Moving over to VariantContext from Variation
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3195 348d0f76-0448-11de-a6fe-93d51630548a
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ebanks
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@ -28,8 +28,8 @@ package org.broadinstitute.sting.gatk.walkers;
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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.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.refdata.VariantContextAdaptors;
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import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
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import org.broadinstitute.sting.utils.genotype.Variation;
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import java.util.Iterator;
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@ -47,7 +47,6 @@ public class PrintRODsWalker extends RodWalker<Integer, Integer> {
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public Integer reduceInit() { return 0; }
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/**
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* For each site of interest, rescore the genotype likelihoods by applying the specified feature set.
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*
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* @param tracker the meta-data tracker
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* @param ref the reference base
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@ -61,7 +60,7 @@ public class PrintRODsWalker extends RodWalker<Integer, Integer> {
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Iterator<GATKFeature> rods = tracker.getAllRods().iterator();
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while ( rods.hasNext() ) {
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Object rod = rods.next().getUnderlyingObject();
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if ( rod instanceof Variation )
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if (VariantContextAdaptors.canBeConvertedToVariantContext(rod) )
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out.println(rod.toString());
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}
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@ -2,20 +2,12 @@ package org.broadinstitute.sting.gatk.walkers.fasta;
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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.utils.GATKFeature;
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import org.broadinstitute.sting.gatk.walkers.DataSource;
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import org.broadinstitute.sting.gatk.walkers.Requires;
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import org.broadinstitute.sting.gatk.walkers.WalkerName;
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import org.broadinstitute.sting.gatk.walkers.*;
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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.Utils;
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import org.broadinstitute.sting.utils.cmdLine.Argument;
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import org.broadinstitute.sting.utils.genotype.Variation;
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import java.io.IOException;
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import java.io.PrintWriter;
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import java.util.Iterator;
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/**
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* Generates an alternative reference sequence over the specified interval. Given variant ROD tracks,
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@ -23,70 +15,35 @@ import java.util.Iterator;
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* allows for a "snpmask" ROD to set overlapping bases to 'N'.
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*/
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@WalkerName("FastaAlternateReferenceMaker")
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@Reference(window=@Window(start=0,stop=50))
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@Requires(value={DataSource.REFERENCE})
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public class FastaAlternateReferenceWalker extends FastaReferenceWalker {
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@Argument(fullName="outputIndelPositions", shortName="indelPositions", doc="output the positions of the indels in the new reference", required=false)
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String indelsFile = null;
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private int deletionBasesRemaining = 0;
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private long basesSeen = 0;
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private PrintWriter indelsWriter = null;
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public void initialize() {
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super.initialize();
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if (indelsFile != null) {
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try {
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indelsWriter = new PrintWriter(indelsFile);
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} catch (IOException e) {
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throw new RuntimeException("Unable to open indel positions output file: " + indelsFile);
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}
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}
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}
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public Pair<GenomeLoc, String> map(RefMetaDataTracker rodData, ReferenceContext ref, AlignmentContext context) {
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String refBase = String.valueOf(ref.getBase());
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public Pair<GenomeLoc, String> map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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if (deletionBasesRemaining > 0) {
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deletionBasesRemaining--;
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return new Pair<GenomeLoc, String>(context.getLocation(), "");
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}
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Iterator<GATKFeature> rods = rodData.getAllRods().iterator();
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while (rods.hasNext()) {
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GATKFeature rod = rods.next();
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if (!(rod.getUnderlyingObject() instanceof Variation))
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continue;
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// if we have multiple variants at a locus, just take the first damn one we see for now
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Variation variant = (Variation) rod.getUnderlyingObject();
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if (!rod.getName().startsWith("snpmask") && variant.isDeletion()) {
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deletionBasesRemaining = variant.getAlleleList().get(0).length();
