Package htsjdk.samtools.seekablestream

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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    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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