zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Updating UnifiedGenotyper to use the new rod binding system.

This commit is contained in:
Ryan Poplin 2011-08-11 11:02:11 -04:00
parent 79c86e211f
commit c7b9a9ef0a
7 changed files with 54 additions and 18 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java
View File

@ -26,6 +26,7 @@
package org.broadinstitute.sting.gatk.walkers.genotyper;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@ -35,6 +36,7 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.util.Map;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
View File

@ -321,7 +321,7 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
haplotypeMap.clear();
if (getAlleleListFromVCF) {
for( final VariantContext vc_input : tracker.getValues(VariantContext.class, "alleles") ) {
for( final VariantContext vc_input : tracker.getValues(UAC.alleles) ) {
if( vc_input != null &&
allowableTypes.contains(vc_input.getType()) &&
ref.getLocus().getStart() == vc_input.getStart()) {

7
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
View File

@ -26,6 +26,7 @@
package org.broadinstitute.sting.gatk.walkers.genotyper;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@ -57,13 +58,13 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC
useAlleleFromVCF = UAC.GenotypingMode == GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES;
}
public static VariantContext getSNPVCFromAllelesRod(RefMetaDataTracker tracker, ReferenceContext ref, boolean requireSNP, Logger logger) {
public static VariantContext getSNPVCFromAllelesRod(RefMetaDataTracker tracker, ReferenceContext ref, 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);
VariantContext vc = null;
// search for usable record
for( final VariantContext vc_input : tracker.getValues(VariantContext.class, "alleles", ref.getLocus()) ) {
for( final VariantContext vc_input : tracker.getValues(allelesBinding) ) {
if ( vc_input != null && ! vc_input.isFiltered() && (! requireSNP || vc_input.isSNP() )) {
if ( vc == null ) {
vc = vc_input;
@ -95,7 +96,7 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC
if ( alternateAlleleToUse != null ) {
bestAlternateAllele = alternateAlleleToUse.getBases()[0];
} else if ( useAlleleFromVCF ) {
VariantContext vc = getSNPVCFromAllelesRod(tracker, ref, true, logger);
VariantContext vc = getSNPVCFromAllelesRod(tracker, ref, true, logger, UAC.alleles);
// ignore places where we don't have a variant
if ( vc == null )

9
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
View File

@ -27,6 +27,9 @@ package org.broadinstitute.sting.gatk.walkers.genotyper;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Hidden;
import org.broadinstitute.sting.commandline.Input;
import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.io.File;
@ -61,6 +64,11 @@ public class UnifiedArgumentCollection {
@Argument(fullName = "computeSLOD", shortName = "sl", doc = "If provided, we will calculate the SLOD", required = false)
public boolean COMPUTE_SLOD = false;
/**
* When the UnifiedGenotyper is put into GENOTYPE_GIVEN_ALLELES mode it will genotype the samples using only the alleles provide in this rod binding
*/
@Input(fullName="alleles", shortName = "alleles", doc="The set of alleles at which to genotype when in GENOTYPE_MODE = GENOTYPE_GIVEN_ALLELES", required=false)
public RodBinding<VariantContext> alleles;
// control the error modes
@Hidden
@ -168,6 +176,7 @@ public class UnifiedArgumentCollection {
uac.OUTPUT_DEBUG_INDEL_INFO = OUTPUT_DEBUG_INDEL_INFO;
uac.INDEL_HAPLOTYPE_SIZE = INDEL_HAPLOTYPE_SIZE;
uac.DO_CONTEXT_DEPENDENT_PENALTIES = DO_CONTEXT_DEPENDENT_PENALTIES;
uac.alleles = alleles;
uac.GET_GAP_PENALTIES_FROM_DATA = GET_GAP_PENALTIES_FROM_DATA;
uac.INDEL_RECAL_FILE = INDEL_RECAL_FILE;

