Added DuplicateReadFilter to filter out reads that are marked as duplicates.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2293 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/filters/DuplicateReadFilter.java

@@ -0,0 +1,43 @@
+package org.broadinstitute.sting.gatk.filters;
+
+import net.sf.picard.filter.SamRecordFilter;
+import net.sf.samtools.SAMRecord;
+
+/*
+ * Copyright (c) 2009 The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: rpoplin
+ * Date: Dec 9, 2009
+ *
+ * Filter out duplicate reads.
+ */
+
+public class DuplicateReadFilter implements SamRecordFilter {
+    public boolean filterOut( final SAMRecord read ) {
+        return read.getDuplicateReadFlag();
+    }
+}