private static BreakEndAdjacency Flip(this BreakEndAdjacency adjacency)
{
var origin = new BreakPoint(adjacency.Partner.Chromosome, adjacency.Partner.Position, !adjacency.Partner.OnReverseStrand);
var partner = new BreakPoint(adjacency.Origin.Chromosome, adjacency.Origin.Position, !adjacency.Origin.OnReverseStrand);
return(new BreakEndAdjacency(origin, partner));
}
private static BreakEndAdjacency[] CreateFromDuplication(IChromosomeInterval interval)
{
// 1 1 . N ]1:10]N
var origin = new BreakPoint(interval.Chromosome, interval.End, false);
var remote = new BreakPoint(interval.Chromosome, interval.Start - 1, false);
var adjacency = new BreakEndAdjacency(origin, remote);
return(new[] { adjacency, adjacency.Flip() });
}
private static BreakEndAdjacency[] CreateFromInversion(IChromosomeInterval interval)
{
// 1 10 . N N]1:20]
// 1 11 . N [1:21[N
var origin = new BreakPoint(interval.Chromosome, interval.Start - 1, false);
var remote = new BreakPoint(interval.Chromosome, interval.End, true);
var adjacency = new BreakEndAdjacency(origin, remote);
var origin2 = new BreakPoint(interval.Chromosome, interval.End + 1, true);
var remote2 = new BreakPoint(interval.Chromosome, interval.Start, false);
var adjacency2 = new BreakEndAdjacency(origin2, remote2);
return(new[] { adjacency, adjacency2 });
}
internal static void GetGeneFusionsByTranscript(this Dictionary <string, IAnnotatedGeneFusion> transcriptIdToGeneFusions,
BreakEndAdjacency adjacency, ITranscript[] originTranscripts, ITranscript[] partnerTranscripts)
{
var geneFusions = new List <IGeneFusion>();
foreach (var originTranscript in originTranscripts)
{
geneFusions.Clear();
bool originOnReverseStrand = originTranscript.Gene.OnReverseStrand ^ adjacency.Origin.OnReverseStrand;
(int originIndex, ITranscriptRegion originRegion) = MappedPositionUtilities.FindRegion(originTranscript.TranscriptRegions, adjacency.Origin.Position);
int?originExon = originRegion.Type == TranscriptRegionType.Exon ? (int?)originRegion.Id : null;
int?originIntron = originRegion.Type == TranscriptRegionType.Intron ? (int?)originRegion.Id : null;
foreach (var partnerTranscript in partnerTranscripts)
{
bool partnerOnReverseStrand = partnerTranscript.Gene.OnReverseStrand ^ adjacency.Partner.OnReverseStrand;
bool differentStrand = originOnReverseStrand != partnerOnReverseStrand;
bool differentTranscriptSource = originTranscript.Source != partnerTranscript.Source;
bool sameGeneSymbol = originTranscript.Gene.Symbol == partnerTranscript.Gene.Symbol;
bool codingRegionAlreadyOverlaps = originTranscript.Translation.CodingRegion.Overlaps(partnerTranscript.Translation.CodingRegion);
if (differentStrand || differentTranscriptSource || sameGeneSymbol || codingRegionAlreadyOverlaps)
{
continue;
}
(int partnerIndex, ITranscriptRegion partnerRegion) = MappedPositionUtilities.FindRegion(partnerTranscript.TranscriptRegions, adjacency.Partner.Position);
int?partnerExon = partnerRegion.Type == TranscriptRegionType.Exon ? (int?)partnerRegion.Id : null;
int?partnerIntron = partnerRegion.Type == TranscriptRegionType.Intron ? (int?)partnerRegion.Id : null;
BreakPointTranscript origin = new BreakPointTranscript(originTranscript, adjacency.Origin.Position, originIndex);
BreakPointTranscript partner = new BreakPointTranscript(partnerTranscript, adjacency.Partner.Position, partnerIndex);
(BreakPointTranscript first, BreakPointTranscript second) = originOnReverseStrand ? (partner, origin) : (origin, partner);
string hgvsCoding = GetHgvsCoding(first, second);
geneFusions.Add(new GeneFusion(partnerExon, partnerIntron, hgvsCoding));
}
if (geneFusions.Count == 0)
{
continue;
}
var annotatedGeneFusion = new AnnotatedGeneFusion(originExon, originIntron, geneFusions.ToArray());
transcriptIdToGeneFusions[originTranscript.Id.WithVersion] = annotatedGeneFusion;
}
}