@Override
public void initialize(
AnnotatorCompatible 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):
if (!isValidRodBinding(walker.getSnpEffRodBinding())) {
canAnnotate = false;
return;
}
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 =
GATKVCFUtils.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);
if (!isValidSnpEffVersionAndCommandLine(snpEffVersionLine, snpEffCommandLine)) {
canAnnotate = false;
return;
}
// 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()));
// Can only be called from VariantAnnotator
if (!(walker instanceof VariantAnnotator)) {
if (walker != null)
logger.warn(
"Annotation will not be calculated, must be called from VariantAnnotator, not "
+ walker.getClass().getName());
else logger.warn("Annotation will not be calculated, must be called from VariantAnnotator");
canAnnotate = false;
return;
}
}
private boolean isValidRodBinding(RodBinding<VariantContext> snpEffRodBinding) {
if (snpEffRodBinding == null || !snpEffRodBinding.isBound()) {
logger.warn(
"The SnpEff annotator requires that a SnpEff VCF output file be provided "
+ "as a rodbinding on the command line via the --snpEffFile option, but "
+ "no SnpEff rodbinding was found.");
return false;
}
return true;
}
private void writeRecord(VariantContext vc, RefMetaDataTracker tracker, GenomeLoc loc) {
if (!wroteHeader) {
wroteHeader = true;
// setup the header fields
Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
hInfo.addAll(GATKVCFUtils.getHeaderFields(getToolkit(), Arrays.asList(variants.getName())));
hInfo.add(VCFStandardHeaderLines.getFormatLine(VCFConstants.GENOTYPE_KEY));
allowedGenotypeFormatStrings.add(VCFConstants.GENOTYPE_KEY);
for (VCFHeaderLine field : hInfo) {
if (field instanceof VCFFormatHeaderLine) {
allowedGenotypeFormatStrings.add(((VCFFormatHeaderLine) field).getID());
}
}
samples = new LinkedHashSet<String>();
if (sampleName != null) {
samples.add(sampleName);
} else {
// try VCF first
samples =
SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(variants.getName()));
if (samples.isEmpty()) {
List<Feature> features = tracker.getValues(variants, loc);
if (features.size() == 0)
throw new IllegalStateException(
"No rod data is present, but we just created a VariantContext");
Feature f = features.get(0);
if (f instanceof RawHapMapFeature)
samples.addAll(Arrays.asList(((RawHapMapFeature) f).getSampleIDs()));
else samples.addAll(vc.getSampleNames());
}
}
vcfwriter.writeHeader(new VCFHeader(hInfo, samples));
}
vc = GATKVariantContextUtils.purgeUnallowedGenotypeAttributes(vc, allowedGenotypeFormatStrings);
vcfwriter.add(vc);
}
private Collection<VariantContext> getVariantContexts(
RefMetaDataTracker tracker, ReferenceContext ref) {
List<Feature> features = tracker.getValues(variants, ref.getLocus());
List<VariantContext> VCs = new ArrayList<VariantContext>(features.size());
for (Feature record : features) {
if (VariantContextAdaptors.canBeConvertedToVariantContext(record)) {
// we need to special case the HapMap format because indels aren't handled correctly
if (record instanceof RawHapMapFeature) {
// is it an indel?
