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simpleMerge UnitTest tests filtered VC merging

This commit is contained in:
Mark DePristo 2011-09-22 17:05:12 -04:00
parent 46ca33dc04
commit 5cf82f9236
2 changed files with 135 additions and 20 deletions
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14
public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
View File

@ -44,6 +44,11 @@ import java.io.Serializable;
import java.util.*;
public class VariantContextUtils {
public final static String MERGE_INTERSECTION = "Intersection";
public final static String MERGE_FILTER_IN_ALL = "FilteredInAll";
public final static String MERGE_REF_IN_ALL = "ReferenceInAll";
public final static String MERGE_FILTER_PREFIX = "filterIn";
final public static JexlEngine engine = new JexlEngine();
static {
engine.setSilent(false); // will throw errors now for selects that don't evaluate properly
@ -609,19 +614,20 @@ public class VariantContextUtils {
if ( filteredRecordMergeType == FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED && nFiltered != VCs.size() )
filters.clear();
if ( annotateOrigin ) { // we care about where the call came from
String setValue;
if ( nFiltered == 0 && variantSources.size() == priorityListOfVCs.size() ) // nothing was unfiltered
setValue = "Intersection";
setValue = MERGE_INTERSECTION;
else if ( nFiltered == VCs.size() ) // everything was filtered out
setValue = "FilteredInAll";
setValue = MERGE_FILTER_IN_ALL;
else if ( variantSources.isEmpty() ) // everyone was reference
setValue = "ReferenceInAll";
setValue = MERGE_REF_IN_ALL;
else {
LinkedHashSet<String> s = new LinkedHashSet<String>();
for ( VariantContext vc : VCs )
if ( vc.isVariant() )
s.add( vc.isFiltered() ? "filterIn" + vc.getSource() : vc.getSource() );
s.add( vc.isFiltered() ? MERGE_FILTER_PREFIX + vc.getSource() : vc.getSource() );
setValue = Utils.join("-", s);
}

141
public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUtilsUnitTest.java
View File

