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Simple walker to randomly break VCF files into (potentially unequal) subsets. Useful for e.g. cutting hapmap into training and evaluation sets. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5333 348d0f76-0448-11de-a6fe-93d51630548a
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ebanks 2011-02-28 16:51:46 +00:00
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commit 8de83725f9
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java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java 100755
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/*
* Copyright (c) 2010, The Broad Institute
*
* 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.gatk.walkers.variantutils;
import org.broad.tribble.util.variantcontext.VariantContext;
import org.broad.tribble.vcf.StandardVCFWriter;
import org.broad.tribble.vcf.VCFHeader;
import org.broad.tribble.vcf.VCFHeaderLine;
import org.broad.tribble.vcf.VCFWriter;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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.SampleUtils;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.vcf.VCFUtils;
import java.io.File;
import java.util.*;
/**
* Takes a VCF file, randomly splits variants into two different sets, and outputs 2 new VCFs with the results.
*/
@Requires(value={},referenceMetaData=@RMD(name="variant", type=VariantContext.class))
public class RandomlySplitVariants extends RodWalker<Integer, Integer> {
@Output(fullName="out1", shortName="o1", doc="File #1 to which variants should be written", required=true)
protected VCFWriter vcfWriter1 = null;
@Output(fullName="out2", shortName="o2", doc="File #2 to which variants should be written", required=true)
// there's a reported bug in the GATK where we can't have 2 @Output writers
protected File file2 = null;
protected StandardVCFWriter vcfWriter2 = null;
@Argument(fullName="fractionToOut1", shortName="fraction", doc="Fraction of records to be placed in out1 (must be 0 >= fraction <= 1); all other records are placed in out2", required=false)
protected double fraction = 0.5;
@Argument(fullName="randomSeed", shortName="seed", doc="Random seed to use; if 0, current time will be used", required=false)
protected long SEED = 0;
protected static final String INPUT_VARIANT_ROD_BINDING_NAME = "variant";
protected Random generator;
protected int iFraction;
/**
* Set up the VCF writer, the sample expressions and regexs, and the JEXL matcher
*/
public void initialize() {
if ( fraction < 0.0 || fraction > 1.0 )
throw new UserException.BadArgumentValue("fractionToOut1", "this value needs to be a number between 0 and 1");
iFraction = (int)(fraction * 1000.0);
// setup the header info
final ArrayList<String> inputNames = new ArrayList<String>();
inputNames.add( INPUT_VARIANT_ROD_BINDING_NAME );
Set<String> samples = SampleUtils.getUniqueSamplesFromRods(getToolkit(), inputNames);
Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
hInfo.addAll(VCFUtils.getHeaderFields(getToolkit(), inputNames));
vcfWriter1.writeHeader(new VCFHeader(hInfo, samples));
vcfWriter2 = new StandardVCFWriter(file2, true);
vcfWriter2.writeHeader(new VCFHeader(hInfo, samples));
if ( SEED == 0 )
generator = new Random();
else
generator = new Random(SEED);
}
/**
* Subset VC record if necessary and emit the modified record (provided it satisfies criteria for printing)
*
* @param tracker the ROD tracker
* @param ref reference information
* @param context alignment info
* @return 1 if the record was printed to the output file, 0 if otherwise
*/
public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
if ( tracker == null )
return 0;
Collection<VariantContext> vcs = tracker.getVariantContexts(ref, INPUT_VARIANT_ROD_BINDING_NAME, null, context.getLocation(), true, false);
for ( VariantContext vc : vcs ) {
int random = generator.nextInt(1000);
if ( random < iFraction )
vcfWriter1.add(vc, ref.getBase());
else
vcfWriter2.add(vc, ref.getBase());
}
return 1;
}
public Integer reduceInit() { return 0; }
public Integer reduce(Integer value, Integer sum) { return value + sum; }
public void onTraversalDone(Integer result) { logger.info(result + " records processed."); }
}