NEWS For End of 2025 Release.

[whitwham]

This is the NEWS update for the end of 2025 release.

It is here for review and is open for updates until the release.

[daviesrob]

Added a few suggested changes to make things clearer. Feel free to make adjustments if you think they need improving.

[daviesrob]

I think this might be a better description?

Suggested change

	* S3 reading code now reads in `chunks` to minimise S3 reading length when
	doing a range request. Also this combines the reading, writing and
	authorisation code into a single file.
	* S3 reading code now reads in "chunks" to limit the amount of data read (and
	therefore egress costs) from the object store when doing a range request.
	Also this combines the reading, writing and authorisation code into a single
	file.

[daviesrob]

Maybe this should count as a bug? The description looked a bit vague, this might be better:

Suggested change

	* Improved operation of filters that work with header data. Filter expressions
	such as rname, mrname, rnext and library were not working well with iterators.
	* Improved operation of filters that work with header data. Filter expressions
	set as an `HTS_OPT_FILTER` on a BAM or CRAM iterator failed to return
	records matching on `rname`, `mrname`, `rnext` or `library`.

[daviesrob]

Suggested change

	* Recognise the tabix comment character (-c) when reading records.
	* Make tabix skip comments (-c) wherever they occur, not just at the start of
	the file.

[daviesrob]

Suggested change

	* Fix embed_ref=2 on SEQ * and MD:Z tag. The combination of no sequence and
	MD:Z with embed_ref=2 caused the slice extents to be miscalculated.
	* Fix embed_ref=2 on SEQ * and MD:Z tag. The combination of no sequence and
	MD:Z with embed_ref=2 caused the slice extents to be miscalculated,
	causing invalid CRAM output to be written.

[daviesrob]

I think this should be in the Updates section, as it's a fairly significant change in behaviour. This came out a bit long, but I think it's important to highlight exactly what changed here.

Suggested change

	* Internally store phase in VCF4.4 format irrespective of input file format.
	This should prevent problems when dealing with different VCF versions.
	* HTSlib 1.22 changed the VCF reader so that it stored GT prefixed phasing
	information, but only for files specifying `fileformat=VCFv4.4` or higher.
	This caused problems when merging files with different versions, so the
	VCF reader will now store prefixed phasing information irrespective of
	the VCF version listed in the file headers. For files up to VCFv4.3, the
	first phasing bit will be set if all other alleles are phased, and cleared
	otherwise (following the rules for VCFv4.4 onwards where no explicit
	phasing symbol is present). This will also happen when reading BCF.
	When accessing GT data, it is no longer safe to assume that the phasing
	is set to zero even if the file reports a version earlier than VCFv4.4.
	Interfaces such as `bcf_gt_allele()` should always be used to access
	GT allele data.
	For compatibility, prefixed phasing will be stripped when writing VCF
	files with version 4.3 or earlier.

[daviesrob]

Suggested change

	* Prevent the dropping of in-flight decode jobs when seeking in
	cram_next_slice().
	* Fix bug where multi-threaded CRAM iterators could drop long alignments
	starting significantly before, but overlapping, the region of interest.