/*
* Copyright (c) 2012 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
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* 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,
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* 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,
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package org.broadinstitute.gatk.tools.walkers.variantutils;
import org.broadinstitute.gatk.utils.commandline.Argument;
import org.broadinstitute.gatk.utils.commandline.ArgumentCollection;
import org.broadinstitute.gatk.utils.commandline.Output;
import org.broadinstitute.gatk.engine.CommandLineGATK;
import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
import org.broadinstitute.gatk.engine.arguments.StandardVariantContextInputArgumentCollection;
import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
import org.broadinstitute.gatk.engine.walkers.RodWalker;
import org.broadinstitute.gatk.utils.SampleUtils;
import org.broadinstitute.gatk.utils.help.HelpConstants;
import org.broadinstitute.gatk.utils.variant.GATKVCFUtils;
import htsjdk.variant.vcf.VCFHeader;
import htsjdk.variant.vcf.VCFHeaderLine;
import org.broadinstitute.gatk.utils.exceptions.UserException;
import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
import htsjdk.variant.variantcontext.VariantContext;
import htsjdk.variant.variantcontext.writer.VariantContextWriter;
import htsjdk.variant.variantcontext.writer.VariantContextWriterFactory;
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.
*/
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARMANIP, extraDocs = {CommandLineGATK.class} )
public class RandomlySplitVariants extends RodWalker<Integer, Integer> {
@ArgumentCollection
protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
@Output(fullName="out1", shortName="o1", doc="File #1 to which variants should be written", required=false, exclusiveOf = "splitToManyFiles")
protected VariantContextWriter vcfWriter1 = null;
@Output(fullName="out2", shortName="o2", doc="File #2 to which variants should be written", required=false, exclusiveOf = "splitToManyFiles")
// there's a reported bug in the GATK where we can't have 2 @Output writers
protected File file2 = null;
protected VariantContextWriter 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="splitToManyFiles", shortName = "splitToMany", doc="split (with uniform distribution) to more than 2 files. numOfFiles and baseOutputName parameters are required", required = false)
protected boolean splitToMany = false;
@Argument(fullName = "numOfOutputVCFFiles", shortName = "N", doc = "number of output VCF files. Only works with SplitToMany = true", required = false, maxRecommendedValue = 20, minValue = 2)
protected int numOfFiles = -1;
@Argument(fullName = "prefixForAllOutputFileNames", shortName = "baseOutputName", doc = "the name of the output VCF file will be: <baseOutputName>.split.<number>.vcf. Required with SplitToMany option", required = false)
protected String baseFileName = null;
private VariantContextWriter[] writers = null;
/**
* 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");
if (splitToMany){
if (numOfFiles < 2)
throw new UserException.BadArgumentValue("numOfFiles", "this value must be greater than 2 when using the splitToMany option");
if (baseFileName == null)
throw new UserException.BadArgumentValue("baseFileName", "this value cannot be null (unprovided) when using the splitToMany option");
}
else{
if(vcfWriter1 == null || vcfWriter2 == null)
throw new UserException.BadArgumentValue("out1 or out2", "this value cannot be null (unprovided) unless you are using the splitToMany option");
}
// setup the header info
final List<String> inputNames = Arrays.asList(variantCollection.variants.getName());
final Set<String> samples = SampleUtils.getUniqueSamplesFromRods(getToolkit(), inputNames);
final Set<VCFHeaderLine> hInfo = new HashSet<>();
hInfo.addAll(GATKVCFUtils.getHeaderFields(getToolkit(), inputNames));
if(splitToMany){
writers = new VariantContextWriter[numOfFiles];
for(int i = 0; i<writers.length; i++){
writers[i] = VariantContextWriterFactory.create(new File(baseFileName+".split."+i+".vcf"), getMasterSequenceDictionary());
writers[i].writeHeader(new VCFHeader(hInfo,samples));
}
}
else {
vcfWriter1.writeHeader(new VCFHeader(hInfo, samples));
vcfWriter2 = VariantContextWriterFactory.create(file2, getMasterSequenceDictionary());
vcfWriter2.writeHeader(new VCFHeader(hInfo, samples));
}
}
/**
* 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(final RefMetaDataTracker tracker, final ReferenceContext ref, final AlignmentContext context) {
if ( tracker == null )
return 0;
final Collection<VariantContext> vcs = tracker.getValues(variantCollection.variants, context.getLocation());
for ( final VariantContext vc : vcs ) {
final double random = GenomeAnalysisEngine.getRandomGenerator().nextDouble();
if(splitToMany){
final int index = (int)(numOfFiles * random);
writers[index].add(vc);
}
else{
if ( random < fraction )
vcfWriter1.add(vc);
else
vcfWriter2.add(vc);
}
}
return 1;
}
public Integer reduceInit() { return 0; }
public Integer reduce(final Integer value, final Integer sum) { return value + sum; }
public void onTraversalDone(final Integer result) {
logger.info(result + " records processed.");
if(splitToMany)
for(final VariantContextWriter writer: writers)
writer.close();
else
vcfWriter2.close();
}
}