public override void WriteHeader()
{
if (Writer == null)
{
throw new IOException("Stream already closed");
}
var currentAssembly = Assembly.GetEntryAssembly().GetName(); //for GetCallingAssembly, originally from .net core
var currentAssemblyVersion = Common.IO.PiscesSuiteAppInfo.Version;
Writer.WriteLine("##fileformat=" + VcfVersion);
Writer.WriteLine("##fileDate=" + string.Format("{0:yyyyMMdd}", DateTime.Now));
Writer.WriteLine("##source=" + currentAssembly.Name + " " + currentAssemblyVersion);
Writer.WriteLine("##" + currentAssembly.Name + "_cmdline=\"" + (_context.QuotedCommandLineString == null? "" : string.Join(" ", _context.QuotedCommandLineString)) + "\"");
Writer.WriteLine("##reference=" + _context.ReferenceName);
//write Alt Allele
Writer.WriteLine("##ALT=<ID=<M>,Description=\"There is an overlapping other allele that has been called in a separate VCF record\">");
// info fields
Writer.WriteLine("##INFO=<ID=" + _formatter.DepthInfo + ",Number=1,Type=Integer,Description=\"Total Depth\">");
// filter fields
var filterStringsForHeader = _formatter.GenerateFilterStringsByType();
foreach (var filter in filterStringsForHeader)
{
Writer.WriteLine(filter.Value);
}
// format fields
Writer.WriteLine("##FORMAT=<ID={0},Number=1,Type=String,Description=\"Genotype\">", _formatter.GenotypeFormat);
Writer.WriteLine("##FORMAT=<ID={0},Number=1,Type=Integer,Description=\"Genotype Quality\">", _formatter.GenotypeQualityFormat);
Writer.WriteLine("##FORMAT=<ID={0},Number=.,Type=Integer,Description=\"Allele Depth\">", _formatter.AlleleDepthFormat);
Writer.WriteLine("##FORMAT=<ID={0},Number=1,Type=Integer,Description=\"Total Depth Used For Variant Calling\">", _formatter.TotalDepthFormat);
Writer.WriteLine("##FORMAT=<ID={0},Number=.,Type=Float,Description=\"Variant Frequency\">", _formatter.VariantFrequencyFormat);
if (_config.ShouldOutputSuspiciousCoverageFraction)
{
Writer.WriteLine("##FORMAT=<ID={0},Number=.,Type=String,Description=\"Suspicious coverage statistics: (confident start coverage, suspicious start coverage, confident end coverage, suspicious end coverage, variant-specific suspicious coverage weighting factor\">", _formatter.FractionSuspiciousCoverageFormat);
}
if (_config.ShouldOutputProbeBias)
{
Writer.WriteLine("##FORMAT=<ID={0},Number=1,Type=Float,Description=\"ProbeBias Score\">", _formatter.ProbeBiasFormat);
}
if (_config.ShouldOutputAmpliconBias)
{
Writer.WriteLine("##FORMAT=<ID={0},Number=1,Type=Float,Description=\"AmpliconBias Score\">", _formatter.AmpliconBiasFormat);
}
if (_config.ShouldOutputStrandBiasAndNoiseLevel)
{
Writer.WriteLine("##FORMAT=<ID={0},Number=1,Type=Integer,Description=\"Applied BaseCall Noise Level\">", _formatter.NoiseLevelFormat);
Writer.WriteLine("##FORMAT=<ID={0},Number=1,Type=Float,Description=\"StrandBias Score\">", _formatter.StrandBiasFormat);
}
if (_config.ShouldOutputNoCallFraction)
{
Writer.WriteLine("##FORMAT=<ID={0},Number=1,Type=Float,Description=\"Fraction of bases which were uncalled or with basecall quality below the minimum threshold\">", _formatter.FractionNoCallFormat);
}
if (_config.ShouldReportGp)
{
Writer.WriteLine("##FORMAT=<ID={0},Number=G,Type=Float,Description=\"Genotype Posterior\">", _formatter.GenotypePosterior);
}
if (_config.ShouldOutputRcCounts)
{
Writer.WriteLine("##FORMAT=<ID={0},Number=.,Type=Integer,Description=\"Supporting read type counts\">", _formatter.UmiStatsFormat);
}
WriteContigs(Writer);
WriteColHeaders(Writer);
}
public override void WriteHeader()
{
