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Variant annotation and effect prediction package.
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package org.snpeff.snpEffect.testCases.unity;

import org.junit.Test;
import org.snpeff.align.VariantRealign;
import org.snpeff.binseq.GenomicSequences;
import org.snpeff.interval.Genome;
import org.snpeff.interval.Variant;
import org.snpeff.util.Gpr;

import junit.framework.Assert;

/**
 *
 * Test cases for variant realignment
 */
public class TestCasesVariantRealignment extends TestCasesBase {

	public TestCasesVariantRealignment() {
		super();
	}

	void checkRealign(String chrName, String chrSequence, int pos, String ref, String alt, String expectedVariantRealign) {
		// Create genome & chromosome
		Genome genome = new Genome("zzz");
		genome.getOrCreateChromosome(chrName).setSequence(chrSequence);

		// Create genomicSequences
		GenomicSequences gs = genome.getGenomicSequences();
		gs.addChromosomeSequence(chrName, chrSequence);
		gs.build();

		// Create variant
		Variant variant = new Variant(genome.getOrCreateChromosome(chrName), pos, ref, alt);

		// Realign variant
		VariantRealign vr = new VariantRealign(variant);
		vr.realign();
		if (verbose) Gpr.debug("Realigned variant: " + vr);

		// Check results
		Assert.assertEquals(expectedVariantRealign, vr.getVariantRealigned().toString());
	}

	@Override
	protected void init() {
		super.init();
		minExons = 2;
		randSeed = 20141128;
		initRand();
	}

	/**
	 * Shift by one position
	 */
	@Test
	public void test_01() {
		Gpr.debug("Test");

		// Change exon's sequence
		if (verbose) Gpr.debug(transcript);

		// Create variant
		Variant variant = new Variant(chromosome, 754, "", "T", "");
		if (verbose) Gpr.debug("Variant: " + variant);

		// Shift variant
		if (verbose) Gpr.debug("Variant (before): " + variant);
		Variant variantShifted = variant.realignLeft();
		if (verbose) Gpr.debug("Variant (after): " + variantShifted);

		// Check that shifted variant is oK
		Assert.assertFalse(variant == variantShifted);
		Assert.assertEquals(756, variantShifted.getStart());
		Assert.assertEquals("", variantShifted.getReference());
		Assert.assertEquals("T", variantShifted.getAlt());
	}

	/**
	 * No shift
	 */
	@Test
	public void test_02() {
		Gpr.debug("Test");

		// Change exon's sequence
		if (verbose) Gpr.debug(transcript);

		// Create variant
		Variant variant = new Variant(chromosome, 754, "", "A", "");
		if (verbose) Gpr.debug("Variant: " + variant);

		// Shift variant
		if (verbose) Gpr.debug("Variant (before): " + variant);
		Variant variantShifted = variant.realignLeft();
		if (verbose) Gpr.debug("Variant (after): " + variantShifted);

		// Check that shifted variant is the same object
		Assert.assertTrue(variant == variantShifted);
	}

	/**
	 * Shift by one position
	 */
	@Test
	public void test_03() {
		Gpr.debug("Test");

		// Change exon's sequence
		if (verbose) Gpr.debug(transcript);

		// Create variant
		Variant variant = new Variant(chromosome, 1025, "", "G", "");
		if (verbose) Gpr.debug("Variant: " + variant);

		// Shift variant
		if (verbose) Gpr.debug("Variant (before): " + variant);
		Variant variantShifted = variant.realignLeft();
		if (verbose) Gpr.debug("Variant (after): " + variantShifted);

		// Check that shifted variant is oK
		Assert.assertFalse(variant == variantShifted);
		Assert.assertEquals(1030, variantShifted.getStart());
		Assert.assertEquals("", variantShifted.getReference());
		Assert.assertEquals("G", variantShifted.getAlt());
	}

	/**
	 * Shift by one position in an intron
	 */
	@Test
	public void test_04_Intron() {
		Gpr.debug("Test");

		// Change exon's sequence
		if (verbose) Gpr.debug(transcript);

		// Create variant
		Variant variant = new Variant(chromosome, 920, "", "C", "");
		if (verbose) Gpr.debug("Variant: " + variant);

		// Shift variant
		if (verbose) Gpr.debug("Variant (before): " + variant);
		Variant variantShifted = variant.realignLeft();
		if (verbose) Gpr.debug("Variant (after): " + variantShifted);

		// Check that shifted variant is oK
		Assert.assertFalse(variant == variantShifted);
		Assert.assertEquals(925, variantShifted.getStart());
	}

	/**
	 * Test case from Savant's poster
	 * http://www.well.ox.ac.uk/savant
	 * (Marton Munz, Elise Ruark, Nazneen Rahman, Gerton Lunter)
	 */
	@Test
	public void test_05_savant() {
		Gpr.debug("Test");
		String seqRef = "AAACTGTATTT";
		String seqAlt = "AAACTATTT";

		VariantRealign vr = new VariantRealign();
		vr.setSequenceRef(seqRef);
		vr.setSequenceAlt(seqAlt);
		vr.realignSeqs();
		if (verbose) Gpr.debug(vr);

		// Check resutls
		Assert.assertEquals("GT", vr.getRefRealign());
		Assert.assertEquals("", vr.getAltRealign());
	}

	@Test
	public void test_05_savant_opposite() {
		Gpr.debug("Test");
		String seqRef = "AAACTATTT";
		String seqAlt = "AAACTGTATTT";

		VariantRealign vr = new VariantRealign();
		vr.setSequenceRef(seqRef);
		vr.setSequenceAlt(seqAlt);
		vr.realignSeqs();
		if (verbose) Gpr.debug(vr);

		// Check resutls
		Assert.assertEquals("", vr.getRefRealign());
		Assert.assertEquals("GT", vr.getAltRealign());
	}

	/**
	 * Same as test Savant's test case, but using variant and GenomicSequences
	 */
	@Test
	public void test_06_savant() {
		Gpr.debug("Test");
		checkRealign("1", "AAACTGTATTT", 4, "TG", "", "chr1:5_GT/");
	}

	/**
	 * Another test case fmor Savant's poster
	 */
	@Test
	public void test_07_savant() {
		Gpr.debug("Test");
		checkRealign("1", "TATGTTTAGGTTTATTGCATTCT", 8, "", "GGG", "chr1:10_/GGG");
	}

	/**
	 * This test should trigger progressive realignment. I.e. requiring more
	 * bases to the right in order to make a good alignment.
	 */
	@Test
	public void test_08_reallyLongRealign() {
		Gpr.debug("Test");
		checkRealign("1", "tatgaccagcagcagcagcagcagcagcagcagcagcagcagcagcaagcccttcagag", 6, "CAG", "", "chr1:44_GCA/");
	}

	/**
	 * This test should trigger (AND fail) to make a progressive realignment.
	 * I.e. requiring more bases to the right in order to make a good
	 * alignment, but there are no more bases available from GenomicSequences.
	 */
	@Test
	public void test_09_reallyLongRealign() {
		Gpr.debug("Test");
		checkRealign("1", "tatgaccagcagcagcagcagcagcagcagcagcag", 6, "CAG", "", "chr1:33_CAG/");
	}

}