fix: clade mismatch against nearest node #1526
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After the query node placement is adjusted during the [greedy tree building](https://docs.nextstrain.org/projects/nextclade/en/stable/user/algorithm/03-phylogenetic-placement.html#tree-building), sometimes the branch needs to be split and a new internal node inserted. Currently we copy the clade of this internal node from the attachment target node. However, this is not always correct and can lead to mismatch between clade of the query node and of the new internal node. Here I add a voting mechanism (simply a mode) between clades involved: of the parent, target and query nodes.
ivan-aksamentov
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…rest node" This reverts commit ee51953.
ivan-aksamentov
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Oct 18, 2024
Followup of: #1526 Additionally to moving clade let's also move "aa" label
rneher
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Oct 18, 2024
This just extends the voting to not only clade_membership clade, but to other clade-like attributes which might be present on the tree (in `.meta.extensions.nextclade`)
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when I try the query sequence linked in the issue with the RSV-A dataset, it seems that the new internal node didn't get a clade assigned for clade-like attribute
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It was missing the `.value`
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Resolves #1525
After the query node placement is adjusted during the greedy tree building, sometimes the branch needs to be split and a new internal node inserted.
Currently we copy the clade of this internal node from the attachment target node. However, this is not always correct and can lead to mismatch between clade of the query node and of the new internal node.
Here I add a voting mechanism (simply a mode) between clades involved: of the parent, target and query nodes.