From 91e330549c9cef439d622db3537d21c102837c59 Mon Sep 17 00:00:00 2001 From: David Roazen Date: Mon, 1 Apr 2024 13:56:09 -0400 Subject: [PATCH] Funcotator: suppress a log message about b37 contigs when not doing b37/hg19 conversion 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. --- .../hellbender/tools/funcotator/FuncotatorEngine.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorEngine.java b/src/main/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorEngine.java index c34b942b148..73a256a794c 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorEngine.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorEngine.java @@ -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; }