From 8bb3e56cbb54f0efddb615b9f5883da50c8f42d8 Mon Sep 17 00:00:00 2001
From: JP Martin <jpmartin@google.com>
Date: Wed, 14 Dec 2016 17:04:35 -0800
Subject: [PATCH 1/4] Add optional wrapper for the underlying
 SeekableByteChannel

This allows users to provide their own buffering or prefetching, without
them having to change htsjdk.
---
 .../htsjdk/samtools/seekablestream/SeekablePathStream.java     | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/src/main/java/htsjdk/samtools/seekablestream/SeekablePathStream.java b/src/main/java/htsjdk/samtools/seekablestream/SeekablePathStream.java
index cb88512df..b7a33e601 100644
--- a/src/main/java/htsjdk/samtools/seekablestream/SeekablePathStream.java
+++ b/src/main/java/htsjdk/samtools/seekablestream/SeekablePathStream.java
@@ -43,6 +43,16 @@ public SeekablePathStream(final Path path, Function<SeekableByteChannel, Seekabl
         ALL_INSTANCES.add(this);
     }
 
+    public SeekablePathStream(final Path path, Function<SeekableByteChannel, SeekableByteChannel> wrapper) throws IOException {
+        this.path = path;
+        if (null==wrapper) {
+            this.sbc = Files.newByteChannel(path);
+        } else {
+            this.sbc = wrapper.apply(Files.newByteChannel(path));
+        }
+        ALL_INSTANCES.add(this);
+    }
+
     @Override
     public long length() {
         try {

From 6693de6d6aaaa13a8491491fbbfb6a9864b101b3 Mon Sep 17 00:00:00 2001
From: JP Martin <jpmartin@google.com>
Date: Wed, 11 Jan 2017 14:14:52 -0800
Subject: [PATCH 2/4] Index wrapper code

---
 src/main/java/htsjdk/samtools/SamInputResource.java            |  8 +++++++-
 src/main/java/htsjdk/samtools/SamReaderFactory.java            | 10 ++++++++--
 .../htsjdk/samtools/seekablestream/SeekablePathStream.java     | 10 ----------
 3 files changed, 15 insertions(+), 13 deletions(-)

diff --git a/src/main/java/htsjdk/samtools/SamInputResource.java b/src/main/java/htsjdk/samtools/SamInputResource.java
index d76694eeb..277c6e5fd 100644
--- a/src/main/java/htsjdk/samtools/SamInputResource.java
+++ b/src/main/java/htsjdk/samtools/SamInputResource.java
@@ -132,7 +132,13 @@ public SamInputResource index(final File file) {
 
     /** Updates the index to point at the provided resource, then returns itself. */
     public SamInputResource index(final Path path) {
-        this.index = new PathInputResource(path, Function.identity());
+        this.index = new PathInputResource(path);
+        return this;
+    }
+
+    /** Updates the index to point at the provided resource, with the provided wrapper, then returns itself. */
+    public SamInputResource index(final Path path, Function<SeekableByteChannel, SeekableByteChannel> wrapper) {
+        this.index = new PathInputResource(path, wrapper);
         return this;
     }
 
diff --git a/src/main/java/htsjdk/samtools/SamReaderFactory.java b/src/main/java/htsjdk/samtools/SamReaderFactory.java
index a5eef5038..bb90ce094 100644
--- a/src/main/java/htsjdk/samtools/SamReaderFactory.java
+++ b/src/main/java/htsjdk/samtools/SamReaderFactory.java
@@ -82,9 +82,15 @@
     abstract public SamReader open(final File file);
 
     public SamReader open(final Path path) {
-        final SamInputResource r = SamInputResource.of(path, getPathWrapper());
+        return open(path, getPathWrapper(), Function.identity());
+    }
+
+    public SamReader open(final Path path,
+            Function<SeekableByteChannel, SeekableByteChannel> pathWrapper,
+            Function<SeekableByteChannel, SeekableByteChannel> indexWrapper) {
+        final SamInputResource r = SamInputResource.of(path, pathWrapper);
         final Path indexMaybe = SamFiles.findIndex(path);
-        if (indexMaybe != null) r.index(indexMaybe);
+        if (indexMaybe != null) r.index(indexMaybe, indexWrapper);
         return open(r);
     }
 
