Genotype merging unit tests for simpleMerge
-- Remaining TODOs are all for GdA
This commit is contained in:
Mark DePristo
parent
4397ce8653
commit
a9f073fa68
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@ -21,14 +21,8 @@
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
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* OTHER DEALINGS IN THE SOFTWARE.
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*/
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// our package
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package org.broadinstitute.sting.utils.variantcontext;
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// the imports for unit testing.
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import net.sf.picard.reference.IndexedFastaSequenceFile;
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import org.apache.log4j.Priority;
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import org.broadinstitute.sting.BaseTest;
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@ -47,7 +41,6 @@ import java.io.File;
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import java.io.FileNotFoundException;
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import java.util.*;
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public class VariantContextUtilsUnitTest extends BaseTest {
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Allele Aref, T, C, delRef, ATC, ATCATC;
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private GenomeLocParser genomeLocParser;
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@ -72,10 +65,22 @@ public class VariantContextUtilsUnitTest extends BaseTest {
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ATCATC = Allele.create("ATCATC");
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}
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private Genotype makeG(String sample, Allele a1, Allele a2) {
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return new Genotype(sample, Arrays.asList(a1, a2));
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}
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private Genotype makeG(String sample, Allele a1, Allele a2, double log10pError) {
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return new Genotype(sample, Arrays.asList(a1, a2), log10pError);
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}
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private VariantContext makeVC(String source, List<Allele> alleles) {
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return makeVC(source, alleles, null, null);
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}
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private VariantContext makeVC(String source, List<Allele> alleles, Genotype... g1) {
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return makeVC(source, alleles, Arrays.asList(g1));
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}
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private VariantContext makeVC(String source, List<Allele> alleles, String filter) {
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return makeVC(source, alleles, filter.equals(".") ? null : new HashSet<String>(Arrays.asList(filter)));
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}
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@ -121,66 +126,66 @@ public class VariantContextUtilsUnitTest extends BaseTest {
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public Object[][] mergeAllelesData() {
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// first, do no harm
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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 MergeAllelesTest(Arrays.asList(Aref),
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Arrays.asList(Aref),
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Arrays.asList(Aref));
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Arrays.asList(Aref),
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Arrays.asList(Aref));
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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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Arrays.asList(Aref, T),
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Arrays.asList(Aref, T));
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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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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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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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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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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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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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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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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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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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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 List<String> priority = vcs2priority(inputs);
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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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@ -281,87 +286,82 @@ public class VariantContextUtilsUnitTest extends BaseTest {
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@DataProvider(name = "mergeFiltered")
