add calculation in MathUtils

Schaudge · Oct 21, 2021 · acecb7b · acecb7b
1 parent 35e7be8
commit acecb7b
Showing 1 changed file with 16 additions and 1 deletion.
diff --git a/src/main/java/org/broadinstitute/hellbender/utils/MathUtils.java b/src/main/java/org/broadinstitute/hellbender/utils/MathUtils.java
@@ -6,7 +6,9 @@
 import org.apache.commons.math3.exception.NumberIsTooLargeException;
 import org.apache.commons.math3.random.RandomGenerator;
 import org.apache.commons.math3.special.Gamma;
+import org.apache.commons.math3.stat.descriptive.moment.Mean;
 import org.apache.commons.math3.stat.descriptive.rank.Median;
+import org.apache.commons.math3.stat.descriptive.summary.Sum;
 import org.apache.commons.math3.stat.descriptive.rank.Percentile;
 import org.apache.commons.math3.util.FastMath;
 import org.apache.commons.math3.util.MathArrays;
@@ -164,13 +166,26 @@ public static int median(final int[] values) {
         Utils.nonNull(values);
         return (int) FastMath.round(new Median().evaluate(Arrays.stream(values).mapToDouble(n -> n).toArray()));
     }
+
+    public double sd(final int[] values) {
+        Utils.nonNull(values);
+        if ( values.length < 2 ) return 0.0;
+        double mean = new Mean().evaluate(Arrays.stream(values).mapToDouble(n -> n).toArray());
+        double square_sum = new Sum().evaluate(Arrays.stream(values).mapToDouble(n -> n - mean).toArray());
+        return Math.sqrt(square_sum / (values.length - 1));
+    }
+
+    public static int mad(final int[] values) {
+        double median = median(values);
+        return (int) FastMath.round(new Median().evaluate(Arrays.stream(values).mapToDouble(n -> n - median).toArray()));
+    }
 
     public static int median(final int[] values, final Percentile.EstimationType type) {
         Utils.nonNull(values);
         return (int) FastMath.round(new Median().withEstimationType(type).evaluate(Arrays.stream(values).mapToDouble(n -> n).toArray()));
     }
 
-    public static double dotProduct(double[] a, double[] b){
+    public static double dotProduct(double[] a, double[] b) {
         return sum(MathArrays.ebeMultiply(Utils.nonNull(a), Utils.nonNull(b)));
     }