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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.interval.Variant;
import org.snpeff.util.Gpr;

/**
 * Test cases: apply a variant (MIXED) to a transcript
 *
 */
public class TestCasesApplyMixed extends TestCasesBaseApply {

	public TestCasesApplyMixed() {
		super();
	}

	/**
	 * Variant before exon
	 */
	@Test
	public void test_apply_variant_01_shorter() {
		Gpr.debug("Test");
		Variant variant = new Variant(transcript.getParent(), 290, "TTTATC", "ACG");
		checkApplyMixed(variant, transcript.cds(), transcript.protein(), 1, 297, 396);
	}

	/**
	 * Variant before exon
	 */
	@Test
	public void test_apply_variant_01_longer() {
		Gpr.debug("Test");
		Variant variant = new Variant(transcript.getParent(), 290, "TTT", "GCATTA");
		checkApplyMixed(variant, transcript.cds(), transcript.protein(), 1, 303, 402);
	}

	/**
	 * Variant before exon
	 */
	@Test
	public void test_apply_variant_02_shorter() {
		Gpr.debug("Test");

		Variant variant = new Variant(transcript.getParent(), 294, "TCGTC", "CG");
		checkApplyMixed(variant, transcript.cds(), transcript.protein(), 1, 297, 396);
	}

	/**
	 * Variant before exon
	 */
	@Test
	public void test_apply_variant_02_longer() {
		Gpr.debug("Test");

		Variant variant = new Variant(transcript.getParent(), 294, "TCG", "AGGACG");
		checkApplyMixed(variant, transcript.cds(), transcript.protein(), 1, 303, 402);
	}

	/**
	 * Variant overlapping exon start
	 */
	@Test
	public void test_apply_variant_03_shorter() {
		Gpr.debug("Test");

		Variant variant = new Variant(transcript.getParent(), 298, "CCTGTT", "ACG");

		String expectedCds = "atgtccgcaggtgaaggcatacacgctgcgcgtatactgatgttacctcgatggattttgtcagaaatatggtgcccaggacgcgaagggcatattatgg" // Exon[0]
				+ "Gtgggaattcacgggcacggttctgcagcaagctgaattggcagctcggcataaatcccgaccccatcgtcacgcacggatcaattcatcctcaacg".toLowerCase() // Exon[1]
				+ "ggtagaggaaaagcacctaacccccattgagcaggatctctttcgtaatactctgtatcgattaccgatttatttgattccccacatttatttcatcggg" // Exon[2]
				;

		checkApplyMixed(variant, expectedCds, null, 1, 300, 396);
	}

	/**
	 * Variant overlapping exon start
	 */
	@Test
	public void test_apply_variant_03_longer() {
		Gpr.debug("Test");

		Variant variant = new Variant(transcript.getParent(), 298, "CCT", "ACGCAA");

		String expectedCds = "atgtccgcaggtgaaggcatacacgctgcgcgtatactgatgttacctcgatggattttgtcagaaatatggtgcccaggacgcgaagggcatattatgg" // Exon[0]
				+ "GCAAgtttgggaattcacgggcacggttctgcagcaagctgaattggcagctcggcataaatcccgaccccatcgtcacgcacggatcaattcatcctcaacg".toLowerCase() // Exon[1]
				+ "ggtagaggaaaagcacctaacccccattgagcaggatctctttcgtaatactctgtatcgattaccgatttatttgattccccacatttatttcatcggg" // Exon[2]
				;

		checkApplyMixed(variant, expectedCds, null, 1, 300, 402);
	}

	/**
	 * Variant at exon start
	 */
	@Test
	public void test_apply_variant_04_shorter() {
		Gpr.debug("Test");

		Variant variant = new Variant(transcript.getParent(), 300, "TGTTTG", "ACG");

		String expectedCds = "atgtccgcaggtgaaggcatacacgctgcgcgtatactgatgttacctcgatggattttgtcagaaatatggtgcccaggacgcgaagggcatattatgg" // Exon[0]
				+ "ACGggaattcacgggcacggttctgcagcaagctgaattggcagctcggcataaatcccgaccccatcgtcacgcacggatcaattcatcctcaacg".toLowerCase() // Exon[1]
				+ "ggtagaggaaaagcacctaacccccattgagcaggatctctttcgtaatactctgtatcgattaccgatttatttgattccccacatttatttcatcggg" // Exon[2]
				;

		checkApplyMixed(variant, expectedCds, null, 1, 300, 396);

