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/*
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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.walkers.variantrecalibration;
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import org.broad.tribble.dbsnp.DbSNPFeature;
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import org.broad.tribble.util.variantcontext.VariantContext;
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import org.broad.tribble.vcf.*;
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import org.broadinstitute.sting.commandline.*;
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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.datasources.simpleDataSources.ReferenceOrderedDataSource;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper;
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import org.broadinstitute.sting.gatk.walkers.RodWalker;
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import org.broadinstitute.sting.utils.*;
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import org.broadinstitute.sting.utils.text.XReadLines;
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import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
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import org.broadinstitute.sting.utils.collections.NestedHashMap;
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import org.broadinstitute.sting.utils.exceptions.UserException;
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import org.broadinstitute.sting.utils.exceptions.StingException;
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import org.broadinstitute.sting.utils.vcf.VCFUtils;
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import java.io.File;
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import java.io.FileNotFoundException;
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import java.io.PrintStream;
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import java.util.*;
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/**
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* Applies calibrated variant cluster parameters to variant calls to produce an accurate and informative variant quality score
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*
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* @author rpoplin
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* @since Mar 17, 2010
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*
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* @help.summary Applies calibrated variant cluster parameters to variant calls to produce an accurate and informative variant quality score
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*/
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public class TestVariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDatum>, ExpandingArrayList<VariantDatum>> {
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/////////////////////////////
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// Inputs
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/////////////////////////////
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@Input(fullName="dataFile", shortName="dataFile", doc="The input cluster file generated by GenerateVariantClusters", required=true)
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private File dataFile;
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@Argument(fullName="target_titv", shortName="titv", doc="The expected novel Ti/Tv ratio to use when calculating FDR tranches and for display on optimization curve output figures. (~~2.07 for whole genome experiments)", required=true)
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private double TARGET_TITV = 2.07;
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@Argument(fullName="FDRtranche", shortName="tranche", doc="The levels of novel false discovery rate (FDR, implied by ti/tv) at which to slice the data. (in percent, that is 1.0 for 1 percent)", required=false)
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private double[] FDR_TRANCHES = null;
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@Argument(fullName="maxElements", shortName="maxElements", doc="The expected novel Ti/Tv ratio to use when calculating FDR tranches and for display on optimization curve output figures. (~~2.07 for whole genome experiments)", required=false)
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private double maxElements = -1;
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@Argument(fullName="sixElementFile", shortName="sixElementFile", doc="", required=false)
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private File sixElementFile = null;
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@Argument(fullName="fourElementFile", shortName="fourElementFile", doc="", required=false)
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private File fourElementFile = null;
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public void initialize() {
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List<VariantDatum> vd = new ArrayList<VariantDatum>();
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try {
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for ( String line : new XReadLines(dataFile, true) ) {
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String[] parts = line.split(" ");
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if ( ! parts[0].equals("QUAL") ) {
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VariantDatum datum = new VariantDatum();
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datum.qual = Double.valueOf(parts[0]);
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datum.isTransition = parts[1].equals("1");
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datum.isKnown = parts[2].equals("1");
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vd.add(datum);
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if ( maxElements != -1 && vd.size() > maxElements )
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break;
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}
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}
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} catch (FileNotFoundException e) {
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throw new StingException("foo", e);
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}
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List<Tranche> tranches = VariantGaussianMixtureModel.findTranches(vd.toArray(new VariantDatum[0]), FDR_TRANCHES, TARGET_TITV);
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System.out.printf(Tranche.tranchesString(tranches));
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if ( sixElementFile != null ) {
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List<Tranche> six = Tranche.readTraches(sixElementFile);
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System.out.printf("six%n");
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System.out.printf(Tranche.tranchesString(six));
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}
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if ( fourElementFile != null ) {
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List<Tranche> four = Tranche.readTraches(fourElementFile);
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System.out.printf("four%n");
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System.out.printf(Tranche.tranchesString(four));
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}
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System.exit(0);
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}
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public ExpandingArrayList<VariantDatum> map( RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context ) {
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return null;
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}
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//---------------------------------------------------------------------------------------------------------------
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//
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// reduce
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//
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//---------------------------------------------------------------------------------------------------------------
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public ExpandingArrayList<VariantDatum> reduceInit() {
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return new ExpandingArrayList<VariantDatum>();
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}
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public ExpandingArrayList<VariantDatum> reduce( final ExpandingArrayList<VariantDatum> mapValue, final ExpandingArrayList<VariantDatum> reduceSum ) {
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reduceSum.addAll( mapValue );
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return reduceSum;
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}
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public void onTraversalDone( ExpandingArrayList<VariantDatum> reduceSum ) {
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}
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}
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