public GeneFusionAnnotation(BreakendTranscriptAnnotation breakendTa)
{
_exon = breakendTa.Exon;
_intron = breakendTa.Intron;
_fusions = new List <GeneFusion>();
_pos1Annotation = breakendTa;
}
public bool IsTranscriptCodingRegionOverlapped(BreakendTranscriptAnnotation other)
{
if (other._referenceName != _referenceName)
{
return(false);
}
if (other._codingEnd < _codingStart || other._codingStart > _codingEnd)
{
return(false);
}
return(true);
}
private string AssignHgvsc(BreakendTranscriptAnnotation pos2Annotation)
{
var hgvsFusionNameBuilder = new StringBuilder(_pos1Annotation.HgvsDescription);
if (_pos1Annotation.ConsistentOrientation == pos2Annotation.ConsistentOrientation)
{
hgvsFusionNameBuilder.Append("_o" + pos2Annotation.HgvsDescription);
}
else
{
hgvsFusionNameBuilder.Append("_" + pos2Annotation.HgvsDescription);
}
return(hgvsFusionNameBuilder.ToString());
}
public bool IsGeneFusion(BreakendTranscriptAnnotation other)
{
if (TranscriptDataSource != other.TranscriptDataSource)
{
return(false);
}
if (!InCodingRegion || !other.InCodingRegion)
{
return(false);
}
if (GeneName == other.GeneName)
{
return(false);
}
if (IsTranscriptCodingRegionOverlapped(other))
{
return(false);
}
return(true);
}
public void AddGeneFusion(BreakendTranscriptAnnotation pos2Annotation)
{
if (!_pos1Annotation.IsGeneFusion(pos2Annotation))
{
return;
}
var fusion = new GeneFusion
{
Exon = pos2Annotation.Exon,
Intron = pos2Annotation.Intron,
HgvsCodingName = AssignHgvsc(pos2Annotation),
Consequences = new List <ConsequenceType>()
};
if (IsUnidirectionalGeneFusion(pos2Annotation))
{
fusion.Consequences.Add(ConsequenceType.UnidirectionalGeneFusion);
}
if (IsBidirectionalGeneFusion(pos2Annotation))
{
fusion.Consequences.Add(ConsequenceType.BidirectionalGeneFusion);
}
_fusions.Add(fusion);
}
private bool IsUnidirectionalGeneFusion(BreakendTranscriptAnnotation pos2Annotation)
{
return(_pos1Annotation.ConsistentOrientation != pos2Annotation.ConsistentOrientation);
}