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public Object[][] mergeFilteredData() {
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new MergeFilteredTest("AllPass",
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makeVC("1", Arrays.asList(Aref, T), VariantContext.PASSES_FILTERS),
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makeVC("2", Arrays.asList(Aref, T), VariantContext.PASSES_FILTERS),
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makeVC("3", Arrays.asList(Aref, T), VariantContext.PASSES_FILTERS),
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VariantContextUtils.MERGE_INTERSECTION);
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makeVC("1", Arrays.asList(Aref, T), VariantContext.PASSES_FILTERS),
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makeVC("2", Arrays.asList(Aref, T), VariantContext.PASSES_FILTERS),
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makeVC("3", Arrays.asList(Aref, T), VariantContext.PASSES_FILTERS),
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VariantContextUtils.MERGE_INTERSECTION);
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new MergeFilteredTest("noFilters",
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makeVC("1", Arrays.asList(Aref, T), "."),
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makeVC("2", Arrays.asList(Aref, T), "."),
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makeVC("3", Arrays.asList(Aref, T), "."),
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VariantContextUtils.MERGE_INTERSECTION);
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makeVC("1", Arrays.asList(Aref, T), "."),
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makeVC("2", Arrays.asList(Aref, T), "."),
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makeVC("3", Arrays.asList(Aref, T), "."),
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VariantContextUtils.MERGE_INTERSECTION);
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new MergeFilteredTest("oneFiltered",
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makeVC("1", Arrays.asList(Aref, T), "."),
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makeVC("2", Arrays.asList(Aref, T), "FAIL"),
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makeVC("3", Arrays.asList(Aref, T), "."),
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String.format("1-%s2", VariantContextUtils.MERGE_FILTER_PREFIX));
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makeVC("1", Arrays.asList(Aref, T), "."),
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makeVC("2", Arrays.asList(Aref, T), "FAIL"),
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makeVC("3", Arrays.asList(Aref, T), "."),
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String.format("1-%s2", VariantContextUtils.MERGE_FILTER_PREFIX));
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new MergeFilteredTest("onePassOneFail",
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makeVC("1", Arrays.asList(Aref, T), VariantContext.PASSES_FILTERS),
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makeVC("2", Arrays.asList(Aref, T), "FAIL"),
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makeVC("3", Arrays.asList(Aref, T), VariantContext.PASSES_FILTERS),
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String.format("1-%s2", VariantContextUtils.MERGE_FILTER_PREFIX));
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makeVC("1", Arrays.asList(Aref, T), VariantContext.PASSES_FILTERS),
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makeVC("2", Arrays.asList(Aref, T), "FAIL"),
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makeVC("3", Arrays.asList(Aref, T), VariantContext.PASSES_FILTERS),
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String.format("1-%s2", VariantContextUtils.MERGE_FILTER_PREFIX));
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new MergeFilteredTest("AllFiltered",
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makeVC("1", Arrays.asList(Aref, T), "FAIL"),
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makeVC("2", Arrays.asList(Aref, T), "FAIL"),
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makeVC("3", Arrays.asList(Aref, T), "FAIL"),
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VariantContextUtils.MERGE_FILTER_IN_ALL);
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makeVC("1", Arrays.asList(Aref, T), "FAIL"),
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makeVC("2", Arrays.asList(Aref, T), "FAIL"),
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makeVC("3", Arrays.asList(Aref, T), "FAIL"),
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VariantContextUtils.MERGE_FILTER_IN_ALL);
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// test ALL vs. ANY
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new MergeFilteredTest("FailOneUnfiltered",
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makeVC("1", Arrays.asList(Aref, T), "FAIL"),
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makeVC("2", Arrays.asList(Aref, T), "."),
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makeVC("3", Arrays.asList(Aref, T), "."),
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VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED,
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String.format("%s1-2", VariantContextUtils.MERGE_FILTER_PREFIX));
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makeVC("1", Arrays.asList(Aref, T), "FAIL"),
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makeVC("2", Arrays.asList(Aref, T), "."),
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makeVC("3", Arrays.asList(Aref, T), "."),
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VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED,
