242 lines
8.8 KiB
Java
242 lines
8.8 KiB
Java
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// our package
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package org.broadinstitute.sting.oneoffprojects.variantcontext;
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// the imports for unit testing.
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import org.broadinstitute.sting.BaseTest;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.GenomeLocParser;
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import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
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import org.junit.Assert;
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import org.junit.Before;
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import org.junit.Test;
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import org.junit.BeforeClass;
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import java.util.Map;
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import java.util.Arrays;
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import java.util.Set;
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import java.util.List;
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import java.io.FileNotFoundException;
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import java.io.File;
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import net.sf.picard.reference.ReferenceSequenceFile;
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/**
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* Basic unit test for RecalData
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*/
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public class VariantContextTest extends BaseTest {
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private static ReferenceSequenceFile seq;
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@BeforeClass
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public static void init() throws FileNotFoundException {
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// sequence
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seq = new IndexedFastaSequenceFile(new File(seqLocation + "/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta"));
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GenomeLocParser.setupRefContigOrdering(seq);
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}
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Allele A, Aref, T, Tref;
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Allele del, delRef, ATC, ATCref;
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// A [ref] / T at 10
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GenomeLoc snpLoc = GenomeLocParser.createGenomeLoc("chr1", 10, 11);
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// - / ATC [ref] from 20-23
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GenomeLoc delLoc = GenomeLocParser.createGenomeLoc("chr1", 20, 23);
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// - [ref] / ATC from 20-20
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GenomeLoc insLoc = GenomeLocParser.createGenomeLoc("chr1", 20, 20);
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// - / A / T / ATC [ref] from 20-23
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GenomeLoc mixedLoc = GenomeLocParser.createGenomeLoc("chr1", 20, 23);
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@Before
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public void before() {
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del = new Allele("-");
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delRef = new Allele("-", true);
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A = new Allele("A");
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Aref = new Allele("A", true);
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T = new Allele("T");
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Tref = new Allele("T", true);
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ATC = new Allele("ATC");
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ATCref = new Allele("ATC", true);
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}
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// todo -- create reference context
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@Test
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public void testCreatingSNPVariantContext() {
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logger.warn("testCreatingSNPVariantContext");
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List<Allele> alleles = Arrays.asList(Aref, T);
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VariantContext vc = new VariantContext(snpLoc, alleles);
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logger.warn("vc = " + vc);
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Assert.assertEquals(vc.getLocation(), snpLoc);
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Assert.assertEquals(vc.getType(), VariantContext.Type.SNP);
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Assert.assertTrue(vc.isSNP());
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Assert.assertFalse(vc.isIndel());
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//Assert.assertFalse(vc.isInsertion());
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//Assert.assertFalse(vc.isDeletion());
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Assert.assertFalse(vc.isMixed());
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Assert.assertTrue(vc.isBiallelic());
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Assert.assertEquals(vc.getNAlleles(), 2);
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Assert.assertEquals(vc.getReference(), Aref);
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Assert.assertEquals(vc.getAlleles().size(), 2);
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Assert.assertEquals(vc.getAlternateAlleles().size(), 1);
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Assert.assertEquals(vc.getAlternateAllele(0), T);
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Assert.assertFalse(vc.hasGenotypes());
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Assert.assertEquals(vc.getSampleNames().size(), 0);
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}
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@Test
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public void testCreatingRefVariantContext() {
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logger.warn("testCreatingRefVariantContext");
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List<Allele> alleles = Arrays.asList(Aref);
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VariantContext vc = new VariantContext(snpLoc, alleles);
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logger.warn("vc = " + vc);
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Assert.assertEquals(vc.getLocation(), snpLoc);
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Assert.assertEquals(vc.getType(), VariantContext.Type.NO_VARIATION);
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Assert.assertFalse(vc.isSNP());
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Assert.assertFalse(vc.isIndel());
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//Assert.assertFalse(vc.isInsertion());
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//Assert.assertFalse(vc.isDeletion());
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Assert.assertFalse(vc.isMixed());
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Assert.assertFalse(vc.isBiallelic());
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Assert.assertEquals(vc.getNAlleles(), 1);
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Assert.assertEquals(vc.getReference(), Aref);
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Assert.assertEquals(vc.getAlleles().size(), 1);
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Assert.assertEquals(vc.getAlternateAlleles().size(), 0);
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//Assert.assertEquals(vc.getAlternateAllele(0), T);
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Assert.assertFalse(vc.hasGenotypes());
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Assert.assertEquals(vc.getSampleNames().size(), 0);
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}
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@Test
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public void testCreatingDeletionVariantContext() {
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logger.warn("testCreatingDeletionVariantContext");
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List<Allele> alleles = Arrays.asList(ATCref, del);
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VariantContext vc = new VariantContext(delLoc, alleles);
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logger.warn("vc = " + vc);
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Assert.assertEquals(vc.getLocation(), delLoc);
