Purple: minor switch of code ordering

hartwigmedical · Feb 18, 2022 · 46c5cb9 · 46c5cb9
1 parent e1f80b2
commit 46c5cb9
Showing 1 changed file with 7 additions and 7 deletions.
diff --git a/purple/src/main/java/com/hartwig/hmftools/purple/germline/GermlineDeletionDrivers.java b/purple/src/main/java/com/hartwig/hmftools/purple/germline/GermlineDeletionDrivers.java
@@ -115,12 +115,7 @@ else if(currentCnChromosome.equals(chromosome) && !copyNumber.chromosome().equal
             if(matchedCopyNumber == null)
                 continue;
 
-            int cohortFrequency = mCohortFrequency.getRegionFrequency(
-                    region.chromosome(), (int)region.start(), (int)region.end(), GERMLINE_DEL_REGION_MATCH_BUFFER);
-
-            final List<String> filters = checkFilters(region, matchedCopyNumber, cohortFrequency);
-
-            findOverlappingDriverGene(region, filters, cohortFrequency);
+            findOverlappingDriverGene(region, matchedCopyNumber);
         }
     }
 
@@ -159,7 +154,7 @@ private List<String> checkFilters(final FittedRegion region, final PurpleCopyNum
         return filters;
     }
 
-    private void findOverlappingDriverGene(final FittedRegion region, final List<String> filters, int cohortFrequency)
+    private void findOverlappingDriverGene(final FittedRegion region, final PurpleCopyNumber matchedCopyNumber)
     {
         // now find genes
         List<GeneData> geneDataList = mGeneDataCache.getChrGeneDataMap().get(region.chromosome());
@@ -198,6 +193,11 @@ private void findOverlappingDriverGene(final FittedRegion region, final List<Str
         if(overlappingGenes.isEmpty() && driverGenes.isEmpty())
             return;
 
+        int cohortFrequency = mCohortFrequency.getRegionFrequency(
+                region.chromosome(), region.start(), region.end(), GERMLINE_DEL_REGION_MATCH_BUFFER);
+
+        final List<String> filters = checkFilters(region, matchedCopyNumber, cohortFrequency);
+
         int exonRankMin = 0;
         int exonRankMax = 0;
         StringJoiner geneNames = new StringJoiner(";");