[v3] error attaching nodes to tree about nextclade HOT 3 CLOSED

I merged #1208, which should solve the first error.

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@jameshadfield Thanks! Not aware. So this is very valuable.

The first error is reproducible. We will check it with Richard.

Regarding the second error, could you please share the tree (or better full dataset) and the sequence in question, so that we can reproduce and trace the execution?

P.S. This may or may not be related and may or may not be useful information for your work on HBV. Back when working on genome annotation branch, I modified the genemap.gff of this dataset: test_datasets/hbv/files/genemap.gff#L6-L16, so that it has proper gene entries as separate lines. In the original they don't exist and genes are just marked as "gene" attributes on CDSes, which is against GFF3 spec. I haven't changed boundaries or anything else (at least I did not mean to). It is important that all three: reference sequence, reference tree and gene map correspond to each other precisely. Any discrepancies can cause errors or just random pink elephants.

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The second part should be addressed in #1211

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