Examples of SeekableBufferedStream

htsjdk.samtools.seekablestream.SeekableBufferedStream
net.sf.samtools.util.SeekableBufferedStream
A wrapper class to provide buffered read access to a SeekableStream. Just wrapping such a stream with a BufferedInputStream will not work as it does not support seeking. In this implementation a seek call is delegated to the wrapped stream, and the buffer reset.

Examples of htsjdk.samtools.seekablestream.SeekableBufferedStream


    private void testReadsLength(int length) throws IOException {
        final int READ_SIZE=100000; //file is 10^6, so make this smaller to be safe.


        SeekableFileStream fileStream = new SeekableFileStream(InputFile);
        SeekableBufferedStream bufferedStream = new SeekableBufferedStream(fileStream, BUFFERED_STREAM_BUFFER_SIZE);


        for (int i = 0; i < READ_SIZE / length; ++i) {
            Assert.assertEquals(bufferedStream.read(buffer, 0, length), length);
        }


    }

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Examples of htsjdk.samtools.seekablestream.SeekableBufferedStream




    private void openIndexFile() {
        try {
            fileStream = new SeekableFileStream(mFile);
            bufferedStream = new SeekableBufferedStream(fileStream,BUFFERED_STREAM_BUFFER_SIZE);
            fileLength=bufferedStream.length();
        }
        catch (IOException exc) {
            throw new ReviewedGATKException("Unable to open index file (" + exc.getMessage() +")" + mFile, exc);
        }

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Examples of net.sf.samtools.util.SeekableBufferedStream

     * @param url         BAM.
     * @param indexFile   Location of index file, or null if indexed access not required.
     * @param eagerDecode eagerDecode if true, decode SAM record entirely when reading it.
     */
    public SAMFileReader(final URL url, final File indexFile, final boolean eagerDecode) {
        init(new SeekableBufferedStream(new SeekableHTTPStream(url)),
                indexFile, eagerDecode, defaultValidationStringency);
    }

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