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Merged bug fix from Stable into Unstable

This commit is contained in:
David Roazen 2011-09-20 17:24:14 -04:00
parent 758ecf2d43 d9ea764611
commit b04d8eab55
5 changed files with 48 additions and 17 deletions
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49
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java
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@ -58,6 +58,13 @@ public class SnpEff extends InfoFieldAnnotation implements ExperimentalAnnotatio
// lacking a SnpEff version number in the VCF header:
public static final String[] SUPPORTED_SNPEFF_VERSIONS = { "2.0.2" };
public static final String SNPEFF_VCF_HEADER_VERSION_LINE_KEY = "SnpEffVersion";
public static final String SNPEFF_VCF_HEADER_COMMAND_LINE_KEY = "SnpEffCmd";
// When we write the SnpEff version number and command line to the output VCF, we change
// the key name slightly so that the output VCF won't be confused in the future for an
// output file produced by SnpEff directly:
public static final String OUTPUT_VCF_HEADER_VERSION_LINE_KEY = "Original" + SNPEFF_VCF_HEADER_VERSION_LINE_KEY;
public static final String OUTPUT_VCF_HEADER_COMMAND_LINE_KEY = "Original" + SNPEFF_VCF_HEADER_COMMAND_LINE_KEY;
// SnpEff aggregates all effects (and effect metadata) together into a single INFO
// field annotation with the key EFF:
@ -165,10 +172,26 @@ public class SnpEff extends InfoFieldAnnotation implements ExperimentalAnnotatio
UNKNOWN
}
public void initialize ( AnnotatorCompatibleWalker walker, GenomeAnalysisEngine toolkit ) {
public void initialize ( AnnotatorCompatibleWalker walker, GenomeAnalysisEngine toolkit, Set<VCFHeaderLine> headerLines ) {
// Make sure that we actually have a valid SnpEff rod binding (just in case the user specified -A SnpEff
// without providing a SnpEff rod via --snpEffFile):
validateRodBinding(walker.getSnpEffRodBinding());
checkSnpEffVersion(walker, toolkit);
RodBinding<VariantContext> snpEffRodBinding = walker.getSnpEffRodBinding();
// Make sure that the SnpEff version number and command-line header lines are present in the VCF header of
// the SnpEff rod, and that the file was generated by a supported version of SnpEff:
VCFHeader snpEffVCFHeader = VCFUtils.getVCFHeadersFromRods(toolkit, Arrays.asList(snpEffRodBinding.getName())).get(snpEffRodBinding.getName());
VCFHeaderLine snpEffVersionLine = snpEffVCFHeader.getOtherHeaderLine(SNPEFF_VCF_HEADER_VERSION_LINE_KEY);
VCFHeaderLine snpEffCommandLine = snpEffVCFHeader.getOtherHeaderLine(SNPEFF_VCF_HEADER_COMMAND_LINE_KEY);
checkSnpEffVersion(snpEffVersionLine);
checkSnpEffCommandLine(snpEffCommandLine);
// If everything looks ok, add the SnpEff version number and command-line header lines to the
// header of the VCF output file, changing the key names so that our output file won't be
// mistaken in the future for a SnpEff output file:
headerLines.add(new VCFHeaderLine(OUTPUT_VCF_HEADER_VERSION_LINE_KEY, snpEffVersionLine.getValue()));
headerLines.add(new VCFHeaderLine(OUTPUT_VCF_HEADER_COMMAND_LINE_KEY, snpEffCommandLine.getValue()));
}
public Map<String, Object> annotate ( RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc ) {
@ -204,12 +227,7 @@ public class SnpEff extends InfoFieldAnnotation implements ExperimentalAnnotatio
}
}
private void checkSnpEffVersion ( AnnotatorCompatibleWalker walker, GenomeAnalysisEngine toolkit ) {
RodBinding<VariantContext> snpEffRodBinding = walker.getSnpEffRodBinding();
VCFHeader snpEffVCFHeader = VCFUtils.getVCFHeadersFromRods(toolkit, Arrays.asList(snpEffRodBinding.getName())).get(snpEffRodBinding.getName());
VCFHeaderLine snpEffVersionLine = snpEffVCFHeader.getOtherHeaderLine(SNPEFF_VCF_HEADER_VERSION_LINE_KEY);
private void checkSnpEffVersion ( VCFHeaderLine snpEffVersionLine ) {
if ( snpEffVersionLine == null || snpEffVersionLine.getValue() == null || snpEffVersionLine.getValue().trim().length() == 0 ) {
throw new UserException("Could not find a " + SNPEFF_VCF_HEADER_VERSION_LINE_KEY + " entry in the VCF header for the SnpEff " +
"input file, and so could not verify that the file was generated by a supported version of SnpEff (" +
@ -224,6 +242,14 @@ public class SnpEff extends InfoFieldAnnotation implements ExperimentalAnnotatio
}
}
private void checkSnpEffCommandLine ( VCFHeaderLine snpEffCommandLine ) {
if ( snpEffCommandLine == null || snpEffCommandLine.getValue() == null || snpEffCommandLine.getValue().trim().length() == 0 ) {
throw new UserException("Could not find a " + SNPEFF_VCF_HEADER_COMMAND_LINE_KEY + " entry in the VCF header for the SnpEff " +
"input file, which should be added by all supported versions of SnpEff (" +
Arrays.toString(SUPPORTED_SNPEFF_VERSIONS) + ")");
}
}
private boolean isSupportedSnpEffVersion ( String versionString ) {
for ( String supportedVersion : SUPPORTED_SNPEFF_VERSIONS ) {
if ( supportedVersion.equals(versionString) ) {
@ -248,10 +274,13 @@ public class SnpEff extends InfoFieldAnnotation implements ExperimentalAnnotatio
List<SnpEffEffect> parsedEffects = new ArrayList<SnpEffEffect>();
Object effectFieldValue = snpEffRecord.getAttribute(SNPEFF_INFO_FIELD_KEY);
List<String> individualEffects;
if ( effectFieldValue == null ) {
return parsedEffects;
}
// The VCF codec stores multi-valued fields as a List<String>, and single-valued fields as a String.
// We can have either in the case of SnpEff, since there may be one or more than one effect in this record.
List<String> individualEffects;
if ( effectFieldValue instanceof List ) {
individualEffects = (List<String>)effectFieldValue;
}

