public int AddCoordinates(EnsemblGtf ensemblGtf, RefSeqGff refSeqGff)
{
foreach (var hgncGene in HgncGenes)
{
var(refSeqGenes, ensemblGene, numMatches) = GetGenes(hgncGene.EntrezGeneId,
refSeqGff.EntrezGeneIdToGene, hgncGene.EnsemblId, ensemblGtf.EnsemblIdToGene);
switch (numMatches)
{
case 0:
break;
case 1:
if (ensemblGene == null)
{
AddCoordinatesFromGene(hgncGene, refSeqGenes[0]);
}
else
{
AddCoordinatesFromGene(hgncGene, ensemblGene);
}
break;
default:
AddCoordinatesFromMultipleGenes(hgncGene, ensemblGene, refSeqGenes);
break;
}
}
return(HgncGenes.Count(hgncGene => hgncGene.Start != 1 && hgncGene.End != -1));
}
private AssemblyDataStore(string description, EnsemblGtf ensemblGtf, RefSeqGff refSeqGff, GlobalCache globalCache)
{
_description = description;
EnsemblGtf = ensemblGtf;
RefSeqGff = refSeqGff;
_globalCache = globalCache;
}