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

Allow appending with the dbSNP ID even if a (different) ID is already present for the variant rod.

This commit is contained in:
Eric Banks 2012-01-25 11:35:54 -05:00
parent ea3d4d60f2
commit e349b4b14b
5 changed files with 30 additions and 8 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

9
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
View File

@ -32,7 +32,6 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.samples.SampleDB;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;
import org.broadinstitute.sting.utils.BaseUtils;
@ -84,7 +83,6 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
@ArgumentCollection
protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
public RodBinding<VariantContext> getVariantRodBinding() { return variantCollection.variants; }
/**
* The INFO field will be annotated with information on the most biologically-significant effect
@ -163,6 +161,13 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
@Argument(fullName="list", shortName="ls", doc="List the available annotations and exit")
protected Boolean LIST = false;
/**
* By default, the dbSNP ID is added only when the ID field in the variant VCF is empty.
*/
@Argument(fullName="alwaysAppendDbsnpId", shortName="alwaysAppendDbsnpId", doc="In conjunction with the dbSNP binding, append the dbSNP ID even when the variant VCF already has the ID field populated")
protected Boolean ALWAYS_APPEND_DBSNP_ID = false;
public boolean alwaysAppendDbsnpId() { return ALWAYS_APPEND_DBSNP_ID; }
@Hidden
@Argument(fullName="vcfContainsOnlyIndels", shortName="dels",doc="Use if you are annotating an indel vcf, currently VERY experimental", required = false)
protected boolean indelsOnly = false;

17
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
View File

@ -195,11 +195,20 @@ public class VariantAnnotatorEngine {
private VariantContext annotateDBs(RefMetaDataTracker tracker, ReferenceContext ref, VariantContext vc, Map<String, Object> infoAnnotations) {
for ( Map.Entry<RodBinding<VariantContext>, String> dbSet : dbAnnotations.entrySet() ) {
if ( dbSet.getValue().equals(VCFConstants.DBSNP_KEY) ) {
String rsID = VCFUtils.rsIDOfFirstRealVariant(tracker.getValues(dbSet.getKey(), ref.getLocus()), vc.getType());
final String rsID = VCFUtils.rsIDOfFirstRealVariant(tracker.getValues(dbSet.getKey(), ref.getLocus()), vc.getType());
// put the DB key into the INFO field
infoAnnotations.put(VCFConstants.DBSNP_KEY, rsID != null);
// annotate dbsnp id if available and not already there
if ( rsID != null && vc.emptyID() )
vc = new VariantContextBuilder(vc).id(rsID).make();
// add the ID if appropriate
if ( rsID != null ) {
if ( vc.emptyID() ) {
vc = new VariantContextBuilder(vc).id(rsID).make();
} else if ( walker.alwaysAppendDbsnpId() && vc.getID().indexOf(rsID) == -1 ) {
final String newRsID = vc.getID() + VCFConstants.ID_FIELD_SEPARATOR + rsID;
vc = new VariantContextBuilder(vc).id(newRsID).make();
}
}
} else {
boolean overlapsComp = false;
for ( VariantContext comp : tracker.getValues(dbSet.getKey(), ref.getLocus()) ) {

2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatibleWalker.java
View File

@ -8,9 +8,9 @@ import java.util.List;
public interface AnnotatorCompatibleWalker {
// getter methods for various used bindings
public abstract RodBinding<VariantContext> getVariantRodBinding();
public abstract RodBinding<VariantContext> getSnpEffRodBinding();
public abstract RodBinding<VariantContext> getDbsnpRodBinding();
public abstract List<RodBinding<VariantContext>> getCompRodBindings();
public abstract List<RodBinding<VariantContext>> getResourceRodBindings();
public abstract boolean alwaysAppendDbsnpId();
}

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

@ -126,10 +126,10 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
@ArgumentCollection
protected DbsnpArgumentCollection dbsnp = new DbsnpArgumentCollection();
public RodBinding<VariantContext> getDbsnpRodBinding() { return dbsnp.dbsnp; }
public RodBinding<VariantContext> getVariantRodBinding() { return null; }
public RodBinding<VariantContext> getSnpEffRodBinding() { return null; }
public List<RodBinding<VariantContext>> getCompRodBindings() { return Collections.emptyList(); }
public List<RodBinding<VariantContext>> getResourceRodBindings() { return Collections.emptyList(); }
public boolean alwaysAppendDbsnpId() { return false; }
/**
* A raw, unfiltered, highly specific callset in VCF format.

8
public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
View File

@ -110,6 +110,14 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
executeTest("getting DB tag with dbSNP", spec);
}
@Test
public void testMultipleIdsWithDbsnp() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " --alwaysAppendDbsnpId --dbsnp " + b36dbSNP129 + " -G Standard --variant " + validationDataLocation + "vcfexample3withIDs.vcf -L " + validationDataLocation + "vcfexample3withIDs.vcf", 1,
Arrays.asList("cd7e3d43b8f5579c461b3e588a295fa8"));
executeTest("adding multiple IDs with dbSNP", spec);
}
@Test
public void testDBTagWithHapMap() {
WalkerTestSpec spec = new WalkerTestSpec(