From dd313defdcdfbf9f53e48ad88eaff3cb3eec6d2c Mon Sep 17 00:00:00 2001
From: Louis Bergelson <louisb@broadinstitute.org>
Date: Wed, 6 Mar 2019 23:01:58 -0500
Subject: [PATCH] Deprecate TestUtil.deleteRecursively (#1315)

* It has been replaced by IOUtil.recursiveDelete()
---
 src/main/java/htsjdk/samtools/util/IOUtil.java   | 15 ++++++++++-----
 src/main/java/htsjdk/samtools/util/TestUtil.java |  4 +++-
 2 files changed, 13 insertions(+), 6 deletions(-)

diff --git a/src/main/java/htsjdk/samtools/util/IOUtil.java b/src/main/java/htsjdk/samtools/util/IOUtil.java
index 41e1081800..b863000b32 100755
--- a/src/main/java/htsjdk/samtools/util/IOUtil.java
+++ b/src/main/java/htsjdk/samtools/util/IOUtil.java
@@ -1318,20 +1318,21 @@ private static String stripQueryStringIfPathIsAnHttpUrl(String path) {
     }
 
     /**
-     * Little test utility to help tests that create multiple levels of subdirectories
-     * clean up after themselves.
+     * Delete a directory and all files in it.
      *
      * @param directory The directory to be deleted (along with its subdirectories)
      */
-    public static void recursiveDelete(final Path directory) throws IOException {
-
+    public static void recursiveDelete(final Path directory) {
+        
         final SimpleFileVisitor<Path> simpleFileVisitor = new SimpleFileVisitor<Path>() {
+            @Override
             public FileVisitResult visitFile(Path file, BasicFileAttributes attrs) throws IOException {
                 super.visitFile(file, attrs);
                 Files.deleteIfExists(file);
                 return FileVisitResult.CONTINUE;
             }
 
+            @Override
             public FileVisitResult postVisitDirectory(Path dir, IOException exc) throws IOException {
                 super.postVisitDirectory(dir, exc);
                 Files.deleteIfExists(dir);
@@ -1339,6 +1340,10 @@ public FileVisitResult postVisitDirectory(Path dir, IOException exc) throws IOEx
             }
         };
 
-        Files.walkFileTree(directory, simpleFileVisitor);
+        try {
+            Files.walkFileTree(directory, simpleFileVisitor);
+        } catch (final IOException e){
+            throw new RuntimeIOException(e);
+        }
     }
 }
diff --git a/src/main/java/htsjdk/samtools/util/TestUtil.java b/src/main/java/htsjdk/samtools/util/TestUtil.java
index 498cca19a5..eb324239fd 100644
--- a/src/main/java/htsjdk/samtools/util/TestUtil.java
+++ b/src/main/java/htsjdk/samtools/util/TestUtil.java
@@ -94,11 +94,13 @@ public static <T extends Serializable> T serializeAndDeserialize(T input) throws
      * clean up after themselves.
      *
      * @param directory The directory to be deleted (along with its subdirectories)
+     * @deprecated Since 3/19, prefer {@link IOUtil#recursiveDelete(Path)}
      */
+    @Deprecated
     public static void recursiveDelete(final File directory) {
         try {
             IOUtil.recursiveDelete(directory.toPath());
-        } catch (IOException e) {
+        } catch (RuntimeIOException e) {
             // bury exception
         }
     }