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[skip ci] v2.17.0 release announcement (#4653)
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cmdcolin authored Nov 14, 2024
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28 changes: 28 additions & 0 deletions website/release_announcement_drafts/v2.17.0.md
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This release adds

- Improved and bugfixed rendering of modified bases from BAM/CRAM files,
particularly, it matches in many ways the IGV rendering of modified bases [^1]
- Improved performance for ultra-long reads from Nanopore, especially with
zooming in and out and scrolling because it caches the mismatches instead of
re-calculating them repeatedly [^2]
- Improved performance for wiggle tracks, multi-wiggle tracks, and SNP coverage
tracks, particularly changing the height for these track types produces less
re-rendering
- A new data adapter loading BLAST tabular -outfmt 6 alignments for the synteny
view
- Fixed interpretation of the 'ts' tag from minimap2 for RNA-seq strandedness

[^1] Importantly, JBrowse 2 now takes into account the ML tag (likelihood) to
better report the results when tools are providing low probability modification
likelihoods, especially for when there are multiple modification possibilities
at each position (e.g. commonly outputted from Dorado which reported as 'm' and
'h' probabilities, we now only choose the highest likelihood for reporting,
which is in line with interpretation from
[the MM/ML tag specification](https://samtools.github.io/hts-specs/SAMtags.pdf))

[^2] As part of this change, the internals of BAM/CRAM records have been
changed. If you have code that was directly accessing any internal attributes of
these records, it may not work anymore. Please use the feature.get('...') on
features to get data of interest. The .get(...) method is the only "official"
API for accessing data on feature objects, and contact us if you run into any
problems!
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