From a5f75cbfd4c03174d8a033935c7bb88f6b97e8b8 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Sun, 20 Dec 2009 02:34:41 +0000
Subject: [PATCH] The previous commit broke the build, so this is a temporary
 patch to get it to compile.  ConcordanceTruthTable should use enums (esp. now
 that all of the concordance variables need to be public), but VariantEval
 will need to be rewritten soon anyways so I'll just push it off until then.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2413 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../walkers/HapmapPoolAllelicInfoWalker.java  | 26 +++++++++++--------
 .../varianteval/ConcordanceTruthTable.java    | 20 +++++++-------
 2 files changed, 25 insertions(+), 21 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/HapmapPoolAllelicInfoWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/HapmapPoolAllelicInfoWalker.java
index 98e188fac..1ad28eaee 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/HapmapPoolAllelicInfoWalker.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/HapmapPoolAllelicInfoWalker.java
@@ -68,11 +68,11 @@ public class HapmapPoolAllelicInfoWalker extends LocusWalker<String, PrintWriter
         long pos = loc.getStart();
         char refBase = Character.toUpperCase(ref.getBase());
         List<Pair<Genotype, Genotype>> chips = getChips(sampleNames, tracker);
-        Pair<Genotype,Pair<Integer,Integer>> alleleFreqInfo = ctt.getPooledAlleleFrequency(chips,refBase);
+        Pair<Integer,Pair<Integer,Integer>> alleleFreqInfo = ctt.getPooledAlleleFrequency(chips,refBase);
         char alternate;
-        if ( alleleFreqInfo.getFirst() != null && alleleFreqInfo.getFirst().isVariant(refBase)) {
+        if ( alleleFreqInfo.first == ConcordanceTruthTable.VARIANT ) {
             //System.out.println(refBase + " " + alleleFreqInfo.getFirst().getBases());
-            alternate = getAlternateBase(alleleFreqInfo.getFirst(),refBase);
+            alternate = getAlternateBase(chips,refBase);
 
         } else {
             return null; // early return
@@ -96,8 +96,8 @@ public class HapmapPoolAllelicInfoWalker extends LocusWalker<String, PrintWriter
 
         // sanity check
         if ( refBase == alternate ) {
-            if ( alleleFreqInfo.getFirst().isVariant(refBase) ) {
-                logger.warn("Called as a variant! Ref: "+ refBase +"Chip data: " + alleleFreqInfo.getFirst().getBases());
+            if ( alleleFreqInfo.first == ConcordanceTruthTable.VARIANT ) {
+                ;//logger.warn("Called as a variant! Ref: "+ refBase +"Chip data: " + alleleFreqInfo.getFirst().getBases());
             }
         }
 
@@ -105,12 +105,16 @@ public class HapmapPoolAllelicInfoWalker extends LocusWalker<String, PrintWriter
 
     }
 
-    public char getAlternateBase(Genotype g, char ref) {
-        char[] bases = g.getBases().toCharArray();
-        if ( Character.toUpperCase(bases[0]) != ref )
-            return bases[0];
-        else
-            return bases[1];
+    public char getAlternateBase(List<Pair<Genotype, Genotype>> chips, char ref) {
+        for ( Pair<Genotype, Genotype> chip : chips ) {
+            Genotype g = chip.first;
+            char[] bases = g.getBases().toCharArray();
+            if ( Character.toUpperCase(bases[0]) != ref )
+                return bases[0];
+            if ( Character.toUpperCase(bases[1]) != ref )
+                return bases[1];
+        }
+        return ref;
     }
 
     public PrintWriter reduce(String s, PrintWriter p) {
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/ConcordanceTruthTable.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/ConcordanceTruthTable.java
index cd75f2659..efa300559 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/ConcordanceTruthTable.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/ConcordanceTruthTable.java
@@ -18,18 +18,18 @@ import java.util.*;
  * the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
  */
 public class ConcordanceTruthTable {
-    private static final int TRUE_POSITIVE = 0;
-    private static final int TRUE_NEGATIVE = 1;
-    private static final int FALSE_POSITIVE = 2;
-    private static final int FALSE_NEGATIVE = 3;
-    private static final int VARIANT = 1;
+    public static final int TRUE_POSITIVE = 0;
+    public static final int TRUE_NEGATIVE = 1;
+    public static final int FALSE_POSITIVE = 2;
+    public static final int FALSE_NEGATIVE = 3;
+    public static final int VARIANT = 1;
     private static final String[] POOL_HEADERS = {"TP","TN","FP","FN"};
 
-    private static final int REF = 0;
-    private static final int VAR_HET = 1;
-    private static final int VAR_HOM = 2;
-    private static final int UNKNOWN = 3;
-    private static final int NO_CALL = 3;   // synonym
+    public static final int REF = 0;
+    public static final int VAR_HET = 1;
+    public static final int VAR_HOM = 2;
+    public static final int UNKNOWN = 3;
+    public static final int NO_CALL = 3;   // synonym
     private static final String[] TRUTH_NAMES = {"IS_REF", "IS_VAR_HET", "IS_VAR_HOM", "UNKNOWN"};
     private static final String[] CALL_NAMES = {"CALLED_REF", "CALLED_VAR_HET", "CALLED_VAR_HOM", "NO_CALL"};