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Fix for performance problem in GGA mode related to previous --regenotype commit. Instead of trying to hack around the determination of the calculation model when it's not needed, just simply overload the calculateGenotypes() method to add one that does simple genotyping. Re-enabling the Pool Caller integration tests.

This commit is contained in:
Eric Banks 2012-08-16 13:05:17 -04:00
parent 04be0c92bf
commit 2df04dc48a
4 changed files with 19 additions and 12 deletions
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12
protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidyIntegrationTest.java
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@ -45,32 +45,32 @@ public class UnifiedGenotyperGeneralPloidyIntegrationTest extends WalkerTest {
executeTest("testPoolCaller:"+name+" args=" + args, spec);
}
@Test(enabled = false)
@Test(enabled = true)
public void testBOTH_GGA_Pools() {
PC_LSV_Test(String.format(" -maxAltAlleles 2 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s",LSV_ALLELES),"LSV_BOTH_GGA","BOTH","0934f72865388999efec64bd9d4a9b93");
}
@Test(enabled = false)
@Test(enabled = true)
public void testINDEL_GGA_Pools() {
PC_LSV_Test(String.format(" -maxAltAlleles 1 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s",LSV_ALLELES),"LSV_INDEL_GGA","INDEL","126581c72d287722437274d41b6fed7b");
}
@Test(enabled = false)
@Test(enabled = true)
public void testINDEL_maxAltAlleles2_ploidy3_Pools_noRef() {
PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","b543aa1c3efedb301e525c1d6c50ed8d");
}
@Test(enabled = false)
@Test(enabled = true)
public void testINDEL_maxAltAlleles2_ploidy1_Pools_noRef() {
PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 1","LSV_INDEL_DISC_NOREF_p1","INDEL","55b20557a836bb92688e68f12d7f5dc4");
}
@Test(enabled = false)
@Test(enabled = true)
public void testMT_SNP_DISCOVERY_sp4() {
PC_MT_Test(CEUTRIO_BAM, " -maxAltAlleles 1 -ploidy 8", "MT_SNP_DISCOVERY_sp4","7eb889e8e07182f4c3d64609591f9459");
}
@Test(enabled = false)
@Test(enabled = true)
public void testMT_SNP_GGA_sp10() {
PC_MT_Test(CEUTRIO_BAM, String.format(" -maxAltAlleles 1 -ploidy 20 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s",NA12891_CALLS), "MT_SNP_GGA_sp10", "db8114877b99b14f7180fdcd24b040a7");
}

15
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
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@ -38,7 +38,6 @@ import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.baq.BAQ;
import org.broadinstitute.sting.utils.classloader.PluginManager;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
@ -259,6 +258,16 @@ public class UnifiedGenotyperEngine {
return calculateGenotypes(tracker, refContext, rawContext, stratifiedContexts, vc, model);
}
/**
* Compute genotypes at a given locus.
*
* @param vc the GL-annotated variant context
* @return the VariantCallContext object
*/
public VariantCallContext calculateGenotypes(VariantContext vc) {
return calculateGenotypes(null, null, null, null, vc, GenotypeLikelihoodsCalculationModel.Model.valueOf("SNP"), false);
}
// ---------------------------------------------------------------------------------------------------------
//
@ -647,10 +656,8 @@ 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 = getVCFromAllelesRod(tracker, refContext, rawContext.getLocation(), false, logger, UAC.alleles);
if ( vcInput == null ) {
models.add(GenotypeLikelihoodsCalculationModel.Model.valueOf(modelPrefix+"SNP"));
if ( vcInput == null )
return models;
}
if ( vcInput.isSNP() ) {
// ignore SNPs if the user chose INDEL mode only

2
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
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@ -568,7 +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(null, ref, context, sub)).filters(sub.getFiltersMaybeNull());
final VariantContextBuilder builder = new VariantContextBuilder(UG_engine.calculateGenotypes(sub)).filters(sub.getFiltersMaybeNull());
addAnnotations(builder, sub);
sub = builder.make();
}

2
public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
View File

@ -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("52cb2f150559ca1457e9df7ec153dbb452cb2f150559ca1457e9df7ec153dbb4")
Arrays.asList("52cb2f150559ca1457e9df7ec153dbb4")
);
executeTest("testRegenotype--" + testFile, spec);