Update Profiled counts to use WES count when gene panel is not available

cBioPortal · Nov 6, 2024 · cace275 · cace275
1 parent 5ccee88
commit cace275
Showing 1 changed file with 1 addition and 2 deletions.
diff --git a/src/main/java/org/cbioportal/service/impl/AlterationCountServiceImpl.java b/src/main/java/org/cbioportal/service/impl/AlterationCountServiceImpl.java
@@ -285,7 +285,6 @@ public List<AlterationCountByGene> getStructuralVariantGenes(StudyViewFilterCont
     private < T extends AlterationCountByGene> List<T> populateAlterationCounts(@NonNull List<T> alterationCounts,
                                                                                 @NonNull StudyViewFilterContext studyViewFilterContext,
                                                                                 @NonNull AlterationType alterationType) {
-        final int profiledCountWithoutGenePanelData = studyViewRepository.getTotalProfiledCountsByAlterationType(studyViewFilterContext, alterationType.toString());
         var profiledCountsMap = studyViewRepository.getTotalProfiledCounts(studyViewFilterContext, alterationType.toString());
         final var matchingGenePanelIdsMap = studyViewRepository.getMatchingGenePanelIds(studyViewFilterContext, alterationType.toString());
         final int sampleProfileCountWithoutGenePanelData = studyViewRepository.getSampleProfileCountWithoutPanelData(studyViewFilterContext, alterationType.toString());
@@ -298,7 +297,7 @@ private < T extends AlterationCountByGene> List<T> populateAlterationCounts(@Non
 
                 int totalProfiledCount = hasGenePanelData(matchingGenePanelIds) 
                     ? profiledCountsMap.getOrDefault(hugoGeneSymbol, 0) + sampleProfileCountWithoutGenePanelData
-                    : profiledCountWithoutGenePanelData;
+                    : sampleProfileCountWithoutGenePanelData;
 
                 alterationCountByGene.setNumberOfProfiledCases(totalProfiledCount);