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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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kiran 2010-08-16 15:07:50 +00:00
parent 20db00a3e8
commit 3d63302b70
1 changed files with 0 additions and 155 deletions
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155
java/src/org/broadinstitute/sting/playground/gatk/walkers/vcftools/VariantSelect.java
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/*
* Copyright (c) 2010.
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.playground.gatk.walkers.vcftools;
import org.apache.commons.jexl2.Expression;
import org.apache.commons.jexl2.JexlContext;
import org.apache.commons.jexl2.MapContext;
import org.broad.tribble.util.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
import org.broadinstitute.sting.gatk.walkers.RMD;
import org.broadinstitute.sting.gatk.walkers.Requires;
import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.utils.vcf.VCFUtils;
import org.broadinstitute.sting.utils.genotype.vcf.*;
import org.broad.tribble.vcf.VCFHeaderLine;
import org.broad.tribble.vcf.VCFFilterHeaderLine;
import org.broad.tribble.vcf.VCFHeader;
import java.util.*;
/**
* 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]
*/
@Requires(value={},referenceMetaData=@RMD(name="variant", type= ReferenceOrderedDatum.class))
public class VariantSelect extends RodWalker<Integer, Integer> {
@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)
protected String[] MATCH_STRINGS = new String[]{null};
private VCFWriter writer = null;
class MatchExp {
String name;
String expStr;
Expression exp;
public MatchExp(String name, String str, Expression exp) {
this.name = name;
this.expStr = str;
this.exp = exp;
}
}
private List<MatchExp> matchExpressions = new ArrayList<MatchExp>();
public void initialize() {
for ( int i = 0; i < MATCH_STRINGS.length; i++ ) {
if ( MATCH_STRINGS[i] != null ) {
try {
Expression filterExpression = VariantContextUtils.engine.createExpression(MATCH_STRINGS[i]);
matchExpressions.add(new MatchExp(String.format("match-%d", i), MATCH_STRINGS[i], filterExpression));
} catch (Exception e) {
throw new StingException("Invalid expression used (" + MATCH_STRINGS[i] + "). Please see the JEXL docs for correct syntax.");
}
}
}
// setup the header fields
Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
hInfo.addAll(VCFUtils.getHeaderFields(getToolkit()));
hInfo.add(new VCFHeaderLine("source", "VariantSelect"));
hInfo.add(new VCFHeaderLine("reference", getToolkit().getArguments().referenceFile.getName()));
for ( MatchExp exp : matchExpressions ) {
hInfo.add(new VCFFilterHeaderLine(exp.name, exp.expStr));
}
writer = new VCFWriterImpl(out);
Set<String> samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList("variant"));
final VCFHeader vcfHeader = new VCFHeader(hInfo, samples);
writer.writeHeader(vcfHeader);
}
public Integer reduceInit() { return 0; }
/**
* For each site of interest, rescore the genotype likelihoods by applying the specified feature set.
*
* @param tracker the meta-data tracker
* @param ref the reference base
* @param context the context for the given locus
* @return 1 if the locus was successfully processed, 0 if otherwise
*/
public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
if ( tracker == null )
return 0;
VariantContext vc = tracker.getVariantContext(ref, "variant", null, context.getLocation(), false);
// ignore places where we don't have a variant
if ( vc == null )
return 0;
boolean someoneMatched = false;
for ( MatchExp exp : matchExpressions ) {
Map<String, Object> infoMap = new HashMap<String, Object>(vc.getAttributes());
infoMap.put("QUAL", String.valueOf(vc.getPhredScaledQual()));
JexlContext jContext = new MapContext(infoMap);
try {
//System.out.printf("Matching %s vs. %s%n", infoMap, exp.expStr);
if ( (Boolean)exp.exp.evaluate(jContext) ) {
//System.out.printf(" => Matched%n");
someoneMatched = true;
break;
}
} catch (Exception e) {
throw new StingException(e.getMessage());
}
}
if ( someoneMatched )
writer.add(vc, ref.getBase());
return 1;
}
public Integer reduce(Integer value, Integer sum) {
return sum + value;
}
public void onTraversalDone(Integer result) {
writer.close();
}
}