UnitTest for simpleMerge for alleles
This commit is contained in:
Mark DePristo
parent
8811bb8668
commit
68da555932
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@ -48,10 +48,8 @@ import java.util.*;
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public class VariantContextUtilsUnitTest extends BaseTest {
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Allele Aref, T, delRef, ATC;
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Genotype ref1, snp1, snp2, indel1, indelref;
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Allele Aref, T, C, delRef, ATC, ATCATC;
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private GenomeLocParser genomeLocParser;
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VariantContext refVC, snpVC1, snpVC2, snpVC3, snpVC4, indelVC1, indelVC2, indelVC3;
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@BeforeSuite
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public void setup() {
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@ -68,22 +66,9 @@ public class VariantContextUtilsUnitTest extends BaseTest {
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Aref = Allele.create("A", true);
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delRef = Allele.create("-", true);
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T = Allele.create("T");
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C = Allele.create("C");
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ATC = Allele.create("ATC");
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ref1 = new Genotype("ref1", Arrays.asList(Aref, Aref), 5, new double[]{0, 5, 10});
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snp1 = new Genotype("snp1", Arrays.asList(Aref,T), 10, new double[]{10, 0, 20});
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snp2 = new Genotype("snp2", Arrays.asList(T,T), 15, new double[]{25, 15, 0});
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indelref = new Genotype("indelref", Arrays.asList(delRef,delRef), 25, new double[]{0, 25, 30});
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indel1 = new Genotype("indel1", Arrays.asList(delRef,ATC), 20, new double[]{20, 0, 30});
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refVC = makeVC("refvc", Arrays.asList(Aref), Arrays.asList(ref1));
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snpVC1 = makeVC("snpvc1", Arrays.asList(Aref, T), Arrays.asList(snp1));
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snpVC2 = makeVC("snpvc2", Arrays.asList(Aref, T), Arrays.asList(snp1, snp2));
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snpVC3 = makeVC("snpvc3", Arrays.asList(Aref, T), Arrays.asList(ref1, snp1));
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snpVC4 = makeVC("snpvc4", Arrays.asList(Aref, T), Arrays.asList(ref1, snp1, snp2));
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indelVC1 = makeVC("indelvc1", Arrays.asList(delRef), Arrays.asList(indelref));
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indelVC2 = makeVC("indelvc2", Arrays.asList(delRef, ATC), Arrays.asList(indel1));
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indelVC3 = makeVC("indelvc3", Arrays.asList(delRef, ATC), Arrays.asList(indelref, indel1));
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ATCATC = Allele.create("ATCATC");
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}
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private VariantContext makeVC(String source, List<Allele> alleles) {
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@ -98,45 +83,124 @@ public class VariantContextUtilsUnitTest extends BaseTest {
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int start = 10;
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int stop = start; // alleles.contains(ATC) ? start + 3 : start;
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return new VariantContext(source, "1", start, stop, alleles,
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VariantContext.genotypeCollectionToMap(new TreeMap<String, Genotype>(), genotypes),
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genotypes == null ? null : VariantContext.genotypeCollectionToMap(new TreeMap<String, Genotype>(), genotypes),
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1.0, filters, null, (byte)'C');
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}
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private class SimpleMergeTest extends TestDataProvider {
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List<VariantContext> inputVCs;
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VariantContext expectedVC;
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// --------------------------------------------------------------------------------
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//
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// Test allele merging
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//
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// --------------------------------------------------------------------------------
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private SimpleMergeTest(VariantContext... vcsArg) {
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super(SimpleMergeTest.class);
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LinkedList<VariantContext> allVCs = new LinkedList<VariantContext>(Arrays.asList(vcsArg));
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expectedVC = allVCs.pollLast();
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inputVCs = allVCs;
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private class MergeAllelesTest extends TestDataProvider {
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List<List<Allele>> inputs;
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List<Allele> expected;
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private MergeAllelesTest(List<Allele>... arg) {
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super(MergeAllelesTest.class);
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LinkedList<List<Allele>> all = new LinkedList<List<Allele>>(Arrays.asList(arg));
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expected = all.pollLast();
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inputs = all;
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}
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public String toString() {
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return String.format("SimpleMergeTest vc=%s expected=%s", inputVCs, expectedVC);
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return String.format("MergeAllelesTest input=%s expected=%s", inputs, expected);
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}
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}
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@DataProvider(name = "simplemergedata")
