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

            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 {

View Full Code Here

    }


    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) {

View Full Code Here

                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);

View Full Code Here


    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();

View Full Code Here

        //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){

View Full Code Here

TOP

Related Classes of org.broad.igv.util.stream.IGVSeekableBufferedStream

org.broad.igv.bbfile.BBFileReader

org.broad.igv.bbfile.BBZoomLevels

org.broad.igv.peaks.PeakParser

org.broad.igv.sam.reader.BAMHttpReader

java.io.IOException

All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.