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Join ancestral state annotations to sources strictly - #1206
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Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #1206 +/- ##
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+ Coverage 92.18% 92.42% +0.24%
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Files 16 16
Lines 4834 4844 +10
Branches 770 766 -4
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+ Hits 4456 4477 +21
+ Misses 273 263 -10
+ Partials 105 104 -1
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The [ancestral_state] annotation was joined to the sources by position, silently treating ambiguous duplicate rows as unknown and only checking REF alleles at duplicate positions. Sources with inconsistent REF alleles were dropped with a warning. - [ancestral_state] accepts include, exclude, regions and targets filters, applied as for sources. - More than one annotation variant at a site after filtering is an error. - Any difference in REF allele at a site, between the sources or between the sources and the annotation, is an error naming the sources and position. Sources may have different ALT alleles. - Ancestral states ".", "N" and "" are unknown, and sites with an unknown ancestral allele are skipped by augment_sites rather than polarised by parsimony.
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The [ancestral_state] annotation was joined to the sources by position, silently treating ambiguous duplicate rows as unknown and only checking REF alleles at duplicate positions.
Closes #1197