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public Object[][] createSimpleMergeData() {
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@DataProvider(name = "mergeAlleles")
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public Object[][] mergeAllelesData() {
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// first, do no harm
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new SimpleMergeTest(refVC, refVC);
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new SimpleMergeTest(snpVC1, snpVC1);
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new SimpleMergeTest(indelVC1, indelVC1);
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new SimpleMergeTest(indelVC3, indelVC3);
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new MergeAllelesTest(Arrays.asList(Aref),
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Arrays.asList(Aref));
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new SimpleMergeTest(refVC, snpVC1, snpVC3);
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new SimpleMergeTest(snpVC1, snpVC2, snpVC2);
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new SimpleMergeTest(refVC, snpVC2, snpVC4);
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new MergeAllelesTest(Arrays.asList(Aref),
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Arrays.asList(Aref),
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Arrays.asList(Aref));
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new SimpleMergeTest(indelVC1, indelVC2, indelVC3);
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new SimpleMergeTest(indelVC1, indelVC3, indelVC3);
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new SimpleMergeTest(indelVC2, indelVC3, indelVC3);
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new MergeAllelesTest(Arrays.asList(Aref),
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Arrays.asList(Aref, T),
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Arrays.asList(Aref, T));
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return SimpleMergeTest.getTests(SimpleMergeTest.class);
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new MergeAllelesTest(Arrays.asList(Aref, C),
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Arrays.asList(Aref, T),
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Arrays.asList(Aref, C, T));
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new MergeAllelesTest(Arrays.asList(Aref, T),
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Arrays.asList(Aref, C),
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Arrays.asList(Aref, C, T)); // sorted by allele
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new MergeAllelesTest(Arrays.asList(Aref, C, T),
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Arrays.asList(Aref, C),
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Arrays.asList(Aref, C, T));
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new MergeAllelesTest(Arrays.asList(Aref, T, C),
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Arrays.asList(Aref, C),
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Arrays.asList(Aref, C, T)); // sorted by allele
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new MergeAllelesTest(Arrays.asList(delRef),
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Arrays.asList(delRef)); // todo -- FIXME me GdA
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new MergeAllelesTest(Arrays.asList(delRef),
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Arrays.asList(delRef, ATC),
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Arrays.asList(delRef, ATC));
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new MergeAllelesTest(Arrays.asList(delRef),
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Arrays.asList(delRef, ATC, ATCATC),
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Arrays.asList(delRef, ATC, ATCATC));
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new MergeAllelesTest(Arrays.asList(delRef, ATCATC),
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Arrays.asList(delRef, ATC, ATCATC),
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Arrays.asList(delRef, ATC, ATCATC));
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new MergeAllelesTest(Arrays.asList(delRef, ATC),
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Arrays.asList(delRef, ATCATC),
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Arrays.asList(delRef, ATC, ATCATC));
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return MergeAllelesTest.getTests(MergeAllelesTest.class);
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}
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@Test(dataProvider = "mergeAlleles")
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public void testMergeAlleles(MergeAllelesTest cfg) {
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final List<String> priority = new ArrayList<String>();
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final List<VariantContext> inputs = new ArrayList<VariantContext>();
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int i = 0;
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for ( final List<Allele> alleles : cfg.inputs ) {
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final String name = "vcf" + ++i;
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priority.add(name);
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inputs.add(makeVC(name, alleles));
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}
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final VariantContext merged = VariantContextUtils.simpleMerge(genomeLocParser,
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inputs, priority,
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VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED,
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VariantContextUtils.GenotypeMergeType.PRIORITIZE, false, false, "set", false, false);
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Assert.assertEquals(merged.getAlleles(), cfg.expected);
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}
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// VariantContext refVC, snpVC1, snpVC2, snpVC3, snpVC4, indelVC1, indelVC2, indelVC3;
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// ref1 = new Genotype("ref1", Arrays.asList(Aref, Aref), 5, new double[]{0, 5, 10});
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// snp1 = new Genotype("snp1", Arrays.asList(Aref,T), 10, new double[]{10, 0, 20});
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// snp2 = new Genotype("snp2", Arrays.asList(T,T), 15, new double[]{25, 15, 0});
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// indelref = new Genotype("indelref", Arrays.asList(delRef,delRef), 25, new double[]{0, 25, 30});
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// indel1 = new Genotype("indel1", Arrays.asList(delRef,ATC), 20, new double[]{20, 0, 30});
