From 2f5064dd1d1e1d8e5b8071bfca3c29b4cc174df1 Mon Sep 17 00:00:00 2001
From: chapmanb <chapmanb@50mail.com>
Date: Mon, 12 Aug 2013 14:36:57 -0400
Subject: [PATCH] Provide close methods to clean up resources used while
 creating AlignmentContexts from BAM file regions. Allows utilization of
 CoveredLocusView via the API

Signed-off-by: David Roazen <droazen@broadinstitute.org>
---
 .../sting/gatk/datasources/reads/BAMScheduler.java        | 8 ++++++++
 .../sting/gatk/datasources/reads/IntervalSharder.java     | 3 +++
 .../sting/gatk/datasources/reads/SAMDataSource.java       | 8 ++++++++
 .../sting/gatk/datasources/reads/ShardBalancer.java       | 3 +++
 4 files changed, 22 insertions(+)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMScheduler.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMScheduler.java
index adb668ff9..2f03edb68 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMScheduler.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMScheduler.java
@@ -246,6 +246,14 @@ public class BAMScheduler implements Iterator<FilePointer> {
      */
     private PeekableIterator<BAMScheduleEntry> bamScheduleIterator = null;
 
+    /**
+     * Clean up underlying BAMSchedule file handles.
+     */
+    public void close() {
+        if(bamScheduleIterator != null)
+            bamScheduleIterator.close();
+    }
+
     /**
      * Get the next overlapping tree of bins associated with the given BAM file.
      * @param currentLocus The actual locus for which to check overlap.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/IntervalSharder.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/IntervalSharder.java
index 048ce17f5..b476945ce 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/IntervalSharder.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/IntervalSharder.java
@@ -62,6 +62,9 @@ public class IntervalSharder implements Iterator<FilePointer> {
         wrappedIterator = new PeekableIterator<FilePointer>(scheduler);
         this.parser = parser;
     }
+    public void close() {
+      wrappedIterator.close();
+    }
 
     public boolean hasNext() {
         return wrappedIterator.hasNext();
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java
index ac2ed4a4c..9dc9734a5 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java
@@ -352,6 +352,14 @@ public class SAMDataSource {
         resourcePool.releaseReaders(readers);
     }
 
+    public void close() {
+        SAMReaders readers = resourcePool.getAvailableReaders();
+        for(SAMReaderID readerID: readerIDs) {
+            SAMFileReader reader = readers.getReader(readerID);
+            reader.close();
+        }
+    }
+
     /**
      * Returns Reads data structure containing information about the reads data sources placed in this pool as well as
      * information about how they are downsampled, sorted, and filtered
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ShardBalancer.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ShardBalancer.java
index ff0fa1127..37f1bcfac 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ShardBalancer.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ShardBalancer.java
@@ -43,4 +43,7 @@ public abstract class ShardBalancer implements Iterable<Shard> {
         this.filePointers = new PeekableIterator<FilePointer>(filePointers);
         this.parser = parser;
     }
+    public void close() {
+      this.filePointers.close();
+    }
 }