/// <summary>
/// Load a list of all variants in a file. This is memory-intensive; don't do this for whole-genome vcf files!
/// </summary>
public static List <CalledAllele> GetAllVariantsInFile(string vcfPath)
{
List <CalledAllele> allVariants = new List <CalledAllele>();
using (AlleleReader reader = new AlleleReader(vcfPath))
{
foreach (CalledAllele variant in reader.GetVariants())
{
allVariants.Add(variant);
}
}
return(allVariants);
}
public static Dictionary <string, List <CandidateAllele> > GetVariantsByChromosome(this AlleleReader reader,
bool variantsOnly = false, bool flagIsKnown = false, List <AlleleCategory> typeFilter = null, Func <CandidateAllele, bool> doSkipCandidate = null)
{
var lookup = new Dictionary <string, List <CandidateAllele> >();
var calledVariants = reader.GetVariants();
foreach (var calledVariant in calledVariants)
{
var candidate = BackToCandiate(calledVariant);
if (candidate.Type != AlleleCategory.Unsupported)
{
if (variantsOnly && candidate.Type == AlleleCategory.Reference)
{
continue;
}
if (typeFilter != null && !typeFilter.Contains(candidate.Type))
{
continue;
}
if (doSkipCandidate != null && doSkipCandidate(candidate))
{
continue;
}
if (flagIsKnown)
{
candidate.IsKnown = true;
}
if (!lookup.ContainsKey(candidate.Chromosome))
{
lookup[candidate.Chromosome] = new List <CandidateAllele>();
}
lookup[candidate.Chromosome].Add(candidate);
}
}
return(lookup);
}