Issues

• Testing audit before v4.0.0

  ncsa/eidolon#819 · Filter by author joshfactorial opened on Oct 6, 2026 · v4.0.0

• Release v4.0.0

  ncsa/eidolon#816 · Filter by author joshfactorial opened on Oct 4, 2026 · v4.0.0

• Germline SVs as a standard feature: data sources, first recall, real-data reference, BED as specimen

  ncsa/eidolon#806 · Filter by author joshfactorial opened on Oct 2, 2026

• Neutral defaults plus a recommended human starting config, validated across organisms

  ncsa/eidolon#805 · Filter by author joshfactorial opened on Oct 2, 2026

• Docs evaluation: ACCESS report germline and somatic sections, and an accuracy sweep

  ncsa/eidolon#804 · Filter by author joshfactorial opened on Oct 2, 2026

• Repo evaluation: duplication, test adequacy, unreviewed code, and NEAT2 divergences without provenance

  ncsa/eidolon#803 · Filter by author joshfactorial opened on Oct 2, 2026
  1

• Model within-GC-bin coverage spread, not just the per-bin weight

  enhancement
  ncsa/eidolon#775 · Filter by author joshfactorial opened on Sep 26, 2026
  1

• Measure indel_probability: the numerator is collected, the denominator never was

  ncsa/eidolon#746 · Filter by author joshfactorial opened on Sep 21, 2026 · v4.1.0

• Further quality-model testing beyond reproducing the fitted library

  testing
  ncsa/eidolon#745 · Filter by author joshfactorial opened on Sep 21, 2026

• Ship a few alternative sequencing-error models, starting with 151 bp

  enhancement
  ncsa/eidolon#744 · Filter by author joshfactorial opened on Sep 21, 2026

• Source a current-chemistry, binned-quality library for a modern default

  ncsa/eidolon#730 · Filter by author joshfactorial opened on Sep 19, 2026
  1

• Scope: set a model's error rate by transforming its quality distribution, not by scaling a summary

  ncsa/eidolon#725 · Filter by author joshfactorial opened on Sep 18, 2026

• Remove the deprecated rneat alias shim (v4.0.0)

  enhancementLow priority
  ncsa/eidolon#710 · Filter by author joshfactorial opened on Sep 13, 2026 · v4.0.0
  1

• Down the road: make eidolon-core a general-purpose, publishable library

  enhancementLow priority
  ncsa/eidolon#704 · Filter by author joshfactorial opened on Sep 13, 2026
  3

• Simulated reads do not stop aligning at long homopolymers (19x, half of cand_per_mb)

  ncsa/eidolon#692 · Filter by author joshfactorial opened on Sep 7, 2026

• De novo germline SV generator: emit a VCF from a reference, without a population catalog

  ncsa/eidolon#686 · Filter by author joshfactorial opened on Sep 6, 2026

• Survey the remaining NEAT2 discrete distributions for ones worth carrying over

  ncsa/eidolon#678 · Filter by author joshfactorial opened on Sep 5, 2026

• [3.4.0 Phase 3] Fit the indel-error context curve from a BAM in gen-bam-models

  ncsa/eidolon#662 · Filter by author joshfactorial opened on Sep 1, 2026
  1

• mapq0_pct: simulated reads are 42x less ambiguous than real ones, cause unknown

  ncsa/eidolon#658 · Filter by author joshfactorial opened on Sep 1, 2026
  1

• Truth VCF and reads are emitted from parallel paths, so they can disagree — make it structurally impossible

  ncsa/eidolon#628 · Filter by author joshfactorial opened on Aug 29, 2026

• Single breakends are a legitimate call, and eidolon rejects them

  ncsa/eidolon#623 · Filter by author joshfactorial opened on Aug 29, 2026

• Clean up existing clippy findings (160 warnings), starting with too_many_arguments

  enhancement
  ncsa/eidolon#617 · Filter by author joshfactorial opened on Aug 28, 2026

• Audit thiserror usage: which error variants are actually discriminated on vs. pure message-wrapping

  enhancement
  ncsa/eidolon#615 · Filter by author joshfactorial opened on Aug 28, 2026

• Investigate adopting CRAM for BAM output/intermediates to cut Delta disk footprint

  enhancement
  ncsa/eidolon#614 · Filter by author joshfactorial opened on Aug 28, 2026
  5

• Investigate coalescent/population-genetics simulation (msprime, SLiM) for cohort-realistic germline variants

  enhancementexpanded-realism
  ncsa/eidolon#602 · Filter by author joshfactorial opened on Aug 26, 2026