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Add alignments track option to 'Hide small indels (less than 10bp)' #4733

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merged 2 commits into from
Dec 19, 2024

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This is something that occurs during long read sequencing a lot

It's hard to find the right balance of what the best behavior is for this setting is as "hifi" reads don't suffer a lot of indels, so it might not make sense to automatically toggle it on, but

for CLR/nanopore where there are a lot of indels, the track can look like this zoomed out

image

but with hide indels turned on, cleans it up a bit...

image

other options include using subpixel rendering so it automatically toggles off at zoomed out scales, this is possible by manually editing the renderer config (minSubfeatureWidth) which could also be exposed via track menu potentially

another option is the 'quick consensus mode' (#4292) but that's a bit trickier. kinda involves calculating snpcoverage type settings, and uses that to inform pileup rendering

@cmdcolin cmdcolin merged commit 1d793a1 into main Dec 19, 2024
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@cmdcolin cmdcolin deleted the hide_small_indels branch December 19, 2024 17:08
@cmdcolin cmdcolin added the enhancement New feature or request label Dec 19, 2024
@cmdcolin cmdcolin changed the title Add option to 'Hide small indels (<10bp)' Add option to 'Hide small indels (less than 10bp)' Jan 29, 2025
@cmdcolin cmdcolin changed the title Add option to 'Hide small indels (less than 10bp)' Add alignments track option to 'Hide small indels (less than 10bp)' Jan 29, 2025
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