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Add --sensitive and --conservative flags #45

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GallVp opened this issue Jul 1, 2024 · 3 comments
Open

Add --sensitive and --conservative flags #45

GallVp opened this issue Jul 1, 2024 · 3 comments
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discussion needed Further discussion is needed enhancement New feature or request

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@GallVp
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GallVp commented Jul 1, 2024

  • By default, turn off enforce_full_intron_support, filter_liftoff_by_hints
@GallVp GallVp self-assigned this Jul 1, 2024
@GallVp GallVp added the enhancement New feature or request label Jul 1, 2024
@GallVp GallVp added this to the 0.4.0 milestone Jul 1, 2024
@GallVp GallVp modified the milestones: 0.4.0, backlog Jul 30, 2024
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GallVp commented Jul 30, 2024 •
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This can create confusion. If --sensitive overrides other parameters, it adds another layer of complexity in understanding how the parameters work.

Perhaps the best solution is to suggest a few parameter profiles in the docs.

@GallVp GallVp modified the milestones: backlog, 0.4.0 Sep 16, 2024
@GallVp GallVp added the discussion needed Further discussion is needed label Sep 23, 2024
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GallVp commented Sep 30, 2024

Add a redirect to conservative/sensitive sets on the main README under usage: https://github.com/PlantandFoodResearch/genepal/tree/dev?tab=readme-ov-file#usage

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GallVp commented Sep 30, 2024

Defer this issue till we have data to show the effect of each parameter.

@GallVp GallVp modified the milestones: 0.4.0, backlog Sep 30, 2024
@GallVp GallVp removed their assignment Nov 20, 2024
@GallVp GallVp removed this from the backlog milestone Nov 21, 2024
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