Examples with IntervalExtender com.github.lindenb.jvarkit.samtools.util.IntervalExtender used on opensource projects

Example 1 with IntervalExtender

use of com.github.lindenb.jvarkit.samtools.util.IntervalExtender in project jvarkit by lindenb.

the class VcfToBed method scan.

private int scan(String uriOrNull, final VCFIterator iter, final PrintWriter pw) {
    try {
        final SAMSequenceDictionary dictIn = iter.getHeader().getSequenceDictionary();
        final IntervalExtender extender = IntervalExtender.of(dictIn, this.extendsStr);
        if (extender.isShriking()) {
            throw new IllegalArgumentException("shrinking interval are not supported " + extender);
        }
        final ContigNameConverter ctgNameConverter;
        final Function<String, SAMSequenceRecord> funGetSSR;
        if (this.samSequenceDictionary != null) {
            ctgNameConverter = ContigNameConverter.fromOneDictionary(this.samSequenceDictionary);
            funGetSSR = C -> samSequenceDictionary.getSequence(C);
        } else if (dictIn != null) {
            ctgNameConverter = ContigNameConverter.fromOneDictionary(dictIn);
            funGetSSR = C -> dictIn.getSequence(C);
        } else {
            ctgNameConverter = null;
            funGetSSR = null;
        }
        while (iter.hasNext()) {
            final VariantContext ctx = iter.next();
            int start = ctx.getStart();
            int end = ctx.getEnd();
            if (!this.ignoreCi && (ctx.hasAttribute("CIPOS") || ctx.hasAttribute("CIEND"))) {
                if (ctx.hasAttribute("CIPOS")) {
                    int x = 0;
                    try {
                        x = ctx.getAttributeAsIntList("CIPOS", 0).get(0);
                    } catch (final Throwable err) {
                        LOG.error(err);
                        x = 0;
                    }
                    start += x;
                }
                if (ctx.hasAttribute("CIEND")) {
                    int x = 0;
                    try {
                        x = ctx.getAttributeAsIntList("CIEND", 0).get(1);
                    } catch (final Throwable err) {
                        LOG.error(err);
                        x = 0;
                    }
                    end += x;
                }
                // it happens for SV=BND
                if (start > end) {
                    final int tmp = start;
                    start = end;
                    end = tmp;
                }
            }
            if (extender.isChanging()) {
                final Locatable extended = extender.apply(new SimpleInterval(ctx.getContig(), start, end));
                start = extended.getStart();
                end = extended.getEnd();
            }
            final String newtContig;
            if (ctgNameConverter != null) {
                newtContig = ctgNameConverter.apply(ctx.getContig());
                if (StringUtil.isBlank(newtContig)) {
                    this.contigsNotFound.add(ctx.getContig());
                    continue;
                }
            } else {
                newtContig = ctx.getContig();
            }
            if (funGetSSR != null) {
                final SAMSequenceRecord ssr = funGetSSR.apply(newtContig);
                if (ssr != null) {
                    end = Math.min(ssr.getSequenceLength(), end);
                }
            }
            start = Math.max(1, start);
            final SimpleInterval interval = new SimpleInterval(newtContig, start, end);
            if (interval.getStart() > interval.getEnd()) {
                LOG.info("negative interval " + interval + " for " + ctx + " in " + uriOrNull);
                continue;
            }
            if (this.minLength != -1 && interval.getLengthOnReference() < this.minLength)
                continue;
            if (this.maxLength != -1 && interval.getLengthOnReference() > this.maxLength)
                continue;
            switch(this.outputFormat) {
                case bed:
                    {
                        pw.print(interval.getContig());
                        pw.print("\t");
                        pw.print(interval.getStart() - 1);
                        pw.print("\t");
                        pw.print(interval.getEnd());
                        pw.print("\t");
                        pw.print(ctx.hasID() ? ctx.getID() : ctx.getAlleles().stream().map(A -> A.getDisplayString()).collect(Collectors.joining(",")));
                        pw.print("\t");
                        pw.print(ctx.hasLog10PError() ? Math.min(1000, (int) ctx.getPhredScaledQual()) : ".");
                        /*
						pw.print("\t");
						pw.print("+");
						pw.print("\t");
						pw.print(interval.getStart()-1);
						pw.print("\t");
						pw.print(interval.getEnd());
						pw.print("\t");
						pw.print("0,0,0");
						*/
                        pw.println();
                        break;
                    }
                case interval:
                    {
                        pw.print(interval.getContig());
                        pw.print(":");
                        pw.print(interval.getStart());
                        pw.print("-");
                        pw.print(interval.getEnd());
                        pw.println();
                        break;
                    }
                default:
                    {
                        throw new IllegalStateException("" + this.outputFormat);
                    }
            }
        }
        return 0;
    } catch (final Exception err) {
        LOG.error(err);
        return -1;
    }
}

