eidolon v3.1.0

What's Changed

• fix(compare-vcfs): inherit header declarations from the source VCF (#444) by @joshfactorial in #461
• fix(delta): measure observed VAF without a genotype call (#450) by @joshfactorial in #463
• fix(delta): fail the signature check below the SNV floor instead of warning by @joshfactorial in #464
• fix(delta): calibrate the SV scorer, compare BND junctions as spans, drop the Python (#457) by @joshfactorial in #462
• fix(delta): scorers must prove they measured what they were given by @joshfactorial in #468
• fix(delta): BNDspan cannot measure junction recall — disable it on probe failure by @joshfactorial in #469
• fix!: de novo BND truth described a rearrangement the reads did not carry by @joshfactorial in #470
• docs: test-adequacy standard; fold v3.0.1 into v3.1.0 by @joshfactorial in #471
• fix(test): restore a silently disabled test; close the BND coverage gaps it hid by @joshfactorial in #472
• test: assert chimeric junction SEQUENCE, not just QNAMEs by @joshfactorial in #473
• test: assert configured purity actually reaches the merged read mix by @joshfactorial in #475
• test: assert the trained quality profile reproduces its POSITIONAL shape by @joshfactorial in #476
• fix(delta): report the binary version, and refuse a stale one by @joshfactorial in #477
• test: assert de novo SV span consistency and exact IUPAC constituents by @joshfactorial in #478
• feat(delta): normalise Manta's inversion representation before scoring by @joshfactorial in #479
• fix!: POS now means the same thing for every symbolic SV type (VCF 4.2) by @joshfactorial in #480
• test: cover INV junction geometry; the "~8% unexplained" was my measurement by @joshfactorial in #481
• test: close the last three vacuous assertions from the audit by @joshfactorial in #482
• feat: eidolon validate — check artifacts against what their consumers accept by @joshfactorial in #483
• feat(delta): gate emitted artifacts through eidolon validate by @joshfactorial in #484
• fix(delta): score BND against the RAW calls, INV against the converted ones by @joshfactorial in #485
• feat: port scn_af_compare.py to eidolon compare-af; closes #466 for that helper by @joshfactorial in #486
• feat!: sample BND geometry instead of emitting head-to-head only (#458 item 2) by @joshfactorial in #487
• docs(report): correct the BND account, extend the defect table, flag what is pending by @joshfactorial in #488
• test(delta): automated tests for the BND geometry harness; stratify BND recall by geometry by @joshfactorial in #489
• fix(delta): score the canonical SVTYPE list, not a glob of the truth directory by @joshfactorial in #490
• fix(core): emit adapter read-through as a soft clip, not an aligned match by @joshfactorial in #491
• docs: engineering audit of three months of AI-assisted development by @joshfactorial in #493
• docs: retract the translocation claims — eidolon has never generated one by @joshfactorial in #492
• docs(P2): measure the PCAWG SV corpus — TRA is 100% inter-chromosomal by @joshfactorial in #494
• test: CI-enforce the SV support matrix by @joshfactorial in #501
• feat(delta): pool truvari results across replicate SV runs by @joshfactorial in #503
• perf(delta): request the whole node's cores; --mem already reserves it by @joshfactorial in #504
• fix(delta): subvaf validation --mem 64G -> 96G; 64 was below the observed peak by @joshfactorial in #506
• fix(delta): decoy displacement must exceed the event; add the missing BND decoy by @joshfactorial in #508
• fix(delta): calibration controls that did not run must fail, and empty SV strata must be reported by @joshfactorial in #509
• fix(sv)!: tag de novo INS with SVTYPE/SVLEN so it is separable from a small indel by @joshfactorial in #510
• fix(delta): stale-binary detection by commit, inline BAM prune, and a disk pre-flight by @joshfactorial in #514
• fix(delta): recover the missed disk pre-flight; pin the large-insertion read gap (#516) by @joshfactorial in #515
• feat(delta): verify planted insertions reach the reads before the BAMs are pruned by @joshfactorial in #517
• fix(sv)!: cap de novo insertions at read_len-1; correct the #516 mechanism; retract the DUP-spanning defect by @joshfactorial in #518
• refactor(delta)!: retire the BND/BNDinv split (#507); verify the query denominator (#511) by @joshfactorial in #520
• fix(delta): scale the disk gate by genome size and coverage instead of a flat 214 GB by @joshfactorial in #521
• docs(delta): link with gcc, not the Cray cc wrapper — and say why by @joshfactorial in #522
• docs(readme): correct the NEAT comparison table and refresh the CLI help block by @joshfactorial in #523
• test(seq-error): assert the transition matrix's content, not that a file appeared by @joshfactorial in #525
• docs: expand CONTRIBUTING and add an ONBOARDING tour for teammates by @joshfactorial in #528
• docs: retire docs/session_handoff.md, migrating the one finding it uniquely held by @joshfactorial in #531
• test(bam): validate MD-tag transition counting against samtools calmd by @joshfactorial in #532
• fix(gen-seq-error-model)!: refuse to substitute the default transition matrix by @joshfactorial in #533
• test(bam): pin the MD reader against a real aligner's output (1000 Genomes HG00096) by @joshfactorial in #535
• docs: roadmap for rebuilding SV confidence from the reads up by @joshfactorial in #538
• docs(sv): record the whole-genome tier — the support matrix was H1N1-only by @joshfactorial in #539
• test(sv): Gate 2 for DEL — assert a real aligner produces the evidence a caller needs by @joshfactorial in #542
• test(sv): Gate 2 for DUP, and a measured mechanism for #499 by @joshfactorial in #543
• test(sv): Gate 2 for INV — and the reads are cleared of the precision artifact by @joshfactorial in #544
• test(sv): Gate 2 for BND — and mated breakends are measured copy-number neutral by @joshfactorial in #545
• docs: a mutation experiment must verify the mutation was applied by @joshfactorial in #547
• docs: split Gate 2 into 2a (realigned) and 2b (golden BAM) by @joshfactorial in #549
• fix(bam)!: golden BAM records were not in reference orientation (Gate 2b) — closes #550, #551 by @joshfactorial in #552
• fix(bam): compute TLEN from realized mate spans by @joshfactorial in #556
• docs: refresh GitNexus index metadata by @joshfactorial in #557
• fix(delta): fail when INS probes are not evaluated by @joshfactorial in #558
• test(bam): verify planted SVs reach golden BAM by @joshfactorial in #559
• docs: record Delta SV characterization baselines by @joshfactorial in #560
• fix(delta): report all-calls SV recall by @joshfactorial in #561
• fix: apply subclone CCF to structural variants by @joshfactorial in #562
• docs: record release candidate SV validation by @joshfactorial in #563
• release: v3.1.0 correctness and validation by @joshfactorial in #564

Full Changelog: v3.0.0...3.1.0