From de68363c23d0a58a2ce8babf9fa5ef3010239bbe Mon Sep 17 00:00:00 2001
From: Guillermo del Angel <delangel@broadinstitute.org>
Date: Fri, 20 Apr 2012 10:58:34 -0400
Subject: [PATCH] Removed experimental feature (aka hack) that was meant for
 1000G consensus but remained in VQSR data manager - QD was being scaled by
 indel length. There's no evidence any more that QD is length-dependent,
 neither in CEU trio data nor in latest 1000G P2 calls

---
 .../walkers/variantrecalibration/VariantDataManager.java  | 8 --------
 .../VariantRecalibrationWalkersIntegrationTest.java       | 6 +++---
 2 files changed, 3 insertions(+), 11 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
index e2d1692d0..3778cffb8 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
@@ -241,14 +241,6 @@ public class VariantDataManager {
                   value += -0.25 + 0.5 * GenomeAnalysisEngine.getRandomGenerator().nextDouble();
             }
 
-            if (vc.isIndel() && annotationKey.equalsIgnoreCase("QD")) {
-            // normalize QD by event length for indel case
-                int eventLength = Math.abs(vc.getAlternateAllele(0).getBaseString().length() - vc.getReference().getBaseString().length()); // ignore multi-allelic complication here for now
-                if (eventLength > 0) { // sanity check
-                    value /= (double)eventLength;
-                }
-            }
-
             if( jitter && annotationKey.equalsIgnoreCase("HaplotypeScore") && MathUtils.compareDoubles(value, 0.0, 0.0001) == 0 ) { value = -0.2 + 0.4*GenomeAnalysisEngine.getRandomGenerator().nextDouble(); }
             if( jitter && annotationKey.equalsIgnoreCase("FS") && MathUtils.compareDoubles(value, 0.0, 0.001) == 0 ) { value = -0.2 + 0.4*GenomeAnalysisEngine.getRandomGenerator().nextDouble(); }
         } catch( Exception e ) {
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 11e093a6c..879a5bfa3 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
@@ -73,9 +73,9 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
     }
 
     VRTest indel = new VRTest("combined.phase1.chr20.raw.indels.sites.vcf",
-            "6d7ee4cb651c8b666e4a4523363caaff",  // tranches
-            "ee5b408c8434a594496118875690c438",  // recal file
-            "5d7e07d8813db96ba3f3dfe4737f83d1"); // cut VCF
+            "da4458d05f6396f5c4ab96f274e5ccdc",  // tranches
+            "cf380d9b0ae04c8918be8425f82035b4",  // recal file
+            "b00e5e5a6807df8ed1682317948e8a6d"); // cut VCF
 
     @DataProvider(name = "VRIndelTest")
     public Object[][] createData2() {