From 0208d201c7c408c340d739ac7b5186a6dab97776 Mon Sep 17 00:00:00 2001
From: aaron <aaron@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 23 Apr 2009 20:47:22 +0000
Subject: [PATCH] Forgot this in the last commit...

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@515 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../dataSources/shards/ReadShardStrategy.java | 82 +++++++++++++++++++
 1 file changed, 82 insertions(+)
 create mode 100755 java/src/org/broadinstitute/sting/gatk/dataSources/shards/ReadShardStrategy.java

diff --git a/java/src/org/broadinstitute/sting/gatk/dataSources/shards/ReadShardStrategy.java b/java/src/org/broadinstitute/sting/gatk/dataSources/shards/ReadShardStrategy.java
new file mode 100755
index 000000000..9d7d7287a
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/gatk/dataSources/shards/ReadShardStrategy.java
@@ -0,0 +1,82 @@
+package org.broadinstitute.sting.gatk.dataSources.shards;
+
+import net.sf.samtools.SAMSequenceDictionary;
+
+import java.util.Iterator;
+
+/**
+ *
+ * User: aaron
+ * Date: Apr 14, 2009
+ * Time: 1:34:28 PM
+ *
+ * The Broad Institute
+ * SOFTWARE COPYRIGHT NOTICE AGREEMENT 
+ * This software and its documentation are copyright 2009 by the
+ * Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
+ *
+ * This software is supplied without any warranty or guaranteed support whatsoever. Neither
+ * the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
+ *
+ */
+
+
+/**
+ * @author aaron
+ * @version 1.0
+ * @date Apr 14, 2009
+ * <p/>
+ * Class ReadShardStrategy
+ * <p/>
+ * A descriptions should go here. Blame aaron if it's missing.
+ */
+public class ReadShardStrategy implements ShardStrategy {
+
+    // do we use unmapped reads in the sharding strategy
+    private boolean unMappedReads = true;
+
+    // our read bucket size, default
+    public long readCount = 100000;
+
+    // our sequence dictionary
+    final private SAMSequenceDictionary dic;
+
+    /**
+     * the default constructor
+     * @param dic the dictionary
+     * @param size the read count to iterate over
+     */
+    ReadShardStrategy(SAMSequenceDictionary dic, long size) {
+        this.dic = dic;
+        readCount = size;    
+    }
+
+    /**
+     * do we have another read shard?
+     * @return
+     */
+    public boolean hasNext() {
+        return true;
+    }
+
+    public Shard next() {
+        return null;  //To change body of implemented methods use File | Settings | File Templates.
+    }
+
+    public void remove() {
+        throw new UnsupportedOperationException("Remove not supported");
+    }
+
+    public Iterator<Shard> iterator() {
+        return this;
+    }
+
+    /**
+     * set the next shards size
+     *
+     * @param size adjust the next size to this
+     */
+    public void adjustNextShardSize(long size) {
+        readCount = size;
+    }
+}