Package htsjdk.tribble.readers

Examples of htsjdk.tribble.readers.LineIterator

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    public MUTCodec(String path, Genome genome) {
        super(Mutation.class);
        this.path = path;
        this.genome = genome;
        try {
            LineIterator reader = new LineIteratorImpl(new AsciiLineReader(ParsingUtils.openInputStream(path)));
            readActualHeader(reader);
        } catch (IOException e) {
            log.error(e.getMessage(), e);
        }
    }
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        if (headerLines != null) {
            String lines = StringUtils.join(headerLines, "\n");
            byte[] bytes = lines.getBytes();
            InputStream is = new ByteArrayInputStream(bytes);
            LineIterator reader = new LineIteratorImpl(new AsciiLineReader(is));
            try {
                codec.readHeader(reader);
            } catch (IOException e) {
                log.error(e.getMessage(), e);
            }
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        List<D> featuresList = new ArrayList<D>();
        String line;
        D feat;

        LineIterator lrw = new LineIteratorImpl(new AsciiLineReader(is));
        lineFeatureDecoder.readActualHeader(lrw);

        while (lrw.hasNext()) {
            line = lrw.next();
            try {
                feat = decode(line);
                if (feat != null) {
                    featuresList.add(feat);
                }
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        final File outputVCF = executeTest("HCTestDanglingTailMergingForDeletions", spec).getFirst().get(0);

        // confirm that the call is the correct one
        final VCFCodec codec = new VCFCodec();
        final FileInputStream s = new FileInputStream(outputVCF);
        final LineIterator lineIterator = codec.makeSourceFromStream(new PositionalBufferedStream(s));
        codec.readHeader(lineIterator);
        final String line = lineIterator.next();
        Assert.assertFalse(line == null);
        final VariantContext vc = codec.decode(line);
        Assert.assertTrue(vc.isBiallelic());
        Assert.assertTrue(vc.getReference().basesMatch("ATGTATG"));
        Assert.assertTrue(vc.getAlternateAllele(0).basesMatch("A"));
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        final File outputVCFAnn = executeTest("testStrandBiasBySample re-annotation of FisherStrand", specAnn).getFirst().get(0);

        // confirm that the FisherStrand values are identical for the two pipelines
        final VCFCodec codec = new VCFCodec();
        final FileInputStream s = new FileInputStream(outputVCF);
        final LineIterator lineIterator = codec.makeSourceFromStream(new PositionalBufferedStream(s));
        codec.readHeader(lineIterator);

        final VCFCodec codecAnn = new VCFCodec();
        final FileInputStream sAnn = new FileInputStream(outputVCFAnn);
        final LineIterator lineIteratorAnn = codecAnn.makeSourceFromStream(new PositionalBufferedStream(sAnn));
        codecAnn.readHeader(lineIteratorAnn);

        while( lineIterator.hasNext() && lineIteratorAnn.hasNext() ) {
            final String line = lineIterator.next();
            Assert.assertFalse(line == null);
            final VariantContext vc = codec.decode(line);

            final String lineAnn = lineIteratorAnn.next();
            Assert.assertFalse(lineAnn == null);
            final VariantContext vcAnn = codecAnn.decode(lineAnn);

            Assert.assertTrue(vc.hasAttribute("FS"));
            Assert.assertTrue(vcAnn.hasAttribute("FS"));
            Assert.assertEquals(vc.getAttributeAsDouble("FS", 0.0), vcAnn.getAttributeAsDouble("FS", -1.0));
        }

