Examples with SeekableByteChannel java.nio.channels.SeekableByteChannel used on opensource projects

Example 16 with SeekableByteChannel

use of java.nio.channels.SeekableByteChannel in project gatk by broadinstitute.

the class SeekableByteChannelPrefetcherTest method testPartialBuffers.

@Test
public void testPartialBuffers() throws Exception {
    SeekableByteChannel chan1 = Files.newByteChannel(Paths.get(input));
    SeekableByteChannel chan2 = new SeekableByteChannelPrefetcher(Files.newByteChannel(Paths.get(input)), 1024);
    // get a partial buffer
    testSeeking(chan1, chan2, (int) chan1.size() - 127);
    // make sure normal reads can use the full buffer
    for (int i = 0; i < 2; i++) {
        testSeeking(chan1, chan2, i * 1024);
    }
    // get a partial buffer, replacing one of the full ones
    testSeeking(chan1, chan2, (int) chan1.size() - 127);
    // make sure the buffers are still OK
    for (int i = 0; i < 2; i++) {
        testSeeking(chan1, chan2, i * 1024);
    }
}

Example 17 with SeekableByteChannel

use of java.nio.channels.SeekableByteChannel in project gatk by broadinstitute.

the class SeekableByteChannelPrefetcherTest method testDoubleWrapping.

@Test(expectedExceptions = IllegalArgumentException.class)
public void testDoubleWrapping() throws Exception {
    SeekableByteChannel chan1 = new SeekableByteChannelPrefetcher(Files.newByteChannel(Paths.get(input)), 1024);
    new SeekableByteChannelPrefetcher(chan1, 1024);
}

Example 18 with SeekableByteChannel

use of java.nio.channels.SeekableByteChannel in project gatk by broadinstitute.

the class SeekableByteChannelPrefetcherTest method testEOF.

@Test
public void testEOF() throws Exception {
    SeekableByteChannel chan1 = Files.newByteChannel(Paths.get(input));
    SeekableByteChannel chan2 = new SeekableByteChannelPrefetcher(Files.newByteChannel(Paths.get(input)), 1024);
    // read the final 128 bytes, exactly.
    testSeeking(chan1, chan2, (int) chan1.size() - 128);
    // read truncated because we're asking for beyond EOF
    testSeeking(chan1, chan2, (int) chan1.size() - 64);
    // read starting past EOF
    testSeeking(chan1, chan2, (int) chan1.size() + 128);
    // read more than a whole block past EOF
    testSeeking(chan1, chan2, (int) chan1.size() + 1024 * 2);
}

Example 19 with SeekableByteChannel

use of java.nio.channels.SeekableByteChannel in project gatk by broadinstitute.

the class SeekableByteChannelPrefetcherTest method testSeek.

@Test
public void testSeek() throws Exception {
    SeekableByteChannel chan1 = Files.newByteChannel(Paths.get(input));
    SeekableByteChannel chan2 = new SeekableByteChannelPrefetcher(Files.newByteChannel(Paths.get(input)), 1024);
    testSeeking(chan1, chan2, 1024);
    testSeeking(chan1, chan2, 1500);
    testSeeking(chan1, chan2, 128);
    testSeeking(chan1, chan2, 256);
    testSeeking(chan1, chan2, 128);
    // yes, testReading - let's make sure that reading more than one block still works
    // even after a seek.
    testReading(chan1, chan2, 1500);
    testSeeking(chan1, chan2, 2048);
    testSeeking(chan1, chan2, 0);
    testSeeking(chan1, chan2, 3000);
    testSeeking(chan1, chan2, 6000);
    testSeeking(chan1, chan2, (int) chan1.size() - 127);
    testSeeking(chan1, chan2, (int) chan1.size() - 128);
    testSeeking(chan1, chan2, (int) chan1.size() - 129);
}

Example 20 with SeekableByteChannel

use of java.nio.channels.SeekableByteChannel in project gatk by broadinstitute.

the class GenomicsDBImport method getReaderFromVCFUri.

/**
     * Creates a feature reader object from a given VCF URI (can also be
     * a local file path) and returns it
     * @param variantPath  URI or file path
     * @return  Feature reader
     */
private AbstractFeatureReader<VariantContext, LineIterator> getReaderFromVCFUri(final String variantPath) {
    final String variantURI = IOUtils.getPath(variantPath).toAbsolutePath().toUri().toString();
    final Function<SeekableByteChannel, SeekableByteChannel> cloudWrapper = (cloudPrefetchBuffer > 0 ? is -> SeekableByteChannelPrefetcher.addPrefetcher(cloudPrefetchBuffer, is) : Function.identity());
    final Function<SeekableByteChannel, SeekableByteChannel> cloudIndexWrapper = (cloudIndexPrefetchBuffer > 0 ? is -> SeekableByteChannelPrefetcher.addPrefetcher(cloudIndexPrefetchBuffer, is) : Function.identity());
    return AbstractFeatureReader.getFeatureReader(variantURI, null, new VCFCodec(), true, cloudWrapper, cloudIndexWrapper);
}