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fix docs
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psathyrella committed Nov 8, 2023
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Expand Up @@ -102,7 +102,7 @@ The following keys are written to output by default:
| qr_gap_seqs | list of query sequences with gaps at shm indel positions (alignment matches gl_gap_seqs) `[per-seq]`
| duplicates | list of "duplicate" sequences for each sequence. If --collapse-duplicate-sequences is set, then after trimming fv/jf insertions, any identical sequences are collapsed during the smith-waterman step (see also the input meta info [multiplicity key](subcommands.md#input-meta-info), as well as --also-remove-duplicate-sequences-with-different-lengths and --dont-remove-framework-insertions). `[per-seq]`
| tree | simulation only: newick-formatted string of the true phylogenetic tree (inferred trees are included in `tree-info`, in order to accomodate multiple trees inferred by different methods)
| tree-info | inferred tree-related information from various methods (e.g. local branching index/ratio, cons-dist-aa), including associated inferred trees. Written for 'get-tree-metrics' action or when --get-tree-metrics or --get-trees are set. Also can include distance to consensus sequence, since this is used similarly to the actual tree metrics.
| tree-info | inferred tree-related information from various methods (e.g. local branching index/ratio, cons-dist-aa), including associated inferred trees. Written for 'get-selection-metrics' action or when --get-selection-metrics or --get-trees are set. Also can include distance to consensus sequence, since this is used similarly to the actual tree metrics.
| alternative-annotations | summary of alternative annotation information (a.t.m. naive sequences and gene calls), where counts of unique sequences have been normalized to give a number between 0 and 1 that can be interpreted as a (heuristically-derived!) probability of each potential naive sequence and gene call. See --calculate-alternative-annotations and the [view-alternative-annotations](subcommands.md#annotation-uncertainties-alternative-annotations) action for details.

The following keys are available in the dictionary in memory, but not written to disk by default (can be written by setting `--extra-annotation-columns key_a:key_b`):
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