Examples with TabixReader htsjdk.tribble.readers.TabixReader used on opensource projects

Example 6 with TabixReader

use of htsjdk.tribble.readers.TabixReader in project ASCIIGenome by dariober.

the class TrackBookmark method addBookmark.

/**
 * Add current genomic position to track.
 * @throws IOException
 * @throws SQLException
 * @throws InvalidRecordException
 * @throws ClassNotFoundException
 * @throws InvalidGenomicCoordsException
 */
@Override
public void addBookmark(GenomicCoords gc, String nameForBookmark) throws IOException, ClassNotFoundException, InvalidRecordException, SQLException, InvalidGenomicCoordsException {
    // Adding a bookmark means re-preparing the bgzip file again.
    // First write the current position to a new tmp file, then append to this file
    // all the bookmarks previously added. Then bgzip and compress replacing the old bookmark file.
    File plainNew = new File(this.getWorkFilename() + ".add");
    plainNew.deleteOnExit();
    BufferedWriter wr = new BufferedWriter(new FileWriter(plainNew));
    InputStream fileStream = new FileInputStream(this.getWorkFilename());
    Reader decoder = new InputStreamReader(new GZIPInputStream(fileStream), "UTF-8");
    BufferedReader br = new BufferedReader(decoder);
    String line;
    while ((line = br.readLine()) != null) {
        if (line.contains("\t__ignore_me__")) {
            // Hack to circumvent issue #38
            continue;
        }
        wr.write(line + "\n");
    }
    // Add new bookamrk
    wr.write(this.positionToGffLine(gc, nameForBookmark) + "\n");
    br.close();
    wr.close();
    // Recompress and index replacing the original bgzip file
    new MakeTabixIndex(plainNew.getAbsolutePath(), new File(this.getWorkFilename()), TabixFormat.GFF);
    plainNew.delete();
    this.tabixReader = new TabixReader(this.getWorkFilename());
    // Update track.
    this.update();
}

Example 7 with TabixReader

use of htsjdk.tribble.readers.TabixReader in project jvarkit by lindenb.

the class VcfRegistryCGI method doWork.

