public void AddAnnotation(IVariantFeature variant)
{
if (!_hasCustomAnnotations)
{
return;
}
variant.AddCustomAnnotation(_customAnnotationReaders);
}
public void AddAnnotation(IVariantFeature variant)
{
if (_saReader == null)
{
return;
}
if (variant.IsStructuralVariant)
{
AddOverlappingIntervals(variant);
}
else
{
variant.SetSupplementaryAnnotation(_saReader);
}
}
public void AddAnnotation(IVariantFeature variant)
{
if (!_hasIntervals)
{
return;
}
_intervalForest.GetAllOverlappingValues(variant.ReferenceIndex, variant.OverlapReferenceBegin,
variant.OverlapReferenceEnd, _overlappingIntervals);
if (_overlappingIntervals.Count == 0)
{
return;
}
variant.AddCustomIntervals(_overlappingIntervals);
}
private void AddOverlappingIntervals(IVariantFeature variant)
{
// get overlapping supplementary intervals.
_overlappingSupplementaryIntervals.Clear();
var firstAltAllele = variant.FirstAlternateAllele;
var variantBegin = firstAltAllele.NirvanaVariantType == VariantType.insertion
? firstAltAllele.End
: firstAltAllele.Start;
var variantEnd = firstAltAllele.End;
_suppIntervalForest.GetAllOverlappingValues(variant.ReferenceIndex, variantBegin, variantEnd,
_overlappingSupplementaryIntervals);
variant.AddSupplementaryIntervals(_overlappingSupplementaryIntervals);
}
public void AnnotateVariant(IVariantFeature variant, List <Transcript> transcripts,
IAnnotatedVariant annotatedVariant, ICompressedSequence sequence)
{
if (variant.IsStructuralVariant)
{
return;
}
CreateTranscriptDictionary(transcripts);
foreach (var altAllele in annotatedVariant.AnnotatedAlternateAlleles)
{
foreach (var transcript in altAllele.EnsemblTranscripts)
{
var lofteeOut = LofteeAnalysis(transcript, altAllele, sequence);
if (lofteeOut != null)
{
if (transcript.AdditionalInfo == null)
{
transcript.AdditionalInfo = new Dictionary <string, string>();
}
transcript.AdditionalInfo["loftee"] = lofteeOut;
}
}
foreach (var transcript in altAllele.RefSeqTranscripts)
{
var lofteeOut = LofteeAnalysis(transcript, altAllele, sequence);
if (lofteeOut != null)
{
if (transcript.AdditionalInfo == null)
{
transcript.AdditionalInfo = new Dictionary <string, string>();
}
transcript.AdditionalInfo["loftee"] = lofteeOut;
}
}
}
}
