From 6b960bd9c5fb54c6b618fcd61edab6378824b634 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Sun, 11 Jul 2010 04:30:15 +0000
Subject: [PATCH] Fix for Steve: genotype filters still want to see the values
 from the VC

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3758 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../variantcontext/VariantContextUtils.java      | 16 +++++++++-------
 .../walkers/filters/VariantFiltrationWalker.java |  2 +-
 2 files changed, 10 insertions(+), 8 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java b/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
index c458e093b..ab51b0918 100755
--- a/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
+++ b/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
@@ -130,27 +130,29 @@ public class VariantContextUtils {
     }
 
     /**
-     * Returns true if exp match VC.  See collection<> version for full docs.
+     * Returns true if exp match VC/g.  See collection<> version for full docs.
+     * @param vc   variant context
      * @param g    genotype
      * @param exp   expression
      * @return true if there is a match
      */
-    public static boolean match(Genotype g, JexlVCMatchExp exp) {
-        return match(g,Arrays.asList(exp)).get(exp);
+    public static boolean match(VariantContext vc, Genotype g, JexlVCMatchExp exp) {
+        return match(vc,g,Arrays.asList(exp)).get(exp);
     }
 
     /**
-     * Matches each JexlVCMatchExp exp against the data contained in vc, and returns a map from these
+     * Matches each JexlVCMatchExp exp against the data contained in vc/g, and returns a map from these
      * expressions to true (if they matched) or false (if they didn't).  This the best way to apply JEXL
-     * expressions to VariantContext records.  Use initializeMatchExps() to create the list of JexlVCMatchExp
+     * expressions to VariantContext records/genotypes.  Use initializeMatchExps() to create the list of JexlVCMatchExp
      * expressions.
      *
+     * @param vc   variant context
      * @param g    genotype
      * @param exps expressions
      * @return true if there is a match
      */
-    public static Map<JexlVCMatchExp, Boolean> match(Genotype g, Collection<JexlVCMatchExp> exps) {
-        return new JEXLMap(exps,g);
+    public static Map<JexlVCMatchExp, Boolean> match(VariantContext vc, Genotype g, Collection<JexlVCMatchExp> exps) {
+        return new JEXLMap(exps,vc,g);
 
     }
 
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java
index 18219ad72..f6cfaa37f 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java
@@ -183,7 +183,7 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
                 Set<String> filters = new LinkedHashSet<String>(g.getFilters());
 
                 for ( VariantContextUtils.JexlVCMatchExp exp : genotypeFilterExps ) {
-                    if ( VariantContextUtils.match(g, exp) )
+                    if ( VariantContextUtils.match(vc, g, exp) )
                         filters.add(exp.name);
                 }