Still working on AS_VarDP

broadinstitute · May 28, 2019 · 789cc37 · 789cc37
1 parent f098d6c
commit 789cc37
Showing 1 changed file with 3 additions and 1 deletion.
diff --git a/.../org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_QualByDepth.java b/.../org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_QualByDepth.java
@@ -16,6 +16,7 @@
 import org.broadinstitute.hellbender.utils.variant.GATKVCFConstants;
 
 import java.util.*;
+import java.util.stream.Collectors;
 
 /**
  * Allele-specific call confidence normalized by depth of sample reads supporting the allele
@@ -118,7 +119,8 @@ public Map<String, Object> finalizeRawData(VariantContext vc, VariantContext ori
 
         final List<Integer> standardDepth;
         if (originalVC.hasAttribute(GATKVCFConstants.AS_VARIANT_DEPTH_KEY)) {
-            standardDepth = originalVC.getAttributeAsString(GATKVCFConstants.AS_VARIANT_DEPTH_KEY, "").split(AnnotationUtils.AS_SPLIT_REGEX);
+            standardDepth = Arrays.stream(originalVC.getAttributeAsString(GATKVCFConstants.AS_VARIANT_DEPTH_KEY, "")
+                    .split(AnnotationUtils.AS_SPLIT_REGEX)).mapToInt(Integer::parseInt).boxed().collect(Collectors.toList());
         } else {
             standardDepth = getAlleleDepths(genotypes);
         }