Two dumb oneoff walkers written to fix & annotate the Baylor indel calls (which came in sans reference, and without coding/intron annotations).
ERIC -- does the IndelAnnotator (the RefSeq lookup code I stole from IndelGentoyperV2) want to be its own Annotation inside VariantAnnotator? Is Andrey already doing this as part of adding indel calling to UG? git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3226 348d0f76-0448-11de-a6fe-93d51630548a
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chartl
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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.StratifiedAlignmentContext;
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import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
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import org.broadinstitute.sting.gatk.refdata.*;
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import org.broadinstitute.sting.gatk.refdata.utils.GATKFeatureIterator;
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import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
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import org.broadinstitute.sting.gatk.walkers.RodWalker;
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import org.broadinstitute.sting.utils.BaseUtils;
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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.genotype.vcf.*;
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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 IndelAnnotator extends RodWalker<Integer,Long>{
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@Argument(fullName="refseq", shortName="refseq",
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doc="Name of RefSeq transcript annotation file. If specified, indels will be annotated with GENOMIC/UTR/INTRON/CODING and with the gene name", required=true)
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String RefseqFileName = null;
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private static String annGenomic = "GENOMIC";
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private static String annIntron = "INTRON";
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private static String annUTR = "UTR";
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private static String annCoding = "CODING";
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private static String annUnknown = "UNKNOWN";
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private SeekableRODIterator refseqIterator;
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private VCFWriter vcfWriter;
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private String getAnnotationString(RODRecordList ann) {
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if ( ann == null ) return annGenomic;
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else {
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StringBuilder b = new StringBuilder();
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if ( rodRefSeq.isExon(ann) ) {
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if ( rodRefSeq.isCodingExon(ann) ) b.append(annCoding); // both exon and coding = coding exon sequence
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else b.append(annUTR); // exon but not coding = UTR
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} else {
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if ( rodRefSeq.isCoding(ann) ) b.append(annIntron); // not in exon, but within the coding region = intron
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else b.append(annUnknown); // we have no idea what this is. this may actually happen when we have a fully non-coding exon...
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}
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b.append('\t');
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b.append(((Transcript)ann.get(0).getUnderlyingObject()).getGeneName()); // there is at least one transcript in the list, guaranteed
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return b.toString();
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}
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}
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public void initialize() {
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if ( RefseqFileName != null ) {
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ReferenceOrderedData<rodRefSeq> refseq = new ReferenceOrderedData<rodRefSeq>("refseq",
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new java.io.File(RefseqFileName), rodRefSeq.class);
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refseqIterator = new SeekableRODIterator(new GATKFeatureIterator(refseq.iterator()));
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logger.info("Using RefSeq annotations from "+RefseqFileName);
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}
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if ( refseqIterator == null ) logger.info("No annotations available");
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Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
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hInfo.addAll(VCFUtils.getHeaderFields(getToolkit()));
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hInfo.add(new VCFHeaderLine("source", "IndelAnnotator"));
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hInfo.add(new VCFHeaderLine("annotatorReference", getToolkit().getArguments().referenceFile.getName()));
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HashSet<VCFInfoHeaderLine> anno = new HashSet<VCFInfoHeaderLine>();
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anno.add(new VCFInfoHeaderLine("type",1,VCFInfoHeaderLine.INFO_TYPE.String,"Genomic interpretation (according to RefSeq)"));
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hInfo.addAll(anno);
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vcfWriter = new VCFWriter(out);
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VCFHeader vcfHeader = new VCFHeader(hInfo, SampleUtils.getUniqueSamplesFromRods(getToolkit()));
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vcfWriter.writeHeader(vcfHeader);
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}
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public Long reduceInit() {
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return 0l;
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}
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public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext con) {
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if ( tracker == null )
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return 0;
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List<Object> rods = tracker.getReferenceMetaData("variant");
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// ignore places where we don't have a variant
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if ( rods.size() == 0 )
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return 0;
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Object variant = rods.get(0);
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if ( variant instanceof RodVCF ) {
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RODRecordList annotationList = (refseqIterator == null ? null : refseqIterator.seekForward(ref.getLocus()));
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String annotationString = (refseqIterator == null ? "" : getAnnotationString(annotationList));
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annotationString = annotationString.split("\\s+")[0];
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((RodVCF) variant).getRecord().addInfoField("type",annotationString);
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vcfWriter.addRecord(((RodVCF) variant).getRecord());
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} else {
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throw new StingException("This one-off walker only deals with VCF files.");
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}
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return 1;
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}
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public Long reduce(Integer i, Long j) {
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return i + j;
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}
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}
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@ -0,0 +1,83 @@
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package org.broadinstitute.sting.oneoffprojects.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.contexts.variantcontext.Allele;
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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.RodWalker;
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import org.broadinstitute.sting.utils.BaseUtils;
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import org.broadinstitute.sting.utils.collections.Pair;
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import org.broadinstitute.sting.utils.SampleUtils;
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import org.broadinstitute.sting.utils.genotype.vcf.*;
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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 13, 2010
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*/
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public class VCFReferenceFixerWalker extends RodWalker<VCFRecord,Long> {
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private VCFWriter vcfWriter;
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public void initialize() {
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TreeSet<String> samples = new TreeSet<String>();
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SampleUtils.getUniquifiedSamplesFromRods(getToolkit(), samples, new HashMap<Pair<String, String>, String>());
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Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
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hInfo.addAll(VCFUtils.getHeaderFields(getToolkit()));
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hInfo.add(new VCFHeaderLine("source", "VariantAnnotator"));
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vcfWriter = new VCFWriter(out);
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VCFHeader vcfHeader = new VCFHeader(hInfo, samples);
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vcfWriter.writeHeader(vcfHeader);
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}
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public VCFRecord map(RefMetaDataTracker tracker, ReferenceContext context, AlignmentContext alicon) {
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if ( tracker == null ) {
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return null;
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}
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List<Object> rods = tracker.getReferenceMetaData("fixme");
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Object rod = rods.get(0);
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RodVCF vcfrod = null;
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if ( rod instanceof RodVCF ) {
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vcfrod = (RodVCF) rod;
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}
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VCFRecord rec = vcfrod.getRecord();
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rec.setReferenceBase(new String(BaseUtils.charSeq2byteSeq(context.getBases())));
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return rec;
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/*
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VariantContext vcon = null;
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if ( rod instanceof RodVCF) {
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vcon = VariantContextAdaptors.toVariantContext("fixme", (RodVCF) rod, new Allele(BaseUtils.charSeq2byteSeq(context.getBases()),true));
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}
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if ( vcon == null ) {
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return null;
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}
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Set<Allele> otherAlleles = vcon.getAlternateAlleles();
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VariantContext fixedContext = new VariantContext(vcon.getName(),context.getLocus(),otherAlleles,vcon.getGenotypes(),vcon.getNegLog10PError(),vcon.getFilters(),vcon.getAttributes());
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return VariantContextAdaptors.toVCF(fixedContext,context.getBase());*/
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}
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public Long reduce(VCFRecord con, Long num) {
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if ( con == null ) {
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return num;
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}
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vcfWriter.addRecord(con);
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return 1 + num;
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}
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public Long reduceInit() {
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return 0l;
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}
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public void onTraversalDone(Long num){
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return;
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}
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}
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