Package htsjdk.samtools.seekablestream

Examples of htsjdk.samtools.seekablestream.SeekableStream.seek()

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    private SAMFileReader getSAMFileReader(String samFile, long startPosition) {
        try {
            SeekableStream stream = IGVSeekableStreamFactory.getInstance().getStreamFor(samFile);
            if (startPosition >= 0) {
                stream.seek(startPosition);
            }
            SAMFileReader reader = new SAMFileReader(stream);
            reader.setValidationStringency(ValidationStringency.SILENT);

            //Need to keep the file source, if loading lazily
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                timeSignalsPath[t] = is.readString();
            }

            chrIndex = new HashMap<String, Long>();

            ss.seek(indexPosition);
            is = new LittleEndianInputStream(new BufferedInputStream(ss));
            int nChrs = is.readInt();
            for (int i = 0; i < nChrs; i++) {
                String chr = is.readString();
                long pos = is.readLong();
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        int startPosition = 500000;
        int length = 50000;

        byte[] buffer1 = new byte[length];
        SeekableStream unBufferedStream = new SeekableFileStream(BAM_FILE);
        unBufferedStream.seek(startPosition);
        int bytesRead = unBufferedStream.read(buffer1, 0, length);
        assertEquals(length, bytesRead);

        byte[] buffer2 = new byte[length];
        SeekableStream bufferedStream = new IGVSeekableBufferedStream(new SeekableHTTPStream(new URL(BAM_URL_STRING)));
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        int bytesRead = unBufferedStream.read(buffer1, 0, length);
        assertEquals(length, bytesRead);

        byte[] buffer2 = new byte[length];
        SeekableStream bufferedStream = new IGVSeekableBufferedStream(new SeekableHTTPStream(new URL(BAM_URL_STRING)));
        bufferedStream.seek(startPosition);
        bytesRead = bufferedStream.read(buffer2, 0, length);
        assertEquals(length, bytesRead);

        assertArraysEqual(buffer1, buffer2);
    }
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        int length = 1000;


        byte[] buffer = new byte[length];
        SeekableStream bufferedStream = new IGVSeekableBufferedStream(new SeekableHTTPStream(new URL(BAM_URL_STRING)));
        bufferedStream.seek(startPosition);
        int bytesRead = bufferedStream.read(buffer, 0, length);
        assertEquals(remainder, bytesRead);

        // Subsequent reads should return -1
        bytesRead = bufferedStream.read(buffer, 0, length);
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        SeekableStream ss = null;
        try {
            ss = IGVSeekableStreamFactory.getInstance().getStreamFor(path);
            int nBytes = (int) (posEnd - posStart);
            byte[] bytes = new byte[nBytes];
            ss.seek(posStart);
            ss.readFully(bytes);
            return bytes;
        } finally {
            if (ss != null) {
                ss.close();
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            is = IGVSeekableStreamFactory.getInstance().getStreamFor(seqFile);

            byte[] bytes = new byte[end - start];
            is.seek(start);
            is.read(bytes);
            return bytes;

        } catch (Exception ex) {
            log.error("Error reading genome sequence from: " + seqFile, ex);
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                            str = new IGVSeekableHTTPStream(url);
                            str.readFully(firstBytes);

                            int end = firstBytes.length;
                            int start = end - 100;
                            str.seek(start);
                            int len = end - start;
                            byte[] buffer = new byte[len];
                            int n = 0;
                            while (n < len) {
                                int count = str.read(buffer, n, len - n);
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        SeekableStream is = null;


        is = IGVSeekableStreamFactory.getInstance().getStreamFor(path);
        is.seek(startPosition);

        BufferedReader reader = new BufferedReader(new InputStreamReader(is), 256000);

        List<MultipleAlignmentBlock> alignments = new ArrayList<MultipleAlignmentBlock>();
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            // Get an estimate of the number of snps (rows).  THIS IS ONLY AN ESTIMATE
            int nRowsEst = chrSummary.getNDataPts();

            SeekableStream is = IGVSeekableStreamFactory.getInstance().getStreamFor(dataResourceLocator.getPath());
            is.seek(chrSummary.getStartPosition());
            AsciiLineReader reader = new AsciiLineReader(is);


            // Create containers to hold data
            IntArrayList startLocations = new IntArrayList(nRowsEst);
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