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Threshold for indicators on SNPCoverage + inverted bargraph of interbase counts for sub-threshold events #1687
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Codecov Report
@@ Coverage Diff @@
## master #1687 +/- ##
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- Coverage 58.94% 58.90% -0.04%
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Files 446 446
Lines 20434 20518 +84
Branches 4805 4842 +37
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+ Hits 12045 12087 +42
- Misses 8089 8129 +40
- Partials 300 302 +2
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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 |
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
two examples from volvox
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