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

java/src/org/broadinstitute/sting/playground/gatk/walkers/ListSampleIds.java

@@ -0,0 +1,56 @@
+
+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;
+    }
+}