From 1e3ea654fbbbb11916a55b7caf44fe54509fc700 Mon Sep 17 00:00:00 2001
From: Jules Jacobsen <j.jacobsen@qmul.ac.uk>
Date: Thu, 22 Feb 2024 23:38:22 +0000
Subject: [PATCH] Revert broken AbstractAnalysisRunner

---
 .../exomiser/core/analysis/AbstractAnalysisRunner.java          | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/AbstractAnalysisRunner.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/AbstractAnalysisRunner.java
index 258eeb8c2..39533b335 100644
--- a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/AbstractAnalysisRunner.java
+++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/AbstractAnalysisRunner.java
@@ -131,7 +131,7 @@ public AnalysisResults run(Sample sample, Analysis analysis) {
         List<Gene> genesToScore = variantsLoaded ? getGenesWithVariants(allGenes) : allGenes.values().stream().filter(genesToScore()).toList();
         // Temporarily add a new PValueGeneScorer so as not to break semver will revert to RawScoreGeneScorer in 14.0.0
         CombinedScorePvalueCalculator combinedScorePvalueCalculator = buildCombinedScorePvalueCalculator(sample, analysis, genesToScore.size());
-        GeneScorer geneScorer = new PvalueGeneScorer(probandIdentifier, sample.getSex(), inheritanceModeAnnotator, combinedScorePvalueCalculator, genomeAnalysisService);
+        GeneScorer geneScorer = new PvalueGeneScorer(probandIdentifier, sample.getSex(), inheritanceModeAnnotator, combinedScorePvalueCalculator);
 
         logger.info("Scoring genes");
         List<Gene> genes = geneScorer.scoreGenes(genesToScore);