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FIX: fix the infra-clade bug#347

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Macabe222 wants to merge 4 commits into
bokulich-lab:mainfrom
Macabe222:taxonomy-merge
Open

FIX: fix the infra-clade bug#347
Macabe222 wants to merge 4 commits into
bokulich-lab:mainfrom
Macabe222:taxonomy-merge

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@Macabe222

@Macabe222 Macabe222 commented Jun 4, 2026

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Description

Addresses a bug where infra-clade nodes could be labeled as is_actual_tip and end up in the table while not being recognized as tips by skbio.Tree.tips(), and thus not ending up in the taxonomy.

Closes #259

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@codecov

codecov Bot commented Jun 4, 2026

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Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 94.53%. Comparing base (044b66f) to head (a66554c).
✅ All tests successful. No failed tests found.

Additional details and impacted files
@@           Coverage Diff           @@
##             main     #347   +/-   ##
=======================================
  Coverage   94.53%   94.53%           
=======================================
  Files          38       38           
  Lines        2854     2854           
  Branches      435      435           
=======================================
  Hits         2698     2698           
  Misses         78       78           
  Partials       78       78           

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@colinvwood

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@misialq, @ebolyen does this look okay?

@misialq misialq changed the title Fixes infra-clade bug FIX: fix the infra-clade bug Jun 11, 2026
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BUG: Error while converting Kraken2 reports (on dereplicated MAGs) to taxonomy

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