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//
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// refVC = makeVC("refvc", Arrays.asList(Aref), Arrays.asList(ref1));
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// snpVC1 = makeVC("snpvc1", Arrays.asList(Aref, T), Arrays.asList(snp1));
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// snpVC2 = makeVC("snpvc2", Arrays.asList(Aref, T), Arrays.asList(snp1, snp2));
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// snpVC3 = makeVC("snpvc3", Arrays.asList(Aref, T), Arrays.asList(ref1, snp1));
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// snpVC4 = makeVC("snpvc4", Arrays.asList(Aref, T), Arrays.asList(ref1, snp1, snp2));
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// indelVC1 = makeVC("indelvc1", Arrays.asList(delRef), Arrays.asList(indelref));
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// indelVC2 = makeVC("indelvc2", Arrays.asList(delRef, ATC), Arrays.asList(indel1));
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// indelVC3 = makeVC("indelvc3", Arrays.asList(delRef, ATC), Arrays.asList(indelref, indel1));
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// --------------------------------------------------------------------------------
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//
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// Test rsID merging
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//
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// --------------------------------------------------------------------------------
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private class SimpleMergeRSIDTest extends TestDataProvider {
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List<String> inputs;
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String expected;
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@ -156,10 +220,13 @@ public class VariantContextUtilsUnitTest extends BaseTest {
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@DataProvider(name = "simplemergersiddata")
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public Object[][] createSimpleMergeRSIDData() {
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new SimpleMergeRSIDTest(".", ".");
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new SimpleMergeRSIDTest(".", ".", ".");
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new SimpleMergeRSIDTest("rs1", "rs1");
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new SimpleMergeRSIDTest("rs1", "rs1", "rs1");
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new SimpleMergeRSIDTest(".", "rs1", "rs1");
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new SimpleMergeRSIDTest("rs1", ".", "rs1");
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new SimpleMergeRSIDTest("rs1", "rs2", "rs1,rs2");
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new SimpleMergeRSIDTest("rs1", "rs2", "rs1", "rs1,rs2"); // duplicates
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new SimpleMergeRSIDTest("rs2", "rs1", "rs2,rs1");
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new SimpleMergeRSIDTest("rs2", "rs1", ".", "rs2,rs1");
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new SimpleMergeRSIDTest("rs2", ".", "rs1", "rs2,rs1");
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@ -171,32 +238,25 @@ public class VariantContextUtilsUnitTest extends BaseTest {
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@Test(dataProvider = "simplemergersiddata")
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public void testRSIDMerge(SimpleMergeRSIDTest cfg) {
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List<VariantContext> inputs = new ArrayList<VariantContext>();
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for ( String id : cfg.inputs ) {
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final VariantContext snpVC1 = makeVC("snpvc1", Arrays.asList(Aref, T));
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final List<VariantContext> inputs = new ArrayList<VariantContext>();
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for ( final String id : cfg.inputs ) {
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MutableVariantContext vc = new MutableVariantContext(snpVC1);
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if ( ! id.equals(".") ) vc.setID(id);
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inputs.add(vc);
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}
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VariantContext merged = myMerge(inputs);
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final VariantContext merged = VariantContextUtils.simpleMerge(genomeLocParser,
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inputs, null,
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VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED,
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VariantContextUtils.GenotypeMergeType.UNSORTED, false, false, "set", false, false);
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Assert.assertEquals(merged.getID(), cfg.expected.equals(".") ? null : cfg.expected);
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}
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private VariantContext myMerge(List<VariantContext> inputs) {
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List<String> priority = new ArrayList<String>();
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for ( VariantContext vc : inputs ) priority.add(vc.getSource());
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return VariantContextUtils.simpleMerge(genomeLocParser,
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inputs, priority,
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VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED,
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VariantContextUtils.GenotypeMergeType.PRIORITIZE, true, false, "set", false, false);
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}
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// todo -- add tests for subset merging, especially with correct PLs
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// todo -- test priority list
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// todo -- test priority list: intersection, filtered in all, reference in all, X-filteredInX, X
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// todo -- test FilteredRecordMergeType
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// todo -- no annotate origin
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// todo -- test set key
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// todo -- test filtered are uncalled
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}
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