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view: opt into htslib dense single-base BED auto-promotion (#2557) #2561

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13 changes: 13 additions & 0 deletions NEWS
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Original file line number Diff line number Diff line change
Expand Up @@ -79,6 +79,19 @@ Changes affecting specific commands:

bcftools +trio-dnm3 --use-ALM

* bcftools view

- `-R FILE` now opts into htslib's `BCF_SR_AUTO_TARGETS_FROM_REGIONS`
when no `-T` is given. Dense single-base BEDs (HGDP+1kGP, AADR 1240k,
PGS Catalog and similar panels) are routed through the streaming-
targets path instead of doing one tabix iterator setup per BED entry;
the htslib-side sniffer decides per-file whether the file qualifies,
and small / sparse / wide BEDs fall back to the existing seek-per-
region default. Pass `--no-regions-fastpath` to disable. Production
panels see roughly 200-300x speedups at the bcftools-view level (1M
entries: 156 s → 0.7 s on the synthetic reproducer). Requires the
matching htslib change (samtools/htslib PR for #2557).


## Release 1.23.1 (18th March 2026)

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300 changes: 300 additions & 0 deletions test/regions-fastpath.bed
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