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Funcotator reference compatibility logging #7757

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jonn-smith opened this issue Apr 6, 2022 · 0 comments · Fixed by #7760
Closed

Funcotator reference compatibility logging #7757

jonn-smith opened this issue Apr 6, 2022 · 0 comments · Fixed by #7760

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@jonn-smith
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Funcotator checks the VCF input sequence dictionary to see if it corresponds to the b37 reference so that it can automatically convert b37 variants to hg19.

In the case where a partial b37 sequence dictionary is provided, funcotator should emit a warning message stating that the sequence dictionary could be b37 but because it's incomplete, it cannot do the automatic conversion.

The code that must be changed for this is in FuncotatorEngine::determineReferenceAndDatasourceCompatibility and FuncotatorUtils::isSequenceDictionaryUsingB37Reference.

droazen pushed a commit that referenced this issue Apr 8, 2022
* Added logging statements to b37 conversion process.

Fixes #7757
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