Examples with VCFHeader htsjdk.variant.vcf.VCFHeader used on opensource projects

Example 41 with VCFHeader

use of htsjdk.variant.vcf.VCFHeader in project jvarkit by lindenb.

the class VcfDoest method run.

private void run(final LineIterator lr, final PrintWriter pw) throws IOException {
    SortingCollection<TranscriptInfo> sorting = null;
    CloseableIterator<TranscriptInfo> iter2 = null;
    try {
        while (lr.hasNext()) {
            VcfIterator in = VCFUtils.createVcfIteratorFromLineIterator(lr, true);
            final VCFHeader header = in.getHeader();
            final Pedigree pedigree = Pedigree.newParser().parse(header);
            if (pedigree.isEmpty()) {
                throw new IOException("No pedigree found in header VCF header. use VcfInjectPedigree to add it");
            }
            final SortedSet<Pedigree.Person> individuals = new TreeSet<>();
            for (final Pedigree.Person individual : pedigree.getPersons()) {
                if (individual.isAffected() || individual.isUnaffected()) {
                    individuals.add(individual);
                }
            }
            boolean first = true;
            pw.println("# samples ( 0: unaffected 1:affected)");
            pw.print("population <- data.frame(family=c(");
            first = true;
            for (final Pedigree.Person person : individuals) {
                if (!first)
                    pw.print(",");
                pw.print("\"" + person.getFamily().getId() + "\"");
                first = false;
            }
            pw.print("),name=c(");
            first = true;
            for (final Pedigree.Person person : individuals) {
                if (!first)
                    pw.print(",");
                pw.print("\"" + person.getId() + "\"");
                first = false;
            }
            pw.print("),status=c(");
            first = true;
            for (final Pedigree.Person person : individuals) {
                if (!first)
                    pw.print(",");
                pw.print(person.isUnaffected() ? 0 : 1);
                first = false;
            }
            pw.println("))");
            sorting = SortingCollection.newInstance(TranscriptInfo.class, new TranscriptInfoCodec(), new TranscriptInfoCmp(), this.writingSortingCollection.getMaxRecordsInRam(), this.writingSortingCollection.getTmpPaths());
            sorting.setDestructiveIteration(true);
            final SAMSequenceDictionaryProgress progess = new SAMSequenceDictionaryProgress(header.getSequenceDictionary());
            /**
             * loop over variants
             */
            while (in.hasNext() && !pw.checkError()) {
                final VariantContext ctx = progess.watch(in.next());
                if (ctx.isFiltered())
                    continue;
                if (ctx.getAlternateAlleles().isEmpty())
                    continue;
                final Allele altAllele = ctx.getAltAlleleWithHighestAlleleCount();
                final MafCalculator mafCalculator = new MafCalculator(altAllele, ctx.getContig());
                boolean genotyped = false;
                for (final Pedigree.Person p : pedigree.getPersons()) {
                    if (!(p.isAffected() || p.isUnaffected()))
                        continue;
                    final Genotype g = ctx.getGenotype(p.getId());
                    if (g == null)
                        throw new IOException("Strange I cannot find individual " + p + " in the pedigree. Aborting.");
                    if (g.isCalled()) {
                        mafCalculator.add(g, p.isMale());
                    }
                    if (g.isHet() || g.isHomVar()) {
                        if (!g.getAlleles().contains(altAllele))
                            continue;
                        genotyped = true;
                        break;
                    }
                }
                if (!genotyped)
                    continue;
                final Interval interval = new Interval(ctx.getContig(), ctx.getStart(), ctx.getEnd());
                final List<KnownGene> genes = this.overlap(interval);
                if (genes.isEmpty())
                    continue;
                for (final KnownGene kg : genes) {
                    final TranscriptInfo trInfo = new TranscriptInfo();
                    trInfo.contig = kg.getContig();
                    trInfo.txStart = kg.getTxStart();
                    trInfo.txEnd = kg.getTxEnd();
                    trInfo.transcriptName = kg.getName();
                    trInfo.strand = (byte) (kg.isPositiveStrand() ? '+' : '-');
                    trInfo.exonCount = kg.getExonCount();
                    trInfo.transcriptLength = kg.getTranscriptLength();
                    trInfo.ctxStart = ctx.getStart();
                    trInfo.ref = ctx.getReference();
                    trInfo.alt = altAllele;
                    trInfo.maf = mafCalculator.getMaf();
                    trInfo.genotypes = new byte[individuals.size()];
