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start of VariantContextUtils UnitTest 

-- tests rsID merging
This commit is contained in:
Mark DePristo 2011-09-22 12:10:39 -04:00
parent 8ca4b5e938
commit ba5f83fee2
2 changed files with 125 additions and 7 deletions
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8
public/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java
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@ -25,16 +25,16 @@ public class Genotype {
protected boolean isPhased = false;
protected boolean filtersWereAppliedToContext;
public Genotype(String sampleName, List<Allele> alleles, double negLog10PError, Set<String> filters, Map<String, ? super Object> attributes, boolean isPhased) {
public Genotype(String sampleName, List<Allele> alleles, double negLog10PError, Set<String> filters, Map<String, ?> attributes, boolean isPhased) {
this(sampleName, alleles, negLog10PError, filters, attributes, isPhased, null);
}
public Genotype(String sampleName, List<Allele> alleles, double negLog10PError, Set<String> filters, Map<String, ? super Object> attributes, boolean isPhased, double[] log10Likelihoods) {
public Genotype(String sampleName, List<Allele> alleles, double negLog10PError, Set<String> filters, Map<String, ?> attributes, boolean isPhased, double[] log10Likelihoods) {
if ( alleles != null )
this.alleles = Collections.unmodifiableList(alleles);
if ( log10Likelihoods != null )
attributes.put(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY, GenotypeLikelihoods.fromLog10Likelihoods(log10Likelihoods));
commonInfo = new InferredGeneticContext(sampleName, negLog10PError, filters, attributes);
if ( log10Likelihoods != null )
commonInfo.putAttribute(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY, GenotypeLikelihoods.fromLog10Likelihoods(log10Likelihoods));
filtersWereAppliedToContext = filters != null;
this.isPhased = isPhased;
validate();

124
public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUtilsUnitTest.java
View File

