org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationSpliceRegion Maven / Gradle / Ivy

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Variant annotation and effect prediction package.

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package org.snpeff.snpEffect.testCases.integration;

import java.util.List;
import java.util.Optional;

import org.junit.Test;
import org.snpeff.snpEffect.EffectType;
import org.snpeff.util.Gpr;
import org.snpeff.vcf.EffFormatVersion;
import org.snpeff.vcf.VcfEffect;
import org.snpeff.vcf.VcfEntry;

import junit.framework.Assert;

/**
 *
 * Test cases for variants
 *
 * @author pcingola
 */
public class TestCasesIntegrationSpliceRegion extends TestCasesIntegrationBase {

	public TestCasesIntegrationSpliceRegion() {
		super();
	}

	/**
	 * Splice region not found in some cases when there is an insertion 
	 */
	@Test
	public void test_01() {
		Gpr.debug("Test");
		String file = path("test.splice_region_01.vcf");
		String args[] = { "-canon" };
		int pos = 117174416;

		// Annotate
		List vcfEntries = snpEffect("testHg19Chr7", file, args, EffFormatVersion.FORMAT_ANN_1);
		if (verbose) vcfEntries.stream().forEach(v -> System.out.println("VcfEffect:" + v));

		// Get variant effects at desired position
		Optional oeff = vcfEntries.stream() //
				.filter(v -> v.getStart() == pos) //
				.flatMap(v -> v.getVcfEffects().stream()) //
				.findFirst();

		// Sanity check
		if (verbose) System.out.println("VcfEffect:" + oeff);
		Assert.assertNotNull("Could not find any variant effect at position " + pos, oeff.isPresent());

		// Get effects
		List effTypes = oeff.get().getEffectTypes();
		if (verbose) System.out.println("effTypes:" + effTypes);
		Assert.assertTrue("Effect type 'SPLICE_SITE_REGION' not found", effTypes.contains(EffectType.SPLICE_SITE_REGION));
	}

}