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 Creation.ReferenceSequence CreateReferenceSequence(FastaSequence fastaSequence, List <Band> cytogeneticBands)
{
Band[] bands = cytogeneticBands.ToArray();
(byte[] buffer, MaskedEntry[] maskedEntries) = TwoBitCompressor.Compress(fastaSequence.Bases);
return(new Creation.ReferenceSequence(buffer, maskedEntries, bands, _beginPosition - 1, fastaSequence.Bases.Length));
}
private static Creation.ReferenceSequence CreateReferenceSequence(FastaSequence fastaSequence)
{
(byte[] buffer, MaskedEntry[] maskedEntries) = TwoBitCompressor.Compress(fastaSequence.Bases);
return(new Creation.ReferenceSequence(buffer, maskedEntries, new Band[0], 0, fastaSequence.Bases.Length));
}