Example 2 with IntervalExtender

use of com.github.lindenb.jvarkit.samtools.util.IntervalExtender in project jvarkit by lindenb.

the class SetFileTools method openSetFileIterator.

private CloseableIterator<SetFileRecord> openSetFileIterator(final List<String> args) throws IOException {
    CloseableIterator<SetFileRecord> iter = null;
    final String input = oneFileOrNull(args);
    final SetFileReaderFactory srf = new SetFileReaderFactory(this.theDict);
    if (input == null) {
        iter = srf.open(IOUtils.openStdinForBufferedReader());
    } else {
        iter = srf.open(IOUtils.openURIForBufferedReading(input));
    }
    if (!StringUtils.isBlank(this.extendStr)) {
        final IntervalExtender xtExtender = IntervalExtender.of(this.theDict, this.extendStr);
        if (xtExtender.isChanging()) {
            iter = new ExtenderIterator(iter, xtExtender);
        }
    }
    if (intersectBedPath != null) {
        iter = new IntersectBedIterator(iter, this.intersectBedPath);
    }
    if (!intersectVcfPath.isEmpty()) {
        iter = new IntersectVcfIterator(iter, IOUtils.unrollPaths(this.intersectVcfPath));
    }
    if (!disable_uniq) {
        iter = new UniqNameIterator(iter);
    }
    return iter;
}

Example 3 with IntervalExtender

use of com.github.lindenb.jvarkit.samtools.util.IntervalExtender in project jvarkit by lindenb.

the class WesCnvSvg method doWork.