@ -30,6 +30,7 @@ package org.broadinstitute.sting.utils.variantcontext;
import net.sf.picard.reference.IndexedFastaSequenceFile;
import org.apache.log4j.Priority;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.gatk.refdata.tracks.FeatureManager;
import org.broadinstitute.sting.utils.GenomeLocParser;
@ -39,6 +40,7 @@ import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
import org.testng.Assert;
import org.testng.annotations.BeforeSuite;
import org.testng.annotations.Test;
import org.testng.annotations.DataProvider;
import java.io.File;
import java.io.FileNotFoundException;
@ -47,8 +49,9 @@ import java.util.*;
public class VariantContextUtilsUnitTest extends BaseTest {
Allele Aref, T, delRef, ATC;
Genotype snp1, snp2, indel1;
Genotype ref1, snp1, snp2, indel1, indelref;
private GenomeLocParser genomeLocParser;
VariantContext refVC, snpVC1, snpVC2, snpVC3, snpVC4, indelVC1, indelVC2, indelVC3;
@BeforeSuite
public void setup() {
@ -67,18 +70,133 @@ public class VariantContextUtilsUnitTest extends BaseTest {
T = Allele.create("T");
ATC = Allele.create("ATC");
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));
}
private VariantContext makeVC(String source, List<Allele> alleles) {
return makeVC(source, alleles, null, null);
}
private VariantContext makeVC(String source, List<Allele> alleles, Collection<Genotype> genotypes) {
return makeVC(source, alleles, genotypes, null);
}
private VariantContext makeVC(String source, List<Allele> alleles, Collection<Genotype> genotypes, Set<String> filters) {
int start = 10;
int stop = alleles.contains(ATC) ? start + 3 : start;
return new VariantContext(source, "1", start, stop, alleles, genotypes, 1.0, filters, null);
int stop = start; // alleles.contains(ATC) ? start + 3 : start;
return new VariantContext(source, "1", start, stop, alleles,
VariantContext.genotypeCollectionToMap(new TreeMap<String, Genotype>(), genotypes),
1.0, filters, null, (byte)'C');
}
private class SimpleMergeTest extends TestDataProvider {
List<VariantContext> inputVCs;
VariantContext expectedVC;
private SimpleMergeTest(VariantContext... vcsArg) {
super(SimpleMergeTest.class);
LinkedList<VariantContext> allVCs = new LinkedList<VariantContext>(Arrays.asList(vcsArg));
expectedVC = allVCs.pollLast();
inputVCs = allVCs;
}
public String toString() {
return String.format("SimpleMergeTest vc=%s expected=%s", inputVCs, expectedVC);
}
}
@DataProvider(name = "simplemergedata")
public Object[][] createSimpleMergeData() {
// first, do no harm
new SimpleMergeTest(refVC, refVC);
new SimpleMergeTest(snpVC1, snpVC1);
new SimpleMergeTest(indelVC1, indelVC1);
new SimpleMergeTest(indelVC3, indelVC3);
new SimpleMergeTest(refVC, snpVC1, snpVC3);
new SimpleMergeTest(snpVC1, snpVC2, snpVC2);
new SimpleMergeTest(refVC, snpVC2, snpVC4);
new SimpleMergeTest(indelVC1, indelVC2, indelVC3);
new SimpleMergeTest(indelVC1, indelVC3, indelVC3);
new SimpleMergeTest(indelVC2, indelVC3, indelVC3);
return SimpleMergeTest.getTests(SimpleMergeTest.class);
}
private class SimpleMergeRSIDTest extends TestDataProvider {
List<String> inputs;
String expected;
private SimpleMergeRSIDTest(String... arg) {
super(SimpleMergeRSIDTest.class);
LinkedList<String> allStrings = new LinkedList<String>(Arrays.asList(arg));
expected = allStrings.pollLast();
inputs = allStrings;
}
public String toString() {
return String.format("SimpleMergeRSIDTest vc=%s expected=%s", inputs, expected);
}
}
@DataProvider(name = "simplemergersiddata")
public Object[][] createSimpleMergeRSIDData() {
new SimpleMergeRSIDTest(".", ".");
new SimpleMergeRSIDTest("rs1", "rs1");
new SimpleMergeRSIDTest(".", "rs1", "rs1");
new SimpleMergeRSIDTest("rs1", ".", "rs1");
new SimpleMergeRSIDTest("rs1", "rs2", "rs1,rs2");
new SimpleMergeRSIDTest("rs2", "rs1", "rs2,rs1");
new SimpleMergeRSIDTest("rs2", "rs1", ".", "rs2,rs1");
new SimpleMergeRSIDTest("rs2", ".", "rs1", "rs2,rs1");
new SimpleMergeRSIDTest("rs1", ".", ".", "rs1");
new SimpleMergeRSIDTest("rs1", "rs2", "rs3", "rs1,rs2,rs3");
return SimpleMergeRSIDTest.getTests(SimpleMergeRSIDTest.class);
}
@Test(dataProvider = "simplemergersiddata")
public void testRSIDMerge(SimpleMergeRSIDTest cfg) {
List<VariantContext> inputs = new ArrayList<VariantContext>();
for ( String id : cfg.inputs ) {
MutableVariantContext vc = new MutableVariantContext(snpVC1);
if ( ! id.equals(".") ) vc.setID(id);
inputs.add(vc);
}
VariantContext merged = myMerge(inputs);
Assert.assertEquals(merged.getID(), cfg.expected.equals(".") ? null : cfg.expected);
}
private VariantContext myMerge(List<VariantContext> inputs) {
List<String> priority = new ArrayList<String>();
for ( VariantContext vc : inputs ) priority.add(vc.getSource());
return VariantContextUtils.simpleMerge(genomeLocParser,
inputs, priority,
VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED,
VariantContextUtils.GenotypeMergeType.PRIORITIZE, true, false, "set", false, false);
}
// todo -- add tests for subset merging, especially with correct PLs
// todo -- test priority list
// todo -- test FilteredRecordMergeType
// todo -- no annotate origin
// todo -- test set key
// todo -- test filtered are uncalled
}