                    int idx = 0;
                    for (final Pedigree.Person individual : individuals) {
                        final Genotype genotype = ctx.getGenotype(individual.getId());
                        final byte b;
                        if (genotype.isHomRef()) {
                            b = 0;
                        } else if (genotype.isHomVar() && genotype.getAlleles().contains(altAllele)) {
                            b = 2;
                        } else if (genotype.isHet() && genotype.getAlleles().contains(altAllele) && genotype.getAlleles().contains(ctx.getReference())) {
                            b = 1;
                        } else /* we treat 0/2 has hom-ref */
                        if (genotype.isHet() && !genotype.getAlleles().contains(altAllele) && genotype.getAlleles().contains(ctx.getReference())) {
                            LOG.warn("Treating " + genotype + " as hom-ref (0) alt=" + altAllele);
                            b = 0;
                        } else /* we treat 2/2 has hom-ref */
                        if (genotype.isHomVar() && !genotype.getAlleles().contains(altAllele)) {
                            LOG.warn("Treating " + genotype + " as hom-ref (0) alt=" + altAllele);
                            b = 0;
                        } else {
                            b = -9;
                        }
                        trInfo.genotypes[idx] = b;
                        ++idx;
                    }
                    KnownGene archetype = kg;
                    /* find gene archetype = longest overlapping */
                    for (final KnownGene kg2 : genes) {
                        if (kg2 == kg)
                            continue;
                        if (archetype.getStrand().equals(kg2.getStrand()) && archetype.getTranscriptLength() < kg2.getTranscriptLength()) {
                            archetype = kg2;
                        }
                    }
                    trInfo.archetypeName = archetype.getName();
                    trInfo.archetypeLength = archetype.getTranscriptLength();
                    boolean ctxWasFoundInExon = false;
                    final int ctxPos0 = ctx.getStart() - 1;
                    int indexInTranscript0 = 0;
                    for (final KnownGene.Exon exon : kg.getExons()) {
                        // variant in exon ?
                        if (!(exon.getStart() > (ctx.getEnd() - 1) || (ctx.getStart() - 1) >= exon.getEnd())) {
                            ctxWasFoundInExon = true;
                            indexInTranscript0 += (ctxPos0 - exon.getStart());
                            if (kg.isNegativeStrand()) {
                                indexInTranscript0 = (kg.getTranscriptLength() - 1) - indexInTranscript0;
                            }
                            trInfo.indexInTranscript0 = indexInTranscript0;
                            trInfo.overlapName = exon.getName();
                            sorting.add(trInfo);
                            break;
                        } else {
                            indexInTranscript0 += (exon.getEnd() - exon.getStart());
                        }
                    }
                    if (ctxWasFoundInExon) {
                        continue;
                    }
                    indexInTranscript0 = 0;
                    // search closest intron/exon junction
                    for (int ex = 0; ex + 1 < kg.getExonCount(); ++ex) {
                        final KnownGene.Exon exon1 = kg.getExon(ex);
                        indexInTranscript0 += (exon1.getEnd() - exon1.getStart());
                        final KnownGene.Exon exon2 = kg.getExon(ex + 1);
                        if (exon1.getEnd() <= ctxPos0 && ctxPos0 < exon2.getStart()) {
                            final int dist_to_exon1 = ctxPos0 - exon1.getEnd();
                            final int dist_to_exon2 = exon2.getStart() - ctxPos0;
                            if (dist_to_exon2 < dist_to_exon1) {
                                indexInTranscript0++;
                            }
                            if (kg.isNegativeStrand()) {
                                indexInTranscript0 = (kg.getTranscriptLength() - 1) - indexInTranscript0;
                            }
                            trInfo.indexInTranscript0 = indexInTranscript0;
                            trInfo.overlapName = exon1.getNextIntron().getName();
                            sorting.add(trInfo);
                            break;
                        }
                    }
                }
            // end loop over genes
            }
            // end while loop over variants
            progess.finish();
            sorting.doneAdding();
            LOG.info("done adding");
            iter2 = sorting.iterator();
            final EqualRangeIterator<TranscriptInfo> eqiter = new EqualRangeIterator<TranscriptInfo>(iter2, new Comparator<TranscriptInfo>() {

