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 static void WritePhasedGenome(PhasedGenomeFile genomeFile) {
genomeFile.Extension = "txt";
Console.Write("Writing phased genome " + genomeFile.Name + "...");
genomeFile.Write(true, new System.Threading.CancellationToken(), null);
Console.WriteLine("completed");
}
public static void AddHistory(PhasedGenomeFile pfile, GenomeFile gfile, int count, IList<Tuple<SegmentMatch, SegmentMatch>> segs) {
DateTime now = DateTime.Now;
pfile.AddComment("## " + DateTime.Now.ToString() + " MatchPhase added " + count.ToString("#,##0") + " phased heterozygous SNPs using " + gfile.Name + ".");
if ((segs != null) && (segs.Count > 0)) {
string filename = Path.Combine(Path.GetDirectoryName(pfile.Filename), pfile.Name + "HISTORY.csv");
List<string> lines = new List<string>();
if (!File.Exists(filename)) {
lines.Add("date,time,source,chromosome,origStart,origEnd,origLen(cM),sides,usedStart,usedEnd,usedLen(cM),newlyPhasedCount");
}
foreach (var tup in segs) {
var match = tup.Item1;
var phased = tup.Item2;
string line = "\"" + now.ToShortDateString() + "\",\"" + now.ToShortTimeString() + "\",\"" + gfile.Name + "\","
+ Snp.ChromosomeToString(match.StartSnp.Chromosome) + "," + match.StartSnp.Position.ToString() + ","
+ match.EndSnp.Position.ToString() + "," + match.CmLength.ToString("#0.00") + ","
+ match.MatchKind.ToString() + "," + phased.StartSnp.Position.ToString() + ","
+ phased.EndSnp.Position.ToString() + "," + phased.CmLength.ToString("#0.00") + ","
+ phased.PhasedSnpCount.ToString();
lines.Add(line);
}
File.AppendAllLines(filename, lines);
}
}
public static PhasedGenomeFile ReadPhasedGenome(SnpCollection refSnps, string filename) {
string phasedFilename = GetPhasedFilename(filename);
if (!File.Exists(phasedFilename)) return null;
PhasedGenomeFile result = new PhasedGenomeFile(phasedFilename);
result.PhasedGenome = new PhasedGenome(1, 23);
Console.Write("Reading phased genome " + result.Name + "...");
result.Read(refSnps, new System.Threading.CancellationToken(), null);
Console.WriteLine("completed");
return result;
}