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String.format("%s1-2", VariantContextUtils.MERGE_FILTER_PREFIX));
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new MergeFilteredTest("OneFailAllUnfilteredArg",
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makeVC("1", Arrays.asList(Aref, T), "FAIL"),
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makeVC("2", Arrays.asList(Aref, T), "."),
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makeVC("3", Arrays.asList(Aref, T), "FAIL"),
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VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ALL_UNFILTERED,
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String.format("%s1-2", VariantContextUtils.MERGE_FILTER_PREFIX));
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makeVC("1", Arrays.asList(Aref, T), "FAIL"),
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makeVC("2", Arrays.asList(Aref, T), "."),
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makeVC("3", Arrays.asList(Aref, T), "FAIL"),
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VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ALL_UNFILTERED,
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String.format("%s1-2", VariantContextUtils.MERGE_FILTER_PREFIX));
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// test excluding allele in filtered record
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new MergeFilteredTest("DontIncludeAlleleOfFilteredRecords",
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makeVC("1", Arrays.asList(Aref, T), "."),
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makeVC("2", Arrays.asList(Aref, T), "FAIL"),
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makeVC("3", Arrays.asList(Aref, T), "."),
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String.format("1-%s2", VariantContextUtils.MERGE_FILTER_PREFIX));
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makeVC("1", Arrays.asList(Aref, T), "."),
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makeVC("2", Arrays.asList(Aref, T), "FAIL"),
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makeVC("3", Arrays.asList(Aref, T), "."),
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String.format("1-%s2", VariantContextUtils.MERGE_FILTER_PREFIX));
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// promotion of site from unfiltered to PASSES
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new MergeFilteredTest("UnfilteredPlusPassIsPass",
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makeVC("1", Arrays.asList(Aref, T), "."),
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makeVC("2", Arrays.asList(Aref, T), VariantContext.PASSES_FILTERS),
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makeVC("3", Arrays.asList(Aref, T), VariantContext.PASSES_FILTERS),
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VariantContextUtils.MERGE_INTERSECTION);
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makeVC("1", Arrays.asList(Aref, T), "."),
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makeVC("2", Arrays.asList(Aref, T), VariantContext.PASSES_FILTERS),
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makeVC("3", Arrays.asList(Aref, T), VariantContext.PASSES_FILTERS),
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VariantContextUtils.MERGE_INTERSECTION);
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new MergeFilteredTest("RefInAll",
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makeVC("1", Arrays.asList(Aref), VariantContext.PASSES_FILTERS),
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makeVC("2", Arrays.asList(Aref), VariantContext.PASSES_FILTERS),
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makeVC("3", Arrays.asList(Aref), VariantContext.PASSES_FILTERS),
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VariantContextUtils.MERGE_REF_IN_ALL);
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makeVC("1", Arrays.asList(Aref), VariantContext.PASSES_FILTERS),
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makeVC("2", Arrays.asList(Aref), VariantContext.PASSES_FILTERS),
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makeVC("3", Arrays.asList(Aref), VariantContext.PASSES_FILTERS),
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VariantContextUtils.MERGE_REF_IN_ALL);
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new MergeFilteredTest("RefInOne",
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makeVC("1", Arrays.asList(Aref), VariantContext.PASSES_FILTERS),
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makeVC("2", Arrays.asList(Aref, T), VariantContext.PASSES_FILTERS),
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makeVC("3", Arrays.asList(Aref, T), VariantContext.PASSES_FILTERS),
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"2");
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makeVC("1", Arrays.asList(Aref), VariantContext.PASSES_FILTERS),
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makeVC("2", Arrays.asList(Aref, T), VariantContext.PASSES_FILTERS),
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makeVC("3", Arrays.asList(Aref, T), VariantContext.PASSES_FILTERS),
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"2");
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return MergeFilteredTest.getTests(MergeFilteredTest.class);
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}
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@Test(dataProvider = "mergeFiltered")
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public void testMergeFiltered(MergeFilteredTest cfg) {
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final List<String> priority = new ArrayList<String>();
