Examples of IGVSeekableBufferedStream

org.broad.igv.util.stream.IGVSeekableBufferedStream
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, we attempt to reuse the buffer if there is overlap between the newly requested range and where the buffer contains data for.

Examples of org.broad.igv.util.stream.IGVSeekableBufferedStream

            indexFile = getIndexFile(locator);
            if (indexFile == null) {
                throw new RuntimeException("Could not load index file for file: " + url.getPath());
            }


            SeekableStream ss = new IGVSeekableBufferedStream(IGVSeekableStreamFactory.getInstance().getStreamFor(url), 128000);
            //SeekableStream ss = getSeekableStream(url);
            log.debug("Initializing SAMFileReader");


            reader = new SAMFileReader(ss, indexFile, false);
        } else {

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Examples of org.broad.igv.util.stream.IGVSeekableBufferedStream

    }


    public CloseableIterator<PicardAlignment> query(String sequence, int start, int end, boolean contained) {
        try {
            if (reader == null) {
                SeekableStream ss = new IGVSeekableBufferedStream(IGVSeekableStreamFactory.getInstance().getStreamFor(url));
                reader = new SAMFileReader(ss, indexFile, false);
            }
            CloseableIterator<SAMRecord> iter = reader.query(sequence, start + 1, end, contained);
            return new WrappedIterator(iter);
        } catch (IOException e) {

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Examples of org.broad.igv.util.stream.IGVSeekableBufferedStream

                long contentLength = ss.length();
                if(contentLength > 0) {
                    bufferSize = (int) Math.min(contentLength, bufferSize);
                }


                IGVSeekableBufferedStream bufferedStream = new IGVSeekableBufferedStream(ss, bufferSize);
                bufferedStream.seek(chrPos);


                reader = new LittleEndianInputStream(bufferedStream);
                int nBytes = reader.readInt();


                byte[] compressedBytes = new byte[nBytes];
                bufferedStream.readFully(compressedBytes);


                byte[] bytes = compressionUtils.decompress(compressedBytes);


                ByteArrayInputStream bis = new ByteArrayInputStream(bytes);
                reader = new LittleEndianInputStream(bis);

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Examples of org.broad.igv.util.stream.IGVSeekableBufferedStream


    public BBFileReader(String path) throws IOException {


        log.debug("Opening BBFile source  " + path);


        fis = new IGVSeekableBufferedStream(IGVSeekableStreamFactory.getInstance().getStreamFor(path), 128000);


        // read in file header
        fileOffset = BBFILE_HEADER_OFFSET;
        fileHeader = new BBFileHeader(path, fis, fileOffset);
        //fileHeader.print();

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Examples of org.broad.igv.util.stream.IGVSeekableBufferedStream

        //this.fis = fis;
        zoomHeadersOffset = fileOffset;
        zoomLevelsCount = zoomLevels;


        // We don't know the exact size of the header fields, so use a buffered stream
        IGVSeekableBufferedStream fis = new IGVSeekableBufferedStream(is, 512000);
        
        // Note: a bad zoom header will result in a 0 count returned
        zoomHeadersRead =  readZoomHeaders(fis, zoomHeadersOffset, zoomLevels, isLowToHigh);


        if(zoomHeadersRead > 0){

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