diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/ListSampleIds.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/ListSampleIds.java new file mode 100644 index 000000000..96df06062 --- /dev/null +++ b/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 +{ + public void initialize() + { + GenomeAnalysisTK toolkit = this.getToolkit(); + SAMFileHeader header = toolkit.getSamReader().getFileHeader(); + List 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; + } +}