Issues

• RJ-17: a deletion of an exon's first bases loses its spliced ALT reads (counted VAF 0.04–0.25 at truth 0.5 on the RNA synthetic set)

  msk-access/gbcms#385 · Filter by author rhshah opened on Oct 31, 2026

• J1e — The carrier guard's masks depend on --min-baseq

  msk-access/gbcms#374 · Filter by author rhshah opened on Oct 30, 2026

• J1d — Spanning: a read that does not reach both ends of a repeat-lengthening stretch (judge vs RJ-1, RJ-27)

  msk-access/gbcms#371 · Filter by author rhshah opened on Oct 30, 2026

• J4b — A repeat-aware band floor (the band gap)

  msk-access/gbcms#369 · Filter by author rhshah opened on Oct 29, 2026
  1

• J4a — Path-align as the judge's default

  msk-access/gbcms#368 · Filter by author rhshah opened on Oct 29, 2026

• J1b — A confident third base at a base an MNP changes: carrier depth under the judge; a delins forgives one

  msk-access/gbcms#366 · Filter by author rhshah opened on Oct 29, 2026

• J1c — The SNV tie rule when a read's own base at X is confident (third-base states)

  msk-access/gbcms#367 · Filter by author rhshah opened on Oct 29, 2026

• J1a — A pure deletion's REF reads in a run ending the contig: REF under the judge, depth under the rules

  msk-access/gbcms#365 · Filter by author rhshah opened on Oct 29, 2026

• J7 — REFBASE: measure a delins-only form (partial at a delins, margin at an MNP)

  msk-access/gbcms#364 · Filter by author rhshah opened on Oct 29, 2026

• R1c — Unprepared deletions of 50+ bp skip the junction judge: measure, then route or declare

  msk-access/gbcms#361 · Filter by author rhshah opened on Oct 29, 2026 · 6.7.0

• R1b — The guard reads stored base qualities, classification reads BAQ-adjusted ones: measure on RNA and --apply-baq

  msk-access/gbcms#360 · Filter by author rhshah opened on Oct 29, 2026 · 6.7.0

• R1a — ASJD applies neither sibling guard: measure the asjd_* effect on RNA rows with a sibling

  msk-access/gbcms#359 · Filter by author rhshah opened on Oct 29, 2026 · 6.7.0

• RNA: pin an edited base inside an insertion's inserted bases

  msk-access/gbcms#346 · Filter by author rhshah opened on Oct 27, 2026 · 6.7.0

• RNA: pin strandedness enforcement for antisense reads carrying another allele

  msk-access/gbcms#345 · Filter by author rhshah opened on Oct 27, 2026 · 6.7.0

• RNA: pin per-transcript counts and ASJD where reads carry another allele

  msk-access/gbcms#344 · Filter by author rhshah opened on Oct 27, 2026 · 6.7.0

• #94 RNA follow-ups: pin decided behaviour

  msk-access/gbcms#343 · Filter by author rhshah opened on Oct 27, 2026 · 6.7.0

• Reads only phasing can decide: ways to recover them without trusting placement

  enhancement
  msk-access/gbcms#340 · Filter by author rhshah opened on Oct 26, 2026

• J6 — Switch-over: defaults, docs, migration notes, changelog

  enhancement
  msk-access/gbcms#337 · Filter by author rhshah opened on Oct 26, 2026 · 6.8.0

• J5 — HPC gate with the judge as the default

  enhancement
  msk-access/gbcms#336 · Filter by author rhshah opened on Oct 26, 2026 · 6.8.0

• J4 — Speed within the agreed bound of the rules judge

  enhancement
  msk-access/gbcms#335 · Filter by author rhshah opened on Oct 26, 2026 · 6.8.0
  3

• J3 — Acceptance at the default: every data type and input, two truth sources, the --min-baseq sweep

  enhancement
  msk-access/gbcms#334 · Filter by author rhshah opened on Oct 26, 2026 · 6.8.0

• J2 — RNA mode under the sequence judge

  enhancement
  msk-access/gbcms#333 · Filter by author rhshah opened on Oct 26, 2026 · 6.8.0

• J1 — Tests and contracts pass with the judge as the default; every output path follows its verdict

  enhancement
  msk-access/gbcms#332 · Filter by author rhshah opened on Oct 26, 2026 · 6.8.0

• J — Make the sequence read judge the default

  enhancement
  msk-access/gbcms#331 · Filter by author rhshah opened on Oct 26, 2026 · 6.8.0
  2

• R5b — Retire the rules read judge one release after the haplotype judge becomes the default

  enhancement
  msk-access/gbcms#328 · Filter by author rhshah opened on Oct 24, 2026 · 6.9.0
  1