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

Example 6 with LineIterator

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

the class TableCodecUnitTest method testDecodeHeader2.

@Test
public void testDecodeHeader2() {
    TableCodec tc = new TableCodec();
    final String str2 = "1:1  1   2   3";
    LineReader reader = makeReader(asList("HEADER a b c", str2));
    LineIterator li = new LineIteratorImpl(reader);
    List<String> hd = tc.readActualHeader(li);
    Assert.assertEquals(hd, asList("HEADER", "a", "b", "c"));
    final TableFeature decode = tc.decode(str2);
    Assert.assertEquals(decode.get("a"), "1");
    Assert.assertEquals(decode.get("b"), "2");
    Assert.assertEquals(decode.get("c"), "3");
    Assert.assertEquals(decode.getLocation().getContig(), "1");
    Assert.assertEquals(decode.getContig(), "1");
    Assert.assertEquals(decode.getLocation().getStart(), 1);
    Assert.assertEquals(decode.getLocation().getEnd(), 1);
}

Example 7 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 8 with LineIterator

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

the class GenomicsDBImportIntegrationTest method testPreserveContigOrderingInHeader.

@Test
public void testPreserveContigOrderingInHeader() throws IOException {
    final String workspace = createTempDir("testPreserveContigOrderingInHeader-").getAbsolutePath() + "/workspace";
    writeToGenomicsDB(Arrays.asList(GENOMICSDB_TEST_DIR + "testHeaderContigLineSorting1.g.vcf", GENOMICSDB_TEST_DIR + "testHeaderContigLineSorting2.g.vcf"), new SimpleInterval("chr20", 17959479, 17959479), workspace, 0, false, 0);
    try (final GenomicsDBFeatureReader<VariantContext, PositionalBufferedStream> genomicsDBFeatureReader = new GenomicsDBFeatureReader<>(new File(workspace, GenomicsDBConstants.DEFAULT_VIDMAP_FILE_NAME).getAbsolutePath(), new File(workspace, GenomicsDBConstants.DEFAULT_CALLSETMAP_FILE_NAME).getAbsolutePath(), workspace, GenomicsDBConstants.DEFAULT_ARRAY_NAME, b38_reference_20_21, null, new BCF2Codec());
        final AbstractFeatureReader<VariantContext, LineIterator> inputGVCFReader = AbstractFeatureReader.getFeatureReader(GENOMICSDB_TEST_DIR + "testHeaderContigLineSorting1.g.vcf", new VCFCodec(), true)) {
        final SAMSequenceDictionary dictionaryFromGenomicsDB = ((VCFHeader) genomicsDBFeatureReader.getHeader()).getSequenceDictionary();
        final SAMSequenceDictionary dictionaryFromInputGVCF = ((VCFHeader) inputGVCFReader.getHeader()).getSequenceDictionary();
        Assert.assertEquals(dictionaryFromGenomicsDB, dictionaryFromInputGVCF, "Sequence dictionary from GenomicsDB does not match original sequence dictionary from input GVCF");
    }
}

Example 9 with LineIterator

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

the class GenotypeGVCFsIntegrationTest method getVariantContexts.

/**
     * Returns a list of VariantContext records from a VCF file
     *
     * @param vcfFile VCF file
     * @return list of VariantContext records
     * @throws IOException if the file does not exist or can not be opened
     */
private static List<VariantContext> getVariantContexts(final File vcfFile) throws IOException {
    final VCFCodec codec = new VCFCodec();
    final FileInputStream s = new FileInputStream(vcfFile);
    final LineIterator lineIteratorVCF = codec.makeSourceFromStream(new PositionalBufferedStream(s));
    codec.readHeader(lineIteratorVCF);
    final List<VariantContext> VCs = new ArrayList<>();
    while (lineIteratorVCF.hasNext()) {
        final String line = lineIteratorVCF.next();
        Assert.assertFalse(line == null);
        VCs.add(codec.decode(line));
    }
    return VCs;
}

Example 10 with LineIterator

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

the class TableCodecUnitTest method testDecodeComment.

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