From 4d4de27ba3d2a56742d8423b2ce0fd7cee0f6eaa Mon Sep 17 00:00:00 2001
From: meganshand <mshand@broadinstitute.org>
Date: Tue, 28 Jul 2015 15:54:21 -0400
Subject: [PATCH] Removes unique(int maxSize) from KBestHaplotypeFinder

---
 .../graphs/KBestHaplotypeFinder.java          | 46 ++++---------------
 1 file changed, 10 insertions(+), 36 deletions(-)

diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KBestHaplotypeFinder.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KBestHaplotypeFinder.java
index 9048046fe..16546b39c 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KBestHaplotypeFinder.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KBestHaplotypeFinder.java
@@ -90,7 +90,7 @@ public class KBestHaplotypeFinder extends AbstractList<KBestHaplotype> implement
     /**
      * The top finder.
      *
-     * <p>If there is only a single source vertex, its finder is the top finder. However whent there
+     * <p>If there is only a single source vertex, its finder is the top finder. However when there
      * is more than one possible source, we create a composite finder that alternates between individual source vertices
      * for their best haplotypes.</p>
      */
@@ -472,44 +472,18 @@ public class KBestHaplotypeFinder extends AbstractList<KBestHaplotype> implement
      *     The resulting list is sorted by the score with more likely haplotype search results first.
      * </p>
      *
-     * @param maxSize maximum number of unique results to return.
-     *
-     * @throws IllegalArgumentException if {@code maxSize} is negative.
-     *
-     * @return never {@code null}, perhaps an empty list.
-     */
-    public List<KBestHaplotype> unique(final int maxSize) {
-        if (maxSize < 0) throw new IllegalArgumentException("maxSize cannot be negative");
-        final int requiredCapacity = Math.min(maxSize,size());
-        final Set<Haplotype> haplotypes = new HashSet<>(requiredCapacity);
-        int resultSize = 0;
-        final List<KBestHaplotype> result = new ArrayList<>(requiredCapacity);
-        for (final KBestHaplotype kbh : this) {
-            if (haplotypes.add(kbh.haplotype())) {
-                result.add(kbh);
-                if (resultSize == maxSize) break;
-            }
-        }
-        return result;
-    }
-
-    /**
-     * Returns a unique list of haplotypes solutions.
-     *
-     * <p>
-     *     The result will not contain more than one haplotype with the same base sequence. The solution of the best
-     *     score is returned.
-     * </p>
-     * <p>
-     *     This makes sense when there are more than one possible path through the graph to create the same haplotype.
-     * </p>
-     * <p>
-     *     The resulting list is sorted by the score with more likely haplotype search results first.
-     * </p>
      *
      * @return never {@code null}, perhaps an empty list.
      */
     public List<KBestHaplotype> unique() {
-        return unique(size());
+        final int requiredCapacity = size();
+        final Set<Haplotype> haplotypes = new HashSet<>(requiredCapacity);
+        final List<KBestHaplotype> result = new ArrayList<>(requiredCapacity);
+        for (final KBestHaplotype kbh : this) {
+            if (haplotypes.add(kbh.haplotype())) {
+                result.add(kbh);
+            }
+        }
+        return result;
     }
 }