Issues

• Truth VCF writes lowercase SV REF and BND anchors on a soft-masked reference

  ncsa/eidolon#790 · Filter by author joshfactorial opened on Sep 30, 2026

• Apply a substitution matrix per read-position bin, with the bin count chosen from data

  enhancement
  ncsa/eidolon#784 · Filter by author joshfactorial opened on Sep 29, 2026

• 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

• Two unreproduced paths to a zero-weight distribution in gen-seq-error-model

  bugLow priority
  ncsa/eidolon#767 · Filter by author joshfactorial opened on Sep 26, 2026

• gen-mut-model discards observed indel lengths when a VCF has only insertions or only deletions

  bugLow priority
  ncsa/eidolon#766 · Filter by author joshfactorial opened on Sep 26, 2026

• Three harness suites have no --mutate, so the CI step proving non-vacuity is itself vacuous

  testing
  ncsa/eidolon#755 · Filter by author joshfactorial opened on Sep 23, 2026

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

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

• 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

• gen-seq-error-model's max_reads takes the first N records, which is one flowcell tile

  bug
  ncsa/eidolon#721 · Filter by author joshfactorial opened on Sep 16, 2026

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

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

• ins_skew 2.4x: fragment model reproduces width and p99 but not asymmetry

  ncsa/eidolon#696 · Filter by author joshfactorial opened on Sep 8, 2026

• 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

• gen-reads plans fragments past the end of a haplotype

  bug
  ncsa/eidolon#691 · Filter by author joshfactorial opened on Sep 6, 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

• somatic_snv_recall sits 4.5 sigma below baseline, replicated on two builds

  ncsa/eidolon#680 · Filter by author joshfactorial opened on Sep 5, 2026
  3

• 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

• 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