RawHapMapFeature hapmap = (RawHapMapFeature) record;
if (hapmap.getAlleles()[0].equals(RawHapMapFeature.NULL_ALLELE_STRING)
|| hapmap.getAlleles()[1].equals(RawHapMapFeature.NULL_ALLELE_STRING)) {
// get the dbsnp object corresponding to this record (needed to help us distinguish
// between insertions and deletions)
VariantContext dbsnpVC = getDbsnp(hapmap.getName());
if (dbsnpVC == null || dbsnpVC.isMixed()) continue;
Map<String, Allele> alleleMap = new HashMap<String, Allele>(2);
alleleMap.put(
RawHapMapFeature.DELETION,
Allele.create(ref.getBase(), dbsnpVC.isSimpleInsertion()));
alleleMap.put(
RawHapMapFeature.INSERTION,
Allele.create(
(char) ref.getBase() + ((RawHapMapFeature) record).getAlleles()[1],
!dbsnpVC.isSimpleInsertion()));
hapmap.setActualAlleles(alleleMap);
// also, use the correct positioning for insertions
hapmap.updatePosition(dbsnpVC.getStart());
if (hapmap.getStart() < ref.getWindow().getStart()) {
logger.warn(
"Hapmap record at "
+ ref.getLocus()
+ " represents an indel too large to be converted; skipping...");
continue;
}
}
}
// ok, we might actually be able to turn this record in a variant context
VariantContext vc =
VariantContextAdaptors.toVariantContext(variants.getName(), record, ref);
if (vc != null) // sometimes the track has odd stuff in it that can't be converted
VCs.add(vc);
}
}
return VCs;
}
public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
if (tracker == null || !BaseUtils.isRegularBase(ref.getBase())) return 0;
Collection<VariantContext> contexts = getVariantContexts(tracker, ref);
for (VariantContext vc : contexts) {
VariantContextBuilder builder = new VariantContextBuilder(vc);
// set the appropriate sample name if necessary
if (sampleName != null && vc.hasGenotypes() && vc.hasGenotype(variants.getName())) {
Genotype g =
new GenotypeBuilder(vc.getGenotype(variants.getName())).name(sampleName).make();
builder.genotypes(g);
}
final VariantContext withID = variantOverlapAnnotator.annotateRsID(tracker, builder.make());
writeRecord(withID, tracker, ref.getLocus());
}
return 1;
}
public void initialize() {
// Initialize VCF header
if (vcfWriter != null) {
Map<String, VCFHeader> header =
GATKVCFUtils.getVCFHeadersFromRodPrefix(getToolkit(), alleles.getName());
samples =
SampleUtils.getSampleList(
header, GATKVariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE);
Set<VCFHeaderLine> headerLines = VCFUtils.smartMergeHeaders(header.values(), true);
headerLines.add(new VCFHeaderLine("source", "GenotypeAndValidate"));
headerLines.add(
GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.GENOTYPE_AND_VALIDATE_STATUS_KEY));
vcfWriter.writeHeader(new VCFHeader(headerLines, samples));
}
// Filling in SNP calling arguments for UG
UnifiedArgumentCollection uac = new UnifiedArgumentCollection();
uac.outputMode = OutputMode.EMIT_ALL_SITES;
uac.alleles = alleles;
// TODO -- if we change this tool to actually validate against the called allele, then this if
// statement is needed;
// TODO -- for now, though, we need to be able to validate the right allele (because we only
// test isVariant below) [EB]
// if (!bamIsTruth)
uac.genotypingOutputMode = GenotypingOutputMode.GENOTYPE_GIVEN_ALLELES;
if (mbq >= 0) uac.MIN_BASE_QUALTY_SCORE = mbq;
if (deletions >= 0) uac.MAX_DELETION_FRACTION = deletions;
else uac.MAX_DELETION_FRACTION = 1.0;
if (emitConf >= 0) uac.genotypeArgs.STANDARD_CONFIDENCE_FOR_EMITTING = emitConf;
if (callConf >= 0) uac.genotypeArgs.STANDARD_CONFIDENCE_FOR_CALLING = callConf;
final GenomeAnalysisEngine toolkit = getToolkit();
uac.GLmodel = GenotypeLikelihoodsCalculationModel.Model.SNP;
snpEngine =
new UnifiedGenotypingEngine(
uac, FixedAFCalculatorProvider.createThreadSafeProvider(toolkit, uac, logger), toolkit);
// Adding the INDEL calling arguments for UG
UnifiedArgumentCollection uac_indel = uac.clone();
uac_indel.GLmodel = GenotypeLikelihoodsCalculationModel.Model.INDEL;
indelEngine =
new UnifiedGenotypingEngine(
uac_indel,
FixedAFCalculatorProvider.createThreadSafeProvider(toolkit, uac, logger),
toolkit);
// make sure we have callConf set to the threshold set by the UAC so we can use it later.
callConf = uac.genotypeArgs.STANDARD_CONFIDENCE_FOR_CALLING;
}