if (Writer == null)
{
throw new Exception("Stream already closed");
}
var currentAssembly = Assembly.GetCallingAssembly().GetName();
Writer.WriteLine("##fileformat=" + VcfVersion);
Writer.WriteLine("##fileDate=" + string.Format("{0:yyyyMMdd}", DateTime.Now));
Writer.WriteLine("##source=" + currentAssembly.Name + " " + currentAssembly.Version);
Writer.WriteLine("##" + currentAssembly.Name + "_cmdline=\"" + (_context.CommandLine == null? "" : string.Join(" ", _context.CommandLine)) + "\"");
Writer.WriteLine("##reference=" + _context.ReferenceName);
// info fields
Writer.WriteLine("##INFO=<ID=" + _formatter.DepthInfo + ",Number=1,Type=Integer,Description=\"Total Depth\">");
// filter fields
var filterStringsForHeader = _formatter.GenerateFilterStringsByType();
// filter fields
if (_config.VariantQualityFilterThreshold.HasValue)
{
Writer.WriteLine(filterStringsForHeader[FilterType.LowVariantQscore]);
}
if (_config.DepthFilterThreshold.HasValue)
{
Writer.WriteLine(filterStringsForHeader[FilterType.LowDepth]);
}
if (_config.StrandBiasFilterThreshold.HasValue && _config.ShouldFilterOnlyOneStrandCoverage)
{
Writer.WriteLine(filterStringsForHeader[FilterType.StrandBias]);
}
else if (_config.StrandBiasFilterThreshold.HasValue)
{
Writer.WriteLine(filterStringsForHeader[FilterType.StrandBias]);
}
else if (_config.ShouldFilterOnlyOneStrandCoverage)
{
Writer.WriteLine(filterStringsForHeader[FilterType.StrandBias]);
}
if (_config.FrequencyFilterThreshold.HasValue)
{
Writer.WriteLine(filterStringsForHeader[FilterType.LowVariantFrequency]);
}
if (_config.GenotypeQualityFilterThreshold.HasValue)
{
Writer.WriteLine(filterStringsForHeader[FilterType.LowGenotypeQuality]);
}
if (_config.IndelRepeatFilterThreshold.HasValue)
{
Writer.WriteLine(filterStringsForHeader[FilterType.IndelRepeatLength]);
}
if (_config.PloidyModel == PloidyModel.Diploid)
{
Writer.WriteLine(filterStringsForHeader[FilterType.MultiAllelicSite]);
}
if (_config.RMxNFilterMaxLengthRepeat.HasValue && _config.RMxNFilterMinRepetitions.HasValue)
{
Writer.WriteLine(filterStringsForHeader[FilterType.RMxN]);
}
// format fields
Writer.WriteLine("##FORMAT=<ID={0},Number=1,Type=String,Description=\"Genotype\">", _formatter.GenotypeFormat);
Writer.WriteLine("##FORMAT=<ID={0},Number=1,Type=Integer,Description=\"Genotype Quality\">", _formatter.GenotypeQualityFormat);
Writer.WriteLine("##FORMAT=<ID={0},Number=.,Type=Integer,Description=\"Allele Depth\">", _formatter.AlleleDepthFormat);
Writer.WriteLine("##FORMAT=<ID={0},Number=1,Type=Integer,Description=\"Total Depth Used For Variant Calling\">", _formatter.TotalDepthFormat);
Writer.WriteLine("##FORMAT=<ID={0},Number=.,Type=Float,Description=\"Variant Frequency\">", _formatter.VariantFrequencyFormat);
if (_config.ShouldOutputStrandBiasAndNoiseLevel)
{
Writer.WriteLine("##FORMAT=<ID={0},Number=1,Type=Integer,Description=\"Applied BaseCall Noise Level\">", _formatter.NoiseLevelFormat);
Writer.WriteLine("##FORMAT=<ID={0},Number=1,Type=Float,Description=\"StrandBias Score\">", _formatter.StrandBiasFormat);
}
if (_config.ShouldOutputNoCallFraction)
{
Writer.WriteLine("##FORMAT=<ID={0},Number=1,Type=Float,Description=\"Fraction of bases which were uncalled or with basecall quality below the minimum threshold\">", _formatter.FractionNoCallFormat);
}
if (_config.ShouldOutputRcCounts)
{
Writer.WriteLine("##FORMAT=<ID={0},Number=.,Type=Integer,Description=\"Supporting read type counts\">", _formatter.UmiStatsFormat);
}
WriteContigs(Writer);
WriteColHeaders(Writer);
}
