private void AddGene(string[] cols, ICollection <EnsemblGene> genes)
{
var chromosome = RefSeqGffReader.GetChromosome(cols[ChromosomeIndex], _refNameToChromosome);
if (chromosome == null)
{
return;
}
try
{
int start = int.Parse(cols[StartIndex]);
int end = int.Parse(cols[EndIndex]);
var infoCols = cols[InfoIndex].Split(';', StringSplitOptions.RemoveEmptyEntries);
var info = GetGffFields(infoCols);
var gene = new EnsemblGene(chromosome, start, end, info.EnsemblGeneId, info.Name);
genes.Add(gene);
}
catch (Exception)
{
Console.WriteLine();
Console.WriteLine("Offending line: {0}", string.Join('\t', cols));
for (var i = 0; i < cols.Length; i++)
{
Console.WriteLine("- col {0}: [{1}]", i, cols[i]);
}
throw;
}
}
private static void AddCoordinatesFromMultipleGenes(HgncGene hgncGene, EnsemblGene ensemblGene, IEnumerable <RefSeqGene> refSeqGenes)
{
if (ensemblGene == null)
{
return;
}
AddCoordinatesFromGene(hgncGene, ensemblGene);
foreach (var refSeqGene in refSeqGenes)
{
if (!IntervalUtilities.Overlaps(hgncGene.Start, hgncGene.End, refSeqGene.Start, refSeqGene.End))
{
continue;
}
AddCoordinatesFromGene(hgncGene, refSeqGene);
}
}