                @Override
                public int compare(final TranscriptInfo o1, final TranscriptInfo o2) {
                    int i = o1.contig.compareTo(o2.contig);
                    if (i != 0)
                        return i;
                    i = o1.transcriptName.compareTo(o2.transcriptName);
                    return i;
                }
            });
            while (eqiter.hasNext()) {
                final List<TranscriptInfo> list = eqiter.next();
                final TranscriptInfo front = list.get(0);
                pw.println("# BEGIN TRANSCRIPT " + front.transcriptName + " ##########################################");
                pw.println("transcript.chrom <- \"" + front.contig + "\"");
                pw.println("transcript.txStart0 <- " + front.txStart + "");
                pw.println("transcript.txEnd0 <- " + front.txEnd + "");
                pw.println("transcript.name <- \"" + front.transcriptName + "\"");
                pw.println("transcript.strand <- \"" + ((char) front.strand) + "\"");
                pw.println("transcript.length <- " + front.transcriptLength + "");
                pw.println("transcript.exonCount <- " + front.exonCount + "");
                pw.println("archetype.name <- \"" + front.archetypeName + "\"");
                pw.println("archetype.length <- " + front.archetypeLength + "");
                pw.print("variants <- data.frame(chrom=c(");
                first = true;
                for (final TranscriptInfo v : list) {
                    if (!first)
                        pw.print(",");
                    pw.print("\"" + v.contig + "\"");
                    first = false;
                }
                pw.print("),chromStart=c(");
                first = true;
                for (final TranscriptInfo v : list) {
                    if (!first)
                        pw.print(",");
                    pw.print(v.ctxStart);
                    first = false;
                }
                pw.print("),chromEnd=c(");
                first = true;
                for (final TranscriptInfo v : list) {
                    if (!first)
                        pw.print(",");
                    pw.print(v.ctxStart + v.ref.length() - 1);
                    first = false;
                }
                pw.print("),refAllele=c(");
                first = true;
                for (final TranscriptInfo v : list) {
                    if (!first)
                        pw.print(",");
                    pw.print("\"" + v.ref.getDisplayString() + "\"");
                    first = false;
                }
                pw.print("),altAllele=c(");
                first = true;
                for (final TranscriptInfo v : list) {
                    if (!first)
                        pw.print(",");
                    pw.print("\"" + v.alt.getDisplayString() + "\"");
                    first = false;
                }
                pw.print("),positionInTranscript1=c(");
                first = true;
                for (final TranscriptInfo v : list) {
                    if (!first)
                        pw.print(",");
                    pw.print(v.indexInTranscript0 + 1);
                    first = false;
                }
                pw.print("),maf=c(");
                first = true;
                for (final TranscriptInfo v : list) {
                    if (!first)
                        pw.print(",");
                    pw.print(v.maf);
                    first = false;
                }
                pw.print("),overlapName=c(");
                first = true;
                for (final TranscriptInfo v : list) {
                    if (!first)
                        pw.print(",");
                    pw.print("\"" + v.overlapName + "\"");
                    first = false;
                }
                pw.println("))");
                pw.println("# genotypes as a list. Should be a multiple of length(samples).");
                pw.println("# 0 is homref (0/0), 1 is het (0/1), 2 is homvar (1/1)");
                pw.println("# if the variant contains another ALT allele: (0/2) and (2/2) are considered 0 (homref)");
                pw.print("genotypes <- c(");
                first = true;
                for (final TranscriptInfo tr : list) {
                    for (byte g : tr.genotypes) {
                        if (!first)
                            pw.print(",");
                        first = false;
                        pw.print((int) g);
                    }
                }
                pw.println(")");
                pw.println("stopifnot(NROW(variants) * NROW(population) == length(genotypes) )");
                if (this.userDefinedFunName == null || this.userDefinedFunName.trim().isEmpty()) {
                    pw.println("## WARNING not user-defined R function was defined");
                } else {
                    pw.println("# consumme data with user-defined R function ");
                    pw.println(this.userDefinedFunName + "()");
                }
                pw.println("# END TRANSCRIPT " + front.transcriptName + " ##########################################");
            }
            // end while eqiter
            eqiter.close();
            iter2.close();
            iter2 = null;
            sorting.cleanup();
            sorting = null;
        }
    } finally {
        CloserUtil.close(iter2);
        if (sorting != null)
            sorting.cleanup();
    }
}

Example 42 with VCFHeader

use of htsjdk.variant.vcf.VCFHeader in project jvarkit by lindenb.

the class VcfAnnotWithBeacon method doVcfToVcf.

