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Funcotator: suppress a log message about b37 contigs when not doing b…
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…37/hg19 conversion (#8758)

Don't print the very long and misleading "The following contigs are present in b37 and
missing in the input VCF sequence dictionary" log message when we're not even doing b37/hg19
conversion.
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droazen committed Apr 1, 2024
1 parent 105b63e commit 724b5bc
Showing 1 changed file with 1 addition and 1 deletion.
Original file line number Diff line number Diff line change
Expand Up @@ -528,7 +528,7 @@ else if ( funcotatorArgs.referenceVersion.equals(BaseFuncotatorArgumentCollectio
}

// Record whether we need to revert the contigs back to B37 after annotation:
if (FuncotatorUtils.isSequenceDictionaryUsingB37Reference(sequenceDictionaryForDrivingVariants) && mustConvertInputContigsToHg19) {
if (mustConvertInputContigsToHg19 && FuncotatorUtils.isSequenceDictionaryUsingB37Reference(sequenceDictionaryForDrivingVariants)) {
this.mustRevertVariantContigsFromHg19ToB37 = true;
}

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