@ -41,6 +41,7 @@ import org.testng.Assert;
import org.testng.annotations.BeforeSuite;
import org.testng.annotations.Test;
import org.testng.annotations.DataProvider;
import org.yaml.snakeyaml.Yaml;
import java.io.File;
import java.io.FileNotFoundException;
@ -75,6 +76,14 @@ public class VariantContextUtilsUnitTest extends BaseTest {
return makeVC(source, alleles, null, null);
}
private VariantContext makeVC(String source, List<Allele> alleles, String filter) {
return makeVC(source, alleles, filter.equals(".") ? null : new HashSet<String>(Arrays.asList(filter)));
}
private VariantContext makeVC(String source, List<Allele> alleles, Set<String> filters) {
return makeVC(source, alleles, null, filters);
}
private VariantContext makeVC(String source, List<Allele> alleles, Collection<Genotype> genotypes) {
return makeVC(source, alleles, genotypes, null);
}
@ -179,22 +188,6 @@ public class VariantContextUtilsUnitTest extends BaseTest {
Assert.assertEquals(merged.getAlleles(), cfg.expected);
}
// VariantContext refVC, snpVC1, snpVC2, snpVC3, snpVC4, indelVC1, indelVC2, indelVC3;
// ref1 = new Genotype("ref1", Arrays.asList(Aref, Aref), 5, new double[]{0, 5, 10});
// snp1 = new Genotype("snp1", Arrays.asList(Aref,T), 10, new double[]{10, 0, 20});
// snp2 = new Genotype("snp2", Arrays.asList(T,T), 15, new double[]{25, 15, 0});
// indelref = new Genotype("indelref", Arrays.asList(delRef,delRef), 25, new double[]{0, 25, 30});
// indel1 = new Genotype("indel1", Arrays.asList(delRef,ATC), 20, new double[]{20, 0, 30});
//
// refVC = makeVC("refvc", Arrays.asList(Aref), Arrays.asList(ref1));
// snpVC1 = makeVC("snpvc1", Arrays.asList(Aref, T), Arrays.asList(snp1));
// snpVC2 = makeVC("snpvc2", Arrays.asList(Aref, T), Arrays.asList(snp1, snp2));
// snpVC3 = makeVC("snpvc3", Arrays.asList(Aref, T), Arrays.asList(ref1, snp1));
// snpVC4 = makeVC("snpvc4", Arrays.asList(Aref, T), Arrays.asList(ref1, snp1, snp2));
// indelVC1 = makeVC("indelvc1", Arrays.asList(delRef), Arrays.asList(indelref));
// indelVC2 = makeVC("indelvc2", Arrays.asList(delRef, ATC), Arrays.asList(indel1));
// indelVC3 = makeVC("indelvc3", Arrays.asList(delRef, ATC), Arrays.asList(indelref, indel1));
// --------------------------------------------------------------------------------
//
// Test rsID merging
@ -254,6 +247,122 @@ public class VariantContextUtilsUnitTest extends BaseTest {
Assert.assertEquals(merged.getID(), cfg.expected.equals(".") ? null : cfg.expected);
}
// --------------------------------------------------------------------------------
//
// Test filtered merging
//
// --------------------------------------------------------------------------------
private class MergeFilteredTest extends TestDataProvider {
List<VariantContext> inputs;
VariantContext expected;
String setExpected;
VariantContextUtils.FilteredRecordMergeType type;
private MergeFilteredTest(String name, VariantContext input1, VariantContext input2, VariantContext expected, String setExpected) {
this(name, input1, input2, expected, VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED, setExpected);
}
private MergeFilteredTest(String name, VariantContext input1, VariantContext input2, VariantContext expected, VariantContextUtils.FilteredRecordMergeType type, String setExpected) {
super(MergeFilteredTest.class, name);
LinkedList<VariantContext> all = new LinkedList<VariantContext>(Arrays.asList(input1, input2));
this.expected = expected;
this.type = type;
inputs = all;
this.setExpected = setExpected;
}
public String toString() {
return String.format("%s input=%s expected=%s", super.toString(), inputs, expected);
}
}
@DataProvider(name = "mergeFiltered")
public Object[][] mergeFilteredData() {
new MergeFilteredTest("AllPass",
makeVC("1", Arrays.asList(Aref, T), VariantContext.PASSES_FILTERS),
makeVC("2", Arrays.asList(Aref, T), VariantContext.PASSES_FILTERS),
makeVC("3", Arrays.asList(Aref, T), VariantContext.PASSES_FILTERS),
VariantContextUtils.MERGE_INTERSECTION);
new MergeFilteredTest("noFilters",
makeVC("1", Arrays.asList(Aref, T), "."),
makeVC("2", Arrays.asList(Aref, T), "."),
makeVC("3", Arrays.asList(Aref, T), "."),
VariantContextUtils.MERGE_INTERSECTION);
new MergeFilteredTest("oneFiltered",
makeVC("1", Arrays.asList(Aref, T), "."),
makeVC("2", Arrays.asList(Aref, T), "FAIL"),
makeVC("3", Arrays.asList(Aref, T), "."),
String.format("1-%s2", VariantContextUtils.MERGE_FILTER_PREFIX));
new MergeFilteredTest("onePassOneFail",
makeVC("1", Arrays.asList(Aref, T), VariantContext.PASSES_FILTERS),
makeVC("2", Arrays.asList(Aref, T), "FAIL"),
makeVC("3", Arrays.asList(Aref, T), VariantContext.PASSES_FILTERS),
String.format("1-%s2", VariantContextUtils.MERGE_FILTER_PREFIX));
new MergeFilteredTest("FailOneUnfiltered",
makeVC("1", Arrays.asList(Aref, T), "FAIL"),
makeVC("2", Arrays.asList(Aref, T), "."),
makeVC("3", Arrays.asList(Aref, T), "."),
String.format("%s1-2", VariantContextUtils.MERGE_FILTER_PREFIX));
new MergeFilteredTest("AllFiltered",
makeVC("1", Arrays.asList(Aref, T), "FAIL"),
makeVC("2", Arrays.asList(Aref, T), "FAIL"),
makeVC("3", Arrays.asList(Aref, T), "FAIL"),
VariantContextUtils.MERGE_FILTER_IN_ALL);
// test ALL vs. ANY
new MergeFilteredTest("OneFailAllUnfilteredArg",
makeVC("1", Arrays.asList(Aref, T), "FAIL"),
makeVC("2", Arrays.asList(Aref, T), "."),
makeVC("3", Arrays.asList(Aref, T), "FAIL"),
VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ALL_UNFILTERED,
String.format("%s1-2", VariantContextUtils.MERGE_FILTER_PREFIX));
// test excluding allele in filtered record
new MergeFilteredTest("DontIncludeAlleleOfFilteredRecords",
makeVC("1", Arrays.asList(Aref, T), "."),
makeVC("2", Arrays.asList(Aref, T), "FAIL"),
makeVC("3", Arrays.asList(Aref, T), "."),
String.format("1-%s2", VariantContextUtils.MERGE_FILTER_PREFIX));
// promotion of site from unfiltered to PASSES
new MergeFilteredTest("UnfilteredPlusPassIsPass",
makeVC("1", Arrays.asList(Aref, T), "."),
makeVC("2", Arrays.asList(Aref, T), VariantContext.PASSES_FILTERS),
makeVC("3", Arrays.asList(Aref, T), VariantContext.PASSES_FILTERS),
VariantContextUtils.MERGE_INTERSECTION);
return MergeFilteredTest.getTests(MergeFilteredTest.class);
}
@Test(dataProvider = "mergeFiltered")
public void testMergeFiltered(MergeFilteredTest cfg) {
final List<String> priority = new ArrayList<String>();
for ( final VariantContext vc : cfg.inputs ) {
priority.add(vc.getSource());
}
final VariantContext merged = VariantContextUtils.simpleMerge(genomeLocParser,
cfg.inputs, priority, cfg.type, VariantContextUtils.GenotypeMergeType.PRIORITIZE, true, false, "set", false, false);
// test alleles are equal
Assert.assertEquals(merged.getAlleles(), cfg.expected.getAlleles());
// test set field
Assert.assertEquals(merged.getAttribute("set"), cfg.setExpected);
// test filter field
Assert.assertEquals(merged.getFilters(), cfg.expected.getFilters());
}
// todo -- add tests for subset merging, especially with correct PLs
// todo -- test priority list: intersection, filtered in all, reference in all, X-filteredInX, X
// todo -- test FilteredRecordMergeType