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Assert.assertEquals(vc.getType(), VariantContext.Type.INDEL);
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Assert.assertFalse(vc.isSNP());
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Assert.assertTrue(vc.isIndel());
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//Assert.assertFalse(vc.isInsertion());
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//Assert.assertFalse(vc.isDeletion());
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Assert.assertFalse(vc.isMixed());
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Assert.assertTrue(vc.isBiallelic());
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Assert.assertEquals(vc.getNAlleles(), 2);
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Assert.assertEquals(vc.getReference(), ATCref);
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Assert.assertEquals(vc.getAlleles().size(), 2);
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Assert.assertEquals(vc.getAlternateAlleles().size(), 1);
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Assert.assertEquals(vc.getAlternateAllele(0), del);
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Assert.assertFalse(vc.hasGenotypes());
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Assert.assertEquals(vc.getSampleNames().size(), 0);
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}
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@Test
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public void testCreatingInsertionVariantContext() {
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logger.warn("testCreatingInsertionVariantContext");
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List<Allele> alleles = Arrays.asList(delRef, ATC);
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VariantContext vc = new VariantContext(insLoc, alleles);
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logger.warn("vc = " + vc);
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Assert.assertEquals(vc.getLocation(), insLoc);
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Assert.assertEquals(vc.getType(), VariantContext.Type.INDEL);
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Assert.assertFalse(vc.isSNP());
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Assert.assertTrue(vc.isIndel());
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//Assert.assertFalse(vc.isInsertion());
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//Assert.assertFalse(vc.isDeletion());
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Assert.assertFalse(vc.isMixed());
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Assert.assertTrue(vc.isBiallelic());
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Assert.assertEquals(vc.getNAlleles(), 2);
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Assert.assertEquals(vc.getReference(), delRef);
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Assert.assertEquals(vc.getAlleles().size(), 2);
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Assert.assertEquals(vc.getAlternateAlleles().size(), 1);
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Assert.assertEquals(vc.getAlternateAllele(0), ATC);
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Assert.assertFalse(vc.hasGenotypes());
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Assert.assertEquals(vc.getSampleNames().size(), 0);
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}
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@Test (expected = IllegalArgumentException.class)
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public void testBadConstructorArgs1() {
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logger.warn("testBadConstructorArgs1");
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new VariantContext(insLoc, Arrays.asList(delRef, ATCref));
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}
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@Test (expected = IllegalArgumentException.class)
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public void testBadConstructorArgs2() {
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logger.warn("testBadConstructorArgs2");
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new VariantContext(insLoc, Arrays.asList(delRef, del));
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}
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@Test (expected = IllegalArgumentException.class)
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public void testBadConstructorArgs3() {
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logger.warn("testBadConstructorArgs3");
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new VariantContext(insLoc, Arrays.asList(del));
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}
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@Test (expected = IllegalArgumentException.class)
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public void testBadConstructorArgsDuplicateAlleles1() {
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logger.warn("testBadConstructorArgsDuplicateAlleles1");
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new VariantContext(insLoc, Arrays.asList(Aref, T, T));
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}
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@Test (expected = IllegalArgumentException.class)
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public void testBadConstructorArgsDuplicateAlleles2() {
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logger.warn("testBadConstructorArgsDuplicateAlleles2");
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new VariantContext(insLoc, Arrays.asList(Aref, A));
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}
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}
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// public Type getType() {
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// public boolean isSNP() { return getType() == Type.SNP; }
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// public boolean isVariant() { return getType() != Type.NO_VARIATION; }
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// public boolean isIndel() { return getType() == Type.INDEL; }
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// public boolean isMixed() { return getType() == Type.MIXED; }
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// public GenomeLoc getLocation() { return loc; }
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// public Allele getReference() {
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// public boolean isBiallelic() {
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// public boolean isMonomorphic() {
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// public boolean isPolymorphic() {
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// public int getNAlleles() {
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// public Set<Allele> getAlleles() { return alleles; }
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// public Set<Allele> getAlternateAlleles() {
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// public Allele getAlternateAllele(int i) {
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// public void setAlleles(Set<Allele> alleles) {
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// public void addAllele(Allele allele) {
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// public void addAllele(Allele allele, boolean allowDuplicates) {
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// public boolean hasGenotypes() { return genotypes.size() > 0; }
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// public Map<String, Genotype> getGenotypes() { return genotypes; }
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// public Set<String> getSampleNames() {
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// public Genotype getGenotype(String sample) {
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// public boolean hasGenotype(String sample) {
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// public void setGenotypes(Genotype genotype) {
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// public void setGenotypes(Collection<Genotype> genotypes) {
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// public void setGenotypes(Map<String, Genotype> genotypes) {
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// public void addGenotype(Genotype genotype) {
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// public void addGenotype(String sampleName, Genotype genotype) {
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// public void addGenotype(String sampleName, Genotype genotype, boolean allowOverwrites) {
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// public void removeGenotype(String sampleName) {
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// public void removeGenotype(Genotype genotype) {
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// public boolean validate() {
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