Examples with BlockCompressedInputStream htsjdk.samtools.util.BlockCompressedInputStream used on opensource projects

Example 6 with BlockCompressedInputStream

use of htsjdk.samtools.util.BlockCompressedInputStream in project jvarkit by lindenb.

the class FindCorruptedFiles method testVcf.

private void testVcf(File f) {
    LOG.fine("Test VCF for " + f);
    Exception error1 = null;
    BlockCompressedInputStream in1 = null;
    try {
        in1 = new BlockCompressedInputStream(f);
        testVcf(f, in1);
    } catch (Exception err) {
        error1 = err;
    } finally {
        if (in1 != null)
            try {
                in1.close();
                in1 = null;
            } catch (IOException e) {
            }
    }
    if (error1 == null) {
        try {
            BlockCompressedInputStream.FileTermination type = BlockCompressedInputStream.checkTermination(f);
            if (type != BlockCompressedInputStream.FileTermination.HAS_TERMINATOR_BLOCK) {
                LOG.warning("bgz:" + type + " for " + f);
                stdout().println(f);
                return;
            }
        } catch (Exception err) {
            stdout().println(f);
            return;
        }
        // TEST BGZF termination
        return;
    }
    GZIPInputStream in2 = null;
    try {
        in2 = new GZIPInputStream(new FileInputStream(f));
        testVcf(f, in2);
        LOG.warning("gzip but not bgzip :" + f);
        return;
    } catch (Exception err) {
        err.printStackTrace();
    } finally {
        if (in2 != null)
            try {
                in2.close();
            } catch (IOException e) {
            }
    }
    LOG.fine("Not a BGZIP file / Error in VCF: " + f);
    stdout().println(f);
}