From 811a7e8cd689f465160102e976f3049c2a2c5d9d Mon Sep 17 00:00:00 2001
From: "Zhaoyuan (Ryan) Fu" <fuzhaoyuan@gmail.com>
Date: Fri, 17 Jan 2025 15:31:15 -0500
Subject: [PATCH] Fix not using correct profiled count

---
 .../cbioportal/service/impl/StudyViewServiceImpl.java    | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/src/main/java/org/cbioportal/service/impl/StudyViewServiceImpl.java b/src/main/java/org/cbioportal/service/impl/StudyViewServiceImpl.java
index 05ea4056aee..67276a42b38 100644
--- a/src/main/java/org/cbioportal/service/impl/StudyViewServiceImpl.java
+++ b/src/main/java/org/cbioportal/service/impl/StudyViewServiceImpl.java
@@ -161,12 +161,15 @@ public List<GenomicDataCountItem> getMutationCountsByGeneSpecific(List<String> s
             .map(Gene::getEntrezGeneId)
             .toList();
 
-        List<AlterationCountByGene> alterationCountByGenes = alterationCountService.getSampleMutationGeneCounts(
+        Pair<List<AlterationCountByGene>, Long> alterationCountsWithProfiledTotal = alterationCountService.getSampleMutationGeneCounts(
             caseIdentifiers,
             Select.byValues(entrezGeneIds),
             true,
             false,
-            alterationFilter).getFirst();
+            alterationFilter);
+        
+        List<AlterationCountByGene> alterationCountByGenes = alterationCountsWithProfiledTotal.getFirst();
+        Long totalProfiledCases = alterationCountsWithProfiledTotal.getSecond();
 
         return genomicDataFilters
             .stream()
@@ -184,7 +187,7 @@ public List<GenomicDataCountItem> getMutationCountsByGeneSpecific(List<String> s
                 
                 int totalCount = sampleIds.size();
                 int mutatedCount = 0;
-                int profiledCount = 0;
+                int profiledCount = Math.toIntExact(totalProfiledCases);
                 
                 if(filteredAlterationCount.isPresent()) {
                     mutatedCount = filteredAlterationCount.get().getNumberOfAlteredCases();