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overlap clipping reproduces fgbio #1090's reference/query distance conflation

Status: Open.

#752 In fulcrumgenomics/fgumi;

· nh13 opened on Aug 14, 2026

codec --rejects omits per-read rejections, so the rejects BAM does not reconcile with --stats

Status: Open.

#751 In fulcrumgenomics/fgumi;

· nh13 opened on Aug 14, 2026

codec rejection reasons are attributed differently from fgbio, making the stats files non-comparable

Status: Open.

#749 In fulcrumgenomics/fgumi;

· nh13 opened on Aug 14, 2026

codec --stats omits five metrics that fgbio emits, though all five are already computed

Status: Open.

#748 In fulcrumgenomics/fgumi;

· nh13 opened on Aug 14, 2026

compare bams prints "Content diffs: 0" when the comparison stopped early

Status: Open.

#747 In fulcrumgenomics/fgumi;

· nh13 opened on Aug 14, 2026

codec exceeds its declared queue memory budget and is OOM-killed when the output device is slow

Status: Open.

#746 In fulcrumgenomics/fgumi;

· nh13 opened on Aug 14, 2026

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

Status: Open.

#726 In fulcrumgenomics/fgumi;

· nh13 opened on Aug 7, 2026

Reads dropped by consensus downsampling are counted as used and never reach --rejects

Status: Open.

#724 In fulcrumgenomics/fgumi;

· nh13 opened on Aug 7, 2026

simplex --max-reads caps the whole MI group instead of each end

Status: Open.

#723 In fulcrumgenomics/fgumi;

· nh13 opened on Aug 7, 2026

Output-collision detection is approximate, and --stats/--metrics are unguarded

Status: Open.

#715 In fulcrumgenomics/fgumi;

· nh13 opened on Aug 5, 2026

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

enhancementNew feature or requestNew feature or request

Status: Open.

#710 In fulcrumgenomics/fgumi;

· nh13 opened on Aug 3, 2026

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

enhancementNew feature or requestNew feature or request

fgumi runall

Status: Open.

#707 In fulcrumgenomics/fgumi;

· nh13 opened on Aug 3, 2026