From 789cc37ade1a0d3c6caa130c801ef125e10d5ae3 Mon Sep 17 00:00:00 2001
From: Laura Gauthier <gauthier@broadinstitute.org>
Date: Tue, 28 May 2019 15:34:26 -0400
Subject: [PATCH] Still working on AS_VarDP

---
 .../walkers/annotator/allelespecific/AS_QualByDepth.java      | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_QualByDepth.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_QualByDepth.java
index d18c0c38f04..69d90d637ef 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_QualByDepth.java
+++ b/src/main/java/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);
         }