Package net.sf.samtools.util

Examples of net.sf.samtools.util.BufferedLineReader

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    /**
     * Prepare to read a SAM text file.
     * @param stream Need not be buffered, as this class provides buffered reading.
     */
    SAMTextReader2(final InputStream stream, final SAMFileReader.ValidationStringency validationStringency, final SAMRecordFactory factory, SAMFileHeader header) {
        mReader = new BufferedLineReader(stream);
        this.validationStringency = validationStringency;
        this.samRecordFactory = factory;
        this.mFileHeader = header;
        advanceLine();
//        readHeader();
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    DataInputStream dis = new DataInputStream(is);
    byte[] bytes = new byte[size];
    dis.readFully(bytes);

    BufferedLineReader r = new BufferedLineReader(new ByteArrayInputStream(
        bytes));
    return new SAMTextHeaderCodec().decode(r, id);
  }
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Related Classes of net.sf.samtools.util.BufferedLineReader

  • net.sf.cram.ReadWrite
  • net.sf.samtools.SAMTextReader2
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