diff --git a/src/main/java/htsjdk/samtools/seekablestream/SeekablePathStream.java b/src/main/java/htsjdk/samtools/seekablestream/SeekablePathStream.java
index b7a33e601..cb88512df 100644
--- a/src/main/java/htsjdk/samtools/seekablestream/SeekablePathStream.java
+++ b/src/main/java/htsjdk/samtools/seekablestream/SeekablePathStream.java
@@ -43,16 +43,6 @@ public SeekablePathStream(final Path path, Function<SeekableByteChannel, Seekabl
         ALL_INSTANCES.add(this);
     }
 
-    public SeekablePathStream(final Path path, Function<SeekableByteChannel, SeekableByteChannel> wrapper) throws IOException {
-        this.path = path;
-        if (null==wrapper) {
-            this.sbc = Files.newByteChannel(path);
-        } else {
-            this.sbc = wrapper.apply(Files.newByteChannel(path));
-        }
-        ALL_INSTANCES.add(this);
-    }
-
     @Override
     public long length() {
         try {

From 496dcbfcc6e22849ebb20cf342e76479e73bd076 Mon Sep 17 00:00:00 2001
From: JP Martin <jpmartin@google.com>
Date: Thu, 19 Jan 2017 14:05:10 -0800
Subject: [PATCH 3/4] Add tests and javadoc

Tested this version with GATK's ReadsDataSourceUnitTest, and it passes.
---
 .../java/htsjdk/samtools/SamReaderFactory.java     | 44 ++++++++-------------
 .../htsjdk/samtools/PathInputResourceTest.java     | 46 ++++++++++++++++++++++
 .../java/htsjdk/samtools/SamReaderFactoryTest.java |  5 +--
 src/test/java/htsjdk/samtools/SamReaderTest.java   |  1 -
 4 files changed, 64 insertions(+), 32 deletions(-)
 create mode 100644 src/test/java/htsjdk/samtools/PathInputResourceTest.java

diff --git a/src/main/java/htsjdk/samtools/SamReaderFactory.java b/src/main/java/htsjdk/samtools/SamReaderFactory.java
index bb90ce094..8f203d5c0 100644
--- a/src/main/java/htsjdk/samtools/SamReaderFactory.java
+++ b/src/main/java/htsjdk/samtools/SamReaderFactory.java
@@ -81,14 +81,26 @@
 
     abstract public SamReader open(final File file);
 
+    /**
+     * Open the specified path (without using any wrappers).
+     *
+     * @param path the SAM or BAM file to open.
+     */
     public SamReader open(final Path path) {
-        return open(path, getPathWrapper(), Function.identity());
+        return open(path, null, null);
     }
 
+    /**
+     * Open the specified path, using the specified wrappers for prefetching/caching.
+     *
+     * @param path the SAM or BAM file to open
+     * @param dataWrapper the wrapper for the data (or null for none)
+     * @param indexWrapper the wrapper for the index (or null for none)
+     */
     public SamReader open(final Path path,
-            Function<SeekableByteChannel, SeekableByteChannel> pathWrapper,
+            Function<SeekableByteChannel, SeekableByteChannel> dataWrapper,
             Function<SeekableByteChannel, SeekableByteChannel> indexWrapper) {
-        final SamInputResource r = SamInputResource.of(path, pathWrapper);
+        final SamInputResource r = SamInputResource.of(path, dataWrapper);
         final Path indexMaybe = SamFiles.findIndex(path);
         if (indexMaybe != null) r.index(indexMaybe, indexWrapper);
         return open(r);
@@ -112,25 +124,6 @@ public SamReader open(final Path path,
     /** Sets a specific Option to a boolean value. * */
     abstract public SamReaderFactory setOption(final Option option, boolean value);
 
