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jannovar-core is a library for the functional annotation of genomic variants

There is a newer version: 0.41

package de.charite.compbio.jannovar.datasource;

import org.ini4j.Profile.Section;

import com.google.common.collect.ImmutableList;

/**
 * {@link DataSource} implementation for data from UCSC.
 *
 * @author Manuel Holtgrewe
 */
final class UCSCDataSource extends DataSource {

	/** expected keys in data source configuration file */
	private final ImmutableList urlKeys = ImmutableList.of("knownCanonical", "knownGene", "knownGeneMrna",
			"kgXref", "knownToLocusLink", "chromInfo", "chrToAccessions");

	UCSCDataSource(DatasourceOptions options, Section iniSection) throws InvalidDataSourceException {
		super(options, iniSection);

		checkURLs();
	}

	@Override
	public JannovarDataFactory getDataFactory() {
		return new UCSCJannovarDataFactory(options, this, iniSection);
	}

	@Override
	protected ImmutableList getURLKeys() {
		return urlKeys;
	}
}