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feat: introduce genome metadata tracking and CSV export #2

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coissac merged 1 commits from push-zrlrptrsrlkk into main 2026-05-22 07:36:11 +00:00
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coissac commented 2026-05-22 07:36:01 +00:00
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This commit replaces raw string genome labels with a structured GenomeInfo type for better metadata tracking. It adds a --meta flag to the index command, and implements a new annotate CLI subcommand to import metadata from CSV files or export it via --dump. Distance and shared-count matrices are now serialized to CSV, with UPGMA clustering trees exported as Newick files. Query outputs now include per-genome k-mer match counts in JSON, while fixing syntax and variable naming issues in index merging and dump generation.

This commit replaces raw string genome labels with a structured `GenomeInfo` type for better metadata tracking. It adds a `--meta` flag to the index command, and implements a new `annotate` CLI subcommand to import metadata from CSV files or export it via `--dump`. Distance and shared-count matrices are now serialized to CSV, with UPGMA clustering trees exported as Newick files. Query outputs now include per-genome k-mer match counts in JSON, while fixing syntax and variable naming issues in index merging and dump generation.
coissac added 1 commit 2026-05-22 07:36:02 +00:00
feat: introduce genome metadata tracking and CSV export 0f8f61d3dd 
This commit replaces raw string genome labels with a structured `GenomeInfo` type for better metadata tracking. It adds a `--meta` flag to the index command, and implements a new `annotate` CLI subcommand to import metadata from CSV files or export it via `--dump`. Distance and shared-count matrices are now serialized to CSV, with UPGMA clustering trees exported as Newick files. Query outputs now include per-genome k-mer match counts in JSON, while fixing syntax and variable naming issues in index merging and dump generation.
coissac merged commit 3d58a32613 into main 2026-05-22 07:36:11 +00:00
coissac deleted branch push-zrlrptrsrlkk 2026-05-22 07:36:11 +00:00
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Reference: OBIKmers/obikmer#2
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