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[skip ci] v2.17.0 release announcement (#4653)
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This release adds | ||
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- 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 | ||
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[^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)) | ||
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[^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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