Deprecated. Use SelectVariants instead.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4043 348d0f76-0448-11de-a6fe-93d51630548a
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/*
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* Copyright (c) 2010.
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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.playground.gatk.walkers.vcftools;
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import org.apache.commons.jexl2.Expression;
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import org.apache.commons.jexl2.JexlContext;
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import org.apache.commons.jexl2.MapContext;
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import org.broad.tribble.util.variantcontext.VariantContext;
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
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import org.broadinstitute.sting.gatk.walkers.RMD;
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import org.broadinstitute.sting.gatk.walkers.Requires;
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import org.broadinstitute.sting.gatk.walkers.RodWalker;
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import org.broadinstitute.sting.utils.StingException;
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import org.broadinstitute.sting.utils.SampleUtils;
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import org.broadinstitute.sting.commandline.Argument;
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import org.broadinstitute.sting.utils.vcf.VCFUtils;
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import org.broadinstitute.sting.utils.genotype.vcf.*;
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import org.broad.tribble.vcf.VCFHeaderLine;
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import org.broad.tribble.vcf.VCFFilterHeaderLine;
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import org.broad.tribble.vcf.VCFHeader;
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import java.util.*;
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/**
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* Selects variant calls for output from a user-supplied VCF file using a number of user-selectable, parameterizable criteria. [TODO -- update to new walker style]
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*/
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@Requires(value={},referenceMetaData=@RMD(name="variant", type= ReferenceOrderedDatum.class))
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public class VariantSelect extends RodWalker<Integer, Integer> {
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@Argument(fullName="match", shortName="match", doc="Expression used with INFO fields to select VCF records for inclusion in the output VCF(see wiki docs for more info)", required=false)
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protected String[] MATCH_STRINGS = new String[]{null};
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private VCFWriter writer = null;
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class MatchExp {
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String name;
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String expStr;
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Expression exp;
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public MatchExp(String name, String str, Expression exp) {
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this.name = name;
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this.expStr = str;
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this.exp = exp;
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}
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}
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private List<MatchExp> matchExpressions = new ArrayList<MatchExp>();
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public void initialize() {
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for ( int i = 0; i < MATCH_STRINGS.length; i++ ) {
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if ( MATCH_STRINGS[i] != null ) {
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try {
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Expression filterExpression = VariantContextUtils.engine.createExpression(MATCH_STRINGS[i]);
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matchExpressions.add(new MatchExp(String.format("match-%d", i), MATCH_STRINGS[i], filterExpression));
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} catch (Exception e) {
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throw new StingException("Invalid expression used (" + MATCH_STRINGS[i] + "). Please see the JEXL docs for correct syntax.");
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}
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}
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}
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// setup the header fields
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Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
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hInfo.addAll(VCFUtils.getHeaderFields(getToolkit()));
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hInfo.add(new VCFHeaderLine("source", "VariantSelect"));
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hInfo.add(new VCFHeaderLine("reference", getToolkit().getArguments().referenceFile.getName()));
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for ( MatchExp exp : matchExpressions ) {
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hInfo.add(new VCFFilterHeaderLine(exp.name, exp.expStr));
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}
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writer = new VCFWriterImpl(out);
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Set<String> samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList("variant"));
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final VCFHeader vcfHeader = new VCFHeader(hInfo, samples);
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writer.writeHeader(vcfHeader);
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}
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public Integer reduceInit() { return 0; }
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/**
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* For each site of interest, rescore the genotype likelihoods by applying the specified feature set.
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*
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* @param tracker the meta-data tracker
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* @param ref the reference base
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* @param context the context for the given locus
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* @return 1 if the locus was successfully processed, 0 if otherwise
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*/
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public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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if ( tracker == null )
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return 0;
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VariantContext vc = tracker.getVariantContext(ref, "variant", null, context.getLocation(), false);
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// ignore places where we don't have a variant
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if ( vc == null )
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return 0;
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boolean someoneMatched = false;
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for ( MatchExp exp : matchExpressions ) {
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Map<String, Object> infoMap = new HashMap<String, Object>(vc.getAttributes());
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infoMap.put("QUAL", String.valueOf(vc.getPhredScaledQual()));
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JexlContext jContext = new MapContext(infoMap);
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try {
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//System.out.printf("Matching %s vs. %s%n", infoMap, exp.expStr);
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if ( (Boolean)exp.exp.evaluate(jContext) ) {
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//System.out.printf(" => Matched%n");
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someoneMatched = true;
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break;
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}
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} catch (Exception e) {
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throw new StingException(e.getMessage());
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}
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}
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if ( someoneMatched )
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writer.add(vc, ref.getBase());
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return 1;
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}
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public Integer reduce(Integer value, Integer sum) {
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return sum + value;
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}
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public void onTraversalDone(Integer result) {
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writer.close();
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}
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}
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