/// <summary>
/// Create a new SegmentMatch struct with the specified values.
/// </summary>
/// <param name="startSnp">The Snp that is the start of the segment.</param>
/// <param name="endSnp">The Snp that is the end of the segment (inclusive).</param>
/// <param name="snpCount">The number of matching Snps within the segment.</param>
/// <param name="halvesMatched">The number of halves matched; either 1 for a half
/// matching segment, or 2 for a full matching segment.</param>
public SegmentMatch(Snp startSnp, Snp endSnp, int snpCount, int phasedSnpCount, int score,
PhasedGenome.Phasing.MatchKind matchKind, int halvesMatched) {
this.startSnp = startSnp;
this.endSnp = endSnp;
this.snpCount = snpCount;
this.phasedSnpCount = phasedSnpCount;
this.score = score;
this.matchKind = matchKind;
this.halvesMatched = halvesMatched;
}
static PhasedGenomeFile SimplePhase(string filename, GenomeFile gfile, SnpCollection refSnps) {
Console.Write("Creating simple phased genome...");
PhasedGenome phased = new PhasedGenome(gfile.Genome);
Console.WriteLine("completed");
PhasedGenomeFile pfile = new PhasedGenomeFile(GetPhasedFilename(filename));
pfile.SetStandardComments();
pfile.AddComment("## history");
pfile.AddComment("## " + DateTime.Now.ToString() + " SimplePhase of " + phased.Count.ToString("#,##0")
+ " homozygous SNPs (of " + gfile.Genome.Count.ToString("#,##0") + " total).");
pfile.PhasedGenome = phased;
return pfile;
}
public void Read(SnpCollection snps, CancellationToken cancel, Progress progress) {
if (snps == null) throw new ArgumentNullException("The SnpCollection cannot be null.");
if (this.filename == null) throw new ArgumentNullException("filename cannot be null.");
if (String.IsNullOrWhiteSpace(filename)) throw new ArgumentOutOfRangeException("filename cannot be empty.");
if (this.genome == null) {
this.genome = new PhasedGenome(1, 23);
} else {
this.genome.Clear();
}
this.comments.Clear();
using (StreamReader reader = new StreamReader(this.filename)) {
long length = 0;
if (progress != null) length = reader.BaseStream.Length;
string line;
string[] columns = new string[4];
while ((line = reader.ReadLine()) != null) {
cancel.ThrowIfCancellationRequested();
if ((line.Length > 0) && (line[0] != '#')) {
int colCount = line.FastSplit('\t', columns);
if ((colCount != 2) && (colCount != 4)) throw new ApplicationException("Not phased genome format.");
string rsId = columns[0];
Snp snp = snps[rsId];
if (snp != null) {
var alleles = columns[colCount - 1];
var phased = new PhasedGenome.Phasing(alleles[0].ToAllele(), alleles[1].ToAllele());
this.genome.Add(snp, phased);
}
} else if ((line.Length > 0) && (genome.Count == 0) && (line != header)) {
this.comments.Add(line);
}
if (progress != null) progress.Set(reader.BaseStream.Position, length);
}
}
if (String.IsNullOrWhiteSpace(genome.Name)) this.genome.Name = Path.GetFileNameWithoutExtension(filename);
}
public void Read(PhasedGenome genome, SnpCollection snps, CancellationToken cancel, Progress progress) {
this.PhasedGenome = genome;
Read(snps, cancel, progress);
}