public static void UpdateCentimorgans(string[] args) {
SnpCollection snps = new SnpCollection(1, 23);
string filename = args[1];
SnpFile.ReadRutgers(snps, filename, new System.Threading.CancellationToken(), null);
for (int i = 1; i <= 23; i++) snps.Add(new Snp("fake" + i, (byte) i, 0, 0, null, null));
SnpCollection refSnps = new SnpCollection(1, 23);
SnpFile.Read(refSnps, "RefSnps.csv");
Snp prevSnp = null;
foreach(Snp snp in refSnps) {
Snp rutgerSnp = null;
if (snps.Contains(snp.RsId)) {
rutgerSnp = snps[snp.RsId];
//if ((rutgerSnp.Chromosome != snp.Chromosome) || (Math.Abs(rutgerSnp.Position-snp.Position) > 10)) {
// Console.WriteLine("mismatched pos for " + snp.RsId + " - " + snp.Chromosome + ":" + snp.Position + " vs. " + rutgerSnp.Chromosome + ":" + rutgerSnp.Position);
// snp.cM = snps.ExtrapolateCentiMorganPosition(snp.Chromosome, snp.Position);
//} else {
// snp.cM = snps[snp.RsId].cM;
//}
snp.Chromosome = rutgerSnp.Chromosome;
snp.Position = rutgerSnp.Position;
}
if ((rutgerSnp != null) && (rutgerSnp.cM > 0)) {
snp.cM = rutgerSnp.cM;
} else {
snp.cM = snps.ExtrapolateCentiMorganPosition(snp.Chromosome, snp.Position);
}
if ((prevSnp != null) && (prevSnp.Chromosome == snp.Chromosome)
&& (prevSnp.cM > snp.cM)) {
Console.WriteLine("cM out of sequence " + prevSnp.RsId + "-" + snp.RsId);
}
prevSnp = snp;
}
SnpFile.Write(refSnps, "RefSnps2.csv");
}
public static void ReadMatchWeights(SnpMap<MatchWeight> matchWeights, SnpCollection snps, string filename,
CancellationToken cancel, Progress progress) {
if (matchWeights == null) throw new ArgumentNullException("The MatchWeights cannot be null.");
if (snps == null) throw new ArgumentNullException("The SnpCollection cannot be null.");
if (filename == null) throw new ArgumentNullException("filename cannot be null.");
if (String.IsNullOrWhiteSpace(filename)) throw new ArgumentOutOfRangeException("filename cannot be empty.");
using (StreamReader reader = new StreamReader(filename)) {
long length = 0;
if (progress != null) length = reader.BaseStream.Length;
string line;
string[] columns = new string[5];
while ((line = reader.ReadLine()) != null) {
cancel.ThrowIfCancellationRequested();
if (line.Length > 0) {
line.FastSplit('\t', columns);
string rsId = columns[0];
string majorAllele = columns[1];
double majorWeight, minorWeight;
double.TryParse(columns[2], out majorWeight);
double.TryParse(columns[4], out minorWeight);
if (snps.Contains(rsId)) {
Snp snp = snps[rsId];
MatchWeight matchWeight = new MatchWeight(Convert.ToInt32(10*majorWeight), Convert.ToInt32(10*minorWeight));
matchWeights.Add(snp, matchWeight);
}
}
if (progress != null) progress.Set(reader.BaseStream.Position, length);
}
}
}