Computes SNP density over the genome. Doesn't work with intervals
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2735 348d0f76-0448-11de-a6fe-93d51630548a
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package org.broadinstitute.sting.playground.gatk.walkers.diagnostics;
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import org.broadinstitute.sting.gatk.walkers.*;
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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.refdata.RODRecordList;
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import org.broadinstitute.sting.gatk.refdata.RodVCF;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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import org.broadinstitute.sting.utils.cmdLine.Argument;
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import org.broadinstitute.sting.utils.StingException;
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import org.broadinstitute.sting.utils.PackageUtils;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.Pair;
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import org.broadinstitute.sting.utils.genotype.Genotype;
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import org.broadinstitute.sting.utils.genotype.Variation;
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import org.broadinstitute.sting.utils.genotype.vcf.VCFRecord;
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import org.broadinstitute.sting.utils.genotype.vcf.VCFGenotypeEncoding;
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import org.broadinstitute.sting.utils.genotype.vcf.VCFGenotypeRecord;
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import org.broadinstitute.sting.playground.gatk.walkers.varianteval.VariantAnalysis;
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import org.broadinstitute.sting.playground.gatk.walkers.diagnostics.newvarianteval.VariantEvaluation;
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import org.broadinstitute.sting.oneoffprojects.variantcontext.VariantContext;
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import org.broadinstitute.sting.oneoffprojects.variantcontext.VariantContextAdaptors;
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import org.apache.commons.jexl.ExpressionFactory;
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import org.apache.commons.jexl.Expression;
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import org.apache.commons.jexl.JexlHelper;
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import org.apache.commons.jexl.JexlContext;
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import java.util.*;
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/**
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* Computes the density of SNPs passing and failing filters in intervals on the genome and emits a table for display
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*/
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@By(DataSource.REFERENCE)
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@Requires(value={},referenceMetaData=@RMD(name="eval",type=RodVCF.class))
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public class SNPDensity extends RefWalker<Pair<VariantContext, GenomeLoc>, SNPDensity.Counter> {
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@Argument(fullName="granularity", shortName="granularity", doc="", required=false)
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private int granularity = 1000000;
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public void initialize() {
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out.printf("chr middlePos linearPos nSNPs nSNPsFiltered unfiltered.density filtered.density%n");
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}
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public class Counter {
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GenomeLoc firstLoc = null;
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long linearOffset = 0;
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int nSNPsCalled = 0;
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int nSNPsFiltered = 0;
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public Counter(Long linearOffset) {
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this.linearOffset = linearOffset;
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//System.out.printf("linear offset %d%n", linearOffset);
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}
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}
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public Pair<VariantContext, GenomeLoc> map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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VariantContext vc = null;
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RODRecordList<ReferenceOrderedDatum> vcfList = tracker.getTrackData("eval", null);
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if (vcfList != null) {
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for (ReferenceOrderedDatum d : vcfList) {
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RodVCF vcfRecord = (RodVCF)d;
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vc = VariantContextAdaptors.vcfToVariantContext(vcfRecord);
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break;
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}
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}
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return new Pair<VariantContext, GenomeLoc>(vc, context.getLocation());
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}
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public Counter reduceInit() {
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return new Counter(0L);
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}
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private void printLine(Counter sum) {
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long offset = granularity / 2 - 1;
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long chrOffset = sum.firstLoc.getStart() + offset;
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out.printf("%s %d %d %d %d %.2e %.2e%n",
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sum.firstLoc.getContig(),
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chrOffset,
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sum.linearOffset + offset,
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sum.nSNPsCalled, sum.nSNPsFiltered,
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(1.0 * sum.nSNPsCalled) / granularity, (1.0 * sum.nSNPsFiltered) / granularity);
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}
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public Counter reduce(Pair<VariantContext, GenomeLoc> p, Counter sum) {
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if ( p == null )
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return sum;
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// System.out.printf("%s %s %d%n", c.getLocation(), sum.firstLoc, sum.nSNPsSeen);
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VariantContext c = p.getFirst();
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GenomeLoc loc = p.getSecond();
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if ( sum.firstLoc != null ) {
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long dist = loc.distance(sum.firstLoc);
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// System.out.printf(" dist = %d%n", dist);
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if ( dist > granularity ) {
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printLine(sum);
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sum = new Counter(sum.linearOffset + granularity);
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}
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}
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if ( sum.firstLoc == null ) sum.firstLoc = loc;
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sum.nSNPsCalled += c != null && c.isNotFiltered() ? 1 : 0;
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sum.nSNPsFiltered += c != null && c.isFiltered() ? 1 : 0;
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return sum;
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}
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public void onTraversalDone(Counter sum) {
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printLine(sum);
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}
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}
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