From b83fdf8a1704c82488816cb80b643cbfd5a603ac Mon Sep 17 00:00:00 2001
From: rpoplin <rpoplin@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 1 Oct 2010 13:09:46 +0000
Subject: [PATCH] Bug fix in AnalyzeAnnotations. Be sure the site is a
 biallelic, unfiltered SNP.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4400 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../AnalyzeAnnotationsWalker.java             | 19 ++++++++++++-------
 .../AnnotationDataManager.java                | 10 ++++------
 2 files changed, 16 insertions(+), 13 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnalyzeAnnotationsWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnalyzeAnnotationsWalker.java
index 4385e719f..3f2f81c68 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnalyzeAnnotationsWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnalyzeAnnotationsWalker.java
@@ -107,18 +107,23 @@ public class AnalyzeAnnotationsWalker extends RodWalker<Integer, Integer> {
             boolean isInTruthSet = false;
             boolean isTrueVariant = false;
             for ( VariantContext vc : VCs ) {
-                if( vc.getName().toUpperCase().startsWith("TRUTH") ) {
-                    isInTruthSet = true;
-                    if (vc.isVariant())
-                        isTrueVariant = true;
+                if( vc != null && vc.isSNP() && !vc.isFiltered() ) {
+                    if( vc.getName().toUpperCase().startsWith("TRUTH") ) {
+                        isInTruthSet = true;
+                        if( vc.isBiallelic() && vc.isVariant() ) {
+                            isTrueVariant = true;
+                        }
+                    }
                 }
             }
             
             // Add each annotation in this VCF Record to the dataManager
             for ( VariantContext vc : VCs ) {
-                if( !vc.getName().toUpperCase().startsWith("TRUTH") ) {
-                    if( vc.isVariant() ) {
-                        dataManager.addAnnotations( vc, SAMPLE_NAME, isInTruthSet, isTrueVariant );
+                if( vc != null && vc.isSNP() && vc.isBiallelic() && !vc.isFiltered() ) {
+                    if( !vc.getName().toUpperCase().startsWith("TRUTH") ) {
+                        if( vc.isVariant() ) {
+                            dataManager.addAnnotations( vc, SAMPLE_NAME, isInTruthSet, isTrueVariant );
+                        }
                     }
                 }
             }
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnnotationDataManager.java b/java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnnotationDataManager.java
index 8a2c54a9f..7513854a5 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnnotationDataManager.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnnotationDataManager.java
@@ -89,12 +89,10 @@ public class AnnotationDataManager {
             final boolean isNovelVariant = !infoField.get(VariantContext.ID_KEY).toString().contains("rs");
 
             // Decide if the variant is a transition or transversion
-            if ( vc.isSNP() ) {
-                if( VariantContextUtils.getSNPSubstitutionType(vc).compareTo(BaseUtils.BaseSubstitutionType.TRANSITION) == 0 ) {
-                    datum.incrementTi( isNovelVariant, isInTruthSet, isTrueVariant );
-                } else {
-                    datum.incrementTv( isNovelVariant, isInTruthSet, isTrueVariant );
-                }
+            if( VariantContextUtils.getSNPSubstitutionType(vc).compareTo(BaseUtils.BaseSubstitutionType.TRANSITION) == 0 ) {
+                datum.incrementTi( isNovelVariant, isInTruthSet, isTrueVariant );
+            } else {
+                datum.incrementTv( isNovelVariant, isInTruthSet, isTrueVariant );
             }
         }
     }