gatk-3.8/java/test/org/broadinstitute/sting/utils/variantcontext/AlleleUnitTest.java

/*
 * Copyright (c) 2010 The Broad Institute
 *
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
 * files (the "Software"), to deal in the Software without
 * restriction, including without limitation the rights to use,
 * copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the
 * Software is furnished to do so, subject to the following
 * conditions:
 *
 * The above copyright notice and this permission notice shall be
 * included in all copies or substantial portions of the Software.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
 * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
 * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
 * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
 * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
 * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
 * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */

// our package
package org.broadinstitute.sting.utils.variantcontext;


// the imports for unit testing.

import org.testng.Assert;
import org.testng.annotations.BeforeSuite;
import org.testng.annotations.BeforeTest;
import org.testng.annotations.Test;

//    public Allele(byte[] bases, boolean isRef) {
//    public Allele(boolean isRef) {
//    public Allele(String bases, boolean isRef) {
//    public boolean isNullAllele()       { return length() == 0; }
//    public boolean isNonNullAllele()    { return ! isNullAllele(); }
//    public boolean isReference()        { return isRef; }
//    public boolean isNonReference()     { return ! isReference(); }
//    public byte[] getBases() { return bases; }
//    public boolean equals(Allele other) {
//    public int length() {

/**
 * Basic unit test for RecalData
 */
public class AlleleUnitTest {
    Allele ARef, del, delRef, A, T, ATIns, ATCIns, NoCall;
    
    @BeforeSuite
    public void before() {
        del = Allele.create("-");
        delRef = Allele.create("-", true);

        A = Allele.create("A");
        ARef = Allele.create("A", true);
        T = Allele.create("T");

        ATIns = Allele.create("AT");
        ATCIns = Allele.create("ATC");

        NoCall = Allele.create(".");
    }

    @Test
    public void testCreatingSNPAlleles() {
        Assert.assertTrue(A.isNonReference());
        Assert.assertFalse(A.isReference());
        Assert.assertTrue(A.basesMatch("A"));
        Assert.assertEquals(A.length(), 1);
        Assert.assertTrue(A.isNonNull());
        Assert.assertFalse(A.isNull());

        Assert.assertTrue(ARef.isReference());
        Assert.assertFalse(ARef.isNonReference());
        Assert.assertTrue(ARef.basesMatch("A"));
        Assert.assertFalse(ARef.basesMatch("T"));

        Assert.assertTrue(T.isNonReference());
        Assert.assertFalse(T.isReference());
        Assert.assertTrue(T.basesMatch("T"));
        Assert.assertFalse(T.basesMatch("A"));
    }

    @Test
    public void testCreatingNoCallAlleles() {
        Assert.assertTrue(NoCall.isNonReference());
        Assert.assertFalse(NoCall.isReference());
        Assert.assertFalse(NoCall.basesMatch("."));
        Assert.assertEquals(NoCall.length(), 0);
        Assert.assertTrue(NoCall.isNonNull());
        Assert.assertFalse(NoCall.isNull());
    }


    @Test
    public void testCreatingIndelAlleles() {
        Assert.assertEquals(ATIns.length(), 2);
        Assert.assertEquals(ATCIns.length(), 3);
        Assert.assertEquals(ATIns.getBases(), "AT".getBytes());
        Assert.assertEquals(ATCIns.getBases(), "ATC".getBytes());

        Assert.assertTrue(del.isNonReference());
        Assert.assertFalse(delRef.isNonReference());
        Assert.assertFalse(del.isReference());
        Assert.assertTrue(delRef.isReference());
        Assert.assertFalse(del.basesMatch("-"));
        Assert.assertTrue(del.basesMatch(""));
        Assert.assertEquals(del.length(), 0);
        Assert.assertFalse(del.isNonNull());
        Assert.assertTrue(del.isNull());
    }


    @Test
    public void testConstructors1() {
        Allele a1 = Allele.create("A");
        Allele a2 = Allele.create("A".getBytes());
        Allele a3 = Allele.create("A");
        Allele a4 = Allele.create("A", true);

        Assert.assertTrue(a1.equals(a2));
        Assert.assertTrue(a1.equals(a3));
        Assert.assertFalse(a1.equals(a4));
    }

    @Test
    public void testDelConstructors() {
        Allele a1 = Allele.create("-");
        Allele a2 = Allele.create("-".getBytes());
        Allele a3 = Allele.create("");
        Allele a4 = Allele.create("", true);

        Assert.assertTrue(a1.equals(a2));
        Assert.assertTrue(a1.equals(a3));
        Assert.assertFalse(a1.equals(a4));
    }

    @Test
    public void testInsConstructors() {
        Allele a1 = Allele.create("AC");
        Allele a2 = Allele.create("AC".getBytes());
        Allele a3 = Allele.create("AC");
        Allele a4 = Allele.create("AC", true);

        Assert.assertTrue(a1.equals(a2));
        Assert.assertTrue(a1.equals(a3));
        Assert.assertFalse(a1.equals(a4));
    }

    @Test
    public void testEquals() {
        Assert.assertTrue(ARef.basesMatch(A));
        Assert.assertFalse(ARef.equals(A));
        Assert.assertFalse(ARef.equals(del));
        Assert.assertFalse(ARef.equals(ATIns));
        Assert.assertFalse(ARef.equals(ATCIns));

        Assert.assertTrue(T.basesMatch(T));
        Assert.assertFalse(T.basesMatch(A));
        Assert.assertFalse(T.equals(A));

        Assert.assertTrue(del.basesMatch(del));
        Assert.assertTrue(del.basesMatch(delRef));
        Assert.assertTrue(del.equals(del));
        Assert.assertFalse(del.equals(delRef));

        Assert.assertTrue(ATIns.equals(ATIns));
        Assert.assertFalse(ATIns.equals(ATCIns));
        Assert.assertTrue(ATIns.basesMatch("AT"));
        Assert.assertFalse(ATIns.basesMatch("A"));
        Assert.assertFalse(ATIns.basesMatch("ATC"));

        Assert.assertTrue(ATIns.basesMatch("AT"));
        Assert.assertFalse(ATIns.basesMatch("ATC"));
    }

    @Test (expectedExceptions = IllegalArgumentException.class)
    public void testBadConstructorArgs1() {
        byte[] foo = null;
        Allele.create(foo);
    }

    @Test (expectedExceptions = IllegalArgumentException.class)
    public void testBadConstructorArgs2() {
        Allele.create("x");
    }

    @Test (expectedExceptions = IllegalArgumentException.class)
    public void testBadConstructorArgs3() {
        Allele.create("--");
    }

    @Test (expectedExceptions = IllegalArgumentException.class)
    public void testBadConstructorArgs4() {
        Allele.create("-A");
    }

    @Test (expectedExceptions = IllegalArgumentException.class)
    public void testBadConstructorArgs5() {
        Allele.create("A A");
    }

    @Test
    public void testExtend() {
        Assert.assertEquals("AT", Allele.extend(Allele.create("A"), "T".getBytes()).toString());
        Assert.assertEquals("ATA", Allele.extend(Allele.create("A"), "TA".getBytes()).toString());
        Assert.assertEquals("A", Allele.extend(Allele.create("-"), "A".getBytes()).toString());
        Assert.assertEquals("A", Allele.extend(Allele.NO_CALL, "A".getBytes()).toString());
        Assert.assertEquals("ATCGA", Allele.extend(Allele.create("AT"), "CGA".getBytes()).toString());
        Assert.assertEquals("ATCGA", Allele.extend(Allele.create("ATC"), "GA".getBytes()).toString());
    }
}