-    /** Sets a wrapper to modify the SeekableByteChannel from an opened Path, e.g. to add
-     * buffering or prefetching. This only works on Path inputs since we need a SeekableByteChannel.
-     *
-     * @param wrapper how to modify the SeekableByteChannel (Function.identity to unset)
-     * @return this
-     */
-    public SamReaderFactory setPathWrapper(Function<SeekableByteChannel, SeekableByteChannel> wrapper) {
-        this.pathWrapper = wrapper;
-        return this;
-    }
-
-    /** Gets the wrapper previously set via setPathWrapper.
-     *
-     * @return the wrapper.
-     */
-    public Function<SeekableByteChannel, SeekableByteChannel> getPathWrapper() {
-        return pathWrapper;
-    }
-
     /** Sets the specified reference sequence * */
     abstract public SamReaderFactory referenceSequence(File referenceSequence);
 
@@ -184,15 +177,10 @@ public static SamReaderFactory make() {
         private CRAMReferenceSource referenceSource;
 
         private SamReaderFactoryImpl(final EnumSet<Option> enabledOptions, final ValidationStringency validationStringency, final SAMRecordFactory samRecordFactory) {
-            this(enabledOptions, validationStringency, samRecordFactory, Function.identity());
-        }
-
-        private SamReaderFactoryImpl(final EnumSet<Option> enabledOptions, final ValidationStringency validationStringency, final SAMRecordFactory samRecordFactory, final Function<SeekableByteChannel, SeekableByteChannel> wrapper) {
             this.enabledOptions = EnumSet.copyOf(enabledOptions);
             this.samRecordFactory = samRecordFactory;
             this.validationStringency = validationStringency;
             this.customReaderFactory = CustomReaderFactory.getInstance();
-            setPathWrapper(wrapper);
         }
    
         @Override
@@ -423,7 +411,7 @@ private boolean isSra(final File sourceFile) {
         }
 
         public static SamReaderFactory copyOf(final SamReaderFactoryImpl target) {
-            return new SamReaderFactoryImpl(target.enabledOptions, target.validationStringency, target.samRecordFactory, target.getPathWrapper());
+            return new SamReaderFactoryImpl(target.enabledOptions, target.validationStringency, target.samRecordFactory);
         }
     }
 
