From cd4cd6db81100d0cce34171807f6c90aabb19ef2 Mon Sep 17 00:00:00 2001
From: flannick <flannick@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 10 Aug 2010 19:55:19 +0000
Subject: [PATCH] Added option to print out discordant sites in
 GenotypeConcordance

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4006 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../varianteval/GenotypeConcordance.java      |  7 +++++++
 .../varianteval/VariantEvalWalker.java        | 19 ++++++++++++++++++-
 2 files changed, 25 insertions(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypeConcordance.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypeConcordance.java
index 9acb4a67b..584c13c71 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypeConcordance.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypeConcordance.java
@@ -62,6 +62,8 @@ public class GenotypeConcordance extends VariantEvaluator implements StandardEva
 
     private static final int MAX_MISSED_VALIDATION_DATA = 100;
 
+		private boolean discordantInteresting = false;
+
     private VariantEvalWalker.EvaluationContext group = null;
 
     static class FrequencyStats implements TableType {
@@ -214,6 +216,7 @@ public class GenotypeConcordance extends VariantEvaluator implements StandardEva
 
     public GenotypeConcordance(VariantEvalWalker parent) {
         super(parent);
+				discordantInteresting = parent.DISCORDANT_INTERESTING;
     }
 
     public String getName() {
@@ -295,6 +298,10 @@ public class GenotypeConcordance extends VariantEvaluator implements StandardEva
                 } else {
                     truth = validation.getGenotype(sample).getType();
                     // interesting = "ConcordanceStatus=FP";
+										if (discordantInteresting && truth.ordinal() != called.ordinal())
+										{
+												interesting = "ConcordanceStatus=" + truth.ordinal() + "/" + called.ordinal();
+										}
                 }
 
                 sampleStats.incrValue(sample, truth, called);
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
index 306175ea0..e7f4fca34 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
@@ -195,6 +195,9 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> {
     @Argument(shortName="aatUseCodons", fullName="aminoAcidsRepresentedByCodons", doc="for the amino acid table, specifiy that the transitions are represented as codon changes, and not directly amino acid names", required = false)
     protected boolean aatUseCodons = false;
 
+    @Argument(shortName="disI", fullName="discordantInteresting", doc="If passed, write discordant sites as interesting", required=false)
+		protected boolean DISCORDANT_INTERESTING = false;
+
     @Argument(fullName="tranchesFile", shortName="tf", doc="The input tranches file describing where to cut the data", required=false)
     private String TRANCHE_FILENAME = null;
 
@@ -530,7 +533,21 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> {
                                     comp.hasNegLog10PError() &&
                                     comp.getNegLog10PError() < (minCompQualScore / 10.0) )
                                 comp = null;
-                            String interesting = evaluation.update2( evalWantsVC ? vc : null, comp, tracker, ref, context, group );
+
+														String interesting = evaluation.update2( evalWantsVC ? vc : null, comp, tracker, ref, context, group );
+
+														/** TODO 
+																-- for Eric: Fix me (current implementation causes GenotypeConcordance
+																to treat sites that don't match JEXL as no-calls)
+
+														String interesting = null;
+														if (evalWantsVC)
+														{
+																interesting = evaluation.update2( evalWantsVC ? vc : null, comp, tracker, ref, context, group );
+														}
+														**/
+
+														
                             if ( interesting != null ) interestingReasons.add(interesting);
                             break;
                         default: