Issues

• feat(simulate): read per-CpG methylation truth from a VCF (--methylation-vcf)

  fulcrumgenomics/fgumi#1009 · Filter by author nh13 opened on Oct 1, 2026

• perf(consensus): D-space accumulation for consensus base calling (follow-up to #973)

  fulcrumgenomics/fgumi#974 · Filter by author nh13 opened on Sep 18, 2026
  1

• feat(codec): warn when a high dovetail fraction indicates untrimmed library structure

  fulcrumgenomics/fgumi#864 · Filter by author nh13 opened on Aug 25, 2026

• Investigate calling CODEC duplex consensus across the full unclipped overlap instead of clamping to the aligned intersection

  enhancementfgumi codec
  fulcrumgenomics/fgumi#862 · Filter by author nh13 opened on Aug 24, 2026
  1

• perf(sort): zero-copy Phase-1 ingest — retain decompressed blocks, ref into them

  fulcrumgenomics/fgumi#847 · Filter by author nh13 opened on Aug 20, 2026
  1

• perf: replace per-read SipHash in IdentityUmiAssigner::assign with a dense-index scan

  enhancementfgumi group
  fulcrumgenomics/fgumi#835 · Filter by author nh13 opened on Aug 19, 2026

• perf(sort): honor --check-crc / skip BGZF CRC in the fgumi-sort reader stack

  fulcrumgenomics/fgumi#817 · Filter by author nh13 opened on Aug 18, 2026

• Tracker: adopt dupblaster IO/dedup optimizations into fgumi

  fulcrumgenomics/fgumi#786 · Filter by author nh13 opened on Aug 16, 2026

• perf(sort): would a Pod queryname key allow radix-sorting queryname?

  enhancementfgumi sort
  fulcrumgenomics/fgumi#726 · Filter by author nh13 opened on Aug 7, 2026

• perf(sort): skip the sort entirely when the input header already declares the requested order

  enhancementfgumi sort
  fulcrumgenomics/fgumi#710 · Filter by author nh13 opened on Aug 3, 2026

• Deadlock watchdog: a ByteBounded edge of zero-heap items reads as zero bytes in flight

  enhancementfgumi runall
  fulcrumgenomics/fgumi#707 · Filter by author nh13 opened on Aug 3, 2026

• umi: paired's k>1 BK-tree path is unmeasured, and the edit index has no -e 2/-e 3 benchmark arm

  fgumi grouphygiene
  fulcrumgenomics/fgumi#664 · Filter by author nh13 opened on Jul 26, 2026

• audit: consensus tag integer widths differ between the BAM and SAM input paths

  bugfgumi filter
  fulcrumgenomics/fgumi#655 · Filter by author nh13 opened on Jul 25, 2026

• perf: TemplateIterator allocates a RawRecord per record; needs a buffer pool

  enhancementraw-bam
  fulcrumgenomics/fgumi#654 · Filter by author nh13 opened on Jul 25, 2026

• sort (feat-runall): --max-memory auto reserves the full budget up front in the arena front

  bugfgumi runallfgumi sort
  fulcrumgenomics/fgumi#481 · Filter by author nh13 opened on Jul 7, 2026

• perf(bgzf): adopt store-only write fast path + optional CRC-skip from bgzf#11

  enhancement
  fulcrumgenomics/fgumi#478 · Filter by author nh13 opened on Jul 4, 2026
  1

• feat(extract): generalize read-name UMI extraction into a delimited-field "read-name structure"

  enhancementfgumi extract
  fulcrumgenomics/fgumi#477 · Filter by author nh13 opened on Jul 3, 2026

• runall: fused extract→filter sort phase OOMs on 30 GiB host at every threads tried (synth-xlarge)

  bugfgumi runall
  fulcrumgenomics/fgumi#382 · Filter by author nh13 opened on Jun 8, 2026
  2

• perf(sort): investigate marginal-spill recovery for k-way merge

  enhancementfgumi sort
  fulcrumgenomics/fgumi#260 · Filter by author nh13 opened on Apr 12, 2026

• Allow variable-length UMIs

  enhancementfgumi correctfgumi group
  fulcrumgenomics/fgumi#189 · Filter by author TimD1 opened on Mar 26, 2026
  1

• chore: revert manual publish workflow after release-plz fixes dev-dep ordering

  continuous-integration
  fulcrumgenomics/fgumi#141 · Filter by author nh13 opened on Feb 28, 2026

• RUSTSEC-2024-0436: paste - no longer maintained

  dependencies
  fulcrumgenomics/fgumi#26 · Filter by author github-actions opened on Jan 27, 2026
  2