From 2eb45340e1b198cb58b581a63e9b4b49e29a19a1 Mon Sep 17 00:00:00 2001
From: Guillermo del Angel <delangel@broadinstitute.org>
Date: Wed, 18 Jan 2012 20:54:10 -0500
Subject: [PATCH] Initial, raw, mostly untested version of new pool caller that
 also does allele discovery. Still needs debugging/refining. Main modification
 is that there is a new operation mode, set by argument
 -ALLELE_DISCOVERY_MODE, which if true will determine optimal alt allele at
 each computable site and will compute AC distribution on it. Current
 implementation is not working yet if there's more than one pool and it will
 only output biallelic sites, no functionality for true multi-allelics yet

---
 .../broadinstitute/sting/utils/MathUtils.java | 44 +++++++++++++++++++
 1 file changed, 44 insertions(+)

diff --git a/public/java/src/org/broadinstitute/sting/utils/MathUtils.java b/public/java/src/org/broadinstitute/sting/utils/MathUtils.java
index 5ffd634cc..5c952b13a 100644
--- a/public/java/src/org/broadinstitute/sting/utils/MathUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/MathUtils.java
@@ -1557,4 +1557,48 @@ public class MathUtils {
         }
         return shuffled;
     }
+
+    /**
+     * Vector operations
+     */
+    public static double[] vectorSum(double v1[], double v2[]) {
+        if (v1.length != v2.length)
+            throw new UserException("BUG: vectors v1, v2 of different size in vectorSum()");
+
+        double result[] = new double[v1.length];
+        for (int k=0; k < v1.length; k++)
+            result[k] = v1[k]+v2[k];
+
+        return result;
+    }
+
+    public static double[] scalarTimesIntVector(double a, int[] v1) {
+
+        double result[] = new double[v1.length];
+        for (int k=0; k < v1.length; k++)
+            result[k] = a*v1[k];
+
+        return result;
+    }
+
+    public static double dotProduct(double v1[], double v2[]) {
+        if (v1.length != v2.length)
+            throw new UserException("BUG: vectors v1, v2 of different size in vectorSum()");
+
+        double result = 0.0;
+        for (int k=0; k < v1.length; k++)
+            result += v1[k]*v2[k];
+
+        return result;
+
+    }
+
+    public static double[] vectorLog10(double v1[]) {
+        double result[] = new double[v1.length];
+        for (int k=0; k < v1.length; k++)
+            result[k] = Math.log10(v1[k]);
+
+        return result;
+
+    }
 }