Examples with LineIterator htsjdk.tribble.readers.LineIterator used on opensource projects

Example 1 with LineIterator

use of htsjdk.tribble.readers.LineIterator 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);
}

Example 2 with LineIterator

use of htsjdk.tribble.readers.LineIterator in project gatk by broadinstitute.

the class TableCodecUnitTest method testDecodeFailsNoHeader.

@Test(expectedExceptions = UserException.MalformedFile.class)
public void testDecodeFailsNoHeader() {
    TableCodec tc = new TableCodec();
    LineReader reader = makeReader(asList("1:1  1   2   3"));
    LineIterator li = new LineIteratorImpl(reader);
    tc.readActualHeader(li);
}

Example 3 with LineIterator

use of htsjdk.tribble.readers.LineIterator in project gatk by broadinstitute.

the class TableCodecUnitTest method testDecodeOnlyComments.

@Test
public void testDecodeOnlyComments() {
    TableCodec tc = new TableCodec();
    LineReader reader = makeReader(asList("#HEADER a b c", "#HEADER d e f"));
    LineIterator li = new LineIteratorImpl(reader);
    final List<String> strings = tc.readActualHeader(li);
    Assert.assertEquals(strings, emptyList());
}

Example 4 with LineIterator

use of htsjdk.tribble.readers.LineIterator in project gatk by broadinstitute.

the class LineIteratorReaderUnitTest method testRead.

@Test(dataProvider = "testParameter")
public void testRead(@SuppressWarnings("unused") final int textSize, @SuppressWarnings("unused") final int lineSize, final int bufferSize, final String text) {
    final LineIterator lineIterator = new TestLineIterator(text);
    final LineIteratorReader reader = new LineIteratorReader(lineIterator);
    final StringBuilder sb = new StringBuilder();
    final char[] buffer = new char[bufferSize];
    int readResult;
    while ((readResult = reader.read(buffer, 0, bufferSize)) >= 0) {
        sb.append(buffer, 0, readResult);
    }
    final String actualText = sb.toString();
    Assert.assertEquals(actualText, text);
}

Example 5 with LineIterator

use of htsjdk.tribble.readers.LineIterator in project gatk by broadinstitute.

the class TableCodecUnitTest method testTwoHeaders.

@Test
public void testTwoHeaders() {
    TableCodec tc = new TableCodec();
    LineReader reader = makeReader(asList("HEADER a b c", "HEADER d e f"));
    LineIterator li = new LineIteratorImpl(reader);
    final List<String> strings = tc.readActualHeader(li);
    Assert.assertEquals(strings, asList("HEADER", "a", "b", "c"));
}