public static GenomeFile ReadGenome(SnpCollection refSnps, string filename) {
GenomeFile result = new GenomeFile(filename);
result.Genome = new Genome(1, 23);
Console.Write("Reading genome " + result.Name + "...");
result.Read(refSnps, new System.Threading.CancellationToken(), null);
Console.WriteLine("completed");
return result;
}
static void Match(string[] args) {
if (args.Length < 4) {
Console.WriteLine("invalid arguments");
ShowHelpMatch();
return;
}
SnpCollection refSnps = ReadRefSnps();
string path = Configuration.GenomePath;
string lastFilename = Path.Combine(path, args[args.Length - 1]);
var testGenomeFile = new GenomeFile(lastFilename);
if (File.Exists(testGenomeFile.Filename)) {
try {
testGenomeFile.Read(refSnps, new System.Threading.CancellationToken(), null);
if (testGenomeFile.Genome.Count > 0) {
int i = 1;
while (File.Exists(Path.Combine(path, "MatchResults(" + i + ").csv"))) i++;
string filename = Path.Combine(path, "MatchResults(" + i + ").csv");
Console.WriteLine("** no filename was specified for the results");
Console.WriteLine("** results will be written to " + filename);
string[] args2 = new string[args.Length + 1];
for (int k = 0; k < args.Length; k++) args2[k] = args[k];
args = args2;
args[args.Length - 1] = filename;
}
}
catch { }
}
string[] filenames = new string[args.Length - 2];
for (int i = 0; i < filenames.Length; i++) {
filenames[i] = args[i + 1];
}
List<Tuple<string, string, SegmentMatch>> results = new List<Tuple<string, string, SegmentMatch>>();
for (int i = 0; i < filenames.Length -1; i++) {
string file1 = Path.Combine(path, filenames[i]);
var phased1 = ReadPhasedGenome(refSnps, file1);
if (phased1 == null) {
var full = ReadGenome(refSnps, file1);
phased1 = SimplePhase(file1, full, refSnps);
WritePhasedGenome(phased1);
}
for (int j = i + 1; j < filenames.Length; j++) {
string file2 = Path.Combine(path, filenames[j]);
var phased2 = ReadPhasedGenome(refSnps, file2);
if (phased2 == null) {
var full = ReadGenome(refSnps, file2);
phased2 = SimplePhase(file2, full, refSnps);
WritePhasedGenome(phased2);
}
Console.Write("Finding matching segments...");
var result = phased1.PhasedGenome.MatchingSegments(phased2.PhasedGenome, Configuration.MaxErrorsToStitch,
Configuration.SegmentMinPhasedSnpCount, Configuration.SegmentMinCmLength,
Configuration.StitchMinPhasedSnpCount, Configuration.StitchMinCmLength);
if (result.Count > 0) {
foreach (var seg in result) results.Add(new Tuple<string, string, SegmentMatch>(phased1.Name, phased2.Name, seg));
} else {
results.Add(new Tuple<string, string, SegmentMatch>(phased1.Name, phased2.Name, default(SegmentMatch)));
}
Console.WriteLine("completed");
}
}
Console.Write("Writing match results to " + args[3] + "...");
WriteSegmentMatches(results, Path.Combine(path, args[args.Length - 1]));
Console.WriteLine("completed");
}