	}

	/**
	 * Variant at exon start
	 */
	@Test
	public void test_apply_variant_04_longer() {
		Gpr.debug("Test");

		Variant variant = new Variant(transcript.getParent(), 300, "TGT", "ACGAAC");

		String expectedCds = "atgtccgcaggtgaaggcatacacgctgcgcgtatactgatgttacctcgatggattttgtcagaaatatggtgcccaggacgcgaagggcatattatgg" // Exon[0]
				+ "ACGAACttgggaattcacgggcacggttctgcagcaagctgaattggcagctcggcataaatcccgaccccatcgtcacgcacggatcaattcatcctcaacg".toLowerCase() // Exon[1]
				+ "ggtagaggaaaagcacctaacccccattgagcaggatctctttcgtaatactctgtatcgattaccgatttatttgattccccacatttatttcatcggg" // Exon[2]
				;

		checkApplyMixed(variant, expectedCds, null, 1, 300, 402);

	}

	/**
	 * Variant in exon
	 */
	@Test
	public void test_apply_variant_05_shorter() {
		Gpr.debug("Test");

		Variant variant = new Variant(transcript.getParent(), 310, "TTCACG", "ACT");

		String expectedCds = "atgtccgcaggtgaaggcatacacgctgcgcgtatactgatgttacctcgatggattttgtcagaaatatggtgcccaggacgcgaagggcatattatgg" // Exon[0]
				+ "tgtttgggaaACTggcacggttctgcagcaagctgaattggcagctcggcataaatcccgaccccatcgtcacgcacggatcaattcatcctcaacg".toLowerCase() // Exon[1]
				+ "ggtagaggaaaagcacctaacccccattgagcaggatctctttcgtaatactctgtatcgattaccgatttatttgattccccacatttatttcatcggg" // Exon[2]
				;

		checkApplyMixed(variant, expectedCds, null, 1, 300, 396);
	}

	/**
	 * Variant in exon
	 */
	@Test
	public void test_apply_variant_05_longer() {
		Gpr.debug("Test");

		Variant variant = new Variant(transcript.getParent(), 310, "TTC", "ACTACG");

		String expectedCds = "atgtccgcaggtgaaggcatacacgctgcgcgtatactgatgttacctcgatggattttgtcagaaatatggtgcccaggacgcgaagggcatattatgg" // Exon[0]
				+ "tgtttgggaaACTACGacgggcacggttctgcagcaagctgaattggcagctcggcataaatcccgaccccatcgtcacgcacggatcaattcatcctcaacg".toLowerCase() // Exon[1]
				+ "ggtagaggaaaagcacctaacccccattgagcaggatctctttcgtaatactctgtatcgattaccgatttatttgattccccacatttatttcatcggg" // Exon[2]
				;

		checkApplyMixed(variant, expectedCds, null, 1, 300, 402);

	}

	/**
	 * Variant in exon
	 */
	@Test
	public void test_apply_variant_06_shorter() {
		Gpr.debug("Test");

		Variant variant = new Variant(transcript.getParent(), 394, "TCAACG", "GAC");

		String expectedCds = "atgtccgcaggtgaaggcatacacgctgcgcgtatactgatgttacctcgatggattttgtcagaaatatggtgcccaggacgcgaagggcatattatgg" // Exon[0]
				+ "tgtttgggaattcacgggcacggttctgcagcaagctgaattggcagctcggcataaatcccgaccccatcgtcacgcacggatcaattcatccGAC".toLowerCase() // Exon[1]
				+ "ggtagaggaaaagcacctaacccccattgagcaggatctctttcgtaatactctgtatcgattaccgatttatttgattccccacatttatttcatcggg" // Exon[2]
				;

		checkApplyMixed(variant, expectedCds, null, 1, 300, 396);
	}

	/**
	 * Variant in exon
	 */
	@Test
	public void test_apply_variant_06_longer() {
		Gpr.debug("Test");

