public static string WriteCountsFile(string vcfIn, string outDir)
{
var variant = new VcfVariant();
var countsPath = Path.Combine(outDir, Path.GetFileName(vcfIn).Replace(".vcf", ".counts"));
var counter = new MutationCounter();
using (VcfReader readerA = new VcfReader(vcfIn))
{
counter.StartWriter(countsPath);
while (readerA.GetNextVariant(variant))
{
try
{
counter.Add(variant);
}
catch (Exception ex)
{
Logger.WriteToLog(string.Format("Fatal error processing vcf; Check {0}, position {1}. Exception: {2}",
variant.ReferenceName, variant.ReferencePosition, ex));
throw;
}
}
counter.CloseFalseCallsWriter();
}
return(countsPath);
}
public static string WriteCountsFile(string vcfIn, string outDir, int lociCount)
{
var variants = new List <CalledAllele>();
var countsPath = Path.Combine(outDir, Path.GetFileName(vcfIn).Replace(".vcf", ".counts"));
var countsPathOld = Path.Combine(outDir, Path.GetFileName(vcfIn).Replace(".vcf", ".counts.original"));
if (File.Exists(countsPath))
{
if (File.Exists(countsPathOld))
{
File.Delete(countsPathOld);
}
File.Copy(countsPath, countsPathOld);
File.Delete(countsPath);
}
var counter = new MutationCounter();
using (AlleleReader readerA = new AlleleReader(vcfIn))
{
counter.StartWriter(countsPath);
while (readerA.GetNextVariants(out variants))
{
foreach (var variant in variants)
{
try
{
counter.Add(variant);
}
catch (Exception ex)
{
Logger.WriteToLog(string.Format("Fatal error processing vcf; Check {0}, position {1}. Exception: {2}",
variant.Chromosome, variant.ReferencePosition, ex));
throw;
}
}
}
if (lociCount > 0)
{
counter.ForceTotalPossibleMutations(lociCount);
}
counter.CloseWriter();
}
return(countsPath);
}
