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No track menu options when changing alignments display to LinearPileupDisplay #1754

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cmdcolin opened this issue Mar 1, 2021 · 6 comments
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@cmdcolin
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cmdcolin commented Mar 1, 2021

Screenshot showing this

Screenshot from 2021-03-01 14-05-57

@cmdcolin cmdcolin added the bug Something isn't working label Mar 1, 2021
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cmdcolin commented Mar 1, 2021

Just for brainstorming purposes, one option is to investigate this and fix it, probably worthwhile anyways

Another option is actually to make a PileupTrack specialized track type, separate from AlignmentsTrack, and then LinearPileupDisplay would be registered to that instead of being selectable in the "Display types" section (similar for LinearSNPCoverageDisplay)

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cmdcolin commented Mar 1, 2021

Note: v1.0.3 did not experience this bug from what I can tell

Also note: refreshing the page restores them

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cmdcolin commented Mar 1, 2021

Git bisect says 0b263b9 may have introduced the issue

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cmdcolin commented Mar 1, 2021

In some ways this is running into the limitations of https://mobx-state-tree.js.org/tips/inheritance

We also lost the ability to set max score on SNPCoverage track, which was a nice benefit of SNPCoverageDisplay being derived from wiggle, but was lost when we defined a composedTrackMenuItems method on SNPCoverageDisplay, because that overrode the one from LinearWiggleDisplay

@rbuels rbuels added this to To do in JBrowse team board via automation Mar 5, 2021
@rbuels rbuels added this to Incoming in JBrowse team board Mar 5, 2021
@rbuels rbuels moved this from Incoming to Prioritized in JBrowse team board Mar 5, 2021
@cmdcolin
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Is this related to code using displays[0] hardcoded? There are quite a number of places in the code that does this now, and may need to be reigned in

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this was fixed I believe by the change to #2226

makes sense in a way :) the old "get trackMenuItems()" may not have accurately caught what was happening, which the new "trackMenuItems()" works

JBrowse team board automation moved this from Prioritized to Done Aug 25, 2021
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