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for ( final VariantContext vc : cfg.inputs ) {
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priority.add(vc.getSource());
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}
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final List<String> priority = vcs2priority(cfg.inputs);
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final VariantContext merged = VariantContextUtils.simpleMerge(genomeLocParser,
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cfg.inputs, priority, cfg.type, VariantContextUtils.GenotypeMergeType.PRIORITIZE, true, false, "set", false, false);
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@ -375,6 +375,148 @@ public class VariantContextUtilsUnitTest extends BaseTest {
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Assert.assertEquals(merged.getFilters(), cfg.expected.getFilters());
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}
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// --------------------------------------------------------------------------------
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//
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// Test genotype merging
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//
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// --------------------------------------------------------------------------------
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private class MergeGenotypesTest extends TestDataProvider {
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List<VariantContext> inputs;
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VariantContext expected;
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List<String> priority;
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private MergeGenotypesTest(String name, String priority, VariantContext... arg) {
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super(MergeGenotypesTest.class, name);
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LinkedList<VariantContext> all = new LinkedList<VariantContext>(Arrays.asList(arg));
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this.expected = all.pollLast();
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inputs = all;
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this.priority = Arrays.asList(priority.split(","));
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}
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public String toString() {
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return String.format("%s input=%s expected=%s", super.toString(), inputs, expected);
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}
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}
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@DataProvider(name = "mergeGenotypes")
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public Object[][] mergeGenotypesData() {
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new MergeGenotypesTest("TakeGenotypeByPriority-1,2", "1,2",
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makeVC("1", Arrays.asList(Aref, T), makeG("s1", Aref, T, 1)),
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makeVC("2", Arrays.asList(Aref, T), makeG("s1", Aref, T, 2)),
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makeVC("3", Arrays.asList(Aref, T), makeG("s1", Aref, T, 1)));
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new MergeGenotypesTest("TakeGenotypeByPriority-1,2-nocall", "1,2",
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makeVC("1", Arrays.asList(Aref, T), makeG("s1", Allele.NO_CALL, Allele.NO_CALL, 1)),
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makeVC("2", Arrays.asList(Aref, T), makeG("s1", Aref, T, 2)),
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makeVC("3", Arrays.asList(Aref, T), makeG("s1", Allele.NO_CALL, Allele.NO_CALL, 1)));
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new MergeGenotypesTest("TakeGenotypeByPriority-2,1", "2,1",
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makeVC("1", Arrays.asList(Aref, T), makeG("s1", Aref, T, 1)),
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makeVC("2", Arrays.asList(Aref, T), makeG("s1", Aref, T, 2)),
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makeVC("3", Arrays.asList(Aref, T), makeG("s1", Aref, T, 2)));
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new MergeGenotypesTest("NonOverlappingGenotypes", "1,2",
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makeVC("1", Arrays.asList(Aref, T), makeG("s1", Aref, T, 1)),
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makeVC("2", Arrays.asList(Aref, T), makeG("s2", Aref, T, 2)),
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makeVC("3", Arrays.asList(Aref, T), makeG("s1", Aref, T, 1), makeG("s2", Aref, T, 2)));
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new MergeGenotypesTest("PreserveNoCall", "1,2",
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makeVC("1", Arrays.asList(Aref, T), makeG("s1", Allele.NO_CALL, Allele.NO_CALL, 1)),
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makeVC("2", Arrays.asList(Aref, T), makeG("s2", Aref, T, 2)),
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makeVC("3", Arrays.asList(Aref, T), makeG("s1", Allele.NO_CALL, Allele.NO_CALL, 1), makeG("s2", Aref, T, 2)));
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new MergeGenotypesTest("PerserveAlleles", "1,2",
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makeVC("1", Arrays.asList(Aref, T), makeG("s1", Aref, T, 1)),
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makeVC("2", Arrays.asList(Aref, C), makeG("s2", Aref, C, 2)),
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makeVC("3", Arrays.asList(Aref, C, T), makeG("s1", Aref, T, 1), makeG("s2", Aref, C, 2)));
