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Allow examples sequences to be loaded together with user submitted by ticking of checkbox
When investigating whether a particular sequences is a contaminant or recombinant, I need to take that sequence in question and spike in some other clades like Delta, Alpha etc.
This is a bit annoying manually, it would be great if there was a checkbox where I could append the example sequences to my user submitted sequence.
this would be quite useful... but we would probably want this to be high quality sequences, rather than our examples with variation in quality.
As a first step I might try to allow dropping or selecting multiple files in Nextclade Web. This way you could provide one file with background sequences and another with the spiked ones. This will look like:
- in the OS file manager or on desktop select multiple files (e.g. holding Shift), and drag them to the drag & drop box together
- click to select a file and select multiple files (e.g. holding Shift, drawing a rectangle around them, or clicking checkboxes if if the file manager has them)
This will only work if the files are dropped/selcted together, i.e. they are easily selectable together (in the same directory). This is somewhat quick and straightforward to implement, I think.
Checkbox with example sequences might be trickier, and will require moving code things around quite a bit, but not impossible.
What if you make ticking of checkbox act like a file being downloaded from URL, while other one is dropped/pasted?
The pain points are twofold right now: 1. Getting the comparison sequences, 2. Joining them together manually
Your suggestion would fix 2, while also being generally useful in broader use cases.
What if you make ticking of checkbox act like a file being downloaded from URL, while other one is dropped/pasted?
Not how it works currently. These 2 places are far away from each other.
Turns out the docs falsely imply that the reference is included in alignment download from web. Am fixing in #693
Having reference by default could be helpful in web downloads in the future.
Implemented in https://github.com/nextstrain/nextclade/pull/859, https://github.com/nextstrain/nextclade/pull/1082