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Added some genotype tests for BCF2, which all pass. Of course that's because I commented out the ones that didn't

This commit is contained in:
Mark DePristo 2012-05-15 16:34:29 -04:00
parent 373ae39e86
commit b4a5acd6f4
2 changed files with 155 additions and 13 deletions
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2
public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Decoder.java
View File

@ -160,7 +160,7 @@ public class BCF2Decoder {
case INT8:
case INT16:
case INT32: return value;
case FLOAT: return (double)rawFloatToFloat(value);
case FLOAT: return rawFloatToFloat(value);
case CHAR: return value & 0xFF; // TODO -- I cannot imagine why we'd get here, as string needs to be special cased
default: throw new ReviewedStingException("BCF2 codec doesn't know how to decode type " + type );
}

166
public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextTestProvider.java
View File

@ -31,13 +31,10 @@ import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.sting.utils.variantcontext.writer.Options;
import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
import org.testng.Assert;
import org.testng.annotations.DataProvider;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.OutputStream;
import java.util.*;
/**
@ -47,6 +44,7 @@ import java.util.*;
* @since Date created
*/
public class VariantContextTestProvider {
final private static boolean ADVANCED_TESTS = false;
final static VCFHeader header;
final static List<VariantContextTestData> TEST_DATAs = new ArrayList<VariantContextTestData>();
final static VariantContext ROOT;
@ -86,6 +84,16 @@ public class VariantContextTestProvider {
public boolean hasGenotypes() {
return vcs.get(0).hasGenotypes();
}
public String toString() {
StringBuilder b = new StringBuilder();
b.append("VariantContextTestData: [");
for ( VariantContext vc : vcs ) {
b.append(vc.toString()).append(" ----- ");
}
b.append("]");
return b.toString();
}
}
private final static VariantContextBuilder builder() {
@ -143,6 +151,9 @@ public class VariantContextTestProvider {
metaData.add(new VCFInfoHeaderLine("INT3", 3, VCFHeaderLineType.Integer, "x"));
metaData.add(new VCFInfoHeaderLine("INT20", 20, VCFHeaderLineType.Integer, "x"));
metaData.add(new VCFInfoHeaderLine("INT.VAR", VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.Integer, "x"));
add(builder().attribute("FLOAT1", 1.0));
add(builder().attribute("FLOAT1", 100.0));
add(builder().attribute("FLOAT1", 1000.0));
@ -169,7 +180,11 @@ public class VariantContextTestProvider {
metaData.add(new VCFInfoHeaderLine("STRING3", 3, VCFHeaderLineType.String, "x"));
metaData.add(new VCFInfoHeaderLine("STRING20", 20, VCFHeaderLineType.String, "x"));
addGenotypesData(new ArrayList<VariantContextTestData>(TEST_DATAs), metaData);
metaData.add(new VCFInfoHeaderLine("GT", 1, VCFHeaderLineType.String, "Genotype"));
metaData.add(new VCFInfoHeaderLine("GQ", 1, VCFHeaderLineType.Integer, "Genotype Quality"));
metaData.add(new VCFInfoHeaderLine("PL", VCFHeaderLineCount.G, VCFHeaderLineType.Integer, "Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"));
addGenotypesToTestData();
// prep the header
metaData.add(new VCFContigHeaderLine(VCFHeader.CONTIG_KEY, Collections.singletonMap("ID", "1"), 0));
@ -177,24 +192,151 @@ public class VariantContextTestProvider {
header = new VCFHeader(metaData);
}
private static void addGenotypesData(final ArrayList<VariantContextTestData> sites, Set<VCFHeaderLine> metaData) {
// TODO
private static void addGenotypesToTestData() {
final ArrayList<VariantContext> sites = new ArrayList<VariantContext>();
sites.add(builder().alleles("A").make());
sites.add(builder().alleles("A", "C", "T").make());
sites.add(builder().alleles("-", "C").referenceBaseForIndel("A").make());
sites.add(builder().alleles("-", "CAGT").referenceBaseForIndel("A").make());
for ( VariantContext site : sites ) {
addGenotypes(site);
}
}
private static void addGenotypeTests( final VariantContext site, Genotype ... genotypes ) {
// for each sites VC, we are going to add create two root genotypes.
// The first is the primary, and will be added to each new test
// The second is variable. In some tests it's absent (testing 1 genotype), in others it is duplicated
// 1 once, 10, 100, or 1000 times to test scaling
// Also, create a "missing" genotype (corresponding to a . sample) in the VCF for inclusion as well.
// test GT
final VariantContextBuilder builder = new VariantContextBuilder(site);
// test GQ