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basesSeen++;
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if (indelsWriter != null)
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indelsWriter.println(fasta.getCurrentID() + ":" + basesSeen + "-" + (basesSeen + variant.getAlleleList().get(0).length()));
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String refBase = String.valueOf(ref.getBase());
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for ( VariantContext vc : tracker.getAllVariantContexts(ref) ) {
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// if we have multiple variants at a locus, just take the first one we see
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if (!vc.getName().startsWith("snpmask") && vc.isDeletion()) {
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deletionBasesRemaining = vc.getReference().length();
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// delete the next n bases, not this one
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return new Pair<GenomeLoc, String>(context.getLocation(), refBase);
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} else if (!rod.getName().startsWith("snpmask") && variant.isInsertion()) {
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basesSeen++;
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if (indelsWriter != null)
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indelsWriter.println(fasta.getCurrentID() + ":" + basesSeen + "-" + (basesSeen + variant.getAlleleList().get(0).length()));
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basesSeen += variant.getAlleleList().get(0).length();
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return new Pair<GenomeLoc, String>(context.getLocation(), refBase.concat(Utils.join("",variant.getAlleleList())));
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} else if (variant.isSNP()) {
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basesSeen++;
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return new Pair<GenomeLoc, String>(context.getLocation(), (rod.getName().startsWith("snpmask") ? "N" : String.valueOf(variant.getAlternativeBaseForSNP())));
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} else if (!vc.getName().startsWith("snpmask") && vc.isInsertion()) {
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return new Pair<GenomeLoc, String>(context.getLocation(), refBase.concat(vc.getAlternateAllele(0).toString()));
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} else if (vc.isSNP()) {
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return new Pair<GenomeLoc, String>(context.getLocation(), (vc.getName().startsWith("snpmask") ? "N" : vc.getAlternateAllele(0).toString()));
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}
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}
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// if we got here then we're just ref
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basesSeen++;
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return new Pair<GenomeLoc, String>(context.getLocation(), refBase);
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}
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public void onTraversalDone(GenomeLoc sum) {
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super.onTraversalDone(sum);
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if (indelsWriter != null)
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indelsWriter.close();
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}
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}
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@ -2,12 +2,9 @@ package org.broadinstitute.sting.gatk.walkers.sequenom;
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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.utils.GATKFeature;
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import org.broadinstitute.sting.gatk.walkers.RodWalker;
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import org.broadinstitute.sting.utils.genotype.Variation;
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import java.util.Iterator;
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/**
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* Create a mask for use with the PickSequenomProbes walker.
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@ -16,15 +13,13 @@ public class CreateSequenomMask extends RodWalker<Integer, Integer> {
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public void initialize() {}
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public Integer map(RefMetaDataTracker rodData, ReferenceContext ref, AlignmentContext context) {
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int result = 0;
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if ( rodData == null ) // apparently, RodWalkers make funky map calls
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public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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if ( tracker == null )
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return 0;
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Iterator<GATKFeature> rods = rodData.getAllRods().iterator();
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while (rods.hasNext()) {
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Object rod = rods.next().getUnderlyingObject();
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if ( rod instanceof Variation && ((Variation)rod).isSNP() ) {
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int result = 0;
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for ( VariantContext vc : tracker.getAllVariantContexts(ref) ) {
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if ( vc.isSNP() ) {
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out.println(context.getLocation());
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result = 1;
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break;
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@ -16,7 +16,7 @@ public class FastaAlternateReferenceIntegrationTest extends WalkerTest {
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executeTest("testFastaReference", spec1);
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WalkerTestSpec spec2 = new WalkerTestSpec(
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"-T FastaAlternateReferenceMaker -R " + oneKGLocation + "reference/human_b36_both.fasta -B indels,PointIndel," + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels -B snpmask,dbsnp,/humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod -L 1:10,075,000-10,075,380;1:10,093,447-10,093,847;1:10,271,252-10,271,452 -o %s",
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"-T FastaAlternateReferenceMaker -R " + oneKGLocation + "reference/human_b36_both.fasta -B indels,VCF," + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf -B snpmask,dbsnp,/humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod -L 1:10,075,000-10,075,380;1:10,093,447-10,093,847;1:10,271,252-10,271,452 -o %s",
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1,
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Arrays.asList("3a48986c3832a768b478c3e95f994b0f"));
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executeTest("testFastaAlternateReferenceIndels", spec2);
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