Expanded UnitTests for VariantContext
Tests for -- getGenotype and getGenotypes -- subContextBySample -- modify routines
This commit is contained in:
Mark DePristo
parent
aa0610ea92
commit
7e66677769
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@ -383,8 +383,8 @@ public class VariantContext implements Feature { // to enable tribble intergrati
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this.stop = stop;
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// intern for efficiency. equals calls will generate NPE if ID is inappropriately passed in as null
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if ( ID == null || ID.equals("") ) throw new IllegalArgumentException("ID field cannot be the null or the empty string");
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this.ID = ID.equals(VCFConstants.EMPTY_ID_FIELD) ? VCFConstants.EMPTY_ID_FIELD : ID;
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if ( this.ID.equals("") ) throw new IllegalArgumentException("ID field cannot be the empty string");
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if ( !genotypesAreUnparsed && attributes != null ) {
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if ( attributes.containsKey(UNPARSED_GENOTYPE_MAP_KEY) ) {
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@ -12,6 +12,7 @@ import org.testng.annotations.DataProvider;
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import org.testng.annotations.Test;
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import org.testng.Assert;
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import java.lang.reflect.Array;
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import java.util.*;
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@ -173,7 +174,7 @@ public class VariantContextUnitTest extends BaseTest {
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@Test
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public void testCreatingRefVariantContext() {
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List<Allele> alleles = Arrays.asList(Aref);
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List<Allele> alleles = Arrays.asList(Aref);
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VariantContext vc = new VariantContext("test", VCFConstants.EMPTY_ID_FIELD, snpLoc,snpLocStart, snpLocStop, alleles);
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Assert.assertEquals(vc.getChr(), snpLoc);
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@ -309,6 +310,16 @@ public class VariantContextUnitTest extends BaseTest {
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new VariantContext("test", VCFConstants.EMPTY_ID_FIELD, delLoc, delLocStart, delLocStop, alleles);
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}
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@Test (expectedExceptions = IllegalArgumentException.class)
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public void testBadID1() {
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new VariantContext("test", null, delLoc, delLocStart, delLocStop, Arrays.asList(Aref, T));
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}
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@Test (expectedExceptions = IllegalArgumentException.class)
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public void testBadID2() {
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new VariantContext("test", "", delLoc, delLocStart, delLocStop, Arrays.asList(Aref, T));
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}
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@Test
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public void testAccessingSimpleSNPGenotypes() {
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List<Allele> alleles = Arrays.asList(Aref, T);
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@ -423,7 +434,7 @@ public class VariantContextUnitTest extends BaseTest {
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}
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@Test
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public void testVCromGenotypes() {
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public void testVCFfromGenotypes() {
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List<Allele> alleles = Arrays.asList(Aref, T, del);
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Genotype g1 = new Genotype("AA", Arrays.asList(Aref, Aref), 10);
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Genotype g2 = new Genotype("AT", Arrays.asList(Aref, T), 10);
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@ -479,6 +490,29 @@ public class VariantContextUnitTest extends BaseTest {
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Assert.assertEquals(0, vc5.getChromosomeCount(Aref));
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}
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public void testGetGenotypeMethods() {
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Genotype g1 = new Genotype("AA", Arrays.asList(Aref, Aref), 10);
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Genotype g2 = new Genotype("AT", Arrays.asList(Aref, T), 10);
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Genotype g3 = new Genotype("TT", Arrays.asList(T, T), 10);
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GenotypesContext gc = GenotypesContext.create(g1, g2, g3);
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VariantContext vc = new VariantContext("genotypes", VCFConstants.EMPTY_ID_FIELD, snpLoc, snpLocStart, snpLocStop, Arrays.asList(Aref, T), gc);
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Assert.assertEquals(vc.getGenotype("AA"), g1);
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Assert.assertEquals(vc.getGenotype("AT"), g2);
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Assert.assertEquals(vc.getGenotype("TT"), g3);
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Assert.assertEquals(vc.getGenotype("CC"), null);
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Assert.assertEquals(vc.getGenotypes(), gc);
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Assert.assertEquals(vc.getGenotypes(Arrays.asList("AA", "AT")), Arrays.asList(g1, g2));
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Assert.assertEquals(vc.getGenotypes(Arrays.asList("AA", "TT")), Arrays.asList(g1, g3));
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Assert.assertEquals(vc.getGenotypes(Arrays.asList("AA", "AT", "TT")), Arrays.asList(g1, g2, g3));
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Assert.assertEquals(vc.getGenotypes(Arrays.asList("AA", "AT", "CC")), Arrays.asList(g1, g2));
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Assert.assertEquals(vc.getGenotype(0), g1);
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Assert.assertEquals(vc.getGenotype(1), g2);
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Assert.assertEquals(vc.getGenotype(2), g3);
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}
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// --------------------------------------------------------------------------------
