internal static string GetHgvsCoding(BreakPointTranscript first, BreakPointTranscript second)
{
(string firstBegin, string firstEnd) = AdjustFirst(first);
(string secondBegin, string secondEnd) = AdjustSecond(second);
return($"{first.Transcript.Gene.Symbol}{{{first.Transcript.Id.WithVersion}}}:c.{firstBegin}_{firstEnd}_{second.Transcript.Gene.Symbol}{{{second.Transcript.Id.WithVersion}}}:c.{secondBegin}_{secondEnd}");
}
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;
}
}
private static (string Begin, string End) AdjustSecond(BreakPointTranscript second)
{
var codingRegion = second.Transcript.Translation.CodingRegion;
int position = second.GenomicPosition;
int codingRegionLength = codingRegion.CdnaEnd - codingRegion.CdnaStart + 1;
if (position < codingRegion.Start)
{
return((position - codingRegion.Start).ToString(), "?");
}
if (position > codingRegion.End)
{
return((position - codingRegion.End + codingRegionLength).ToString(), "?");
}
return(HgvsUtilities.GetCdnaPositionOffset(second.Transcript, position, second.RegionIndex).Value, codingRegionLength.ToString());
}
private static (string Begin, string End) AdjustFirst(BreakPointTranscript first)
{
var codingRegion = first.Transcript.Translation.CodingRegion;
int position = first.GenomicPosition;
int codingRegionLength = codingRegion.CdnaEnd - codingRegion.CdnaStart + 1;
if (position < codingRegion.Start)
{
return("?", (position - codingRegion.Start).ToString());
}
if (position > codingRegion.End)
{
return("?", (position - codingRegion.End + codingRegionLength).ToString());
}
return("1", HgvsUtilities.GetCdnaPositionOffset(first.Transcript, position, first.RegionIndex).Value);
}
