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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 (DEL) to a transcript
 *
 */
public class TestCasesApplyDel extends TestCasesBaseApply {

	public TestCasesApplyDel() {
		super();
	}

	/**
	 * Variant before exon
	 */
	@Test
	public void test_apply_variant_01() {
		Gpr.debug("Test");
		Variant variant = new Variant(transcript.getParent(), 290, "TTT", "");
		checkApplyDel(variant, transcript.cds(), transcript.protein(), 1, 297, 396);
	}

	/**
	 * Variant right before exon start
	 */
	@Test
	public void test_apply_variant_02() {
		Gpr.debug("Test");

		Variant variant = new Variant(transcript.getParent(), 297, "TCC", "");
		checkApplyDel(variant, transcript.cds(), transcript.protein(), 1, 297, 396);
	}

	/**
	 * Variant overlapping exon start
	 */
	@Test
	public void test_apply_variant_03() {
		Gpr.debug("Test");

		Variant variant = new Variant(transcript.getParent(), 299, "CTG", "");

		String expectedCds = "atgtccgcaggtgaaggcatacacgctgcgcgtatactgatgttacctcgatggattttgtcagaaatatggtgcccaggacgcgaagggcatattatgg" // Exon[0]
				+ "tttgggaattcacgggcacggttctgcagcaagctgaattggcagctcggcataaatcccgaccccatcgtcacgcacggatcaattcatcctcaacg" // Exon[1]
				+ "ggtagaggaaaagcacctaacccccattgagcaggatctctttcgtaatactctgtatcgattaccgatttatttgattccccacatttatttcatcggg" // Exon[2]
		;

		checkApplyDel(variant, expectedCds, null, 1, 299, 396);
	}

	/**
	 * Variant at exon start
	 */
	@Test
	public void test_apply_variant_04() {
		Gpr.debug("Test");

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

		String expectedCds = "atgtccgcaggtgaaggcatacacgctgcgcgtatactgatgttacctcgatggattttgtcagaaatatggtgcccaggacgcgaagggcatattatgg" // Exon[0]
				+ "ttgggaattcacgggcacggttctgcagcaagctgaattggcagctcggcataaatcccgaccccatcgtcacgcacggatcaattcatcctcaacg" // Exon[1]
				+ "ggtagaggaaaagcacctaacccccattgagcaggatctctttcgtaatactctgtatcgattaccgatttatttgattccccacatttatttcatcggg" // Exon[2]
		;

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

	}

	/**
	 * Variant in exon
	 */
	@Test
	public void test_apply_variant_05() {
		Gpr.debug("Test");

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

		String expectedCds = "atgtccgcaggtgaaggcatacacgctgcgcgtatactgatgttacctcgatggattttgtcagaaatatggtgcccaggacgcgaagggcatattatgg" // Exon[0]
				+ "tgtttgggaaacgggcacggttctgcagcaagctgaattggcagctcggcataaatcccgaccccatcgtcacgcacggatcaattcatcctcaacg" // Exon[1]
				+ "ggtagaggaaaagcacctaacccccattgagcaggatctctttcgtaatactctgtatcgattaccgatttatttgattccccacatttatttcatcggg" // Exon[2]
		;

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

	}

	/**
	 * Variant right before exon end
	 */
	@Test
	public void test_apply_variant_06() {
		Gpr.debug("Test");

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

		String expectedCds = "atgtccgcaggtgaaggcatacacgctgcgcgtatactgatgttacctcgatggattttgtcagaaatatggtgcccaggacgcgaagggcatattatgg" // Exon[0]
				+ "tgtttgggaattcacgggcacggttctgcagcaagctgaattggcagctcggcataaatcccgaccccatcgtcacgcacggatcaattcatcctca" // Exon[1]
				+ "ggtagaggaaaagcacctaacccccattgagcaggatctctttcgtaatactctgtatcgattaccgatttatttgattccccacatttatttcatcggg" // Exon[2]
		;

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

	}

	/**
	 * Variant overlapping exon end
	 */
	@Test
	public void test_apply_variant_07() {
		Gpr.debug("Test");

		Variant variant = new Variant(transcript.getParent(), 398, "CGA", "");

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

		checkApplyDel(variant, expectedCds, null, 1, 300, 397);

	}

	/**
	 * Variant right after exon end
	 */
	@Test
	public void test_apply_variant_08() {
		Gpr.debug("Test");

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

	/**
	 * Variant after exon end
	 */
	@Test
	public void test_apply_variant_09() {
		Gpr.debug("Test");

