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Primers missing from HTML file #19

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DrownedMala opened this issue Nov 4, 2024 · 2 comments
Open

Primers missing from HTML file #19

DrownedMala opened this issue Nov 4, 2024 · 2 comments

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@DrownedMala
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DrownedMala commented Nov 4, 2024

Hello devs,
as suggested in issue #13, I'm opening a new issue for the absence of graphical primers in the HTML output of olivar tiling.
Here I attach the screenshots from my last generated primers (of today):
full
Full screen

partial_olivar
Zoomed-in view: a primer should be seen starting at pos. 71

For reference, I used the olivar-validate python script with the snps module to build the variant file and ran olivar build with default settings, using the eukar db from NCBI as background.
Anyway, even by other means (different tools than the olivar-validate), I still get no primers in the HTML file.

Let me know if I can give you any further helpful info.
Cheers,
Simone

edit: In addition, let me attach the HTML output of olivar-validate validate for the same case:
versus

@mxwang66
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mxwang66 commented Nov 4, 2024

@DrownedMala Thanks for opening this issue!

I did notice people might have different html outputs. Could you share your plotly version and your OS? And I assume you justed used the default parameters for Olivar?

@DrownedMala
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My plotly version is 5.24.1.
OS is Ubuntu 20.04.6 LTS.

Yes, I did run it with default parameters, changing only temperature… But I've also tried leaving temperature as default, and it doesn't change the resulting HTML.
By the way, previous versions of olivar did display the primers correctly.

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