nextstrain/nextclade: 1.10.0

Nextclade Web 1.13.0, Nextclade CLI 1.10.0, Nextalign CLI 1.10.0 (2022-01-24) [Feature] Detailed split of private mutations (Nextclade) #689

Private mutations (differences between a query sequence and nearest neighbour in reference tree) are now split into three categories:

1. Reversion to reference genotype
2. (SARS-CoV-2 only for now) Mutation to a genotype common in at least 1 clade get labeled with that clade
3. Mutations that are neither reversions nor labeled (called "unlabeled")

Which category a mutation belongs to is visible by hovering over the "Mut." column in Nextclade Web and in various "privateNucMutations" fields in csv/tsv/json outputs.

[Change] "Private mutations" QC rule now accounts for reversions and labeled mutations

Reversions and labeled mutations (see feature above) are particularly common in contaminated samples, coinfections and recombination. To draw the user's attention to such sequences, both types of private mutation now get higher weights in the "Private mutations" QC rule (denoted as "P" in Nextclade Web, and qc.privateMutations in output files).

[Feature] Insertions now also available as amino acids #692

Aminoacid insertions in the query peptides relative to the corresponding reference peptide are now displayed in the "Ins." column in Nextclade Web and are emitted as "aaInsertions" and "totalAminoacidInsertions" fields in Nextalign and Nextclade output files. Note, that similarly to nucleotide insertions, aminoacid insertions are stripped from the output alignment.

[Fix] Gaps in query sequences are now stripped correctly #696

When query sequences contained gaps (-), e.g. when inputting aligned sequences, gaps were not stripped correctly since v1.7.0 (web v1.10.0), which could lead to - showing up in insertions.