diff --git a/java/src/org/broadinstitute/sting/gatk/filters/MissingReadGroupFilter.java b/java/src/org/broadinstitute/sting/gatk/filters/MissingReadGroupFilter.java new file mode 100755 index 000000000..e46d1f09d --- /dev/null +++ b/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; + } +} \ No newline at end of file