Add keep_all option for additional_inputs and sequence_source column#123
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Add keep_all option for additional_inputs and sequence_source column#123
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Additional inputs specified under `additional_inputs` in the config are now subsampled by default (preserving previous behavior). Setting `keep_all: True` on an additional input force-includes all its sequences, bypassing subsampling and quality filters. A `sequence_source` metadata column is added whenever any additional inputs are present, labeling sequences by their input name or "Pathoplexus" for background sequences. This enables coloring and filtering by origin in Auspice. Addresses [this issue](#122). Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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Additional inputs specified under
additional_inputsin the config are now subsampled by default (preserving previous behavior). Settingkeep_all: Trueon an additional input force-includes all its sequences, bypassing subsampling and quality filters.A
sequence_sourcemetadata column is added whenever any additional inputs are present, labeling sequences by their input name or "Pathoplexus" for background sequences. This enables coloring and filtering by origin in Auspice.Addresses this issue.