From e051a566748ee30c3bac50dce2a49230251c0918 Mon Sep 17 00:00:00 2001
From: Nikolai Karulin <Nikolai_Karulin@epam.com>
Date: Wed, 17 Jan 2018 20:25:59 +0300
Subject: [PATCH] make SortingCollection.spillToDisk public(#1061)

downstream users need access to this method in order to create parallel implementations
---
 .../samtools/util/SortingCollection.java      |  4 ++--
 .../samtools/util/SortingCollectionTest.java  | 23 ++++++++++++++++++-
 2 files changed, 24 insertions(+), 3 deletions(-)

diff --git a/src/main/java/htsjdk/samtools/util/SortingCollection.java b/src/main/java/htsjdk/samtools/util/SortingCollection.java
index 0dacb56c93..46b84c117b 100644
--- a/src/main/java/htsjdk/samtools/util/SortingCollection.java
+++ b/src/main/java/htsjdk/samtools/util/SortingCollection.java
@@ -1,7 +1,7 @@
 /*
  * The MIT License
  *
- * Copyright (c) 2009 The Broad Institute
+ * Copyright (c) 2018 The Broad Institute
  *
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal
@@ -215,7 +215,7 @@ public void setDestructiveIteration(boolean destructiveIteration) {
     /**
      * Sort the records in memory, write them to a file, and clear the buffer of records in memory.
      */
-    private void spillToDisk() {
+    public void spillToDisk() {
         try {
             Arrays.sort(this.ramRecords, 0, this.numRecordsInRam, this.comparator);
             final Path f = newTempFile();
diff --git a/src/test/java/htsjdk/samtools/util/SortingCollectionTest.java b/src/test/java/htsjdk/samtools/util/SortingCollectionTest.java
index 7254a877a4..9722de8a9e 100644
--- a/src/test/java/htsjdk/samtools/util/SortingCollectionTest.java
+++ b/src/test/java/htsjdk/samtools/util/SortingCollectionTest.java
@@ -1,7 +1,7 @@
 /*
  * The MIT License
  *
- * Copyright (c) 2009 The Broad Institute
+ * Copyright (c) 2018 The Broad Institute
  *
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal
@@ -103,6 +103,27 @@ public void testPositive(final String testName, final int numStringsToGenerate,
         Assert.assertEquals(tmpDir().list().length, 0);
     }
 
+    @Test
+    public void spillToDiskTest() {
+        final SortingCollection<String> sortingCollection = makeSortingCollection(10);
+        final String[] strings = new String[] {
+                "1", "2", "3"
+        };
+
+        for (String str : strings) {
+            sortingCollection.add(str);
+        }
+
+        Assert.assertEquals(tmpDir().list().length, 0);
+        sortingCollection.spillToDisk();
+        Assert.assertEquals(tmpDir().list().length, 1);
+
+        assertIteratorEqualsList(strings, sortingCollection.iterator());
+
+        sortingCollection.cleanup();
+        Assert.assertEquals(tmpDir().list().length, 0);
+    }
+
     private void assertIteratorEqualsList(final String[] strings, final Iterator<String> sortingCollection) {
         int i = 0;
         while (sortingCollection.hasNext()) {