@Override
protected int doVcfToVcf(String inputName, final VcfIterator iter, final VariantContextWriter out) {
    CloseableHttpClient httpClient = null;
    InputStream contentInputStream = null;
    try {
        final org.apache.http.impl.client.HttpClientBuilder hb = HttpClients.custom();
        if (this.ignoreCertErrors) {
            // http://stackoverflow.com/questions/24720013/apache-http-client-ssl-certificate-error
            System.setProperty("jsse.enableSNIExtension", "false");
            final SSLContext sslContext = org.apache.http.conn.ssl.SSLContexts.custom().loadTrustMaterial(null, new org.apache.http.conn.ssl.TrustStrategy() {

                @Override
                public boolean isTrusted(final X509Certificate[] chain, final String authType) throws CertificateException {
                    return true;
                }
            }).useTLS().build();
            final org.apache.http.conn.ssl.SSLConnectionSocketFactory connectionFactory = new org.apache.http.conn.ssl.SSLConnectionSocketFactory(sslContext, new org.apache.http.conn.ssl.AllowAllHostnameVerifier());
            hb.setSSLSocketFactory(connectionFactory);
        }
        httpClient = hb.build();
        HttpGet httpGetRequest = null;
        final Set<String> available_chromosomes = new HashSet<>();
        try {
            httpGetRequest = new HttpGet(baseurl + "/chromosomes");
            httpGetRequest.setHeader("Accept", ContentType.APPLICATION_JSON.getMimeType());
            contentInputStream = httpClient.execute(httpGetRequest).getEntity().getContent();
            JsonParser jsonparser = new JsonParser();
            final JsonElement root = jsonparser.parse(new InputStreamReader(contentInputStream));
            Iterator<JsonElement> jsr = root.getAsJsonArray().iterator();
            while (jsr.hasNext()) {
                final String ctg = jsr.next().getAsString();
                available_chromosomes.add(ctg);
            }
            LOG.debug(available_chromosomes);
        } catch (final Exception err) {
            LOG.error(err);
            return -1;
        } finally {
            CloserUtil.close(contentInputStream);
        }
        final Set<String> available_alleles = new HashSet<>();
        try {
            httpGetRequest = new HttpGet(baseurl + "/alleles");
            httpGetRequest.setHeader("Accept", ContentType.APPLICATION_JSON.getMimeType());
            contentInputStream = httpClient.execute(httpGetRequest).getEntity().getContent();
            JsonParser jsonparser = new JsonParser();
            final JsonElement root = jsonparser.parse(new InputStreamReader(contentInputStream));
            Iterator<JsonElement> jsr = root.getAsJsonArray().iterator();
            while (jsr.hasNext()) {
                final String allele = jsr.next().getAsString();
                available_alleles.add(allele);
            }
            LOG.debug(available_alleles);
        } catch (final Exception err) {
            LOG.error(err);
            return -1;
        } finally {
            CloserUtil.close(contentInputStream);
        }
        final StoredResponseBinding storedResponseBinding = new StoredResponseBinding();
        final VCFHeader header = new VCFHeader(iter.getHeader());
        final VCFInfoHeaderLine infoHeaderLine = new VCFInfoHeaderLine(this.infoTag, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.String, "Tag inserted with " + getProgramName());
        header.addMetaDataLine(infoHeaderLine);
        DatabaseEntry key = new DatabaseEntry();
        DatabaseEntry data = new DatabaseEntry();
        out.writeHeader(header);
        while (iter.hasNext()) {
            final VariantContext ctx = iter.next();
            if (!ctx.isVariant() || ctx.getReference().isSymbolic()) {
                out.add(ctx);
                continue;
            }
            if (ctx.hasAttribute(infoHeaderLine.getID()) && this.dontUpdateIfInfoIsPresent) {
                out.add(ctx);
                continue;
            }
            String beaconContig = ctx.getContig();
            if (!available_chromosomes.contains(beaconContig)) {
                if (beaconContig.startsWith("chr")) {
                    beaconContig = beaconContig.substring(3);
                }
                if (!available_chromosomes.contains(beaconContig)) {
                    out.add(ctx);
                    continue;
                }
            }
            final List<Allele> altAlleles = ctx.getAlternateAlleles();
            if (altAlleles.isEmpty()) {
                out.add(ctx);
                continue;
            }
            final Set<String> newInfo = new HashSet<>();
            for (final Allele alt : altAlleles) {
                if (alt.isSymbolic() || alt.isNoCall())
                    continue;
