public void FilterSites(PolymorphismFilter filterToApply)
{
var goodPolys = filterToApply.FilterPolys(this).Select(x => x.Position).ToDictionary(z => z, u => u);
List <int> toRemove = this.Select(x => x.position).Where(y => !goodPolys.ContainsKey(y)).ToList();
foreach (var v in toRemove)
{
polymorphisms.Remove(v);
}
}
/// <summary>
/// Call SNPs from the sorted list of sequences using the pile-up method.
/// </summary>
/// <returns>The SN ps.</returns>
/// <param name="sequences">Sequences.</param>
public static SNPCallerReport CallSNPs(IEnumerable <CompactSAMSequence> sequences)
{
// Get a pile up and convert it to genotypes
var pileups = PileUpProducer.CreatePileupFromReads(sequences);
var genotypes = ContinuousGenotypeCaller.CallContinuousGenotypes(pileups).ToList();
// Filter down to a usable set
var usable = genotypes.Where(x => x.ResultType == GenotypeCallResult.GenotypeCalled && x.OriginalPosition.HasValue).ToList();
if (usable.Count == 0)
{
return(new SNPCallerReport(AlgorithmResult.Failed));
}
// Get median coverage at sites
var data_counts = usable.Select(x => x.TotalObservedBases).ToList();
data_counts.Sort();
var median = data_counts[data_counts.Count / 2];
//now create a cut-off for required coverage as the square root of the median.
var cut_off = Math.Sqrt(median);
//Get a list of genotypes, and if a simple SNP, make a polymorphism if it doesn't match
//the reference
var genotypedPositions = new HashSet <int> ();
List <Polymorphism> polys = new List <Polymorphism> ();
foreach (var geno in usable)
{
if (geno.TotalObservedBases >= cut_off)
{
genotypedPositions.Add(geno.OriginalPosition.Value);
var org_bp = ReferenceGenome.GetReferenceBaseAt_rCRSPosition(geno.OriginalPosition.Value);
var cur_bp = geno.GetMostFrequentGenotype();
if (org_bp != cur_bp[0])
{
var poly = new Polymorphism(geno.OriginalPosition.Value, MutationAssigner.getBase(cur_bp));
polys.Add(poly);
}
}
}
//Now assign haplotype
HaplotypeSearcher hts = new HaplotypeSearcher();
PolymorphismFilter pf = new PolymorphismFilter(p => p.IsSNP && genotypedPositions.Contains(p.Position));
var simpSample = new SimpleSample("Pileup", polys, pf);
var hap_report = hts.GetHaplotypeReport(simpSample);
return(new SNPCallerReport(genotypes, hap_report));
}