diff --git a/src/test/java/htsjdk/samtools/PathInputResourceTest.java b/src/test/java/htsjdk/samtools/PathInputResourceTest.java
new file mode 100644
index 000000000..a45605ddf
--- /dev/null
+++ b/src/test/java/htsjdk/samtools/PathInputResourceTest.java
@@ -0,0 +1,46 @@
+package htsjdk.samtools;
+
+import java.nio.channels.SeekableByteChannel;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.HashMap;
+import java.util.function.Function;
+import junit.framework.Assert;
+import org.testng.annotations.Test;
+
+public class PathInputResourceTest {
+  final String localBam = "src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam";
+
+  @Test
+  public void testWrappersAreAccessed() throws Exception {
+    Path path = Paths.get(localBam);
+    Path indexPath = Paths.get(localBam + ".bai");
+    HashMap<String, Boolean> fired = new HashMap<>();
+    Function<SeekableByteChannel, SeekableByteChannel> wrapData = (SeekableByteChannel in) -> {
+      fired.put("data", true);
+      return in;
+    };
+    Function<SeekableByteChannel, SeekableByteChannel> wrapIndex = (SeekableByteChannel in) -> {
+      fired.put("index", true);
+      return in;
+    };
+    SamInputResource in = SamInputResource.of(path, wrapData);
+    in.index(indexPath, wrapIndex);
+    InputResource indexResource = in.indexMaybe();
+    Assert.assertNotNull(indexResource);
+
+    Assert.assertFalse(fired.containsKey("data"));
+    Assert.assertFalse(fired.containsKey("index"));
+
+    indexResource.asUnbufferedSeekableStream();
+
+    Assert.assertFalse(fired.containsKey("data"));
+    Assert.assertTrue(fired.containsKey("index"));
+
+    in.data().asUnbufferedSeekableStream();
+
+    Assert.assertTrue(fired.containsKey("data"));
+    Assert.assertTrue(fired.containsKey("index"));
+  }
+
+}
\ No newline at end of file
diff --git a/src/test/java/htsjdk/samtools/SamReaderFactoryTest.java b/src/test/java/htsjdk/samtools/SamReaderFactoryTest.java
index 4c045d9d8..1d5163346 100644
--- a/src/test/java/htsjdk/samtools/SamReaderFactoryTest.java
+++ b/src/test/java/htsjdk/samtools/SamReaderFactoryTest.java
@@ -6,6 +6,7 @@
 import htsjdk.samtools.seekablestream.SeekableHTTPStream;
 import htsjdk.samtools.seekablestream.SeekableStreamFactory;
 import htsjdk.samtools.util.*;
+import java.net.URI;
 import java.nio.ByteBuffer;
 import java.nio.channels.SeekableByteChannel;
 import java.nio.file.Paths;
@@ -92,8 +93,7 @@ public void testWrap() throws IOException {
         final SamReader wrappedReader =
             SamReaderFactory
                 .makeDefault()
-                .setPathWrapper(SamReaderFactoryTest::addHeader)
-                .open(input);
+                .open(input, SamReaderFactoryTest::addHeader, null);
         int records = countRecords(wrappedReader);
         Assert.assertEquals(10, records);
     }
@@ -289,7 +289,6 @@ public void openPath() throws IOException {
         }
     }
 
-
     final Set<List<SAMRecord>> observedRecordOrdering1 = new HashSet<List<SAMRecord>>();
     final Set<List<SAMRecord>> observedRecordOrdering3 = new HashSet<List<SAMRecord>>();
     final Set<List<SAMRecord>> observedRecordOrdering20 = new HashSet<List<SAMRecord>>();
diff --git a/src/test/java/htsjdk/samtools/SamReaderTest.java b/src/test/java/htsjdk/samtools/SamReaderTest.java
index 093dffbeb..02364f318 100644
--- a/src/test/java/htsjdk/samtools/SamReaderTest.java
+++ b/src/test/java/htsjdk/samtools/SamReaderTest.java
@@ -23,7 +23,6 @@
  */
 package htsjdk.samtools;
 
-import htsjdk.samtools.cram.CRAMException;
 import htsjdk.samtools.util.CloseableIterator;
 import htsjdk.samtools.util.CloserUtil;
 import org.testng.Assert;

From 031cee93c186c7ad4c106b3327f5e394d160ae2e Mon Sep 17 00:00:00 2001
From: JP Martin <jpmartin@google.com>
Date: Fri, 20 Jan 2017 11:59:54 -0800
Subject: [PATCH 4/4] Fix import

---
 src/test/java/htsjdk/samtools/PathInputResourceTest.java | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/test/java/htsjdk/samtools/PathInputResourceTest.java b/src/test/java/htsjdk/samtools/PathInputResourceTest.java
index a45605ddf..1bc2aa161 100644
--- a/src/test/java/htsjdk/samtools/PathInputResourceTest.java
+++ b/src/test/java/htsjdk/samtools/PathInputResourceTest.java
@@ -5,7 +5,7 @@
 import java.nio.file.Paths;
 import java.util.HashMap;
 import java.util.function.Function;
-import junit.framework.Assert;
+import org.testng.Assert;
 import org.testng.annotations.Test;
 
 public class PathInputResourceTest {
@@ -43,4 +43,4 @@ public void testWrappersAreAccessed() throws Exception {
     Assert.assertTrue(fired.containsKey("index"));
   }
 
-}
\ No newline at end of file
+}