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Selects a single sample on which to operate. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3080 348d0f76-0448-11de-a6fe-93d51630548a
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kiran 2010-03-26 20:50:58 +00:00
parent 20e3ba15ca
commit 8048b709a0
1 changed files with 16 additions and 0 deletions
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16
java/src/org/broadinstitute/sting/gatk/filters/SampleFilter.java 100755
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package org.broadinstitute.sting.gatk.filters;
import net.sf.picard.filter.SamRecordFilter;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMReadGroupRecord;
import org.broadinstitute.sting.utils.cmdLine.Argument;
public class SampleFilter implements SamRecordFilter {
@Argument(fullName = "sample_to_keep", shortName = "goodSM", doc="The name of the sample to keep, filtering out all others", required=true)
private String SAMPLE_TO_KEEP = null;
public boolean filterOut( final SAMRecord read ) {
final SAMReadGroupRecord readGroup = read.getReadGroup();
return !( readGroup != null && readGroup.getSample().equals( SAMPLE_TO_KEEP ) );
}
}