From 504103bd157e81b64a747e02f445f4c651bf5de3 Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 7 May 2010 21:34:18 +0000
Subject: [PATCH] Misc. additions to correct utilities

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3329 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../org/broadinstitute/sting/utils/BaseUtils.java |  4 ++++
 .../org/broadinstitute/sting/utils/MathUtils.java | 15 +++++++++++++--
 2 files changed, 17 insertions(+), 2 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/utils/BaseUtils.java b/java/src/org/broadinstitute/sting/utils/BaseUtils.java
index e106859b5..975a8c112 100644
--- a/java/src/org/broadinstitute/sting/utils/BaseUtils.java
+++ b/java/src/org/broadinstitute/sting/utils/BaseUtils.java
@@ -192,6 +192,10 @@ public class BaseUtils {
         return isRegularBase((char)base);
     }
 
+    static public boolean isNBase(char base) {
+        return isNBase((byte)base);
+    }
+
     static public boolean isNBase(byte base) {
         return base == 'N';
     }
diff --git a/java/src/org/broadinstitute/sting/utils/MathUtils.java b/java/src/org/broadinstitute/sting/utils/MathUtils.java
index bd99f88ba..209588fff 100755
--- a/java/src/org/broadinstitute/sting/utils/MathUtils.java
+++ b/java/src/org/broadinstitute/sting/utils/MathUtils.java
@@ -710,9 +710,20 @@ public class MathUtils {
 
     }
 
-
     public static byte getQScoreMedian(List<SAMRecord> reads, List<Integer> offsets) {
         return getQScoreOrderStatistic(reads, offsets, (int)Math.floor(reads.size()/2.));
     }
-    
+
+
+    //
+    // useful common utility routines
+    //
+    public static double rate(long n, long d)           { return n / (1.0 * Math.max(d, 1)); }
+    public static double rate(int n, int d)             { return n / (1.0 * Math.max(d, 1)); }
+
+    public static long inverseRate(long n, long d)      { return n == 0 ? 0 : d / Math.max(n, 1); }
+    public static long inverseRate(int n, int d)        { return n == 0 ? 0 : d / Math.max(n, 1); }
+
+    public static double ratio(int num, int denom)      { return ((double)num) / (Math.max(denom, 1)); }
+    public static double ratio(long num, long denom)    { return ((double)num) / (Math.max(denom, 1)); }
 }