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new MergeGenotypesTest("TakeGenotypePartialOverlap-1,2", "1,2",
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makeVC("1", Arrays.asList(Aref, T), makeG("s1", Aref, T, 1)),
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makeVC("2", Arrays.asList(Aref, T), makeG("s1", Aref, T, 2), makeG("s3", Aref, T, 3)),
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makeVC("3", Arrays.asList(Aref, T), makeG("s1", Aref, T, 1), makeG("s3", Aref, T, 3)));
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new MergeGenotypesTest("TakeGenotypePartialOverlap-2,1", "2,1",
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makeVC("1", Arrays.asList(Aref, T), makeG("s1", Aref, T, 1)),
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makeVC("2", Arrays.asList(Aref, T), makeG("s1", Aref, T, 2), makeG("s3", Aref, T, 3)),
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makeVC("3", Arrays.asList(Aref, T), makeG("s1", Aref, T, 2), makeG("s3", Aref, T, 3)));
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// todo -- GDA -- add tests for merging correct PLs
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return MergeGenotypesTest.getTests(MergeGenotypesTest.class);
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}
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// todo -- add test for GenotypeMergeType UNIQUIFY, REQUIRE_UNIQUE
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@Test(dataProvider = "mergeGenotypes")
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public void testMergeGenotypes(MergeGenotypesTest cfg) {
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final VariantContext merged = VariantContextUtils.simpleMerge(genomeLocParser,
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cfg.inputs, cfg.priority, VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED,
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VariantContextUtils.GenotypeMergeType.PRIORITIZE, true, false, "set", false, false);
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// test alleles are equal
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Assert.assertEquals(merged.getAlleles(), cfg.expected.getAlleles());
|
||||
|
||||
// test genotypes
|
||||
assertGenotypesAreMostlyEqual(merged.getGenotypes(), cfg.expected.getGenotypes());
|
||||
}
|
||||
|
||||
// necessary to not overload equals for genotypes
|
||||
private void assertGenotypesAreMostlyEqual(Map<String, Genotype> actual, Map<String, Genotype> expected) {
|
||||
if (actual == expected) {
|
||||
return;
|
||||
}
|
||||
|
||||
if (actual == null || expected == null) {
|
||||
Assert.fail("Maps not equal: expected: " + expected + " and actual: " + actual);
|
||||
}
|
||||
|
||||
if (actual.size() != expected.size()) {
|
||||
Assert.fail("Maps do not have the same size:" + actual.size() + " != " + expected.size());
|
||||
}
|
||||
|
||||
for (Map.Entry<String, Genotype> entry : actual.entrySet()) {
|
||||
String key = entry.getKey();
|
||||
Genotype value = entry.getValue();
|
||||
Genotype expectedValue = expected.get(key);
|
||||
|
||||
Assert.assertEquals(value.alleles, expectedValue.alleles);
|
||||
Assert.assertEquals(value.getNegLog10PError(), expectedValue.getNegLog10PError());
|
||||
Assert.assertEquals(value.hasLikelihoods(), expectedValue.hasLikelihoods());
|
||||
if ( value.hasLikelihoods() )
|
||||
Assert.assertEquals(value.getLikelihoods(), expectedValue.getLikelihoods());
|
||||
}
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testMergeGenotypesUniquify() {
|
||||
final VariantContext vc1 = makeVC("1", Arrays.asList(Aref, T), makeG("s1", Aref, T, 1));
|
||||
final VariantContext vc2 = makeVC("2", Arrays.asList(Aref, T), makeG("s1", Aref, T, 2));
|
||||
|
||||
final VariantContext merged = VariantContextUtils.simpleMerge(genomeLocParser,
|
||||
Arrays.asList(vc1, vc2), null, VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED,
|
||||
VariantContextUtils.GenotypeMergeType.UNIQUIFY, false, false, "set", false, false);
|
||||
|
||||
// test genotypes
|
||||
Assert.assertEquals(merged.getGenotypes().keySet(), new HashSet<String>(Arrays.asList("s1.1", "s1.2")));
|
||||
}
|
||||
|
||||
@Test(expectedExceptions = UserException.class)
|
||||
public void testMergeGenotypesRequireUnique() {
|
||||
final VariantContext vc1 = makeVC("1", Arrays.asList(Aref, T), makeG("s1", Aref, T, 1));
|
||||
final VariantContext vc2 = makeVC("2", Arrays.asList(Aref, T), makeG("s1", Aref, T, 2));
|
||||
|
||||
final VariantContext merged = VariantContextUtils.simpleMerge(genomeLocParser,
|
||||
Arrays.asList(vc1, vc2), null, VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED,
|
||||
VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE, false, false, "set", false, false);
|
||||
}
|
||||
|
||||
// --------------------------------------------------------------------------------
|
||||
//
|
||||
// Misc. tests
|
||||
//
|
||||
// --------------------------------------------------------------------------------
|
||||
|
||||
@Test
|
||||
public void testAnnotationSet() {
|
||||
for ( final boolean annotate : Arrays.asList(true, false)) {
|
||||
|
|
@ -395,6 +537,13 @@ public class VariantContextUtilsUnitTest extends BaseTest {
|
|||
}
|
||||
}
|
||||
|
||||
// todo -- add tests for subset merging, especially with correct PLs
|
||||
// todo -- test priority list
|
||||
private static final List<String> vcs2priority(final Collection<VariantContext> vcs) {
|
||||
final List<String> priority = new ArrayList<String>();
|
||||
|
||||
for ( final VariantContext vc : vcs ) {
|
||||
priority.add(vc.getSource());
|
||||
}
|
||||
|
||||
return priority;
|
||||
}
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue