.9287	86.7137	86.6245	0.1443	3
+0.02	52.2317	51.5383	0.0050	99.9218	99.9221	99.9293	93.1659	93.1087	0.1395	3
+0.05	52.0120	51.3520	0.0053	99.9200	99.9205	99.9285	97.1594	97.1411	0.4015	3
+0.1	51.9807	51.3210	0.0070	99.9202	99.9207	99.9287	98.6376	98.6291	1.0858	3
+0.25	52.0021	51.3475	0.0080	99.9199	99.9202	99.9276	99.5399	99.5361	3.5592	3
+0.5	52.0909	51.4305	0.0066	99.9197	99.9201	99.9275	99.8460	99.8450	8.3327	3
+0.6	52.0024	51.3501	0.0068	99.9179	99.9184	99.9256	99.8949	99.8942	11.9381	3
+0.7	52.0225	51.3680	0.0069	99.9188	99.9191	99.9267	99.9331	99.9326	17.9501	3
+0.8	52.0097	51.3543	0.0070	99.9153	99.9157	99.9235	99.9593	99.9590	26.5814	3
+0.9	52.0161	51.3586	0.0070	99.9200	99.9203	99.9287	99.9829	99.9828	46.7696	3
+0.95	52.0212	51.3645	0.0071	99.9220	99.9227	99.9293	99.9921	99.9921	65.7875	3
+0.99	52.0165	51.3599	0.0069	99.8933	99.8967	99.9067	99.9979	99.9980	87.9740	3

xenofilx/benchmark/tables/table-s7-parameter-grid.tsv

@@ -0,0 +1,13 @@
+t	p	modern_recall	modern_spec	modern_f1	modern_frags	legacy_recall	legacy_spec	legacy_f1	legacy_frags	conventional_recall	conventional_spec	conventional_f1	conventional_frags	n
+5	8	51.6177	99.9181	68.0647	310,034	50.5244	99.9185	67.1069	303,472	0.0046	99.9258	0.0092	325	3
+5	10	51.6177	99.9181	68.0647	310,034	50.5244	99.9185	67.1069	303,472	0.0046	99.9258	0.0092	325	3
+5	12	51.6177	99.9181	68.0647	310,034	50.5244	99.9185	67.1069	303,472	0.0046	99.9258	0.0092	325	3
+6	8	52.0024	99.9179	68.3985	312,343	51.3501	99.9184	67.8316	308,427	0.0068	99.9256	0.0135	338	3
+6	10	52.0024	99.9179	68.3985	312,343	51.3501	99.9184	67.8316	308,427	0.0068	99.9256	0.0135	338	3
+6	12	52.0024	99.9179	68.3985	312,343	51.3501	99.9184	67.8316	308,427	0.0068	99.9256	0.0135	338	3
+7	8	52.2246	99.9177	68.5904	313,677	51.6993	99.9181	68.1357	310,524	0.0105	99.9253	0.0210	362	3
+7	10	52.2246	99.9177	68.5904	313,677	51.6993	99.9181	68.1357	310,524	0.0105	99.9253	0.0210	362	3
+7	12	52.2246	99.9177	68.5904	313,677	51.6993	99.9181	68.1357	310,524	0.0105	99.9253	0.0210	362	3
+8	8	52.2941	99.9176	68.6504	314,094	51.8356	99.9177	68.2539	311,343	0.0149	99.9249	0.0298	390	3
+8	10	52.2941	99.9176	68.6504	314,094	51.8356	99.9177	68.2539	311,343	0.0149	99.9249	0.0298	390	3
+8	12	52.2941	99.9176	68.6504	314,094	51.8356	99.9177	68.2539	311,343	0.0149	99.9249	0.0298	390	3