                final StringBuilder buildUrl = new StringBuilder();
                buildUrl.append("chrom=");
                buildUrl.append(URLEncoder.encode(beaconContig, "UTF-8"));
                buildUrl.append("&pos=");
                /*
					 * "Coordinate within a chromosome. Position is a number and is 0-based"
					 * .
					 */
                buildUrl.append(ctx.getStart() - 1);
                buildUrl.append("&allele=");
                final String allele;
                if (ctx.getReference().length() > alt.length()) {
                    // del
                    allele = "D";
                } else if (ctx.getReference().length() > alt.length()) {
                    // ins
                    allele = "I";
                } else {
                    allele = alt.getDisplayString();
                }
                if (!available_alleles.contains(allele))
                    continue;
                buildUrl.append(allele);
                buildUrl.append("&ref=");
                buildUrl.append(URLEncoder.encode(this.genomeBuild, "UTF-8"));
                final String queryUrl = buildUrl.toString();
                boolean foundInBdb = false;
                Set<String> foundIn = null;
                if (this.beaconDatabase != null) {
                    StringBinding.stringToEntry(queryUrl, key);
                    if (this.beaconDatabase.get(this.txn, key, data, LockMode.DEFAULT) == OperationStatus.SUCCESS) {
                        StoredResponse response = storedResponseBinding.entryToObject(data);
                        if (// TODO check how old is
                        response.timeStamp < 0) // that data
                        {
                            response = null;
                            this.beaconDatabase.delete(this.txn, key);
                        }
                        if (response != null) {
                            foundInBdb = true;
                            foundIn = response.foundIn;
                        }
                    }
                }
                if (foundIn == null) {
                    foundIn = new HashSet<>();
                    try {
                        httpGetRequest = new HttpGet(baseurl + "/responses?" + queryUrl);
                        httpGetRequest.setHeader("Accept", ContentType.APPLICATION_JSON.getMimeType());
                        LOG.debug(httpGetRequest.getURI());
                        contentInputStream = httpClient.execute(httpGetRequest).getEntity().getContent();
                        JsonParser jsonparser = new JsonParser();
                        final JsonElement root = jsonparser.parse(new InputStreamReader(contentInputStream));
                        Iterator<JsonElement> jsr = root.getAsJsonArray().iterator();
                        while (jsr.hasNext()) {
                            final JsonObject b = jsr.next().getAsJsonObject();
                            if (!(b.has("beacon") && b.has("response")))
                                continue;
                            final String beacon_id = b.get("beacon").getAsJsonObject().get("id").getAsString();
                            final JsonElement response_prim = b.get("response");
                            if (response_prim.isJsonPrimitive() && response_prim.getAsBoolean()) {
                                foundIn.add(beacon_id);
                            }
                        }
                    } catch (final Exception err) {
                        LOG.error(err);
                        if (stopOnNetworkError) {
                            throw new RuntimeIOException(err);
                        }
                    } finally {
                        CloserUtil.close(contentInputStream);
                    }
                }
                if (this.beaconDatabase != null && !foundInBdb) {
                    StoredResponse response = new StoredResponse();
                    response.timeStamp = System.currentTimeMillis();
                    response.foundIn = foundIn;
                }
                // 17&pos=41244981&=G&ref=GRCh37")
                newInfo.addAll(foundIn.stream().map(S -> alt.getDisplayString() + "|" + S).collect(Collectors.toSet()));
            }
            if (newInfo.isEmpty()) {
                out.add(ctx);
                continue;
            }
            final VariantContextBuilder vcb = new VariantContextBuilder(ctx);
            vcb.attribute(infoHeaderLine.getID(), new ArrayList<String>(newInfo));
            out.add(vcb.make());
        }
        return 0;
    } catch (final Exception err) {
        LOG.error(err);
        return -1;
    } finally {
        CloserUtil.close(httpClient);
    }
}

Example 43 with VCFHeader

use of htsjdk.variant.vcf.VCFHeader in project jvarkit by lindenb.

the class EigenVariants method initialize.

