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Better tests for Genotype parsing

This commit is contained in:
Mark DePristo 2012-06-05 14:36:10 -04:00
parent 4a4d3cde3d
commit 249d5e5533
2 changed files with 81 additions and 3 deletions
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6
public/java/test/org/broadinstitute/sting/utils/codecs/bcf2/BCF2EncoderDecoderUnitTest.java
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@ -31,7 +31,6 @@ package org.broadinstitute.sting.utils.codecs.bcf2;
import org.apache.commons.lang.ArrayUtils;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.utils.exceptions.StingException;
import org.testng.Assert;
import org.testng.annotations.BeforeSuite;
import org.testng.annotations.DataProvider;
@ -41,7 +40,10 @@ import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.util.*;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.List;
public class BCF2EncoderDecoderUnitTest extends BaseTest {

78
public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextTestProvider.java
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@ -29,6 +29,7 @@ import org.broad.tribble.FeatureCodec;
import org.broad.tribble.FeatureCodecHeader;
import org.broad.tribble.readers.PositionalBufferedStream;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.codecs.bcf2.BCF2Codec;
import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.sting.utils.collections.Pair;
@ -107,7 +108,14 @@ public class VariantContextTestProvider {
final VariantContext vc = vcs.get(0);
final VariantContextBuilder builder = new VariantContextBuilder(vc);
builder.noGenotypes();
b.append(builder.make().toString()).append(" nGenotypes = ").append(vc.getNSamples());
b.append(builder.make().toString());
if ( vc.getNSamples() < 5 ) {
for ( final Genotype g : vc.getGenotypes() )
b.append(g.toString());
} else {
b.append(" nGenotypes = ").append(vc.getNSamples());
}
if ( vcs.size() > 1 ) b.append(" ----- with another ").append(vcs.size() - 1).append(" VariantContext records");
b.append("]");
return b.toString();
@ -235,6 +243,8 @@ public class VariantContextTestProvider {
add(builder().attribute("STRING20", Arrays.asList("s1", "s2", "s3", "s4", "s5", "s6", "s7", "s8", "s9", "s10", "s11", "s12", "s13", "s14", "s15", "s16", "s17", "s18", "s19", "s20")));
addGenotypesToTestData();
addComplexGenotypesTest();
}
private static void addGenotypesToTestData() {
@ -531,6 +541,72 @@ public class VariantContextTestProvider {
Assert.assertEquals(actual, expected);
}
public static void addComplexGenotypesTest() {
final List<Allele> allAlleles = Arrays.asList(
Allele.create("A", true),
Allele.create("C", false),
Allele.create("G", false));
for ( int nAlleles : Arrays.asList(2, 3) ) {
for ( int highestPloidy : Arrays.asList(1, 2, 3) ) {
// site alleles
final List<Allele> siteAlleles = allAlleles.subList(0, nAlleles);
// possible alleles for genotypes
final List<Allele> possibleGenotypeAlleles = new ArrayList<Allele>(siteAlleles);
possibleGenotypeAlleles.add(Allele.NO_CALL);
// there are n^ploidy possible genotypes
final List<List<Allele>> possibleGenotypes = makeAllGenotypes(possibleGenotypeAlleles, highestPloidy);
final int nPossibleGenotypes = possibleGenotypes.size();
VariantContextBuilder vb = new VariantContextBuilder("unittest", "1", 1, 1, siteAlleles);
// first test -- create n copies of each genotype
for ( int i = 0; i < nPossibleGenotypes; i++ ) {
final List<Genotype> samples = new ArrayList<Genotype>(3);
samples.add(GenotypeBuilder.create("sample" + i, possibleGenotypes.get(i)));
add(vb.genotypes(samples));
}
// second test -- create one sample with each genotype
{
final List<Genotype> samples = new ArrayList<Genotype>(nPossibleGenotypes);
for ( int i = 0; i < nPossibleGenotypes; i++ ) {
samples.add(GenotypeBuilder.create("sample" + i, possibleGenotypes.get(i)));
}
add(vb.genotypes(samples));
}
// test mixed ploidy
for ( int i = 0; i < nPossibleGenotypes; i++ ) {
for ( int ploidy = 1; ploidy < highestPloidy; ploidy++ ) {
final List<Genotype> samples = new ArrayList<Genotype>(highestPloidy);
final List<Allele> genotype = possibleGenotypes.get(i).subList(0, ploidy);
samples.add(GenotypeBuilder.create("sample" + i, genotype));
add(vb.genotypes(samples));
}
}
}
}
}
private static final List<List<Allele>> makeAllGenotypes(final List<Allele> alleles, final int highestPloidy) {
final List<List<Allele>> combinations = new ArrayList<List<Allele>>();
if ( highestPloidy == 1 ) {
for ( final Allele a : alleles )
combinations.add(Collections.singletonList(a));
} else {
final List<List<Allele>> sub = makeAllGenotypes(alleles, highestPloidy - 1);
for ( List<Allele> subI : sub ) {
for ( final Allele a : alleles ) {
combinations.add(Utils.cons(a, subI));
}
}
}
return combinations;
}
public static void assertEquals(final VCFHeader actual, final VCFHeader expected) {
Assert.assertEquals(actual.getMetaData().size(), expected.getMetaData().size());