From c752b9bca668b951dc6e7e4c3409299618cebcb8 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Wed, 13 May 2015 11:10:23 -0400
Subject: [PATCH] Fixed a small feature/bug that I introduced with the spanning
 deletions genotyping.

In the case where there's a low quality SNP under a spanning deletion in the gvcfs:
if the SNP is not genotyped by GenotypeGVCFs (because it's just noise) we were still
emitting a record with just the symbolic DEL allele (because that allele is high quality).

We no longer do that.
---
 .../tools/walkers/variantutils/GenotypeGVCFs.java    | 12 +++++++++++-
 .../variantutils/GenotypeGVCFsIntegrationTest.java   | 11 +++++++++++
 2 files changed, 22 insertions(+), 1 deletion(-)

diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFs.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFs.java
index e003bef9d..9e71a0818 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFs.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFs.java
@@ -261,7 +261,7 @@ public class GenotypeGVCFs extends RodWalker<VariantContext, VariantContextWrite
         // only re-genotype polymorphic sites
         if ( result.isVariant() ) {
             VariantContext regenotypedVC = genotypingEngine.calculateGenotypes(result);
-            if ( regenotypedVC == null) {
+            if ( ! isProperlyPolymorphic(regenotypedVC) ) {
                 if (!INCLUDE_NON_VARIANTS)
                     return null;
             }
@@ -295,6 +295,16 @@ public class GenotypeGVCFs extends RodWalker<VariantContext, VariantContextWrite
         return result;
     }
 
+    /**
+     * Determines whether the provided VariantContext has real alternate alleles
+     *
+     * @param vc  the VariantContext to evaluate
+     * @return true if it has proper alternate alleles, false otherwise
+     */
+    private boolean isProperlyPolymorphic(final VariantContext vc) {
+        return ( vc != null && !vc.isSymbolic() );
+    }
+
     /**
      * Add genotyping-based annotations to the new VC
      *
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java
index 514eb5901..d1ac6eca0 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java
@@ -480,4 +480,15 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
         spec.disableShadowBCF();
         executeTest("testMultipleSpanningDeletionsMD5", spec);
     }
+
+    @Test(enabled = true)
+    public void testSpanningDeletionDoesNotGetGenotypedWithNoOtherAlleles() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                "-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
+                        " -V " + privateTestDir + "spanningDel.delOnly.g.vcf",
+                1,
+                Arrays.asList("46169d08f93e5ff57856c7b64717314b"));
+        spec.disableShadowBCF();
+        executeTest("testSpanningDeletionDoesNotGetGenotypedWithNoOtherAlleles", spec);
+    }
 }
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