Package htsjdk.tribble

Examples of htsjdk.tribble.AbstractFeatureReader

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                "Hs.594545", "LONG_FEATURE"));

        // Interval index
        TestUtils.createIndex(bedFile, IgvTools.LINEAR_INDEX, 500);

        AbstractFeatureReader bfr = AbstractFeatureReader.getFeatureReader(bedFile, new IGVBEDCodec());
        Iterator<BasicFeature> iter = bfr.query(chr, start, end);
        int countInterval = 0;
        while (iter.hasNext()) {
            BasicFeature feature = iter.next();
            Assert.assertTrue(feature.getEnd() >= start && feature.getStart() <= end);
            Assert.assertTrue(expectedNames.contains(feature.getName()));
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                "Hs.594545", "LONG_FEATURE"));

        // Interval index
        TestUtils.createIndex(bedFile, IgvTools.INTERVAL_INDEX, 1);

        AbstractFeatureReader bfr = AbstractFeatureReader.getFeatureReader(bedFile, new IGVBEDCodec());
        Iterator<BasicFeature> iter = bfr.query(chr, start, end);
        int countInterval = 0;
        while (iter.hasNext()) {
            BasicFeature feature = iter.next();
            Assert.assertTrue(feature.getEnd() >= start && feature.getStart() <= end);
            Assert.assertTrue(expectedNames.contains(feature.getName()));
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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());
            if (count == 0) {
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        convert(args[0], args[1]);
    }

    public static void convert(String vcfFile, String bedFile) throws IOException {

        AbstractFeatureReader basicReader = null;
        PrintWriter writer = null;
        try {
            writer = new PrintWriter(new BufferedWriter(new FileWriter(bedFile)));
            Genome genome = null; // Don't do alias converting
            FeatureCodec codec = CodecFactory.getCodec(vcfFile, genome);
            boolean isVCF = codec.getClass().isAssignableFrom(VCFCodec.class);
            basicReader = AbstractFeatureReader.getFeatureReader(vcfFile, codec, true);

            Iterator<VariantContext> iter = basicReader.iterator();

            while (iter.hasNext()) {

                VariantContext vc = iter.next();
                String chr = vc.getChr();
                if (!chr.startsWith("chr")) {
                    chr = "chr" + chr;
                }

                int start = vc.getStart() - 1;
                int end = vc.getEnd();
                String id = vc.getID();
                if(id == null) {
                    id = ".";
                }
                String af = vc.getAttributeAsString("AF", "");

                writer.println(chr + "\t" + start + "\t" + end + "\t" + id + "\t" + af);

            }
        }
        finally {
            if (basicReader != null)
                basicReader.close();
            if (writer != null)
                writer.close();
        }

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    private Pair<AbstractFeatureReader, SAMSequenceDictionary> getFeatureSource(FeatureManager.FeatureDescriptor descriptor,
                                                                        String name,
                                                                        File inputFile,
                                                                        RMDStorageType storageType) {
        // Feature source and sequence dictionary to use as the ultimate reference
        AbstractFeatureReader featureSource = null;
        SAMSequenceDictionary sequenceDictionary = null;

        // Detect whether or not this source should be indexed.
        boolean canBeIndexed = (storageType == RMDStorageType.FILE);
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Related Classes of htsjdk.tribble.AbstractFeatureReader

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  • org.broad.igv.data.GenomeSummaryDataTest
  • org.broad.igv.dev.db.SQLCodecSourceTest
  • org.broad.igv.feature.FeatureUtilsTest
  • org.broad.igv.feature.JunctionsBedTest
  • org.broad.igv.feature.tribble.TribbleIndexTest
  • org.broad.igv.tools.IGVToolsTest
  • org.broad.igv.tools.parsers.TestBEDCodecs
  • org.broad.igv.track.TrackMenuUtilsTest
  • org.broad.igv.variant.util.VCFtoBed
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