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rationalize column headers across CSV output files #1555
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might want to include duplicate columns for backwards compat... everything in genome-grist and charcoal will break if we swizzle the names 😆 specific example: gather output has |
I was thinking that a ~clean way to do this would be to add two options, one to use current column names (default in v4.x) and one to switch column names (new); then swizzle the defaults for v5, and deprecate the current column names in 5; and then remove the old column names in v6. |
starting to work on this: https://hackmd.io/EdrdrkByQ7a2GuyiN5oyGQ and #2274 |
note, docs requested for ANI columns 😓 #2367 (comment) |
note that we should now also update these in the rust layer, e.g. https://github.com/sourmash-bio/sourmash/blob/latest/src/core/src/index/mod.rs#L57-L64 |
…stead of name (#3078) This PR enables loading from gather lineages files that contain 'match_name' instead of name. Rationale: - we generally plan to replace 'name' with 'match_name' in gather output (#1555) - branchwater plugin's fastmultigather already uses 'match_name' --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
prefetch and gather use different CSV column headers for their output, and I'm sure so does search and other commands.
Would be good to fix this in v5.
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