Colin Diesh

This is an experimental PR that is somewhat of a large refactor aiming to fix issues like https://github.com/GMOD/jbrowse-components/issues/3965 The use of mixins allows shared functionality but it also has caused...

Performing whole genome overviews, like with proposed synteny viewer launcher puts a very large list of displayedRegions into the session This overloads localStorage We could create a custom encoding Possible...

Possible fix for https://github.com/GMOD/jbrowse-components/issues/4844 The layout does not get 'cleaned up' as long as you stay at the same zoom level, and now feature data is stored in the layout...

Potential fix for [https://github.com/GMOD/jbrowse-components/security/code-scanning/13](https://github.com/GMOD/jbrowse-components/security/code-scanning/13) To mitigate prototype pollution risk, we must prevent dangerous property names such as `__proto__`, `constructor`, and (optionally) `prototype` from being copied or merged. The best way...

Create helper functions for static blocks and dynamic blocks calculations, and tests to ensure synchronized settings

2

Alternate approach to https://github.com/GMOD/jbrowse-components/pull/5237 Instead of calculateDynamicBlocks derive from calculateStaticBlocks, which involves having to undo various things that static blocks does (e.g. the calculateDynamicBlocks in #5237 has to 'merge blocks'...

Follow ups to multi-variant rendering

16

- allow deleting rows - allow renaming rows - add legend - add ability to customize color - add ability to cluster individual haplotype rows from phased VCF - configurable...

Support CS tag in synteny rendering

2

CS tag is an alternative to CIGAR that makes it easier to tell where SNPs are https://github.com/lh3/minimap2#the-cs-optional-tag Currently we draw insertions and deletions, but showing where mismatches are would likely...

Showing whole-genome overviews can be slow because large amounts of CIGAR data and other tags can slow down the data fetching and display code. This proposes making our make-pif format...

Initialize pluginManager without any tracks loaded at first, and then load rest of config secondarily

1

this could open the door to allowing plugins the ability to pre-process an entire config This might help with use cases such as the genomes.jbrowse.org jb2hubs (example motivation related to...

Optionally use "Virtual scrollbars" instead of native scrollbars on per-track scrolling

2

This PR adds the option to change per-track scrolls into "virtual scrollbars" that do not respect normal vertical wheel scroll by default Instead, you must do the following to perform...