From d7430c23f86ef10d364e0e9b0c93d2f330cc3fc0 Mon Sep 17 00:00:00 2001
From: rpoplin <rpoplin@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 14 Jun 2011 20:23:43 +0000
Subject: [PATCH] Bringing VQSR up to date with the 1000G v2b changes

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6000 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/annotator/FisherStrand.java           | 3 +--
 .../sting/gatk/walkers/annotator/HaplotypeScore.java         | 5 ++---
 .../walkers/variantrecalibration/VariantDataManager.java     | 5 ++++-
 3 files changed, 7 insertions(+), 6 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
index af2bd7a9a..66d927e1c 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
@@ -47,10 +47,9 @@ public class FisherStrand implements InfoFieldAnnotation, StandardAnnotation {
     private static final double MIN_PVALUE = 1E-320;
 
     public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
-        if ( ! vc.isVariant() || vc.isFiltered()  )
+        if ( ! vc.isVariant() || vc.isFiltered() )
             return null;
 
-
         int[][] table;
 
         if (vc.isBiallelic() && vc.isSNP())
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
index 05914d4b5..cb7bcbeed 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
@@ -101,7 +101,6 @@ public class HaplotypeScore implements InfoFieldAnnotation, StandardAnnotation {
                         }
                         else
                             return null;
-
                     }
                 }
             }
@@ -168,13 +167,13 @@ public class HaplotypeScore implements InfoFieldAnnotation, StandardAnnotation {
 
         // Now retrieve the N most popular haplotypes
         if (consensusHaplotypeQueue.size() > 0) {
-            // Since the consensus haplotypes are in a quality-ordered priority queue, the two best haplotypes are just the first two in the queue
+            // The consensus haplotypes are in a quality-ordered priority queue, so the best haplotypes are just the ones at the front of the queue
             final Haplotype haplotype1 = consensusHaplotypeQueue.poll();
 
             List<Haplotype>hlist = new ArrayList<Haplotype>();
             hlist.add(new Haplotype(haplotype1.getBasesAsBytes(), 60));
 
-            for (int k=1;k < haplotypesToCompute; k++) {
+            for (int k=1; k < haplotypesToCompute; k++) {
                 Haplotype haplotype2 = consensusHaplotypeQueue.poll();
                 if(haplotype2 == null ) { haplotype2 = haplotype1; } // Sometimes only the reference haplotype can be found
                 hlist.add(new Haplotype(haplotype2.getBasesAsBytes(), 20));
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
index 2aaa4c04b..72282e6d8 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
@@ -211,14 +211,17 @@ public class VariantDataManager {
         try {
             if( annotationKey.equalsIgnoreCase("QUAL") ) {
                 value = vc.getPhredScaledQual();
+            } else if( annotationKey.equalsIgnoreCase("DP") ) {
+                value = Double.parseDouble( (String)vc.getAttribute( "DP" ) ) / Double.parseDouble( (String)vc.getAttribute( "AN" ) );
             } else {
                 value = Double.parseDouble( (String)vc.getAttribute( annotationKey ) );
                 if( Double.isInfinite(value) ) { value = Double.NaN; }
-                if( annotationKey.equalsIgnoreCase("InbreedingCoeff") && value > 0.01 ) { value = Double.NaN; }
+                if( annotationKey.equalsIgnoreCase("InbreedingCoeff") && value > 0.05 ) { value = Double.NaN; }
                 if( jitter && annotationKey.equalsIgnoreCase("HRUN") ) { // Integer valued annotations must be jittered a bit to work in this GMM
                       value += -0.25 + 0.5 * GenomeAnalysisEngine.getRandomGenerator().nextDouble();
                 }
                 if( annotationKey.equalsIgnoreCase("HaplotypeScore") && MathUtils.compareDoubles(value, 0.0, 0.0001) == 0 ) { value = -0.2 + 0.4*GenomeAnalysisEngine.getRandomGenerator().nextDouble(); }
+                if( annotationKey.equalsIgnoreCase("FS") && MathUtils.compareDoubles(value, 0.0, 0.01) == 0 ) { value = -0.2 + 0.4*GenomeAnalysisEngine.getRandomGenerator().nextDouble(); }
             }
 
          } catch( final Exception e ) {