Examples of VCFCodec

Examples of htsjdk.variant.vcf.VCFCodec

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    static AbstractFeatureReader<VariantContext, ?> bfr;

    @BeforeClass
    public static void setUpClass() throws IOException {
        File idxFile = new File(testFile + ".idx");
        FeatureCodec codec = new VCFCodec();
        createIndex(idxFile, codec);

        bfr = AbstractFeatureReader.getFeatureReader(testFile, codec);
    }
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Examples of htsjdk.variant.vcf.VCFCodec

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    }

    @Test
    public void testIntervalIndex40() throws Exception {
        String testFile = TestUtils.LARGE_DATA_DIR + "CEU.SRP000032.2010_03_v4.0.genotypes.head.vcf";
        FeatureCodec codec = new VCFCodec();
        tstIntervalIndex(testFile, codec);
    }
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Examples of htsjdk.variant.vcf.VCFCodec

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        if (fn.endsWith(".vcf3")) {
            return new VCFWrapperCodec(new VCF3Codec(), genome);
        }
        if (fn.endsWith(".vcf4")) {
            return new VCFWrapperCodec(new VCFCodec(), genome);
        } else if (fn.endsWith(".vcf")) {
            return new VCFWrapperCodec(getVCFCodec(locator), genome);
        } else if (fn.endsWith(".bcf")) {
            return new BCF2WrapperCodec(new BCF2Codec(), genome);
        } else if (fn.endsWith(".bed")) {
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Examples of htsjdk.variant.vcf.VCFCodec

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                    if (tmp.length > 1) {
                        String version = tmp[1].toLowerCase();
                        if (version.startsWith("vcfv3")) {
                            return new VCF3Codec();
                        } else {
                            return new VCFCodec();
                        }
                    }
                }
                lineCount++;
            }

        } catch (IOException e) {
            log.error("Error checking VCF Version");

        } finally {
            if (reader != null) try {
                reader.close();
            } catch (IOException e) {

            }
        }
        // Should never get here, but as a last resort assume this is a VCF 4.x file.
        return new VCFCodec();
    }
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Examples of htsjdk.variant.vcf.VCFCodec

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        String chr = "chr9";
        // Linear index
        TestUtils.createIndex(file);

        // First test query
        AbstractFeatureReader bfr = AbstractFeatureReader.getFeatureReader(file, new VCFCodec());
        Iterator<htsjdk.variant.variantcontext.VariantContext> iter = bfr.query(chr, 5073767 - 5, 5073767 + 5);
        int count = 0;
        while (iter.hasNext()) {
            htsjdk.variant.variantcontext.VariantContext feat = iter.next();
            assertEquals("chr9", feat.getChr());
            assertEquals(feat.getStart(), 5073767);
            assertTrue(feat.hasAttribute("MapQs"));
            count++;
        }
        assertEquals(1, count);

        // Test non-indexed access (iterator)
        iter = bfr.iterator();
        count = 0;
        while (iter.hasNext()) {
            htsjdk.variant.variantcontext.VariantContext feat = iter.next();
            assertEquals("chr9", feat.getChr());
            assertEquals(feat.getStart(), 5073767);
            assertTrue(feat.hasAttribute("MapQs"));
            count++;
        }
        assertEquals(1, count);

        //Do similar as above, but have a different test file
        file = TestUtils.DATA_DIR + "vcf/outputPileup.flt1.vcf";
        chr = "1";
        // Linear index
        TestUtils.createIndex(file);

        bfr = AbstractFeatureReader.getFeatureReader(file, new VCFCodec());
        iter = bfr.query(chr, 984163 - 5, 984163 + 5);
        count = 0;
        while (iter.hasNext()) {
            htsjdk.variant.variantcontext.VariantContext feat = iter.next();
            assertEquals(chr, feat.getChr());
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Examples of htsjdk.variant.vcf.VCFCodec

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                "##FORMAT=<ID=HQ, Number=2, Type=Integer, Description=\"Haplotype quality\">\n"+
                "##FORMAT=<ID=GQ, Number=1, Type=Integer, Description=\"Genotype quality\">\n"+
                "#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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Examples of htsjdk.variant.vcf.VCFCodec

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    @Test(enabled=true)
    public void testNRD_testNRS_testMargins() {
        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);
        int[][] table = metrics.getOverallGenotypeConcordance().getTable();
        // set up the table
        table[0] = new int[] {30, 12, 7, 5, 6, 0};
        table[1] = new int[] {10, 100, 5, 1, 7, 1};
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Examples of htsjdk.variant.vcf.VCFCodec

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        Assert.assertEquals(metrics.getOverallGenotypeConcordance().getnCompGenotypes(GenotypeType.HOM_VAR),EXPEC_COMP_VAR);
    }

    @Test(enabled=true)
    public void testRobustness() {
        VCFCodec codec = new VCFCodec();
        VCFHeader evalHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_3_HEADER_1))));
        VCFHeader disjointCompHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_3_HEADER_2))));
        VCFHeader overlapCompHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_3_HEADER_3))));
        ConcordanceMetrics disjointMetrics = new ConcordanceMetrics(evalHeader,disjointCompHeader,null);
        ConcordanceMetrics overlapMetrics = new ConcordanceMetrics(evalHeader,overlapCompHeader,null);

        // test what happens if you put in disjoint sets and start making requests
        Assert.assertEquals(0,disjointMetrics.getPerSampleGenotypeConcordance().size());
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Examples of htsjdk.variant.vcf.VCFCodec

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        return Arrays.asList(site1,site2,site3,site4,site5,site6,site7);
    }

    @Test(enabled = true)
    public void testSites() {
        VCFCodec codec = new VCFCodec();
        VCFHeader evalHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_2_HEADER))));
        VCFHeader compHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_2_HEADER))));
        ConcordanceMetrics metrics = new ConcordanceMetrics(evalHeader,compHeader,null);

        List<Pair<VariantContext,VariantContext>> data = getData7();

        int idx = 0;
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Examples of htsjdk.variant.vcf.VCFCodec

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        final String base = String.format("-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -R %s -I %s", REF, NA12878_BAM) + " --no_cmdline_in_header -o %s -L 20:10130740-10130800 --allowNonUniqueKmersInRef";
        final WalkerTestSpec spec = new WalkerTestSpec(base, 1, Arrays.asList(""));
        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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