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Simple walker to print all of the sample names present in a merged bam file. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@500 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
jmaguire 2009-04-23 12:26:56 +00:00
parent ef4a107548
commit 8c1905c7d9
1 changed files with 56 additions and 0 deletions
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56
java/src/org/broadinstitute/sting/playground/gatk/walkers/ListSampleIds.java 100644
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package org.broadinstitute.sting.playground.gatk.walkers;
import net.sf.samtools.*;
import org.broadinstitute.sting.gatk.*;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
import org.broadinstitute.sting.gatk.refdata.rodGFF;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.gatk.LocusContext;
import org.broadinstitute.sting.playground.gatk.walkers.AlleleFrequencyWalker;
import org.broadinstitute.sting.playground.utils.AlleleFrequencyEstimate;
import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.cmdLine.Argument;
import java.util.*;
public class ListSampleIds extends LocusWalker<Boolean, Boolean>
{
public void initialize()
{
GenomeAnalysisTK toolkit = this.getToolkit();
SAMFileHeader header = toolkit.getSamReader().getFileHeader();
List<SAMReadGroupRecord> read_groups = header.getReadGroups();
for (int i = 0; i < read_groups.size(); i++)
{
String sample_name = read_groups.get(i).getSample();
out.println(sample_name);
}
}
public Boolean map(RefMetaDataTracker tracker, char ref, LocusContext context)
{
return true;
}
public void onTraversalDone()
{
return;
}
public Boolean reduceInit()
{
return true;
}
public Boolean reduce(Boolean mapresult, Boolean sum)
{
out.flush();
System.exit(0);
return true;
}
}