Automated flagging of dubious sequences

[theosanderson]

We want to be able to flag questionable sequences

          We also may not have captured in issues @emmahodcroft's (and the rest of us)'s concept around flagging "dubious" sequences

Originally posted by @theosanderson in https://github.com/loculus-project/loculus/issues/1272#issuecomment-1986219631

After handling manual flagging of sequences in: https://github.com/loculus-project/loculus/issues/813 we should move to this more automated flagging, which would probably come from the preprocessing pipeline

• [ ] Add preprocessing warnings/flags to sequence page: https://github.com/loculus-project/loculus/issues/1272
• [ ] Warn if we suspect sequence data is wrong
• [ ] Warn if we suspect sequence data is filled with reference
• [ ] Warn if we suspect sequence data lab adapted strain

[emmahodcroft]

Idea here is if a sequence is suspected to be, ex:

• filled with reference
• vaccine strain
• lab adapted strain

One cannot 'fix' it, but should be able to curate-flag it so it is not included in searches by defaults, and shows up as somehow 'dubious' when people view sequences