@Override
public int doWork(final List<String> args) {
    XMLStreamWriter w = null;
    BufferedReader r = null;
    OutputStream fout = null;
    VCFReader vcfReader = null;
    try {
        this.indexedFastaSequenceFile = ReferenceSequenceFileFactory.getReferenceSequenceFile(this.faidx);
        final SAMSequenceDictionary refDict = SequenceDictionaryUtils.extractRequired(this.indexedFastaSequenceFile);
        final IntervalExtender extender = IntervalExtender.of(refDict, this.extendWhat);
        if (extender.isShriking()) {
            LOG.error("extend factor <1.0");
            return -1;
        }
        final ContigNameConverter contigNameConverter = ContigNameConverter.fromOneDictionary(refDict);
        final ContigDictComparator contigDictCompare = new ContigDictComparator(refDict);
        final List<CaptureInterval> userIntervals = this.intervalListProvider.stream().map(loc -> contigNameConverter.convertToSimpleInterval(loc).<RuntimeException>orElseThrow(() -> new RuntimeException(new JvarkitException.ContigNotFoundInDictionary(loc.getContig(), refDict)))).map(extender).collect(HtsCollectors.mergeIntervals()).map(L -> new CaptureInterval(L)).sorted(contigDictCompare.createLocatableComparator()).collect(Collectors.toCollection(ArrayList::new));
        if (userIntervals.isEmpty()) {
            LOG.error("no interval or bed defined");
            return -1;
        }
        this.countBasesToBeDisplayed = userIntervals.stream().mapToInt(R -> R.getLengthOnReference()).sum();
        if (this.countBasesToBeDisplayed < 1) {
            LOG.error("Nothing to display. BED count==0");
            return -1;
        } else {
            double x1 = 0;
            for (int i = 0; i < userIntervals.size(); ++i) {
                final CaptureInterval ci = userIntervals.get(i);
                ci.pixelx = x1;
                x1 += ci.getPixelWidth();
            }
        }
        /* distinct ordered contigs */
        final List<String> distinctContigs = userIntervals.stream().map(R -> R.getContig()).collect(Collectors.toSet()).stream().sorted(contigDictCompare).collect(Collectors.toList());
        final SamReaderFactory srf = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.LENIENT).referenceSequence(this.faidx);
        for (final Path bamFile : IOUtils.unrollPaths(args)) {
            final BamInput bi = new BamInput();
            bi.bamPath = bamFile;
            try (SamReader samReader = srf.open(bamFile)) {
                final SAMSequenceDictionary samDict = SequenceDictionaryUtils.extractRequired(samReader.getFileHeader());
                if (!SequenceUtil.areSequenceDictionariesEqual(refDict, samDict)) {
                    throw new JvarkitException.DictionariesAreNotTheSame(refDict, samDict);
                }
                bi.sample = samReader.getFileHeader().getReadGroups().stream().map(V -> V.getSample()).filter(S -> !StringUtil.isBlank(S)).findFirst().orElse(IOUtils.getFilenameWithoutCommonSuffixes(bamFile));
                final CoverageFactory covFactory = new CoverageFactory().setMappingQuality(this.minMappingQuality);
                for (final String contig : distinctContigs) {
                    final List<CaptureInterval> contig_intervals = userIntervals.stream().filter(R -> R.getContig().equals(contig)).collect(Collectors.toList());
                    final CoverageFactory.SimpleCoverage coverage = covFactory.getSimpleCoverage(samReader, contig_intervals, null);
                    for (CaptureInterval rgn : contig_intervals) {
                        final double[] array = coverage.getSubCoverage(rgn).scale(this.scaleType, (int) rgn.getPixelWidth());
                        bi.coverages.add(array);
                    }
                }
            }
            this.bamInputs.add(bi);
        }
        if (this.bamInputs.isEmpty()) {
            LOG.error("no bam input");
            return -1;
        }
        if (this.vcfFile != null) {
            vcfReader = VCFReaderFactory.makeDefault().open(this.vcfFile, true);
            final SAMSequenceDictionary vcfDict = vcfReader.getHeader().getSequenceDictionary();
            if (vcfDict != null)
                SequenceUtil.assertSequenceDictionariesEqual(refDict, vcfDict);
        }
        final XMLOutputFactory xof = XMLOutputFactory.newFactory();
        if (this.outputFile == null) {
            w = xof.createXMLStreamWriter(stdout(), "UTF-8");
        } else {
            fout = Files.newOutputStream(this.outputFile);
            w = xof.createXMLStreamWriter(fout, "UTF-8");
        }
        final Function<List<Point2D.Double>, String> points2str = (L) -> L.stream().map(S -> format(S.getX()) + "," + format(S.getY())).collect(Collectors.joining(" "));
        final Consumer<List<Point2D.Double>> simplifyPoints = (L) -> {
            for (int z = 0; z + 1 < L.size(); ++z) {
                if (L.get(z).getY() == L.get(z + 1).getY()) {
                    L.get(z).x = L.get(z + 1).x;
                    L.remove(z + 1);
                }
            }
        };
        w.writeStartDocument("UTF-8", "1.0");
        final Dimension dim = new Dimension(this.drawinAreaWidth, 0);
