Package htsjdk.tribble.readers

Examples of htsjdk.tribble.readers.LineIteratorImpl

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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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    }


    public LineIterator getLineIterator() {
        try {
            return new LineIteratorImpl(LineReaderUtil.fromBufferedStream(new PositionalBufferedStream(new FileInputStream(hapMapFile))));
        } catch (FileNotFoundException e) {
            Assert.fail("Unable to open hapmap file : " + hapMapFile);
        }
        return null; // for intellij, it doesn't know that assert.fail is fatal
    }
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Related Classes of htsjdk.tribble.readers.LineIteratorImpl

  • org.broad.igv.cli_plugin.AsciiDecoder
  • org.broad.igv.dev.db.SQLCodecSource
  • org.broad.igv.feature.tribble.MUTCodec
  • org.broadinstitute.gatk.utils.codecs.hapmap.HapMapUnitTest
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