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
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@ -208,8 +208,6 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
engine = new VariantAnnotatorEngine(annotationGroupsToUse, annotationsToUse, this, getToolkit());
engine.initializeExpressions(expressionsToUse);
engine.invokeAnnotationInitializationMethods();
// setup the header fields
// note that if any of the definitions conflict with our new ones, then we want to overwrite the old ones
Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
@ -219,6 +217,8 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
hInfo.add(line);
}
engine.invokeAnnotationInitializationMethods(hInfo);
VCFHeader vcfHeader = new VCFHeader(hInfo, samples);
vcfWriter.writeHeader(vcfHeader);

6
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
View File

@ -114,13 +114,13 @@ public class VariantAnnotatorEngine {
dbAnnotations.put(rod, rod.getName());
}
public void invokeAnnotationInitializationMethods() {
public void invokeAnnotationInitializationMethods( Set<VCFHeaderLine> headerLines ) {
for ( VariantAnnotatorAnnotation annotation : requestedInfoAnnotations ) {
annotation.initialize(walker, toolkit);
annotation.initialize(walker, toolkit, headerLines);
}
for ( VariantAnnotatorAnnotation annotation : requestedGenotypeAnnotations ) {
annotation.initialize(walker, toolkit);
annotation.initialize(walker, toolkit, headerLines);
}
}

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java
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@ -25,9 +25,11 @@
package org.broadinstitute.sting.gatk.walkers.annotator.interfaces;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import java.util.List;
import java.util.Set;
@DocumentedGATKFeature(enable = true, groupName = "VariantAnnotator annotations", summary = "VariantAnnotator annotations")
public abstract class VariantAnnotatorAnnotation {
@ -35,5 +37,5 @@ public abstract class VariantAnnotatorAnnotation {
public abstract List<String> getKeyNames();
// initialization method (optional for subclasses, and therefore non-abstract)
public void initialize ( AnnotatorCompatibleWalker walker, GenomeAnalysisEngine toolkit ) { }
public void initialize ( AnnotatorCompatibleWalker walker, GenomeAnalysisEngine toolkit, Set<VCFHeaderLine> headerLines ) { }
}

2
public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
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@ -134,7 +134,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
validationDataLocation + "1kg_exomes_unfiltered.AFR.unfiltered.vcf --snpEffFile " + validationDataLocation +
"snpEff.AFR.unfiltered.vcf -L 1:1-1,500,000",
1,
Arrays.asList("486fc6a5ca1819f5ab180d5d72b1ebc9")
Arrays.asList("ed9d1b37b0bd8b65ff9ce2688e0e102e")
);
executeTest("Testing SnpEff annotations", spec);
}