        final int bed_header_height = 20;
        dim.height += bed_header_height;
        dim.height += (int) this.bamInputs.stream().mapToDouble(B -> B.getPixelHeight()).sum();
        LOG.debug("drawing area: " + dim);
        w.writeStartElement("svg");
        w.writeAttribute("width", String.valueOf(dim.width));
        w.writeAttribute("height", String.valueOf(dim.height));
        w.writeDefaultNamespace(SVG.NS);
        w.writeNamespace("xlink", XLINK.NS);
        // https://stackoverflow.com/questions/15717970
        w.writeStartElement("style");
        if (this.cssFile != null) {
            w.writeCharacters(IOUtil.slurp(this.cssFile));
        } else {
            w.writeCharacters("g.maing {stroke:black;stroke-width:0.5px;fill:whitesmoke;font-size:10pt;}\n" + "text.sampleLabel {stroke:none;stroke-width:0.5px;fill:blue;}" + "text.captureLabel {stroke:none;stroke-width:0.5px;fill:slategrey;text-anchor:middle;}" + "polygon.area {stroke:darkgray;stroke-width:0.5px;fill:url('#grad01');}" + "line.linedp {stroke:darkcyan;stroke-width:0.3px;opacity:0.4;}" + "text.linedp {fill-opacity:0.6;font-size:7px;stroke:none;stroke-width:0.5px;fill:darkcyan;}" + "rect.sampleFrame { fill:none;stroke:slategray;stroke-width:0.3px;}" + "rect.clickRgn {fill:none;stroke:none;pointer-events:all;}" + "polyline.gc {stroke:lightcoral;stroke-width:0.3px;fill:none;}" + "polyline.clipping {stroke:orange;stroke-width:0.8px;fill:none;}" + "circle.ar {fill:orange;stroke:none;}" + "circle.aa {fill:red;stroke:none;}" + "circle.rr {fill:green;stroke:none;}");
        }
        // style
        w.writeEndElement();
        w.writeStartElement("title");
        w.writeCharacters(this.domSvgTitle);
        w.writeEndElement();
        w.writeStartElement("defs");
        // alleles
        final double genotype_radius = Double.parseDouble(this.dynaParams.getOrDefault("gt.radius", "1.5"));
        w.writeEmptyElement("circle");
        w.writeAttribute("r", format(genotype_radius));
        w.writeAttribute("id", "rr");
        w.writeAttribute("class", "rr");
        w.writeEmptyElement("circle");
        w.writeAttribute("r", format(genotype_radius));
        w.writeAttribute("id", "ar");
        w.writeAttribute("class", "ar");
        w.writeEmptyElement("circle");
        w.writeAttribute("r", format(genotype_radius));
        w.writeAttribute("id", "aa");
        w.writeAttribute("class", "aa");
        // gradient
        w.writeStartElement("linearGradient");
        w.writeAttribute("id", "grad01");
        w.writeAttribute("x1", "50%");
        w.writeAttribute("x2", "50%");
        w.writeAttribute("y1", "0%");
        w.writeAttribute("y2", "100%");
        w.writeEmptyElement("stop");
        w.writeAttribute("offset", "0%");
        w.writeAttribute("style", "stop-color:lightgray;stop-opacity:1;");
        w.writeEmptyElement("stop");
        w.writeAttribute("offset", "100%");
        w.writeAttribute("style", "stop-color:gray;stop-opacity:1;");
        w.writeEndElement();
        // gc percent
        for (final CaptureInterval ci : userIntervals) {
            final GenomicSequence genomicSequence = new GenomicSequence(this.indexedFastaSequenceFile, ci.getContig());
            final int gc_percent_width = (int) ci.getPixelWidth();
            final List<Point2D.Double> points = new ArrayList<>(gc_percent_width);
            for (int x = 0; x < gc_percent_width; ++x) {
                int pos1 = ci.getStart() + (int) (((x + 0) / ci.getPixelWidth()) * ci.getLengthOnReference());
                int pos2 = ci.getStart() + (int) (((x + 1) / ci.getPixelWidth()) * ci.getLengthOnReference());
                double gc_percent = getGcPercent(genomicSequence, pos1, pos2);
                double y = this.sampleTrackHeight - this.sampleTrackHeight * gc_percent;
                points.add(new Point2D.Double(x, y));
            }
            simplifyPoints.accept(points);
            w.writeStartElement("polyline");
            w.writeAttribute("class", "gc");
            w.writeAttribute("id", "z" + ci.getId());
            w.writeAttribute("points", points2str.apply(points));
            w.writeStartElement("title");
            w.writeCharacters("GC %");
            w.writeEndElement();
            w.writeEndElement();
        }
        // defs
        w.writeEndElement();
        w.writeStartElement("script");
        final StringBuilder openBrowserFunction = new StringBuilder("function openGenomeBrowser(contig,chromStart,chromEnd) {\n");
        if (!this.hyperlinkType.isEmpty()) {
            openBrowserFunction.append("var url=\"" + this.hyperlinkType.getPattern() + "\".replace(/__CHROM__/g,contig).replace(/__START__/g,chromStart).replace(/__END__/g,chromEnd);\n");
            openBrowserFunction.append("window.open(url,'_blank');\n");
        } else {
        // nothing
        }
        openBrowserFunction.append("}\n");
        w.writeCData(openBrowserFunction.toString() + "function clicked(evt,contig,chromStart,chromEnd){\n" + "    var e = evt.target;\n" + "    var dim = e.getBoundingClientRect();\n" + "    var x = 1.0 * evt.clientX - dim.left;\n" + "    var cLen = 1.0* (chromEnd - chromStart); if(cLen<1) cLen=1.0;\n" + "    var pos1 = chromStart + parseInt(((x+0)/dim.width)*cLen);\n" + "    var pos2 = chromStart + parseInt(((x+1)/dim.width)*cLen);\n" + "   openGenomeBrowser(contig,pos1,pos2);\n" + "}\n");
