Examples of SeekableFileStream

Examples of net.sf.samtools.util.SeekableFileStream

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    if (params.cramFile != null) {
      FileInputStream fis = new FileInputStream(params.cramFile);
      if (params.locations == null || params.locations.isEmpty())
        is = new BufferedInputStream(fis);
      else
        is = new SeekableFileStream(params.cramFile);
    } else
      is = System.in;

    if (params.decrypt) {
      CipherInputStream_256 cipherInputStream_256 = new CipherInputStream_256(
          is, pass, 128);
      is = cipherInputStream_256.getCipherInputStream();
      if (params.locations != null && !params.locations.isEmpty()) {
        is = new SeekableCipherStream_256(new SeekableFileStream(
            params.cramFile), pass, 1, 128);
      }
    }

    long offset = 0;
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Examples of net.sf.samtools.util.SeekableFileStream

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      return emptyIterator;

    SeekableStream s = null;
    if (file != null) {
      try {
        s = new SeekableFileStream(file);
      } catch (FileNotFoundException e) {
        throw new RuntimeException(e);
      }
    } else if (is instanceof SeekableStream)
      s = (SeekableStream) is;
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Examples of net.sf.samtools.util.SeekableFileStream

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    final long startOfLastLinearBin = getIndex().getStartOfLastLinearBin();

    SeekableStream s = null;
    if (file != null) {
      try {
        s = new SeekableFileStream(file);
      } catch (FileNotFoundException e) {
        throw new RuntimeException(e);
      }
    } else if (is instanceof SeekableStream)
      s = (SeekableStream) is;
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