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Bugfix for hom ref records that aren't GVCF blocks.

This commit is contained in:
Ryan Poplin 2013-09-27 11:24:35 -04:00
parent f3a67edc24
commit ef1d58b7ff
3 changed files with 34 additions and 2 deletions
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2
protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
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@ -374,7 +374,7 @@ public class UnifiedGenotyperEngine {
final VariantContext vc,
final GenotypeLikelihoodsCalculationModel.Model model,
final Map<String, org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap> perReadAlleleLikelihoodMap) {
return calculateGenotypes(tracker, refContext, rawContext, stratifiedContexts, vc, model, false,perReadAlleleLikelihoodMap);
return calculateGenotypes(tracker, refContext, rawContext, stratifiedContexts, vc, model, false, perReadAlleleLikelihoodMap);
}
/**

5
protected/java/src/org/broadinstitute/sting/utils/gvcf/GVCFWriter.java
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@ -46,6 +46,9 @@
package org.broadinstitute.sting.utils.gvcf;
import org.broadinstitute.sting.gatk.walkers.haplotypecaller.ReferenceConfidenceModel;
import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.variant.variantcontext.Genotype;
import org.broadinstitute.variant.variantcontext.GenotypeBuilder;
import org.broadinstitute.variant.variantcontext.VariantContext;
@ -284,7 +287,7 @@ public class GVCFWriter implements VariantContextWriter {
}
final Genotype g = vc.getGenotype(0);
if ( g.isHomRef() ) {
if ( g.isHomRef() && vc.hasAlternateAllele(GATKVariantContextUtils.NON_REF_SYMBOLIC_ALLELE) ) {
// create bands
final VariantContext maybeCompletedBand = addHomRefSite(vc, g);
if ( maybeCompletedBand != null ) underlyingWriter.add(maybeCompletedBand);

29
protected/java/test/org/broadinstitute/sting/utils/gvcf/GVCFWriterUnitTest.java
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@ -129,6 +129,16 @@ public class GVCFWriterUnitTest extends BaseTest {
return vcb.genotypes(gb.make()).make();
}
private VariantContext makeHomRefAlt(final String contig, final int start, final int GQ) {
final VariantContextBuilder vcb = new VariantContextBuilder("test", contig, start, start, Arrays.asList(REF, ALT));
final GenotypeBuilder gb = new GenotypeBuilder(SAMPLE_NAME, Arrays.asList(REF, REF));
gb.GQ(GQ);
gb.DP(10);
gb.AD(new int[]{1, 2});
gb.PL(new int[]{0, 10, 100});
return vcb.genotypes(gb.make()).make();
}
private VariantContext makeNonRef(final String contig, final int start, final int GQ) {
final VariantContextBuilder vcb = new VariantContextBuilder("test", contig, start, start, Arrays.asList(REF, ALT));
final GenotypeBuilder gb = new GenotypeBuilder(SAMPLE_NAME, Arrays.asList(REF, ALT));
@ -305,6 +315,25 @@ public class GVCFWriterUnitTest extends BaseTest {
assertGoodVC(mockWriter.emitted.get(2), "20", 6, 7, false);
}
@Test
public void testHomRefAlt() {
final GVCFWriter writer = new GVCFWriter(mockWriter, standardPartition);
writer.add(makeHomRef("20", 1, 0));
writer.add(makeHomRef("20", 2, 0));
writer.add(makeHomRefAlt("20", 3, 0));
writer.add(makeHomRef("20", 4, 0));
writer.add(makeHomRef("20", 5, 0));
writer.add(makeHomRef("20", 6, 0));
writer.add(makeHomRef("20", 7, 0));
writer.close();
Assert.assertEquals(mockWriter.emitted.size(), 3);
assertGoodVC(mockWriter.emitted.get(0), "20", 1, 2, false);
Assert.assertFalse(mockWriter.emitted.get(1).hasAttribute("END"));
Assert.assertFalse(mockWriter.emitted.get(1).hasAttribute("BLOCK_SIZE"));
assertGoodVC(mockWriter.emitted.get(2), "20", 4, 7, false);
}
@DataProvider(name = "BandPartitionData")
public Object[][] makeBandPartitionData() {
List<Object[]> tests = new ArrayList<>();