Package htsjdk.samtools.seekablestream

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

252
253
254
255
256
257
258
259
260
261
262
        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)));
View Full Code Here
32
33
34
35
36
37
38
39
40
41
42
    @Test
    public void testSeek() throws Exception {
        String expectedLine = "chr22\t14000000\t15000000\trecombRate\t0.182272\t0.20444\t0.160104\t0\t0\t0\t0\t0\t0";
        File testFile = new File(TestUtils.DATA_DIR + "igv/recombRate.igv.txt");
        SeekableFileStream is = new SeekableFileStream(testFile);
        is.seek(149247);
        AsciiLineReader reader = new AsciiLineReader(is);
        String nextLine = reader.readLine();
        assertEquals(expectedLine, nextLine);
    }
}
View Full Code Here
TOP
Copyright © 2018 www.massapi.com. All rights reserved.
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.