113 lines
4.0 KiB
Java
Executable File
113 lines
4.0 KiB
Java
Executable File
/*
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* Copyright (c) 2010 The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
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* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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*/
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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.text.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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