Merge pull request #344 from lbergelson/lb_library_read_filter

Adding LibraryReadFilter.

public/java/src/org/broadinstitute/sting/gatk/filters/LibraryReadFilter.java

@@ -0,0 +1,49 @@
+/*
+* Copyright (c) 2012 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.samtools.SAMReadGroupRecord;
+import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.gatk.filters.ReadFilter;
+
+/**
+ * Only use reads from the specified library
+ *
+ * @author kcibul
+ * @since Aug 15, 2012
+ *
+ */
+
+public class LibraryReadFilter extends ReadFilter {
+    @Argument(fullName = "library", shortName = "library", doc="The name of the library to keep, filtering out all others", required=true)
+    private String LIBRARY_TO_KEEP = null;
+
+    public boolean filterOut( final SAMRecord read ) {
+        final SAMReadGroupRecord readGroup = read.getReadGroup();
+        return ( readGroup == null || readGroup.getLibrary() == null || !readGroup.getLibrary().equals( LIBRARY_TO_KEEP ) );
+    }
+}