From 6dfcc486e81a4ac3350ebfc3ffa8d4659d700005 Mon Sep 17 00:00:00 2001
From: Khalid Shakir <kshakir@broadinstitute.org>
Date: Fri, 13 Jul 2012 15:40:56 -0400
Subject: [PATCH] In ApplyRecalibration marking filter as PASS instead of '.'
 when the site passes by calling .passFilters().

---
 .../ApplyRecalibration.java                   |  6 ++++--
 ...ntRecalibrationWalkersIntegrationTest.java | 20 +++++++++++++++----
 2 files changed, 20 insertions(+), 6 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
index f95e5647c..0dfdd4ba1 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
@@ -172,7 +172,7 @@ public class ApplyRecalibration extends RodWalker<Integer, Integer> implements T
         vcfWriter.writeHeader(vcfHeader);
     }
 
-    public static final void addVQSRStandardHeaderLines(final Set<VCFHeaderLine> hInfo) {
+    public static void addVQSRStandardHeaderLines(final Set<VCFHeaderLine> hInfo) {
         hInfo.add(VCFStandardHeaderLines.getInfoLine(VCFConstants.END_KEY));
         hInfo.add(new VCFInfoHeaderLine(VariantRecalibrator.VQS_LOD_KEY, 1, VCFHeaderLineType.Float, "Log odds ratio of being a true variant versus being false under the trained gaussian mixture model"));
         hInfo.add(new VCFInfoHeaderLine(VariantRecalibrator.CULPRIT_KEY, 1, VCFHeaderLineType.String, "The annotation which was the worst performing in the Gaussian mixture model, likely the reason why the variant was filtered out"));
@@ -236,7 +236,9 @@ public class ApplyRecalibration extends RodWalker<Integer, Integer> implements T
                     filterString = tranches.get(0).name+"+";
                 }
 
-                if( !filterString.equals(VCFConstants.PASSES_FILTERS_v4) ) {
+                if( filterString.equals(VCFConstants.PASSES_FILTERS_v4) ) {
+                    builder.passFilters();
+                } else {
                     builder.filters(filterString);
                 }
 
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
index 393905961..2411f9e08 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
@@ -18,6 +18,11 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
             this.recalMD5 = recalMD5;
             this.cutVCFMD5 = cutVCFMD5;
         }
+
+        @Override
+        public String toString() {
+            return "VRTest{inVCF='" + inVCF +"'}";
+        }
     }
 
     VRTest lowPass = new VRTest("phase1.projectConsensus.chr20.raw.snps.vcf",
@@ -69,14 +74,21 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
         executeTest("testApplyRecalibration-"+params.inVCF, spec);
     }
 
-    VRTest indel = new VRTest("combined.phase1.chr20.raw.indels.sites.vcf",
+    VRTest indelUnfiltered = new VRTest(
+            "combined.phase1.chr20.raw.indels.unfiltered.sites.vcf", // all FILTERs as .
             "b7589cd098dc153ec64c02dcff2838e4",  // tranches
             "a04a9001f62eff43d363f4d63769f3ee",  // recal file
-            "888eb042dd33b807bcbb8630896fda94"); // cut VCF
+            "64f576881e21323dd4078262604717a2"); // cut VCF
+
+    VRTest indelFiltered = new VRTest(
+            "combined.phase1.chr20.raw.indels.filtered.sites.vcf", // all FILTERs as PASS
+            "b7589cd098dc153ec64c02dcff2838e4",  // tranches
+            "a04a9001f62eff43d363f4d63769f3ee",  // recal file
+            "af22c55d91394c56a222fd40d6d54781"); // cut VCF
 
     @DataProvider(name = "VRIndelTest")
-    public Object[][] createData2() {
-        return new Object[][]{ {indel} };
+    public Object[][] createTestVariantRecalibratorIndel() {
+        return new Object[][]{ {indelUnfiltered}, {indelFiltered} };
     }
 
     @Test(dataProvider = "VRIndelTest")