public static MitoHeteroplasmyProvider GetProvider()
{
var assembly = Assembly.GetExecutingAssembly();
using var stream = assembly.GetManifestResourceStream(ResourceName);
if (stream == null)
{
throw new NullReferenceException("Unable to read from the Mitochondrial Heteroplasmy file");
}
using var gzStream = new GZipStream(stream, CompressionMode.Decompress);
using var reader = new StreamReader(gzStream);
reader.ReadLine();
var heteroplasmyProvider = new MitoHeteroplasmyProvider();
while (true)
{
string line = reader.ReadLine();
if (line == null)
{
break;
}
var fields = line.OptimizedSplit('\t');
var position = int.Parse(fields[PositionIndex]);
var vrfs = fields[VrfIndex].Split(',').Select(double.Parse);
var alleleDepths = fields[AlleleDepthIndex].Split(',').Select(int.Parse).ToArray();
heteroplasmyProvider.Add(position, fields[AltIndex], vrfs, alleleDepths);
}
return(heteroplasmyProvider);
}
public static MitoHeteroplasmyProvider GetProvider()
{
var assembly = Assembly.GetExecutingAssembly();
using var stream = assembly.GetManifestResourceStream(ResourceName);
if (stream == null)
{
throw new NullReferenceException("Unable to read from the Mitochondrial Heteroplasmy file");
}
using var gzStream = new GZipStream(stream, CompressionMode.Decompress);
using var reader = new StreamReader(gzStream);
string line;
var heteroplasmyProvider = new MitoHeteroplasmyProvider();
while ((line = reader.ReadLine()) != null)
{
if (line.StartsWith("#"))
{
continue;
}
var fields = line.OptimizedSplit('\t');
var position = int.Parse(fields[PositionIndex]);
var refAllele = fields[RefIndex];
var altAllele = fields[AltIndex];
if (altAllele == "." || !(refAllele.Length == 1 && altAllele.Length == 1))
{
continue;
}
var vrfs = fields[VrfBinsIndex].Split(',').Select(double.Parse);
var alleleDepths = fields[VrfCountsIndex].Split(',').Select(int.Parse).ToArray();
heteroplasmyProvider.Add(position, altAllele, vrfs.ToArray(), alleleDepths);
}
return(heteroplasmyProvider);
}
