Add a method to conditionally apply a Consumer on a nullable input

src/main/java/htsjdk/samtools/util/CodeUtil.java

@@ -1,14 +1,26 @@
 package htsjdk.samtools.util;
 
+import java.util.function.Consumer;
+
 /**
  * Miscellaneous util methods that don't fit anywhere else.
  */
 public class CodeUtil {
 
-    /** Mimic of Oracle's nvl() - returns the first value if not null, otherwise the second value. */
+    /**
+     * Mimic of Oracle's nvl() - returns the first value if not null, otherwise the second value.
+     */
     public static <T> T getOrElse(final T value1, final T value2) {
-        if (value1 != null) return value1;
-        else return value2;
+        if (value1 != null) {
+            return value1;
+        } else {
+            return value2;
+        }
     }
 
+    public static <T> void applyIfNotNull(final T input, Consumer<T> action) {
+        if (input != null) {
+            action.accept(input);
+        }
+    }
 }

src/main/java/htsjdk/samtools/util/IOUtil.java

@@ -30,7 +30,6 @@
 import htsjdk.samtools.seekablestream.SeekableHTTPStream;
 import htsjdk.samtools.seekablestream.SeekableStream;
 import htsjdk.samtools.util.nio.DeleteOnExitPathHook;
-import htsjdk.tribble.Tribble;
 
 import java.io.BufferedInputStream;
 import java.io.BufferedOutputStream;
@@ -68,7 +67,6 @@
 import java.util.Collection;
 import java.util.Collections;
 import java.util.HashMap;
-import java.util.HashSet;
 import java.util.LinkedList;
 import java.util.List;
 import java.util.Scanner;

src/test/java/htsjdk/samtools/util/IOUtilTest.java

@@ -114,6 +114,10 @@ public void testFileReadingAndWriting() throws IOException {
         String randomizedTestString = TEST_STRING + System.currentTimeMillis();
         for (String ext : TEST_FILE_EXTENSIONS) {
             File f = File.createTempFile(TEST_FILE_PREFIX, ext);
+            IOUtil.assertFileIsReadable(f);
+
+            CodeUtil.applyIfNotNull(f,IOUtil::assertFileIsReadable);
+
             f.deleteOnExit();
 
             OutputStream os = IOUtil.openFileForWriting(f);