From 6566dd6ca94dd3bc92788c868f33de61bcedec69 Mon Sep 17 00:00:00 2001
From: Ryan Poplin <rpoplin@broadinstitute.org>
Date: Fri, 21 Mar 2014 13:47:05 -0400
Subject: [PATCH] Fix for dropping of reference sample depth in the DP
 annotation. -- In the case of hierarchical merge we can't assume that we have
 only one genotype. -- Removed use of deprecated VC annotation access
 functions.

---
 .../gatk/walkers/variantutils/GenotypeGVCFs.java    |  2 +-
 .../variantutils/GenotypeGVCFsIntegrationTest.java  | 13 +++++++++++++
 .../utils/variant/GATKVariantContextUtils.java      |  9 ++++++---
 3 files changed, 20 insertions(+), 4 deletions(-)

diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeGVCFs.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeGVCFs.java
index 09c291955..89faa29d4 100644
--- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeGVCFs.java
+++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeGVCFs.java
@@ -251,7 +251,7 @@ public class GenotypeGVCFs extends RodWalker<VariantContext, VariantContextWrite
 
             // move the MIN_DP to DP
             if ( oldGT.hasExtendedAttribute("MIN_DP") ) {
-                depth = oldGT.getAttributeAsInt("MIN_DP", 0);
+                depth = Integer.parseInt((String)oldGT.getAnyAttribute("MIN_DP"));
                 builder.DP(depth);
                 attrs.remove("MIN_DP");
             }
diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeGVCFsIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeGVCFsIntegrationTest.java
index 1e2b30fee..fab5a4384 100644
--- a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeGVCFsIntegrationTest.java
+++ b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeGVCFsIntegrationTest.java
@@ -81,6 +81,19 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
         executeTest("combineSingleSamplePipelineGVCF_includeNonVariants", spec);
     }
 
+    @Test(enabled = true)
+    public void combineSingleSamplePipelineGVCFHierarchical() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                baseTestString(" -V " + privateTestDir + "combine.single.sample.pipeline.combined.vcf" +
+                        " -V:sample1 " + privateTestDir + "combine.single.sample.pipeline.1.vcf" +
+                        " -V:sample2 " + privateTestDir + "combine.single.sample.pipeline.2.vcf" +
+                        " -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" +
+                        " -L 20:10,000,000-20,000,000", b37KGReference),
+                1,
+                Arrays.asList("ba07b64d677b0c8306e71695867fd946"));
+        executeTest("combineSingleSamplePipelineGVCFHierarchical", spec);
+    }
+
     @Test(enabled = true)
     public void combineSingleSamplePipelineGVCF_addDbsnp() {
         WalkerTestSpec spec = new WalkerTestSpec(
diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/variant/GATKVariantContextUtils.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/variant/GATKVariantContextUtils.java
index 5670f5871..6fc65bfb3 100644
--- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/variant/GATKVariantContextUtils.java
+++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/variant/GATKVariantContextUtils.java
@@ -1095,10 +1095,13 @@ public class GATKVariantContextUtils {
             mergeRefConfidenceGenotypes(genotypes, vc, remappedAlleles, allelesList);
 
             // special case DP (add it up) for all events
-            if ( vc.hasAttribute(VCFConstants.DEPTH_KEY) )
+            if ( vc.hasAttribute(VCFConstants.DEPTH_KEY) ) {
                 depth += vc.getAttributeAsInt(VCFConstants.DEPTH_KEY, 0);
-            else if ( vc.getNSamples() == 1 && vc.getGenotype(0).hasExtendedAttribute("MIN_DP") ) // handle the gVCF case from the HaplotypeCaller
-                depth += vc.getGenotype(0).getAttributeAsInt("MIN_DP", 0);
+            } else { // handle the gVCF case from the HaplotypeCaller
+                for( final Genotype gt : vc.getGenotypes() ) {
+                    depth += (gt.hasExtendedAttribute("MIN_DP") ? Integer.parseInt((String)gt.getAnyAttribute("MIN_DP")) : (gt.hasDP() ? gt.getDP() : 0));
+                }
+            }
 
             if ( loc.getStart() != vc.getStart() )
                 continue;