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

Example 1 with AbstractVCFCodec

use of htsjdk.variant.vcf.AbstractVCFCodec 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 2 with AbstractVCFCodec

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

the class VCFUtils method findCodecFromLines.

/**
 * find a codec from the lines header. if not found, return default codec
 */
public static AbstractVCFCodec findCodecFromLines(final List<String> list) {
    for (final String line : list) {
        String formatString = line;
        if (formatString.startsWith("##")) {
            formatString = formatString.substring(2);
        }
        int eq = formatString.indexOf('=');
        if (eq == -1)
            continue;
        if (!VCFHeaderVersion.isFormatString(formatString.substring(0, eq)))
            continue;
        VCFHeaderVersion version = VCFHeaderVersion.getHeaderVersion(line);
        if (version == null)
            continue;
        switch(version) {
            case VCF3_2:
            case VCF3_3:
                return new VCF3Codec();
            case VCF4_0:
            case VCF4_1:
            case VCF4_2:
                return new VCFCodec();
        }
    }
    return createDefaultVCFCodec();
}

Example 3 with AbstractVCFCodec

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

the class FixVCF method doWork.

private int doWork(String filenameIn, InputStream vcfStream, VariantContextWriter w) throws IOException {
    final AbstractVCFCodec vcfCodec = VCFUtils.createDefaultVCFCodec();
    LineIterator r = new LineIteratorImpl(new SynchronousLineReader(vcfStream));
    final VCFHeader header = (VCFHeader) vcfCodec.readActualHeader(r);
    // samples names have been changed by picard api and reordered !!!
    // re-create the original order
    List<String> sampleNamesInSameOrder = new ArrayList<String>(header.getSampleNamesInOrder().size());
    for (int col = 0; col < header.getSampleNamesInOrder().size(); ++col) {
        for (String sample : header.getSampleNameToOffset().keySet()) {
            if (header.getSampleNameToOffset().get(sample) == col) {
                sampleNamesInSameOrder.add(sample);
                break;
            }
        }
    }
    if (sampleNamesInSameOrder.size() != header.getSampleNamesInOrder().size()) {
        throw new IllegalStateException();
    }
    VCFHeader h2 = new VCFHeader(header.getMetaDataInInputOrder(), sampleNamesInSameOrder);
    File tmp = IOUtil.newTempFile("tmp", ".vcf.gz", new File[] { tmpDir });
    tmp.deleteOnExit();
    PrintWriter pw = new PrintWriter(new GZIPOutputStream(new FileOutputStream(tmp)));
    while (r.hasNext()) {
        String line = r.next();
        pw.println(line);
        VariantContext ctx = null;
        try {
            ctx = vcfCodec.decode(line);
        } catch (Exception err) {
            pw.close();
            LOG.error(line);
            LOG.error(err);
            return -1;
        }
        for (String f : ctx.getFilters()) {
            if (h2.getFilterHeaderLine(f) != null)
                continue;
            // if(f.equals(VCFConstants.PASSES_FILTERS_v4)) continue; hum...
            if (f.isEmpty() || f.equals(VCFConstants.UNFILTERED))
                continue;
            LOG.info("Fixing missing Filter:" + f);
            h2.addMetaDataLine(new VCFFilterHeaderLine(f));
        }
        for (String tag : ctx.getAttributes().keySet()) {
            if (h2.getInfoHeaderLine(tag) != null)
                continue;
            LOG.info("Fixing missing INFO:" + tag);
            h2.addMetaDataLine(new VCFInfoHeaderLine(tag, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.String, "undefined. Saved by " + getClass()));
        }
    }
    pw.flush();
    pw.close();
    pw = null;
    LOG.info("re-reading VCF frm tmpFile:" + tmp);
    h2.addMetaDataLine(new VCFHeaderLine(getClass().getSimpleName(), "Saved VCF FILTER AND INFO from " + filenameIn));
    // save header in memory
    ByteArrayOutputStream baos = new ByteArrayOutputStream();
    VariantContextWriter w2 = VCFUtils.createVariantContextWriterToOutputStream(baos);
    w2.writeHeader(h2);
    w2.close();
    baos.close();
    // reopen tmp file
    @SuppressWarnings("resource") VcfIterator in = new VcfIteratorImpl(new SequenceInputStream(new ByteArrayInputStream(baos.toByteArray()), new GZIPInputStream(new FileInputStream(tmp))));
    w.writeHeader(h2);
    while (in.hasNext()) {
        w.add(in.next());
    }
    in.close();
    tmp.delete();
    return 0;
}