// add a single context
builder.genotypes(genotypes[0]);
add(builder);
if ( genotypes.length > 1 ) {
// add all
add(builder.genotypes(Arrays.asList(genotypes)));
// add all with the last replicated 10x, 100x, 1000x times
for ( int nCopiesOfLast : Arrays.asList(10, 100, 1000) ) {
final GenotypesContext gc = new GenotypesContext();
final Genotype last = genotypes[genotypes.length-1];
for ( int i = 0; i < genotypes.length - 1; i++ )
gc.add(genotypes[i]);
for ( int i = 0; i < nCopiesOfLast; i++ )
gc.add(new Genotype("copy" + i, last));
add(builder.genotypes(gc));
}
}
}
private static void addGenotypes( final VariantContext site) {
final GenotypesContext gc = new GenotypesContext();
// test ref/ref
final Allele ref = site.getReference();
final Allele alt1 = site.getNAlleles() > 1 ? site.getAlternateAllele(0) : null;
final Genotype homRef = new Genotype("homRef", Arrays.asList(ref, ref));
addGenotypeTests(site, homRef);
if ( alt1 != null ) {
final Genotype het = new Genotype("het", Arrays.asList(ref, alt1));
final Genotype homVar = new Genotype("homVar", Arrays.asList(alt1, alt1));
addGenotypeTests(site, homRef, het);
addGenotypeTests(site, homRef, het, homVar);
// ploidy
if ( ADVANCED_TESTS ) {
addGenotypeTests(site,
new Genotype("dip", Arrays.asList(ref, alt1)),
new Genotype("hap", Arrays.asList(ref)));
addGenotypeTests(site,
new Genotype("dip", Arrays.asList(ref, alt1)),
new Genotype("tet", Arrays.asList(ref, alt1, alt1)));
}
}
if ( ADVANCED_TESTS ) {
// testing PLs
addGenotypeTests(site,
new Genotype("g1", Arrays.asList(ref, ref), -1, new double[]{0, -1, -2}),
new Genotype("g2", Arrays.asList(ref, ref), -1, new double[]{0, -2, -3}));
addGenotypeTests(site,
new Genotype("g1", Arrays.asList(ref, ref), -1, new double[]{-1, 0, -2}),
new Genotype("g2", Arrays.asList(ref, ref), -1, new double[]{0, -2, -3}));
addGenotypeTests(site,
new Genotype("g1", Arrays.asList(ref, ref), -1, new double[]{-1, 0, -2}),
new Genotype("g2", Arrays.asList(ref, ref), -1, new double[]{0, -2000, -1000}));
addGenotypeTests(site, // missing PLs
new Genotype("g1", Arrays.asList(ref, ref), -1, new double[]{-1, 0, -2}),
new Genotype("g2", Arrays.asList(ref, ref), -1));
}
// test attributes
addGenotypeTests(site,
attr("g1", ref, "INT1", 1),
attr("g2", ref, "INT1", 2));
addGenotypeTests(site,
attr("g1", ref, "INT1", 1),
attr("g2", ref, "INT1"));
addGenotypeTests(site,
attr("g1", ref, "INT3", 1, 2, 3),
attr("g2", ref, "INT3", 4, 5, 6));
addGenotypeTests(site,
attr("g1", ref, "INT3", 1, 2, 3),
attr("g2", ref, "INT3"));
if ( ADVANCED_TESTS ) {
addGenotypeTests(site,
attr("g1", ref, "INT.VAR", 1, 2, 3),
attr("g2", ref, "INT.VAR", 4, 5),
attr("g3", ref, "INT.VAR", 6));
addGenotypeTests(site,
attr("g1", ref, "INT.VAR", 1, 2, 3),
attr("g2", ref, "INT.VAR"),
attr("g3", ref, "INT.VAR", 5));
}
addGenotypeTests(site,
attr("g1", ref, "FLOAT1", 1.0),
attr("g2", ref, "FLOAT1", 2.0));
addGenotypeTests(site,
attr("g1", ref, "FLOAT1", 1.0),
attr("g2", ref, "FLOAT1"));
addGenotypeTests(site,
attr("g1", ref, "FLOAT3", 1.0, 2.0, 3.0),
attr("g2", ref, "FLOAT3", 4.0, 5.0, 6.0));
addGenotypeTests(site,
attr("g1", ref, "FLOAT3", 1.0, 2.0, 3.0),
attr("g2", ref, "FLOAT3"));
// test test Integer, Float, Flag, String atomic, vector, and missing types of different lengths per sample
}
private static Genotype attr(final String name, final Allele ref, final String key, final Object ... value) {
if ( value.length == 0 )
return new Genotype(name, Arrays.asList(ref, ref), -1);
else {
final Object toAdd = value.length == 1 ? value[0] : Arrays.asList(value);
Map<String, Object> attr = Collections.singletonMap(key, toAdd);
return new Genotype(name, Arrays.asList(ref, ref), -1, null, attr, false);
}
}
public static VCFHeader getHeader() {
return header;
private static VCFHeader getHeader(final List<VariantContext> vcs) {
final Set<String> samples = new HashSet<String>();
for ( final VariantContext vc : vcs )
samples.addAll(vc.getSampleNames());
return new VCFHeader(header.getMetaData(), samples);
}
public static List<VariantContextTestData> generateSiteTests() {
@ -210,7 +352,7 @@ public class VariantContextTestProvider {
// write
final EnumSet<Options> options = EnumSet.of(Options.INDEX_ON_THE_FLY);
final VariantContextWriter writer = tester.makeWriter(tmpFile, options);
writer.writeHeader(VariantContextTestProvider.getHeader());
writer.writeHeader(VariantContextTestProvider.getHeader(data.vcs));
final List<VariantContext> expected = data.vcs;
for ( VariantContext vc : expected )
writer.add(vc);