minor updates

broadinstitute · Nov 25, 2024 · 5a8e612 · 5a8e612
1 parent 76bd38c
commit 5a8e612
Showing 1 changed file with 1 addition and 5 deletions.
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/gvs/extract/ExtractCohortEngine.java b/src/main/java/org/broadinstitute/hellbender/tools/gvs/extract/ExtractCohortEngine.java
@@ -310,6 +310,7 @@ public void traverse() {
                     fullYngMap.get(location).putIfAbsent(ref, new HashMap<>());
                     fullYngMap.get(location).get(ref).put(alt, yng);
                 }
+                logger.info("Processed " + recordsProcessed + " filter set info records, dropped " + recordsDropped + ".");
                 processBytesScanned(reader);
             }
         }
@@ -1106,8 +1107,6 @@ private VariantIterables createVariantIterablesFromUnsortedBigQueryRanges(
                 vbs);
 
         return new VariantIterables(sortedVet, sortedReferenceRange);
-
-        // createVariantsFromSortedRanges(sampleIdsToExtract, sortedVet, sortedReferenceRange, fullScoreMap, fullVQScoreMap, fullYngMap, samplePloidyMap, siteFilterMap, noVQScoreFilteringRequested);
     }
 
     //
@@ -1138,7 +1137,6 @@ private VariantIterables createVariantIterablesFromUnsortedExtractTableBigQueryR
                 localSortMaxRecordsInRam,
                 vbs);
 
-        // createVariantsFromSortedRanges(sampleIdsToExtract, sortedVet, sortedReferenceRange, fullScoreMap, fullVQScoreMap, fullYngMap, samplePloidyMap, siteFilterMap, noVQScoreFilteringRequested);
         return new VariantIterables(sortedVet, sortedReferenceRange);
     }
 
@@ -1224,8 +1222,6 @@ private VariantIterables createVariantsIterablesFromUnsortedAvroRanges(
             sortedReferenceRange = localSortedReferenceRange;
         }
 
-        // createVariantsFromSortedRanges(sampleIdsToExtract, sortedVet, sortedReferenceRange, fullScoreMap, fullVQScoreMap, fullYngMap, samplePloidyMap, siteFilterMap, noVQScoreFilteringRequested);
-
         return new VariantIterables(sortedVet, sortedReferenceRange);
     }