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Threshold for indicators on SNPCoverage + inverted bargraph of interbase counts for sub-threshold events #1687

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merged 14 commits into from
Feb 19, 2021

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Current code for drawing the insertion draws an indicator if there is even 1 insertion, which can make too many insertion indicators for long noisy reads especially

This adds a threshold based on this so that at least 30% of reads by default would share the indicator. This filters out many false positives I think

In addition to drawing the indicator, I added a "upside down histogram" of the interbase info such as clip/insertion. The upside-down nature emphasizes that these do not contribute to the count in the pileup. This captures things below 30%, and that is especially handy when there is a "region" that has a lot of clipping or the insertion has a fuzzy position by the aligner, which I think is biologically a real phenomenon (see cuteSV paper for how they call fuzzy insertion positions)

Sort of xref #1065

localhost_3000__config=test_data%2Fvolvox%2Fconfig json session=local-zG1O8Um2E (6)
localhost_3000__config=test_data%2Fvolvox%2Fconfig json session=local-zG1O8Um2E (5)
two examples from volvox

localhost_3000__config=test_data%2Fconfig_demo json session=local-9I4yxqofW (1)

example from human, sometimes there are tiny things that can catch your eye that stand out more than background but might not trigger the "indicatorThreshold"

note that the settings for "drawIndicators" and "drawInterbaseFuzz" are configurable booleans, and could be made track menu items

@github-actions github-actions bot added the needs label triage Needs a label to show in changelog (breaking, enhancement, bug, documentation, or internal) label Feb 11, 2021
@cmdcolin cmdcolin marked this pull request as draft February 11, 2021 03:41
@cmdcolin cmdcolin changed the title Threshold for indicators on SNPCoverage a inverted bargraph of interbase counts for sub-threshold events Threshold for indicators on SNPCoverage + inverted bargraph of interbase counts for sub-threshold events Feb 11, 2021
@cmdcolin cmdcolin added enhancement New feature or request and removed needs label triage Needs a label to show in changelog (breaking, enhancement, bug, documentation, or internal) labels Feb 11, 2021
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codecov bot commented Feb 11, 2021

Codecov Report

Merging #1687 (121ab19) into master (045eb53) will decrease coverage by 0.03%.
The diff coverage is 64.86%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master    #1687      +/-   ##
==========================================
- Coverage   58.94%   58.90%   -0.04%     
==========================================
  Files         446      446              
  Lines       20434    20518      +84     
  Branches     4805     4842      +37     
==========================================
+ Hits        12045    12087      +42     
- Misses       8089     8129      +40     
- Partials      300      302       +2     
Impacted Files Coverage Δ
...rc/LinearSNPCoverageDisplay/models/configSchema.ts 100.00% <ø> (ø)
...archicalTrackSelectorWidget/components/Category.js 86.66% <ø> (ø)
...otplot-view/src/DotplotRenderer/DotplotRenderer.ts 64.93% <0.00%> (ø)
...lot-view/src/DotplotView/components/ImportForm.tsx 12.50% <0.00%> (-0.33%) ⬇️
...tenyRenderer/components/LinearSyntenyRendering.tsx 1.75% <0.00%> (-0.07%) ⬇️
...ew/src/LinearSyntenyView/components/ImportForm.tsx 6.66% <0.00%> (-0.16%) ⬇️
plugins/linear-comparative-view/src/index.tsx 35.13% <0.00%> (-1.49%) ⬇️
...aseLinearDisplay/models/BaseLinearDisplayModel.tsx 73.86% <ø> (ø)
...LinearWiggleDisplay/components/SetMinMaxDialog.tsx 3.84% <0.00%> (-1.16%) ⬇️
...se-react-linear-genome-view/src/createViewState.ts 42.85% <0.00%> (ø)
... and 28 more

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@cmdcolin cmdcolin force-pushed the indicator_threshold branch 6 times, most recently from ac99b5c to 6025e18 Compare February 16, 2021 04:45
@cmdcolin cmdcolin force-pushed the indicator_threshold branch from 6025e18 to 569c3bd Compare February 16, 2021 21:52
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Marking this as ready for review. I think the indicators end up being much more reasonable than having an indicator for every insertion

@cmdcolin cmdcolin marked this pull request as ready for review February 16, 2021 22:02
@rbuels rbuels merged commit 4b62426 into master Feb 19, 2021
@rbuels rbuels deleted the indicator_threshold branch February 19, 2021 21:19
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