        Assert.assertFalse(lineIterator.hasNext());
        Assert.assertFalse(lineIteratorAnn.hasNext());
    }
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        // confirm that the QD values are present in the new file for all biallelic variants
        // QD values won't be identical because some filtered reads are missing during re-annotation

        final VCFCodec codec = new VCFCodec();
        final FileInputStream s = new FileInputStream(outputVCF);
        final LineIterator lineIterator = codec.makeSourceFromStream(new PositionalBufferedStream(s));
        codec.readHeader(lineIterator);

        final VCFCodec codecAnn = new VCFCodec();
        final FileInputStream sAnn = new FileInputStream(outputVCFAnn);
        final LineIterator lineIteratorAnn = codecAnn.makeSourceFromStream(new PositionalBufferedStream(sAnn));
        codecAnn.readHeader(lineIteratorAnn);

        while( lineIterator.hasNext() && lineIteratorAnn.hasNext() ) {
            final String line = lineIterator.next();
            Assert.assertFalse(line == null);
            final VariantContext vc = codec.decode(line);

            final String lineAnn = lineIteratorAnn.next();
            Assert.assertFalse(lineAnn == null);
            final VariantContext vcAnn = codecAnn.decode(lineAnn);

      Assert.assertTrue(vc.hasAttribute("QD"));
      Assert.assertTrue(vcAnn.hasAttribute("QD"));
        }

        Assert.assertFalse(lineIterator.hasNext());
        Assert.assertFalse(lineIteratorAnn.hasNext());
    }
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        final File outputVCF = executeTest("testMultiAllelics", spec).getFirst().get(0);

        final VCFCodec codec = new VCFCodec();
        final FileInputStream originalStream = new FileInputStream(MultiAllelicsTest);
        final LineIterator originalLineIterator = codec.makeSourceFromStream(new PositionalBufferedStream(originalStream));
        codec.readHeader(originalLineIterator);
        int numOriginalRecords = 0;
        while ( originalLineIterator.hasNext() ) {
            originalLineIterator.next();
            numOriginalRecords++;
        }

        final FileInputStream newStream = new FileInputStream(outputVCF);
        final LineIterator newLineIterator = codec.makeSourceFromStream(new PositionalBufferedStream(newStream));
        codec.readHeader(newLineIterator);
        int numNewRecords = 0;
        while ( newLineIterator.hasNext() ) {
            newLineIterator.next();
            numNewRecords++;
        }

        Assert.assertTrue(numOriginalRecords > 0);
        Assert.assertEquals(numNewRecords, numOriginalRecords);
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     * be equal (i.e. they return the same object).
     */
    @Test
    public void testReadHeader() {
        RawHapMapCodec codec = new RawHapMapCodec();
        final LineIterator reader = getLineIterator();
        try {
            String header = reader.next();
            Assert.assertTrue(header.equals(codec.readActualHeader(getLineIterator())));
        } finally {
            codec.close(reader);
        }
    }
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    @Test
    public void testReadCorrectNumberOfRecords() {
        // setup the record for reading our 500 line file (499 records, 1 header line)
        RawHapMapCodec codec = new RawHapMapCodec();
        final LineIterator reader = getLineIterator();

        int count = 0;
        try {
            codec.readHeader(reader);
            while (reader.hasNext()) {
                codec.decode(reader.next());
                ++count;
            }
        } catch (IOException e) {
            Assert.fail("IOException " + e.getMessage());
        } finally {
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    @Test
    public void testGetSampleNames() {
        // setup the record for reading our 500 line file (499 records, 1 header line)
        RawHapMapCodec codec = new RawHapMapCodec();
        final LineIterator reader = getLineIterator();

        String line;
        try {
            codec.readHeader(reader);
            line = reader.next();
            RawHapMapFeature feature = (RawHapMapFeature) codec.decode(line);
            Assert.assertEquals(feature.getSampleIDs().length,87);

        } catch (IOException e) {
            Assert.fail("IOException " + e.getMessage());
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Related Classes of htsjdk.tribble.readers.LineIterator

  • org.broad.igv.cli_plugin.AsciiDecoder
  • org.broad.igv.dev.db.SQLCodecSource
  • org.broad.igv.feature.tribble.MUTCodec
  • org.broadinstitute.gatk.tools.walkers.annotator.VariantAnnotatorIntegrationTest
  • org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCallerIntegrationTest
  • org.broadinstitute.gatk.tools.walkers.phasing.PhaseByTransmissionIntegrationTest
  • org.broadinstitute.gatk.utils.codecs.hapmap.HapMapUnitTest
  • org.broadinstitute.gatk.utils.variant.GATKVCFUtils
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