54 lines
1.7 KiB
Java
54 lines
1.7 KiB
Java
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package org.broadinstitute.sting.utils;
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import net.sf.samtools.SAMReadGroupRecord;
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import net.sf.samtools.SAMFileHeader;
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import java.util.*;
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import org.broadinstitute.sting.utils.genotype.Genotype;
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import org.broadinstitute.sting.utils.genotype.SampleBacked;
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/**
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* SampleUtils is a static class (no instantiation allowed!) with some utility methods for getting samples
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* quality scores.
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*
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* @author ebanks
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*/
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public class SampleUtils {
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/**
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* Private constructor. No instantiating this class!
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*/
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private SampleUtils() {}
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/**
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* Pull out the samples from a SAMFileHeader;
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* note that we use a TreeSet so that they are sorted
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*
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* @param header the sam file header
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* @return list of strings representing the sample names
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*/
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public static Set<String> getSAMFileSamples(SAMFileHeader header) {
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// get all of the unique sample names
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Set<String> samples = new TreeSet<String>();
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List<SAMReadGroupRecord> readGroups = header.getReadGroups();
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for ( SAMReadGroupRecord readGroup : readGroups )
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samples.add(readGroup.getSample());
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return samples;
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}
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/**
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* get the samples names from genotype objects if they are backed by samples
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*
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* @param genotypes the genotype list
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* @return list of strings representing the sample names
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*/
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public static List<String> getGenotypeSamples(List<Genotype> genotypes) {
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List<String> samples = new ArrayList<String>();
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for ( Genotype genotype : genotypes ) {
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if ( genotype instanceof SampleBacked )
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samples.add(((SampleBacked)genotype).getSampleName());
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}
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return samples;
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}
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}
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