private static List <Creation.ReferenceSequence> CreateReferenceSequences(IEnumerable <FastaSequence> fastaSequences, IReadOnlyList <List <Band> > cytogeneticBandsByRef)
{
var referenceSequences = new List <Creation.ReferenceSequence>();
foreach (var fastaSequence in fastaSequences)
{
Band[] cytogeneticBands = cytogeneticBandsByRef[fastaSequence.Chromosome.Index].ToArray();
(byte[] buffer, MaskedEntry[] maskedEntries) = TwoBitCompressor.Compress(fastaSequence.Bases);
var referenceSequence = new Creation.ReferenceSequence(buffer, maskedEntries,
cytogeneticBands, 0, fastaSequence.Bases.Length);
referenceSequences.Add(referenceSequence);
}
return(referenceSequences);
}
private static void CreateReferenceSequenceFile(GenomeAssembly genomeAssembly, IReadOnlyCollection <IChromosome> chromosomes, Creation.ReferenceSequence referenceSequence)
{
using (var writer = new ReferenceSequenceWriter(FileUtilities.GetCreateStream(_outputCompressedPath),
chromosomes, genomeAssembly, 0))
{
writer.Write(new List <Creation.ReferenceSequence> {
referenceSequence
});
}
}
