private void AnnotateAltAllele(VariantFeature variant, VariantAlternateAllele altAllele, Transcript transcript)
{
// handle upstream or downstream transcripts
if (!Overlap.Partial(transcript.Start, transcript.End, altAllele.Start, altAllele.End))
{
return;
}
var ta = new TranscriptAnnotation
{
AlternateAllele = altAllele,
HasValidCdnaCodingStart = false,
HasValidCdsStart = false
};
MapCdnaCoordinates(transcript, ta, altAllele);
_pianoVariant.CreateAnnotationObject(transcript, altAllele);
GetCodingAnnotations(transcript, ta, _compressedSequence);
var consequence = new Consequences(new VariantEffect(ta, transcript, variant.InternalCopyNumberType));
consequence.DetermineVariantEffects(variant.InternalCopyNumberType);
_pianoVariant.FinalizeAndAddAnnotationObject(transcript, ta, consequence.GetConsequenceStrings());
}
private List <MutableGene> GetValidGenes(MutableGene seedGene, List <MutableGene> genes, out int start,
out int end)
{
var validGenes = new List <MutableGene>();
start = seedGene.Start;
end = seedGene.End;
foreach (var gene in genes)
{
if (gene.Invalid || seedGene.OnReverseStrand != gene.OnReverseStrand ||
seedGene.ReferenceIndex != gene.ReferenceIndex || !Overlap.Partial(start, end, gene.Start, gene.End))
{
continue;
}
validGenes.Add(gene);
if (gene.Start < start)
{
start = gene.Start;
}
if (gene.End > end)
{
end = gene.End;
}
}
return(validGenes);
}
private static MutableGene GetFlattenedGene(MutableGene seedGene, List <MutableGene> genesWithSameGeneId,
int overlapStart, int overlapEnd)
{
var flattenedGene = MutableGene.Clone(seedGene);
bool useOverlap = overlapStart != -1 && overlapEnd != -1;
foreach (var gene in genesWithSameGeneId)
{
if (gene.Invalid || flattenedGene.OnReverseStrand != gene.OnReverseStrand ||
flattenedGene.ReferenceIndex != gene.ReferenceIndex)
{
continue;
}
if (useOverlap && !Overlap.Partial(overlapStart, overlapEnd, gene.Start, gene.End))
{
continue;
}
if (!useOverlap && !Overlap.Partial(flattenedGene.Start, flattenedGene.End, gene.Start, gene.End))
{
continue;
}
UpdateCoordinates(gene, flattenedGene);
gene.Invalid = true;
}
return(flattenedGene);
}
private static bool HasCds(CdnaCoordinateMap exon, int codingRegionStart, int codingRegionEnd)
{
if (codingRegionStart == -1 || codingRegionEnd == -1)
{
return(false);
}
return(Overlap.Partial(exon.GenomicStart, exon.GenomicEnd, codingRegionStart, codingRegionEnd));
}
/// <summary>
/// constructor
/// </summary>
public FeatureVariantEffects(ReferenceAnnotationInterval feature, VariantType vt, int refBegin, int refEnd, bool isSV, VariantType internalCopyNumberType)
{
_isSV = isSV;
_completelyOverlaps = Overlap.Complete(feature.Start, feature.End, refBegin, refEnd);
_overlaps = Overlap.Partial(feature.Start, feature.End, refBegin, refEnd);
_completelyWithin = refBegin >= feature.Start && refEnd <= feature.End;
_lossOrDeletion = vt == VariantType.copy_number_loss || vt == VariantType.deletion || internalCopyNumberType == VariantType.copy_number_loss;
_gainOrDuplication = vt == VariantType.copy_number_gain || vt == VariantType.duplication ||
vt == VariantType.tandem_duplication || internalCopyNumberType == VariantType.copy_number_gain;
_isInsertionDeletion = vt == VariantType.indel;
_isInsertion = vt == VariantType.insertion;
}
public void AddCustomIntervals(List <ICustomInterval> overlappingCustomIntervals)
{
if (overlappingCustomIntervals == null)
{
return;
}
foreach (var customInterval in overlappingCustomIntervals)
{
if (Overlap.Partial(this, customInterval))
{
CustomIntervals.Add(customInterval);
}
}
}
public int Extract()
{
var count = 0;
var interval = _reader.GetNextCustomInterval();
while (interval != null)
{
if (Overlap.Partial(interval.Start, interval.End, _begin, _end))
{
_writer.WriteInterval(interval);
count++;
}
interval = _reader.GetNextCustomInterval();
}
_writer.Dispose();
return(count);
}