From 724b5bcb5860dadceb2aa6610dfe2f910cf7d462 Mon Sep 17 00:00:00 2001
From: droazen <droazen@broadinstitute.org>
Date: Mon, 1 Apr 2024 15:27:23 -0400
Subject: [PATCH] Funcotator: suppress a log message about b37 contigs when not
 doing b37/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.
---
 .../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;
         }