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rationalize column headers across CSV output files #1555

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ctb opened this issue May 26, 2021 · 5 comments
Open

rationalize column headers across CSV output files #1555

ctb opened this issue May 26, 2021 · 5 comments
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5.0 issues to address for a 5.0 release
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5.0

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@ctb
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ctb commented May 26, 2021

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.
@ctb ctb added the 5.0 issues to address for a 5.0 release label Jan 6, 2022
@ctb
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ctb commented Jan 6, 2022

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 name, prefetch output has match_name. Grr.

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ctb commented Mar 12, 2022

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.

@ctb ctb mentioned this issue Apr 15, 2022
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@bluegenes bluegenes mentioned this issue Apr 15, 2022
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This was referenced Apr 27, 2022
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@bluegenes bluegenes mentioned this issue Apr 27, 2022
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@ctb ctb mentioned this issue Jun 2, 2022
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@ctb ctb mentioned this issue Sep 8, 2022
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@ctb
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ctb commented Sep 8, 2022

starting to work on this: https://hackmd.io/EdrdrkByQ7a2GuyiN5oyGQ and #2274

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ctb commented Jan 8, 2023

note, docs requested for ANI columns 😓 #2367 (comment)

This was referenced Aug 24, 2023
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@luizirber luizirber added this to the 5.0 milestone Dec 1, 2023
@ctb ctb mentioned this issue Feb 29, 2024
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@bluegenes
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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

@bluegenes bluegenes mentioned this issue Mar 12, 2024
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bluegenes added a commit that referenced this issue Mar 12, 2024
@bluegenes @pre-commit-ci
MRG: enable loading lineages from annotated gather with match_name in…
69edb60 
…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>
@ctb ctb mentioned this issue May 1, 2024
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