From 761347b8d5b71e54bc1db01ec686efe323602c67 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Thu, 30 Jun 2011 15:26:09 -0400
Subject: [PATCH] The VariantContext utility method used by SelectVariants
 wasn't checking the filter status (unfiltered vs. passing filters) and always
 returned a VC that was passing filters.  This is fixed and the md5 from the
 VCF Streaming test has been re-updated.

---
 .../sting/utils/variantcontext/VariantContext.java            | 2 +-
 .../walkers/variantutils/VCFStreamingIntegrationTest.java     | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
index 92262f1bf..3d375aba2 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
@@ -414,7 +414,7 @@ public class VariantContext implements Feature { // to enable tribble intergrati
      * @return vc subcontext
      */
     public VariantContext subContextFromGenotypes(Collection<Genotype> genotypes, Set<Allele> alleles) {
-        return new VariantContext(getSource(), contig, start, stop, alleles, genotypes, getNegLog10PError(), getFilters(), getAttributes());
+        return new VariantContext(getSource(), contig, start, stop, alleles, genotypes, getNegLog10PError(), filtersWereApplied() ? getFilters() : null, getAttributes());
     }
 
 
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VCFStreamingIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VCFStreamingIntegrationTest.java
index 4ed9718fd..cf0673ee6 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VCFStreamingIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VCFStreamingIntegrationTest.java
@@ -60,7 +60,7 @@ public class VCFStreamingIntegrationTest extends WalkerTest {
                     " --NO_HEADER" +
                     " -o %s",
             1,
-            Arrays.asList("995c07ccd593fe1c35d0d28155112a55")
+            Arrays.asList("debbbf3e661b6857cc8d99ff7635bb1d")
         );
 
         executeTest("testSimpleVCFStreaming", spec);
@@ -98,7 +98,7 @@ public class VCFStreamingIntegrationTest extends WalkerTest {
             " -EV CompOverlap -noEV -noST" +
             " -o %s",
             1,
-            Arrays.asList("f60729c900bc8368717653b3fad80d1e")
+            Arrays.asList("f60729c900bc8368717653b3fad80d1e")           //"f60729c900bc8368717653b3fad80d1e"
         );
         executeTest("testVCFStreamingChain", selectTestSpec);