88 lines
2.9 KiB
Java
88 lines
2.9 KiB
Java
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package org.broadinstitute.sting.gatk.refdata;
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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 org.broadinstitute.sting.utils.xReadLines;
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import java.util.*;
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import java.util.regex.Matcher;
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import java.util.regex.Pattern;
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import java.io.IOException;
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import java.io.File;
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import java.io.FileNotFoundException;
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public class BeagleROD extends BasicReferenceOrderedDatum {
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GenomeLoc loc;
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List<String> sampleNames = null;
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Map<String, List<String>> sampleGenotypes = new HashMap<String, List<String>>();
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public BeagleROD(String name) {
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super(name);
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}
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public String toString() { return "BeagleRod"; }
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public String delimiterRegex() {
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return " ";
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}
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public GenomeLoc getLocation() {
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return loc;
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}
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public List<String> getSampleNames() {
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return sampleNames;
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}
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public Map<String, List<String>> getGenotypes() {
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return sampleGenotypes;
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}
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public Object initialize(final File source) throws FileNotFoundException {
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String firstLine = new xReadLines(source).next();
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String[] parts = firstLine.split(" ");
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if ( parts[0].equals("I") ) {
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// I id NA12891 NA12891 NA12892 NA12892
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sampleNames = Arrays.asList(parts).subList(2, parts.length);
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return sampleNames;
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} else {
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throw new IllegalStateException("Beagle file " + source + " doesn't have required header line I");
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}
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}
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private static Pattern MARKER_PATTERN = Pattern.compile("c(.+)_p([0-9]+)");
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public static GenomeLoc parseMarkerName(String markerName) {
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Matcher m = MARKER_PATTERN.matcher(markerName);
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if ( m.matches() ) {
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String contig = m.group(1);
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long start = Long.valueOf(m.group(2));
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return GenomeLocParser.createGenomeLoc(contig, start, start);
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} else {
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throw new IllegalArgumentException("Malformatted family structure string: " + markerName + " required format is mom+dad=child");
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}
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}
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public boolean parseLine(final Object header, final String[] parts) throws IOException {
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//System.out.printf("Parsing beagle parts=%s header=%s%n", parts, header);
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List<String> sampleNames = (List<String>)header;
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if ( parts.length == 0 || ! parts[0].equals("M") )
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return false;
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else {
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loc = parseMarkerName(parts[1]);
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for ( int i = 2; i < parts.length; i++ ) {
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String sampleName = sampleNames.get(i-2);
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if ( ! sampleGenotypes.containsKey(sampleName) ) {
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sampleGenotypes.put(sampleName, new ArrayList<String>());
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}
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sampleGenotypes.get(sampleName).add(parts[i]);
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}
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return true;
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}
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}
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}
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