add Alignments track read grouping

[rbuels]

trafficstars

Group reads by:

• read strand
• first-of-pair strand
• sample
• library
• read group
• chromosome of mate
• pair orientation
• supplementary flag
• read order
• tag
• base at XXXX (centerline position)

[rbuels]

implementation sketch:

• make a new layout class called GroupedLayout that manages a set of GranularRectLayouts, one per grouping
• make the PileupRenderer use this layout for certain render props

[cmdcolin]

just gotta give a +1 to this one, i think it would be really good and it often really clarifies the data to view it in read groups

exciting screenshots like https://pbs.twimg.com/media/Eq66gYtUYAAzZAy?format=png&name=4096x4096 show grouping by haplotype HP tag is quite nice.

[cmdcolin]

note that we can sort of make a hackey approach to group by for example if we (a) copy track and (b) filter by tag in the copied track (once #1473 is added)

[rbuels]

@cmdcolin just noticed this issue was marked "In Progress", what's its status?

[cmdcolin]

It is perhaps stalled? I dunno. I'm not actively working on it but would be cool to see it make progress somehow. We could introduce an extra category on the board if it helps

[cmdcolin]

See https://github.com/GMOD/jbrowse-components/pull/1942 for working demo of this though

[cmdcolin]

periodic motivation for this https://user-images.githubusercontent.com/82141791/215484889-6a032cc0-9c90-4a26-9689-7d5cb41a2ab5.png

from https://github.com/katerinakazantseva/stRainy

[cmdcolin]

my current thinking on this is to make e.g. spawn multiple alignments tracks. this is the easiest implementation wise, is the most general. it may have a bit less usability but it will create e.g. a separate SNPCoverage track for each group which i think can be valuable (igv does not do this)