From 56092a0fc21ebb4670cd9ea2cad5b19dcae200e6 Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 19 Mar 2010 13:18:08 +0000
Subject: [PATCH] Slight cleanup for mathutils

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3042 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/walkers/TrioGenotyperWalker.java       |  2 +-
 .../broadinstitute/sting/utils/MathUtils.java   | 17 ++++++++++++++---
 2 files changed, 15 insertions(+), 4 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/TrioGenotyperWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/TrioGenotyperWalker.java
index 0b4b4378e..216323fbc 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/TrioGenotyperWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/TrioGenotyperWalker.java
@@ -122,7 +122,7 @@ public class TrioGenotyperWalker extends RefWalker<VariantContext, Integer>{
                 }
             }
 
-            double[] posteriors = MathUtils.log10posteriorsFromLog10L(L);
+            double[] posteriors = MathUtils.normalizeFromLog10(L, true);
             log10POfGenotype = posteriors[bestIndex];
         }
         //log10POfViolation = Math.min(log10POfViolation, 0);
diff --git a/java/src/org/broadinstitute/sting/utils/MathUtils.java b/java/src/org/broadinstitute/sting/utils/MathUtils.java
index 4fcd28092..d93ec1137 100755
--- a/java/src/org/broadinstitute/sting/utils/MathUtils.java
+++ b/java/src/org/broadinstitute/sting/utils/MathUtils.java
@@ -277,9 +277,13 @@ public class MathUtils {
 
     /**
      * normalizes the log10-based array
+     *
      * @param array  the array to be normalized
+     * @param takeLog10OfOutput if true, the output will be transformed back into log10 units
+     *
+     * @return a newly allocated array corresponding the normalized values in array, maybe log10 transformed
     */
-    public static double[] normalizeFromLog10(double[] array) {
+    public static double[] normalizeFromLog10(double[] array, boolean takeLog10OfOutput) {
         double[] normalized = new double[array.length];
 
         // for precision purposes, we need to add (or really subtract, since they're
@@ -292,9 +296,16 @@ public class MathUtils {
         double sum = 0.0;
         for (int i = 0; i < array.length; i++)
             sum += normalized[i];
-        for (int i = 0; i < array.length; i++)
-            normalized[i] /= sum;
+        for (int i = 0; i < array.length; i++) {
+            double x = normalized[i] / sum;
+            if ( takeLog10OfOutput ) x = Math.log10(x);
+            normalized[i] = x;
+        }
 
         return normalized;
     }
+
+    public static double[] normalizeFromLog10(double[] array) {
+        return normalizeFromLog10(array, false);
+    }
 }