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

Status: Open.

#473 In fg-labs/bwa-mem3;

· nh13 opened on Sep 5, 2026

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

Status: Open.

#438 In fg-labs/bwa-mem3;

· 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)

Status: Open.

#402 In fg-labs/bwa-mem3;

· 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)

Status: Open.

#375 In fg-labs/bwa-mem3;

· nh13 opened on Aug 16, 2026

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

Status: Open.

#238 In fg-labs/bwa-mem3;

· nh13 opened on Jul 21, 2026

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

Status: Open.

#196 In fg-labs/bwa-mem3;

· matthdsm opened on Jul 2, 2026

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

Status: Open.

#188 In fg-labs/bwa-mem3;

· nh13 opened on Jun 30, 2026

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

Status: Open.

#159 In fg-labs/bwa-mem3;

· nh13 opened on Jun 18, 2026

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

Status: Open.

#146 In fg-labs/bwa-mem3;

· nh13 opened on Jun 17, 2026

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

Status: Open.

#136 In fg-labs/bwa-mem3;

· nh13 opened on Jun 15, 2026

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

Status: Open.

#127 In fg-labs/bwa-mem3;

· 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

Status: Open.

#120 In fg-labs/bwa-mem3;

· nh13 opened on May 20, 2026