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Recombinant lineages #179

Merged
merged 4 commits into from
Jul 25, 2023
Merged

Recombinant lineages #179

merged 4 commits into from
Jul 25, 2023

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Taepper
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@Taepper Taepper commented Jul 24, 2023

Resolves #143

fengelniederhammer
fengelniederhammer reviewed Jul 25, 2023
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I'm not yet sure what the logic should be exactly.

E.g. XB is defined as

  "XB": [
    "B.1.634",
    "B.1.631"
  ]

Should XB also be recognized as sublineage of B.1.634?

If I interpret this PR correctly, so far this is only about "if the alias is array-valued, then we cannot resolve this any further, since it's a recombinant". Are we missing something on that end?

src/silo/preprocessing/pango_lineage_count.cpp Outdated Show resolved Hide resolved
src/silo/storage/pango_lineage_alias.cpp Outdated Show resolved Hide resolved
@Taepper
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Taepper commented Jul 25, 2023

I'm not yet sure what the logic should be exactly.

E.g. XB is defined as

  "XB": [
    "B.1.634",
    "B.1.631"
  ]

Should XB also be recognized as sublineage of B.1.634?

If I interpret this PR correctly, so far this is only about "if the alias is array-valued, then we cannot resolve this any further, since it's a recombinant". Are we missing something on that end?

I asked chaoran about this. All recombinants are to be treated as a new root

@Taepper Taepper merged commit dd69112 into main Jul 25, 2023
4 of 5 checks passed
@Taepper Taepper deleted the recombinantLineages branch July 25, 2023 18:18
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@fengelniederhammer fengelniederhammer fengelniederhammer approved these changes

@chaoran-chen chaoran-chen Awaiting requested review from chaoran-chen

@JonasKellerer JonasKellerer Awaiting requested review from JonasKellerer

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Consider recombinant lineages
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@Taepper @fengelniederhammer