/*
* Copyright (c) 2012 The Broad Institute
*
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* obtaining a copy of this software and associated documentation
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* 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,
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* 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,
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package org.broadinstitute.gatk.engine.filters;
import htsjdk.samtools.SAMReadGroupRecord;
import htsjdk.samtools.SAMRecord;
import org.broadinstitute.gatk.utils.commandline.Argument;
/**
* Only use reads from the specified read group.
*
* @author rpoplin
* @since Nov 27, 2009
*
*/
public class SingleReadGroupFilter extends ReadFilter {
@Argument(fullName = "read_group_to_keep", shortName = "goodRG", doc="The name of the read group to keep, filtering out all others", required=true)
private String READ_GROUP_TO_KEEP = null;
public boolean filterOut( final SAMRecord read ) {
final SAMReadGroupRecord readGroup = read.getReadGroup();
return !( readGroup != null && readGroup.getReadGroupId().equals( READ_GROUP_TO_KEEP ) );
}
}