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Add "Group by" method for alignments tracks #4519

Merged
merged 2 commits into from
Aug 19, 2024
Merged

Add "Group by" method for alignments tracks #4519

merged 2 commits into from
Aug 19, 2024

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cmdcolin
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@cmdcolin cmdcolin commented Aug 16, 2024

This creates a 'Group by' feature for alignments tracks. It uses a sort of 'slight of hand' by dynamically adding a series of sessionTracks to the users session, and then launching them individually

Example: there are haplotypes 0 and 1 in the HP tag for a bam file, it create trackname-HP:0 and tracknamee-HP:1 as session tracks with each track having filterBy set to either HP==0 or HP==1, and then launches them

Pros:

  • Fairly easy solution. the software engineering required to change the alignments track to have arbitrary "grouped" subtracks is sort of complicated from what I have tried.
  • Each 'new track' has it's own SNPCoverage track as well as all individualized track settings (this is actually different from igv group by, and could be considered a 'strength' of this approach perhaps)

Cons:

  • Creates a number of subtracks that could by a bit overwhelming for the users config
  • Each subtrack having all individualized track settings makes it hard to change e.g. just the compactness setting across all of them (this is a general problem though even without group by...)
  • Does not 'observe' the current set of tags available after scroll, so can miss things
  • Has to be enabled by going through the "Group by..." dialog, you can't set e.g. colorBy:tag in the config and then it automatically sets this up
  • Has to parse through the data multiple times for each subtrack

fixes #912

@cmdcolin
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result on HP tag in volvox demo

image

menu item

image

dialog box

image

@cmdcolin
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the previous "state of the art" was sort by+color by, which helps distinguish somewhat but is not a full 'group by' solution (picture below)

image

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add Alignments track read grouping
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