private static FastaSequence GetFastaSequence(string fastaPath, IDictionary <string, IChromosome> refNameToChromosome)
{
var references = new List <FastaSequence>();
FastaReader.AddReferenceSequences(new GZipStream(FileUtilities.GetReadStream(fastaPath), CompressionMode.Decompress), refNameToChromosome, references);
if (references.Count != 1)
{
throw new InvalidDataException($"Expected 1 reference, but found {references.Count} references.");
}
var reference = references[0];
int length = _endPosition - _beginPosition + 1;
string substring = reference.Bases.Substring(_beginPosition - 1, length);
return(new FastaSequence(reference.Chromosome, substring));
}
private static List <FastaSequence> GetFastaSequences(string fastaPrefix, IDictionary <string, IChromosome> refNameToChromosome)
{
string directory = Path.GetDirectoryName(fastaPrefix);
string prefix = Path.GetFileName(fastaPrefix);
string[] fastaFiles = Directory.GetFiles(directory, $"{prefix}*.fa.gz");
var references = new List <FastaSequence>();
foreach (string filePath in fastaFiles)
{
Console.Write($" - parsing {Path.GetFileName(filePath)}... ");
FastaReader.AddReferenceSequences(new GZipStream(FileUtilities.GetReadStream(filePath), CompressionMode.Decompress), refNameToChromosome, references);
Console.WriteLine($"total: {references.Count} sequences");
}
return(references.OrderBy(x => x.Chromosome.Index).ToList());
}