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

	/**
	 * Variant over exon: variant is larger than exon, starts before exon and overlaps the whole exon
	 */
	@Test
	public void test_apply_variant_10() {
		Gpr.debug("Test");

		Variant variant = new Variant(transcript.getParent() //
				, 290 //
				, "tttatcgtcctgtttgggaattcacgggcacggttctgcagcaagctgaattggcagctcggcataaatcccgaccccatcgtcacgcacggatcaattcatcctcaacgaaagggagct" //
				, "" //
		);

		String expectedCds = "atgtccgcaggtgaaggcatacacgctgcgcgtatactgatgttacctcgatggattttgtcagaaatatggtgcccaggacgcgaagggcatattatgg" // Exon[0]
				+ "" // Exon[1]
				+ "ggtagaggaaaagcacctaacccccattgagcaggatctctttcgtaatactctgtatcgattaccgatttatttgattccccacatttatttcatcggg" // Exon[2]
		;

		// Note: Since the original exon 1 is deleted, we check coordinates 
		// for exon 2 (that becomes exon 1 in the new transcript)
		checkApplyDel(variant, expectedCds, null, 1, 780, 879);
	}

	/**
	 * Variant over exon: variant is larger than exon and starts right at exons start and ends after exon end
	 */
	@Test
	public void test_apply_variant_11() {
		Gpr.debug("Test");

		Variant variant = new Variant(transcript.getParent() //
				, 300 //
				, "TGTTTGGGAATTCACGGGCACGGTTCTGCAGCAAGCTGAATTGGCAGCTCGGCATAAATCCCGACCCCATCGTCACGCACGGATCAATTCATCCTCAACGAAAGGGAGCTAGCGCTGTAC" //
				, "" //
		);

		String expectedCds = "atgtccgcaggtgaaggcatacacgctgcgcgtatactgatgttacctcgatggattttgtcagaaatatggtgcccaggacgcgaagggcatattatgg" // Exon[0]
				+ "" // Exon[1]
				+ "ggtagaggaaaagcacctaacccccattgagcaggatctctttcgtaatactctgtatcgattaccgatttatttgattccccacatttatttcatcggg" // Exon[2]
		;

		// Note: Since the original exon 1 is deleted, we check coordinates 
		// for exon 2 (that becomes exon 1 in the new transcript)
		checkApplyDel(variant, expectedCds, null, 1, 780, 879);
	}

	/**
	 * Variant over exon: variant is larger than exon, starts before exon start and end right at exon end
	 */
	@Test
	public void test_apply_variant_12() {
		Gpr.debug("Test");

		Variant variant = new Variant(transcript.getParent()//
				, 280 //
				, "aaccgctaactttatcgtcctgtttgggaattcacgggcacggttctgcagcaagctgaattggcagctcggcataaatcccgaccccatcgtcacgcacggatcaattcatcctcaacg".toUpperCase() //
				, "" //
		);

		String expectedCds = "atgtccgcaggtgaaggcatacacgctgcgcgtatactgatgttacctcgatggattttgtcagaaatatggtgcccaggacgcgaagggcatattatgg" // Exon[0]
				+ "" // Exon[1]
				+ "ggtagaggaaaagcacctaacccccattgagcaggatctctttcgtaatactctgtatcgattaccgatttatttgattccccacatttatttcatcggg" // Exon[2]
		;

		// Note: Since the original exon 1 is deleted, we check coordinates 
		// for exon 2 (that becomes exon 1 in the new transcript)
		checkApplyDel(variant, expectedCds, null, 1, 780, 879);

	}

	/**
	 * Variant over exon: variant is on the same coordiantes as exon
	 */
	@Test
	public void test_apply_variant_13() {
		Gpr.debug("Test");

		Variant variant = new Variant(transcript.getParent() //
				, 300 //
				, "tgtttgggaattcacgggcacggttctgcagcaagctgaattggcagctcggcataaatcccgaccccatcgtcacgcacggatcaattcatcctcaacg".toUpperCase() //
				, "" //
		);

		String expectedCds = "atgtccgcaggtgaaggcatacacgctgcgcgtatactgatgttacctcgatggattttgtcagaaatatggtgcccaggacgcgaagggcatattatgg" // Exon[0]
				+ "" // Exon[1]
				+ "ggtagaggaaaagcacctaacccccattgagcaggatctctttcgtaatactctgtatcgattaccgatttatttgattccccacatttatttcatcggg" // Exon[2]
		;

		// Note: Since the original exon 1 is deleted, we check coordinates 
		// for exon 2 (that becomes exon 1 in the new transcript)
		checkApplyDel(variant, expectedCds, null, 1, 800, 899);
	}

}