Checkin for Eric (IndelDBRateWalker is a prelude to a VariantEval module for comparisons for indels)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3234 348d0f76-0448-11de-a6fe-93d51630548a
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chartl
parent
c7b4f78316
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@ -110,4 +110,8 @@ public class IndelAnnotator extends RodWalker<Integer,Long>{
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return i + j;
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}
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public void onTraversalDone(Long l) {
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return;
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}
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}
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@ -0,0 +1,258 @@
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package org.broadinstitute.sting.oneoffprojects.walkers;
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import org.broadinstitute.sting.commandline.Argument;
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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.VariantContext;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.refdata.RodVCF;
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import org.broadinstitute.sting.gatk.refdata.VariantContextAdaptors;
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import org.broadinstitute.sting.gatk.walkers.Reference;
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import org.broadinstitute.sting.gatk.walkers.RodWalker;
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import org.broadinstitute.sting.gatk.walkers.Window;
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import org.broadinstitute.sting.utils.SampleUtils;
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import org.broadinstitute.sting.utils.StingException;
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import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
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import org.broadinstitute.sting.utils.genotype.vcf.VCFHeader;
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import org.broadinstitute.sting.utils.genotype.vcf.VCFHeaderLine;
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import org.broadinstitute.sting.utils.genotype.vcf.VCFUtils;
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import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
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import java.io.PrintStream;
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import java.util.*;
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/**
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* IF THERE IS NO JAVADOC RIGHT HERE, YELL AT chartl
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*
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* @Author chartl
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* @Date Apr 21, 2010
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*/
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public class IndelDBRateWalker extends RodWalker<OverlapTable,OverlapTabulator> {
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@Argument(fullName="indelWindow",doc="size of the window in which to look for indels; max 40",required=false)
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int indelWindow = 10;
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@Argument(fullName="writeVCF",doc="Writes \"overlapping\" variants to this vcf",required=false)
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PrintStream outVCF;
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VCFWriter vcfWriter;
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private List<VariantContext> compContexts = new ArrayList<VariantContext>(50); // not going to be more than 50 contexts in a size-40 window
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private List<VariantContext> evalContexts = new ArrayList<VariantContext>(50);
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public void initialize() {
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if ( indelWindow > 40 ) {
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throw new StingException("Indel windows have a maximum size of 40");
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}
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if ( outVCF != null ) {
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vcfWriter = new VCFWriter(outVCF);
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Set<VCFHeaderLine> header = new HashSet<VCFHeaderLine>();
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header.addAll(VCFUtils.getHeaderFields(getToolkit()));
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VCFHeader vcfHeader = new VCFHeader(header, SampleUtils.getUniqueSamplesFromRods(getToolkit()));
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vcfWriter.writeHeader(vcfHeader);
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}
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}
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public OverlapTabulator reduceInit() {
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return new OverlapTabulator();
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}
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public OverlapTabulator reduce(OverlapTable oTable, OverlapTabulator tabulator) {
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if ( oTable != null ) {
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tabulator.update(oTable);
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}
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return tabulator;
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}
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private void finalUpdate(OverlapTabulator tab) {
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while ( ! evalContexts.isEmpty() ) {
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tab.update(emptyOverlapTable());
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}
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}
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public void onTraversalDone(OverlapTabulator tabulation) {
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finalUpdate(tabulation);
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out.printf("%s\t%s\t%s\t%s\t%s%n","Num_eval_sites","Num_comp_within_2bp","Num_comp_within_4bp","Num_comp_within_window","Total_comp_%");
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out.printf("%s",tabulation.tabulateString());
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}
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public OverlapTable map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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// step 1: get the eval and compare contexts
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if ( tracker == null ) {
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return null;
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}
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Object eval = tracker.getReferenceMetaData("eval") != null &&
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tracker.getReferenceMetaData("eval").size() != 0 ? tracker.getReferenceMetaData("eval").get(0) : null ;
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VariantContext evalContext;
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if ( eval != null ) {
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evalContext = VariantContextAdaptors.toVariantContext("eval",eval);
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} else {
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evalContext = null;
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}
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Object comp = tracker.getReferenceMetaData("comp") != null &&
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tracker.getReferenceMetaData("comp").size() != 0 ? tracker.getReferenceMetaData("comp").get(0) : null;
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VariantContext compContext;
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if ( comp != null ) {
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compContext = VariantContextAdaptors.toVariantContext("comp",comp);
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} else {
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compContext = null;
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}
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// step 2: add indel contexts to the queue
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addToQueue(compContexts,compContext);
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addToQueue(evalContexts,evalContext);
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// step 3: check to see if we have exceeded the window size for the top eval contexts of the queue
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// and do the work
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return getOverlapTable(ref);
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}
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public void addToQueue(List<VariantContext> queue, VariantContext con) {
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if ( con != null && con.isIndel() ) {
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queue.add(con);
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}
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}
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public OverlapTable getOverlapTable(ReferenceContext ref) {
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// step 1: check that the eval queue is non-empty and that we are outside the window
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if ( evalContexts.isEmpty() || evalContexts.get(0).getLocation().distance(ref.getLocus()) <= indelWindow ) {
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return null;
