Filter for reads with missing read groups so we can safely assume all reads have valid read groups

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1717 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -0,0 +1,44 @@
+/*
+ * 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.
+ */
+
+package org.broadinstitute.sting.gatk.filters;
+
+import net.sf.picard.filter.SamRecordFilter;
+import net.sf.samtools.SAMRecord;
+
+/**
+ * Filter out reads without read groups.
+ *
+ * @author ebanks
+ * @version 0.1
+ */
+
+public class MissingReadGroupFilter implements SamRecordFilter {
+    public boolean filterOut(SAMRecord rec) {
+        String RG = (String)(rec.getAttribute("RG"));
+        return RG == null ||
+               rec.getHeader() == null ||
+               rec.getHeader().getReadGroup(RG) == null;
+    }
+}