private void doWork(XMLStreamWriter w, final GroupFile gf) throws XMLStreamException {
    Position pos = parsePosition();
    if (pos == null)
        return;
    w.writeStartElement("div");
    w.writeStartElement("h2");
    w.writeCharacters(pos.chrom + ":" + pos.pos);
    w.writeEndElement();
    w.writeStartElement("table");
    w.writeStartElement("thead");
    w.writeStartElement("tr");
    for (String header : new String[] { "CHROM", "POS", "ID", "REF", "QUAL", "Sample", "Alleles", "DP", "GQ", "File" }) {
        w.writeStartElement("th");
        w.writeCharacters(header);
        // td
        w.writeEndElement();
    }
    // tr
    w.writeEndElement();
    // thead
    w.writeEndElement();
    w.writeStartElement("tbody");
    Set<String> samplesWithGenotypes = new HashSet<String>();
    Set<String> allSamples = new HashSet<String>();
    for (VcfFile f : getVcfFiles(gf)) {
        TabixReader tabixReader = null;
        TabixReader.Iterator iter = null;
        BlockCompressedInputStream bgzin = null;
        VCFHeader header = null;
        AbstractVCFCodec vcfCodec = VCFUtils.createDefaultVCFCodec();
        LineIterator lineIterator = null;
        for (int i = 0; i < 2; i++) {
            try {
                if (i == 0) {
                    bgzin = new BlockCompressedInputStream(f.file);
                    lineIterator = new LineIteratorImpl(new SynchronousLineReader(bgzin));
                    header = (VCFHeader) vcfCodec.readActualHeader(lineIterator);
                    allSamples.addAll(header.getGenotypeSamples());
                } else {
                    tabixReader = new TabixReader(f.file.getPath());
                    String line;
                    int[] x = tabixReader.parseReg(pos.chrom + ":" + pos.pos + "-" + (pos.pos));
                    if (x != null && x.length > 2 && x[0] != -1) {
                        iter = tabixReader.query(x[0], x[1], x[2]);
                    } else {
                    }
                    while (iter != null && (line = iter.next()) != null) {
                        VariantContext var = vcfCodec.decode(line);
                        for (String sample : header.getSampleNamesInOrder()) {
                            final Genotype genotype = var.getGenotype(sample);
                            if (genotype == null || !genotype.isCalled())
                                continue;
                            if (!genotype.isAvailable())
                                continue;
                            samplesWithGenotypes.add(sample);
                            w.writeStartElement("tr");
                            w.writeStartElement("td");
                            w.writeCharacters(var.getContig());
                            w.writeEndElement();
                            w.writeStartElement("td");
                            w.writeCharacters(String.valueOf(var.getStart()));
                            w.writeEndElement();
                            if (var.hasID()) {
                                w.writeStartElement("td");
                                if (var.getID().matches("rs[0-9]+")) {
                                    w.writeStartElement("a");
                                    w.writeAttribute("href", "http://www.ncbi.nlm.nih.gov/snp/" + var.getID().substring(2));
                                    w.writeCharacters(var.getID());
                                    // a
                                    w.writeEndElement();
                                } else {
                                    w.writeCharacters(var.getID());
                                }
                                // td
                                w.writeEndElement();
                            } else {
                                w.writeEmptyElement("td");
                            }
                            if (var.getReference() != null) {
                                w.writeStartElement("td");
                                w.writeCharacters(var.getReference().getBaseString());
                                w.writeEndElement();
                            } else {
                                w.writeEmptyElement("td");
                            }
                            if (var.hasLog10PError()) {
                                w.writeStartElement("td");
                                w.writeCharacters(String.valueOf((int) var.getPhredScaledQual()));
                                w.writeEndElement();
                            } else {
                                w.writeEmptyElement("td");
                            }
                            w.writeStartElement("td");
                            w.writeCharacters(sample);
                            w.writeEndElement();
                            List<Allele> alleles = genotype.getAlleles();
                            w.writeStartElement("td");
                            w.writeStartElement("span");
                            if (genotype.isHomRef()) {
                                w.writeAttribute("style", "color:green;");
                            } else if (genotype.isHomVar()) {
                                w.writeAttribute("style", "color:red;");
                            } else if (genotype.isHet()) {
                                w.writeAttribute("style", "color:blue;");
                            }
                            for (int j = 0; j < alleles.size(); ++j) {
                                if (j > 0)
                                    w.writeCharacters(genotype.isPhased() ? "|" : "/");
                                w.writeCharacters(alleles.get(j).getBaseString());
                            }
                            // span
                            w.writeEndElement();
                            w.writeEndElement();
                            if (genotype.hasDP()) {
                                w.writeStartElement("td");
                                w.writeCharacters(String.valueOf(genotype.getDP()));
                                w.writeEndElement();
                            } else {
                                w.writeEmptyElement("td");
                            }
                            if (genotype.hasGQ()) {
                                w.writeStartElement("td");
                                w.writeCharacters(String.valueOf(genotype.getGQ()));
                                w.writeEndElement();
                            } else {
                                w.writeEmptyElement("td");
                            }
                            w.writeStartElement("td");
                            w.writeCharacters(f.file.getName());
                            w.writeEndElement();
                            // tr
                            w.writeEndElement();
                            w.flush();
                        }
                    }
                }
            } catch (Exception err) {
                w.writeComment("BOUM " + err);
                header = null;
                lastException = err;
            } finally {
                CloserUtil.close(lineIterator);
                CloserUtil.close(bgzin);
                CloserUtil.close(tabixReader);
                CloserUtil.close(iter);
            }
            if (i == 0 && header == null)
                break;
        }
        w.flush();
    }
    // tbody
    w.writeEndElement();
    // table
    w.writeEndElement();
    allSamples.removeAll(samplesWithGenotypes);
    if (!allSamples.isEmpty()) {
        w.writeStartElement("h3");
        w.writeCharacters("Samples not found");
        w.writeEndElement();
        w.writeStartElement("ol");
        for (String sample : new TreeSet<String>(allSamples)) {
            w.writeStartElement("li");
            w.writeCharacters(sample);
            w.writeEndElement();
        }
        w.writeEndElement();
    }
    writeHTMLException(w, this.lastException);
    // div
    w.writeEndElement();
}

Example 8 with TabixReader

use of htsjdk.tribble.readers.TabixReader in project ASCIIGenome by dariober.

the class MakeTabixFileTest method canCompressAndIndexSortedFile.

