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Added SingleReadGroupFilter to only use reads from a specific read group, filtering out all others. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2172 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2009-11-27 20:33:59 +00:00
parent 91f5672a32
commit 26db15be5c
2 changed files with 74 additions and 0 deletions
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25
java/src/org/broadinstitute/sting/gatk/filters/NoOriginalQualityScoresFilter.java
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@ -3,6 +3,31 @@ 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

49
java/src/org/broadinstitute/sting/gatk/filters/SingleReadGroupFilter.java 100755
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@ -0,0 +1,49 @@
package org.broadinstitute.sting.gatk.filters;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMReadGroupRecord;
import net.sf.picard.filter.SamRecordFilter;
import org.broadinstitute.sting.utils.cmdLine.Argument;
/*
* 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: Nov 27, 2009
*
* Only use reads from the specified read group.
*/
public class SingleReadGroupFilter implements SamRecordFilter {
@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(SAMRecord read) {
SAMReadGroupRecord readGroup = read.getReadGroup();
return !( readGroup != null && readGroup.getReadGroupId().equals( READ_GROUP_TO_KEEP ) );
}
}