From b807ff63efe7b9f92afe3dae8302c986e64fea99 Mon Sep 17 00:00:00 2001
From: Ryan Poplin <rpoplin@broadinstitute.org>
Date: Mon, 2 Jul 2012 16:37:39 -0400
Subject: [PATCH] HaplotypeCaller now creates MNP and complex substitutions by
 using LD information to decide if events segregate together on haplotypes.
 Added unit test.

---
 .../gatk/walkers/annotator/ClippingRankSumTest.java      | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ClippingRankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ClippingRankSumTest.java
index aeb01bf3e..f41a40621 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ClippingRankSumTest.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ClippingRankSumTest.java
@@ -25,6 +25,9 @@ public class ClippingRankSumTest extends RankSumTest {
     public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("ClippingRankSum", 1, VCFHeaderLineType.Float, "Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases")); }
 
     protected void fillQualsFromPileup(byte ref, List<Byte> alts, ReadBackedPileup pileup, List<Double> refQuals, List<Double> altQuals) {
+        return;
+        // This working implementation below needs to be tested for the UG pipeline
+        /*
         for ( final PileupElement p : pileup ) {
             if ( isUsableBase(p) ) {
                 if ( p.getBase() == ref ) {
@@ -34,6 +37,7 @@ public class ClippingRankSumTest extends RankSumTest {
                 }
             }
         }
+        */
     }
 
     protected void fillQualsFromPileup(final Allele ref, final List<Allele> alts, final int refLoc, final Map<Allele, List<GATKSAMRecord>> stratifiedContext, final List<Double> refQuals, final List<Double> altQuals) {
@@ -53,6 +57,10 @@ public class ClippingRankSumTest extends RankSumTest {
     }
 
     protected void fillIndelQualsFromPileup(ReadBackedPileup pileup, List<Double> refQuals, List<Double> altQuals) {
+        return;
+        // This working implementation below needs to be tested for the UG pipeline
+
+        /*
         // equivalent is whether indel likelihoods for reads corresponding to ref allele are more likely than reads corresponding to alt allele ?
         HashMap<PileupElement,LinkedHashMap<Allele,Double>> indelLikelihoodMap = IndelGenotypeLikelihoodsCalculationModel.getIndelLikelihoodMap();
         for (final PileupElement p: pileup) {
@@ -78,5 +86,6 @@ public class ClippingRankSumTest extends RankSumTest {
                     altQuals.add((double)AlignmentUtils.getNumHardClippedBases(p.getRead()));
             }
         }
+        */
     }
 }