        // script
        w.writeEndElement();
        w.writeStartElement("g");
        w.writeAttribute("class", "maing");
        int y = 0;
        w.writeStartElement("g");
        w.writeComment("interval background");
        for (final CaptureInterval ci : userIntervals) {
            w.writeStartElement("text");
            w.writeAttribute("class", "captureLabel");
            w.writeAttribute("textLength", String.valueOf(ci.getPixelWidth() * 0.8));
            w.writeAttribute("lengthAdjust", "spacing");
            w.writeAttribute("x", String.valueOf(ci.getPixelX1() + ci.getPixelWidth() / 2.0));
            w.writeAttribute("y", String.valueOf(bed_header_height - 2));
            w.writeCharacters(ci.getName());
            w.writeStartElement("title");
            w.writeCharacters(ci.toNiceString());
            // title
            w.writeEndElement();
            // text
            w.writeEndElement();
            w.writeStartElement("rect");
            w.writeAttribute("style", "stroke:black;fill:none;");
            w.writeAttribute("x", String.valueOf(ci.getPixelX1()));
            w.writeAttribute("y", "0");
            w.writeAttribute("width", String.valueOf(ci.getPixelWidth()));
            w.writeAttribute("height", String.valueOf(dim.height));
            w.writeStartElement("title");
            w.writeCharacters(ci.getName());
            w.writeEndElement();
            w.writeEndElement();
        }
        // interval background
        w.writeEndElement();
        y += bed_header_height;
        for (final BamInput bi : this.bamInputs) {
            w.writeComment(bi.bamPath.toString());
            w.writeStartElement("g");
            w.writeAttribute("transform", "translate(0," + y + ")");
            if (normalize_on_median_flag) {
                final double medianDepth = Math.max(1.0, Percentile.median().evaluate(bi.coverages.stream().flatMapToDouble(B -> Arrays.stream(B)).toArray()).orElse(1.0));
                LOG.info("median" + medianDepth);
                for (final double[] coverage_array : bi.coverages) {
                    for (int px = 0; px < coverage_array.length; px++) {
                        coverage_array[px] /= medianDepth;
                    }
                }
            }
            final double maxDepth = bi.coverages.stream().flatMapToDouble(B -> Arrays.stream(B)).max().orElse(1.0);
            for (int ridx = 0; ridx < userIntervals.size(); ridx++) {
                final CaptureInterval ci = userIntervals.get(ridx);
                final String clickedAttribute = "clicked(evt,\"" + ci.getContig() + "\"," + ci.getStart() + "," + ci.getEnd() + ")";
                final double[] coverage_array = bi.coverages.get(ridx);
                final double leftx = ci.getPixelX1();
                w.writeStartElement("g");
                w.writeAttribute("transform", "translate(" + leftx + ",0)");
                final int segment_width = (int) ci.getPixelWidth();
                // coverage
                {
                    final List<Point2D.Double> points = new ArrayList<>(segment_width);
                    points.add(new Point2D.Double(0, bi.getPixelHeight()));
                    for (int px = 0; px < coverage_array.length; px++) {
                        final double y_avg_cov = coverage_array[px];
                        final double new_y = bi.getPixelHeight() - (y_avg_cov / maxDepth) * bi.getPixelHeight();
                        points.add(new Point2D.Double(px, new_y));
                    }
                    points.add(new Point2D.Double(ci.getPixelWidth(), bi.getPixelHeight()));
                    simplifyPoints.accept(points);
                    // close
                    points.add(new Point2D.Double(leftx, bi.getPixelHeight()));
                    w.writeEmptyElement("polygon");
                    w.writeAttribute("class", "area");
                    w.writeAttribute("title", ci.toNiceString());
                    // w.writeAttribute("onclick", clickedAttribute);
                    w.writeAttribute("points", points2str.apply(points));
                }
                // w.writeEndElement();//g
                int depthshift = 1;
                for (; ; ) {
                    final int numdiv = (int) (maxDepth / depthshift);
                    if (numdiv <= 10)
                        break;
                    depthshift *= 10;
                }
                int depth = depthshift;
                while (depth < maxDepth) {
                    double new_y = bi.getPixelHeight() - (depth / maxDepth) * bi.getPixelHeight();
                    w.writeStartElement("text");
                    w.writeAttribute("class", "linedp");
                    w.writeAttribute("x", "1");
                    w.writeAttribute("y", String.valueOf(new_y + 1));
                    w.writeCharacters(String.valueOf(depth));
                    // text
                    w.writeEndElement();