		Variant variant = new Variant(transcript.getParent(), 397, "ACG", "GACAGT");

		String expectedCds = "atgtccgcaggtgaaggcatacacgctgcgcgtatactgatgttacctcgatggattttgtcagaaatatggtgcccaggacgcgaagggcatattatgg" // Exon[0]
				+ "tgtttgggaattcacgggcacggttctgcagcaagctgaattggcagctcggcataaatcccgaccccatcgtcacgcacggatcaattcatcctcaGAC".toLowerCase() // Exon[1]
				+ "ggtagaggaaaagcacctaacccccattgagcaggatctctttcgtaatactctgtatcgattaccgatttatttgattccccacatttatttcatcggg" // Exon[2]
				;

		checkApplyMixed(variant, expectedCds, null, 1, 300, 399);
	}

	/**
	 * Variant overlapping exon end
	 */
	@Test
	public void test_apply_variant_07_shorter() {
		Gpr.debug("Test");

		Variant variant = new Variant(transcript.getParent(), 397, "ACGAAA", "TGC");

		String expectedCds = "atgtccgcaggtgaaggcatacacgctgcgcgtatactgatgttacctcgatggattttgtcagaaatatggtgcccaggacgcgaagggcatattatgg" // Exon[0]
				+ "tgtttgggaattcacgggcacggttctgcagcaagctgaattggcagctcggcataaatcccgaccccatcgtcacgcacggatcaattcatcctcaTGC".toLowerCase() // Exon[1]
				+ "ggtagaggaaaagcacctaacccccattgagcaggatctctttcgtaatactctgtatcgattaccgatttatttgattccccacatttatttcatcggg" // Exon[2]
				;

		checkApplyMixed(variant, expectedCds, null, 1, 300, 399);
	}

	/**
	 * Variant overlapping exon end
	 */
	@Test
	public void test_apply_variant_07_longer() {
		Gpr.debug("Test");

		Variant variant = new Variant(transcript.getParent(), 397, "ACG", "TGCATG");

		String expectedCds = "atgtccgcaggtgaaggcatacacgctgcgcgtatactgatgttacctcgatggattttgtcagaaatatggtgcccaggacgcgaagggcatattatgg" // Exon[0]
				+ "tgtttgggaattcacgggcacggttctgcagcaagctgaattggcagctcggcataaatcccgaccccatcgtcacgcacggatcaattcatcctcaTGC".toLowerCase() // Exon[1]
				+ "ggtagaggaaaagcacctaacccccattgagcaggatctctttcgtaatactctgtatcgattaccgatttatttgattccccacatttatttcatcggg" // Exon[2]
				;

		checkApplyMixed(variant, expectedCds, null, 1, 300, 399);
	}

	/**
	 * Variant right after exon end
	 */
	@Test
	public void test_apply_variant_08_shorter() {
		Gpr.debug("Test");

		Variant variant = new Variant(transcript.getParent(), 400, "AAAGGG", "CAT");
		checkApplyMixed(variant, transcript.cds(), transcript.protein(), 1, 300, 399);
	}

	/**
	 * Variant right after exon end
	 */
	@Test
	public void test_apply_variant_08_longer() {
		Gpr.debug("Test");

		Variant variant = new Variant(transcript.getParent(), 400, "AAA", "CATTGC");
		checkApplyMixed(variant, transcript.cds(), transcript.protein(), 1, 300, 399);
	}

	/**
	 * Variant after exon end
	 */
	@Test
	public void test_apply_variant_09_shorter() {
		Gpr.debug("Test");

		Variant variant = new Variant(transcript.getParent(), 410, "AGCGCT", "TCG");
		checkApplyMixed(variant, transcript.cds(), transcript.protein(), 1, 300, 399);
	}

	/**
	 * Variant after exon end
	 */
	@Test
	public void test_apply_variant_09_longer() {
		Gpr.debug("Test");

		Variant variant = new Variant(transcript.getParent(), 410, "AGC", "TCGACT");
		checkApplyMixed(variant, transcript.cds(), transcript.protein(), 1, 300, 399);
	}

}