@Override
public void initialize() {
    logger.info("opening eigen directory :" + eigenDir);
    IOUtil.assertDirectoryIsReadable(eigenDir);
    this.annotator = new EigenInfoAnnotator(this.eigenDir);
    if (this.tabixPrefix != null) {
        logger.info("changing eigen file prefix from  :" + this.annotator.getTabixPrefix() + " to " + this.tabixPrefix);
        this.annotator.setTabixFilePrefix(this.tabixPrefix);
    }
    final VCFHeader header1 = super.getVcfHeader();
    final VCFHeader h2 = new VCFHeader(header1);
    for (final VCFInfoHeaderLine vihl : this.annotator.getInfoHeaderLines()) {
        if (h2.getInfoHeaderLine(vihl.getID()) != null) {
            throw new UserException.MalformedVCFHeader("VCF INFO " + vihl.getID() + " already defined in input VCF.");
        }
        h2.addMetaDataLine(vihl);
    }
    super.writer.writeHeader(h2);
    super.initialize();
}

Example 44 with VCFHeader

use of htsjdk.variant.vcf.VCFHeader in project jvarkit by lindenb.

the class SoftClipAnnotator method initialize.

public void initialize() {
    final Set<VCFHeaderLine> hInfo = new HashSet<>();
    final List<String> rodName = Arrays.asList(variantCollection.variants.getName());
    final Set<String> samples = SampleUtils.getUniqueSamplesFromRods(getToolkit(), rodName);
    for (final String sample : samples) {
        this.sample2bam.put(sample, new ArrayList<>());
    }
    for (final VCFHeaderLine line : GATKVCFUtils.getHeaderFields(getToolkit(), rodName)) {
        if (isUniqueHeaderLine(line, hInfo))
            hInfo.add(line);
    }
    VCFHeader vcfHeader = new VCFHeader(hInfo, samples);
    VCFHeader header2 = new VCFHeader(vcfHeader);
    header2.addMetaDataLine(this.numClipInGenotypeFormatHeaderLine);
    header2.addMetaDataLine(this.filterHaveClipInVariant);
    vcfWriter.writeHeader(header2);
    final SamReaderFactory srf = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.LENIENT);
    for (final File samFilename : IOUtil.unrollFiles(this.samFilenames, ".bam")) {
        logger.info("opening " + samFilename);
        final SamReader r = srf.open(samFilename);
        final Set<String> sampleset = new HashSet<>();
        for (final SAMReadGroupRecord g : r.getFileHeader().getReadGroups()) {
            if (g.getSample() == null || !this.sample2bam.containsKey(g.getSample()))
                continue;
            sampleset.add(g.getSample());
        }
        if (sampleset.isEmpty()) {
            logger.info("no VCF sample in " + samFilename);
            CloserUtil.close(r);
            continue;
        }
        this.samReaders.add(r);
        for (final String sample : sampleset) {
            if (!this.sample2bam.containsKey(sample))
                continue;
            this.sample2bam.get(sample).add(r);
        }
    }
}

Example 45 with VCFHeader

use of htsjdk.variant.vcf.VCFHeader in project jvarkit by lindenb.

the class WindowVariants method initialize.

@Override
public void initialize() {
    if (this.window_size <= 0) {
        throw new UserException("Bad window size.");
    }
    if (this.window_shift <= 0) {
        throw new UserException("Bad window shift.");
    }
    if (this.winName == null || this.winName.isEmpty()) {
        throw new UserException("Bad INFO ID windowName");
    }
    final Map<String, String> exprMap = new HashMap<>();
    for (final String expStr : this.selectExpressions) {
        exprMap.put("expr" + (1 + exprMap.size()), expStr);
    }
    this.jexls = VariantContextUtils.initializeMatchExps(exprMap);
    final VCFHeader header = new VCFHeader(super.getVcfHeader());
    if (header.getInfoHeaderLine(this.winName) != null) {
        throw new UserException("VCF header already contains the INFO header ID=" + this.winName);
    }
    header.addMetaDataLine(new VCFInfoHeaderLine(this.winName, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.String, "Window : start|end|number-of-matching-variants|number-of-non-matching-variants"));
    super.writer.writeHeader(header);
    super.initialize();
}