private static void FilterAndStreamOut(List <CalledAllele> alleles, VcfFileWriter writer, GeometricFilter filter)
{
alleles = filter.DoFiltering(alleles);
try
{
writer.Write(alleles);
}
catch (Exception ex)
{
Logger.WriteWarningToLog("Problem writing alleles to vcf.");
Logger.WriteExceptionToLog(ex);
return;
}
writer.FlushBuffer();
}
public static void DoReformating(string inputFile, bool crush)
{
var outputFile = inputFile.Replace(".vcf", ".uncrushed.vcf");
if (crush)
{
Console.WriteLine("crushing " + inputFile + "...");
outputFile = inputFile.Replace(".vcf", ".crushed.vcf");
}
else
{
Console.WriteLine("uncrushing " + inputFile + "...");
}
if (File.Exists(outputFile))
{
File.Delete(outputFile);
}
var config = new VcfWriterConfig()
{
AllowMultipleVcfLinesPerLoci = !crush
};
using (VcfFileWriter writer = new VcfFileWriter(outputFile, config, new VcfWriterInputContext()))
{
writer.WriteHeader();
using (VcfReader reader = new VcfReader(inputFile, false))
{
var currentAllele = new CalledAllele();
var backLogVcfVariant = new VcfVariant();
var backLogExists = reader.GetNextVariant(backLogVcfVariant);
while (backLogExists)
{
var backLogAlleles = backLogExists ? VcfVariantUtilities.Convert(new List <VcfVariant> {
backLogVcfVariant
}).ToList() : null;
foreach (var allele in backLogAlleles)
{
try
{
writer.Write(new List <CalledAllele>()
{
allele
});
}
catch (Exception ex)
{
Console.WriteLine("Problem writing " + allele.ToString());
Console.WriteLine("Exception: " + ex);
return;
}
}
backLogExists = reader.GetNextVariant(backLogVcfVariant);
if (backLogAlleles[0].Chromosome != backLogVcfVariant.ReferenceName)
{
//we have switched to the next chr. flush the buffer.
writer.FlushBuffer();
}
}
writer.FlushBuffer();
}
}
}
