private static Dictionary <string, List <Interval> > LoadBedRegions(IFileLocation bedFile,
GenomeMetadata genomeMetadata)
{
return(File.ReadAllLines(bedFile.FullName)
.Select(line =>
{
var bits = line.Split('\t');
return (Chromosome: bits[0], Interval: new Interval(int.Parse(bits[1]) + 1, int.Parse(bits[2])));
})
.GroupByAdjacent(bedEntry => bedEntry.Chromosome)
.Where(kvp => genomeMetadata.GetSequence(kvp.Key) != null)
.ToDictionary(
chromosomeElements => chromosomeElements.Key,
chromosomeElements => GetValidatedIntervals(chromosomeElements.Value,
genomeMetadata.GetSequence(chromosomeElements.Key).Length).ToList()));
}
public ChrReference GetChrReference(string chrName)
{
var sequenceSource = _genomeSource.GetSequence(chrName);
if (sequenceSource == null)
{
return(null);
}
return(new ChrReference
{
Name = chrName,
Sequence = sequenceSource.GetBases(true),
FastaPath = sequenceSource.FastaPath
});
}