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//
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// Test allele merging
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@ -545,4 +579,159 @@ public class VariantContextUnitTest extends BaseTest {
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Assert.assertFalse(vc.hasAllele(missingAllele));
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Assert.assertFalse(vc.hasAllele(missingAllele, true));
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}
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}
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private class SitesAndGenotypesVC extends TestDataProvider {
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VariantContext vc, copy;
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private SitesAndGenotypesVC(String name, VariantContext original) {
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super(SitesAndGenotypesVC.class, name);
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this.vc = original;
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this.copy = new VariantContext(original);
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}
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public String toString() {
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return String.format("%s input=%s", super.toString(), vc);
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}
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}
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@DataProvider(name = "SitesAndGenotypesVC")
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public Object[][] MakeSitesAndGenotypesVCs() {
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Genotype g1 = new Genotype("AA", Arrays.asList(Aref, Aref), 10);
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Genotype g2 = new Genotype("AT", Arrays.asList(Aref, T), 10);
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Genotype g3 = new Genotype("TT", Arrays.asList(T, T), 10);
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VariantContext sites = new VariantContext("sites", VCFConstants.EMPTY_ID_FIELD, snpLoc, snpLocStart, snpLocStop, Arrays.asList(Aref, T));
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VariantContext genotypes = new VariantContext("genotypes", VCFConstants.EMPTY_ID_FIELD, snpLoc, snpLocStart, snpLocStop, Arrays.asList(Aref, T), Arrays.asList(g1, g2, g3));
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new SitesAndGenotypesVC("sites", sites);
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new SitesAndGenotypesVC("genotypes", genotypes);
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return SitesAndGenotypesVC.getTests(SitesAndGenotypesVC.class);
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}
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// --------------------------------------------------------------------------------
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//
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// Test modifying routines
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//
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// --------------------------------------------------------------------------------
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@Test(dataProvider = "SitesAndGenotypesVC")
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public void runModifyVCTests(SitesAndGenotypesVC cfg) {
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VariantContext modified = VariantContext.modifyLocation(cfg.vc, "chr2", 123, 123);
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Assert.assertEquals(modified.getChr(), "chr2");
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Assert.assertEquals(modified.getStart(), 123);
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Assert.assertEquals(modified.getEnd(), 123);
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modified = VariantContext.modifyID(cfg.vc, "newID");
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Assert.assertEquals(modified.getID(), "newID");
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Set<String> newFilters = Collections.singleton("newFilter");
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modified = VariantContext.modifyFilters(cfg.vc, newFilters);
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Assert.assertEquals(modified.getFilters(), newFilters);
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modified = VariantContext.modifyAttribute(cfg.vc, "AC", 1);
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Assert.assertEquals(modified.getAttribute("AC"), 1);
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modified = VariantContext.modifyAttribute(modified, "AC", 2);
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Assert.assertEquals(modified.getAttribute("AC"), 2);
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modified = VariantContext.modifyAttributes(modified, null);
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Assert.assertTrue(modified.getAttributes().isEmpty());
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Genotype g1 = new Genotype("AA2", Arrays.asList(Aref, Aref), 10);
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Genotype g2 = new Genotype("AT2", Arrays.asList(Aref, T), 10);
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Genotype g3 = new Genotype("TT2", Arrays.asList(T, T), 10);
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GenotypesContext gc = GenotypesContext.create(g1,g2,g3);
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modified = VariantContext.modifyGenotypes(cfg.vc, gc);
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Assert.assertEquals(modified.getGenotypes(), gc);
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modified = VariantContext.modifyGenotypes(cfg.vc, null);
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Assert.assertTrue(modified.getGenotypes().isEmpty());
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// test that original hasn't changed
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Assert.assertEquals(cfg.vc.getChr(), cfg.copy.getChr());
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Assert.assertEquals(cfg.vc.getStart(), cfg.copy.getStart());
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Assert.assertEquals(cfg.vc.getEnd(), cfg.copy.getEnd());
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Assert.assertEquals(cfg.vc.getAlleles(), cfg.copy.getAlleles());
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Assert.assertEquals(cfg.vc.getAttributes(), cfg.copy.getAttributes());
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Assert.assertEquals(cfg.vc.getID(), cfg.copy.getID());
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Assert.assertEquals(cfg.vc.getGenotypes(), cfg.copy.getGenotypes());
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Assert.assertEquals(cfg.vc.getNegLog10PError(), cfg.copy.getNegLog10PError());
