From 7bbb5d49416b1ba24ae082f507e6f86e950bb1c9 Mon Sep 17 00:00:00 2001
From: Chris Norman <cnorman@broadinstitute.org>
Date: Tue, 8 Feb 2022 18:57:36 -0500
Subject: [PATCH] Make LocatableCache and strategy classes serializable.

---
 .../engine/cache/DrivingFeatureInputCacheStrategy.java       | 5 ++++-
 .../hellbender/engine/cache/LocatableCache.java              | 4 +++-
 .../hellbender/engine/cache/LocatableCacheStrategy.java      | 3 +--
 .../hellbender/engine/cache/SideReadInputCacheStrategy.java  | 5 ++++-
 4 files changed, 12 insertions(+), 5 deletions(-)

diff --git a/src/main/java/org/broadinstitute/hellbender/engine/cache/DrivingFeatureInputCacheStrategy.java b/src/main/java/org/broadinstitute/hellbender/engine/cache/DrivingFeatureInputCacheStrategy.java
index a11000b41de..cd356007c61 100644
--- a/src/main/java/org/broadinstitute/hellbender/engine/cache/DrivingFeatureInputCacheStrategy.java
+++ b/src/main/java/org/broadinstitute/hellbender/engine/cache/DrivingFeatureInputCacheStrategy.java
@@ -5,6 +5,7 @@
 import org.broadinstitute.hellbender.exceptions.GATKException;
 import org.broadinstitute.hellbender.utils.SimpleInterval;
 
+import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.Deque;
 import java.util.Iterator;
@@ -22,7 +23,9 @@
  *
  * @param <CACHED_FEATURE> type Feature being cached
  */
-public class DrivingFeatureInputCacheStrategy<CACHED_FEATURE extends Feature> implements LocatableCacheStrategy<CACHED_FEATURE> {
+public class DrivingFeatureInputCacheStrategy<CACHED_FEATURE extends Feature>
+        implements LocatableCacheStrategy<CACHED_FEATURE>, Serializable {
+    private static final long serialVersionUID = 1L;
 
     /**
      * When we trimCache our cache to a new start position, this is the maximum number of
diff --git a/src/main/java/org/broadinstitute/hellbender/engine/cache/LocatableCache.java b/src/main/java/org/broadinstitute/hellbender/engine/cache/LocatableCache.java
index d6f85bfc3c8..f454ff2a819 100644
--- a/src/main/java/org/broadinstitute/hellbender/engine/cache/LocatableCache.java
+++ b/src/main/java/org/broadinstitute/hellbender/engine/cache/LocatableCache.java
@@ -6,6 +6,7 @@
 import org.apache.logging.log4j.Logger;
 import org.broadinstitute.hellbender.utils.Utils;
 
+import java.io.Serializable;
 import java.util.*;
 
 /**
@@ -23,7 +24,8 @@
  *
  * @param <T> Type of Locatable record we are caching
  */
-public class LocatableCache<T extends Locatable> {
+public class LocatableCache<T extends Locatable> implements Serializable {
+    private static final long serialVersionUID = 1L;
     private static final Logger logger = LogManager.getLogger(LocatableCache.class);
 
     /**
diff --git a/src/main/java/org/broadinstitute/hellbender/engine/cache/LocatableCacheStrategy.java b/src/main/java/org/broadinstitute/hellbender/engine/cache/LocatableCacheStrategy.java
index 97bb978f372..ce098f5157e 100644
--- a/src/main/java/org/broadinstitute/hellbender/engine/cache/LocatableCacheStrategy.java
+++ b/src/main/java/org/broadinstitute/hellbender/engine/cache/LocatableCacheStrategy.java
@@ -1,14 +1,13 @@
 package org.broadinstitute.hellbender.engine.cache;
 
 import htsjdk.samtools.util.Locatable;
-import org.broadinstitute.hellbender.utils.SimpleInterval;
 
 import java.util.Deque;
 import java.util.Iterator;
 import java.util.List;
 
 /**
- * Interface for implemented by cache strategy objects for {@code LocatableCache}.
+ * Interface implemented by cache strategy objects for {@code LocatableCache}.
  *
  * {@code LocatableCacheStrategy} implementations determine the following policies for the cache:
  *
diff --git a/src/main/java/org/broadinstitute/hellbender/engine/cache/SideReadInputCacheStrategy.java b/src/main/java/org/broadinstitute/hellbender/engine/cache/SideReadInputCacheStrategy.java
index 8bf72cd29e0..b67e072c512 100644
--- a/src/main/java/org/broadinstitute/hellbender/engine/cache/SideReadInputCacheStrategy.java
+++ b/src/main/java/org/broadinstitute/hellbender/engine/cache/SideReadInputCacheStrategy.java
@@ -7,6 +7,7 @@
 import org.broadinstitute.hellbender.utils.SimpleInterval;
 import org.broadinstitute.hellbender.utils.read.GATKRead;
 
+import java.io.Serializable;
 import java.util.*;
 import java.util.function.Function;
 
@@ -23,7 +24,9 @@
  *
  * @param <CACHED_READ> Type of Locatable being cached.
  */
-public class SideReadInputCacheStrategy<CACHED_READ extends GATKRead> implements LocatableCacheStrategy<CACHED_READ> {
+public class SideReadInputCacheStrategy<CACHED_READ extends GATKRead>
+        implements LocatableCacheStrategy<CACHED_READ>, Serializable {
+    private static final long serialVersionUID = 1L;
     private static final Logger logger = LogManager.getLogger(LocatableCache.class);
     private static final int EXPECTED_MAX_OVERLAPPING_READS_DURING_CACHE_TRIM = 128;