Cosmetic change to list sampling functions: the typical usage of n and k were reversed. No change in functionality of the classes has been made and unit tests still pass.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1736 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/playground/gatk/walkers/CoverageEvalWalker.java

@@ -75,7 +75,7 @@ public class CoverageEvalWalker extends LocusWalker<List<String>, String> {
             for (int coverage : coverage_levels) {
                 coverage = Math.min(coverage_available, coverage); // don't exceed max available coverage
                 for (int r=0; r<downsampling_repeats; r++) {
-                    List<Integer> subset_indices = ListUtils.sampleIndicesWithReplacement(coverage, coverage_available);
+                    List<Integer> subset_indices = ListUtils.sampleIndicesWithReplacement(coverage_available, coverage);
                     List<SAMRecord> sub_reads = ListUtils.sliceListByIndices(subset_indices, reads);
                     List<Integer> sub_offsets = ListUtils.sliceListByIndices(subset_indices, offsets);
 

java/src/org/broadinstitute/sting/utils/ListUtils.java

@@ -18,16 +18,16 @@ public class ListUtils {
     /**
      * Returns n random indices drawn with replacement from the range 0..(k-1)
      *
-     * @param n  the number of random indices to draw (with replacement)
+     * @param n the total number of indices sampled from
-     * @param k  the total number of indices allowed
+     * @param k the number of random indices to draw (with replacement)
-     * @return a list of random indices ranging from 0 to (k-1) with possible duplicates
+     * @return a list of k random indices ranging from 0 to (n-1) with possible duplicates
      */
     static public ArrayList<Integer> sampleIndicesWithReplacement(int n, int k) {
 
-        ArrayList<Integer> chosen_balls = new ArrayList <Integer>();
+        ArrayList<Integer> chosen_balls = new ArrayList <Integer>(k);
-        for (int i=0; i<n; i++) {
+        for (int i=0; i< k; i++) {
             //Integer chosen_ball = balls[rand.nextInt(k)];
-            chosen_balls.add(rand.nextInt(k));
+            chosen_balls.add(rand.nextInt(n));
             //balls.remove(chosen_ball);
         }
 
@@ -37,9 +37,9 @@ public class ListUtils {
     /**
      * Returns n random indices drawn without replacement from the range 0..(k-1)
      *
-     * @param n  the number of random indices to draw (without replacement)
+     * @param n the total number of indices sampled from
-     * @param k  the total number of indices allowed
+     * @param k the number of random indices to draw (without replacement)
-     * @return a list of random indices ranging from 0 to (k-1) without duplicates
+     * @return a list of k random indices ranging from 0 to (n-1) without duplicates
      */
     static public ArrayList<Integer> sampleIndicesWithoutReplacement(int n, int k) {
         ArrayList<Integer> chosen_balls = new ArrayList<Integer>(k);

java/test/org/broadinstitute/sting/utils/ListUtilsTest.java

@@ -4,10 +4,8 @@ import org.junit.Assert;
 import org.junit.BeforeClass;
 import org.junit.Test;
 import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.MathUtils;
 
 
-import java.io.File;
 import java.util.List;
 import java.util.ArrayList;
 import java.util.Collections;
@@ -27,15 +25,15 @@ public class ListUtilsTest extends BaseTest {
         logger.warn("Executing testRandomIndicesWithReplacement");
 
         // Check that the size of the list returned is correct
-        Assert.assertTrue(ListUtils.sampleIndicesWithReplacement(0, 5).size() == 0);
+        Assert.assertTrue(ListUtils.sampleIndicesWithReplacement(5, 0).size() == 0);
-        Assert.assertTrue(ListUtils.sampleIndicesWithReplacement(1, 5).size() == 1);
+        Assert.assertTrue(ListUtils.sampleIndicesWithReplacement(5, 1).size() == 1);
         Assert.assertTrue(ListUtils.sampleIndicesWithReplacement(5, 5).size() == 5);
-        Assert.assertTrue(ListUtils.sampleIndicesWithReplacement(1000, 5).size() == 1000);
+        Assert.assertTrue(ListUtils.sampleIndicesWithReplacement(5, 1000).size() == 1000);
 
         // Check that the list contains only the k element range that as asked for - no more, no less
         List<Integer> Five = new ArrayList<Integer>();
         Collections.addAll(Five, 0, 1, 2, 3, 4);
-        List<Integer> BigFive = ListUtils.sampleIndicesWithReplacement(10000, 5);
+        List<Integer> BigFive = ListUtils.sampleIndicesWithReplacement(5, 10000);
         Assert.assertTrue(BigFive.containsAll(Five));
         Assert.assertTrue(Five.containsAll(BigFive));
     }
@@ -53,7 +51,7 @@ public class ListUtilsTest extends BaseTest {
         Collections.addAll(Five, 0, 1, 2, 3, 4);
         List<Character> FiveAlpha = new ArrayList<Character>();
         Collections.addAll(FiveAlpha, 'a', 'b', 'c', 'd', 'e');
-        List<Integer> BigFive = ListUtils.sampleIndicesWithReplacement(10000, 5);
+        List<Integer> BigFive = ListUtils.sampleIndicesWithReplacement(5, 10000);
         List<Character> BigFiveAlpha = ListUtils.sliceListByIndices(BigFive, FiveAlpha);
         Assert.assertTrue(BigFiveAlpha.containsAll(FiveAlpha));
         Assert.assertTrue(FiveAlpha.containsAll(BigFiveAlpha));