@Test
public void canCompressAndIndexSortedFile() throws IOException, InvalidRecordException, ClassNotFoundException, SQLException {
    String infile = "test_data/overlapped.bed";
    File outfile = new File("test_data/tmp.bed.gz");
    outfile.deleteOnExit();
    File expectedTbi = new File(outfile.getAbsolutePath() + TabixUtils.STANDARD_INDEX_EXTENSION);
    expectedTbi.deleteOnExit();
    new MakeTabixIndex(infile, outfile, TabixFormat.BED);
    assertTrue(outfile.exists());
    assertTrue(outfile.length() > 80);
    assertTrue(expectedTbi.exists());
    assertTrue(expectedTbi.length() > 80);
    TabixReader tbx = new TabixReader(outfile.getAbsolutePath());
    Iterator x = tbx.query("chr1", 1, 1000000);
    assertTrue(x.next().startsWith("chr1"));
}

Example 9 with TabixReader

use of htsjdk.tribble.readers.TabixReader in project ASCIIGenome by dariober.

the class MakeTabixFileTest method canCompressAndIndexSortedGzipFile.

@Test
public void canCompressAndIndexSortedGzipFile() throws IOException, InvalidRecordException, ClassNotFoundException, SQLException {
    String infile = "test_data/hg19_genes.gtf.gz";
    File outfile = new File("test_data/tmp2.bed.gz");
    outfile.deleteOnExit();
    File expectedTbi = new File(outfile.getAbsolutePath() + TabixUtils.STANDARD_INDEX_EXTENSION);
    expectedTbi.deleteOnExit();
    new MakeTabixIndex(infile, outfile, TabixFormat.GFF);
    assertTrue(outfile.exists());
    assertTrue(outfile.length() > 7000000);
    assertTrue(expectedTbi.exists());
    assertTrue(expectedTbi.length() > 500000);
    TabixReader tbx = new TabixReader(outfile.getAbsolutePath());
    Iterator x = tbx.query("chr1", 1, 1000000);
    assertTrue(x.next().startsWith("chr1"));
}

Example 10 with TabixReader

use of htsjdk.tribble.readers.TabixReader in project jvarkit by lindenb.

the class VCFTabixml method doVcfToVcf.

