81 lines
2.1 KiB
Java
81 lines
2.1 KiB
Java
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package org.broadinstitute.sting.gatk.refdata;
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import java.util.Iterator;
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import java.io.IOException;
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import java.io.File;
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import edu.mit.broad.picard.genotype.geli.GeliFileReader;
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import edu.mit.broad.picard.genotype.geli.GenotypeLikelihoods;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.GenomeLocParser;
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import net.sf.samtools.util.CloseableIterator;
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/**
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* This class wraps Picard Geli CHiP data and presents it as a ROD.
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*/
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public class rodGELI extends BasicReferenceOrderedDatum {
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// ----------------------------------------------------------------------
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//
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// Constructors
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//
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// ----------------------------------------------------------------------
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private GenotypeLikelihoods gh = null;
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public rodGELI(final String name, GenotypeLikelihoods gh) {
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super(name);
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this.gh = gh;
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}
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@Override
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public GenomeLoc getLocation() {
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return GenomeLocParser.createGenomeLoc(gh.getSequenceIndex(), gh.getPosition());
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}
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/** Required by ReferenceOrderedDatum interface. This implementation provides its own iterator,
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* so this method does nothing at all (always returns false).
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*
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*/
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@Override
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public boolean parseLine(Object header, String[] parts) throws IOException {
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return false;
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}
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@Override
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public String toString() {
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return gh.toString();
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}
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private static class rodGELIIterator implements Iterator<rodGELI> {
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private String rodName = null;
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private GeliFileReader parser = null;
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private CloseableIterator<GenotypeLikelihoods> iterator = null;
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rodGELIIterator(String name, File f) {
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rodName = name;
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parser = new GeliFileReader(f);
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iterator = parser.iterator();
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}
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public boolean hasNext() {
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return iterator.hasNext();
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}
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public rodGELI next() {
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return new rodGELI(rodName, iterator.next());
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}
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public void remove() {
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throw new UnsupportedOperationException("'remove' operation is not supported for GELIs");
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}
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}
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public static Iterator<rodGELI> createIterator(String name, File file) {
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return new rodGELI.rodGELIIterator(name,file);
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}
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}
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