private VD.Gene[] ConvertGenes()
{
var genes = new VD.Gene[_mergedGenes.Count];
for (int i = 0; i < _mergedGenes.Count; i++)
{
genes[i] = _mergedGenes[i].ToGene();
}
return(genes);
}
public Transcript(BioType biotype, Exon[] transExons, Gene gene, Translation translation, VariantEffectFeatureCache cache, Slice slice,
bool onReverseStrand, bool isCanonical, int cdnaCodingStart, int cdnaCodingEnd, ushort referenceIndex, int start, int end,
string ccdsId, string databaseId, string proteinId, string refSeqId, string geneStableId, string stableId, string geneSymbol,
GeneSymbolSource geneSymbolSource, int hgncId, byte version, SimpleInterval[] microRnas)
: base(referenceIndex, start, end)
{
BioType = biotype;
CcdsId = ccdsId;
CompDnaCodingEnd = cdnaCodingEnd;
CompDnaCodingStart = cdnaCodingStart;
DatabaseId = databaseId;
Gene = gene;
GeneStableId = geneStableId;
GeneSymbol = geneSymbol;
GeneSymbolSource = geneSymbolSource;
HgncId = hgncId;
IsCanonical = isCanonical;
MicroRnas = microRnas;
OnReverseStrand = onReverseStrand;
ProteinId = proteinId;
RefSeqId = refSeqId;
Slice = slice;
StableId = stableId;
TransExons = transExons;
Translation = translation;
VariantEffectCache = cache;
Version = version;
var entrezId = ImportDataStore.TranscriptSource == TranscriptDataSource.Ensembl
? CompactId.Empty
: CompactId.Convert(geneStableId);
var ensemblId = ImportDataStore.TranscriptSource == TranscriptDataSource.Ensembl
? CompactId.Convert(geneStableId)
: CompactId.Empty;
FinalGene = new VariantAnnotation.DataStructures.Gene(referenceIndex, start, end, onReverseStrand,
geneSymbol, hgncId, entrezId, ensemblId, -1);
GenerateHashCode();
}
/// <summary>
/// constructor
/// </summary>
public Transcript(ushort referenceIndex, int start, int end, CompactId id, byte version,
Translation translation, BioType bioType, Gene gene, int totalExonLength, byte startExonPhase,
bool isCanonical, SimpleInterval[] introns, SimpleInterval[] microRnas, CdnaCoordinateMap[] cdnaMaps,
int siftIndex, int polyPhenIndex, TranscriptDataSource transcriptSource) : base(referenceIndex, start, end)
{
Id = id;
Version = version;
Translation = translation;
BioType = bioType;
Gene = gene;
TotalExonLength = totalExonLength;
StartExonPhase = startExonPhase;
IsCanonical = isCanonical;
Introns = introns;
MicroRnas = microRnas;
CdnaMaps = cdnaMaps;
SiftIndex = siftIndex;
PolyPhenIndex = polyPhenIndex;
TranscriptSource = transcriptSource;
TotalExonLength = TranscriptUtilities.GetTotalExonLength(cdnaMaps);
}
