From 81cd1626f73018506e949bfeb5668f6b947c30d1 Mon Sep 17 00:00:00 2001
From: Tom White <tom.e.white@gmail.com>
Date: Tue, 3 Sep 2019 17:36:24 +0100
Subject: [PATCH] Serializable identityFunction

---
 .../hellbender/engine/FeatureDataSource.java         |  6 +++---
 .../org/broadinstitute/hellbender/utils/Utils.java   | 12 ++++++++++++
 2 files changed, 15 insertions(+), 3 deletions(-)

diff --git a/src/main/java/org/broadinstitute/hellbender/engine/FeatureDataSource.java b/src/main/java/org/broadinstitute/hellbender/engine/FeatureDataSource.java
index 9710bcdf810..460dc1a2241 100644
--- a/src/main/java/org/broadinstitute/hellbender/engine/FeatureDataSource.java
+++ b/src/main/java/org/broadinstitute/hellbender/engine/FeatureDataSource.java
@@ -269,8 +269,8 @@ public FeatureDataSource(final FeatureInput<T> featureInput, final int queryLook
             Utils.nonNull(genomicsDBOptions, "GenomicsDBOptions must not be null. Calling tool may not read from a GenomicsDB data source.");
         }
 
-        final Function<SeekableByteChannel, SeekableByteChannel> cloudWrapper = (cloudPrefetchBuffer > 0 ? is -> SeekableByteChannelPrefetcher.addPrefetcher(cloudPrefetchBuffer, is) : Function.identity());
-        final Function<SeekableByteChannel, SeekableByteChannel> cloudIndexWrapper = (cloudIndexPrefetchBuffer > 0 ? is -> SeekableByteChannelPrefetcher.addPrefetcher(cloudIndexPrefetchBuffer, is) : Function.identity());
+        final Function<SeekableByteChannel, SeekableByteChannel> cloudWrapper = (cloudPrefetchBuffer > 0 ? is -> SeekableByteChannelPrefetcher.addPrefetcher(cloudPrefetchBuffer, is) : Utils.identityFunction());
+        final Function<SeekableByteChannel, SeekableByteChannel> cloudIndexWrapper = (cloudIndexPrefetchBuffer > 0 ? is -> SeekableByteChannelPrefetcher.addPrefetcher(cloudIndexPrefetchBuffer, is) : Utils.identityFunction());
 
         // Create a feature reader without requiring an index.  We will require one ourselves as soon as
         // a query by interval is attempted.
@@ -369,7 +369,7 @@ private static <T extends Feature> FeatureReader<T> getFeatureReader(final Featu
             if (BucketUtils.isCloudStorageUrl(featureInput)) {
                 return AbstractFeatureReader.getFeatureReader(absoluteRawPath, null, codec, requireIndex, cloudWrapper, cloudIndexWrapper);
             } else {
-                return AbstractFeatureReader.getFeatureReader(absoluteRawPath, null, codec, requireIndex, Function.identity(), Function.identity());
+                return AbstractFeatureReader.getFeatureReader(absoluteRawPath, null, codec, requireIndex, Utils.identityFunction(), Utils.identityFunction());
             }
         } catch (final TribbleException e) {
             throw new GATKException("Error initializing feature reader for path " + featureInput.getFeaturePath(), e);
diff --git a/src/main/java/org/broadinstitute/hellbender/utils/Utils.java b/src/main/java/org/broadinstitute/hellbender/utils/Utils.java
index b51658114b7..af4f808088d 100644
--- a/src/main/java/org/broadinstitute/hellbender/utils/Utils.java
+++ b/src/main/java/org/broadinstitute/hellbender/utils/Utils.java
@@ -19,6 +19,7 @@
 import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.IOException;
+import java.io.Serializable;
 import java.lang.reflect.Array;
 import java.math.BigInteger;
 import java.nio.file.Files;
@@ -1102,6 +1103,17 @@ public static <T> Stream<T> stream(final Iterator<T> iterator) {
         return stream(() -> iterator);
     }
 
+    /**
+     * Returns a function that always returns its input argument. Unlike {@link Function#identity()} the returned
+     * function is also serializable.
+     *
+     * @param <T> the type of the input and output objects to the function
+     * @return a function that always returns its input argument
+     */
+    public static <T> Function<T, T> identityFunction() {
+        return (Function & Serializable) t -> t;
+    }
+
     /**
      * Like Guava's {@link Iterators#transform(Iterator, com.google.common.base.Function)}, but runs a fixed number
      * ({@code numThreads}) of transformations in parallel, while maintaining ordering of the output iterator.