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Assert.assertEquals(cfg.vc.getFilters(), cfg.copy.getFilters());
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}
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// --------------------------------------------------------------------------------
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//
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// Test subcontext
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//
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// --------------------------------------------------------------------------------
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private class SubContextTest extends TestDataProvider {
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Set<String> samples;
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boolean updateAlleles;
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private SubContextTest(Collection<String> samples, boolean updateAlleles) {
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super(SubContextTest.class);
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this.samples = new HashSet<String>(samples);
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this.updateAlleles = updateAlleles;
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}
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public String toString() {
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return String.format("%s samples=%s updateAlleles=%b", super.toString(), samples, updateAlleles);
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}
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}
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@DataProvider(name = "SubContextTest")
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public Object[][] MakeSubContextTest() {
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for ( boolean updateAlleles : Arrays.asList(true, false)) {
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new SubContextTest(Collections.<String>emptySet(), updateAlleles);
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new SubContextTest(Collections.singleton("AA"), updateAlleles);
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new SubContextTest(Collections.singleton("AT"), updateAlleles);
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new SubContextTest(Collections.singleton("TT"), updateAlleles);
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new SubContextTest(Arrays.asList("AA", "AT"), updateAlleles);
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new SubContextTest(Arrays.asList("AA", "AT", "TT"), updateAlleles);
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}
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return SubContextTest.getTests(SubContextTest.class);
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}
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private final static void SubContextTest() {
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}
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@Test(dataProvider = "SubContextTest")
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public void runSubContextTest(SubContextTest cfg) {
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Genotype g1 = new Genotype("AA", Arrays.asList(Aref, Aref), 10);
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Genotype g2 = new Genotype("AT", Arrays.asList(Aref, T), 10);
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Genotype g3 = new Genotype("TT", Arrays.asList(T, T), 10);
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GenotypesContext gc = GenotypesContext.create(g1, g2, g3);
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VariantContext vc = new VariantContext("genotypes", VCFConstants.EMPTY_ID_FIELD, snpLoc, snpLocStart, snpLocStop, Arrays.asList(Aref, T), gc);
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VariantContext sub = cfg.updateAlleles ? vc.subContextFromSamples(cfg.samples) : vc.subContextFromSamples(cfg.samples, vc.getAlleles());
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// unchanged attributes should be the same
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Assert.assertEquals(sub.getChr(), vc.getChr());
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Assert.assertEquals(sub.getStart(), vc.getStart());
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Assert.assertEquals(sub.getEnd(), vc.getEnd());
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Assert.assertEquals(sub.getNegLog10PError(), vc.getNegLog10PError());
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Assert.assertEquals(sub.getFilters(), vc.getFilters());
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Assert.assertEquals(sub.getID(), vc.getID());
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Assert.assertEquals(sub.getReferenceBaseForIndel(), vc.getReferenceBaseForIndel());
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Assert.assertEquals(sub.getAttributes(), vc.getAttributes());
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Set<Genotype> expectedGenotypes = new HashSet<Genotype>();
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if ( cfg.samples.contains(g1.getSampleName()) ) expectedGenotypes.add(g1);
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if ( cfg.samples.contains(g2.getSampleName()) ) expectedGenotypes.add(g2);
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if ( cfg.samples.contains(g3.getSampleName()) ) expectedGenotypes.add(g3);
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GenotypesContext expectedGC = GenotypesContext.copy(expectedGenotypes);
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// these values depend on the results of sub
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if ( cfg.updateAlleles ) {
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// do the work to see what alleles should be here, and which not
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Set<Allele> alleles = new HashSet<Allele>();
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for ( final Genotype g : expectedGC ) alleles.addAll(g.getAlleles());
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if ( ! alleles.contains(Aref) ) alleles.add(Aref); // always have the reference
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Assert.assertEquals(new HashSet<Allele>(sub.getAlleles()), alleles);
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} else {
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// not updating alleles -- should be the same
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Assert.assertEquals(sub.getAlleles(), vc.getAlleles());
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}
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// same sample names => success
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Assert.assertEquals(sub.getGenotypes().getSampleNames(), expectedGC.getSampleNames());
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}
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}
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