37
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
View File

@ -25,10 +25,7 @@
package org.broadinstitute.sting.gatk.walkers.genotyper;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.ArgumentCollection;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.DownsampleType;
import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@ -69,9 +66,35 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
*/
@ArgumentCollection protected DbsnpArgumentCollection dbsnp = new DbsnpArgumentCollection();
public RodBinding<VariantContext> getDbsnpRodBinding() { return dbsnp.dbsnp; }
public RodBinding<SnpEffFeature> getSnpEffRodBinding() { return null; }
public List<RodBinding<VariantContext>> getCompRodBindings() { return Collections.emptyList(); }
public List<RodBinding<VariantContext>> getResourceRodBindings() { return Collections.emptyList(); }
/**
* The INFO field will be annotated with information on the most biologically-significant effect
* listed in the SnpEff output file for each variant.
*/
@Input(fullName="snpEffFile", shortName = "snpEffFile", doc="SnpEff file", required=false)
public RodBinding<SnpEffFeature> snpEffFile;
public RodBinding<SnpEffFeature> getSnpEffRodBinding() { return snpEffFile; }
/**
* If a record in the 'variant' track overlaps with a record from the provided comp track, the INFO field will be annotated
* as such in the output with the track name (e.g. -comp:FOO will have 'FOO' in the INFO field). Records that are filtered in the comp track will be ignored.
* Note that 'dbSNP' has been special-cased (see the --dbsnp argument).
*/
@Input(fullName="comp", shortName = "comp", doc="comparison VCF file", required=false)
public List<RodBinding<VariantContext>> comps = Collections.emptyList();
public List<RodBinding<VariantContext>> getCompRodBindings() { return comps; }
/**
* An external resource VCF file or files from which to annotate.
*
* One can add annotations from one of the resource VCFs to the output.
* For example, if you want to annotate your 'variant' VCF with the AC field value from the rod bound to 'resource',
* you can specify '-E resource.AC' and records in the output VCF will be annotated with 'resource.AC=N' when a record exists in that rod at the given position.
* If multiple records in the rod overlap the given position, one is chosen arbitrarily.
*/
@Input(fullName="resource", shortName = "resource", doc="external resource VCF file", required=false)
public List<RodBinding<VariantContext>> resources = Collections.emptyList();
public List<RodBinding<VariantContext>> getResourceRodBindings() { return resources; }
// control the output
@Output(doc="File to which variants should be written",required=true)

5
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
View File

@ -58,6 +58,7 @@ public class UnifiedGenotyperEngine {
// the unified argument collection
private final UnifiedArgumentCollection UAC;
public UnifiedArgumentCollection getUAC() { return UAC; }
// the annotation engine
private final VariantAnnotatorEngine annotationEngine;
@ -232,7 +233,7 @@ public class UnifiedGenotyperEngine {
private VariantCallContext generateEmptyContext(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, AlignmentContext rawContext) {
VariantContext vc;
if ( UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ) {
VariantContext vcInput = SNPGenotypeLikelihoodsCalculationModel.getSNPVCFromAllelesRod(tracker, ref, false, logger);
VariantContext vcInput = SNPGenotypeLikelihoodsCalculationModel.getSNPVCFromAllelesRod(tracker, ref, false, logger, UAC.alleles);
if ( vcInput == null )
return null;
vc = new VariantContext("UG_call", vcInput.getChr(), vcInput.getStart(), vcInput.getEnd(), vcInput.getAlleles());
@ -630,7 +631,7 @@ public class UnifiedGenotyperEngine {
// no extended event pileup
// 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) {
VariantContext vcInput = SNPGenotypeLikelihoodsCalculationModel.getSNPVCFromAllelesRod(tracker, refContext, false, logger);
VariantContext vcInput = SNPGenotypeLikelihoodsCalculationModel.getSNPVCFromAllelesRod(tracker, refContext, false, logger, UAC.alleles);
if (vcInput == null)
return null;

10
public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
View File

@ -45,7 +45,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
GenomeAnalysisEngine.resetRandomGenerator();
WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
baseCommand + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -B:alleles,vcf " + result.get(0).getAbsolutePath() + " -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,050,000", 1,
baseCommand + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + result.get(0).getAbsolutePath() + " -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,050,000", 1,
Arrays.asList(md5));
executeTest("test MultiSample Pilot2 with alleles passed in", spec2);
}
@ -53,12 +53,12 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
@Test
public void testWithAllelesPassedIn() {
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
baseCommand + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -B:alleles,vcf " + validationDataLocation + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1,
baseCommand + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1,
Arrays.asList("811ddc0bd8322b14f14f58df8c627aa9"));
executeTest("test MultiSample Pilot2 with alleles passed in", spec1);
WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
baseCommand + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -B:alleles,vcf " + validationDataLocation + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1,
baseCommand + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1,
Arrays.asList("5cf08dd7ac3d218082f7be3915ce0b15"));
executeTest("test MultiSample Pilot2 with alleles passed in and emitting all sites", spec2);
}
@ -286,13 +286,13 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
@Test
public void testWithIndelAllelesPassedIn() {
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -B:alleles,vcf " + validationDataLocation + "indelAllelesForUG.vcf -I " + validationDataLocation +
baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "indelAllelesForUG.vcf -I " + validationDataLocation +
"pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
Arrays.asList("69b0b3f089c80b9864294d838a061336"));
executeTest("test MultiSample Pilot2 indels with alleles passed in", spec1);
WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
baseCommandIndels + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -B:alleles,vcf "
baseCommandIndels + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles "
+ validationDataLocation + "indelAllelesForUG.vcf -I " + validationDataLocation +
"pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
Arrays.asList("c90174cfd7dd68bdef36fe2c60145e10"));