                    w.writeStartElement("line");
                    w.writeAttribute("class", "linedp");
                    w.writeAttribute("stroke-dasharray", "4");
                    w.writeAttribute("x1", "0");
                    w.writeAttribute("x2", String.valueOf(ci.getPixelWidth()));
                    w.writeAttribute("y1", String.valueOf(new_y));
                    w.writeAttribute("y2", String.valueOf(new_y));
                    w.writeStartElement("title");
                    w.writeCharacters(String.valueOf(depth));
                    w.writeEndElement();
                    // line
                    w.writeEndElement();
                    depth += depthshift;
                }
                // polyline
                w.writeEmptyElement("use");
                w.writeAttribute("xlink", XLINK.NS, "href", "#z" + ci.getId());
                w.writeAttribute("x", "0");
                w.writeAttribute("y", "0");
                // click
                w.writeStartElement("rect");
                w.writeAttribute("class", "clickRgn");
                w.writeAttribute("onclick", clickedAttribute);
                w.writeAttribute("x", "0");
                w.writeAttribute("y", "0");
                w.writeAttribute("width", String.valueOf(ci.getPixelWidth()));
                w.writeAttribute("height", String.valueOf(bi.getPixelHeight()));
                w.writeEndElement();
                // genotype
                if (vcfReader != null) {
                    try (CloseableIterator<VariantContext> iter = vcfReader.query(ci)) {
                        while (iter.hasNext()) {
                            final VariantContext ctx = iter.next();
                            final Genotype gt = ctx.getGenotype(bi.sample);
                            if (gt == null)
                                break;
                            String allele_id = null;
                            switch(gt.getType()) {
                                case HET:
                                    allele_id = "ar";
                                    break;
                                case HOM_REF:
                                    allele_id = "rr";
                                    break;
                                case HOM_VAR:
                                    allele_id = "aa";
                                    break;
                                default:
                                    allele_id = null;
                                    break;
                            }
                            if (allele_id != null) {
                                w.writeEmptyElement("use");
                                w.writeAttribute("xlink", XLINK.NS, "href", "#" + allele_id);
                                w.writeAttribute("x", format(((ctx.getStart() - ci.getStart()) / (double) ci.getLengthOnReference()) * ci.getPixelWidth()));
                                w.writeAttribute("y", format(bi.getPixelHeight() - 2 * genotype_radius));
                            }
                        }
                    }
                }
                // g
                w.writeEndElement();
            }
            // frame for this sample
            w.writeStartElement("rect");
            w.writeAttribute("class", "sampleFrame");
            w.writeAttribute("x", "0");
            w.writeAttribute("y", "0");
            w.writeAttribute("width", String.valueOf(dim.width));
            w.writeAttribute("height", String.valueOf(bi.getPixelHeight()));
            // rect
            w.writeEndElement();
            w.writeStartElement("text");
            w.writeAttribute("class", "sampleLabel");
            w.writeAttribute("x", "5");
            w.writeAttribute("y", "12");
            w.writeStartElement("title");
            w.writeCharacters(bi.bamPath.toString());
            w.writeEndElement();
            w.writeCharacters(bi.sample);
            // text
            w.writeEndElement();
            // g
            w.writeEndElement();
            y += bi.getPixelHeight();
        }
        w.writeStartElement("g");
        w.writeComment("interval lines");
        for (int n = 0; n <= userIntervals.size(); n++) {
            w.writeEmptyElement("line");
            String x1 = n < userIntervals.size() ? String.valueOf(userIntervals.get(n).getPixelX1()) : String.valueOf(dim.width);
            w.writeAttribute("x1", x1);
            w.writeAttribute("y1", "0");
            w.writeAttribute("x2", x1);
            w.writeAttribute("y2", String.valueOf(dim.height));
        }
        // interval lines
        w.writeEndElement();
        // g
        w.writeEndElement();
        // svg
        w.writeEndElement();
        w.writeEndDocument();
        w.flush();
        w.close();
        return 0;
    } catch (final Exception err) {
        LOG.error(err);
        return -1;
    } finally {
        CloserUtil.close(vcfReader);
        CloserUtil.close(w);
        CloserUtil.close(fout);
        CloserUtil.close(r);
        CloserUtil.close(this.indexedFastaSequenceFile);
        CloserUtil.close(this.bamInputs);
    }
}