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Fixing behavior of the --regenotype argument in SelectVariants to properly run in GenotypeGivenAlleles mode. Added integration tests to cover recent SV changes.

This commit is contained in:
Eric Banks 2012-08-14 14:21:42 -04:00
parent 34b62fa092
commit 8e3774fb0e
3 changed files with 16 additions and 13 deletions
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10
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
View File

@ -646,15 +646,17 @@ public class UnifiedGenotyperEngine {
// if we're genotyping given alleles and we have a requested SNP at this position, do SNP
if ( UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ) {
final VariantContext vcInput = UnifiedGenotyperEngine.getVCFromAllelesRod(tracker, refContext, rawContext.getLocation(), false, logger, UAC.alleles);
if ( vcInput == null )
final VariantContext vcInput = getVCFromAllelesRod(tracker, refContext, rawContext.getLocation(), false, logger, UAC.alleles);
if ( vcInput == null ) {
models.add(GenotypeLikelihoodsCalculationModel.Model.valueOf(modelPrefix+"SNP"));
return models;
}
if ( vcInput.isSNP() ) {
// ignore SNPs if the user chose INDEL mode only
if ( UAC.GLmodel.name().toUpperCase().contains("BOTH") || UAC.GLmodel.name().toUpperCase().contains("SNP") )
models.add(GenotypeLikelihoodsCalculationModel.Model.valueOf(modelPrefix+"SNP"));
}
}
else if ( vcInput.isIndel() || vcInput.isMixed() ) {
// ignore INDELs if the user chose SNP mode only
if ( UAC.GLmodel.name().toUpperCase().contains("BOTH") || UAC.GLmodel.name().toUpperCase().contains("INDEL") )
@ -759,7 +761,7 @@ public class UnifiedGenotyperEngine {
public static VariantContext getVCFromAllelesRod(RefMetaDataTracker tracker, ReferenceContext ref, GenomeLoc loc, boolean requireSNP, Logger logger, final RodBinding<VariantContext> allelesBinding) {
if ( tracker == null || ref == null || logger == null )
throw new ReviewedStingException("Bad arguments: tracker=" + tracker + " ref=" + ref + " logger=" + logger);
return null;
VariantContext vc = null;
// search for usable record

3
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
View File

@ -470,6 +470,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
final UnifiedArgumentCollection UAC = new UnifiedArgumentCollection();
UAC.GLmodel = GenotypeLikelihoodsCalculationModel.Model.BOTH;
UAC.OutputMode = UnifiedGenotyperEngine.OUTPUT_MODE.EMIT_ALL_SITES;
UAC.GenotypingMode = GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES;
UAC.NO_SLOD = true;
UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, null, null, samples, VariantContextUtils.DEFAULT_PLOIDY);
headerLines.addAll(UnifiedGenotyper.getHeaderInfo(UAC, null, null));
@ -567,7 +568,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
VariantContext sub = subsetRecord(vc, EXCLUDE_NON_VARIANTS);
if ( REGENOTYPE && sub.isPolymorphicInSamples() && hasPLs(sub) ) {
final VariantContextBuilder builder = new VariantContextBuilder(UG_engine.calculateGenotypes(tracker, ref, context, sub)).filters(sub.getFiltersMaybeNull());
final VariantContextBuilder builder = new VariantContextBuilder(UG_engine.calculateGenotypes(null, ref, context, sub)).filters(sub.getFiltersMaybeNull());
addAnnotations(builder, sub);
sub = builder.make();
}

16
public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
View File

@ -34,7 +34,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(" -sn A -sn B -sn C --variant " + testfile),
1,
Arrays.asList("3d98a024bf3aecbd282843e0af89d0e6")
Arrays.asList("125d1c9fa111cd38dfa2ff3900f16b57")
);
executeTest("testRepeatedLineSelection--" + testfile, spec);
@ -49,7 +49,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
+ b37hapmapGenotypes + " -disc " + testFile
+ " -o %s --no_cmdline_in_header -U LENIENT_VCF_PROCESSING",
1,
Arrays.asList("54289033d35d32b8ebbb38c51fbb614c")
Arrays.asList("c0b937edb6a8b6392d477511d4f1ebcf")
);
spec.disableShadowBCF();
@ -135,7 +135,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants -R " + b36KGReference + " -sn NA12892 --variant:dbsnp " + testFile + " -o %s --no_cmdline_in_header",
1,
Arrays.asList("d12ae1617deb38f5ed712dc326935b9a")
Arrays.asList("a554459c9ccafb9812ff6d8c06c11726")
);
executeTest("testUsingDbsnpName--" + testFile, spec);
@ -148,7 +148,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants -R " + b36KGReference + " -regenotype -sn NA12892 --variant " + testFile + " -o %s --no_cmdline_in_header",
1,
Arrays.asList("c22ad8864d9951403672a24c20d6c3c2")
Arrays.asList("52cb2f150559ca1457e9df7ec153dbb452cb2f150559ca1457e9df7ec153dbb4")
);
executeTest("testRegenotype--" + testFile, spec);
@ -161,10 +161,10 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants -R " + b36KGReference + " -sn NA12892 --variant " + testFile + " -o %s --no_cmdline_in_header",
1,
Arrays.asList("")
Arrays.asList("a554459c9ccafb9812ff6d8c06c11726")
);
executeTest("testRegenotype--" + testFile, spec);
executeTest("testRemoveMLE--" + testFile, spec);
}
@Test
@ -174,10 +174,10 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants -R " + b36KGReference + " -regenotype -sn NA12892 --variant " + testFile + " -o %s --no_cmdline_in_header",
1,
Arrays.asList("")
Arrays.asList("52cb2f150559ca1457e9df7ec153dbb4")
);
executeTest("testRegenotype--" + testFile, spec);
executeTest("testRemoveMLEAndRegenotype--" + testFile, spec);
}
@Test