Package htsjdk.tribble.readers

Examples of htsjdk.tribble.readers.PositionalBufferedStream

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    //Quick method for checking if a bcf file has the magic header
    @Ignore
    //@Test
    public void rawTestFile() throws Exception {
        String path = "/path/to/myfile.bcf";
        PositionalBufferedStream ps = new PositionalBufferedStream(new FileInputStream(path));

        BCF2Codec codec = new BCF2Codec();
        codec.readHeader(ps);

    }
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    public void basicTestReadBinary() throws Exception {
        ResultSet rs = DBManagerTest.getAllFromSQLTable("sql/unigene.db", "unigene");
        SQLInputStream is = new SQLInputStream(rs, false, 1, 3);

        FeatureCodec featCodec = new ExampleBinaryCodec();
        PositionalBufferedStream pbs = new PositionalBufferedStream(is);
        int count = 0;
        while (!rs.isAfterLast()) {
            Feature feat = featCodec.decode(pbs);
            checkFeatureIntegrity(feat, "chr2");
            count++;
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        return path.endsWith(".bcf");
    }

    @Override
    public LocationAware makeIndexableSourceFromStream(final InputStream bufferedInputStream) {
        final PositionalBufferedStream pbs;
        if (bufferedInputStream instanceof PositionalBufferedStream) {
            pbs = (PositionalBufferedStream) bufferedInputStream;
        } else {
            pbs = new PositionalBufferedStream(bufferedInputStream);
        }
        return new AsciiLineReaderIterator(new AsciiLineReader(pbs));
    }
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        positionalBufferedStream.close();
    }

    @Override
    public PositionalBufferedStream makeSourceFromStream(final InputStream bufferedInputStream) {
        return new PositionalBufferedStream(bufferedInputStream);
    }
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        this.codec = codec;
    }

    @Override
    public Iterator<D> decodeAll(InputStream is, boolean strictParsing) throws IOException {
        PositionalBufferedStream pis = new PositionalBufferedStream(is);

        this.codec.readHeader(pis);

        List<D> features = new ArrayList<D>();
        while (!pis.isDone()) {
            try {
                D feature = this.codec.decode(pis);
                if (feature != null) {
                    features.add(feature);
                }
            } catch (Exception e) {
                log.error(e.getMessage(), e);
                if (strictParsing) {
                    throw new RuntimeException(e);
                }
            } finally {
                pis.close();
            }
        }
        return features.iterator();
    }
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                "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\n";

    private VCFHeader createHeader(String headerStr) {
        VCFCodec codec = new VCFCodec();
        VCFHeader head = null;
        head = (VCFHeader) codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(headerStr))));
        return head;
    }
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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());
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    public void testSimpleComparison() {
        Pair<VariantContext,VariantContext> data = getData1();
        VariantContext eval = data.getFirst();
        VariantContext truth = data.getSecond();
        VCFCodec codec = new VCFCodec();
        VCFHeader evalHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_1_HEADER))));
        VCFHeader compHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_1_HEADER))));
        ConcordanceMetrics metrics = new ConcordanceMetrics(evalHeader,compHeader,null);
        metrics.update(eval,truth);
        Assert.assertEquals(eval.getGenotype("test1_sample2").getType().ordinal(), 2);
        Assert.assertEquals(truth.getGenotype("test1_sample2").getType().ordinal(),1);
        Assert.assertEquals(metrics.getGenotypeConcordance("test1_sample2").getnMismatchingAlt(),0);
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    public void testMismatchingAlleleInAlleleSubset() {
        Pair<VariantContext,VariantContext> data = getData2();
        VariantContext eval = data.getFirst();
        VariantContext truth = data.getSecond();
        VCFCodec codec = new VCFCodec();
        VCFHeader evalHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_1_HEADER))));
        VCFHeader compHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_1_HEADER))));
        ConcordanceMetrics metrics = new ConcordanceMetrics(evalHeader,compHeader,null);
        metrics.update(eval,truth);
        Assert.assertEquals(eval.getGenotype("test1_sample2").getType().ordinal(), 2);
        Assert.assertEquals(truth.getGenotype("test1_sample2").getType().ordinal(),2);
        Assert.assertEquals(metrics.getGenotypeConcordance("test1_sample2").getnMismatchingAlt(),1);
        Assert.assertEquals(metrics.getGenotypeConcordance("test1_sample2").getTable()[2][1],0);
        Assert.assertEquals(metrics.getGenotypeConcordance("test1_sample3").getTable()[2][1],0);
        Assert.assertEquals(metrics.getGenotypeConcordance("test1_sample3").getTable()[2][3],1);
        Assert.assertEquals(metrics.getOverallGenotypeConcordance().getTable()[1][1],1);
        Assert.assertEquals(metrics.getOverallSiteConcordance().getSiteConcordance()[ConcordanceMetrics.SiteConcordanceType.EVAL_SUPERSET_TRUTH.ordinal()],1);
        Assert.assertEquals(metrics.getOverallSiteConcordance().getSiteConcordance()[ConcordanceMetrics.SiteConcordanceType.ALLELES_DO_NOT_MATCH.ordinal()],0);
        Assert.assertEquals(metrics.getOverallSiteConcordance().getSiteConcordance()[ConcordanceMetrics.SiteConcordanceType.ALLELES_MATCH.ordinal()],0);

        // now flip them around

        eval = data.getSecond();
        truth = data.getFirst();
        codec = new VCFCodec();
        evalHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_1_HEADER))));
        compHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_1_HEADER))));
        metrics = new ConcordanceMetrics(evalHeader,compHeader,null);
        metrics.update(eval,truth);
        Assert.assertEquals(eval.getGenotype("test1_sample2").getType().ordinal(), 2);
        Assert.assertEquals(truth.getGenotype("test1_sample2").getType().ordinal(),2);
        Assert.assertEquals(metrics.getGenotypeConcordance("test1_sample2").getnMismatchingAlt(),1);
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    public void testComplex() {
        Pair<VariantContext,VariantContext> data = getData3();
        VariantContext eval = data.getFirst();
        VariantContext truth = data.getSecond();
        VCFCodec codec = new VCFCodec();
        VCFHeader evalHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_1_HEADER))));
        VCFHeader compHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_1_HEADER))));
        ConcordanceMetrics metrics = new ConcordanceMetrics(evalHeader,compHeader,null);
        metrics.update(eval,truth);
        Assert.assertEquals(metrics.getGenotypeConcordance("test1_sample1").getnMismatchingAlt(),1);
        Assert.assertEquals(metrics.getGenotypeConcordance("test1_sample2").getTable()[2][1],0);
        Assert.assertEquals(metrics.getGenotypeConcordance("test1_sample2").getTable()[3][3],1);
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Related Classes of htsjdk.tribble.readers.PositionalBufferedStream

  • org.broad.igv.cli_plugin.FeatureCodecDecoder
  • org.broad.igv.dev.db.SQLInputStreamTest
  • org.broad.igv.feature.tribble.BCF2WrapperCodec
  • org.broad.igv.variant.vcf.BCFReaderTest
  • org.broadinstitute.gatk.tools.walkers.annotator.VariantAnnotatorIntegrationTest
  • org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCallerIntegrationTest
  • org.broadinstitute.gatk.tools.walkers.phasing.PhaseByTransmissionIntegrationTest
  • org.broadinstitute.gatk.tools.walkers.variantutils.CombineVariantsUnitTest
  • org.broadinstitute.gatk.tools.walkers.variantutils.ConcordanceMetricsUnitTest
  • org.broadinstitute.gatk.utils.codecs.hapmap.HapMapUnitTest
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