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The --fast mode noticeably reduce mapping accuracy

Status: Open.

#202 In fg-labs/bwa-mem3;

· lh3 opened on Jul 5, 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

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

Status: Open.

#91 In fg-labs/bwa-mem3;

· nh13 opened on May 11, 2026

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

Status: Open.

#61 In fg-labs/bwa-mem3;

· nh13 opened on Apr 27, 2026

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

Status: Open.

#46 In fg-labs/bwa-mem3;

· nh13 opened on Apr 24, 2026