@Override
protected int doVcfToVcf(String inputName, VcfIterator r, VariantContextWriter w) {
    TabixReader tabixReader = null;
    try {
        LOG.info("opening BED" + BEDFILE);
        tabixReader = new TabixReader(this.BEDFILE);
        Pattern tab = Pattern.compile("[\t]");
        LOG.info("loading xslt " + STYLESHEET);
        this.stylesheet = TransformerFactory.newInstance().newTemplates(new StreamSource(STYLESHEET));
        Transformer transformer = this.stylesheet.newTransformer();
        transformer.setOutputProperty(OutputKeys.METHOD, "xml");
        final VCFHeader header = r.getHeader();
        final VCFHeader h2 = new VCFHeader(header);
        LOG.info("reading Tags " + TAGS);
        BufferedReader rT = IOUtils.openFileForBufferedReading(TAGS);
        String line;
        while ((line = rT.readLine()) != null) {
            if (!line.startsWith(VCFHeader.METADATA_INDICATOR)) {
                throw new RuntimeException("should start with " + VCFHeader.METADATA_INDICATOR + ":" + line);
            }
            if (!line.startsWith(VCFConstants.INFO_HEADER_START)) {
                throw new RuntimeException("should start with " + VCFConstants.INFO_HEADER_START + ":" + line);
            }
            VCFInfoHeaderLine hi = new VCFInfoHeaderLine(line.substring(7), VCFHeaderVersion.VCF4_1);
            if (hi.getCount() != 1) {
                throw new IllegalArgumentException("VCFHeaderLineCount not supported : " + hi);
            }
            switch(hi.getType()) {
                case String:
                    break;
                default:
                    throw new IllegalArgumentException("VCFHeaderLineTyoe not supported : " + hi);
            }
            LOG.info(hi.toString());
            h2.addMetaDataLine(hi);
        }
        rT.close();
        LOG.info("writing header");
        w.writeHeader(h2);
        JAXBContext jaxbCtx = JAXBContext.newInstance(Properties.class, Property.class);
        Unmarshaller unmarshaller = jaxbCtx.createUnmarshaller();
        while (r.hasNext()) {
            VariantContext ctx = r.next();
            HashMap<String, Set<String>> insert = new LinkedHashMap<String, Set<String>>();
            int[] array = tabixReader.parseReg(ctx.getContig() + ":" + (ctx.getStart()) + "-" + (ctx.getEnd() + 1));
            TabixReader.Iterator iter = null;
            if (array != null && array.length == 3 && array[0] != -1 && array[1] >= 0 && array[2] >= 0) {
                iter = tabixReader.query(array[0], array[1], array[2]);
            } else {
                LOG.info("Cannot get " + ctx.getContig() + ":" + (ctx.getStart()) + "-" + (ctx.getEnd() + 1));
            }
            String line2 = null;
            while (iter != null && (line2 = iter.next()) != null) {
                String[] tokens2 = tab.split(line2, 5);
                if (tokens2.length < 4) {
                    LOG.error("[VCFTabixml] VCF. Error not enough columns in tabix.line " + line2);
                    return -1;
                }
                int chromStart = Integer.parseInt(tokens2[1]);
                int chromEnd = Integer.parseInt(tokens2[2]);
                if (chromStart + 1 != chromEnd) {
                    LOG.error("Error in " + this.BEDFILE + " extected start+1=end int " + tokens2[0] + ":" + tokens2[1] + "-" + tokens2[2]);
                    continue;
                }
                if (ctx.getStart() - 1 != chromStart)
                    continue;
                transformer.setParameter("vcfchrom", ctx.getContig());
                transformer.setParameter("vcfpos", ctx.getStart());
                transformer.setParameter("vcfref", ctx.getReference().getBaseString());
                transformer.setParameter("vcfalt", ctx.getAltAlleleWithHighestAlleleCount().getBaseString());
                try {
                    StringWriter sw = new StringWriter();
                    StreamSource src = new StreamSource(new StringReader(tokens2[3]));
                    StreamResult rez = new StreamResult(sw);
                    transformer.transform(src, rez);
                    Properties props = unmarshaller.unmarshal(new StreamSource(new StringReader(sw.toString())), Properties.class).getValue();
                    for (Property p : props.getProperty()) {
                        if (p.key.isEmpty())
                            continue;
                        if (h2.getInfoHeaderLine(p.key) == null) {
                            LOG.info("ignoring key " + p.key + " you could set it to:\n" + "##INFO=<ID=" + p.key + ",Number=1,Type=String,Description=\"" + p.key + " from " + BEDFILE + "\">");
                            continue;
                        }
                        Set<String> x = insert.get(p.key);
                        if (x == null) {
                            x = new LinkedHashSet<String>();
                            insert.put(p.key, x);
                        }
                        x.add(p.value);
                    }
                } catch (Exception e) {
                    e.printStackTrace();
                    throw new RuntimeException("error", e);
                }
            }
            if (insert.isEmpty()) {
                w.add(ctx);
                continue;
            }
            VariantContextBuilder b = new VariantContextBuilder(ctx);
            for (String key : insert.keySet()) {
                for (String s2 : insert.get(key)) {
                    b.attribute(key, s2);
                    // limit 1
                    break;
                }
            }
            w.add(b.make());
        }
        return 0;
    } catch (IOException err) {
        err.printStackTrace();
        return -1;
    } catch (Throwable err) {
        err.printStackTrace();
        return -1;
    }
}