Issues

• --dedup-reads never memoizes the first (sliced) batch; a fix measured no gain on a human panel

  fg-labs/bwa-mem3#592 · Filter by author nh13 opened on Oct 13, 2026

• in-process ALT post-processing

  fg-labs/bwa-mem3#570 · Filter by author milkschen opened on Oct 9, 2026

• Make fmi_seed_open failure-safe for C callers (recoverable load_index errors)

  fg-labs/bwa-mem3#487 · Filter by author nh13 opened on Sep 6, 2026

• Investigate promoting --rescue-skip into --fast (gated on exome truth concordance)

  fg-labs/bwa-mem3#473 · Filter by author nh13 opened on Sep 5, 2026
  1

• Whole-aligner uninitialized-read smoke (cover the kswv mate-rescue padded-lane path in situ)

  fg-labs/bwa-mem3#438 · Filter by author nh13 opened on Sep 1, 2026

• feat(mem): opt-in --huge-pages to back the index with 1 GB pages when available (safe no-op otherwise)

  fg-labs/bwa-mem3#402 · Filter by author nh13 opened on Aug 19, 2026

• test: no coverage of -W or the -x long-read presets in the bwa-parity arm (how #310 survived)

  fg-labs/bwa-mem3#375 · Filter by author nh13 opened on Aug 16, 2026

• Long-read (HiFi/ONT) support: bound extension-buffer memory (design + adversarial review)

  fg-labs/bwa-mem3#238 · Filter by author nh13 opened on Jul 21, 2026

• Feature: uBam/uCram input OR fastq header parsing for UMI data

  fg-labs/bwa-mem3#196 · Filter by author matthdsm opened on Jul 2, 2026
  2

• Order-invariant DP chaining: make the --seed-order / --smem-dedup wins default-safe

  fg-labs/bwa-mem3#188 · Filter by author nh13 opened on Jun 30, 2026

• docs(perf): backfill hic-1M / sbx-1M into the mem2-vs-mem3 speedup table

  fg-labs/bwa-mem3#159 · Filter by author nh13 opened on Jun 18, 2026

• [Tracking] 8-bit long-read banded-SW follow-ups: correctness, cleanup, perf

  fg-labs/bwa-mem3#146 · Filter by author nh13 opened on Jun 17, 2026
  3

• mem --meth: pair MAPQ deflated in segmental duplications because C→T/G→A scoring discards copy-distinguishing bases

  fg-labs/bwa-mem3#136 · Filter by author nh13 opened on Jun 15, 2026

• track(correctness): pin the source PR for FG-SUPP-ADDITIONS extra supplementary alignments

  fg-labs/bwa-mem3#127 · Filter by author nh13 opened on Jun 8, 2026

• perf(fmi): cp_count[4] is int64_t but max occ fits in 32 bits for hg-scale references

  fg-labs/bwa-mem3#120 · Filter by author nh13 opened on May 20, 2026

• test: migrate test_bismark_tags.sh from cargo-from-SHA holodeck to pixi-pinned holodeck

  fg-labs/bwa-mem3#91 · Filter by author nh13 opened on May 11, 2026

• track(smem): int16_t cursor overflow at >32Kbp in lockstep SMEM driver

  fg-labs/bwa-mem3#61 · Filter by author nh13 opened on Apr 27, 2026

• track(correctness): investigate unreliable supplementary-alignment MAPQ (upstream #260)

  fg-labs/bwa-mem3#46 · Filter by author nh13 opened on Apr 24, 2026