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}
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// step 2: discard all comp variations which come before the window
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while ( ! compContexts.isEmpty() && compContexts.get(0).getLocation().isBefore(ref.getLocus()) &&
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compContexts.get(0).getLocation().distance(ref.getLocus()) > indelWindow) {
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compContexts.remove(0);
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}
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// step 3: see if there are any contexts left; if so then they must be within the window
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if ( ! compContexts.isEmpty() ) {
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return nonEmptyOverlapTable();
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} else {
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return emptyOverlapTable();
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}
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}
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public OverlapTable emptyOverlapTable() {
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// only eval, no comp
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OverlapTable ot = new OverlapTable();
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ot.setEvalSizeAndType(evalContexts.get(0));
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return ot;
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}
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public OverlapTable nonEmptyOverlapTable() {
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if ( vcfWriter != null ) {
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int i = 0;
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while ( i < compContexts.size() && compContexts.get(i).getLocation().isBefore(evalContexts.get(0).getLocation())) {
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vcfWriter.addRecord(VariantContextAdaptors.toVCF(compContexts.get(i),(char)compContexts.get(i).getReference().getBases()[0]));
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i++;
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}
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vcfWriter.addRecord(VariantContextAdaptors.toVCF(evalContexts.get(0),(char) evalContexts.get(0).getReference().getBases()[0]));
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while ( i < compContexts.size() && compContexts.get(i).getLocation().distance(evalContexts.get(0).getLocation()) <= indelWindow) {
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vcfWriter.addRecord(VariantContextAdaptors.toVCF(compContexts.get(i),(char) compContexts.get(i).getReference().getBases()[0]));
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i++;
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}
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}
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OverlapTable ot = new OverlapTable();
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ot.setCompOverlaps(compContexts.size());
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ot.setDistances(compContexts,evalContexts.get(0), indelWindow);
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return ot;
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}
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}
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class OverlapTable {
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private int numOverlaps;
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private ExpandingArrayList<Integer> distances; // currently unused
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private int evalSize;
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private boolean isDeletion;
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public OverlapTable() {
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numOverlaps = 0;
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}
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public void setEvalSizeAndType(VariantContext context) {
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int size = context.getAlternateAllele(0).length();
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evalSize = size;
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isDeletion = context.isDeletion();
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}
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public void setCompOverlaps(int overlaps) {
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numOverlaps = overlaps;
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}
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public void setDistances(List<VariantContext> comps, VariantContext eval, int winsize) {
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distances = new ExpandingArrayList<Integer>();
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for ( VariantContext comp : comps ) {
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if ( comp.getLocation().distance(eval.getLocation()) <= winsize ) {
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distances.add(comp.getLocation().distance(eval.getLocation()));
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}
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}
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}
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public int getNumOverlaps() {
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return numOverlaps;
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}
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public int getSize() {
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return evalSize;
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}
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public boolean isDeletion() {
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return isDeletion;
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}
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public ExpandingArrayList<Integer> getDistances() {
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return distances;
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}
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}
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class OverlapTabulator {
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HashMap<Integer,Long> hitsToCounts;
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int totalEvalVariants;
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public OverlapTabulator() {
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hitsToCounts = new HashMap<Integer,Long>();
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totalEvalVariants = 0;
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}
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public void update(OverlapTable table) {
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totalEvalVariants++;
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if ( table.getNumOverlaps() != 0 ) {
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if ( hitsToCounts.containsKey(table.getNumOverlaps()) ) {
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hitsToCounts.put(table.getNumOverlaps(),hitsToCounts.get(table.getNumOverlaps())+1);
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} else {
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hitsToCounts.put(table.getNumOverlaps(),1l);
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}
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}
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}
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public String tabulateString() {
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StringBuffer sb = new StringBuffer();
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sb.append(totalEvalVariants);
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sb.append("\t");
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long lt2counts = 0l;
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long lt4counts = 0l;
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long totalCounts = 0l;
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for ( int i = 0; i < 40; i ++ ) {
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long counts = 0;
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if ( hitsToCounts.containsKey(i) ) {
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counts = hitsToCounts.get(i);
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}
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if ( i <= 2 ) {
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lt2counts += counts;
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}
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if ( i <= 4 ) {
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lt4counts += counts;
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}
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totalCounts += counts;
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}
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sb.append(lt2counts);
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sb.append("\t");
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sb.append(lt4counts);
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sb.append("\t");
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sb.append(totalCounts);
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sb.append("\t");
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sb.append(String.format("%.2f", 100*( (double) totalCounts)/( (double) totalEvalVariants)));
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return sb.toString();
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}
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}
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